@article {hachicha_combined_2024,
	title = {Combined biological treatments of olive mill wastewater using fungi and microalgae},
	journal = {Euro-Mediterranean Journal for Environmental Integration},
	year = {2024},
	month = {jan},
	abstract = {Olive mill wastewaters (OMWs), which are mainly composed of phenolic compounds, present an important environmental issue. This effluent was treated using fungal laccases from Tetraselmis sp. and Chlorella sp. and two green microalgae. In the first step in the removal of phenolic compounds, enzymatic pretreatment of diluted OMWs (30\% v/v) with the fungal laccases led to a 57.79 {\textpm} 2.21\% decrease in phenol concentration and a 54.79 {\textpm} 3.44\% decrease in the dark coloration of the diluted OMWs. This preatreated wastewater was suitable for microalgae culture under mixotrophy. The growth and biochemical composition of the two microalgae strains were determined and compared to those obtained from a control culture under autotrophy. Under mixotrophy, the growth of Chlorella sp. and Tetraselmis sp. reduced dramatically. Moroever, their photosynthetic pigment productivities (0.0071 {\textpm} 0.08 mg/104 cells/mL/day for Chlorella sp. and 0.011 {\textpm} 0.002 mg/104 cells/ mL/day for Tetraselmis sp.) were decreased when compared to those attained under autotrophy. In terms of starch and lipid production, the highest final contents of starch and lipids were obtained under autotrophy: 13.38 {\textpm} 2.17\% and 4.2 {\textpm} 0.35\% for Chlorella sp. and 15.66 {\textpm} 0.92\% and 5.22 {\textpm} 0.79\% for Tetraselmis sp., respectively. The mixotrophic cultivation mode of Chlorella sp. reinforces protein synthesis. These results highlight the opportunity to achieve high-value biomass production by the mixotrophic cultivation of microalgae using pretreated OMWs as a low-cost raw material.},
	keywords = {RCC288},
	issn = {2365-6433, 2365-7448},
	doi = {10.1007/s41207-023-00451-6},
	url = {https://link.springer.com/10.1007/s41207-023-00451-6},
	author = {Hachicha, Rihab and Dammak, Mouna and Hachicha, Ridha and Dubessay, Pascal and Abdelkafi, Slim and Michaud, Philippe and Fendri, Imen}
}
@article {rihtman_coordinated_2024,
	title = {Coordinated transcriptional response to environmental stress by a \textit{Synechococcus virus},
	journal = {The ISME Journal},
	year = {2024},
	month = {mar},
	pages = {wrae032},
	abstract = {Viruses are a major control on populations of microbes. Often, their virulence is examined in controlled laboratory conditions. Yet, in nature, environmental conditions lead to changes in host physiology and fitness that may impart both costs and benefits on viral success.},
	keywords = {rcc752},
	issn = {1751-7362, 1751-7370},
	doi = {10.1093/ismejo/wrae032},
	url = {https://academic.oup.com/ismej/advance-article/doi/10.1093/ismejo/wrae032/7618445},
	author = {Rihtman, Branko and Torcello-Requena, Alberto and Mikhaylina, Alevtina and Puxty, Richard J and Clokie, Martha R J and Millard, Andrew D and Scanlan, David J}
}
@article {varga_cytotoxicity_2024,
	title = {Cytotoxicity of Prymnesium parvum extracts and prymnesin analogs on epithelial fish gill cells RTgill-W1 and the human colon cell line HCEC-1CT},
	journal = {Archives of Toxicology},
	year = {2024},
	month = {jan},
	abstract = {Harmful algal blooms kill fish populations worldwide, as exemplified by the haptophyte microalga Prymnesium~parvum. The suspected causative agents are prymnesins, categorized as A-, B-, and C-types based on backbone carbon atoms. Impacts of P.~parvum extracts and purified prymnesins were tested on the epithelial rainbow trout fish gill cell line RTgill-W1 and on the human colon epithelial cells HCEC-1CT. Cytotoxic potencies ranked A > C > B-type with concentrations spanning from low (A- and C-type) to middle (B-type) nM ranges. Although RTgill-W1 cells were about twofold more sensitive than HCEC-1CT, the cytotoxicity of prymnesins is not limited to fish gills. Both cell lines responded rapidly to prymnesins; with EC50 values for B-types in RTgill-W1 cells of 110 {\textpm} 11~nM and 41.5 {\textpm} 0.6~nM after incubations times of 3 and 24~h. Results of fluorescence imaging and measured lytic effects suggest plasma membrane interactions. Postulating an osmotic imbalance as mechanisms of toxicity, incubations with prymnesins in media lacking either Cl-, Na+, or Ca2+ were performed. Cl- removal reduced morphometric rearrangements observed in RTgill-W1 and cytotoxicity in HCEC-1CT cells. Ca2+-free medium in RTgill-W1 cells exacerbated effects on the cell nuclei. Prymnesin composition of different P.~parvum strains showed that analog composition within one type scarcely influenced the cytotoxic potential, while analog type potentially dictate potency. Overall, A-type prymnesins were the most potent ones in both cell lines followed by the C-types, and lastly B-types. Disturbance of Ca2+ and Cl- ionoregulation may be integral to prymnesin toxicity.},
	keywords = {Fluorescence microscopy, Ichthyotoxin, Ionoregulation, Microalgae, MS, RCC1436, RCC191, UHPLC},
	issn = {1432-0738},
	doi = {10.1007/s00204-023-03663-5},
	url = {https://doi.org/10.1007/s00204-023-03663-5},
	author = {Varga, Elisabeth and Prause, H{\'e}l{\`e}ne-Christine and Riepl, Matthias and Hochmayr, Nadine and Berk, Deniz and Attakpah, Eva and Kiss, Endre and Medi{\'c}, Nikola and Del Favero, Giorgia and Larsen, Thomas Ostenfeld and Hansen, Per Juel and Marko, Doris}
}
@article {roux_ecophysiological_2024,
	title = {Ecophysiological response of the cupped oyster Crassostrea gigas exposed to the green dinoflagellate Lepidodinium chlorophorum},
	journal = {Aquaculture},
	year = {2024},
	month = {feb},
	pages = {740644},
	keywords = {RCC6911},
	issn = {00448486},
	doi = {10.1016/j.aquaculture.2024.740644},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0044848624001054},
	author = {Roux, Pauline and Garc{\'\i}a-Corona, Jos{\'e} Luis and Ragueneau, Stacy and Schapira, Mathilde and Siano, Raffaele and Pernet, Fabrice and Queau, Isabelle and Malestroit, Pascale and Tallec, Kevin and Fleury, Elodie}
}
@article {koslova_endogenous_2024,
	title = {Endogenous virophages are active and mitigate giant virus infection in the marine protist Cafeteria burkhardae},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {121},
	number = {11},
	year = {2024},
	note = {Publisher: Proceedings of the National Academy of Sciences},
	month = {mar},
	pages = {e2314606121},
	abstract = {Endogenous viral elements (EVEs) are common genetic passengers in various protists. Some EVEs represent viral fossils, whereas others are still active. The marine heterotrophic flagellate Cafeteria burkhardae contains several EVE types related to the virophage mavirus, a small DNA virus that parasitizes the lytic giant virus CroV. We hypothesized that endogenous virophages may act as an antiviral defense system in protists, but no protective effect of virophages in wild host populations has been shown so far. Here, we tested the activity of virophage EVEs and studied their impact on giant virus replication. We found that endogenous mavirus-like elements (EMALEs) from globally distributed Cafeteria populations produced infectious virus particles specifically in response to CroV infection. However, reactivation was stochastic, often inefficient, and poorly reproducible. Interestingly, only one of eight EMALE types responded to CroV infection, implying that other EMALEs may be linked to different giant viruses. We isolated and cloned several reactivated virophages and characterized their particles, genomes, and infection dynamics. All tested virophages inhibited the production of CroV during coinfection, thereby preventing lysis of the host cultures in a dose-dependent manner. Comparative genomics of different C. burkhardae strains revealed that inducible EMALEs are common and are not linked to specific geographic locations. We demonstrate that naturally occurring virophage EVEs reactivate upon giant virus infection, thus providing a striking example that eukaryotic EVEs can become active under specific conditions. Moreover, our results support the hypothesis that virophages can act as an adaptive antiviral defense system in protists.},
	keywords = {RCC970},
	doi = {10.1073/pnas.2314606121},
	url = {https://www.pnas.org/doi/full/10.1073/pnas.2314606121},
	author = {Koslov{\'a}, Anna and Hackl, Thomas and Bade, Felix and Sanchez Kasikovic, Alexander and Barenhoff, Karina and Schimm, Fiona and Mersdorf, Ulrike and Fischer, Matthias G.}
}
@article {dulong_exopolysaccharide_2024,
	title = {Exopolysaccharide from marine microalgae belonging to the \textit{Glossomastix genus: fragile gel behavior and suspension stability},
	journal = {Bioengineered},
	volume = {15},
	number = {1},
	year = {2024},
	note = {Publisher: Taylor \& Francis _eprint: https://doi.org/10.1080/21655979.2023.2296257},
	month = {dec},
	pages = {2296257},
	abstract = {With the aim to find new polysaccharides of rheological interest with innovated properties, rhamnofucans produced as exopolysaccharides (EPS) in a photobioreactor (PBR) and an airlift bioreactor (ABR) by the marine microalgae Glossomastix sp. RCC3707 and RCC3688 were fully studied. Chemical characterizations have been conducted (UHPLC {\textendash} MS HR). Analyses by size-exclusion chromatography (SEC) coupled online with a multiangle light scattering detector (MALS) and a differential refractive index detector showed the presence of large structures with molar masses higher than 106 g.mol-1. The rheological studies of these EPS solutions, conducted at different concentrations and salinities, have evidenced interesting and rare behavior characteristic of weak and fragile hydrogels i.e. gel behavior with very low elastic moduli (between 10-2 and 10 Pa) and yield stresses (between 10-2 and 2 Pa) according to the EPS source, concentration, and salinity. These results were confirmed by diffusing wave spectroscopy. Finally, as one of potential application, solutions of EPS from Glossomastix sp. have evidenced very good properties as anti-settling stabilizers, using microcrystalline cellulose particles as model, studied by multiple light scattering (MLS) with utilization in cosmetic or food industry. Compared to alginate solution with same viscosity for which sedimentation is observed over few hours, microalgae EPS leads to a stable suspension over few days.},
	keywords = {fragile gel, Glossomastix, Microalgae, Polysaccharide, RCC3688, RCC3707, stabilizer},
	issn = {2165-5979},
	doi = {10.1080/21655979.2023.2296257},
	url = {https://doi.org/10.1080/21655979.2023.2296257},
	author = {Dulong, Virginie and Rihouey, Christophe and Gaignard, Cl{\'e}ment and Bridiau, Nicolas and Gourvil, Priscilla and Laroche, C{\'e}line and Pierre, Guillaume and Varacavoudin, Tony and Probert, Ian and Maugard, Thierry and Michaud, Philippe and Picton, Luc and Le Cerf, Didier}
}
@article {cho_genomic_2024,
	title = {Genomic analyses of Symbiomonas scintillans show no evidence for endosymbiotic bacteria but does reveal the presence of giant viruses},
	journal = {PLOS Genetics},
	volume = {20},
	number = {4},
	year = {2024},
	note = {Publisher: Public Library of Science},
	pages = {e1011218},
	abstract = {Symbiomonas scintillans Guillou et Chr{\'e}tiennot-Dinet, 1999 is a tiny (1.4 μm) heterotrophic microbial eukaryote. The genus was named based on the presence of endosymbiotic bacteria in its endoplasmic reticulum, however, like most such endosymbionts neither the identity nor functional association with its host were known. We generated both amplification-free shotgun metagenomics and whole genome amplification sequencing data from S. scintillans strains RCC257 and RCC24, but were unable to detect any sequences from known lineages of endosymbiotic bacteria. The absence of endobacteria was further verified with FISH analyses. Instead, numerous contigs in assemblies from both RCC24 and RCC257 were closely related to prasinoviruses infecting the green algae Ostreococcus lucimarinus, Bathycoccus prasinos, and Micromonas pusilla (OlV, BpV, and MpV, respectively). Using the BpV genome as a reference, we assembled a near-complete 190 kbp draft genome encoding all hallmark prasinovirus genes, as well as two additional incomplete assemblies of closely related but distinct viruses from RCC247, and three similar draft viral genomes from RCC24, which we collectively call SsVs. A multi-gene tree showed the three SsV genome types branched within highly supported clades with each of BpV2, OlVs, and MpVs, respectively. Interestingly, transmission electron microscopy also revealed a 190 nm virus-like particle similar the morphology and size of the endosymbiont originally reported in S. scintillans. Overall, we conclude that S. scintillans currently does not harbour an endosymbiotic bacterium, but is associated with giant viruses.},
	keywords = {Eukaryota, Gene prediction, genomics, metagenomics, RCC24, RCC257, Shotgun sequencing, Transcriptome analysis, Viral genomics, Whole genome amplification},
	issn = {1553-7404},
	doi = {10.1371/journal.pgen.1011218},
	url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1011218},
	author = {Cho, Anna and Lax, Gordon and Livingston, Samuel J. and Masukagami, Yumiko and Naumova, Mariia and Millar, Olivia and Husnik, Filip and Keeling, Patrick J.}
}
@mastersthesis {mauro_influence_2024,
	title = {The influence of acclimation to density on organisms{\textquoteright} traits and population growth in \textit{Synechococcus sp. RS 9909},
	year = {2024},
	school = {Universit{\'e} catholique de Louvain},
	type = {masters},
	abstract = {In a constantly changing environment, it is essential to understand how different factors can affect the growth of populations, including its dependence on density, commonly referred to as density dependence. These factors can affect population growth directly, by inducing a higher mortality rate for example, but also indirectly by changing organisms{\textquoteright} traits, such as their size or their pigment content, enabling them to better cope with the changing environmental conditions in which they find themselves. This process, also known as acclimation, can have a strong influence on the density dependence of populations. It is therefore necessary, when studying population growth and density dependence, to take into account the initial conditions in which individuals have lived. Surprisingly, while many studies have looked at how acclimation to external conditions (light, temperature, pH) can affect density dependence, the impact of initial population density conditions on growth has never been studied. In this master{\textquoteright}s thesis, we studied how acclimation of a cyanobacterium of the genus Synechococcus to different population densities could impact organisms{\textquoteright} traits and population growth, including the density dependence. We found that populations acclimated to higher densities showed higher mean trait values for all but one trait, but less variability. Growth modelling showed the emergence of a non-linear density dependence from a certain initial acclimation density. In addition, comparison of these functions showed that populations acclimated to higher densities had higher growth rates and lower density dependence. This study is the first to show how initial population density conditions can affect individual characteristics and population growth, including density dependence, and demonstrates that it is important to take a more general interest in all the historical conditions experienced by populations in order to better predict their dynamics.},
	keywords = {RCC2383, ⛔ No DOI found},
	author = {Mauro, Nicola}
}
@article {harcourt_intraspecific_2024,
	title = {Intraspecific trait variation modulates the temperature effect on elemental quotas and stoichiometry in marine Synechococcus},
	journal = {PLOS ONE},
	volume = {19},
	number = {3},
	year = {2024},
	note = {Publisher: Public Library of Science},
	month = {mar},
	pages = {e0292337},
	abstract = {Diverse phytoplankton modulate the coupling between the ocean carbon and nutrient cycles through life-history traits such as cell size, elemental quotas, and ratios. Biodiversity is mostly considered at broad functional levels, but major phytoplankton lineages are themselves highly diverse. As an example, Synechococcus is found in nearly all ocean regions, and we demonstrate contains extensive intraspecific variation. Here, we grew four closely related Synechococcus isolates in serially transferred cultures across a range of temperatures (16{\textendash}25{\textdegree}C) to quantify for the relative role of intraspecific trait variation vs. environmental change. We report differences in cell size (p<0.01) as a function of strain and clade (p<0.01). The carbon (QC), nitrogen (QN), and phosphorus (QP) cell quotas all increased with cell size. Furthermore, cell size has an inverse relationship to growth rate. Within our experimental design, temperature alone had a weak physiological effect on cell quota and elemental ratios. Instead, we find systemic intraspecific variance of C:N:P, with cell size and N:P having an inverse relationship. Our results suggest a key role for intraspecific life history traits in determining elemental quotas and stoichiometry. Thus, the extensive biodiversity harbored within many lineages may modulate the impact of environmental change on ocean biogeochemical cycles.},
	keywords = {Biogeochemistry, Cell enumeration techniques, Oceans, Particulates, Phylogenetics, phytoplankton, RCC1086, RCC2673, RCC515, Stoichiometry, Synechococcus},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0292337},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0292337},
	author = {Harcourt, Renne and Garcia, Nathan S. and Martiny, Adam C.}
}
@article {merritt_variability_2024,
	title = {Variability in spectral absorption within cryptophyte phycobiliprotein types},
	journal = {Journal of Phycology},
	volume = {n/a},
	number = {n/a},
	year = {2024},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jpy.13439},
	abstract = {Cryptophytes are known to vary widely in coloration among species. These differences in color arise primarily from the presence of phycobiliprotein accessory pigments. There are nine defined cryptophyte phycobiliprotein (Cr-PBP) types, named for their wavelength of maximal absorbance. Because Cr-PBP type has traditionally been regarded as a categorical trait, there is a paucity of information about how spectral absorption characteristics of Cr-PBPs vary among species. We investigated variability in primary and secondary peak absorbance wavelengths and full width at half max (FWHM) values of spectra of Cr-PBPs extracted from 75 cryptophyte strains (55 species) grown under full spectrum irradiance. We show that there may be substantial differences in spectral shapes within Cr-PBP types, with Cr-Phycoerythrin (Cr-PE) 545 showing the greatest variability with two, possibly three, subtypes, while Cr-PE 566 spectra were the least variable, with only {\textpm}1 nm of variance around the mean absorbance maximum of 565 nm. We provide additional criteria for classification in cases where the wavelength of maximum absorbance alone is not definitive. Variations in spectral characteristics among strains containing the same presumed Cr-PBP type may indicate differing chromophore composition and/or the presence of more than one Cr-PBP in a single cryptophyte species.},
	keywords = {absorbance, Absorption, chromophore, cryptomonad, cryptophyte, phycobilin, phycobiliprotein, RCC1505, RCC2614, RCC3072, RCC350, RCC3575, RCC4102, RCC4116, RCC439, RCC4444, RCC4474, RCC4787, RCC4843, RCC4857},
	issn = {1529-8817},
	doi = {10.1111/jpy.13439},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.13439},
	author = {Merritt, Kristia{\"a}n A. and Richardson, Tammi L.}
}
@article {bouquet_artificial_2023,
	title = {Artificial Substrates Coupled with qPCR (AS-qPCR) Assay for the Detection of the Toxic Benthopelagic Dinoflagellate Vulcanodinium rugosum},
	journal = {Toxins},
	volume = {15},
	number = {3},
	year = {2023},
	note = {Number: 3 Publisher: Multidisciplinary Digital Publishing Institute},
	month = {mar},
	pages = {217},
	abstract = {Vulcanodinium rugosum is an emerging benthopelagic neuro-toxic dinoflagellate species responsible for seasonal Pinnatoxins and Portimines contaminations of shellfish and marine animals. This species is challenging to detect in the environment, as it is present in low abundance and difficult to be identified using light microscopy. In this work, we developed a method using artificial substrates coupled with qPCR (AS-qPCR) to detect V. rugosum in a marine environment. This sensitive, specific and easy-to-standardize alternative to current techniques does not require specialized expertise in taxonomy. After determining the limits and specificity of the qPCR, we searched for the presence of V. rugosum in four French Mediterranean lagoons using artificial substrates collected every two weeks for one year. The AS-qPCR method revealed its occurrences in summer 2021 in every studied lagoon and detected cells in more samples than light microscopy. As V. rugosum development induces shellfish contamination even at low microalga densities, the AS-qPCR method is accurate and relevant for monitoring V. rugosum in a marine environment.},
	keywords = {artificial substrate, benthopelagic, detection, PCR, RCC6328, RCC6338, RCC6344, RCC6548, RCC6550, toxins, \textitVulcanodinium rugosum},
	issn = {2072-6651},
	doi = {10.3390/toxins15030217},
	url = {https://www.mdpi.com/2072-6651/15/3/217},
	author = {Bouquet, Aur{\'e}lien and Felix, Christine and Masseret, Estelle and Reymond, Coralie and Abadie, Eric and Laabir, Mohamed and Rolland, Jean Luc}
}
@article {strauss_bay_2023,
	title = {The Bay of Bengal exposes abundant photosynthetic picoplankton and newfound diversity along salinity-driven gradients},
	journal = {Environmental Microbiology},
	year = {2023},
	abstract = {The Bay of Bengal (BoB) is a 2,600,000 km2 expanse in the Indian Ocean upon which many humans rely. However, the primary producers underpinning food chains here remain poorly characterized. We examined phytoplankton abundance and diversity along strong BoB latitudinal and vertical salinity gradients-which have low temperature variation (27-29{\textdegree}C) between the surface and subsurface chlorophyll maximum (SCM). In surface waters, Prochlorococcus averaged 11.7 {\textpm} 4.4 {\texttimes} 104  cells ml-1 , predominantly HLII, whereas LLII and {\textquoteright}rare{\textquoteright} ecotypes, HLVI and LLVII, dominated in the SCM. Synechococcus averaged 8.4 {\textpm} 2.3 {\texttimes} 104  cells ml-1 in the surface, declined rapidly with depth, and population structure of dominant Clade II differed between surface and SCM; Clade X was notable at both depths. Across all sites, Ostreococcus Clade OII dominated SCM eukaryotes whereas communities differentiated strongly moving from Arabian Sea-influenced high salinity (southerly; prasinophytes) to freshwater-influenced low salinity (northerly; stramenopiles, specifically, diatoms, pelagophytes, and dictyochophytes, plus the prasinophyte Micromonas) surface waters. Eukaryotic phytoplankton peaked in the south (1.9 {\texttimes} 104  cells ml-1 , surface) where a novel Ostreococcus was revealed, named here Ostreococcus bengalensis. We expose dominance of a single picoeukaryote and hitherto {\textquoteright}rare{\textquoteright} picocyanobacteria at depth in this complex ecosystem where studies suggest picoplankton are replacing larger phytoplankton due to climate change.},
	keywords = {RCC393, RCC809},
	issn = {1462-2920},
	doi = {10.1111/1462-2920.16431},
	author = {Strauss, Jan and Choi, Chang Jae and Grone, Jonathan and Wittmers, Fabian and Jimenez, Valeria and Makareviciute-Fichtner, Kriste and Bachy, Charles and Jaeger, Gualtiero Spiro and Poirier, Camille and Eckmann, Charlotte and Spezzano, Rachele and L{\"o}scher, Carolin R. and Sarma, V. V. S. S. and Mahadevan, Amala and Worden, Alexandra Z.}
}
@article {letscher_biodiversity_2023,
	title = {Biodiversity and stoichiometric plasticity increase pico-phytoplankton contributions to marine net primary productivity and the biological pump},
	journal = {Global Biogeochemical Cycles},
	volume = {n/a},
	number = {n/a},
	year = {2023},
	note = {_eprint: https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2023GB007756},
	pages = {e2023GB007756},
	abstract = {Earth System Models generally predict increasing upper ocean stratification from 21st century warming, which will cause a decrease in the vertical nutrient flux forcing declines in marine net primary productivity (NPP) and carbon export. Recent advances in quantifying marine ecosystem carbon to nutrient stoichiometry have identified large latitudinal and biome variability, with low-latitude oligotrophic systems harboring pico-sized phytoplankton exhibiting large phosphorus to carbon cellular plasticity. Climate forced changes in nutrient flux stoichiometry and phytoplankton community composition is thus likely to alter the ocean{\textquoteright}s biogeochemical response and feedback with the carbon-climate system. We have added three pico-phytoplankton functional types within the Biogeochemical Elemental Cycling component of the Community Earth System Model while incorporating variable cellular phosphorus to carbon stoichiometry for all represented phytoplankton types. The model simulates Prochlorococcus and Synechococcus populations that dominate the productivity and sinking carbon export of the tropical and subtropical ocean, and pico-eukaryote populations that contribute significantly to productivity and export within the subtropical to mid-latitude transition zone, with the western subtropical regions of each basin supporting the most P-poor stoichiometries. Subtropical gyre recirculation regions along the poleward flanks of surface western boundary currents are identified as regional hotspots of enhanced carbon export exhibiting C-rich/P-poor stoichiometry, preferentially inhabited by pico-eukaryotes and diatoms. Collectively, pico-phytoplankton contribute \~{}58\% of global NPP and \~{}46\% of global particulate organic carbon export below 100 meters through direct and ecosystem processing pathways. Biodiversity and cellular nutrient plasticity in marine pico-phytoplankton combine to increase their contributions to ocean productivity and the biological carbon pump. This article is protected by copyright. All rights reserved.},
	keywords = {carbon export, net primary productivity, pico-phytoplankton, rcc162, rcc1677, rcc212, rcc289, rcc296, rcc30, rcc438, variable C:P},
	issn = {1944-9224},
	doi = {10.1029/2023GB007756},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1029/2023GB007756},
	author = {Letscher, Robert T. and Moore, J. Keith and Martiny, Adam C. and Lomas, Michael W.}
}
@booklet {dennu_biological_2023,
	title = {Biological and genomic resources for the cosmopolitan phytoplankton Bathycoccus: Insights into genetic diversity and major structural variations},
	year = {2023},
	note = {Pages: 2023.10.16.562038 Section: New Results},
	month = {oct},
	publisher = {bioRxiv},
	abstract = {Population-scale sequencing has become a standard practice to explore the natural genetic diversity underlying adaptation, notably in land plants. However, current sequencing initiatives for eukaryotic phytoplankton primarily concentrate on creating reference genomes for model organisms and characterizing natural communities through metagenomics approaches. Consequently, few species have been thoroughly sequenced and intraspecific genetic diversity remains virtually undescribed, limiting our understanding of diversity and adaptation mechanisms. Here we report a biological and genomic resource to explore the genetic diversity of the cosmopolitan and ecologically important Bathycoccus genus. To span broad geographical and temporal scales, we selected available strains but also isolated and genotyped strains from both the Banyuls bay (Mediterranean sea) and the Baffin bay (Arctic ocean). By combining ONT long reads and Illumina short reads technologies, we produced and annotated 28 Bathycoccus sp. de novo assembled genomes of high quality, including 24 genomes of Bathycoccus prasinos strains along a latitudinal gradient between 40{\textdegree} and 78{\textdegree} North, one reference genome of the Bathycoccus calidus species and 3 genomes of a yet undescribed Bathycoccus species named Bathycoccus catiminus. We assessed the genetic diversity of this genus through phylogenomic analyses and highlighted the central role of this genomic resource in providing new insights into the diversity of outlier chromosomal structures. The Bathycoccus biological and genomic resources offer a robust framework for investigating the diversity and adaptation mechanisms of eukaryotic phytoplankton in the Ocean. Significance statement Comparative and functional approaches for the study of eukaryotic phytoplankton and their adaptation to latitudes and seasons that rely on extensive biological and genomic resources are currently lacking. Here we report such resources and describe the natural diversity of the cosmopolitan phytoplankton Bathycoccus, providing insights into its species and intraspecific diversity and establishing it as a robust model for functional and ecological studies.},
	keywords = {RCC1615, RCC1868, RCC4222, RCC4752, RCC5417, RCC685, RCC716},
	doi = {10.1101/2023.10.16.562038},
	url = {https://www.biorxiv.org/content/10.1101/2023.10.16.562038v1},
	author = {Dennu, Louis and Devic, Martine and Rigonato, Janaina and Falciatore, Angela and Lozano, Jean-Claude and Verg{\'e}, Val{\'e}rie and Mariac, C{\'e}dric and Jaillon, Olivier and Team, The Dark Edge genomics sampling and Sabot, Fran{\c c}ois and Bouget, Fran{\c c}ois-Yves}
}
@article {cruz_bioprospecting_2023,
	title = {Bioprospecting for industrially relevant exopolysaccharide-producing cyanobacteria under Portuguese simulated climate},
	journal = {Scientific Reports},
	volume = {13},
	number = {1},
	year = {2023},
	note = {Number: 1 Publisher: Nature Publishing Group},
	pages = {13561},
	abstract = {Cyanobacterial exopolysaccharides (EPS) are potential candidates for the production of sustainable biopolymers. Although the bioactive and physicochemical properties of cyanobacterial-based EPS are attractive, their commercial exploitation is limited by the high production costs. Bioprospecting and characterizing novel EPS-producing strains for industrially relevant conditions is key to facilitate their implementation in various biotechnological applications and fields. In the present work, we selected twenty-five Portuguese cyanobacterial strains from a diverse taxonomic range (including some genera studied for the first time) to be grown in diel light and temperature, simulating the Portuguese climate conditions, and evaluated their growth performance and proximal composition of macronutrients. Synechocystis and Cyanobium genera, from marine and freshwater origin, were highlighted as fast-growing (0.1{\textendash}0.2~g~L-1~day-1) with distinct biomass composition. Synechocystis sp. LEGE 07367 and Chroococcales cyanobacterium LEGE 19970, showed a production of 0.3 and 0.4~g~L-1 of released polysaccharides (RPS). These were found to be glucan-based polymers with high molecular weight and a low number of monosaccharides than usually reported for cyanobacterial EPS. In addition, the absence of known cyanotoxins in these two RPS producers was also confirmed. This work provides the initial steps for the development of cyanobacterial EPS bioprocesses under the Portuguese climate.},
	keywords = {Biochemistry, Biotechnology, Microbiology, rcc2380},
	issn = {2045-2322},
	doi = {10.1038/s41598-023-40542-6},
	url = {https://www.nature.com/articles/s41598-023-40542-6},
	author = {Cruz, Jos{\'e} Diogo and Delattre, C{\'e}dric and Felpeto, Aldo Barreiro and Pereira, Hugo and Pierre, Guillaume and Morais, Jo{\~a}o and Petit, Emmanuel and Silva, Joana and Azevedo, Joana and Elboutachfaiti, Redouan and Maia, In{\^e}s B. and Dubessay, Pascal and Michaud, Philippe and Vasconcelos, Vitor}
}
@article {arnaldo_comparison_2023,
	title = {Comparison of different small-scale cultivation methods towards the valorization of a marine benthic diatom strain for lipid production},
	journal = {Algal Research},
	year = {2023},
	pages = {103327},
	keywords = {RCC5813},
	issn = {22119264},
	doi = {10.1016/j.algal.2023.103327},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2211926423003600},
	author = {Arnaldo, Mary Dianne Grace and Gamage, Nadeeshani Dehel and Jaffrenou, Agathe and Rabesaotra, Vony and Mossion, Aur{\'e}lie and Wielgosz-Collin, Ga{\"e}tane and M{\'e}l{\'e}der, Vona}
}
@booklet {de_vries_critical_2023,
	title = {A critical trade-off between nitrogen quota and growth allows Coccolithus braarudii life cycle phases{\textquoteright} to exploit varying environment},
	year = {2023},
	publisher = {Biodiversity and Ecosystem Function: Marine},
	type = {preprint},
	abstract = {Coccolithophores have a distinct haplo-diplontic life cycle, which allows them to grow and divide in two different life cycle phases (haploid and diploid). These life cycle phases vary significantly in inorganic carbon content and morphology, and inhabit distinct niches, with haploids generally preferring low-nutrient and high-temperature and -light environments. This niche contrast indicates different physiology of the life cycle phases, which is considered here in the context of a trait trade-off 5 framework, in which a particular set of traits comes with both costs and benefits. However, coccolithophore{\textquoteright}s phase trade-offs are not fully identified, limiting our understanding of the functionality of the coccolithophore life cycle. Here, we investigate the response of the two life cycle phases of the coccolithophore Coccolithus braarudii to key environmental drivers: light, temperature and nutrients, using laboratory experiments. With this data, we identify the main trade-offs of each life cycle phase and use models to test the role of such trade-offs under different environmental conditions.},
	keywords = {RCC1200, RCC1203, RCC3777, RCC3779, RCC6535},
	doi = {10.5194/egusphere-2023-880},
	url = {https://egusphere.copernicus.org/preprints/2023/egusphere-2023-880/},
	author = {De Vries, Joost and Monteiro, Fanny and Langer, Gerald and Brownlee, Colin and Wheeler, Glen}
}
@article {coleman_fine-tuning_2023,
	title = {Fine-tuning the flavor of Tetraselmis chuii by modifying nitrogen supply},
	journal = {Algal Research},
	year = {2023},
	pages = {103208},
	abstract = {Dried Tetraselmis chuii biomass has potential as flavoring agent for the development of plant-based seafood alternatives because of its seafood-like aroma and strong umami taste. Depending on the cultivation conditions, microalgae can adapt their metabolism, resulting in a change in biochemical composition. The aim of this study was to assess if the flavor of T. chuii could be modified by changing the nitrogen (N) supply in the cultivation medium in order to maximize the potential of T. chuii as flavoring agent. The sensory evaluation by a trained panel showed that the T. chuii biomass obtained from N starved cultivation conditions (N-deplete) is characterized by a significantly stronger odor intensity and earthy-like off-odor compared to T. chuii biomass obtained from N sufficient cultivation conditions (N-replete). The analysis of volatile organic compounds (VOCs) using SPME-GC{\textendash}MS showed that these odor features of N-deplete biomass are attributed to an increased formation of odor-active VOCs including 2,3-butanedione, 3-methylbutanal, 3-methylbutanol and sulfur-containing dimethyl sulfide and dimethyl disulfide. In contrast, the T. chuii N-replete biomass possessed a significantly stronger taste intensity, umami and salty taste compared to the T. chuii N-deplete biomass. The higher umami is attributed to the significantly higher free glutamic acid (Glu) and adenosine monophosphate (AMP) concentrations in N-replete biomass compared to N-deplete biomass. This study illustrates that flavor and palatability of microalgae biomass is strongly affected by cultivating conditions and modifying these conditions can be an important tool in the development of plant-based seafood alternatives.},
	keywords = {Microalgae, Nitrogen starvation, RCC128, Sensory evaluation, Umami, Volatile organic compounds},
	issn = {2211-9264},
	doi = {10.1016/j.algal.2023.103208},
	url = {https://www.sciencedirect.com/science/article/pii/S2211926423002412},
	author = {Coleman, Bert and Van Poucke, Christof and Dewitte, Bavo and Casciaro, Valentina and Moerdijk-Poortvliet, Tanja and Muylaert, Koenraad and Robbens, Johan}
}
@article {ruvindy_genomic_2023,
	title = {Genomic copy number variability at the genus, species and population levels impacts in situ ecological analyses of dinoflagellates and harmful algal blooms},
	journal = {ISME Communications},
	volume = {3},
	number = {1},
	year = {2023},
	note = {Number: 1 Publisher: Nature Publishing Group},
	month = {jul},
	pages = {1{\textendash}11},
	abstract = {The application of meta-barcoding, qPCR, and metagenomics to aquatic eukaryotic microbial communities requires knowledge of genomic copy number variability (CNV). CNV may be particularly relevant to functional genes, impacting dosage and expression, yet little is known of the scale and role of CNV in microbial eukaryotes. Here, we quantify CNV of rRNA and a gene involved in Paralytic Shellfish Toxin (PST) synthesis (sxtA4), in 51 strains of 4 Alexandrium (Dinophyceae) species. Genomes varied up to threefold within species and \textasciitilde7-fold amongst species, with the largest (A. pacificum, 130 {\textpm} 1.3 pg cell-1 /\textasciitilde127 Gbp) in the largest size category of any eukaryote. Genomic copy numbers (GCN) of rRNA varied by 6 orders of magnitude amongst Alexandrium (102{\textendash} 108 copies cell-1) and were significantly related to genome size. Within the population CNV of rRNA was 2 orders of magnitude (105 {\textendash} 107 cell-1) in 15 isolates from one population, demonstrating that quantitative data based on rRNA genes needs considerable caution in interpretation, even if validated against locally isolated strains. Despite up to 30 years in laboratory culture, rRNA CNV and genome size variability were not correlated with time in culture. Cell volume was only weakly associated with rRNA GCN (20{\textendash}22\% variance explained across dinoflagellates, 4\% in Gonyaulacales). GCN of sxtA4 varied from 0{\textendash}102 copies cell-1, was significantly related to PSTs (ng cell-1), displaying a gene dosage effect modulating PST production. Our data indicate that in dinoflagellates, a major marine eukaryotic group, low-copy functional genes are more reliable and informative targets for quantification of ecological processes than unstable rRNA genes.},
	keywords = {Molecular ecology, Molecular Evolution, RCC3145, RCC4874, RCC4876, RCC4877, RCC4879},
	issn = {2730-6151},
	doi = {10.1038/s43705-023-00274-0},
	url = {https://www.nature.com/articles/s43705-023-00274-0},
	author = {Ruvindy, Rendy and Barua, Abanti and Bolch, Christopher J. S. and Sarowar, Chowdhury and Savela, Henna and Murray, Shauna A.}
}
@article {lopez-pacheco_growth_2023,
	title = {Growth Behavior, Biomass Composition and Fatty Acid Methyl Esters (FAMEs) Production Potential of Chlamydomonas reinhardtii, and Chlorella vulgaris Cultures},
	journal = {Marine Drugs},
	volume = {21},
	number = {8},
	year = {2023},
	month = {aug},
	pages = {450},
	abstract = {The production of biomolecules by microalgae has a wide range of applications in the development of various materials and products, such as biodiesel, food supplements, and cosmetics. Microalgae biomass can be produced using waste and in a smaller space than other types of crops (e.g., soja, corn), which shows microalgae{\textquoteright}s great potential as a source of biomass. Among the produced biomolecules of greatest interest are carbohydrates, proteins, lipids, and fatty acids. In this study, the production of these biomolecules was determined in two strains of microalgae (Chlamydomonas reinhardtii and Chlorella vulgaris) when exposed to different concentrations of nitrogen, phosphorus, and sulfur. Results show a significant microalgal growth (3.69 g L-1) and carbohydrates (163 mg g-1) increase in C. reinhardtii under low nitrogen concentration. Also, higher lipids content was produced under low sulfur concentration (246 mg g-1). It was observed that sulfur variation could affect in a negative way proteins production in C. reinhardtii culture. In the case of C. vulgaris, a higher biomass production was obtained in the standard culture medium (1.37 g L-1), and under a low-phosphorus condition, C. vulgaris produced a higher lipids concentration (248 mg g-1). It was observed that a low concentration of nitrogen had a better effect on the accumulation of fatty acid methyl esters (FAMEs) (C16-C18) in both microalgae. These results lead us to visualize the effects that the variation in macronutrients can have on the growth of microalgae and their possible utility for the production of microalgae-based subproducts.},
	keywords = {RCC2488},
	issn = {1660-3397},
	doi = {10.3390/md21080450},
	url = {https://www.mdpi.com/1660-3397/21/8/450},
	author = {L{\'o}pez-Pacheco, Itzel Y. and Ayala-Moreno, Victoria Guadalupe and Mejia-Melara, Catherinne Arlette and Rodr{\'\i}guez-Rodr{\'\i}guez, Jos{\'e} and Cuellar-Bermudez, Sara P. and Gonz{\'a}lez-Gonz{\'a}lez, Reyna Berenice and Coronado-Apodaca, Karina G. and Farfan-Cabrera, Leonardo I. and Gonz{\'a}lez-Meza, Georgia Mar{\'\i}a and Iqbal, Hafiz M. N. and Parra-Sald{\'\i}var, Roberto}
}
@booklet {devic_indel_2023,
	title = {An INDEL genomic approach to explore population diversity of phytoplankton : \textit{Bathycoccus , a case study},
	year = {2023},
	publisher = {Ecology},
	type = {preprint},
	abstract = {Abstract Although metabarcoding has generated large dataset on world-wide phytoplankton species diversity, little is known about the intraspecies diversity underlying adaptation to environmental niches. To gain insight into population diversity, a novel INDEL based method was developed on Bathycoccus prasinos . Oxford Nanopore Technology (ONT) sequencing was first used to characterise structural variants (SV) among the genomes of Bathycoccus sampled from geographically distinct regions in the world ocean. Markers derived from INDEL were validated by PCR and sequencing in the world-wide strains. These markers were then used to genotype 55 Bathycoccus strains isolated during the winter bloom 2018-2019 in the bay of Banyuls-sur-Mer. With five markers, eight Multi Loci Genotypes (MLG) were determined, two of which represented 53\% and 29\% of the isolates. Physiological studies confirmed that isolates are phenotypically different, cells isolated in February growing better at low temperature than those isolated in December and January. When tested directly on environmental samples, two diversity markers showed a similar allele frequency in sea water as in individual Bathycoccus strains isolated at the same period. We conclude that these markers constitute a resource to identify the most abundant variant alleles in a given bloom. A follow-up on three consecutive blooms revealed differences in allele abundance during the course of a bloom, particularly at initiation and between years. This INDEL-based genotyping constitutes a new methodological approach that may be used to assess the population structure and diversity of other species.},
	keywords = {RCC1613, RCC1615, RCC1868, RCC4222, RCC4752, RCC5417, RCC685},
	doi = {10.1101/2023.02.09.527951},
	url = {http://biorxiv.org/lookup/doi/10.1101/2023.02.09.527951},
	author = {Devic, Martine and Mariac, C{\'e}dric and Verg{\'e}, Val{\'e}rie and Schatt, Philipe and Dennu, Louis and Lozano, Jean-Claude and Bouget, Fran{\c c}ois-Yves and Sabot, Fran{\c c}ois}
}
@article {moreno-cabezuelo_integrated_2023,
	title = {Integrated Proteomic and Metabolomic Analyses Show Differential Effects of Glucose Availability in Marine Synechococcus and Prochlorococcus},
	journal = {Microbiology Spectrum},
	year = {2023},
	month = {feb},
	pages = {e03275{\textendash}22},
	abstract = {<p>We compared changes induced by the addition of 100 nM and 5 mM glucose on the proteome and metabolome complements in Synechococcus sp. strains WH8102, WH7803, and BL107 and Prochlorococcus sp. strains MED4, SS120, and MIT9313, grown either under standard light conditions or in darkness. Our results suggested that glucose is metabolized by these cyanobacteria, using primarily the oxidative pentoses and Calvin pathways, while no proof was found for the involvement of the EntnerDoudoroff pathway in this process. We observed differences in the effects of glucose availability, both between genera and between Prochlorococcus MED4 and SS120 strains, which might be related to their specific adaptations to the environment. We found evidence for fermentation in Prochlorococcus sp. strain SS120 and Synechococcus sp. strain WH8102 after 5 mM glucose addition. Our results additionally suggested that marine cyanobacteria can detect nanomolar glucose concentrations in the environment and that glucose might be used to sustain metabolism under darkness. Furthermore, the KaiB and KaiC proteins were also affected in Synechococcus sp. WH8102, pointing to a direct link between glucose assimilation and circadian rhythms in marine cyanobacteria. In conclusion, our study provides a wide overview on the metabolic effects induced by glucose availability in representative strains of the diverse marine picocyanobacteria, providing further evidence for the importance of mixotrophy in marine picocyanobacteria.</p>
},
	keywords = {RCC156, RCC407, RCC515, rcc539, rcc752},
	issn = {2165-0497},
	doi = {10.1128/spectrum.03275-22},
	url = {https://journals.asm.org/doi/10.1128/spectrum.03275-22},
	author = {Moreno-Cabezuelo, Jos{\'e} {\'A}ngel and G{\'o}mez-Baena, Guadalupe and D{\'\i}ez, Jes{\'u}s and Garc{\'\i}a-Fern{\'a}ndez, Jos{\'e} Manuel},
	editor = {Hom, Erik F. Y.}
}
@article {barbosa_microalga_2023,
	title = {The microalga \textit{Dunaliella and its applications: a review},
	journal = {Applied Phycology},
	volume = {4},
	number = {1},
	year = {2023},
	pages = {99{\textendash}120},
	keywords = {RCC3579, RCC5},
	issn = {2638-8081},
	doi = {10.1080/26388081.2023.2222318},
	url = {https://www.tandfonline.com/doi/full/10.1080/26388081.2023.2222318},
	author = {Barbosa, Miguel and In{\'a}cio, Leonardo Garcia and Afonso, Cl{\'e}lia and Maranh{\~a}o, Paulo}
}
@article {mertens_morpho-molecular_2023,
	title = {Morpho-molecular analysis of podolampadacean dinoflagellates (Dinophyceae), with the description of two new genera},
	journal = {Phycologia},
	year = {2023},
	note = {Publisher: Taylor \& Francis _eprint: https://doi.org/10.1080/00318884.2022.2158281},
	month = {feb},
	pages = {1{\textendash}19},
	abstract = {Sequences were obtained for 58 podolampadacean single cells from France, Reunion Island (French territories) and Japan (6 SSU rDNA only, 40 SSU+LSU and 12 LSU only). The sequenced taxa belong to five of the eight described genera: Podolampas, Blepharocysta, Lissodinium, Gaarderiella and Mysticella. Two new genera, Alatosphaera and Pseudalatosphaera, were erected to accommodate {\textquoteleft}Blepharocysta{\textquoteright} hermosillae and {\textquoteleft}Blepharocysta{\textquoteright} denticulata. Most genera are well supported by concatenated LSU{\textendash}SSU rDNA phylogenies, with the least support for Lissodinium. Metabarcoding of podolampadaceans using the V4 region of SSU rDNA showed a resolution too low to discriminate genera or species. Roscoffia and Cabra are here considered podolampadaceans, whilst Lessardia is considered to belong in a separate family. The relationship of Rhinodinium to the Podolampadaceae needs further study. Desmoschisis was recorded for the first time in Alatosphaera and Pseudalatosphaera. Several ribotypes need further study to attribute a species name to them.},
	keywords = {Alatosphaera, Blepharocysta, desmoschisis, Gaarderiella, Lissodinium, LSU rDNA, Mysticella, Podolampas, Pseudalatosphaera, SSU rDNA},
	issn = {0031-8884},
	doi = {10.1080/00318884.2022.2158281},
	url = {https://doi.org/10.1080/00318884.2022.2158281},
	author = {Mertens, Kenneth Neil and Carbonell-Moore, M. Consuelo and Chom{\'e}rat, Nicolas and Bilien, Gwenael and Boulben, Sylviane and Guillou, Laure and Romac, Sarah and Probert, Ian and Ishikawa, Akira and N{\'e}zan, Elisabeth}
}
@booklet {wang_novel_2023,
	title = {Novel dimethylsulfoniopropionate biosynthesis enzymes in diverse marine bacteria, cyanobacteria and abundant algae},
	year = {2023},
	month = {mar},
	publisher = {In Review},
	type = {preprint},
	abstract = {Abstract Dimethylsulfoniopropionate (DMSP) is an abundant marine organosulfur compound[1] with roles in stress protection[2, 3], chemotaxis[4], nutrient and sulfur cycling[5] and, potentially, climate regulation[6, 7]. Marine algae and bacteria are considered significant DMSP producers, but many diverse representatives lack known DMSP synthesis genes/enzymes[8, 9]. Here, new DMSP biosynthesis enzymes were identified that considerably increase the number and diversity of potential DMSP-producing organisms, inferring new and significant global DMSP producers. A novel bifunctional DMSP biosynthesis enzyme, DsyGD, identified in the rhizobacterium Gynuella sunshinyii, produces DMSP at levels higher than any other bacterium from methylthiohydroxybutyrate (MTHB) via an N-terminal MTHB S-methyltransferase domain (termed DsyG) and a C-terminal dimethylsulfoniohydroxybutyrate (DMSHB) decarboxylase domain (termed DsyD, which is the first reported enzyme with this activity). DsyGD is also found in some filamentous cyanobacteria, not previously known to produce DMSP. Regulation of DMSP production and dsyGD transcription was consistent with their role in osmoprotection. Indeed, cloned dsyGD conferred osmotolerance to bacteria deficient in osmolyte production, something not previously demonstrated for any known DMSP synthesis gene, and which could be exploited for biotechnology e.g., engineering salt tolerance. DsyGD characterisation led to identification of phylogenetically distinct DsyG-like proteins, termed DSYE, with MTHB S-methyltransferase activity, in diverse and environmentally abundant Chlorophyta, Chlorachniophyta, Ochraphyta, Haptophyta and Bacillariophyta algae. These algae comprise a mix of low, high and previously unknown DMSP producers[10]. Algae containing DSYE, particularly bloom-forming Pelagophyceae species, which we showed to accumulate medium-high intracellular DMSP levels, were globally more abundant DMSP producers than Haptophyta, Dinophyta and Bacillariophyta with DSYB and/or TpMMT. This highlights the potential importance of Pelagophyceae and other DSYE containing algae in global DMSP production and sulfur cycling.},
	keywords = {RCC100, RCC2956, RCC4094, RCC4422, RCC6172},
	doi = {10.21203/rs.3.rs-2678769/v1},
	url = {https://www.researchsquare.com/article/rs-2678769/v1},
	author = {Wang, Jinyan and Zhou, Shun and Curson, Andrew and Vieira, Ana and Walsham, Keanu and Monaco, Serena and Li, Chun-Yang and Rivera, Peter Paolo and Wang, Xiao-Di and Hanwell, Libby and Zhu, Xiao-Yu and Le{\~a}o, Pedro and Lea-Smith, David J. and Zhang, Yuzhong and Zhang, Xiaohua and Todd, Jonathan}
}
@article {concordio-reis_novel_2023,
	title = {Novel exopolysaccharide produced by the marine dinoflagellate Heterocapsa AC210: Production, characterization, and biological properties},
	journal = {Algal Research},
	volume = {70},
	year = {2023},
	pages = {103014},
	abstract = {Marine microalgae are promising sources of novel valuable biomolecules such as polysaccharides. In this study, the dinoflagellate Heterocapsa sp. AC210 was described as a new exopolysaccharide (EPS) producer. The cultivation and EPS production in bioreactor was evaluated for the first time in detail. The EPS was composed of seven different sugar monomers, including fucose and glucosamine, which are quite rare and have never been reported in dinoflagellates{\textquoteright} EPS. Moreover, the EPS had a high content of sulphate, which is often associated with biological properties. Cytotoxicity was accessed and the results showed that the EPS did not reduce cell viability for concentrations up to 1~g~L-1. Additionally, antioxidant and anti-inflammatory assays demonstrated that the EPS reduced by 18~\% the intracellular reactive oxygen species and decreased up to 79.3~\% and 46.2~\% of IL-8 and IL-6 secretion in keratinocytes, which supports its potential application in the cosmeceutical and biomedical fields.},
	keywords = {Anti-inflammatory, Cytotoxicity, Dinoflagellates, Exopolysaccharide production, Marine microalgae, RCC1514, sp. AC210},
	issn = {2211-9264},
	doi = {10.1016/j.algal.2023.103014},
	url = {https://www.sciencedirect.com/science/article/pii/S2211926423000474},
	author = {Conc{\'o}rdio-Reis, Patr{\'\i}cia and Cardeira, Martim and Macedo, Ana Catarina and Ferreira, S{\'o}nia S. and Serra, Ana Teresa and Coimbra, Manuel A. and Amorim, Ana and Reis, Maria A. M. and Freitas, Filomena}
}
@article {noordally_phospho-dawn_2023,
	title = {A phospho-dawn of protein modification anticipates light onset in the picoeukaryote \textit{O. tauri},
	journal = {Journal of Experimental Botany},
	year = {2023},
	month = {jul},
	pages = {erad290},
	abstract = {Abstract Diel regulation of protein levels and protein modification had been less studied than transcript rhythms. Here, we compare transcriptome data under light-dark cycles to partial proteome and phosphoproteome data, assayed using shotgun mass-spectrometry, from the alga Ostreococcus tauri, the smallest free-living eukaryote. 10\% of quantified proteins but two-thirds of phosphoproteins were rhythmic. Mathematical modelling showed that light-stimulated protein synthesis can account for the observed clustering of protein peaks in the daytime. Prompted by night-peaking and apparently dark-stable proteins, we also tested cultures under prolonged darkness, where the proteome changed less than under the diel cycle. Among the dark-stable proteins were prasinophyte-specific sequences that were also reported to accumulate when O. tauri formed lipid droplets. In the phosphoproteome, 39\% of rhythmic phospho-sites reached peak levels just before dawn. This anticipatory phosphorylation suggests that a clock-regulated phospho-dawn prepares green cells for daytime functions. Acid-directed and proline-directed protein phosphorylation sites were regulated in antiphase, implicating the clock-related, casein kinases 1 and 2 in phase-specific regulation, alternating with the CMGC protein kinase family. Understanding the dynamic phosphoprotein network should be facilitated by the minimal kinome and proteome of O. tauri. The data are available from ProteomeXchange, with identifiers PXD001734, PXD001735 and PXD002909.},
	keywords = {RCC745},
	issn = {0022-0957, 1460-2431},
	doi = {10.1093/jxb/erad290},
	url = {https://academic.oup.com/jxb/advance-article/doi/10.1093/jxb/erad290/7229478},
	author = {Noordally, Zeenat B and Hindle, Matthew M and Martin, Sarah F and Seaton, Daniel D and Simpson, T Ian and Le Bihan, Thierry and Millar, Andrew J}
}
@booklet {devic_population_2023,
	title = {Population dynamics of the cosmopolitan eukaryotic picophytoplankton Bathycoccus during seasonal blooms in the bay of Banyuls sur Mer (North Western Mediterranean sea)},
	year = {2023},
	publisher = {BioRxiv},
	type = {preprint},
	abstract = {Abstract Although Bathycoccus is one of the most abundant picophytoplankton, little is known about the genetic diversity underlying its adaptation to ecological niches. In this study, the diversity of Bathycoccus populations during their annual bloom in the Mediterranean bay of Banyuls France was assessed by an INDEL based approach. Oxford Nanopore Technology (ONT) was used to characterise structural variants (SV) among the genomes of Bathycoccus sampled from geographically distinct regions in the world ocean. Markers derived from INDEL were validated by PCR and sequencing in the world-wide strains. These markers were then used to genotype 55 Bathycoccus strains isolated during the winter bloom 2018-2019 in Banyuls. With five markers, eight Multi Loci Genotypes (MLG) were determined, two of which represented 53\% and 29\% of the isolates. Physiological studies confirmed that isolates are phenotypically different, cells isolated in February growing better at low temperature than those isolated in December. When tested on environmental samples, two diversity markers showed a similar allele frequency in sea water as in individual Bathycoccus strains isolated at the same period. We conclude that these markers constitute a resource to identify the most abundant variant alleles in a given bloom. A follow-up on three consecutive blooms revealed differences in allele abundance during the course of a bloom, particularly at initiation, and between years. In addition to Bathycoccus prasinos , two other species of Bathycoccus were identified including the recently described species B. calidus and a novel species B. catiminus , suggesting that species diversity of the genus Bathycoccus may be underestimated.},
	keywords = {RCC1613, RCC1615, RCC1868, RCC4222, RCC4752, RCC5417, RCC685},
	doi = {10.1101/2023.02.09.527951},
	url = {http://biorxiv.org/lookup/doi/10.1101/2023.02.09.527951},
	author = {Devic, Martine and Mariac, C{\'e}dric and Verg{\'e}, Val{\'e}rie and Schatt, Philipe and Dennu, Louis and Lozano, Jean-Claude and Bouget, Fran{\c c}ois-Yves and Sabot, Fran{\c c}ois}
}
@article {zhang_stimulating_2023,
	title = {Stimulating and toxic effect of chromium on growth and photosynthesis of a marine chlorophyte},
	journal = {New Phytologist},
	volume = {n/a},
	number = {n/a},
	year = {2023},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19376},
	abstract = {Marine phytoplankton can interchange trace metals in various biochemical functions, particularly under metal-limiting conditions. Here, we investigate the stimulating and toxicity effect of chromium (Cr) on a marine Chlorophyceae Osetreococcus tauri under Fe-replete and Fe-deficient conditions. We determined the growth, photosynthesis, and proteome expressions of Osetreococcus tauri cultured under different Cr and Fe concentrations. In Fe-replete conditions, the presence of Cr(VI) stimulated significantly the growth rate and the maximum yield of photochemistry of photosystem II (Fv/Fm) of the phytoplankton, while the functional absorption cross-section of photosystem II (σPSII) did not change. Minor additions of Cr(VI) partially rescued phytoplankton growth under Fe-limited conditions. Proteomic analysis of this alga grown in Fe-replete normal and Fe-replete with Cr addition media (10 μM Cr) showed that the presence of Cr significantly decreased the expression of phosphate-transporting proteins and photosynthetic proteins, while increasing the expression of proteins related to carbon assimilation. Cr can stimulate the growth and photosynthesis of O. tauri, but the effects are dependent on both the Cr(VI) concentration and the availability of Fe. The proteomic results further suggest that Cr(VI) addition might significantly increase starch production and carbon fixation.},
	keywords = {chromium, Photosynthesis, phytoplankton, proteomics, RCC1, RCC1242, trace metal},
	issn = {1469-8137},
	doi = {10.1111/nph.19376},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19376},
	author = {Zhang, Qiong and Charles, Philip D. and Bendif, El Mahdi and Hester, Svenja S. and Mohammad, Shabaz and Rickaby, Rosalind E. M.}
}
@article {alonso-saez_transcriptional_2023,
	title = {Transcriptional Mechanisms of Thermal Acclimation in \textit{Prochlorococcus},
	journal = {mBio},
	year = {2023},
	pages = {e03425{\textendash}22},
	abstract = {Low temperature limits the growth and the distribution of the key oceanic primary producer Prochlorococcus, which does not proliferate above a latitude of ca. 40{\textdegree}. Yet, the molecular basis of thermal acclimation in this cyanobacterium remains unexplored. We analyzed the transcriptional response of the Prochlorococcus marinus strain MIT9301 in long-term acclimations and in natural Prochlorococcus populations along a temperature range enabling its growth (17 to 30{\textdegree}C). MIT9301 upregulated mechanisms of the global stress response at the temperature minimum (17{\textdegree}C) but maintained the expression levels of genes involved in essential metabolic pathways (e.g., ATP synthesis and carbon fixation) along the whole thermal niche. Notably, the declining growth of MIT9301 from the optimum to the minimum temperature was coincident with a transcriptional suppression of the photosynthetic apparatus and a dampening of its circadian expression patterns, indicating a loss in their regulatory capacity under cold conditions. Under warm conditions, the cellular transcript inventory of MIT9301 was strongly streamlined, which may also induce regulatory imbalances due to stochasticity in gene expression. The daytime transcriptional suppression of photosynthetic genes at low temperature was also observed in metatranscriptomic reads mapping to MIT9301 across the global ocean, implying that this molecular mechanism may be associated with the restricted distribution of Prochlorococcus to temperate zones.},
	keywords = {RCC3377},
	issn = {2150-7511},
	doi = {10.1128/mbio.03425-22},
	url = {https://journals.asm.org/doi/10.1128/mbio.03425-22},
	author = {Alonso-S{\'a}ez, Laura and Palacio, Antonio S. and Cabello, Ana M. and Robaina-Est{\'e}vez, Semid{\'a}n and Gonz{\'a}lez, Jos{\'e} M. and Garczarek, Laurence and L{\'o}pez-Urrutia, {\'A}ngel},
	editor = {Martiny, Jennifer B. H.}
}
@article {syhapanha_transcriptomicsguided_2023,
	title = {Transcriptomics-guided identification of an algicidal protease of the marine bacterium Kordia algicida OT-1},
	journal = {MicrobiologyOpen},
	volume = {12},
	number = {5},
	year = {2023},
	pages = {e1387},
	abstract = {In recent years, interest in algicidal bacteria has risen due to their ecological importance and their potential as biotic regulators of harmful algal blooms. Algicidal bacteria shape the plankton communities of the oceans by inhibiting or lysing microalgae and by consuming the released nutrients. Kordia algicida strain OT-1 is a model marine algicidal bacterium that was isolated from a bloom of the diatom Skeletonema costatum. Previous work has suggested that algicidal activity is mediated by secreted proteases. Here, we utilize a transcriptomics-guided approach to identify the serine protease gene KAOT1_RS09515, hereby named alpA1 as a key element in the algicidal activity of K. algicida. The protease AlpA1 was expressed and purified from a heterologous host and used in in vitro bioassays to validate its activity. We also show that K. algicida is the only algicidal species within a group of four members of the Kordia genus. The identification of this algicidal protease opens the possibility of real-time monitoring of the ecological impact of algicidal bacteria in natural phytoplankton blooms., Algicidal bacteria shape the plankton communities of the oceans by lysing microalgae and consuming the released nutrients. Kordia algicida is an environmentally relevant marine bacterium whose algicidal activity is mediated by secreted proteases. In this study, we utilize a transcriptomics-guided approach to identify the secreted serine protease AlpA1 as a key factor in the algicidal process. This discovery offers new approaches for the real-time monitoring and manipulation of algicidal bacteria in algal blooms.},
	keywords = {RCC75},
	issn = {2045-8827},
	doi = {10.1002/mbo3.1387},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10565126/},
	author = {Syhapanha, Kristy S. and Russo, David A. and Deng, Yun and Meyer, Nils and Poulin, Remington X. and Pohnert, Georg}
}
@article {yee_v-type_2023,
	title = {The V-type ATPase enhances photosynthesis in marine phytoplankton and further links phagocytosis to symbiogenesis},
	journal = {Current Biology},
	year = {2023},
	month = {may},
	pages = {S0960982223006152},
	abstract = {Diatoms, dinoflagellates, and coccolithophores are dominant groups of marine eukaryotic phytoplankton that are collectively responsible for the majority of primary production in the ocean.1 These phytoplankton contain additional intracellular membranes around their chloroplasts, which are derived from ancestral engulfment of red microalgae by unicellular heterotrophic eukaryotes that led to secondary and tertiary endosymbiosis.2 However, the selectable evolutionary advantage of these membranes and the physiological significance for extant phytoplankton remain poorly understood. Since intracellular digestive vacuoles are ubiquitously acidified by V-type H+-ATPase (VHA),3 proton pumps were proposed to acidify the microenvironment around secondary chloroplasts to promote the dehydration of dissolved inorganic carbon (DIC) into CO2, thus enhancing photosynthesis.4,5 We report that VHA is localized around the chloroplasts of centric diatoms and that VHA significantly contributes to their photosynthesis across a wide range of oceanic irradiances. Similar results in a pennate diatom, dinoflagellate, and coccolithophore, but not green or red microalgae, imply the co-option of phagocytic VHA activity into a carbon-concentrating mechanism (CCM) is common to secondary endosymbiotic phytoplankton. Furthermore, analogous mechanisms in extant photosymbiotic marine invertebrates6{\textendash}8 provide functional evidence for an adaptive advantage throughout the transition from endosymbiosis to symbiogenesis. Based on the contribution of diatoms to ocean biogeochemical cycles, VHA-mediated enhancement of photosynthesis contributes at least 3.5 Gtons of fixed carbon per year (or 7\% of primary production in the ocean), providing an example of a symbiosis-derived evolutionary innovation with global environmental implications.},
	keywords = {RCC3387},
	issn = {09609822},
	doi = {10.1016/j.cub.2023.05.020},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982223006152},
	author = {Yee, Daniel P. and Samo, Ty J. and Abbriano, Raffaela M. and Shimasaki, Bethany and Vernet, Maria and Mayali, Xavier and Weber, Peter K. and Mitchell, B. Greg and Hildebrand, Mark and Decelle, Johan and Tresguerres, Martin}
}
@article {ferrieux_comparative_2022,
	title = {Comparative Thermophysiology of Marine Synechococcus CRD1 Strains Isolated From Different Thermal Niches in Iron-Depleted Areas},
	journal = {Frontiers in Microbiology},
	volume = {13},
	year = {2022},
	abstract = {Marine Synechococcus cyanobacteria are ubiquitous in the ocean, a feature likely related to their extensive genetic diversity. Amongst the major lineages, clades I and IV preferentially thrive in temperate and cold, nutrient-rich waters, whilst clades II and III prefer warm, nitrogen or phosphorus-depleted waters. The existence of such cold (I/IV) and warm (II/III) thermotypes is corroborated by physiological characterization of representative strains. A fifth clade, CRD1, was recently shown to dominate the Synechococcus community in iron-depleted areas of the world ocean and to encompass three distinct ecologically significant taxonomic units (ESTUs CRD1A-C) occupying different thermal niches, suggesting that distinct thermotypes could also occur within this clade. Here, using comparative thermophysiology of strains representative of these three CRD1 ESTUs we show that the CRD1A strain MITS9220 is a warm thermotype, the CRD1B strain BIOS-U3-1 a cold temperate thermotype, and the CRD1C strain BIOS-E4-1 a warm temperate stenotherm. Curiously, the CRD1B thermotype lacks traits and/or genomic features typical of cold thermotypes. In contrast, we found specific physiological traits of the CRD1 strains compared to their clade I, II, III, and IV counterparts, including a lower growth rate and photosystem II maximal quantum yield at most temperatures and a higher turnover rate of the D1 protein. Together, our data suggests that the CRD1 clade prioritizes adaptation to low-iron conditions over temperature adaptation, even though the occurrence of several CRD1 thermotypes likely explains why the CRD1 clade as a whole occupies most iron-limited waters.},
	keywords = {RCC2374, RCC2385, RCC2533, RCC2534, RCC2571, RCC515, rcc539, rcc791},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2022.893413},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2022.893413},
	author = {Ferrieux, Mathilde and Dufour, Louison and Dor{\'e}, Hugo and Ratin, Morgane and Gu{\'e}neugu{\`e}s, Audrey and Chasselin, L{\'e}o and Marie, Dominique and Rigaut-jalabert, Fabienne and Le Gall, Florence and Sciandra, Th{\'e}o and Monier, Garance and Hoebeke, Mark and Corre, Erwan and Xia, Xiaomin and Liu, Hongbin and Scanlan, David J. and Partensky, Fr{\'e}d{\'e}ric and Garczarek, Laurence}
}
@article {grebert_diversity_2022,
	title = {Diversity and evolution of pigment types in marine \textit{Synechococcus cyanobacteria},
	journal = {Genome Biology and Evolution},
	year = {2022},
	pages = {evac035},
	abstract = {DNA integration and site-specific recombination, suggesting that their genomic variability relies D in part on a {\textquoteleft}tycheposon{\textquoteright}-like mechanism. Comparison of the phylogenies obtained for PBS and E core genes revealed that the evolutionary history of PBS rod genes differs from the core T genome and is characterized by the co-existence of different alleles and frequent allelic P exchange. We propose a scenario for the evolution of the different pigment types and highlight E the importance of incomplete lineage sorting in maintaining a wide diversity of pigment types in C different Synechococcus lineages despite multiple speciation events.},
	keywords = {RCC307, to add},
	issn = {1759-6653},
	doi = {10.1093/gbe/evac035},
	url = {https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evac035/6547267},
	author = {Gr{\'e}bert, Th{\'e}ophile and Garczarek, Laurence and Daubin, Vincent and Humily, Florian and Marie, Dominique and Ratin, Morgane and Devailly, Alban and Farrant, Gregory K. and Mary, Isabelle and Mella-Flores, Daniella and Tanguy, Gwenn and Labadie, Karine and Wincker, Patrick and Kehoe, David M. and Partensky, Fr{\'e}d{\'e}ric},
	editor = {Angert, Esther}
}
@article {guerin_genomic_2022,
	title = {Genomic adaptation of the picoeukaryote Pelagomonas calceolata to iron-poor oceans revealed by a chromosome-scale genome sequence},
	journal = {Communications Biology},
	volume = {5},
	number = {1},
	year = {2022},
	note = {Number: 1 Publisher: Nature Publishing Group},
	pages = {1{\textendash}14},
	abstract = {The smallest phytoplankton species are key actors in oceans biogeochemical cycling and their abundance and distribution are affected with global environmental changes. Among them, algae of the Pelagophyceae class encompass coastal species causative of harmful algal blooms while others are cosmopolitan and abundant. The lack of genomic reference in this lineage is a main limitation to study its ecological importance. Here, we analysed Pelagomonas calceolata relative abundance, ecological niche and potential for the adaptation in all oceans using a complete chromosome-scale assembled genome sequence. Our results show that P. calceolata is one of the most abundant eukaryotic species in the oceans with a relative abundance favoured by high temperature, low-light and iron-poor conditions. Climate change projections based on its relative abundance suggest an extension of the P. calceolata habitat toward the poles at the end of this century. Finally, we observed a specific gene repertoire and expression level variations potentially explaining its ecological success in low-iron and low-nitrate environments. Collectively, these findings reveal the ecological importance of P. calceolata and lay the foundation for a global scale analysis of the adaptation and acclimation strategies of this small phytoplankton in a changing environment. Genomic inference reveals potential climate change-driven range expansion of the phytoplankton species Pelagomonas calceolata.},
	keywords = {Biogeography, comparative genomics, metagenomics, RCC100, Water microbiology},
	issn = {2399-3642},
	doi = {10.1038/s42003-022-03939-z},
	url = {https://www.nature.com/articles/s42003-022-03939-z},
	author = {Gu{\'e}rin, Nina and Ciccarella, Marta and Flamant, Elisa and Fr{\'e}mont, Paul and Mangenot, Sophie and Istace, Benjamin and Noel, Benjamin and Belser, Caroline and Bertrand, Laurie and Labadie, Karine and Cruaud, Corinne and Romac, Sarah and Bachy, Charles and Gachenot, Martin and Pelletier, Eric and Alberti, Adriana and Jaillon, Olivier and Wincker, Patrick and Aury, Jean-Marc and Carradec, Quentin}
}
@article {vazquez_high-co2_2022,
	title = {High-CO2 Levels Rather than Acidification Restrict Emiliania huxleyi Growth and Performance},
	journal = {Microbial Ecology},
	year = {2022},
	abstract = {The coccolithophore Emiliania huxleyi shows a variety of responses to ocean acidification (OA) and to high-CO2 concentrations, but there is still controversy on differentiating between these two factors when using different strains and culture methods. A heavily calcified type A strain isolated from the Norwegian Sea was selected and batch cultured in order to understand whether acclimation to OA was mediated mainly by CO2 or H+, and how it impacted cell growth performance, calcification, and physiological stress management. Emiliania huxleyi responded differently to each acidification method. CO2-enriched aeration (1200 {\textmu}atm, pH 7.62) induced a negative effect on the cells when compared to acidification caused by decreasing pH alone (pH 7.60). The growth rates of the coccolithophore were more negatively affected by high pCO2 than by low pH without CO2 enrichment with respect to the control (400 {\textmu}atm, pH 8.1). High CO2 also affected cell viability and promoted the accumulation of reactive oxygen species (ROS), which was not observed under low pH. This suggests a possible metabolic imbalance induced by high CO2 alone. In contrast, the affinity for carbon uptake was negatively affected by both low pH and high CO2. Photochemistry was only marginally affected by either acidification method when analysed by PAM fluorometry. The POC and PIC cellular quotas and the PIC:POC ratio shifted along the different phases of the cultures; consequently, calcification did not follow the same pattern observed in cell stress and growth performance. Specifically, acidification by HCl addition caused a higher proportion of severely deformed coccoliths, than CO2 enrichment. These results highlight the capacity of CO2 rather than acidification itself to generate metabolic stress, not reducing calcification.},
	keywords = {Calcification, coccolithophores, Emiliania huxleyi, Ocean acidification, pCO2, Photochemistry, phytoplankton, rcc1226, Stress},
	issn = {1432-184X},
	doi = {10.1007/s00248-022-02035-3},
	url = {https://doi.org/10.1007/s00248-022-02035-3},
	author = {V{\'a}zquez, V{\'\i}ctor and Le{\'o}n, Pablo and Gordillo, Francisco J. L. and Jim{\'e}nez, Carlos and Concepci{\'o}n, I{\~n}iguez and Mackenzie, Kevin and Bresnan, Eileen and Segovia, Mar{\'\i}a}
}
@article {biller_isolation_2022,
	title = {Isolation and Characterization of Cyanobacterial Extracellular Vesicles},
	journal = {Journal of Visualized Experiments},
	year = {2022},
	month = {feb},
	abstract = {Cyanobacteria are a diverse group of photosynthetic, Gram-negative bacteria that play critical roles in global ecosystems and serve as essential biotechnology models. Recent work has demonstrated that both marine and freshwater cyanobacteria produce extracellular vesicles - small membrane-bound structures released from the outer surface of the microbes. While vesicles likely contribute to diverse biological processes, their specific functional roles in cyanobacterial biology remain largely unknown. To encourage and advance research in this area, a detailed protocol is presented for isolating, concentrating, and purifying cyanobacterial extracellular vesicles. The current work discusses methodologies that have successfully isolated vesicles from large cultures of Prochlorococcus, Synechococcus, and Synechocystis. Methods for quantifying and characterizing vesicle samples from these strains are presented. Approaches for isolating vesicles from aquatic field samples are also described. Finally, typical challenges encountered with cyanobacterial vesicle purification, methodological considerations for different downstream applications, and the trade-offs between approaches are also discussed.},
	doi = {10.3791/63481},
	author = {Biller, Steven and Mu{\~n}oz Marin, Maria and Lima, Steeve and Matinha-Cardoso, Jorge and Tamagnini, Paula and Oliveira, Paulo}
}
@article {dominguez-martin_marine_2022,
	title = {Marine \textit{Synechococcus sp. Strain WH7803 Shows Specific Adaptative Responses to Assimilate Nanomolar Concentrations of Nitrate},
	journal = {Microbiology Spectrum},
	volume = {10},
	number = {4},
	year = {2022},
	month = {aug},
	pages = {e00187{\textendash}22},
	abstract = {Marine Synechococcus, together with Prochlorococcus, contribute to a significant proportion of the primary production on Earth. The spatial distribution of these two groups of marine picocyanobacteria depends on different factors such as nutrient availability and temperature. Some Synechococcus ecotypes thrive in mesotrophic and moderately oligotrophic waters, where they exploit both oxidized and reduced forms of nitrogen. Here, we present a comprehensive study, which includes transcriptomic and proteomic analyses of the response of Synechococcus sp. strain WH7803 to nanomolar concentrations of nitrate, compared to micromolar ammonium or nitrogen starvation. We found that Synechococcus has a specific response to a nanomolar nitrate concentration that differs from the response shown under nitrogen starvation or the presence of standard concentrations of either ammonium or nitrate. This fact suggests that the particular response to the uptake of nanomolar concentrations of nitrate could be an evolutionary advantage for marine Synechococcus against Prochlorococcus in the natural environment.},
	keywords = {rcc752},
	issn = {2165-0497},
	doi = {10.1128/spectrum.00187-22},
	url = {https://journals.asm.org/doi/10.1128/spectrum.00187-22},
	author = {Dom{\'\i}nguez-Mart{\'\i}n, Maria Agustina and L{\'o}pez-Lozano, Antonio and Melero-Rubio, Yesica and G{\'o}mez-Baena, Guadalupe and Jim{\'e}nez-Estrada, Juan Andr{\'e}s and Kukil, Kateryna and D{\'\i}ez, Jes{\'u}s and Garc{\'\i}a-Fern{\'a}ndez, Jos{\'e} Manuel},
	editor = {Hom, Erik F. Y.}
}
@article {koppelle_mixotrophy_2022,
	title = {Mixotrophy in the bloom-forming genus Phaeocystis and other haptophytes},
	journal = {Harmful Algae},
	volume = {117},
	year = {2022},
	pages = {102292},
	abstract = {Phaeocystis is a globally widespread marine phytoplankton genus, best known for its colony-forming species that can form large blooms and odorous foam during bloom decline. In the North Sea, Phaeocystis globosa typically becomes abundant towards the end of the spring bloom, when nutrients are depleted and the share of mixo- trophic protists increases. Although mixotrophy is widespread across the eukaryotic tree of life and is also found amongst haptophytes, a mixotrophic nutrition has not yet been demonstrated in Phaeocystis. Here, we sampled two consecutive Phaeocystis globosa spring blooms in the coastal North Sea. In both years, bacterial cells were observed inside 0.6 {\textendash} 2\% of P. globosa cells using double CARD-FISH hybridizations in combination with laser scanning confocal microscopy. Incubation experiments manipulating light and nutrient availability showed a trend towards higher occurrence of intracellular bacteria under P-deplete conditions. Based on counts of bacteria inside P. globosa cells in combination with theoretical values of prey digestion times, maximum ingestion rates of up to 0.08 bacteria cell- 1 h- 1 were estimated. In addition, a gene-based predictive model was applied to the transcriptome assemblies of seven Phaeocystis strains and 24 other haptophytes to assess their trophic mode. This model predicted a phago-mixotrophic feeding strategy in several (but not all) strains of P. globosa, P. antarctica and other haptophytes that were previously assumed to be autotrophic. The observation of bacterial cells inside P. globosa and the gene-based model predictions strongly suggest that the phago-mixotrophic feeding strategy is widespread among members of the Phaeocystis genus and other haptophytes, and might contribute to their remarkable success to form nuisance blooms under nutrient-limiting conditions.},
	keywords = {RCC1130, RCC1303, rcc1383, RCC1455, RCC1486, RCC1523, RCC1537, RCC918},
	issn = {15689883},
	doi = {10.1016/j.hal.2022.102292},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1568988322001202},
	author = {Koppelle, Sebastiaan and L{\'o}pez-Escard{\'o}, David and Brussaard, Corina P.D. and Huisman, Jef and Philippart, Catharina J.M. and Massana, Ramon and Wilken, Susanne}
}
@article {johnson_nutritional_2022,
	title = {Nutritional response of a coccolithophore to changing pH and temperature},
	journal = {Limnology and Oceanography},
	volume = {n/a},
	number = {n/a},
	year = {2022},
	note = {_eprint: https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.1002/lno.12204},
	abstract = {Coccolithophores are a calcifying unicellular phytoplankton group that are at the base of the marine food web, and their lipid content provides a source of energy to consumers. Coccolithophores are vulnerable to ocean acidification and warming, therefore it is critical to establish the effects of climate change on these significant marine primary producers, and determine potential consequences that these changes can have on their consumers. Here, we quantified the impact of changes in pH and temperature on the nutritional condition (lipid content, particulate organic carbon/nitrogen), growth rate, and morphology of the most abundant living coccolithophore species, Emiliania huxleyi. We used a regression type approach with nine pH levels (ranging from 7.66 to 8.44) and two temperatures (15{\textdegree}C and 20{\textdegree}C). Lipid production was greater under reduced pH, and growth rates were distinctly lower at 15{\textdegree}C than at 20{\textdegree}C. The production potential of lipids, which estimates the availability of lipids to consumers, increased under 20{\textdegree}C, but decreased under low pH. The results indicate that, while consumers will benefit energetically under ocean warming, this benefit will be mitigated by ocean acidification. The carbon to nitrogen ratio was higher at 20{\textdegree}C and low pH, indicating that the nutritional quality of coccolithophores for consumers will decline under climate change. The impact of low pH on the structural integrity of the coccosphere may also mean that coccolithophores are easier to digest for consumers. Many responses suggest cellular stress, indicating that increases in temperature and reductions in pH may have a negative impact on the ecophysiology of coccolithophores.},
	keywords = {RCC1832},
	issn = {1939-5590},
	doi = {10.1002/lno.12204},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1002/lno.12204},
	author = {Johnson, Roberta and Langer, Gerald and Rossi, Sergio and Probert, Ian and Mammone, Marta and Ziveri, Patrizia}
}
@article {lacour_photoacclimation_2022,
	title = {Photoacclimation of the polar diatom Chaetoceros neogracilis at low temperature},
	journal = {PLOS ONE},
	volume = {17},
	number = {9},
	year = {2022},
	note = {Publisher: Public Library of Science},
	month = {sep},
	pages = {e0272822},
	abstract = {Polar microalgae face two major challenges: 1- growing at temperatures (-1.7 to 5{\textdegree}C) that limit enzyme kinetics; and 2- surviving and exploiting a wide range of irradiance. The objective of this study is to understand the adaptation of an Arctic diatom to its environment by studying its ability to acclimate to changes in light and temperature. We acclimated the polar diatom Chaetoceros neogracilis to various light levels at two different temperatures and studied its growth and photosynthetic properties using semi-continuous cultures. Rubisco content was high, to compensate for low catalytic rates, but did not change detectably with growth temperature. Contrary to what is observed in temperate species, in C. neogracilis, carbon fixation rate (20 min 14C incorporation) equaled net growth rate (μ) suggesting very low or very rapid (<20 min) re-oxidation of the newly fixed carbon. The comparison of saturation irradiances for electron transport, oxygen net production and carbon fixation revealed alternative electron pathways that could provide energy and reducing power to the cell without consuming organic carbon which is a very limiting product at low temperatures. High protein contents, low re-oxidation of newly fixed carbon and the use of electron pathways alternative to carbon fixation may be important characteristics allowing efficient growth under those extreme environmental conditions.},
	keywords = {5-bisphosphate carboxylase oxygenase, Carbon fixation, diatoms, Fluorescence, Light, Photons, Photosynthesis, pigments, RCC2278, Ribulose-1},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0272822},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0272822},
	author = {Lacour, Thomas and Larivi{\`e}re, Jade and Ferland, Joannie and Morin, Philippe-Isra{\"e}l and Grondin, Pierre-Luc and Donaher, Natalie and Cockshutt, Amanda and Campbell, Douglas A. and Babin, Marcel}
}
@article {meyer_pronounced_2022,
	title = {Pronounced Uptake and Metabolism of Organic Substrates by Diatoms Revealed by Pulse-Labeling Metabolomics},
	journal = {Frontiers in Marine Science},
	volume = {9},
	year = {2022},
	pages = {821167},
	abstract = {Diatoms contribute as a dominant group of microalgae to approximately 20\% of the global carbon fixation. In the plankton, these photosynthetic algae are exposed to a plethora of metabolites, especially when competing algae are lysed. It is well established that diatoms can take up specific metabolites, such as vitamins, amino acids as nitrogen source, or dimethylsulfoniopropoionate to compensate for changes in water salinity. It is, however, unclear to which extent diatoms take up other organic resources and if these are incorporated into the cell{\textasciiacute}s metabolism. Here, we explore the general scope of uptake of metabolites from competitors. Using labeled metabolites released during lysis of algae grown under a 13CO2 atmosphere, we show that the cosmopolitan diatom Chaetoceros didymus takes up even dilute organic substrates from these lysates with little bias for molecular weight or polarity. This is reflected by a high degree of labeling in the metabolome of the exposed cells. The newly developed pulse label/mass spectrometry metabolomics approach reveals that polarity and molecular weight has no detectable influence on uptake. We further show that the taken-up metabolites are partly maintained without metabolic modification within the cells, but also a substantial part is subject to catabolic and anabolic transformation. One of the most dominant phytoplankton groups thus has the potential to compete with heterotrophs, suggesting that the observed osmotrophy may substantially impact organic material fluxes in the oceans. Our findings call for the refinement of our understanding of competition in the plankton.},
	keywords = {RCC75},
	issn = {2296-7745},
	doi = {10.3389/fmars.2022.821167},
	url = {https://www.frontiersin.org/articles/10.3389/fmars.2022.821167/full},
	author = {Meyer, Nils and Rydzyk, Aljoscha and Pohnert, Georg}
}
@article {pilatova_revisiting_2022,
	title = {Revisiting biocrystallization: purine crystalline inclusions are widespread in eukaryotes},
	journal = {The ISME Journal},
	year = {2022},
	month = {jun},
	keywords = {RCC1350, RCC745},
	issn = {1751-7362, 1751-7370},
	doi = {10.1038/s41396-022-01264-1},
	url = {https://www.nature.com/articles/s41396-022-01264-1},
	author = {Pil{\'a}tov{\'a}, Jana and P{\'a}nek, Tom{\'a}{\v s} and Obornik, Miroslav and {\v C}epi{\v c}ka, Ivan and Mojze{\v s}, Peter}
}
@article {de_la_broise_scale-up_2022,
	title = {Scale-Up to Pilot of a Non-Axenic Culture of Thraustochytrids Using Digestate from Methanization as Nitrogen Source},
	journal = {Marine Drugs},
	volume = {20},
	number = {8},
	year = {2022},
	month = {aug},
	pages = {499},
	abstract = {The production of non-fish based docosahexaenoic acid (DHA) for feed and food has become a critical need in our global context of over-fishing. The industrial-scale production of DHA{\textendash}rich Thraustochytrids could be an alternative, if costs turned out to be competitive. In order to reduce production costs, this study addresses the feasibility of the non-axenic (non-sterile) cultivation of Aurantiochytrium mangrovei on industrial substrates (as nitrogen and mineral sources and glucose syrup as carbon and energy sources), and its scale-up from laboratory (250 mL) to 500 L cultures. Pilot-scale reactors were airlift cylinders. Batch and fed-batch cultures were tested. Cultures over 38 to 62 h achieved a dry cell weight productivity of 3.3 to 5.5 g.L-1.day-1, and a substrate to biomass yield of up to 0.3. DHA productivity ranged from 10 to 0.18 mg.L-1.day-1. Biomass productivity appears linearly related to oxygen transfer rate. Bacterial contamination of cultures was low enough to avoid impacts on fatty acid composition of the biomass. A specific work on microbial risks assessment (in supplementary files) showed that the biomass can be securely used as feed. However, to date, there is a law void in EU legislation regarding the recycling of nitrogen from digestate from animal waste for microalgae biomass and its usage in animal feed. Overall, the proposed process appears similar to the industrial yeast production process (non-axenic heterotrophic process, dissolved oxygen supply limiting growth, similar cell size). Such similarity could help in further industrial developments.},
	keywords = {RCC893},
	issn = {1660-3397},
	doi = {10.3390/md20080499},
	url = {https://www.mdpi.com/1660-3397/20/8/499},
	author = {de la Broise, Denis and Ventura, Mariana and Chauchat, Luc and Guerreiro, Maurean and Michez, Teo and Vinet, Thibaud and Gautron, Nicolas and Le Grand, Fabienne and Bideau, Antoine and Go{\"\i}c, Nelly Le and Bidault, Adeline and Lambert, Christophe and Soudant, Philippe}
}
@article {croteau_shifts_2022,
	title = {Shifts in growth light optima among diatom species support their succession during the spring bloom in the Arctic},
	journal = {Journal of Ecology},
	volume = {n/a},
	number = {n/a},
	year = {2022},
	note = {_eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2745.13874},
	abstract = {1. Diatoms of the Arctic Ocean annually experience extreme changes of light environment linked to photoperiodic cycles and seasonal variations of the snow and sea-ice cover extent and thickness which attenuate light penetration in the water column. Arctic diatom communities exploit this complex seasonal dynamic through a well-documented species succession during spring, beginning in sea-ice and culminating in massive phytoplankton blooms underneath sea-ice and in the marginal ice zone. The pattern of diatom taxa sequentially dominating this succession is relatively well conserved interannually, and taxonomic shifts seem to align with habitat transitions. 2. To understand whether differential photoadaptation strategies among diatom taxa explain these recurring succession sequences, we coupled lab experiments with field work in Baffin Bay at 67.5{\textdegree}N. Based on field data, we selected five diatom species typical of different ecological niches and measured their growth rates under light intensity ranges representative of their natural habitats. To characterize their photoacclimative responses, we sampled pigments and total particulate carbon, and conducted 14C-uptake photosynthesis response curves and variable fluorescence measurements. 3. We documented a gradient in species respective light intensity for maximal growth suggesting divergent light response plasticity, which for the most part align with species sequential dominance. Other photophysiological parameters supported this ecophysiological framing, although contrasts were always clear only between succession endmembers, Nitzschia frigida and Chaetoceros neogracilis. To validate that these photoacclimative responses are representative of in situ dynamics, we compared them to the chlorophyll a-specific light-limited slope (α*) and saturated rate of photosynthesis (P*M), monitored in Baffin Bay on sea-ice and planktonic communities. This complementary approach confirmed that unusual responses in α* and P*M as a function of light history intensity are similar between sentinel sympagic species N. frigida and natural ice-core communities. While no light-history-dependent trends were observed in planktonic communities, their α* and P*M values were in the range of measurements from our monospecific cultures. 4. Synthesis. Our results suggest that Arctic diatoms species photoadaptation strategy is tuned to the light environment of the habitats in which they dominate and indeed drives the seasonal taxonomic succession.},
	keywords = {Arctic Ocean, diatoms, Ecophysiology, photoacclimation, photoadaptation, primary production, RCC2046, RCC2278, seasonal species succession, spring bloom},
	issn = {1365-2745},
	doi = {10.1111/1365-2745.13874},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/1365-2745.13874},
	author = {Croteau, D. and Lacour, T. and Schiffrine, N. and Morin, P.-I. and Forget, M.-H. and Bruyant, F. and Ferland, J. and Lafond, A. and Campbell, D. A. and Tremblay, J.-E. and Babin, M. and Lavaud, J.}
}
@article {calo_tor_2022,
	title = {TOR signaling in the green picoalga Ostreococcus tauri},
	journal = {Plant Science},
	volume = {323},
	year = {2022},
	month = {oct},
	pages = {111390},
	abstract = {Target of rapamycin (TOR) is a master regulator that controls growth and metabolism by integrating external and internal signals. Although there was a great progress in the study of TOR in plants and in the model alga Chlamydomonas, scarce data are available in other green algae. Thus, in this work we studied TOR signaling in Ostreococcus tauri, the smallest free-living eukaryote described to date. This picoalga is particularly important because it has a key site at the base of the green lineage and is part of the marine phytoplankton, contributing to global photosynthesis. We investigated OtTOR complex in silico and experimentally, by using first- and second-generation TOR inhibitors, such as rapamycin and PP242. We analyzed the effect of TOR down-regulation on cell growth and on the accumulation of carbon reserves. The results showed that O. tauri responds to TOR inhibitors more similarly to plants than to Chlamydomonas, being PP242 a valuable tool to study this pathway. Besides, Ottor expression analysis revealed that the kinase is dynamically regulated under nutritional stress. Our data indicate that TOR signaling is conserved in O. tauri and we propose this alga as a good and simple model for studying TOR kinase and its regulation.},
	keywords = {Carbon reserves, Green algae, Growth, Nitrogen deprivation, RCC745, TOR inhibitors, TOR kinase},
	issn = {0168-9452},
	doi = {10.1016/j.plantsci.2022.111390},
	url = {https://www.sciencedirect.com/science/article/pii/S016894522200214X},
	author = {Cal{\'o}, Gonzalo and De Marco, Mar{\'\i}a Agustina and Salerno, Graciela Lidia and Mart{\'\i}nez-No{\"e}l, Giselle Mar{\'\i}a Astrid}
}
@article {stewart_altitudinal_2021,
	title = {Altitudinal Zonation of Green Algae Biodiversity in the French Alps},
	journal = {Frontiers in Plant Science},
	volume = {12},
	year = {2021},
	pages = {1066},
	abstract = {Mountain environments are marked by an altitudinal zonation of habitat types. They are home to a multitude of terrestrial green algae, who have to cope with abiotic conditions specific to high elevation, e.g., high UV irradiance, alternating desiccation, rain and snow precipitations, extreme diurnal variations in temperature and chronic scarceness of nutrients. Even though photosynthetic green algae are primary producers colonizing open areas and potential markers of climate change, their overall biodiversity in the Alps has been poorly studied so far, in particular in soil, where algae have been shown to be key components of microbial communities. Here, we investigated whether the spatial distribution of green algae followed the altitudinal zonation of the Alps, based on the assumption that algae settle in their preferred habitats under the pressure of parameters correlated with elevation. We did so by focusing on selected representative elevational gradients at distant locations in the French Alps, where soil samples were collected at different depths. Soil was considered as either a potential natural habitat or temporary reservoir of algae. We showed that algal DNA represented a relatively low proportion of the overall eukaryotic diversity as measured by a universal Eukaryote marker. We designed two novel green algae metabarcoding markers to amplify the Chlorophyta phylum and its Chlorophyceae class, respectively. Using our newly developed markers, we showed that elevation was a strong correlate of species and genus level distribution. Altitudinal zonation was thus determined for about fifty species, with proposed accessions in reference databases. In particular, Planophila laetevirens and Bracteococcus ruber related species as well as the snow alga Sanguina genus were only found in soil starting at 2,000 m above sea level. Analysis of environmental and bioclimatic factors highlighted the importance of pH and nitrogen/carbon ratios in the vertical distribution in soil. Capacity to grow heterotrophically may determine the Trebouxiophyceae over Chlorophyceae ratio. The intensity of freezing events (freezing degree days), proved also determinant in Chlorophyceae distribution. Guidelines are discussed for future, more robust and precise analyses of environmental algal DNA in mountain ecosystems and address green algae species distribution and dynamics in response to environmental changes.},
	keywords = {rcc, RCC1055, RCC130, RCC1563, RCC2501, RCC2960, RCC3402, RCC443, RCC4743, RCC537, RCC581, RCC6, RCC7, RCC891},
	issn = {1664-462X},
	doi = {10.3389/fpls.2021.679428},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2021.679428},
	author = {Stewart, Adeline and Rioux, Delphine and Boyer, Fr{\'e}deric and Gielly, Ludovic and Pompanon, Fran{\c c}ois and Saillard, Am{\'e}lie and Thuiller, Wilfried and Valay, Jean-Gabriel and Mar{\'e}chal, {\'E}ric and Coissac, Eric}
}
@article {Trefaut2020,
	title = {Annual phytoplankton dynamics in coastal waters from fildes bay, western antarctic peninsula},
	journal = {Scientific Reports},
	volume = {11},
	number = {1},
	year = {2021},
	note = {tex.mendeley-tags: RCC2265,RCC2289,RCC4582,RCC4586,RCC5152},
	month = {dec},
	pages = {1368},
	abstract = {Year-round reports of phytoplankton dynamics in the West Antarctic Peninsula are rare and mainly limited to microscopy and/or pigment-based studies. We analyzed the phytoplankton community from coastal waters of Fildes Bay in the West Antarctic Peninsula between January 2014 and 2015 using metabarcoding of the nuclear and plastidial 18/16S rRNA gene from both size-fractionated and flow cytometry sorted samples. Overall 14 classes of photosynthetic eukaryotes were present in our samples with the following dominating: Bacillariophyta (diatoms), Pelagophyceae and Dictyochophyceae for division Ochrophyta, Mamiellophyceae and Pyramimonadophyceae for division Chlorophyta, Haptophyta and Cryptophyta. Each metabarcoding approach yielded a different image of the phytoplankton community with for example Prymnesiophyceae more prevalent in plastidial metabarcodes and Mamiellophyceae in nuclear ones. Diatoms were dominant in the larger size fractions and during summer, while Prymnesiophyceae and Cryptophyceae were dominant in colder seasons. Pelagophyceae were particularly abundant towards the end of autumn (May). In addition of Micromonas polaris and Micromonas sp. clade B3, both previously reported in Arctic waters, we detected a new Micromonas 18S rRNA sequence signature, close to, but clearly distinct from M. polaris , which potentially represents a new clade specific of the Antarctic. These results highlight the need for complementary strategies as well as the importance of year-round monitoring for a comprehensive description of phytoplankton communities in Antarctic coastal waters.},
	keywords = {RCC2265, RCC2289, RCC4582, RCC4586, RCC5152},
	issn = {2045-2322},
	doi = {10.1038/s41598-020-80568-8},
	url = {http://biorxiv.org/content/early/2020/10/27/2020.10.27.356600.abstract http://www.nature.com/articles/s41598-020-80568-8},
	author = {Trefault, Nicole and de la Iglesia, Rodrigo and Moreno-Pino, Mario and Lopes dos Santos, Adriana and G{\'e}rikas Ribeiro, Catherine and Parada-Pozo, G{\'e}nesis and Cristi, Antonia and Marie, Dominique and Vaulot, Daniel}
}
@article {roux_bacteria_2021,
	title = {Bacteria enhance the production of extracellular polymeric substances by the green dinoflagellate Lepidodinium chlorophorum},
	journal = {Scientific Reports},
	volume = {11},
	number = {1},
	year = {2021},
	note = {Number: 1 Publisher: Nature Publishing Group},
	pages = {1{\textendash}15},
	abstract = {High biomasses of the marine dinoflagellate Lepidodinium chlorophorum cause green seawater discolorations along Southern Brittany (NE Atlantic, France). The viscosity associated to these phenomena has been related to problems in oyster cultivation. The harmful effect of L. chlorophorum might originate from the secretion of Extracellular Polymeric Substances (EPS). To understand whether the EPS are produced by L. chlorophorum or its associated bacteria, or if they are a product of their interaction, batch cultures were performed under non-axenic and pseudo-axenic conditions for three strains. Maximum dinoflagellate cell abundances were observed in pseudo-axenic cultures. The non-sinking fraction of polymers (Soluble Extracellular Polymers, SEP), mainly composed of proteins and the exopolysaccharide sulphated galactan, slightly increased in pseudo-axenic cultures. The amount of Transparent Exopolymer Particles (TEP) per cell increased under non-axenic conditions. Despite the high concentrations of Particulate Organic Carbon (POC) measured, viscosity did not vary. These results suggest that the L. chlorophorum-bacteria interaction could have a detrimental consequence on the dinoflagellate, translating in a negative effect on L. chlorophorum growth, as well as EPS overproduction by the dinoflagellate, at concentrations that should not affect seawater viscosity.},
	keywords = {RCC1489},
	issn = {2045-2322},
	doi = {10.1038/s41598-021-84253-2},
	url = {http://www.nature.com/articles/s41598-021-84253-2},
	author = {Roux, Pauline and Siano, Raffaele and Collin, Karine and Bilien, Gwenael and Sinquin, Corinne and Marchand, Laetitia and Zykwinska, Agata and Delbarre-Ladrat, Christine and Schapira, Mathilde}
}
@article {pollara_bacterial_2021,
	title = {Bacterial Quorum-Sensing Signal Arrests Phytoplankton Cell Division and Impacts Virus-Induced Mortality},
	journal = {mSphere},
	volume = {6},
	number = {3},
	year = {2021},
	pages = {e00009{\textendash}21, /msphere/6/3/mSph.00009{\textendash}21.atom},
	abstract = {Interactions between phytoplankton and heterotrophic bacteria fundamentally shape marine ecosystems by controlling primary production, structuring marine food webs, mediating carbon export, and influencing global climate. Phytoplankton-bacterium interactions are facilitated by secreted compounds; however, linking these chemical signals, their mechanisms of action, and their resultant ecological consequences remains a fundamental challenge. The bacterial quorumsensing signal 2-heptyl-4-quinolone (HHQ) induces immediate, yet reversible, cellular stasis (no cell division or mortality) in the coccolithophore Emiliania huxleyi; however, the mechanism responsible remains unknown. Using transcriptomic and proteomic approaches in combination with diagnostic biochemical and fluorescent cell-based assays, we show that HHQ exposure leads to prolonged S-phase arrest in phytoplankton coincident with the accumulation of DNA damage and a lack of repair despite the induction of the DNA damage response (DDR). While this effect is reversible, HHQ-exposed phytoplankton were also protected from viral mortality, ascribing a new role of quorum-sensing signals in regulating multitrophic interactions. Furthermore, our data demonstrate that in situ measurements of HHQ coincide with areas of enhanced micro- and nanoplankton biomass. Our results suggest bacterial communication signals as emerging players that may be one of the contributing factors that help structure complex microbial communities throughout the ocean.},
	keywords = {rcc1731},
	issn = {2379-5042},
	doi = {10.1128/mSphere.00009-21},
	url = {https://msphere.asm.org/content/6/3/e00009-21},
	author = {Pollara, Scott B. and Becker, Jamie W. and Nunn, Brook L. and Boiteau, Rene and Repeta, Daniel and Mudge, Miranda C. and Downing, Grayton and Chase, Davis and Harvey, Elizabeth L. and Whalen, Kristen E.},
	editor = {McMahon, Katherine}
}
@article {uwizeye_cytoklepty_2021,
	title = {Cytoklepty in the plankton: A host strategy to optimize the bioenergetic machinery of endosymbiotic algae},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {118},
	number = {27},
	year = {2021},
	note = {Publisher: National Academy of Sciences Section: Biological Sciences},
	month = {jul},
	abstract = {Endosymbioses have shaped the evolutionary trajectory of life and remain ecologically important. Investigating oceanic photosymbioses can illuminate how algal endosymbionts are energetically exploited by their heterotrophic hosts and inform on putative initial steps of plastid acquisition in eukaryotes. By combining three-dimensional subcellular imaging with photophysiology, carbon flux imaging, and transcriptomics, we show that cell division of endosymbionts (Phaeocystis) is blocked within hosts (Acantharia) and that their cellular architecture and bioenergetic machinery are radically altered. Transcriptional evidence indicates that a nutrient-independent mechanism prevents symbiont cell division and decouples nuclear and plastid division. As endosymbiont plastids proliferate, the volume of the photosynthetic machinery volume increases 100-fold in correlation with the expansion of a reticular mitochondrial network in close proximity to plastids. Photosynthetic efficiency tends to increase with cell size, and photon propagation modeling indicates that the networked mitochondrial architecture enhances light capture. This is accompanied by 150-fold higher carbon uptake and up-regulation of genes involved in photosynthesis and carbon fixation, which, in conjunction with a ca.15-fold size increase of pyrenoids demonstrates enhanced primary production in symbiosis. Mass spectrometry imaging revealed major carbon allocation to plastids and transfer to the host cell. As in most photosymbioses, microalgae are contained within a host phagosome (symbiosome), but here, the phagosome invaginates into enlarged microalgal cells, perhaps to optimize metabolic exchange. This observation adds evidence that the algal metamorphosis is irreversible. Hosts, therefore, trigger and benefit from major bioenergetic remodeling of symbiotic microalgae with potential consequences for the oceanic carbon cycle. Unlike other photosymbioses, this interaction represents a so-called cytoklepty, which is a putative initial step toward plastid acquisition.},
	keywords = {3D electron microscopy, oceanic plankton, Photosynthesis, rcc, rcc1383, single-cell transcriptomics, symbiosis},
	issn = {0027-8424, 1091-6490},
	doi = {10.1073/pnas.2025252118},
	url = {https://www.pnas.org/content/118/27/e2025252118},
	author = {Uwizeye, Clarisse and Brisbin, Margaret Mars and Gallet, Benoit and Chevalier, Fabien and LeKieffre, Charlotte and Schieber, Nicole L. and Falconet, Denis and Wangpraseurt, Daniel and Schertel, Lukas and Stryhanyuk, Hryhoriy and Musat, Niculina and Mitarai, Satoshi and Schwab, Yannick and Finazzi, Giovanni and Decelle, Johan}
}
@article {morais_detection_2021,
	title = {Detection of Alexandrium minutum dinoflagellate in environ- mental samples using electrochemical genosensor},
	journal = {Chemistry Proceedings},
	year = {2021},
	pages = {7},
	abstract = {Dinoflagellates are aquatic microorganisms that inhabit both salt and fresh waters. These microorganisms are mostly harmless, however, under certain conditions, some species rapidly reproduce forming water blooms that not only discolor the waters but also compromise the health of every organism in the vicinity, as some dinoflagellates produce potent toxins deemed unsafe for human health (e.g. Alexandrium minutum). In this work, a disposable electrochemical genosensor for the detection of the toxic dinoflagellate Alexandrium minutum was developed. The analytical platform methodology consisted in a sandwich format heterogeneous hybridization of complementary DNA sequences assay. The 70 bp A. minutum-specific targeting probe, the 45 bp fluorescein isothiocyanate-labelled signaling DNA probe and the 25 bp thiolated-DNA-capture probe were designed, after analyzing public databases. To maximize the complementary DNA hybridization and to avoid the formation of strong secondary structures, a mixed mercaptohexanol (MCH) and self-assembled monolayer (SAM) A. minutum-specific DNA-capture probe was immobilized onto disposable screen-printed gold electrodes (SPGE). Using chronoamperometric measurements, the enzymatic amplification of the electrochemical signal was obtained with a concentration range from 0.12 to 1.0 nM, a LD of 24.78 pM with a RSD < 5.2 \%. This electrochemical genosensor was successfully applied to the selective analysis of the targeted A. minutum specific region of denatured genomic DNA, extracted from toxic dinoflagellates present in the Atlantic Ocean.},
	keywords = {? No DOI found, RCC3029},
	author = {Morais, Stephanie L and Barros, Piedade and Santos, Marlene and Delerue-Matos, Cristina and Gomes, Andreia C and Barroso, M F{\'a}tima}
}
@article {robla_determination_2021,
	title = {Determination of the efficiency of filtration of cultures from microalgae and bacteria using hollow fiber filters},
	journal = {Environmental Science: Water Research \& Technology},
	volume = {7},
	number = {7},
	year = {2021},
	note = {Publisher: The Royal Society of Chemistry},
	month = {jul},
	pages = {1230{\textendash}1239},
	abstract = {The most important question in sampling is {\textquotedblleft}Is the sample representative of the target population?{\textquotedblright} This question is necessary to understand how valid the sample taken is to the original population and if generalizations can be made from the sample. Samples taken for water quality measurement range from 1 mL for bacterial contamination to 100 mL or up to 1000 L for protozoan parasites. With larger samples taken, the confidence in detecting rare events increases dramatically. Here we illustrate that hollow fiber filters as routinely used for kidney dialysis can be adapted for environmental use. The filters retain all organisms down to viral particles and organic matter above 70 kDA, the molecular cutoff for urea, one of the waste products removed in kidney dialysis. With these filters, 50 liters of water can be filtered in about 90 minutes. Backflush of the filters recovers viable cells with minimal cell lysis that can be processed downstream for molecular analysis. Recovery rates were as high as 89\% and 75\% for phytoplankton and bacteria, respectively.},
	keywords = {rcc, RCC1507},
	issn = {2053-1419},
	doi = {10.1039/D0EW00927J},
	url = {https://pubs.rsc.org/en/content/articlelanding/2021/ew/d0ew00927j},
	author = {Robla, J. and Garc{\'\i}a-Hierrro, J. and Alguacil, F. J. and Dittami, S. M. and Marie, D. and Villa, E. and Deragon, E. and Guillebault, D. and Mengs, G. and Medlin, L. K.}
}
@article {long_dinophyceae_2021,
	title = {Dinophyceae can use exudates as weapons against the parasite Amoebophrya sp. (Syndiniales)},
	journal = {ISME Communications},
	volume = {1},
	number = {1},
	year = {2021},
	note = {Bandiera_abtest: a Cg_type: Nature Research Journals Number: 1 Primary_atype: Research Publisher: Nature Publishing Group Subject_term: Microbial ecology;Plant ecology;Water microbiology Subject_term_id: microbial-ecology;plant-ecology;water-microbiology},
	pages = {1{\textendash}10},
	abstract = {Parasites in the genus Amoebophrya sp. infest dinoflagellate hosts in marine ecosystems and can be determining factors in the demise of blooms, including toxic red tides. These parasitic protists, however, rarely cause the total collapse of Dinophyceae blooms. Experimental addition of parasite-resistant Dinophyceae (Alexandrium minutum or Scrippsiella donghaienis) or exudates into a well-established host-parasite coculture (Scrippsiella acuminata-Amoebophrya sp.) mitigated parasite success and increased the survival of the sensitive host. This effect was mediated by waterborne molecules without the need for a physical contact. The strength of the parasite defenses varied between dinoflagellate species, and strains of A. minutum and was enhanced with increasing resistant host cell concentrations. The addition of resistant strains or exudates never prevented the parasite transmission entirely. Survival time of Amoebophrya sp. free-living stages (dinospores) decreased in presence of A. minutum but not of S. donghaienis. Parasite progeny drastically decreased with both species. Integrity of the dinospore membrane was altered by A. minutum, providing a first indication on the mode of action of anti-parasitic molecules. These results demonstrate that extracellular defenses can be an effective strategy against parasites that protects not only the resistant cells producing them, but also the surrounding community.},
	keywords = {microbial ecology, Plant ecology, rcc, RCC1627, RCC4383, RCC4714, RCC749, Water microbiology},
	issn = {2730-6151},
	doi = {10.1038/s43705-021-00035-x},
	url = {http://www.nature.com/articles/s43705-021-00035-x},
	author = {Long, Marc and Marie, Dominique and Szymczak, Jeremy and Toullec, Jordan and Bigeard, Estelle and Sourisseau, Marc and Le Gac, Micka{\"e}l and Guillou, Laure and Jauzein, C{\'e}cile}
}
@booklet {marc_dinophyceae_2021,
	title = {Dinophyceae use exudates as weapons against the parasite Amoebophrya sp. (Syndiniales)},
	year = {2021},
	note = {Company: Cold Spring Harbor Laboratory Distributor: Cold Spring Harbor Laboratory Label: Cold Spring Harbor Laboratory Section: New Results Type: article},
	month = {jan},
	pages = {2021.01.05.425281},
	abstract = {Parasites of the genus Amoebophrya sp. are important contributors to marine ecosystems and can be determining factors in the demise of blooms of Dinophyceae, including microalgae commonly responsible for toxic red tides. Yet they rarely lead to the total collapse of Dinophyceae blooms. The addition of resistant Dinophyceae (Alexandrium minutum or Scrippsiella donghaienis) or their exudate into a well-established host-parasite culture (Scrippsiella acuminata-Amoebophrya sp.) mitigated the success of the parasite and increased the survival of the sensitive host. Effect were mediated via water-borne molecules without the need of a physical contact. Severity of the anti-parasitic defenses fluctuated depending on the species, the strain and its concentration, but never totally prevented the parasite transmission. The survival time of Amoebophrya sp. free-living stages (dinospores) decreased in presence of A. minutum but not of S. donghaienis. The progeny drastically decreased with both species. Integrity of the membrane of dinospores was altered by A. minutum which provided a first indication on the mode of action of these anti-parasitic molecules. These results demonstrate that extracellular defenses are an effective strategy against parasites that does not only protect the resistant cells but also have the potential to affect the whole surrounding community.},
	keywords = {rcc, RCC1627, RCC4383, RCC4714, RCC749},
	doi = {10.1101/2021.01.05.425281},
	url = {https://www.biorxiv.org/content/10.1101/2021.01.05.425281v1},
	author = {Marc, Long and Dominique, Marie and Jeremy, Szymczak and Jordan, Toullec and Estelle, Bigeard and Marc, Sourisseau and Mickael, Le Gac and Laure, Guillou and C{\'e}cile, Jauzein}
}
@article {geffroy_sxta4_2021,
	title = {From the sxtA4 Gene to Saxitoxin Production: What Controls the Variability Among Alexandrium minutum and Alexandrium pacificum Strains?},
	journal = {Frontiers in Microbiology},
	volume = {12},
	year = {2021},
	pages = {613199},
	abstract = {Paralytic shellfish poisoning (PSP) is a human foodborne syndrome caused by the consumption of shellfish that accumulate paralytic shellfish toxins (PSTs, saxitoxin group). In PST-producing dinoflagellates such as Alexandrium spp., toxin synthesis is encoded in the nuclear genome via a gene cluster (sxt). Toxin production is supposedly associated with the presence of a 4th domain in the sxtA gene (sxtA4), one of the core genes of the PST gene cluster. It is postulated that gene expression in dinoflagellates is partially constitutive, with both transcriptional and post-transcriptional processes potentially co-occurring. Therefore, gene structure and expression mode are two important features to explore in order to fully understand toxin production processes in dinoflagellates. In this study, we determined the intracellular toxin contents of twenty European Alexandrium minutum and Alexandrium pacificum strains that we compared with their genome size and sxtA4 gene copy numbers. We observed a significant correlation between the sxtA4 gene copy number and toxin content, as well as a moderate positive correlation between the sxtA4 gene copy number and genome size. The 18 toxic strains had several sxtA4 gene copies (9{\textendash}187), whereas only one copy was found in the two observed non-toxin producing strains. Exploration of allelic frequencies and expression of sxtA4 mRNA in 11 A. minutum strains showed both a differential expression and specific allelic forms in the non-toxic strains compared with the toxic ones. Also, the toxic strains exhibited a polymorphic sxtA4 mRNA sequence between strains and between gene copies within strains. Finally, our study supported the hypothesis of a genetic determinism of toxin synthesis (i.e., the existence of several genetic isoforms of the sxtA4 gene and their copy numbers), and was also consistent with the hypothesis that constitutive gene expression and moderation by transcriptional and post-transcriptional regulation mechanisms are the cause of the observed variability in the production of toxins by A. minutum.},
	keywords = {RCC2644, RCC2645, RCC3327, RCC4871, RCC4872, RCC4890, RCC7037, RCC7038, RCC7039},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2021.613199},
	url = {https://www.frontiersin.org/articles/10.3389/fmicb.2021.613199/full},
	author = {Geffroy, Sol{\`e}ne and Lechat, Marc-Marie and Le Gac, Micka{\"e}l and Rovillon, Georges-Augustin and Marie, Dominique and Bigeard, Estelle and Malo, Florent and Amzil, Zouher and Guillou, Laure and Caruana, Amandine M. N.}
}
@article {Wang2021,
	title = {Group 2i Isochrysidales produce characteristic alkenones reflecting sea ice distribution},
	journal = {Nature Communications},
	volume = {12},
	number = {1},
	year = {2021},
	note = {Publisher: Springer US tex.mendeley-tags: RCC107,RCC1195,RCC1334,RCC5486},
	month = {dec},
	pages = {15},
	abstract = {Alkenones are biomarkers produced solely by algae in the order Isochrysidales that have been used to reconstruct sea surface temperature (SST) since the 1980s. However, alkenone-based SST reconstructions in the northern high latitude oceans show significant bias towards warmer temperatures in core-tops, diverge from other SST proxies in down core records, and are often accompanied by anomalously high relative abundance of the C 37 tetra-unsaturated methyl alkenone (\%C 37:4 ). Elevated \%C 37:4 is widely interpreted as an indicator of low sea surface salinity from polar water masses, but its biological source has thus far remained elusive. Here we identify a lineage of Isochrysidales that is responsible for elevated C 37:4 methyl alkenone in the northern high latitude oceans through next-generation sequencing and lab-culture experiments. This Isochrysidales lineage co-occurs widely with sea ice in marine environments and is distinct from other known marine alkenone-producers, namely Emiliania huxleyi and Gephyrocapsa oceanica . More importantly, the \%C 37:4 in seawater filtered particulate organic matter and surface sediments is significantly correlated with annual mean sea ice concentrations. In sediment cores from the Svalbard region, the \%C 37:4 concentration aligns with the Greenland temperature record and other qualitative regional sea ice records spanning the past 14 kyrs, reflecting sea ice concentrations quantitatively. Our findings imply that \%C 37:4 is a powerful proxy for reconstructing sea ice conditions in the high latitude oceans on thousand- and, potentially, on million-year timescales.},
	keywords = {RCC107, RCC1195, RCC1334, RCC5486},
	issn = {2041-1723},
	doi = {10.1038/s41467-020-20187-z},
	url = {http://dx.doi.org/10.1038/s41467-020-20187-z http://www.nature.com/articles/s41467-020-20187-z},
	author = {Wang, Karen Jiaxi and Huang, Yongsong and Majaneva, Markus and Belt, Simon T. and Liao, Sian and Novak, Joseph and Kartzinel, Tyler R. and Herbert, Timothy D. and Richter, Nora and Cabedo-Sanz, Patricia}
}
@article {Magalhaes2018,
	title = {Hemiselmis aquamarina sp . nov . (Cryptomonadales , Cryptophyceae), a cryptomonad with a novel phycobiliprotein type (Cr-PC 564)},
	journal = {Protist},
	volume = {in press},
	year = {2021},
	keywords = {RCC4102, RCC5634, to add},
	doi = {10.1016/j.protis.2021.125832},
	url = {https://doi.org/10.1016/j.protis.2021.125832},
	author = {Magalh{\~a}es, Karoline and Lopes dos Santos, Adriana and Vaulot, Daniel and de Oliveira, Mariana Cabral}
}
@article {zhang_isotope_2021,
	title = {An isotope label method for empirical detection of carbonic anhydrase in the calcification pathway of the coccolithophore Emiliania huxleyi},
	journal = {Geochimica et Cosmochimica Acta},
	volume = {292},
	year = {2021},
	pages = {78{\textendash}93},
	abstract = {Coccolithophores are a group of phytoplankton widely distributed in the ocean, which secrete extracellular calcite plates termed coccoliths. Coccoliths have been increasingly employed as an archive for geochemical, ecological and paleoclimate studies in recent years. A robust application of coccolith-based geochemical proxies relies on understanding the carbon acquisition strategies and the pathways of carbon supply for calcification. Carbonic anhydrase (CA) plays important roles in the carbon concentrating mechanism s of aquatic algae and potentially also in calcification. However, it is difficult to independently assess the role of CA in carbon supply for photosynthesis versus calcification. To fill this gap, we explored a new method to detect the CA activity inside coccolithophore. To achieve this, coccolithophores were cultured with oxygen and carbon isotope labeled dissolved inorganic carbon (DIC). By exploiting the different behavior of oxygen and carbon isotopes with (sea)water, this double label method can elucidate the significance of CA activity in the calcification pathway. Application of this method to Emiliania huxleyi shows that CA is present in the calcification pathway, and that there is no significant difference in the CA activity between a high and low CO2 treatment. However, under low CO2 treatment E. huxleyi enhanced the bicarbonate pumping rate on both cell and chloroplast membranes. This novel method could be performed on other species of coccolithophores in the future and have a potential to extend our knowledge on coccolith oxygen isotope vital effects.},
	keywords = {Carbonic anhjydrase, ccm, coccolithophore, Isotopic labelling, rcc, rcc1258},
	issn = {0016-7037},
	doi = {10.1016/j.gca.2020.09.008},
	url = {https://www.sciencedirect.com/science/article/pii/S0016703720305597},
	author = {Zhang, Hongrui and Blanco-Ameijeiras, Sonia and Hopkinson, Brian M. and Bernasconi, Stefano M. and Mejia, Luz Maria and Liu, Chuanlian and Stoll, Heather}
}
@article {schapira_les_2021,
	title = {Les Efflorescences de Lepidodinium chlorophorum au large de la Loire et de la Vilaine : D{\'e}terminisme et cons{\'e}quences sur la qualit{\'e} des masses d{\textquoteright}eau c{\^o}ti{\`e}res},
	year = {2021},
	abstract = {Ce projet, organis{\'e} en trois actions, avait pour objectif de mieux {\'e}valuer les risques d{\textquoteright}eaux color{\'e}es vertes se produisant sur le secteur c{\^o}tier situ{\'e} au large de la Loire et de la Vilaine, en termes (i) de fr{\'e}quence de ces {\'e}pisodes, (ii) d{\textquoteright}abondance et (iii) de localisation des zones {\`a} risque. Action 1 : Am{\'e}lioration du recensement des eaux vertes {\`a} L. chlorophorum Action 2 : Optimisation de l{\textquoteright}estimation des abondances de L. chlorophorum Action 3 : Identification des zones {\`a} risque au large de la Loire et de la Vilaine.},
	keywords = {? No DOI found, rcc, RCC1489},
	url = {https://archimer.ifremer.fr/doc/00724/83598/},
	author = {Schapira, Mathilde and Roux, Pauline and Andre, Coralie and Mertens, Kenneth and Bilien, Gwenael and Terre Terrillon, Aouregan and Le Gac-Abernot, Chantal and Siano, Raffaele and Qu{\'e}r{\'e}, Julien and Bizzozero, Lucie and Bonneau, Francoise and Bouget, Jean-Francois and Cochennec-Laureau, Nathalie and Collin, Karine and Fortune, Mireille and Gabellec, Raoul and Le Merrer, Yoann and Manach, Soazig and Pierre-Duplessix, Olivier and Retho, Michael and Schmitt, Anne and Souchu, Philippe and Stachowski-Haberkorn, Sabine}
}
@article {six_marine_2021,
	title = {Marine Synechococcus  picocyanobacteria: Light utilization across latitudes},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {118},
	number = {38},
	year = {2021},
	note = {Publisher: National Academy of Sciences Section: Biological Sciences},
	abstract = {<p>The most ubiquitous cyanobacteria, Synechococcus, have colonized different marine thermal niches through the evolutionary specialization of lineages adapted to different ranges of temperature seawater. We used the strains of Synechococcus temperature ecotypes to study how light utilization has evolved in the function of temperature. The tropical Synechococcus (clade II) was unable to grow under 16 {\textdegree}C but, at temperatures \&gt;25 {\textdegree}C, induced very high growth rates that relied on a strong synthesis of the components of the photosynthetic machinery, leading to a large increase in photosystem cross-section and electron flux. By contrast, the Synechococcus adapted to subpolar habitats (clade I) grew more slowly but was able to cope with temperatures \&lt;10 {\textdegree}C. We show that growth at such temperatures was accompanied by a large increase of the photoprotection capacities using the orange carotenoid protein (OCP). Metagenomic analyzes revealed that Synechococcus natural communities show the highest prevalence of the ocp genes in low-temperature niches, whereas most tropical clade II Synechococcus have lost the gene. Moreover, bioinformatic analyzes suggested that the OCP variants of the two cold-adapted Synechococcus clades I and IV have undergone evolutionary convergence through the adaptation of the molecular flexibility. Our study points to an important role of temperature in the evolution of the OCP. We, furthermore, discuss the implications of the different metabolic cost of these physiological strategies on the competitiveness of Synechococcus in a warming ocean. This study can help improve the current hypotheses and models aimed at predicting the changes in ocean carbon fluxes in response to global warming.</p>
},
	keywords = {?? Invalid DOI, RCC2035, rcc2382, RCC2385, RCC2421, RCC2527, RCC2535, RCC2553, RCC2570, RCC515, rcc539, rcc752, rcc791, to add},
	issn = {0027-8424, 1091-6490},
	doi = {10.1073/pnas.2111300118},
	url = {http://www.pnas.org/content/118/38/e2111300118},
	author = {Six, Christophe and Ratin, Morgane and Marie, Dominique and Corre, Erwan}
}
@article {uwizeye_morphological_2021,
	title = {Morphological bases of phytoplankton energy management and physiological responses unveiled by 3D subcellular imaging},
	journal = {Nature Communications},
	volume = {12},
	number = {1},
	year = {2021},
	note = {Number: 1 Publisher: Nature Publishing Group},
	month = {feb},
	pages = {1{\textendash}12},
	abstract = {Phytoplankton account for a large proportion of global primary production and comprise a number of phylogenetically distinct lineages. Here, Uwizeye et al. use FIB-SEM to study ultrastructural plasticity of 7 distinct taxa and describe how subcellular organisation is linked to energy metabolism.},
	keywords = {RCC100, RCC4014, RCC827, RCC909},
	issn = {2041-1723},
	doi = {10.1038/s41467-021-21314-0},
	url = {http://www.nature.com/articles/s41467-021-21314-0},
	author = {Uwizeye, Clarisse and Decelle, Johan and Jouneau, Pierre-Henri and Flori, Serena and Gallet, Benoit and Keck, Jean-baptiste and Bo, Davide Dal and Moriscot, Christine and Seydoux, Claire and Chevalier, Fabien and Schieber, Nicole L. and Templin, Rachel and Allorent, Guillaume and Courtois, Florence and Curien, Gilles and Schwab, Yannick and Schoehn, Guy and Zeeman, Samuel C. and Falconet, Denis and Finazzi, Giovanni}
}
@article {decamp_new_2021,
	title = {A New, Quick, and Simple Protocol to Evaluate Microalgae Polysaccharide Composition},
	journal = {Marine Drugs},
	volume = {19},
	number = {2},
	year = {2021},
	pages = {101},
	abstract = {In this work, a new methodological approach, relying on the high specificity of enzymes in a complex mixture, was developed to estimate the composition of bioactive polysaccharides produced by microalgae, directly in algal cultures. The objective was to set up a protocol to target oligomers commonly known to be associated with exopolysaccharides{\textquoteright} (EPS) nutraceutical and pharmaceutical activities (i.e., rhamnose, fucose, acidic sugars, etc.) without the constraints classically associated with chromatographic methods, while maintaining a resolution sufficiently high to enable their monitoring in the culture system. Determination of the monosaccharide content required the application of acid hydrolysis (2 M trifluoroacetic acid) followed by NaOH (2 M) neutralization. Quantification was then carried out directly on the fresh hydrolysate using enzyme kits corresponding to the main monosaccharides in a pre-determined composition of the polysaccharides under analysis. Initial results showed that the enzymes were not sensitive to the presence of TFA and NaOH, so the methodology could be carried out on fresh hydrolysate. The limits of quantification of the method were estimated as being in the order of the log of nanograms of monosaccharides per well, thus positioning it among the chromatographic methods in terms of analytical performance. A comparative analysis of the results obtained by the enzymatic method with a reference method (high-performance anion-exchange chromatography) confirmed good recovery rates, thus validating the closeness of the protocol. Finally, analyses of raw culture media were carried out and compared to the results obtained in miliQ water; no differences were observed. The new approach is a quick, functional analysis method allowing routine monitoring of the quality of bioactive polysaccharides in algal cultures grown in photobioreactors.},
	keywords = {rcc2380, RCC3438},
	issn = {1660-3397},
	doi = {10.3390/md19020101},
	url = {https://www.mdpi.com/1660-3397/19/2/101},
	author = {Decamp, Antoine and Michelo, Orane and Rabbat, Christelle and Laroche, C{\'e}line and Grizeau, Dominique and Pruvost, J{\'e}r{\'e}my and Gon{\c c}alves, Olivier}
}
@article {harada_novel_2021,
	title = {A novel characteristic of a phytoplankton as a potential source of straight-chain alkanes},
	journal = {Scientific Reports},
	volume = {11},
	number = {1},
	year = {2021},
	note = {Bandiera_abtest: a Cc_license_type: cc_by Cg_type: Nature Research Journals Number: 1 Primary_atype: Research Publisher: Nature Publishing Group Subject_term: Biofuels;Biological techniques Subject_term_id: biofuels;biological-techniques},
	pages = {14190},
	abstract = {Biosynthesis of hydrocarbons is a promising approach for the production of alternative sources of energy because of the emerging need to reduce global consumption of fossil fuels. However, the suitability of biogenic hydrocarbons as fuels is limited because their range of the number of carbon atoms is small, and/or they contain unsaturated carbon bonds. Here, we report that a marine phytoplankton, Dicrateria rotunda, collected from the western Arctic Ocean, can synthesize a series of saturated hydrocarbons (n-alkanes) from C10H22 to C38H78, which are categorized as petrol (C10{\textendash}C15), diesel oils (C16{\textendash}C20), and fuel oils (C21{\textendash}C38). The observation that these n-alkanes were also produced by ten other cultivated strains of Dicrateria collected from the Atlantic and Pacific oceans suggests that this capability is a common characteristic of Dicrateria. We also identified that the total contents of the n-alkanes in the Arctic D. rotunda strain increased under dark and nitrogen-deficient conditions. The unique characteristic of D. rotunda could contribute to the development of a new approach for the biosynthesis of n-alkanes.},
	keywords = {RCC3437, RCC4217, RCC4577, RCC4578, RCC5635, RCC5639},
	issn = {2045-2322},
	doi = {10.1038/s41598-021-93204-w},
	url = {http://www.nature.com/articles/s41598-021-93204-w},
	author = {Harada, Naomi and Hirose, Yuu and Chihong, Song and Kurita, Hirofumi and Sato, Miyako and Onodera, Jonaotaro and Murata, Kazuyoshi and Itoh, Fumihiro}
}
@article {russo_production_2021,
	title = {Production of Omega-3 Oil by Aurantiochytrium mangrovei Using Spent Osmotic Solution from Candied Fruit Industry as Sole Organic Carbon Source},
	journal = {Processes},
	volume = {9},
	number = {10},
	year = {2021},
	note = {Number: 10 Publisher: Multidisciplinary Digital Publishing Institute},
	month = {oct},
	pages = {1834},
	abstract = {Osmotic dehydration is an important phase in the production of dried products, including most fruits and vegetables, in the food industry. The drying process for candied fruit produces a liquid waste called {\textquotedblleft}spent osmotic solution{\textquotedblright}, which is characterized by a high content of organic compounds, mostly dissolved sugars. The sugar content of this food by-product could be valorized through the growth of biomass with a high added value. In this study, the spent osmotic solution from the candied fruit industry was used as an organic carbon source for the growth and production of docosahexaenoic acid (DHA) in the cultivation of Aurantiochytrium mangrovei RCC893. The carbon content of the standard media was completely replaced by the sugars present in this food by-product. After that, the growth condition of this strain was optimized through response surface methodologies using a central composite design (CCD), and the optimal combination of the spent osmotic solution and nitrogen was established. Moreover, a scale-up trial was performed using the optimal conditions obtained after CCD to evaluate the scalability of the process.},
	keywords = {DHA, food waste, Microalgae, PUFA, rcc, RCC893, sustainability},
	doi = {10.3390/pr9101834},
	url = {https://www.mdpi.com/2227-9717/9/10/1834},
	author = {Russo, Giovanni L. and Langellotti, Antonio L. and Blasco, Thierry and Oliviero, Maria and Sacchi, Raffaele and Masi, Paolo}
}
@article {Farhat2021,
	title = {Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp.},
	journal = {BMC Biology},
	year = {2021},
	note = {Publisher: BMC Biology tex.mendeley-tags: RCC4383,RCC4398},
	pages = {1{\textendash}21},
	keywords = {Dinoflagellate, genome, Introner elements, Non-canonical introns, parasite, RCC4383, RCC4398},
	doi = {10.1186/s12915-020-00927-9},
	author = {Farhat, Sarah and Le, Phuong and Kayal, Ehsan and Noel, Benjamin and Bigeard, Estelle and Corre, Erwan and Maumus, Florian and Florent, Isabelle and Alberti, Adriana and Aury, Jean-Marc and Barbeyron, Tristan and Cai, Ruibo and Silva, Corinne Da and Istace, Benjamin and Labadie, Karine and Marie, Dominique and Mercier, Jonathan and Rukwavu, Tsinda and Szymczak, Jeremy and Tonon, Thierry and Alves-de-Souza, Catharina and Rouze, Pierre and de Peer, Yves Van and Wincker, Patrick and Rombauts, Stephane and Porcel, Betina M and Guillou, Laure}
}
@article {kawachi_rappemonads_2021,
	title = {Rappemonads are haptophyte phytoplankton},
	journal = {Current Biology},
	year = {2021},
	month = {mar},
	abstract = {Rapidly accumulating genetic data from environmental sequencing approaches have revealed an extraordinary level of unsuspected diversity within marine phytoplankton,1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 which is responsible for around 50\% of global net primary production.12,13 However, the phenotypic identity of many of the organisms distinguished by environmental DNA sequences remains unclear. The rappemonads represent a plastid-bearing protistan lineage that to date has only been identified by environmental plastid 16S rRNA sequences.14, 15, 16, 17 The phenotypic identity of this group, which does not confidently cluster in any known algal clades in 16S rRNA phylogenetic reconstructions,15 has remained unknown since the first report of environmental sequences over two decades ago. We show that rappemonads are closely related to a haptophyte microalga, Pavlomulina ranunculiformis gen. nov. et sp. nov., and belong to a new haptophyte class, the Rappephyceae. Organellar phylogenomic analyses provide strong evidence for the inclusion of this lineage within the Haptophyta as a sister group to the Prymnesiophyceae. Members of this new class have a cosmopolitan distribution in coastal and oceanic regions. The relative read abundance of Rappephyceae in a large environmental barcoding dataset was comparable to, or greater than, those of major haptophyte species, such as the bloom-forming Gephyrocapsa huxleyi and Prymnesium parvum, and this result indicates that they likely have a significant impact as primary producers. Detailed characterization of Pavlomulina allowed for reconstruction of the ancient evolutionary history of the Haptophyta, a group that is one of the most important components of extant marine phytoplankton communities.},
	keywords = {environmental DNA sequences, morphological evolution, organellar phylogenomics, phytoplankton diversity, RCC3430, transmission electron microscopy},
	issn = {0960-9822},
	doi = {10.1016/j.cub.2021.03.012},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982221003511},
	author = {Kawachi, Masanobu and Nakayama, Takuro and Kayama, Motoki and Nomura, Mami and Miyashita, Hideaki and Bojo, Othman and Rhodes, Lesley and Sym, Stuart and Pienaar, Richard N. and Probert, Ian and Inouye, Isao and Kamikawa, Ryoma}
}
@article {langer_role_2021,
	title = {Role of silicon in the development of complex crystal shapes in coccolithophores},
	journal = {New Phytologist},
	volume = {231},
	number = {5},
	year = {2021},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.17230},
	pages = {1845{\textendash}1857},
	abstract = {The development of calcification by the coccolithophores had a profound impact on ocean carbon cycling, but the evolutionary steps leading to the formation of these complex biomineralized structures are not clear. Heterococcoliths consisting of intricately shaped calcite crystals are formed intracellularly by the diploid life cycle phase. Holococcoliths consisting of simple rhombic crystals can be produced by the haploid life cycle stage but are thought to be formed extracellularly, representing an independent evolutionary origin of calcification. We use advanced microscopy techniques to determine the nature of coccolith formation and complex crystal formation in coccolithophore life cycle stages. We find that holococcoliths are formed in intracellular compartments in a similar manner to heterococcoliths. However, we show that silicon is not required for holococcolith formation and that the requirement for silicon in certain coccolithophore species relates specifically to the process of crystal morphogenesis in heterococcoliths. We therefore propose an evolutionary scheme in which the lower complexity holococcoliths represent an ancestral form of calcification in coccolithophores. The subsequent recruitment of a silicon-dependent mechanism for crystal morphogenesis in the diploid life cycle stage led to the emergence of the intricately shaped heterococcoliths, enabling the formation of the elaborate coccospheres that underpin the ecological success of coccolithophores.},
	keywords = {biomineralization, Calcification, coccolith, coccolithophore, evolution, rcc, RCC1178, RCC1181, RCC1456, RCC1460, RCC1461, RCC1477, RCC1800, RCC1801, RCC3777, RCC6506, silicon},
	issn = {1469-8137},
	doi = {10.1111/nph.17230},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.17230},
	author = {Langer, Gerald and Taylor, Alison R. and Walker, Charlotte E. and Meyer, Erin M. and Ben Joseph, Oz and Gal, Assaf and Harper, Glenn M. and Probert, Ian and Brownlee, Colin and Wheeler, Glen L.}
}
@article {castillo_seasonal_2021,
	title = {Seasonal dynamics of natural Ostreococcus viral infection at the single cell level using VirusFISH},
	journal = {Environmental Microbiology},
	volume = {n/a},
	number = {n/a},
	year = {2021},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.15504},
	abstract = {Ostreococcus is a cosmopolitan marine genus of phytoplankton found in mesotrophic and oligotrophic waters, and the smallest free-living eukaryotes known to date, with a cell diameter close to 1 μm. Ostreococcus has been extensively studied as a model system to investigate viral{\textendash}host dynamics in culture, yet the impact of viruses in naturally occurring populations is largely unknown. Here, we used Virus Fluorescence in situ Hybridization (VirusFISH) to visualize and quantify viral-host dynamics in natural populations of Ostreococcus during a seasonal cycle in the central Cantabrian Sea (Southern Bay of Biscay). Ostreococcus were predominantly found during summer and autumn at surface and 50 m depth, in coastal, mid-shelf and shelf waters, representing up to 21\% of the picoeukaryotic communities. Viral infection was only detected in surface waters, and its impact was variable but highest from May to July and November to December, when up to half of the population was infected. Metatranscriptomic data available from the mid-shelf station unveiled that the Ostreococcus population was dominated by the species O. lucimarinus. This work represents a proof of concept that the VirusFISH technique can be used to quantify the impact of viruses on targeted populations of key microbes from complex natural communities. This article is protected by copyright. All rights reserved.},
	keywords = {RCC2590, RCC4221, RCC809},
	issn = {1462-2920},
	doi = {10.1111/1462-2920.15504},
	url = {http://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.15504},
	author = {Castillo, Yaiza M. and Forn, Irene and Yau, Sheree and Mor{\'a}n, Xos{\'e} Anxelu G. and Alonso-S{\'a}ez, Laura and Arandia-Gorostidi, N{\'e}stor and Vaqu{\'e}, Dolors and Sebasti{\'a}n, Marta}
}
@article {decelle_subcellular_2021,
	title = {Subcellular architecture and metabolic connection in the planktonic photosymbiosis between Collodaria (radiolarians) and their microalgae},
	journal = {bioRxiv},
	year = {2021},
	note = {Company: Cold Spring Harbor Laboratory Distributor: Cold Spring Harbor Laboratory Label: Cold Spring Harbor Laboratory Section: New Results Type: article},
	pages = {2021.03.13.435225},
	abstract = {Photosymbiosis is widespread and ecologically important in the oceanic plankton but remains poorly studied. Here, we used multimodal subcellular imaging to investigate the photosymbiosis between colonial Collodaria and their microalga dinoflagellate (Brandtodinium) collected in surface seawaters. We showed that this symbiosis is a very dynamic system whereby symbionts interact with different host cells via extracellular vesicles within the {\textquotedblleft}greenhouse-like{\textquotedblright} colony. 3D electron microscopy revealed that the volume of the photosynthetic apparatus (plastid and pyrenoid) of the microalgae increased in symbiosis compared to free-living while the mitochondria volume was similar. Stable isotope probing coupled with NanoSIMS showed that carbon and nitrogen were assimilated and stored in the symbiotic microalga in starch granules and purine crystals, respectively. Nitrogen was also allocated to the algal nucleus (nucleolus). After 3 hours, low 13C and 15N transfer was detected in the host Golgi. Metal mapping revealed that intracellular iron concentration was similar in free-living and symbiotic microalgae (ca 40 ppm) and two-fold higher in the host, whereas copper concentration increased in symbiotic microalgae (up to 6900 ppm) and was detected in the host cell and extracellular vesicles. Sulfur mapping also pinpointed the importance of this nutrient for the algal metabolism. This study, which revealed subcellular changes of the morphology and nutrient homeostasis in symbiotic microalgae, improves our understanding on the metabolism of this widespread and abundant oceanic symbiosis and paves the way for more studies to investigate the metabolites exchanged.},
	doi = {10.1101/2021.03.13.435225},
	url = {https://www.biorxiv.org/content/10.1101/2021.03.13.435225v1},
	author = {Decelle, Johan and Veronesi, Giulia and LeKieffre, Charlotte and Gallet, Benoit and Chevalier, Fabien and Stryhanyuk, Hryhoriy and Marro, Sophie and Ravanel, St{\'e}phane and Tucoulou, R{\'e}mi and Schieber, Nicole and Finazzi, Giovanni and Schwab, Yannick and Musat, Niculina}
}
@article {muller_temperature_2021,
	title = {Temperature Induced Physiological Reaction Norms of the Coccolithophore Gephyrocapsa oceanica and Resulting Coccolith Sr/Ca and Mg/Ca Ratios},
	journal = {Frontiers in Earth Science},
	volume = {9},
	year = {2021},
	pages = {273},
	abstract = {Coccolithophores are one of the major contributors to the pelagic production of calcium carbonate and their fossilized remains are a key component of the biogeochemical cycles of calcium (Ca), magnesium (Mg), and other divalent cations present in the intracellular precipitated calcitic structures (coccoliths). The geochemical signature of coccoliths (e.g., Sr/Ca and Mg/Ca ratios) is used as paleoproxy to reconstruct past environmental conditions and to understand the underlying physiological precipitation kinetics. Here, we present the elemental fractionation of Sr and Mg in calcite of the coccolithophore Gephyrocapsa oceanica from controlled laboratory experiments applying an extended temperature gradient (12 to 27{\textdegree}C). The physiological reaction norm of G. oceanica, in terms of growth rate, exhibited optimum behavior while the partition coefficient of Sr (DSr) was linearly correlated with temperature and DMg indicated no specific trend. Our results indicate: (1) a presumably secondary physiological control of DSr, and (2) the importance of calibrating coccolithophore-based proxies using experiments that include the full physiological reaction norms (i.e., a possible non-linear response) to environmental drivers (e.g., temperature, salinity, and pH, etc.). The presented results contribute to an improved understanding of the underlying physiological kinetics involved in regulating coccolith elemental fractionation and give additional implications for designing future laboratory experiments to calibrate and apply coccolithophore based paleoproxies on the fossil sediment record.},
	keywords = {rcc, RCC1303},
	issn = {2296-6463},
	doi = {10.3389/feart.2021.582521},
	url = {https://www.frontiersin.org/article/10.3389/feart.2021.582521},
	author = {M{\"u}ller, Marius N. and Blanco-Ameijeiras, Sonia and Stoll, Heather M. and M{\'e}ndez-Vicente, Ana and Lebrato, Mario}
}
@article {labban_temperature_2021,
	title = {Temperature Responses of Heterotrophic Bacteria in Co-culture With a Red Sea Synechococcus Strain},
	journal = {Frontiers in Microbiology},
	volume = {12},
	year = {2021},
	pages = {612732},
	abstract = {Interactions between autotrophic and heterotrophic bacteria are fundamental for marine biogeochemical cycling. How global warming will affect the dynamics of these essential microbial players is not fully understood. The aims of this study were to identify the major groups of heterotrophic bacteria present in a Synechococcus culture originally isolated from the Red Sea and assess their joint responses to experimental warming within the metabolic ecology framework. A co-culture of Synechococcus sp. RS9907 and their associated heterotrophic bacteria, after determining their taxonomic affiliation by 16S rRNA gene sequencing, was acclimated and maintained in the lab at different temperatures (24{\textendash}34{\textdegree}C). The abundance and cellular properties of Synechococcus and the three dominant heterotrophic bacterial groups (pertaining to the genera Paracoccus, Marinobacter, and Muricauda) were monitored by flow cytometry. The activation energy of Synechococcus, which grew at 0.94{\textendash}1.38 d{\textendash}1, was very similar (0.34 {\textpm} 0.02 eV) to the value hypothesized by the metabolic theory of ecology (MTE) for autotrophs (0.32 eV), while the values of the three heterotrophic bacteria ranged from 0.16 to 1.15 eV and were negatively correlated with their corresponding specific growth rates (2.38{\textendash}24.4 d{\textendash}1). The corresponding carrying capacities did not always follow the inverse relationship with temperature predicted by MTE, nor did we observe a consistent response of bacterial cell size and temperature. Our results show that the responses to future ocean warming of autotrophic and heterotrophic bacteria in microbial consortia might not be well described by theoretical universal rules.},
	keywords = {rcc, RCC546},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2021.612732},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8141594/},
	author = {Labban, Abbrar and Palacio, Antonio S. and Garc{\'\i}a, Francisca C. and Hadaidi, Ghaida and Ansari, Mohd I. and L{\'o}pez-Urrutia, {\'A}ngel and Alonso-S{\'a}ez, Laura and Hong, Pei-Ying and Mor{\'a}n, Xos{\'e} Anxelu G.}
}
@booklet {roquis_tropical_2021,
	title = {The tropical coral Pocillopora acuta displays an unusual chromatin structure and shows histone H3 clipping plasticity upon bleaching},
	number = {6:195},
	year = {2021},
	note = {Type: article},
	month = {jul},
	publisher = {Wellcome Open Research},
	abstract = {<p>Background: Pocillopora acuta is a hermatypic coral with strong ecological importance. Anthropogenic disturbances and global warming are major threats that can induce coral bleaching, the disruption of the mutualistic symbiosis between the coral host and its endosymbiotic algae. Previous works have shown that somaclonal colonies display different levels of survival depending on the environmental conditions they previously faced. Epigenetic mechanisms are good candidates to explain this phenomenon. However, almost no work had been published on the P. acuta epigenome, especially on histone modifications. In this study, we aim at providing the first insight into chromatin structure of this species. Methods: We aligned the amino acid sequence of P. acuta core histones with histone sequences from various phyla. We developed a centri-filtration on sucrose gradient to separate chromatin from the host and the symbiont. The presence of histone H3 protein and specific histone modifications were then detected by western blot performed on histone extraction done from bleached and healthy corals. Finally, micrococcal nuclease (MNase) digestions were undertaken to study nucleosomal organization. Results: The centri-filtration enabled coral chromatin isolation with less than 2\% of contamination by endosymbiont material. Histone sequences alignments with other species show that P. acuta displays on average \textasciitilde90\% of sequence similarities with mice and \textasciitilde96\% with other corals. H3 detection by western blot showed that H3 is clipped in healthy corals while it appeared to be intact in bleached corals. MNase treatment failed to provide the usual mononucleosomal digestion, a feature shared with some cnidarian, but not all; suggesting an unusual chromatin structure. Conclusions: These results provide a first insight into the chromatin, nucleosome and histone structure of P. acuta . The unusual patterns highlighted in this study and partly shared with other cnidarian will need to be further studied to better understand its role in corals.</p>
},
	keywords = {chromatin structure, Histone H3 clipping, invertebrate epigenetics, Pocillopora acuta, Pocillopora damicornis, rcc, RCC4017},
	doi = {10.12688/wellcomeopenres.17058.1},
	url = {https://wellcomeopenresearch.org/articles/6-195},
	author = {Roquis, David and Cosseau, C{\'e}line and Raffalli, Kelly Brener and Romans, Pascal and Masanet, Patrick and Mitta, Guillaume and Grunau, Christoph and Vidal-Dupiol, Jeremie}
}
@article {barbeyron_zobellia_2021,
	title = {Zobellia roscoffensis sp. nov. and Zobellia nedashkovskayae sp. nov., two flavobacteria from the epiphytic microbiota of the brown alga Ascophyllum nodosum, and emended description of the genus Zobellia},
	journal = {International Journal of Systematic and Evolutionary Microbiology},
	volume = {71},
	number = {8},
	year = {2021},
	abstract = {Four marine bacterial strains were isolated from a thallus of the brown alga Ascophyllum nodosum collected in Roscoff, France. Cells were Gram-s- tain--negative, strictly aerobic, non-f-lagellated, gliding, rod--shaped and grew optimally at 25{\textendash}30 {\textdegree}C, at pH 7{\textendash}8 and with 2{\textendash}4 \% NaCl. Phylogenetic analyses of their 16S rRNA gene sequences showed that the bacteria were affiliated to the genus Zobellia (family Flavobacteriaceae, phylum Bacteroidetes). The four strains exhibited 97.8{\textendash}100 \% 16S rRNA gene sequence similarity values among themselves, 97.9{\textendash}99.1 \% to the type strains of Zobellia amurskyensis KMM 3526T and Zobellia laminariae KMM 3676T, and less than 99 \% to other species of the genus Zobellia. The DNA G+C content of the four strains ranged from 36.7 to 37.7 mol\%. Average nucleotide identity and digital DNA{\textendash}DNA hybridization calculations between the new strains and other members of the genus Zobellia resulted in values of 76.4{\textendash}88.9 \% and below 38.5 \%, respectively. Phenotypic, phylogenetic and genomic analyses showed that the four strains are distinct from species of the genus Zobellia with validly published names. They represent two novel species of the genus Zobellia, for which the names Zobellia roscoffensis sp. nov. and Zobellia nedashkovskayae sp. nov. are proposed with Asnod1--F08T (RCC6906T=KMM 6823T=CIP 111902T) and Asnod2--B07--BT (RCC6908T=KMM 6825T=CIP 111904T), respectively, as the type strains.},
	keywords = {RCC6906, RCC6907, RCC6908, RCC6909},
	issn = {1466-5026, 1466-5034},
	doi = {10.1099/ijsem.0.004913},
	url = {https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.004913},
	author = {Barbeyron, Tristan and Thi{\'e}baud, Manon and Le Duff, Nolwen and Martin, Marjolaine and Corre, Erwan and Tanguy, Gwenn and Vandenbol, Micheline and Thomas, Fran{\c c}ois}
}
@article {Pan2020,
	title = {Assessments of first feeding protocols on the larviculture of California grunion Leuresthes tenuis (Osteichthyes: Atherinopsidae)},
	journal = {Aquaculture Research},
	volume = {51},
	number = {7},
	year = {2020},
	note = {Publisher: Blackwell Publishing Ltd tex.mendeley-tags: RCC350},
	month = {jul},
	pages = {3054{\textendash}3058},
	keywords = {California grunion, Copepod, larval rearing, live feed, quiescent egg, RCC350},
	issn = {13652109},
	doi = {10.1111/are.14637},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/are.14637},
	author = {Pan, Yen Ju and D{\'e}pos{\'e}, Emilien and Souissi, Anissa and H{\'e}nard, St{\'e}phane and Schaadt, Mike and Mastro, Ed and Souissi, Sami}
}
@article {Palacio2020,
	title = {Changes in population age-structure obscure the temperature-size rule in marine cyanobacteria},
	journal = {Frontiers in Microbiology},
	volume = {11},
	year = {2020},
	note = {Publisher: Frontiers Media S.A. tex.mendeley-tags: RCC2382,RCC3377},
	month = {aug},
	pages = {2059},
	abstract = {The temperature-size Rule (TSR) states that there is a negative relationship between ambient temperature and body size. This rule has been independently evaluated for different phases of the life cycle in multicellular eukaryotes, but mostly for the average population in unicellular organisms. We acclimated two model marine cyanobacterial strains (Prochlorococcus marinus MIT9301 and Synechococcus sp. RS9907) to a gradient of temperatures and measured the changes in population age-structure and cell size along their division cycle. Both strains displayed temperature-dependent diel changes in cell size, and as a result, the relationship between temperature and average cell size varied along the day. We computed the mean cell size of new-born cells in order to test the prediction of the TSR on a single-growth stage. Our work reconciles previous inconsistent results when testing the TSR on unicellular organisms, and shows that when a single-growth stage is considered the predicted negative response to temperature is revealed.},
	keywords = {cell cycle, Cell Division, cell size, Prochlorococcus, rcc2382, RCC3377, Synechococcus, temperature, temperature-size rule},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2020.02059},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2020.02059/full},
	author = {Palacio, Antonio S. and Cabello, Ana Mar{\'\i}a and Garc{\'\i}a, Francisca C. and Labban, Abbrar and Mor{\'a}n, Xos{\'e} Anxelu G. and Garczarek, Laurence and Alonso-S{\'a}ez, Laura and L{\'o}pez-Urrutia, {\'A}ngel}
}
@article {Mucko2020,
	title = {Characterization of a lipid-producing thermotolerant marine photosynthetic pico-alga in the genus Picochlorum (Trebouxiophyceae)},
	journal = {European Journal of Phycology},
	volume = {00},
	number = {00},
	year = {2020},
	note = {Publisher: Taylor \& Francis tex.mendeley-tags: RCC1034,RCC13,RCC14,RCC289,RCC475,RCC6905,RCC846,RCC9,RCC945},
	month = {aug},
	pages = {1{\textendash}16},
	keywords = {morphology, photosynthetic picoeukaryotes, phylogeny, physiology, Picochlorum, RCC1034, RCC13, RCC14, rcc289, RCC475, RCC6905, RCC846, RCC9, RCC945},
	issn = {0967-0262},
	doi = {10.1080/09670262.2020.1757763},
	url = {https://doi.org/10.1080/09670262.2020.1757763 https://www.tandfonline.com/doi/full/10.1080/09670262.2020.1757763},
	author = {Mucko, Maja and Padis{\'a}k, Judit and Gligora Udovi{\v c}, Marija and P{\'a}lmai, Tam{\'a}s and Novak, Tihana and Medi{\'c}, Nikola and Ga{\v s}parovi{\'c}, Bla{\v z}enka and Peharec {\v S}tefani{\'c}, Petra and Orli{\'c}, Sandi and Ljube{\v s}i{\'c}, Zrinka}
}
@article {Carrigee2020,
	title = {CpeY is a phycoerythrobilin lyase for cysteine 82 of the phycoerythrin I <span class="nocase">α</span>-subunit in marine Synechococcus},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	year = {2020},
	note = {Publisher: Elsevier B.V tex.mendeley-tags: RCC555},
	month = {apr},
	pages = {148215},
	keywords = {rcc555},
	issn = {00052728},
	doi = {10.1016/j.bbabio.2020.148215},
	url = {https://doi.org/10.1016/j.bbamem.2019.183135 https://linkinghub.elsevier.com/retrieve/pii/S0005272820300657},
	author = {Carrigee, Lyndsay A. and Mahmoud, Rania M. and Sanfilippo, Joseph E. and Frick, Jacob P. and Strnat, Johann A. and Karty, Jonathan A. and Chen, Bo and Kehoe, David M. and Schluchter, Wendy M.}
}
@article {Cai2020,
	title = {Cryptic species in the parasitic Amoebophrya species complex revealed by a polyphasic approach},
	journal = {Scientific Reports},
	volume = {10},
	number = {1},
	year = {2020},
	note = {Publisher: Springer US tex.mendeley-tags: RCC1627,RCC1720,RCC3018,RCC3043,RCC3044,RCC3047,RCC3048,RCC3049,RCC3145,RCC3278,RCC3596,RCC4381,RCC4382,RCC4383,RCC4384,RCC4385,RCC4386,RCC4387,RCC4388,RCC4389,RCC4390,RCC4391,RCC4392,RCC4393,RCC4394,RCC4395,RCC4396,RCC4397,RCC4398,RCC4399,RCC4400,RCC4401,RCC4402,RCC4403,RCC4404,RCC4405,RCC4406,RCC4407,RCC4408,RCC4409,RCC4410,RCC4411,RCC4412,RCC4413,RCC4414,RCC4415,RCC4416,RCC4711,RCC4712,RCC4713,RCC4715,RCC4716,RCC4722,RCC4723,RCC4726,RCC4728,RCC4729,RCC4732,RCC4733,RCC4734,RCC5984,RCC5985,RCC5986,RCC5987,RCC5988,RCC5989,RCC5990,RCC5991,RCC5992,RCC5993,RCC5994,RCC5995,RCC5997,RCC5998,RCC5999,RCC6000,RCC6001,RCC6002,RCC6003,RCC6004,RCC6005,RCC6006,RCC6007,RCC6008,RCC6009,RCC6010,RCC6079,RCC6080,RCC6081,RCC6082,RCC6083,RCC6084,RCC6085,RCC6087,RCC6088,RCC6094,RCC6096,RCC6100,RCC6101,RCC6102,RCC6103,RCC6104,RCC6105,RCC6106,RCC6107,RCC6108,RCC6109,RCC6110,RCC6111,RCC6112,RCC6113,RCC6115,RCC6116,RCC6117,RCC6118,RCC6119,RCC6120,RCC6121},
	month = {dec},
	pages = {2531},
	keywords = {RCC1627, RCC1720, RCC3018, RCC3043, RCC3044, RCC3047, RCC3048, RCC3049, RCC3145, RCC3278, RCC3596, RCC4381, RCC4382, RCC4383, RCC4384, RCC4385, RCC4386, RCC4387, RCC4388, RCC4389, RCC4390, RCC4391, RCC4392, RCC4393, RCC4394, RCC4395, RCC4396, RCC4397, RCC4398, RCC4399, RCC4400, RCC4401, RCC4402, RCC4403, RCC4404, RCC4405, RCC4406, RCC4407, RCC4408, RCC4409, RCC4410, RCC4411, RCC4412, RCC4413, RCC4414, RCC4415, RCC4416, RCC4711, RCC4712, RCC4713, RCC4715, RCC4716, RCC4722, RCC4723, RCC4726, RCC4728, RCC4729, RCC4732, RCC4733, RCC4734, RCC5984, RCC5985, RCC5986, RCC5987, RCC5988, RCC5989, RCC5990, RCC5991, RCC5992, RCC5993, RCC5994, RCC5995, RCC5997, RCC5998, RCC5999, RCC6000, RCC6001, RCC6002, RCC6003, RCC6004, RCC6005, RCC6006, RCC6007, RCC6008, RCC6009, RCC6010, RCC6079, RCC6080, RCC6081, RCC6082, RCC6083, RCC6084, RCC6085, RCC6087, RCC6088, RCC6094, RCC6096, RCC6100, RCC6101, RCC6102, RCC6103, RCC6104, RCC6105, RCC6106, RCC6107, RCC6108, RCC6109, RCC6110, RCC6111, RCC6112, RCC6113, RCC6115, RCC6116, RCC6117, RCC6118, RCC6119, RCC6120, RCC6121},
	issn = {2045-2322},
	doi = {10.1038/s41598-020-59524-z},
	url = {http://dx.doi.org/10.1038/s41598-020-59524-z http://www.nature.com/articles/s41598-020-59524-z},
	author = {Cai, Ruibo and Kayal, Ehsan and Alves-de-Souza, Catharina and Bigeard, Estelle and Corre, Erwan and Jeanthon, Christian and Marie, Dominique and Porcel, Betina M and Siano, Raffaele and Szymczak, Jeremy and Wolf, Matthias and Guillou, Laure}
}
@article {Ribeiro2020,
	title = {Culturable diversity of Arctic phytoplankton during pack ice melting},
	journal = {Elementa: Science of the Anthropocene},
	volume = {8},
	number = {1},
	year = {2020},
	note = {tex.mendeley-tags: RCC5197,RCC5198,RCC5199,RCC5200,RCC5201,RCC5202,RCC5203,RCC5204,RCC5205,RCC5206,RCC5207,RCC5208,RCC5209,RCC5210,RCC5211,RCC5212,RCC5213,RCC5214,RCC5215,RCC5216,RCC5217,RCC5218,RCC5219,RCC5220,RCC5221,RCC5222,RCC5223,RCC5224,RCC5225,RCC5226,RCC5227,RCC5228,RCC5229,RCC5230,RCC5231,RCC5232,RCC5233,RCC5234,RCC5235,RCC5236,RCC5237,RCC5238,RCC5239,RCC5240,RCC5241,RCC5242,RCC5243,RCC5244,RCC5245,RCC5246,RCC5247,RCC5248,RCC5249,RCC5250,RCC5251,RCC5252,RCC5253,RCC5254,RCC5255,RCC5256,RCC5257,RCC5258,RCC5259,RCC5260,RCC5261,RCC5262,RCC5263,RCC5264,RCC5265,RCC5266,RCC5267,RCC5268,RCC5269,RCC5270,RCC5271,RCC5272,RCC5273,RCC5274,RCC5275,RCC5276,RCC5277,RCC5278,RCC5279,RCC5280,RCC5281,RCC5282,RCC5283,RCC5284,RCC5285,RCC5286,RCC5287,RCC5288,RCC5289,RCC5290,RCC5291,RCC5292,RCC5293,RCC5294,RCC5295,RCC5296,RCC5297,RCC5298,RCC5299,RCC5300,RCC5301,RCC5302,RCC5303,RCC5304,RCC5305,RCC5306,RCC5307,RCC5308,RCC5309,RCC5310,RCC5311,RCC5312,RCC5313,RCC5314,RCC5315,RCC5316,RCC5317,RCC5318,RCC5319,RCC5320,RCC5321,RCC5322,RCC5323,RCC5324,RCC5325,RCC5326,RCC5327,RCC5328,RCC5329,RCC5330,RCC5331,RCC5332,RCC5333,RCC5334,RCC5335,RCC5336,RCC5337,RCC5338,RCC5339,RCC5340,RCC5341,RCC5342,RCC5343,RCC5344,RCC5345,RCC5346,RCC5347,RCC5348,RCC5349,RCC5350,RCC5351,RCC5352,RCC5353,RCC5354,RCC5355,RCC5356,RCC5357,RCC5358,RCC5359,RCC5360,RCC5361,RCC5362,RCC5363,RCC5364,RCC5365,RCC5366,RCC5367,RCC5368,RCC5369,RCC5370,RCC5371,RCC5372,RCC5373,RCC5374,RCC5375,RCC5376,RCC5377,RCC5378,RCC5379,RCC5380,RCC5381,RCC5382,RCC5383,RCC5384,RCC5385,RCC5386,RCC5387,RCC5388,RCC5389,RCC5390,RCC5391,RCC5392,RCC5393,RCC5394,RCC5395,RCC5396,RCC5397,RCC5398,RCC5399,RCC5400,RCC5401,RCC5402,RCC5403,RCC5404,RCC5405,RCC5406,RCC5407,RCC5408,RCC5409,RCC5410,RCC5411,RCC5412,RCC5413,RCC5414,RCC5415,RCC5416,RCC5417,RCC5418,RCC5419,RCC5420,RCC5421,RCC5422,RCC5423,RCC5424,RCC5425,RCC5426,RCC5427,RCC5428,RCC5429,RCC5430,RCC5431,RCC5432,RCC5433,RCC5434,RCC5435,RCC5436,RCC5437,RCC5438,RCC5439,RCC5440,RCC5441,RCC5442,RCC5443,RCC5444,RCC5445,RCC5446,RCC5447,RCC5448,RCC5449,RCC5450,RCC5451,RCC5452,RCC5453,RCC5454,RCC5455,RCC5456,RCC5457,RCC5458,RCC5459,RCC5460,RCC5461,RCC5462,RCC5463,RCC5464,RCC5465,RCC5466,RCC5467,RCC5468,RCC5469,RCC5470,RCC5471,RCC5472,RCC5473,RCC5474,RCC5475,RCC5476,RCC5477,RCC5478,RCC5479,RCC5480,RCC5481,RCC5482,RCC5483,RCC5484,RCC5485,RCC5486,RCC5487,RCC5488,RCC5489,RCC5490,RCC5491,RCC5492,RCC5493,RCC5494,RCC5495,RCC5496,RCC5497,RCC5498,RCC5499,RCC5500,RCC5501,RCC5502,RCC5503,RCC5504,RCC5505,RCC5506,RCC5507,RCC5508,RCC5509,RCC5510,RCC5511,RCC5512,RCC5513,RCC5514,RCC5515,RCC5516,RCC5517,RCC5518,RCC5519,RCC5520,RCC5521,RCC5522,RCC5523,RCC5524,RCC5525,RCC5526,RCC5527,RCC5528,RCC5529,RCC5530,RCC5531,RCC5532,RCC5533,RCC5534,RCC5535,RCC5536,RCC5537,RCC5538,RCC5539,RCC5540,RCC5541,RCC5542,RCC5543,RCC5544,RCC5545,RCC5546,RCC5547,RCC5548,RCC5549,RCC5550,RCC5551,RCC5552,RCC5553,RCC5554,RCC5555,RCC5556,RCC5557,RCC5558,RCC5559,RCC5560,RCC5561,RCC5562,RCC5563,RCC5564,RCC5565,RCC5566,RCC5567,RCC5568,RCC5569,RCC5570,RCC5571,RCC5572,RCC5573,RCC5574,RCC5575,RCC5576,RCC5577,RCC5578,RCC5579,RCC5580,RCC5581,RCC5582,RCC5583,RCC5584,RCC5585,RCC5586,RCC5587,RCC5588,RCC5589,RCC5590,RCC5591,RCC5592,RCC5593,RCC5594,RCC5595,RCC5596,RCC5597,RCC5598,RCC5599,RCC5600,RCC5601,RCC5602,RCC5603,RCC5604,RCC5605,RCC5606,RCC5607,RCC5608,RCC5609,RCC5610,RCC5611,RCC5612},
	month = {feb},
	pages = {6},
	abstract = {Massive phytoplankton blooms develop at the Arctic ice edge, sometimes extending far under the pack ice. An extensive culturing effort was conducted before and during a phytoplankton bloom in Baffin Bay between April and July 2016. Different isolation strategies were applied, including flow cytometry cell sorting, manual single cell pipetting and serial dilution. Although all three techniques yielded the most common organisms, each technique retrieved specific taxa, highlighting the importance of using several methods to maximize the number and diversity of isolated strains. More than 1,000 cultures were obtained, characterized by 18S rRNA sequencing and optical microscopy and de-replicated to a subset of 276 strains presented in this work. Strains grouped into 57 genotypes defined by 100\% 18S rRNA sequence similarity. These genotypes spread across five divisions: Heterokontophyta, Chlorophyta, Cryptophyta, Haptophyta and Dinophyta. Diatoms were the most abundant group (193 strains), mostly represented by the genera Chaetoceros and Attheya. The genera Rhodomonas and Pyramimonas were the most abundant non-diatom nanoplankton strains, while Micromonas polaris dominated the picoplankton. Diversity at the class level was higher during the peak of the bloom. Potentially new species were isolated, in particular within the genera Navicula, Nitzschia, Coscinodiscus, Thalassiosira, Pyramimonas, Mantoniella and Isochrysis.},
	keywords = {RCC5197, RCC5198, RCC5199, RCC5200, RCC5201, RCC5202, RCC5203, RCC5204, RCC5205, RCC5206, RCC5207, RCC5208, RCC5209, RCC5210, RCC5211, RCC5212, RCC5213, RCC5214, RCC5215, RCC5216, RCC5217, RCC5218, RCC5219, RCC5220, RCC5221, RCC5222, RCC5223, RCC5224, RCC5225, RCC5226, RCC5227, RCC5228, RCC5229, RCC5230, RCC5231, RCC5232, RCC5233, RCC5234, RCC5235, RCC5236, RCC5237, RCC5238, RCC5239, RCC5240, RCC5241, RCC5242, RCC5243, RCC5244, RCC5245, RCC5246, RCC5247, RCC5248, RCC5249, RCC5250, RCC5251, RCC5252, RCC5253, RCC5254, RCC5255, RCC5256, RCC5257, RCC5258, RCC5259, RCC5260, RCC5261, RCC5262, RCC5263, RCC5264, RCC5265, RCC5266, RCC5267, RCC5268, RCC5269, RCC5270, RCC5271, RCC5272, RCC5273, RCC5274, RCC5275, RCC5276, RCC5277, RCC5278, RCC5279, RCC5280, RCC5281, RCC5282, RCC5283, RCC5284, RCC5285, RCC5286, RCC5287, RCC5288, RCC5289, RCC5290, RCC5291, RCC5292, RCC5293, RCC5294, RCC5295, RCC5296, RCC5297, RCC5298, RCC5299, RCC5300, RCC5301, RCC5302, RCC5303, RCC5304, RCC5305, RCC5306, RCC5307, RCC5308, RCC5309, RCC5310, RCC5311, RCC5312, RCC5313, RCC5314, RCC5315, RCC5316, RCC5317, RCC5318, RCC5319, RCC5320, RCC5321, RCC5322, RCC5323, RCC5324, RCC5325, RCC5326, RCC5327, RCC5328, RCC5329, RCC5330, RCC5331, RCC5332, RCC5333, RCC5334, RCC5335, RCC5336, RCC5337, RCC5338, RCC5339, RCC5340, RCC5341, RCC5342, RCC5343, RCC5344, RCC5345, RCC5346, RCC5347, RCC5348, RCC5349, RCC5350, RCC5351, RCC5352, RCC5353, RCC5354, RCC5355, RCC5356, RCC5357, RCC5358, RCC5359, RCC5360, RCC5361, RCC5362, RCC5363, RCC5364, RCC5365, RCC5366, RCC5367, RCC5368, RCC5369, RCC5370, RCC5371, RCC5372, RCC5373, RCC5374, RCC5375, RCC5376, RCC5377, RCC5378, RCC5379, RCC5380, RCC5381, RCC5382, RCC5383, RCC5384, RCC5385, RCC5386, RCC5387, RCC5388, RCC5389, RCC5390, RCC5391, RCC5392, RCC5393, RCC5394, RCC5395, RCC5396, RCC5397, RCC5398, RCC5399, RCC5400, RCC5401, RCC5402, RCC5403, RCC5404, RCC5405, RCC5406, RCC5407, RCC5408, RCC5409, RCC5410, RCC5411, RCC5412, RCC5413, RCC5414, RCC5415, RCC5416, RCC5417, RCC5418, RCC5419, RCC5420, RCC5421, RCC5422, RCC5423, RCC5424, RCC5425, RCC5426, RCC5427, RCC5428, RCC5429, RCC5430, RCC5431, RCC5432, RCC5433, RCC5434, RCC5435, RCC5436, RCC5437, RCC5438, RCC5439, RCC5440, RCC5441, RCC5442, RCC5443, RCC5444, RCC5445, RCC5446, RCC5447, RCC5448, RCC5449, RCC5450, RCC5451, RCC5452, RCC5453, RCC5454, RCC5455, RCC5456, RCC5457, RCC5458, RCC5459, RCC5460, RCC5461, RCC5462, RCC5463, RCC5464, RCC5465, RCC5466, RCC5467, RCC5468, RCC5469, RCC5470, RCC5471, RCC5472, RCC5473, RCC5474, RCC5475, RCC5476, RCC5477, RCC5478, RCC5479, RCC5480, RCC5481, RCC5482, RCC5483, RCC5484, RCC5485, RCC5486, RCC5487, RCC5488, RCC5489, RCC5490, RCC5491, RCC5492, RCC5493, RCC5494, RCC5495, RCC5496, RCC5497, RCC5498, RCC5499, RCC5500, RCC5501, RCC5502, RCC5503, RCC5504, RCC5505, RCC5506, RCC5507, RCC5508, RCC5509, RCC5510, RCC5511, RCC5512, RCC5513, RCC5514, RCC5515, RCC5516, RCC5517, RCC5518, RCC5519, RCC5520, RCC5521, RCC5522, RCC5523, RCC5524, RCC5525, RCC5526, RCC5527, RCC5528, RCC5529, RCC5530, RCC5531, RCC5532, RCC5533, RCC5534, RCC5535, RCC5536, RCC5537, RCC5538, RCC5539, RCC5540, RCC5541, RCC5542, RCC5543, RCC5544, RCC5545, RCC5546, RCC5547, RCC5548, RCC5549, RCC5550, RCC5551, RCC5552, RCC5553, RCC5554, RCC5555, RCC5556, RCC5557, RCC5558, RCC5559, RCC5560, RCC5561, RCC5562, RCC5563, RCC5564, RCC5565, RCC5566, RCC5567, RCC5568, RCC5569, RCC5570, RCC5571, RCC5572, RCC5573, RCC5574, RCC5575, RCC5576, RCC5577, RCC5578, RCC5579, RCC5580, RCC5581, RCC5582, RCC5583, RCC5584, RCC5585, RCC5586, RCC5587, RCC5588, RCC5589, RCC5590, RCC5591, RCC5592, RCC5593, RCC5594, RCC5595, RCC5596, RCC5597, RCC5598, RCC5599, RCC5600, RCC5601, RCC5602, RCC5603, RCC5604, RCC5605, RCC5606, RCC5607, RCC5608, RCC5609, RCC5610, RCC5611, RCC5612},
	issn = {2325-1026},
	doi = {10.1525/elementa.401},
	url = {https://www.biorxiv.org/content/10.1101/642264v1 https://www.elementascience.org/article/10.1525/elementa.401/},
	author = {Ribeiro, Catherine G{\'e}rikas and dos Santos, Adriana Lopes and Gourvil, Priscillia and Le Gall, Florence and Marie, Dominique and Tragin, Margot and Probert, Ian and Vaulot, Daniel}
}
@article {Avrahami2020,
	title = {Detection of phagotrophy in the marine phytoplankton group of the coccolithophores (calcihaptophycidae, haptophyta) during Nutrient-replete and Phosphate-limited growth},
	journal = {Journal of Phycology},
	year = {2020},
	note = {tex.mendeley-tags: RCC1130,RCC1131,RCC1178,RCC1216,RCC1217,RCC3779},
	month = {apr},
	pages = {jpy.12997},
	abstract = {Mixotrophic algae that combine photoautotrophy with phagotrophy in a single cell are prevalent in marine ecosystems. Here, we assessed the ability of food ingestion in coccolithophores, an important group of calcifying haptophytes inhabiting the oceans. We tested four species from different coccolithophore lineages (Emiliania huxleyi, Calcidiscus leptoporus, Coccolithus braarudii, and Calyptrosphaera sphaeroidea). For both E. huxleyi and C. leptoporus we included different life phases (haploid and diploid). For C. braarudii we only tested diploid heterococcolithophore cells, while for C. sphaeroidea we only tested haploid holococcolithophore cells. Phagotrophy was assessed using fluorescently labeled bacteria (FLB) as model prey item, under nutrient-replete and phosphate-limited conditions. We detected by microscopy ingestion of FLB by all species, except the diploid C. braarudii strain. However, a previous study detected ingestion by haploid cells of C. braarudii. These overall results indicate that mixotrophy and the ability to ingest prey is widespread in coccolithophores. Yet, in all tested species the ingestion of FLB was low ({\textexclamdown}1\% of the population contained prey at all time points over 2 days), namely for E. huxleyi and the diploid cells from C. leptoporus where detection of ingestion was sporadic. Moreover, no clear differences were detected between life phases in E. huxleyi and C. leptoporus under equal circumstances, or between replete and limited growth conditions.},
	keywords = {bacterivory, coccolithophores, life cycle, mixotrophy, phytoplankton, RCC1130, RCC1131, RCC1178, RCC1216, rcc1217, RCC3779},
	issn = {0022-3646},
	doi = {10.1111/jpy.12997},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.12997},
	author = {Avrahami, Yoav and Frada, Miguel J.},
	editor = {Mock, T.}
}
@article {Altenburger2020,
	title = {Dimorphism in cryptophytes{\textemdash}The case of Teleaulax amphioxeia / Plagioselmis prolonga and its ecological implications},
	journal = {Science Advances},
	volume = {6},
	number = {37},
	year = {2020},
	note = {tex.mendeley-tags: RCC5152},
	month = {sep},
	pages = {eabb1611},
	abstract = {Growing evidence suggests that sexual reproduction might be common in unicellular organisms, but observations are sparse. Limited knowledge of sexual reproduction constrains understanding of protist ecology. Although Teleaulax amphioxeia and Plagioselmis prolonga are common marine cryptophytes worldwide, and are also important plastid donors for some kleptoplastic ciliates and dinoflagellates, the ecology and development of these protists are poorly known. We demonstrate that P. prolonga is the haploid form of the diploid T. amphioxeia and describe the seasonal dynamics of these two life stages. The diploid T. amphioxeia dominates during periods of high dissolved inorganic nitrogen (DIN) and low irradiance, temperature, and grazing (winter and early spring), whereas the haploid P. prolonga becomes more abundant during the summer, when DIN is low and irradiance, temperature, and grazing are high. Dimorphic sexual life cycles might explain the success of this species by fostering high genetic diversity and enabling endurance in adverse conditions.},
	keywords = {RCC5152},
	issn = {2375-2548},
	doi = {10.1126/sciadv.abb1611},
	url = {https://advances.sciencemag.org/lookup/doi/10.1126/sciadv.abb1611},
	author = {Altenburger, A and Blossom, H E and Garcia-Cuetos, L. and Jakobsen, H H and Carstensen, J and Lundholm, N. and Hansen, P. J. and Moestrup, {\O}. and Haraguchi, L.}
}
@article {Kayal2020,
	title = {Dinoflagellate host chloroplasts and mitochondria remain functional during amoebophrya infection},
	journal = {Frontiers in Microbiology},
	volume = {11},
	number = {December},
	year = {2020},
	note = {tex.mendeley-tags: RCC1627,RCC4398},
	month = {dec},
	pages = {1{\textendash}11},
	abstract = {Dinoflagellates are major components of phytoplankton that play critical roles in many microbial food webs, many of them being hosts of countless intracellular parasites. The phototrophic dinoflagellate Scrippsiella acuminata (Dinophyceae) can be infected by the microeukaryotic parasitoids Amoebophrya spp. (Syndiniales), some of which primarily target and digest the host nucleus. Early digestion of the nucleus at the beginning of the infection is expected to greatly impact the host metabolism, inducing the knockout of the organellar machineries that highly depend upon nuclear gene expression, such as the mitochondrial OXPHOS pathway and the plastid photosynthetic carbon fixation. However, previous studies have reported that chloroplasts remain functional in swimming host cells infected by Amoebophrya . We report here a multi-approach monitoring study of S. acuminata organelles over a complete infection cycle by nucleus-targeting Amoebophrya sp. strain A120. Our results show sustained and efficient photosystem II activity as a hallmark of functional chloroplast throughout the infection period despite the complete digestion of the host nucleus. We also report the importance played by light on parasite production, i.e., the amount of host biomass converted to parasite infective propagules. Using a differential gene expression analysis, we observed an apparent increase of all 3 mitochondrial and 9 out of the 11 plastidial genes involved in the electron transport chains (ETC) of the respiration pathways during the first stages of the infection. The longer resilience of organellar genes compared to those encoded by the nucleus suggests that both mitochondria and chloroplasts remain functional throughout most of the infection. This extended organelle functionality, along with higher parasite production under light conditions, suggests that host bioenergetic organelles likely benefit the parasite Amoebophrya sp. A120 and improve its fitness during the intracellular infective stage.},
	keywords = {amoebophrya, chloroplast, Dinoflagellate, frontiers in microbiology, frontiersin, kleptoplast, marine plankton, org, organelles, parasitism, RCC1627, RCC4398, www},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2020.600823},
	url = {https://www.frontiersin.org/articles/10.3389/fmicb.2020.600823/full},
	author = {Kayal, Ehsan and Alves-de-Souza, Catharina and Farhat, Sarah and Velo-Suarez, Lourdes and Monjol, Joanne and Szymczak, Jeremy and Bigeard, Estelle and Marie, Dominique and Noel, Benjamin and Porcel, Betina M and Corre, Erwan and Six, Christophe and Guillou, Laure}
}
@article {Arsenieff2020,
	title = {Diversity and dynamics of relevant nanoplanktonic diatoms in the Western English Channel},
	journal = {The ISME Journal},
	year = {2020},
	note = {Publisher: Springer US tex.mendeley-tags: RCC4657,RCC4658,RCC4659,RCC4660,RCC4661,RCC4662,RCC4663,RCC4664,RCC4665,RCC4666,RCC5154,RCC5839,RCC5840,RCC5841,RCC5842,RCC5843,RCC5844,RCC5845,RCC5846,RCC5847,RCC5848,RCC5849,RCC5850,RCC5851,RCC5852,RCC5853,RCC5854,RCC5855,RCC5856,RCC5857,RCC5859,RCC5860,RCC5861,RCC5862,RCC5863,RCC5864,RCC5865,RCC5866,RCC5867,RCC5868,RCC5869,RCC5870,RCC5871,RCC5872,RCC5873,RCC5875,RCC5876,RCC5877,RCC5878,RCC5879,RCC5880,RCC5881,RCC5882,RCC5883,RCC5884,RCC5885,RCC5886,RCC5887,RCC5921},
	month = {apr},
	keywords = {RCC4657, RCC4658, RCC4659, RCC4660, RCC4661, RCC4662, RCC4663, RCC4664, RCC4665, RCC4666, RCC5154, RCC5839, RCC5840, RCC5841, RCC5842, RCC5843, RCC5844, RCC5845, RCC5846, RCC5847, RCC5848, RCC5849, RCC5850, RCC5851, RCC5852, RCC5853, RCC5854, RCC5855, RCC5856, RCC5857, RCC5859, RCC5860, RCC5861, RCC5862, RCC5863, RCC5864, RCC5865, RCC5866, RCC5867, RCC5868, RCC5869, RCC5870, RCC5871, RCC5872, RCC5873, RCC5875, RCC5876, RCC5877, RCC5878, RCC5879, RCC5880, RCC5881, RCC5882, RCC5883, RCC5884, RCC5885, RCC5886, RCC5887, RCC5921},
	issn = {1751-7362},
	doi = {10.1038/s41396-020-0659-6},
	url = {http://dx.doi.org/10.1038/s41396-020-0659-6 http://www.nature.com/articles/s41396-020-0659-6},
	author = {Arsenieff, Laure and Le Gall, Florence and Rigaut-jalabert, Fabienne and Mah{\'e}, Fr{\'e}d{\'e}ric and Sarno, Diana and Gouhier, L{\'e}na and Baudoux, Anne-claire and Simon, Nathalie}
}
@article {Coelho2020,
	title = {Ectocarpus: an evo-devo model for the brown algae},
	journal = {EvoDevo},
	volume = {11},
	number = {1},
	year = {2020},
	note = {ISBN: 1322702000164 Publisher: BioMed Central},
	month = {dec},
	pages = {19},
	keywords = {Brown algae, complex, Complex multicellularity, cycle, Ectocarpus, ectocarpus is a genus, filamentous, Gametophyte, life-cycle, Marine, multicellu-, multicellularity, natural habitat and life, of small, Phaeoviruses, Sex determination, Sporophyte},
	issn = {2041-9139},
	doi = {10.1186/s13227-020-00164-9},
	url = {https://doi.org/10.1186/s13227-020-00164-9 https://evodevojournal.biomedcentral.com/articles/10.1186/s13227-020-00164-9},
	author = {Coelho, Susana M and Peters, Akira F and M{\"u}ller, Dieter and Cock, J Mark}
}
@article {Morais2020,
	title = {Electrochemical genosensor for the detection of Alexandrium minutum dinoflagellates},
	journal = {Talanta},
	year = {2020},
	note = {Publisher: Elsevier B.V. tex.mendeley-tags: RCC3029},
	pages = {121416},
	keywords = {RCC3029},
	issn = {00399140},
	doi = {10.1016/j.talanta.2020.121416},
	url = {https://doi.org/10.1016/j.talanta.2020.121416 https://linkinghub.elsevier.com/retrieve/pii/S0039914020307074},
	author = {Morais, Stephanie L. and Barros, Piedade and Santos, Marlene and Delerue-Matos, Cristina and Gomes, Andreia C. and F{\'a}tima Barroso, M.}
}
@article {Hackl2019,
	title = {Four high-quality draft genome assemblies of the marine heterotrophic nanoflagellate Cafeteria roenbergensis},
	journal = {Scientific Data},
	volume = {7},
	number = {1},
	year = {2020},
	note = {tex.mendeley-tags: RCC4623,RCC4624,RCC4625,RCC970},
	month = {dec},
	pages = {29},
	keywords = {RCC4623, RCC4624, RCC4625, RCC970},
	issn = {2052-4463},
	doi = {10.1038/s41597-020-0363-4},
	url = {http://www.nature.com/articles/s41597-020-0363-4},
	author = {Hackl, Thomas and Martin, Roman and Barenhoff, Karina and Duponchel, Sarah and Heider, Dominik and Fischer, Matthias G.}
}
@article {Belisle2020,
	title = {Genome sequences of synechococcus sp. Strain MIT S9220 and cocultured cyanophage SynMITS9220M01},
	journal = {Microbiology Resource Announcements},
	volume = {9},
	number = {30},
	year = {2020},
	note = {tex.mendeley-tags: RCC2571},
	month = {jul},
	pages = {28{\textendash}30},
	abstract = {Synechococcus bacteria are unicellular cyanobacteria that contribute significantly to global marine primary production. We report the nearly complete genome sequence of Synechococcus sp. strain MIT S9220, which lacks the nitrate utilization genes present in most marine Synechococcus genomes. Assembly also produced the complete genome sequence of a cyanophage present in the MIT S9220 culture.},
	keywords = {RCC2571},
	issn = {2576-098X},
	doi = {10.1128/MRA.00481-20},
	url = {https://mra.asm.org/content/9/30/e00481-20},
	author = {Belisle, B. Shafer and Avila Paz, Andres A. and Carpenter, Angelina R. and Cormier, Tayla C. and Lewis, Adam J. and Menin, Linnea S. and Oliveira, Daniel R and Song, Bukyung and Szeto, Amy and Tchantouridze, Elizabeth I and Watson, Kayleigh A and Yohannes, Mary T and Ahlgren, Nathan A},
	editor = {Putonti, Catherine}
}
@article {Carrillo2020,
	title = {Identification and characterization of ChlreSEX4, a novel glucan phosphatase from Chlamydomonas reinhardtii green alga},
	journal = {Archives of Biochemistry and Biophysics},
	volume = {680},
	year = {2020},
	note = {Publisher: Academic Press Inc.},
	month = {feb},
	pages = {108235},
	abstract = {Chlamydomonas reinhardtii is the best known unicellular green alga model which has long been used to investigate all kinds of cellular processes, including starch metabolism. Here we identified and characterized a novel enzyme, ChlreSEX4, orthologous to glucan phosphatase SEX4 from Arabidopsis thaliana, that is capable of binding and dephosphorylating amylopectin in vitro. We also reported that cysteine 224 and tryptophan 305 residues are critical for enzyme catalysis and substrate binding. Furthermore, we verified that ChlreSEX4 gene is expressed in vivo and that glucan phosphatase activity is measurable in Chlamydomonas protein extracts. In view of the results presented, we suggest ChlreSEX4 as a functional phosphoglucan phosphatase from C. reinhardtii. Our data obtained so far contribute to understanding the phosphoglucan phosphatases evolutionary process in the green lineage and their role in starch reversible phosphorylation. In addition, this allows to position Chlamydomonas as a potential tool to obtain starches with different degrees of phosphorylation for industrial or biotechnological purposes.},
	keywords = {Chlamydomonas Reinhardtii, ChlreSEX4, Glucan phosphatase, SEX4, Starch phosphorylation},
	issn = {10960384},
	doi = {10.1016/j.abb.2019.108235},
	author = {Carrillo, Julieta B. and Torresi, Florencia and Morales, Luisina L. and Ricordi, Micaela and Gomez-Casati, Diego F. and Busi, Maria V. and Mart{\'\i}n, Mariana}
}
@article {Uwizeye2020,
	title = {In-cell quantitative structural imaging of phytoplankton using 3D electron microscopy},
	journal = {bioRxiv},
	year = {2020},
	note = {tex.mendeley-tags: RCC100,RCC4014,RCC827,RCC909},
	month = {jan},
	pages = {2020.05.19.104166},
	abstract = {Phytoplankton is a minor fraction of the global biomass playing a major role in primary production and climate. Despite improved understanding of phytoplankton diversity and genomics, we lack nanoscale subcellular imaging approaches to understand their physiology and cell biology. Here, we present a complete Focused Ion Beam - Scanning Electron Microscopy (FIB-SEM) workflow (from sample preparation to image processing) to generate nanometric 3D phytoplankton models. Tomograms of entire cells, representatives of six ecologically-successful phytoplankton unicellular eukaryotes, were used for quantitative morphometric analysis. Besides lineage-specific cellular architectures, we observed common features related to cellular energy management: i) conserved cell-volume fractions occupied by the different organelles; ii) consistent plastid-mitochondria interactions, iii) constant volumetric ratios in these energy-producing organelles. We revealed detailed subcellular features related to chromatin organization and to biomineralization. Overall, this approach opens new perspectives to study phytoplankton acclimation responses to abiotic and biotic factors at a relevant biological scale.Competing Interest StatementThe authors have declared no competing interest.},
	keywords = {RCC100, RCC4014, RCC827, RCC909},
	doi = {10.1101/2020.05.19.104166},
	url = {http://biorxiv.org/content/early/2020/05/20/2020.05.19.104166.abstract},
	author = {Uwizeye, Clarisse and Decelle, Johan and Jouneau, Pierre-Henri and Gallet, Benoit and Keck, Jean-baptiste and Schwab, Yannick and Schoehn, Guy and Zeeman, Samuel C and Falconet, Denis and Finazzi, Giovanni and Moriscot, Christine and Chevalier, Fabien and Schieber, Nicole L and Templin, Rachel and Curien, Gilles and Schwab, Yannick and Schoehn, Guy and Zeeman, Samuel C and Falconet, Denis and Finazzi, Giovanni}
}
@article {Langer2020,
	title = {Li partitioning into coccoliths of Emiliania huxleyi : evaluating the general role of {\textquotedblleft}vital effects{\textquotedblright} in explaining element partitioning in biogenic carbonates},
	journal = {Geochemistry, Geophysics, Geosystems},
	year = {2020},
	note = {ISBN: 0000000272 tex.mendeley-tags: RCC3652},
	month = {jun},
	pages = {0{\textendash}2},
	abstract = {Abstract Emiliania huxleyi cells were grown in artificial seawater of different Li and Ca concentrations and coccolith Li/Ca ratios determined. Coccolith Li/Ca ratios were positively correlated to seawater Li/Ca ratios only if the seawater Li concentration was changed, not if the seawater Ca concentration was changed. This Li partitioning pattern of E. huxleyi was previously also observed in the benthic foraminifer Amphistegina lessonii and inorganically precipitated calcite. We argue that Li partitioning in both E. huxleyi and A. lessonii is dominated by a coupled transmembrane transport of Li and Ca from seawater to the site of calcification. We present a refined version of a recently proposed transmembrane transport model for Li and Ca. The model assumes that Li and Ca enter the cell via Ca channels, the Li flux being dependent on the Ca flux. While the original model features a linear function to describe the experimental data, our refined version uses a power function, changing the stoichiometry of Li and Ca. The version presented here accurately predicts the observed dependence of DLi on seawater Li/Ca ratios. Our data demonstrate that minor element partitioning in calcifying organisms is partly mediated by biological processes even if the partitioning behaviour of the calcifying organism is indistinguishable from that of inorganically precipitated calcium carbonate.},
	keywords = {RCC3652},
	issn = {1525-2027},
	doi = {10.1029/2020GC009129},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1029/2020GC009129},
	author = {Langer, Gerald and Sadekov, Aleksey and Greaves, Mervyn and Nehrke, Gernot and Probert, Ian and Misra, Sambuddha and Thoms, Silke}
}
@article {Aveiro2020,
	title = {The polar lipidome of cultured emiliania huxleyi: A source of bioactive lipids with relevance for biotechnological applications},
	journal = {Biomolecules},
	volume = {10},
	number = {10},
	year = {2020},
	note = {tex.ids= Aveiro2020a tex.mendeley-tags: RCC1250 publisher: Multidisciplinary Digital Publishing Institute},
	pages = {1434},
	abstract = {Polar lipids from microalgae have aroused greater interest as a natural source of omega-3 (n-3) polyunsaturated fatty acids (PUFA), an alternative to fish, but also as bioactive compounds with multiple applications. The present study aims to characterize the polar lipid profile of cultured microalga Emiliania huxleyi using hydrophilic interaction liquid chromatography coupled with high-resolution mass spectrometry (HILIC{\textendash}MS) and fatty acids (FA) analysis by gas chromatography (GC{\textendash}MS). The lipidome of E. huxleyi revealed the presence of distinct n-3 PUFA (40\% of total FA), namely docosahexaenoic acid (22:6n-3) and stearidonic acid (18:4n-3), which give this microalga an increased commercial value as a source of n-3 PUFA present in the form of polar lipids. A total of 134 species of polar lipids were identified and some of these species, particularly glycolipids, have already been reported for their bioactive properties. Among betaine lipids, the diacylglyceryl carboxyhydroxymethylcholine (DGCC) class is the least reported in microalgae. For the first time, monomethylphosphatidylethanolamine (MMPE) has been found in the lipidome of E. huxleyi. Overall, this study highlights the potential of E. huxleyi as a sustainable source of high-value polar lipids that can be exploited for different applications, namely human and animal nutrition, cosmetics, and pharmaceuticals.},
	keywords = {Emiliania huxleyi, haptophyta, Lipidomics, Mass spectrometry, Microalgae, RCC1250},
	issn = {2218-273X},
	doi = {10.3390/biom10101434},
	url = {https://www.mdpi.com/2218-273X/10/10/1434},
	author = {Aveiro, Susana S. and Melo, T{\^a}nia and Figueiredo, Ana and Domingues, Pedro and Pereira, Hugo and Maia, In{\^e}s B. and Silva, Joana and Domingues, M. Ros{\'a}rio and Nunes, Cl{\'a}udia and Moreira, Ana S. P.}
}
@article {Avilan2020,
	title = {ppGpp influences protein protection, growth and photosynthesis in Phaeodactylum tricornutum},
	journal = {bioRxiv},
	year = {2020},
	note = {Publisher: Cold Spring Harbor Laboratory tex.mendeley-tags: RCC2967},
	month = {mar},
	pages = {2020.03.05.978130},
	abstract = {{\textbullet} Chloroplasts retain elements of a bacterial stress response pathway that is mediated by the signalling nucleotides guanosine penta-and tetraphosphate, or (p)ppGpp. In the model flowering plant Arabidopsis, ppGpp acts as a potent regulator of plastid gene expression and influences photosynthesis, plant growth and development. However, little is known about ppGpp metabolism or its evolution in other photosynthetic eukaryotes. {\textbullet} Here, we studied the function of ppGpp in the diatom P. tricornutum using transgenic lines containing an inducible system for ppGpp accumulation. We used these lines to investigate the effects of ppGpp on growth, photosynthesis, lipid metabolism and protein expression. {\textbullet} We demonstrate that ppGpp accumulation reduces photosynthetic capacity and promotes a quiescent-like state with reduced proliferation and ageing. Strikingly, using non-targeted proteomics, we discovered that ppGpp accumulation also leads to the coordinated upregulation of a protein protection response in multiple cellular compartments. {\textbullet} Our findings highlight the importance of ppGpp as a fundamental regulator of chloroplast function across different domains of life, and lead to new questions about the molecular mechanisms and roles of (p)ppGpp signalling in photosynthetic eukaryotes.},
	keywords = {chloroplast, diatoms, lipid droplets, Phaeodactylum tricornutum, Photosynthesis, ppGpp, proteome, RCC2967},
	doi = {10.1101/2020.03.05.978130},
	url = {https://doi.org/10.1101/2020.03.05.978130},
	author = {Avilan, Luisana and Lebrun, Regine and Puppo, Carine and Citerne, Sylvie and Cuin{\'e}, Stephane and Li-Beisson, Yonghua and Menand, Benoit and Field, Ben and Gontero, Brigitte}
}
@article {Morales-Sanchez2020,
	title = {Production of carbohydrates, lipids and polyunsaturated fatty acids (PUFA) by the polar marine microalga Chlamydomonas malina RCC2488},
	journal = {Algal Research},
	volume = {50},
	number = {July},
	year = {2020},
	note = {tex.mendeley-tags: RCC2488},
	month = {sep},
	pages = {102016},
	keywords = {RCC2488},
	issn = {22119264},
	doi = {10.1016/j.algal.2020.102016},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2211926420303477},
	author = {Morales-S{\'a}nchez, Daniela and Schulze, Peter S.C. and Kiron, Viswanath and Wijffels, Ren{\'e} H.}
}
@article {Meyer2020,
	title = {Sr in coccoliths of Scyphosphaera apsteinii: Partitioning behavior and role in coccolith morphogenesis},
	journal = {Geochimica et Cosmochimica Acta},
	volume = {285},
	year = {2020},
	note = {Publisher: Elsevier Ltd tex.mendeley-tags: RCC1456},
	month = {sep},
	pages = {41{\textendash}54},
	abstract = {Coccolithophores are important contributors to global calcium carbonate through their species-specific production of calcite coccoliths. Nannofossil coccolith calcite remains an important tool for paleoreconstructions through geochemical analysis of isotopic and trace element incorporation including Sr, which is a potential indicator of past surface ocean temperature and productivity. Scyphosphaera apsteinii (Zygodiscales) exhibits an unusually high Sr/Ca ratio and correspondingly high partitioning coefficient (DSr = 2.5) in their two morphologically distinct types of coccoliths: flat muroliths and barrel-like lopadoliths. Whether or not this reflects mechanistic differences in calcification compared to other coccolithophores is unknown. We therefore examined the possible role of Sr in S. apsteinii calcification by growing cells in deplete (0.33 mmol/mol Sr/Ca), ambient (9 mmol/mol Sr/Ca), and higher than ambient Sr conditions (36 and 72 mmol/mol Sr/Ca). The effects on growth, quantum efficiency of photosystem II (Fv/Fm), coccolith morphology, and calcite DSr were evaluated. No effect on S. apsteinii growth rate or Fv/Fm was observed when cells were grown in Sr/Ca between 0.33{\textendash}36 mmol/mol. However, at 72 mmol/mol Sr/Ca growth rate was significantly reduced, although Fv/Fm was unaffected. Reducing the Sr/Ca from ambient (9 mmol/mol) did not significantly alter the frequency of malformed and aberrant muroliths and lopadoliths, but at higher than ambient Sr/Ca conditions coccolith morphology was significantly disrupted. This implies that Sr is not a critical determining factor in normal coccolith calcite morphology in this dimorphic species. Using energy dispersive spectroscopy (EDS) we observed an increase in [Sr] and decrease in DSr of coccoliths as the Sr/Ca of the growth medium increased. Interestingly, muroliths had significantly lower Sr/Ca than lopadoliths at ambient and elevated [Sr], and lopadolith tips had lower Sr than bases in ambient conditions. In summary, the Sr fractionation behavior of S. apsteinii is distinct from other coccolithophores because of an unusually high DSr and inter- and intra-coccolith variability in Sr/Ca. These observations could be explained by mechanistic differences in the selectivity of the Ca2+ transport pathway or in the Sr-and Ca-binding capacity of organic components, such as polysaccharides associated with coccolithogenesis.},
	keywords = {biomineralization, Calcification, coccolith, coccolithophore, Energy dispersive spectroscopy, Fractionation, RCC1456, Sr/Ca, Strontium, Trace element},
	issn = {00167037},
	doi = {10.1016/j.gca.2020.06.023},
	author = {Meyer, Erin M. and Langer, Gerald and Brownlee, Colin and Wheeler, Glen L. and Taylor, Alison R.}
}
@article {Derilus2020,
	title = {Synergism between the Black Queen effect and the proteomic constraint on genome size reduction in the photosynthetic picoeukaryotes},
	journal = {Scientific Reports},
	volume = {10},
	number = {1},
	year = {2020},
	note = {Publisher: Springer US tex.mendeley-tags: RCC1110,RCC1116,RCC809},
	pages = {8918},
	keywords = {RCC1110, RCC1116, RCC809},
	issn = {2045-2322},
	doi = {10.1038/s41598-020-65476-1},
	url = {http://dx.doi.org/10.1038/s41598-020-65476-1 http://www.nature.com/articles/s41598-020-65476-1},
	author = {Derilus, D and Rahman, M Z and Pinero, F and Massey, S E}
}
@article {Yau2020,
	title = {Virus-host coexistence in phytoplankton through the genomic lens},
	journal = {Science Advances},
	volume = {6},
	number = {14},
	year = {2020},
	note = {tex.mendeley-tags: RCC2590,RCC2596},
	month = {apr},
	pages = {eaay2587},
	abstract = {Virus-microbe interactions in the ocean are commonly described by {\textquotedblleft}boom and bust{\textquotedblright} dynamics, whereby a numerically dominant microorganism is lysed and replaced by a virus-resistant one. Here, we isolated a microalga strain and its infective dsDNA virus whose dynamics are characterized instead by parallel growth of both the microalga and the virus. Experimental evolution of clonal lines revealed that this viral production originates from the lysis of a minority of virus-susceptible cells, which are regenerated from resistant cells. Whole-genome sequencing demonstrated that this resistant-susceptible switch involved a large deletion on one chromosome. Mathematical modeling explained how the switch maintains stable microalga-virus population dynamics consistent with their observed growth pattern. Comparative genomics confirmed an ancient origin of this {\textquotedblleft}accordion{\textquotedblright} chromosome despite a lack of sequence conservation. Together, our results show how dynamic genomic rearrangements may account for a previously overlooked coexistence mechanism in microalgae-virus interactions.},
	keywords = {RCC2590, RCC2596},
	issn = {2375-2548},
	doi = {10.1126/sciadv.aay2587},
	url = {https://advances.sciencemag.org/lookup/doi/10.1126/sciadv.aay2587},
	author = {Yau, Sheree and Krasovec, Marc and Benites, L. Felipe and Rombauts, Stephane and Groussin, Mathieu and Vancaester, Emmelien and Aury, Jean-Marc and Derelle, Evelyne and Desdevises, Yves and Escande, Marie-Line and Grimsley, Nigel and Guy, Julie and Moreau, Herv{\'e} and Sanchez-Brosseau, Sophie and Van de Peer, Yves and Vandepoele, Klaas and Gourbi{\`e}re, S{\'e}bastien and Piganeau, Gwenael}
}
@article {Castillo2020,
	title = {Visualization of viral infection dynamics in a unicellular eukaryote and quantification of viral production using virus fluorescence in situ hybridization},
	journal = {Frontiers in Microbiology},
	volume = {11},
	year = {2020},
	note = {Publisher: Frontiers Media S.A. tex.mendeley-tags: RCC4221},
	month = {jul},
	pages = {1559},
	abstract = {One of the major challenges in viral ecology is to assess the impact of viruses in controlling the abundance of specific hosts in the environment. To this end, techniques that enable the detection and quantification of virus-host interactions at the single-cell level are essential. With this goal in mind, we implemented virus fluorescence in situ hybridization (VirusFISH) using as a model the marine picoeukaryote Ostreococcus tauri and its virus Ostreococcus tauri virus 5 (OtV5). VirusFISH allowed the visualization and quantification of the proportion of infected cells during an infection cycle in experimental conditions. We were also able to quantify the abundance of free viruses released during cell lysis, discriminating OtV5 from other mid-level fluorescence phages in our non-axenic infected culture that were not easily distinguishable with flow cytometry. Our results showed that although the major lysis of the culture occurred between 24 and 48 h after OtV5 inoculation, some new viruses were already produced between 8 and 24 h. With this work, we demonstrate that VirusFISH is a promising technique to study specific virus-host interactions in non-axenic cultures and establish a framework for its application in complex natural communities.},
	keywords = {culture system, marine picoeukaryote, Ostreococcus tauri, Ostreococcus tauri virus 5, RCC4221, virus fluorescence in situ hybridization, virus-host interactions},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2020.01559},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2020.01559/full},
	author = {Castillo, Yaiza M. and Sebasti{\'a}n, Marta and Forn, Irene and Grimsley, Nigel and Yau, Sheree and Moraru, Cristina and Vaqu{\'e}, Dolors}
}
@article {Decelle2019,
	title = {Algal remodeling in a ubiquitous planktonic photosymbiosis},
	journal = {Current Biology},
	volume = {29},
	number = {6},
	year = {2019},
	note = {Publisher: Cell Press tex.mendeley-tags: RCC1719},
	month = {mar},
	pages = {968{\textendash}978.e4},
	abstract = {Photosymbiosis between single-celled hosts and microalgae is common in oceanic plankton, especially in oligotrophic surface waters. However, the functioning of this ecologically important cell-cell interaction and the subcellular mechanisms allowing the host to accommodate and benefit from its microalgae remain enigmatic. Here, using a combination of quantitative single-cell structural and chemical imaging techniques (FIB-SEM, nanoSIMS, Synchrotron X-ray fluorescence), we show that the structural organization, physiology, and trophic status of the algal symbionts (the haptophyte Phaeocystis) significantly change within their acantharian hosts compared to their free-living phase in culture. In symbiosis, algal cell division is blocked, photosynthesis is enhanced, and cell volume is increased by up to 10-fold with a higher number of plastids (from 2 to up to 30) and thylakoid membranes. The multiplication of plastids can lead to a 38-fold increase of the total plastid volume in a cell. Subcellular mapping of nutrients (nitrogen and phosphorous) and their stoichiometric ratios shows that symbiotic algae are impoverished in phosphorous and suggests a higher investment in energy-acquisition machinery rather than in growth. Nanoscale imaging also showed that the host supplies a substantial amount of trace metals (e.g., iron and cobalt), which are stored in algal vacuoles at high concentrations (up to 660 ppm). Sulfur mapping reveals a high concentration in algal vacuoles that may be a source of antioxidant molecules. Overall, this study unveils an unprecedented morphological and metabolic transformation of microalgae following their integration into a host, and it suggests that this widespread symbiosis is a farming strategy wherein the host engulfs and exploits microalgae.},
	keywords = {RCC1719},
	issn = {0960-9822},
	doi = {10.1016/J.CUB.2019.01.073},
	url = {https://www.sciencedirect.com/science/article/abs/pii/S0960982219301320$\#$undfig1},
	author = {Decelle, Johan and Stryhanyuk, Hryhoriy and Gallet, Benoit and Veronesi, Giulia and Schmidt, Matthias and Balzano, Sergio and Marro, Sophie and Uwizeye, Clarisse and Jouneau, Pierre-Henri and Lupette, Josselin and Jouhet, Juliette and Mar{\'e}chal, {\'E}ric and Schwab, Yannick and Schieber, Nicole L. and Tucoulou, R{\'e}mi and Richnow, Hans and Finazzi, Giovanni and Musat, Niculina}
}
@article {Zimmerman2019,
	title = {Closely related viruses of the marine picoeukaryotic alga Ostreococcus lucimarinus exhibit different ecological strategies},
	journal = {Environmental Microbiology},
	volume = {00},
	year = {2019},
	note = {tex.mendeley-tags: RCC3401,RCC393,RCC829},
	abstract = {SUMMARY In marine ecosystems viruses are major disrupters of the direct flow of carbon and nutrients to higher trophic levels. While the genetic diversity of several eukaryotic phytoplankton virus groups has been characterized, their infection dynamics are less understood, such that the physiological and ecological implications of their diversity remain unclear. We compared genomes and infection phenotypes of the two most closely related cultured phycodnaviruses infecting the widespread picoprasinophyte Ostreococcus lucimarinus under standard- (1.3 divisions d-1) and limited-light (0.41 divisions d-1) nutrient replete conditions. OlV7 infection caused early arrest of the host cell cycle, coinciding with a significantly higher proportion of infected cells than OlV1-amended treatments, regardless of host growth rate. OlV7 treatments showed a near-50-fold increase of progeny virions at the higher host growth rate, contrasting with OlV1{\textquoteright}s 16-fold increase. However, production of OlV7 virions was more sensitive than OlV1 production to reduced host growth rate, suggesting fitness trade-offs between infection efficiency and resilience to host physiology. Moreover, while organic matter released from OlV1- and OlV7-infected hosts had broadly similar chemical composition, some distinct molecular signatures were observed. Collectively, these results suggest that current views on viral relatedness through marker and core gene analyses underplay operational divergence and consequences for host ecology. This article is protected by copyright. All rights reserved.},
	keywords = {rcc3401, RCC393, RCC829},
	issn = {14622920},
	doi = {10.1111/1462-2920.14608},
	author = {Zimmerman, Amy E. and Bachy, Charles and Ma, Xiufeng and Roux, Simon and Jang, Ho Bin and Sullivan, Matthew B. and Waldbauer, Jacob R. and Worden, Alexandra Z.}
}
@article {kusch_dead_2019,
	title = {Dead in the Water: The Vicious Cycle of Blanks During Natural Level 14 C Manipulation of Marine Algal Cultures},
	journal = {Frontiers in Marine Science},
	volume = {6},
	year = {2019},
	note = {Publisher: Frontiers},
	abstract = {Authentic biomarker standards were obtained from algal cultures in an attempt to accurately determine blank C added during sample processing for compound-specific radiocarbon analysis. Emiliania huxleyi and Thalassiosira pseudonana were grown under manipulated Δ14C dissolved inorganic carbon (DIC) levels and chlorophyll a and either alkenones (E. huxleyi) or low molecular weight (LMW) alkanoic acids (T. pseudonana) were isolated from the respective biomass using preparative liquid chromatography (LC), wet chemical techniques or preparative gas chromatography, respectively. DI14C in the seawater medium was determined pre- and post-growth. Biomarker Δ14C values mostly agree within 1-2? analytical uncertainties. In those cases where biomarker Δ14C values differ significantly, chlorophyll a is up to 104{\textperthousand} more 14C-depleted than alkenones or LMW alkanoic acids, consistent with a larger LC blank compared to the other purification methods. However, in the majority of experimental setups pre- and post-growth DIC Δ14C values seem to be compromised by an unknown and variable blank C contribution. DIC Δ14C values deviate strongly from the anticipated Δ14C values (by up to ca. 560{\textperthousand}), pre- and post-growth Δ14C values differ significantly (by up to ca. 460{\textperthousand}), and changes are not unidirectional. Accordingly, since the substrate Δ14C value cannot unequivocally be constrained, blank C contributions for the different biomarker purification methods cannot be accurately calculated. This study illustrates the challenges and problems of producing authentic standards that are not readily commercially available and exemplifies how a laborious and time-consuming culturing approach may enter a vicious cycle of blank C contamination hampering accurate blank C determination.},
	keywords = {Algal cultures, Alkanoic acids, alkenones, Authentic standards, Blank, chlorophyll a, Compound-specific radiocarbon analysis, natural level 14 C manipulation, rcc1238},
	issn = {2296-7745},
	doi = {10.3389/fmars.2019.00780},
	url = {https://www.frontiersin.org/articles/10.3389/fmars.2019.00780/full},
	author = {Kusch, Stephanie and Benthien, Albert and Richter, Klaus-Uwe and Rost, Bj{\"o}rn and Mollenhauer, Gesine}
}
@article {Lacour2019,
	title = {Decoupling light harvesting, electron transport and carbon fixation during prolonged darkness supports rapid recovery upon re-illumination in the Arctic diatom Chaetoceros neogracilis},
	journal = {Polar Biology},
	year = {2019},
	note = {ISBN: 0123456789 Publisher: Springer Berlin Heidelberg tex.mendeley-tags: RCC2278},
	month = {may},
	keywords = {Arctic microalgae, Darkness, Diatom, GROWTH RATE, Photosynthesis, Polar night, RCC2278, temperature},
	issn = {0722-4060},
	doi = {10.1007/s00300-019-02507-2},
	url = {https://doi.org/10.1007/s00300-019-02507-2 http://link.springer.com/10.1007/s00300-019-02507-2},
	author = {Lacour, Thomas and Morin, Philippe-Isra{\"e}l and Sciandra, Th{\'e}o and Donaher, Natalie and Campbell, Douglas A. and Ferland, Joannie and Babin, Marcel}
}
@article {Weiss2019,
	title = {Hydrogen isotope fractionation response to salinity and alkalinity in a calcifying strain of Emiliania huxleyi},
	journal = {Organic Geochemistry},
	year = {2019},
	note = {Publisher: Elsevier Ltd tex.mendeley-tags: RCC2050},
	month = {jun},
	keywords = {RCC2050},
	issn = {01466380},
	doi = {10.1016/j.orggeochem.2019.06.001},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0146638019301020},
	author = {Weiss, Gabriella M. and Roepert, Anne and Middelburg, Jack J. and Schouten, Stefan and Sinninghe Damst{\'e}, Jaap S. and van der Meer, Marcel T.J.}
}
@article {LevyKarin2019,
	title = {MetaEuk {\textendash} sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics},
	journal = {bioRxiv},
	year = {2019},
	month = {jan},
	pages = {851964},
	abstract = {Background: Metagenomics is revolutionizing the study of microorganisms and their involvement in biological, biomedical, and geochemical processes, allowing us to investigate by direct sequencing a tremendous diversity of organisms without the need for prior cultivation. Unicellular eukaryotes play essential roles in most microbial communities as chief predators, decomposers, phototrophs, bacterial hosts, symbionts and parasites to plants and animals. Investigating their roles is therefore of great interest to ecology, biotechnology, human health, and evolution. However, the generally lower sequencing coverage, their more complex gene and genome architectures, and a lack of eukaryote-specific experimental and computational procedures have kept them on the sidelines of metagenomics. Results: MetaEuk is a toolkit for high-throughput, reference-based discovery and annotation of protein-coding genes in eukaryotic metagenomic contigs. It performs fast searches with 6-frame-translated fragments covering all possible exons and optimally combines matches into multi-exon proteins. We used a benchmark of seven diverse, annotated genomes to show that MetaEuk is highly sensitive even under conditions of low sequence similarity to the reference database. To demonstrate MetaEuk\&\#039;s power to discover novel eukaryotic proteins in large-scale metagenomic data, we assembled contigs from 912 samples of the Tara Oceans project. MetaEuk predicted \&gt;12,000,000 protein-coding genes in eight days on ten 16-core servers. Most of the discovered proteins are highly diverged from known proteins and originate from very sparsely sampled eukaryotic supergroups. Conclusion: The open-source (GPLv3) MetaEuk software (https://github.com/soedinglab/metaeuk) enables large-scale eukaryotic metagenomics through reference-based, sensitive taxonomic and functional annotation.},
	doi = {10.1101/851964},
	url = {http://biorxiv.org/content/early/2019/11/25/851964.abstract},
	author = {Levy Karin, Eli and Mirdita, Milot and Soeding, Johannes}
}
@article {Iglesias2019,
	title = {NMR characterization and evaluation of antibacterial and antiobiofilm activity of organic extracts from stationary phase batch cultures of five marine microalgae (Dunaliella sp., D. salina, Chaetoceros calcitrans, C. gracilis and Tisochrysis lutea)},
	journal = {Phytochemistry},
	volume = {164},
	number = {April},
	year = {2019},
	note = {Publisher: Elsevier tex.mendeley-tags: RCC1349,RCC1811,RCC3579,RCC5,RCC5953},
	month = {aug},
	pages = {192{\textendash}205},
	keywords = {Antibacterial, Antibiofilm, Chaetoceros, Dunaliella, Metabolite identification, NMR, RCC1349, RCC1811, RCC3579, RCC5, RCC5953, Tisochrysis},
	issn = {00319422},
	doi = {10.1016/j.phytochem.2019.05.001},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0031942219300184},
	author = {Iglesias, Ma Jos{\'e} and Soengas, Raquel and Probert, Ian and Guilloud, Emilie and Gourvil, Priscillia and Mehiri, Mohamed and L{\'o}pez, Yuly and Cepas, Virginio and Guti{\'e}rrez-del-R{\'\i}o, Ignacio and Redondo-Blanco, Sa{\'u}l and Villar, Claudio J. and Lomb{\'o}, Felipe and Soto, Sara and Ortiz, Fernando L{\'o}pez}
}
@article {Demory2019,
	title = {Picoeukaryotes of the Micromonas genus: sentinels of a warming ocean},
	journal = {The ISME Journal},
	volume = {13},
	number = {1},
	year = {2019},
	note = {tex.ids= Demory2018 tex.mendeley-tags: RCC114,RCC1697,RCC1862,RCC2257,RCC2306,RCC299,RCC451,RCC497,RCC746,RCC829,RCC834 publisher: Nature Publishing Group},
	month = {jan},
	pages = {132{\textendash}146},
	abstract = {Photosynthetic picoeukaryotesx in the genus Micromonas show among the widest latitudinal distributions on Earth, experiencing large thermal gradients from poles to tropics. Micromonas comprises at least four different species often found in sympatry. While such ubiquity might suggest a wide thermal niche, the temperature response of the different strains is still unexplored, leaving many questions as for their ecological success over such diverse ecosystems. Using combined experiments and theory, we characterize the thermal response of eleven Micromonas strains belonging to four species. We demonstrate that the variety of specific responses to temperature in the Micromonas genus makes this environmental factor an ideal marker to describe its global distribution and diversity. We then propose a diversity model for the genus Micromonas, which proves to be representative of the whole phytoplankton diversity. This prominent primary producer is therefore a sentinel organism of phytoplankton diversity at the global scale. We use the diversity within Micromonas to anticipate the potential impact of global warming on oceanic phytoplankton. We develop a dynamic, adaptive model and run forecast simulations, exploring a range of adaptation time scales, to probe the likely responses to climate change. Results stress how biodiversity erosion depends on the ability of organisms to adapt rapidly to temperature increase.},
	keywords = {Biogeography, change ecology, Climate, microbial ecology, RCC114, RCC1697, RCC1862, RCC2257, RCC2306, RCC299, RCC451, RCC497, RCC746, RCC829, RCC834},
	issn = {1751-7362},
	doi = {10.1038/s41396-018-0248-0},
	url = {http://www.nature.com/articles/s41396-018-0248-0},
	author = {Demory, David and Baudoux, Anne-claire and Monier, Adam and Simon, Nathalie and Six, Christophe and Ge, Pei and Rigaut-jalabert, Fabienne and Marie, Dominique and Sciandra, Antoine and Bernard, Olivier and Rabouille, Sophie}
}
@article {Gaignard2019,
	title = {Screening of marine microalgae: Investigation of new exopolysaccharide producers},
	journal = {Algal Research},
	volume = {44},
	year = {2019},
	note = {tex.ids= Gaignard2019a tex.mendeley-tags: RCC1084,RCC1196,RCC1504,RCC1714,RCC1774,RCC1786,RCC1863,RCC1978,RCC1983,RCC2035,RCC232,RCC2350,RCC2352,RCC2368,RCC2380,RCC2381,RCC2383,RCC2436,RCC2558,RCC2598,RCC2608,RCC2614,RCC2624,RCC2638,RCC269,RCC2696,RCC2703,RCC2932,RCC3069,RCC3072,RCC3092,RCC3093,RCC3436,RCC3649,RCC377,RCC4094,RCC4438,RCC4555,RCC4621,RCC4631,RCC4657,RCC76,RCC775,RCC821,RCC97 publisher: Elsevier},
	month = {dec},
	pages = {101711},
	abstract = {Biopolymers, such as exopolysaccharides are widely exploited by industry as hydrocolloids (gelling, thickening agents) and biological agents (anti-inflammatory, anti-parasitic, antioxidant, etc.). In this study, 166 marine microalgae and cyanobacteria species have been screened in order to identify strains producing original exopolysaccharides. This screening allowed the highlighting of 45 positive strains. In a second time, the monosaccharide compositions from 20 EPS of them were determined by GC/MS and HPAEC-PAD. The results led to a discovery of 8 new genera of microalgae producing EPS, including polymers with a very original composition like richness in GlcA. Finally, a phylogenic tree has been contructed in order to assess the link between the phylogeny of microalgae and the global composition of their exopolymers, based on data obtained in this study and from the literature.},
	keywords = {rcc1084, RCC1196, RCC1504, RCC1714, RCC1774, RCC1786, RCC1863, RCC1978, RCC1983, RCC2035, RCC232, RCC2350, RCC2352, RCC2368, rcc2380, RCC2381, RCC2383, RCC2436, RCC2558, RCC2598, RCC2608, RCC2614, RCC2624, RCC2638, RCC269, RCC2696, RCC2703, RCC2932, RCC3069, RCC3072, RCC3092, RCC3093, RCC3436, RCC3649, RCC377, RCC4094, RCC4438, RCC4555, RCC4621, RCC4631, RCC4657, RCC76, RCC775, RCC821, RCC97},
	issn = {22119264},
	doi = {10.1016/j.algal.2019.101711},
	url = {https://www.sciencedirect.com/science/article/pii/S2211926419303261 https://linkinghub.elsevier.com/retrieve/pii/S2211926419303261},
	author = {Gaignard, C. and Laroche, C. and Pierre, G. and Dubessay, P. and Delattre, C. and Gardarin, C. and Gourvil, P. and Probert, I. and Dubuffet, A. and Michaud, P.}
}
@article {Sanchez2019,
	title = {Simplified transformation of ostreococcus tauri using polyethylene glycol},
	journal = {Genes},
	volume = {10},
	number = {5},
	year = {2019},
	note = {tex.mendeley-tags: RCC4221},
	month = {may},
	pages = {399},
	abstract = {Ostreococcustauri is an easily cultured representative of unicellular algae (class Mamiellophyceae) that abound in oceans worldwide. Eight complete 13{\textendash}22 Mb genomes of phylogenetically divergent species within this class are available, and their DNA sequences are nearly always present in metagenomic data produced from marine samples. Here we describe a simplified and robust transformation protocol for the smallest of these algae (O. tauri). Polyethylene glycol (PEG) treatment was much more efficient than the previously described electroporation protocol. Short (2 min or less) incubation times in PEG gave {\textquestiondown}104 transformants per microgram DNA. The time of cell recovery after transformation could be reduced to a few hours, permitting the experiment to be done in a day rather than overnight as used in previous protocols. DNA was randomly inserted in the O. tauri genome. In our hands PEG was 20{\textendash}40-fold more efficient than electroporation for the transformation of O. tauri, and this improvement will facilitate mutagenesis of all of the dispensable genes present in the tiny O. tauri genome.},
	keywords = {bioluminescence, Chlorophyta, Ecosystem, Gene Expression, luciferase, mamiellophyceae, Ostreococcus, picoeukaryote, plankton, Prasinophyte, promoter, RCC4221},
	issn = {2073-4425},
	doi = {10.3390/genes10050399},
	url = {https://www.mdpi.com/2073-4425/10/5/399},
	author = {Sanchez, Fr{\'e}d{\'e}ric and Geffroy, Sol{\`e}ne and Norest, Manon and Yau, Sheree and Moreau, Herv{\'e} and Grimsley, Nigel}
}
@article {Kashiyama2019,
	title = {Taming chlorophylls by early eukaryotes underpinned algal interactions and the diversification of the eukaryotes on the oxygenated Earth},
	journal = {The ISME Journal},
	year = {2019},
	note = {Publisher: Springer US tex.mendeley-tags: RCC164,RCC22,RCC24,RCC375,RCC916},
	month = {feb},
	pages = {1},
	abstract = {Extant eukaryote ecology is primarily sustained by oxygenic photosynthesis, in which chlorophylls play essential roles. The exceptional photosensitivity of chlorophylls allows them to harvest solar energy for photosynthesis, but on the other hand, they also generate cytotoxic reactive oxygen species. A risk of such phototoxicity of the chlorophyll must become particularly prominent upon dynamic cellular interactions that potentially disrupt the mechanisms that are designed to quench photoexcited chlorophylls in the phototrophic cells. Extensive examination of a wide variety of phagotrophic, parasitic, and phototrophic microeukaryotes demonstrates that a catabolic process that converts chlorophylls into nonphotosensitive 132,173-cyclopheophorbide enols (CPEs) is phylogenetically ubiquitous among extant eukaryotes. The accumulation of CPEs is identified in phagotrophic algivores belonging to virtually all major eukaryotic assemblages with the exception of Archaeplastida, in which no algivorous species have been reported. In addition, accumulation of CPEs is revealed to be common among phototrophic microeukaryotes (i.e., microalgae) along with dismantling of their secondary chloroplasts. Thus, we infer that CPE-accumulating chlorophyll catabolism (CACC) primarily evolved among algivorous microeukaryotes to detoxify chlorophylls in an early stage of their evolution. Subsequently, it also underpinned photosynthetic endosymbiosis by securing close interactions with photosynthetic machinery containing abundant chlorophylls, which led to the acquisition of secondary chloroplasts. Our results strongly suggest that CACC, which allowed the consumption of oxygenic primary producers, ultimately permitted the successful radiation of the eukaryotes throughout and after the late Proterozoic global oxygenation.},
	keywords = {Biochemistry, Biogeochemistry, Cellular microbiology, microbial ecology, RCC164, RCC22, RCC24, RCC375, RCC916},
	issn = {1751-7362},
	doi = {10.1038/s41396-019-0377-0},
	url = {http://www.nature.com/articles/s41396-019-0377-0},
	author = {Kashiyama, Yuichiro and Yokoyama, Akiko and Shiratori, Takashi and Hess, Sebastian and Not, Fabrice and Bachy, Charles and Gutierrez-Rodriguez, Andres and Kawahara, Jun and Suzaki, Toshinobu and Nakazawa, Masami and Ishikawa, Takahiro and Maruyama, Moe and Wang, Mengyun and Chen, Man and Gong, Yingchun and Seto, Kensuke and Kagami, Maiko and Hamamoto, Yoko and Honda, Daiske and Umetani, Takahiro and Shihongi, Akira and Kayama, Motoki and Matsuda, Toshiki and Taira, Junya and Yabuki, Akinori and Tsuchiya, Masashi and Hirakawa, Yoshihisa and Kawaguchi, Akane and Nomura, Mami and Nakamura, Atsushi and Namba, Noriaki and Matsumoto, Mitsufumi and Tanaka, Tsuyoshi and Yoshino, Tomoko and Higuchi, Rina and Yamamoto, Akihiro and Maruyama, Tadanobu and Yamaguchi, Aika and Uzuka, Akihiro and Miyagishima, Shinya and Tanifuji, Goro and Kawachi, Masanobu and Kinoshita, Yusuke and Tamiaki, Hitoshi}
}
@article {Liu2019,
	title = {Transcriptome of thalassicolla nucleata holobiont reveals details of a radiolarian symbiotic relationship},
	journal = {Frontiers in Marine Science},
	volume = {6},
	number = {June},
	year = {2019},
	note = {tex.mendeley-tags: RCC3387},
	month = {jun},
	pages = {1{\textendash}11},
	keywords = {Brandtodinium, holobiont, photosymbiosis, radiolarian, RCC3387, Transcriptome},
	issn = {2296-7745},
	doi = {10.3389/fmars.2019.00284},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2019.00284/full},
	author = {Liu, Zhenfeng and Mesrop, Lisa Y. and Hu, Sarah K. and Caron, David A.}
}
@article {Breton2019,
	title = {Unveiling membrane thermoregulation strategies in marine picocyanobacteria},
	journal = {New Phytologist},
	number = {July},
	year = {2019},
	note = {ISBN: 0000000244022 tex.mendeley-tags: RCC2374,RCC2385,RCC515,RCC539},
	month = {oct},
	pages = {nph.16239},
	keywords = {RCC2374, RCC2385, RCC515, rcc539},
	issn = {0028-646X},
	doi = {10.1111/nph.16239},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.16239},
	author = {Breton, Sol{\`e}ne and Jouhet, Juliette and Guyet, Ulysse and Gros, Val{\'e}rie and Pittera, Justine and Demory, David and Partensky, Fr{\'e}d{\'e}ric and Dor{\'e}, Hugo and Ratin, Morgane and Mar{\'e}chal, {\'E}ric and Nguyen, Ngoc An and Garczarek, Laurence and Six, Christophe}
}
@article {Pierre2019,
	title = {What is in store for EPS microalgae in the next decade?},
	journal = {Molecules},
	volume = {24},
	number = {23},
	year = {2019},
	month = {nov},
	pages = {4296},
	abstract = {Microalgae and their metabolites have been an El Dorado since the turn of the 21st century. Many scientific works and industrial exploitations have thus been set up. These developments have often highlighted the need to intensify the processes for biomass production in photo-autotrophy and exploit all the microalgae value including ExoPolySaccharides (EPS). Indeed, the bottlenecks limiting the development of low value products from microalgae are not only linked to biology but also to biological engineering problems including harvesting, recycling of culture media, photoproduction, and biorefinery. Even respecting the so-called {\textquotedblleft}Biorefinery Concept{\textquotedblright}, few applications had a chance to emerge and survive on the market. Thus, exploiting EPS from microalgae for industrial applications in some low-value markets such as food is probably not a mature proposition considering the competitiveness of polysaccharides from terrestrial plants, macroalgae, and bacteria. However, it does not imply drawing a line on their uses but rather {\textquotedblleft}thinking them{\textquotedblright} differently. This review provides insights into microalgae, EPS, and their exploitation. Perspectives on issues affecting the future of EPS microalgae are also addressed with a critical point of view.},
	keywords = {application, eps, exopolysaccharides, market, Microalgae},
	issn = {1420-3049},
	doi = {10.3390/molecules24234296},
	url = {https://www.mdpi.com/1420-3049/24/23/4296},
	author = {Pierre, Guillaume and Delattre, C{\'e}dric and Dubessay, Pascal and Jubeau, S{\'e}bastien and Vialleix, Carole and Cadoret, Jean-Paul and Probert, Ian and Michaud, Philippe}
}
@article {Cheng2018,
	title = {10KP: A phylodiverse genome sequencing plan},
	journal = {GigaScience},
	volume = {7},
	number = {3},
	year = {2018},
	pages = {1{\textendash}9},
	keywords = {10kp, 12 february 2018, 2018, 4, accepted, access article distributed under, and reproduction in any, attribution license, biodiversity, by, c the author, creative commons, creativecommons, Distribution, genome sequencing, genomics, http, licenses, medium, mgiseq, open community, org, phylogenomics, PLANTS, press, published by oxford university, received, s, samples, the terms of the, this is an open, which permits unrestricted reuse},
	issn = {2047-217X},
	doi = {10.1093/gigascience/giy013},
	url = {https://academic.oup.com/gigascience/article/7/3/1/4880447},
	author = {Cheng, Shifeng and Melkonian, Michael and Smith, Stephen A and Brockington, Samuel and Archibald, John M and Delaux, Pierre-Marc and Li, Fay-Wei and Melkonian, Barbara and Mavrodiev, Evgeny V and Sun, Wenjing and Fu, Yuan and Yang, Huanming and Soltis, Douglas E and Graham, Sean W and Soltis, Pamela S and Liu, Xin and Xu, Xun and Wong, Gane Ka-Shu}
}
@article {Meng2018,
	title = {Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network},
	journal = {Molecular Ecology},
	year = {2018},
	note = {tex.mendeley-tags: RCC1491,RCC1516,RCC3387,RCC3468,RCC3507},
	pages = {0{\textendash}2},
	abstract = {Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and used a sequence similarity network (SSN) to compare the underlying genomic basis of functional features within the group. This approach constitutes the most comprehensive picture to date of the genomic potential of dinoflagellates. A core predicted proteome composed of 252 connected components (CCs) of putative conserved protein domains (pCDs) was identified. Of these, 206 were novel and 16 lacked any functional annotation in public databases. Integration of functional information in our network analyses allowed investigation of pCDs specifically associated to functional traits. With respect to toxicity, sequences homologous to those of proteins found in species with toxicity potential (e.g. sxtA4 and sxtG) were not specific to known toxin-producing species. Although not fully specific to symbiosis, the most represented functions associated with proteins involved in the symbiotic trait were related to membrane processes and ion transport. Overall, our SSN approach led to identification of 45,207 and 90,794 specific and constitutive pCDs of respectively the toxic and symbiotic species represented in our analyses. Of these, 56\% and 57\% respectively (i.e. 25,393 and 52,193 pCDs) completely lacked annotation in public databases. This stresses the extent of our lack of knowledge, while emphasizing the potential of SSNs to identify candidate pCDs for further functional genomic characterization. This article is protected by copyright. All rights reserved.},
	keywords = {Genomics/Proteomics, Microbial Biology, Molecular Evolution, Protists, rcc1491, RCC1516, RCC3387, rcc3468, rcc3507, transcriptomics},
	issn = {09621083},
	doi = {10.1111/mec.14579},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/29624751\%0Ahttp://doi.wiley.com/10.1111/mec.14579},
	author = {Meng, Arnaud and Corre, Erwan and Probert, Ian and Gutierrez-Rodriguez, Andres and Siano, Raffaele and Annamale, Anita and Alberti, Adriana and Da Silva, Corinne and Wincker, Patrick and Le Crom, St{\'e}phane and Not, Fabrice and Bittner, Lucie}
}
@article {Fox2018,
	title = {Calcein staining as a tool to investigate coccolithophore calcification},
	journal = {Frontiers in Marine Science},
	volume = {5},
	number = {September},
	year = {2018},
	note = {tex.mendeley-tags: RCC 1461,RCC 3777,RCC1130,RCC1303,RCC1456},
	abstract = {This brief paper summarizes the literature on academic accommodations for students with psychiatric disabilities. A definition of psychiatric disability precedes a brief summary of the following specific psychiatric diagnoses: depression, bipolar affective disorder; borderline personality disorder; schizophrenia; and anxiety disorders. Also noted are behavior or personality disorders specifically excluded from coverage under the Americans with Disabilities Act. Functional limitations of this population that may affect academic performance are then listed and defined. Among these are medication side effects, sustaining concentration, maintaining stamina, interacting with others, responding to negative feedback, responding to change, and severe test anxiety. Examples of appropriate instructional strategies are followed by a discussion of reasonable accommodations to provide these students with equal access to the curriculum. Examples are then given of classroom accommodations, examination accommodations, and assignment accommodations. Characteristics of accommodations that are not reasonable are also listed. The paper concludes with a resource list including Web site and contact information for the DO-IT (Disabilities, Opportunities, Internetworking, and Technology) Project. (DB)},
	keywords = {bet hedging, calcein, Calcification, coccolith, coccolithophore, flow cytometry, haptophyte, RCC1130, RCC1303, RCC1456, RCC1461, RCC3777, secretion},
	issn = {2296-7745},
	doi = {10.3389/fmars.2018.00326},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2018.00326/full},
	author = {Fox, Emily and Meyer, Erin and Panasiak, Natalie and Taylor, Alison R.}
}
@article {McQuaid2018,
	title = {Carbonate-sensitive phytotransferrin controls high-affinity iron uptake in diatoms},
	journal = {Nature},
	volume = {555},
	number = {7697},
	year = {2018},
	note = {Publisher: Nature Publishing Group tex.mendeley-tags: RCC2967},
	month = {mar},
	pages = {534{\textendash}537},
	abstract = {Iron is an essential nutrient for photosynthetic plankton (phytoplankton), but owing to its low solubility in vast areas of the ocean the concentration of this metal is low, limiting the growth of the phytoplankton. Andrew Allen and co-workers show that the phytoplankton Phaeodactylum tricornutum has developed a specific iron acquisition mechanism that relies on activity of the ISIP2A protein. ISIP2A represents a functional analogue of transferrin{\textemdash}a metazoan protein that binds iron with high affinity{\textemdash}as both proteins use similar iron binding, internalization and release mechanisms, suggesting their independent and convergent evolution. Both proteins bind iron through a synergistic interaction of ferric iron and CO32-, and because ocean acidification decreases CO32- concentration it may also decrease phytoplankton iron uptake and growth.},
	keywords = {RCC2967},
	issn = {0028-0836},
	doi = {10.1038/nature25982},
	url = {http://dx.doi.org/10.1038/nature25982 http://www.nature.com/doifinder/10.1038/nature25982},
	author = {McQuaid, Jeffrey B. and Kustka, Adam B. and Obornik, Miroslav and Horak, Ales and McCrow, John P. and Karas, Bogumil J. and Zheng, Hong and Kindeberg, Theodor and Andersson, Andreas J. and Barbeau, Katherine A. and Allen, Andrew E.}
}
@article {Paerl2018,
	title = {Carboxythiazole is a key microbial nutrient currency and critical component of thiamin biosynthesis},
	journal = {Scientific Reports},
	volume = {8},
	number = {1},
	year = {2018},
	note = {Publisher: Springer US tex.mendeley-tags: RCC4222,RCC745},
	pages = {5940},
	keywords = {RCC4222, RCC745},
	issn = {2045-2322},
	doi = {10.1038/s41598-018-24321-2},
	url = {http://www.nature.com/articles/s41598-018-24321-2},
	author = {Paerl, Ryan W. and Bertrand, Erin M. and Rowland, Elden and Schatt, Phillippe and Mehiri, Mohamed and Niehaus, Thomas D. and Hanson, Andrew D. and Riemann, Lasse and Yves-Bouget, Francois}
}
@article {Partensky2018,
	title = {Comparison of photosynthetic performances of marine picocyanobacteria with different configurations of the oxygen-evolving complex},
	journal = {Photosynthesis Research},
	volume = {138},
	number = {1},
	year = {2018},
	note = {tex.mendeley-tags: RCC752},
	pages = {57{\textendash}71},
	abstract = {The extrinsic PsbU and PsbV proteins are known to play a critical role in stabilizing the Mn4CaO5 cluster of the PSII oxygen-evolving complex (OEC). However, most isolates of the marine cyanobacterium Prochlorococcus naturally miss these proteins, even though they have kept the main OEC protein, PsbO. A structural homology model of the PSII of such a natural deletion mutant strain (P. marinus MED4) did not reveal any obvious compensation mechanism for this lack. To assess the physiological consequences of this unusual OEC, we compared oxygen evolution between Prochlorococcus strains missing psbU and psbV (PCC 9511 and SS120) and two marine strains possessing these genes (Prochlorococcus sp. MIT9313 and Synechococcus sp. WH7803). While the low light-adapted strain SS120 exhibited the lowest maximal O2 evolution rates (Pmax per divinyl-chlorophyll a, per cell or per photosystem II) of all four strains, the high light-adapted strain PCC 9511 displayed even higher PChlmax and PPSIImax at high irradiance than Synechococcus sp. WH7803. Furthermore, thermoluminescence glow curves did not show any alteration in the B-band shape or peak position that could be related to the lack of these extrinsic proteins. This suggests an efficient functional adaptation of the OEC in these natural deletion mutants, in which PsbO alone is seemingly sufficient to ensure proper oxygen evolution. Our study also showed that Prochlorococcus strains exhibit negative net O2 evolution rates at the low irradiances encountered in minimum oxygen zones, possibly explaining the very low O2 concentrations measured in these environments, where Prochlorococcus is the dominant oxyphototroph.},
	keywords = {rcc752},
	issn = {1573-5079},
	doi = {10.1007/s11120-018-0539-3},
	url = {https://doi.org/10.1007/s11120-018-0539-3},
	author = {Partensky, Fr{\'e}d{\'e}ric and Mella-Flores, Daniella and Six, Christophe and Garczarek, Laurence and Czjzek, Mirjam and Marie, Dominique and Kotabov{\'a}, Eva and Felcmanov{\'a}, Kristina and Pr{\'a}{\v s}il, Ond{\v r}ej}
}
@article {Engesmo2018,
	title = {Development of a qPCR assay to detect and quantify ichthyotoxic flagellates along the Norwegian coast, and the first Norwegian record of Fibrocapsa japonica (Raphidophyceae)},
	journal = {Harmful Algae},
	volume = {75},
	year = {2018},
	note = {Publisher: Elsevier B.V. tex.mendeley-tags: RCC1501,RCC1502},
	pages = {105{\textendash}117},
	abstract = {Blooms of ichthyotoxic microalgae pose a great challenge to the aquaculture industry world-wide, and there is a need for fast and specific methods for their detection and quantification in monitoring programs. In this study, quantitative real-time PCR (qPCR) assays for the detection and enumeration of three ichthyotoxic flagellates: the dinoflagellate Karenia mikimotoi (Miyake \& Kominami ex Oda) Hansen \& Moestrup and the two raphidophytes Heterosigma akashiwo (Hada) Hada ex Hara \& Chihara and Fibrocapsa japonica Toriumi \& Takano were developed. Further, a previously published qPCR assay for the dinoflagellate Karlodinium veneficum (Ballantine) Larsen was used. Monthly samples collected for three years (Aug 2009{\textendash}Jun 2012) in outer Oslofjorden, Norway were analysed, and the results compared with light microscopy cell counts. The results indicate a higher sensitivity and a lower detection limit (down to 1 cell L-1) for both qPCR assays. Qualitative and semi-quantitative results were further compared with those obtained by environmental 454 high throughput sequencing (HTS, metabarcoding) and scanning electron microscopy (SEM) examination from the same samplings. All four species were detected by qPCR and HTS and/or SEM in outer Oslofjorden (Aug 2009{\textendash}Jun 2012); Karlodinium veneficum was present year-round, whereas Karenia mikimotoi, Heterosigma akashiwo and Fibrocapsa japonica appeared mainly during the autumn in all three years. This is the first observation of Fibrocapsa japonica in Norwegian coastal waters. This species has previously been recorded off the Swedish west coast and German Bight, which may suggest a northward dispersal.},
	keywords = {454 high throughput environmental sequencing, Heterosigma akashiwo, Karenia mikimotoi, Karlodinium veneficum, Molecular monitoring, rcc1501, rcc1502, RDNA, SEM},
	issn = {15689883},
	doi = {10.1016/j.hal.2018.04.007},
	url = {https://doi.org/10.1016/j.hal.2018.04.007},
	author = {Engesmo, Anette and Strand, David and Gran-Stadnicze{\~n}ko, Sandra and Edvardsen, Bente and Medlin, Linda K. and Eikrem, Wenche}
}
@article {Kazamia2018,
	title = {Endocytosis-mediated siderophore uptake as a strategy for Fe acquisition in diatoms},
	journal = {Science Advances},
	volume = {4},
	number = {5},
	year = {2018},
	note = {tex.mendeley-tags: RCC2967},
	month = {may},
	pages = {eaar4536},
	keywords = {RCC2967},
	issn = {2375-2548},
	doi = {10.1126/sciadv.aar4536},
	url = {http://advances.sciencemag.org/lookup/doi/10.1126/sciadv.aar4536},
	author = {Kazamia, Elena and Sutak, Robert and Paz-Yepes, Javier and Dorrell, Richard G and Vieira, Fabio Rocha Jimenez and Mach, Jan and Morrissey, Joe and Leon, S{\'e}bastien and Lam, France and Pelletier, Eric and Camadro, Jean-michel and Bowler, Chris and Lesuisse, Emmanuel}
}
@article {Garcia2018,
	title = {High variability in cellular stoichiometry of carbon, nitrogen, and phosphorus within classes of marine eukaryotic phytoplankton under sufficient nutrient conditions},
	journal = {Frontiers in Microbiology},
	volume = {9},
	number = {March},
	year = {2018},
	note = {tex.mendeley-tags: RCC103,RCC1242,RCC1562,RCC4023,RCC449,RCC931},
	pages = {1{\textendash}10},
	abstract = {Current hypotheses suggest that cellular elemental stoichiometry of marine eukaryotic phytoplankton such as the ratios of cellular carbon:nitrogen:phosphorus (C:N:P) vary between phylogenetic groups based traits like evolutionary history and cell size. To investigate how phylogenetic structure, cell volume, growth rate and temperature interact to affect the cellular elemental stoichiometry of marine eukaryotic phytoplankton, we examined the C:N:P composition in 30 isolates across 7 classes of marine phytoplankton that were grown with a sufficient supply of nutrients with nitrate as the nitrogen source. The isolates covered a wide range in cell volume (5 orders of magnitude), growth rate ({\textexclamdown}0.01-0.9 d-1), and habitat temperature (2-24{\textdegree}C). Our analysis indicates that C:N:P is highly variable, with statistical model residuals accounting for over half of the total variance with no relationship between phylogeny and elemental stoichiometry. Furthermore, our data indicated that variability in C:P, N:P and C:N within Bacillariophyceae (diatoms) was as high as that among all of the isolates that we examined. In addition, a linear statistical model identified a positive relationship between diatom cell volume and C:P and N:P. Among all of the isolates that we examined, the statistical model identified temperature as a significant factor, consistent with the temperature-dependent translation efficiency model, but temperature only explained 5\% of the total statistical model variance. While some of our results support data from previous field studies, the high variability of elemental ratios within Bacillariophyceae contradicts previous work that suggests that this cosmopolitan group of microalgae has consistently low C:P and N:P ratios in comparison with other groups.},
	keywords = {cell size, Diatom, Dinoflagellate, eukaryote, frontiers in microbiology, frontiersin, Growth, org, protist, prymnesiophyte, RCC103, RCC1242, RCC1562, RCC4023, RCC449, RCC931, temperature, www},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2018.00543},
	url = {http://journal.frontiersin.org/article/10.3389/fmicb.2018.00543/full},
	author = {Garcia, Nathan S. and Sexton, Julie and Riggins, Tracey and Brown, Jeff and Lomas, Michael W. and Martiny, Adam C.}
}
@article {Carrillo2018,
	title = {Identification and analysis of OsttaDSP, a phosphoglucan phosphatase from Ostreococcus tauri},
	journal = {PLOS ONE},
	volume = {13},
	number = {1},
	year = {2018},
	note = {tex.mendeley-tags: RCC745},
	month = {jan},
	pages = {e0191621},
	keywords = {RCC745},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0191621},
	url = {http://dx.plos.org/10.1371/journal.pone.0191621},
	author = {Carrillo, Julieta B and Gomez-Casati, Diego F. and Mart{\'\i}n, Mariana and Busi, Maria V.},
	editor = {Permyakov, Eugene A.}
}
@article {Moniruzzaman2018,
	title = {Infection by a giant virus (AaV) induces widespread physiological reprogramming in aureococcus anophagefferens CCMP1984 {\textendash} a harmful bloom algae},
	journal = {Frontiers in Microbiology},
	volume = {9},
	number = {April},
	year = {2018},
	note = {tex.mendeley-tags: RCC4094},
	month = {apr},
	pages = {1{\textendash}16},
	abstract = {While viruses with distinct phylogenetic origins and different nucleic acid types can infect and lyse eukaryotic phytoplankton, " giant " dsDNA viruses have been found to be associated with important ecological processes, including the collapse of algal blooms. However, the molecular aspects of giant virus {\textendash} host interactions remain largely unknown. AaV, a giant virus in the Mimiviridae clade, is known to play a critical role in regulating the fate of brown tide blooms caused by the pelagophyte Aureococcus anophagefferens. To understand the physiological response of A. anophagefferens CCMP1984 upon AaV infection, we studied the transcriptomic landscape of this host-virus pair over an entire infection cycle using a RNA-sequencing approach. A massive transcriptional reprogramming of the host was evident as early as 5 min post-infection, with modulation of specific processes likely related to both host defense mechanism(s) and viral takeover of the cell. Infected Aureococcus showed a relative suppression of host-cell transcripts associated with photosynthesis, cytoskeleton formation, fatty acid and carbohydrate biosynthesis. In contrast, host cell processes related to protein synthesis, polyamine biosynthesis, cellular respiration, transcription and RNA processing were overrepresented compared to the healthy cultures at different stages of the infection cycle. A large number of redox active host-selenoproteins were overexpressed, which suggested that viral replication and assembly progresses in a highly oxidative environment. The majority (99.2\%) of annotated AaV genes were expressed at some point during the infection cycle and demonstrated a clear temporal-expression pattern and an increasing relative expression for the majority of the genes through the time course. We detected a putative early promoter motif for AaV, which was highly similar to the early promoter elements of two other Mimiviridae members, indicating some degree of evolutionary conservation of gene regulation within this clade. This large-scale transcriptome study provides the insight into the Aureococcus {\textquoteright}virocell{\textquoteright}, and establishes a foundation to test hypotheses regarding metabolic and regulatory processes critical for AaV and other Mimiviridae members.},
	keywords = {Algal viruses, brown, Host-virus interaction, Mimiviridae, RCC4094, transcriptional profiles},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2018.00752},
	url = {http://dx.doi.org/10.1101/256149 http://journal.frontiersin.org/article/10.3389/fmicb.2018.00752/full},
	author = {Moniruzzaman, Mohammad and Gann, Eric R and Wilhelm, Steven W}
}
@article {Piedade2018,
	title = {Influence of irradiance and temperature on the virus MpoV - 45T infecting the arctic picophytoplankter micromonas polaris},
	journal = {Viruses},
	year = {2018},
	note = {tex.mendeley-tags: RCC2257,RCC2258},
	pages = {1{\textendash}17},
	abstract = {Arctic marine ecosystems are currently undergoing rapid changes in temperature and light availability. Picophytoplankton, such as Micromonas polaris, are predicted to benefit from such changes. However, little is known about how these environmental changes affect the viruses that exert a strong mortality pressure on these small but omnipresent algae. Here we report on one-step infection experiments, combined with measurements of host physiology and viability, with 2 strains of M. polaris and the virus MpoV-45T under 3 light intensities (5, 60 and 160 ??mol quanta m-2 s-1), 2 light period regimes (16:8 and 24:0 h light:dark cycle) and 2 temperatures (3 and 7 {\textdegree}C). Our results show that low light intensity (16:8 h light:dark) delayed the decline in photosynthetic efficiency and cell lysis, while decreasing burst size by 46\%. In contrast, continuous light (24:0 h light:dark) shortened the latent period by 5 h for all light intensities, and even increased the maximum virus production rate and burst size under low light (by 157 and 69\%, respectively). Higher temperature (7 {\textdegree}C vs 3 {\textdegree}C) led to earlier cell lysis and increased burst size (by 19\%), except for the low light conditions. These findings demonstrate the ecological importance of light in combination with temperature as a controlling factor for Arctic phytoplankton host and virus dynamics seasonally, even more so in the light of global warming.},
	keywords = {arctic algal viruses, global climate change, light intensity, light regime, RCC2257, RCC2258, virus growth},
	issn = {1999-4915},
	doi = {10.3390/v10120676},
	author = {Piedade, Gon{\c c}alo J and Wesdorp, Ella M and Borbolla, Elena Montenegro and Maat, Douwe S}
}
@article {Smallwood2018,
	title = {Integrated systems biology and imaging of the smallest free-living eukaryote Ostreococcus tauri},
	journal = {bioRxiv},
	year = {2018},
	note = {tex.mendeley-tags: RCC745},
	keywords = {? No DOI found, RCC745},
	author = {Smallwood, Authors Chuck R and Chen, Jian-hua and Kumar, Neeraj and Chrisler, William and Samuel, O and Kyle, Jennifer E and Nicora, Carrie D and Boudreau, Rosanne and Ekman, Axel and Kim, K and Moore, Ronald J and Mcdermott, Gerry and Cannon, William R and Evans, James E}
}
@article {Rastogi2017,
	title = {Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms},
	journal = {Scientific Reports},
	volume = {8},
	number = {1},
	year = {2018},
	note = {ISBN: 4159801823106 Publisher: Springer US tex.mendeley-tags: RCC2967},
	month = {dec},
	pages = {4834},
	abstract = {2 3 Diatoms are one of the most successful and ecologically important groups of eukaryotic 4 phytoplankton in the modern ocean. Deciphering their genomes is a key step towards better 5 understanding of their biological innovations, evolutionary origins, and ecological 6 underpinnings. Here, we have used 90 RNA-Seq datasets from different growth conditions 7 combined with published expressed sequence tags and protein sequences from multiple taxa 8 to explore the genome of the model diatom Phaeodactylum tricornutum, and introduce 1,489 9 novel genes. The new annotation additionally permitted the discovery for the first time of 10 extensive alternative splicing (AS) in diatoms, including intron retention and exon skipping 11 which increases the diversity of transcripts to regulate gene expression in response to nutrient 12 limitations. In addition, we have used up-to-date reference sequence libraries to dissect the 13 taxonomic origins of diatom genomes. We show that the P. tricornutum genome is replete in 14 lineage-specific genes, with up to 47\% of the gene models present only possessing 15 orthologues in other stramenopile groups. Finally, we have performed a comprehensive de 16 novo annotation of repetitive elements showing novel classes of TEs such as SINE, MITE, LINE 17 and TRIM/LARD. This work provides a solid foundation for future studies of diatom gene 18 function, evolution and ecology.},
	keywords = {RCC2967},
	issn = {2045-2322},
	doi = {10.1038/s41598-018-23106-x},
	url = {https://www.biorxiv.org/content/early/2017/08/14/176024\%0Ahttp://dx.doi.org/10.1101/176024 http://www.nature.com/articles/s41598-018-23106-x},
	author = {Rastogi, Achal and Maheswari, Uma and Dorrell, Richard G. and Vieira, Fabio Rocha Jimenez and Maumus, Florian and Kustka, Adam and McCarthy, James and Allen, Andy E. and Kersey, Paul and Bowler, Chris and Tirichine, Leila}
}
@article {Partensky2018,
	title = {A novel species of the marine cyanobacterium Acaryochloris with a unique pigment content and lifestyle},
	journal = {Scientific Reports},
	volume = {8},
	number = {1},
	year = {2018},
	note = {tex.mendeley-tags: RCC1774},
	month = {dec},
	pages = {9142},
	keywords = {RCC1774},
	issn = {2045-2322},
	doi = {10.1038/s41598-018-27542-7},
	url = {http://www.nature.com/articles/s41598-018-27542-7},
	author = {Partensky, Fr{\'e}d{\'e}ric and Six, Christophe and Ratin, Morgane and Garczarek, Laurence and Vaulot, Daniel and Probert, Ian and Calteau, Alexandra and Gourvil, Priscillia and Marie, Dominique and Gr{\'e}bert, Th{\'e}ophile and Bouchier, Christiane and Le Panse, Sophie and Gachenot, Martin and Rodr{\'\i}guez, Francisco and Garrido, Jos{\'e} L.}
}
@article {Henriquez-Castillo2018,
	title = {Ostreococcus tauri luminescent reporter lines as biosensors for detecting pollution from copper-mine tailing effluents in coastal environments},
	journal = {Frontiers in Environmental Science},
	volume = {6},
	number = {May},
	year = {2018},
	note = {tex.mendeley-tags: RCC745},
	month = {may},
	pages = {1{\textendash}11},
	keywords = {biosensors, CDKA, copper pollution, ferritin, frontiers in environmental science, frontiersin, luciferase reporter, mine tailings, org, Ostreococcus, RCC745, www},
	issn = {2296-665X},
	doi = {10.3389/fenvs.2018.00022},
	url = {https://www.frontiersin.org/article/10.3389/fenvs.2018.00022/full},
	author = {Henr{\'\i}quez-Castillo, Carlos and Botebol, Hugo and Mouton, Adelaide and Ram{\'\i}rez-Flandes, Salvador and Lozano, Jean-Claude and Lelandais, Gaelle and Andrade, Santiago and Trefault, Nicole and de la Iglesia, Rodrigo and Bouget, Fran{\c c}ois-Yves}
}
@article {Moldovan2018,
	title = {Pangenomic definition of prokaryotic species and the phylogenetic structure of prochlorococcus spp.},
	journal = {Frontiers in Microbiology},
	volume = {9},
	number = {March},
	year = {2018},
	note = {tex.mendeley-tags: RCC158,RCC162,RCC269,RCC278,RCC3307,RCC407},
	pages = {1{\textendash}11},
	keywords = {monophyly, pangenome, paraphyly, prokaryotic species, RCC158, rcc162, RCC269, RCC278, RCC3307, RCC407, species definition, taxonomy},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2018.00428},
	url = {http://journal.frontiersin.org/article/10.3389/fmicb.2018.00428/full},
	author = {Moldovan, Mikhail A. and Gelfand, Mikhail S.}
}
@article {Mizrachi2018,
	title = {Phenotypic variability in chloroplast redox state predicts cell fate in a marine diatom},
	journal = {bioRxiv},
	year = {2018},
	note = {arXiv: 319517 tex.arxivid: 319517 tex.mendeley-tags: RCC2967},
	keywords = {RCC2967},
	doi = {10.1101/319517},
	author = {Mizrachi, Avia and Graff, Shiri and Creveld, Van and Shapiro, Orr H and Rosenwasser, Shilo}
}
@article {yau_rapidity_2018,
	title = {Rapidity of Genomic Adaptations to Prasinovirus Infection in a Marine Microalga},
	journal = {Viruses},
	volume = {10},
	number = {8},
	year = {2018},
	note = {Number: 8 Publisher: Multidisciplinary Digital Publishing Institute},
	pages = {441},
	abstract = {Prasinoviruses are large dsDNA viruses commonly found in aquatic systems worldwide, where they can infect and lyse unicellular prasinophyte algae such as Ostreococcus. Host susceptibility is virus strain-specific, but resistance of susceptible Ostreococcus tauri strains to a virulent virus arises frequently. In clonal resistant lines that re-grow, viruses are usually present for many generations, and genes clustered on chromosome 19 show physical rearrangements and differential expression. Here, we investigated changes occurring during the first two weeks after inoculation of the prasinovirus OtV5. By serial dilutions of cultures at the time of inoculation, we estimated the frequency of resistant cells arising in virus-challenged O. tauri cultures to be 10\&minus;3\&ndash;10\&minus;4 of the inoculated population. Re-growing resistant cells were detectable by flow cytometry 3 days post-inoculation (dpi), visible re-greening of cultures occurred by 6 dpi, and karyotypic changes were visually detectable at 8 dpi. Resistant cell lines showed a modified spectrum of host-virus specificities and much lower levels of OtV5 adsorption.},
	keywords = {adsorption, Chromosome, host range, karyotype, mamiellophyceae, phycodnaviridae, RCC1105, RCC4221, RCC4223, rearrangement, resistance, specificity, \textitOstreococcus tauri},
	doi = {10.3390/v10080441},
	url = {https://www.mdpi.com/1999-4915/10/8/441},
	author = {Yau, Sheree and Caravello, Ga{\"e}tan and Fonvieille, Nad{\`e}ge and Desgranges, Elodie and Moreau, Herv{\'e} and Grimsley, Nigel}
}
@article {EMI4:EMI412614,
	title = {Relative stability of ploidy in a marine Synechococcus across various growth conditions},
	journal = {Environmental Microbiology Reports},
	year = {2018},
	note = {tex.mendeley-tags: RCC752},
	month = {feb},
	pages = {in press},
	abstract = {Marine picocyanobacteria of the genus Synechococcus are ubiquitous phototrophs in oceanic systems. Consistent with these organisms occupying vast tracts of the nutrient impoverished ocean, most marine Synechococcus so far studied are monoploid i.e. contain a single chromosome copy. The exception is the oligoploid strain Synechococcus sp. WH7803, which on average possesses around 4 chromosome copies. Here, we set out to understand the role of resource availability (through nutrient deplete growth) and physical stressors (UV, exposure to low and high temperature) in regulating ploidy level in this strain. Using qPCR to assay ploidy status we demonstrate the relative stability of chromosome copy number in Synechococcus sp. WH7803. Such robustness in maintaining an oligoploid status even under nutrient and physical stress is indicative of a fundamental role, perhaps facilitating recombination of damaged DNA regions as a result of prolonged exposure to oxidative stress, or allowing added flexibility in gene expression via possessing multiple alleles. This article is protected by copyright. All rights reserved.},
	keywords = {rcc752},
	issn = {17582229},
	doi = {10.1111/1758-2229.12614},
	url = {http://dx.doi.org/10.1111/1758-2229.12614 http://doi.wiley.com/10.1111/1758-2229.12614},
	author = {Perez-Sepulveda, Blanca and Pitt, Frances and N{\textquoteright}Guyen, An Ngoc and Ratin, Morgane and Garczarek, Laurence and Millard, Andrew and Scanlan, David J}
}
@article {Muller2018,
	title = {Stable isotope fractionation of strontium in coccolithophore calcite: Influence of temperature and carbonate chemistry},
	journal = {Geobiology},
	volume = {16},
	number = {3},
	year = {2018},
	note = {Publisher: John Wiley \& Sons, Ltd (10.1111) tex.mendeley-tags: RCC1200},
	month = {may},
	pages = {297{\textendash}306},
	abstract = {Abstract Marine calcifying eukaryotic phytoplankton (coccolithophores) is a major contributor to the pelagic production of CaCO3 and plays an important role in the biogeochemical cycles of C, Ca and other divalent cations present in the crystal structure of calcite. The geochemical signature of coccolithophore calcite is used as palaeoproxy to reconstruct past environmental conditions and to understand the underlying physiological mechanisms (vital effects) and precipitation kinetics. Here, we present the stable Sr isotope fractionation between seawater and calcite (?88/86Sr) of laboratory cultured coccolithophores in individual dependence of temperature and seawater carbonate chemistry. Coccolithophores were cultured within a temperature and a pCO2 range from 10 to 25{\textdegree}C and from 175 to 1,240 ?atm, respectively. Both environmental drivers induced a significant linear increase in coccolith stable Sr isotope fractionation. The temperature correlation at constant pCO2 for Emiliania huxleyi and Coccolithus braarudii is expressed as ?88/86Sr = ?7.611 ? 10?3 T + 0.0061. The relation of ?88/86Sr to pCO2 was tested in Emiliania huxleyi at 10 and 20{\textdegree}C and resulted in ?88/86Sr = ?5.394 ? 10?5 pCO2 ? 0.0920 and ?88/86Sr = ?5.742 ? 10?5 pCO2 ? 0.1351, respectively. No consistent relationship was found between coccolith ?88/86Sr and cellular physiology impeding a direct application of fossil coccolith ?88/86Sr as coccolithophore productivity proxy. An overall significant correlation was detected between the elemental distribution coefficient (DSr) and ?88/86Sr similar to inorganic calcite with a physiologically induced offset. Our observations indicate (i) that temperature and pCO2 induce specific effects on coccolith ?88/86Sr values and (ii) that strontium elemental ratios and stable isotope fractionation are mainly controlled by precipitation kinetics when embedded into the crystal lattice and subject to vital effects during the transmembrane transport from seawater to the site of calcification. These results provide an important step to develop a coccolith ?88/86Sr palaeoproxy complementing the existing toolbox of palaeoceanography.},
	keywords = {coccolithophores, paleoproxy calibration, phytoplankton, RCC1200, stable Sr isotope fractionation},
	issn = {1472-4677},
	doi = {10.1111/gbi.12276},
	url = {https://doi.org/10.1111/gbi.12276},
	author = {M{\"u}ller, M N and Krabbenh{\"o}ft, A and Vollstaedt, H and Brandini, F P and Eisenhauer, A}
}
@article {Mahmoud2017,
	title = {Adaptation to blue light in marine synechococcus requires MpeU, an enzyme with similarity to phycoerythrobilin lyase isomerases},
	journal = {Frontiers in Microbiology},
	volume = {8},
	number = {February},
	year = {2017},
	note = {tex.mendeley-tags: 2017,rcc555,sbr?hyto?app},
	month = {feb},
	pages = {243},
	abstract = {Marine Synechococcus cyanobacteria have successfully adapted to environments with different light colors, which likely contributes to this genus being the second most abundant photosynthetic microorganism worldwide. Populations of Synechococcus that grow in deep, blue ocean waters contain large amounts of the blue-light absorbing chromophore phycourobilin (PUB) in their light harvesting complexes (phycobilisomes). Here we show that all Synechococcus strains adapted to blue light possess a gene called mpeU. MpeU is structurally similar to phycobilin lyases, enzymes that ligate chromophores to phycobiliproteins. Interruption of mpeU caused a reduction in PUB content, produced impaired phycobilisomes and reduced growth rate more strongly in blue than green light. When mpeU was reintroduced in the mpeU mutant background, the mpeU-less phenotype was complemented in terms of PUB content and phycobilisome content. Fluorescence spectra of mpeU mutant cells and purified phycobilisomes revealed red-shifted phycoerythrin emission peaks, likely indicating a defect in chromophore ligation to phycoerythrin-I (PE-I) or phycoerythrin-II (PE-II). Our results suggest that MpeU is a lyase-isomerase that attaches a phycoerythrobilin to a PEI or PEII subunit and isomerizes it to PUB. MpeU is therefore an important determinant in adaptation of Synechococcus spp. to capture photons in blue light environments throughout the world{\textquoteright}s oceans.},
	keywords = {2017, Blue light, light harvesting complex, Lyase isomerase, marine cyanobacteria, Marine Synechococcus, phycobilin, Phycobilisome, Phycoerythrin, Phycourobilin, rcc555, sbr?hyto?app},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2017.00243},
	url = {http://journal.frontiersin.org/article/10.3389/fmicb.2017.00243/full},
	author = {Mahmoud, Rania M. and Sanfilippo, Joseph E. and Nguyen, Adam A. and Strnat, Johann A. and Partensky, Fr{\'e}d{\'e}ric and Garczarek, Laurence and Abo El Kassem, Nabil and Kehoe, David M. and Schluchter, Wendy M.}
}
@article {Ni2016,
	title = {Arctic Micromonas uses protein pools and non-photochemical quenching to cope with temperature restrictions on Photosystem II protein turnover},
	journal = {Photosynthesis Research},
	volume = {131},
	number = {2},
	year = {2017},
	note = {ISBN: 1112001603 Publisher: Springer Netherlands tex.mendeley-tags: 2016,RCC806},
	month = {feb},
	pages = {203{\textendash}220},
	keywords = {2016, {\'a}, Photoinactivation, photoinactivation {\'a} xanthophyll cycle, Photosystem II, Prasinophyte, prasinophyte {\'a} photosystem ii, RCC806, Xanthophyll cycle},
	issn = {0166-8595},
	doi = {10.1007/s11120-016-0310-6},
	url = {http://link.springer.com/10.1007/s11120-016-0310-6},
	author = {Ni, Guangyan and Zimbalatti, Gabrielle and Murphy, Cole D. and Barnett, Audrey B. and Arsenault, Christopher M. and Li, Gang and Cockshutt, Amanda M. and Campbell, Douglas A.}
}
@article {Gnouma2017,
	title = {Changes in fatty acids profile, monosaccharide profile and protein content during batch growth of Isochrysis galbana (T.iso)},
	journal = {Aquaculture Research},
	volume = {48},
	number = {9},
	year = {2017},
	note = {Publisher: John Wiley \& Sons, Ltd (10.1111) tex.mendeley-tags: RCC1349},
	month = {sep},
	pages = {4982{\textendash}4990},
	abstract = {Abstract To investigate the nutritional value of the marine micro-alga Isochrysis galbana Tahitian Isochrysis strain (T.iso) as an alternative feed for aquaculture during culture age, its biochemical composition was studied under autotrophic and controlled culture conditions at different growth stages: exponential phase, early and late stationary phases and decay phase. Analysis showed that C14:0, C16:0, C16:1, C18:4 (n-3) and C22:6 (n-3) were the most abundant fatty acids in this alga at different growth stages. The highest values of monounsaturated fatty acids were recorded at the late stationary and the decay phases. However, the highest levels of polyunsaturated fatty acids were observed at the early stationary phase. At all growth stages, I. galbana (T.iso) contained arabinose, xylose, mannose, galactose and glucose. Glucose represented the main sugar, and its content per dry alga biomass weight increased with increasing age of the culture and reached about fourfold in the decay phase. The maximum protein content was also observed during this last phase.},
	keywords = {fatty acids, growth phases, Isochrysis galbana (T.iso), monosaccharides, proteins, RCC1349},
	issn = {1355-557X},
	doi = {10.1111/are.13316},
	url = {https://doi.org/10.1111/are.13316},
	author = {Gnouma, Asma and Sadovskaya, Irina and Souissi, Anissa and Sebai, Khaled and Medhioub, Amel and Grard, Thierry and Souissi, Sami}
}
@article {Dorrell2017,
	title = {Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome},
	journal = {eLife},
	volume = {6},
	year = {2017},
	month = {may},
	pages = {1{\textendash}45},
	abstract = {Plastids are supported by a wide range of proteins encoded within the nucleus and imported from the cytoplasm. These plastid-targeted proteins may originate from the endosymbiont, the host, or other sources entirely. Here, we identify and characterise 770 plastid-targeted proteins that are conserved across the ochrophytes, a major group of algae including diatoms, pelagophytes and kelps, that possess plastids derived from red algae. We show that the ancestral ochrophyte plastid proteome was an evolutionary chimera, with 25\% of its phylogenetically tractable nucleus-encoded proteins deriving from green algae. We additionally show that functional mixing of host and plastid proteomes, such as through dual-targeting, is an ancestral feature of plastid evolution. Finally, we detect a clear phylogenetic signal from one ochrophyte subgroup, the lineage containing pelagophytes and dictyochophytes, in plastid-targeted proteins from another major algal lineage, the haptophytes. This may represent a possible serial endosymbiosis event deep in eukaryotic evolutionary history.},
	keywords = {2017, RCC1486, RCC1523, RCC1537, RCC1587, SBR$_\textrmP$hyto$_\textrmE$PPO},
	issn = {2050-084X},
	doi = {10.7554/eLife.23717},
	url = {http://elifesciences.org/lookup/doi/10.7554/eLife.23717},
	author = {Dorrell, Richard G and Gile, Gillian and McCallum, Giselle and M{\'e}heust, Rapha{\"e}l and Bapteste, Eric P and Klinger, Christen M and Brillet-Gu{\'e}guen, Loraine and Freeman, Katalina D and Richter, Daniel J and Bowler, Chris}
}
@article {LopesdosSantos2017,
	title = {Chloropicophyceae, a new class of picophytoplanktonic prasinophytes},
	journal = {Scientific Reports},
	volume = {7},
	number = {1},
	year = {2017},
	note = {tex.mendeley-tags: 2017,RCC1019,RCC1021,RCC1032,RCC1043,RCC1124,RCC138,RCC15,RCC1871,RCC19,RCC227,RCC2335,RCC2337,RCC2339,RCC287,RCC297,RCC3368,RCC3373,RCC3374,RCC3375,RCC3376,RCC3402,RCC4429,RCC4430,RCC4434,RCC4572,RCC4656,RCC696,RCC700,RCC701,RCC712,RCC713,RCC717,RCC719,RCC722,RCC726,RCC856,RCC857,RCC887,RCC917,RCC996,RCC997,RCC998,RCC999,sbr?hyto$_\textrmd$ipo},
	month = {dec},
	pages = {14019},
	keywords = {2017, RCC1019, RCC1021, RCC1032, RCC1043, RCC1124, RCC138, RCC15, RCC1871, RCC19, RCC227, RCC2335, RCC2337, RCC2339, RCC287, RCC297, RCC3368, RCC3373, RCC3374, RCC3375, RCC3376, RCC3402, RCC4429, RCC4430, RCC4434, RCC4572, RCC4656, RCC696, RCC700, RCC701, RCC712, RCC713, RCC717, RCC719, RCC722, RCC726, RCC856, RCC857, RCC887, RCC917, RCC996, RCC997, RCC998, RCC999, sbr?hyto$_\textrmd$ipo},
	issn = {2045-2322},
	doi = {10.1038/s41598-017-12412-5},
	url = {http://www.nature.com/articles/s41598-017-12412-5},
	author = {Lopes dos Santos, Adriana and Pollina, Thibaut and Gourvil, Priscillia and Corre, Erwan and Marie, Dominique and Garrido, Jos{\'e} Luis and Rodr{\'\i}guez, Francisco and No{\"e}l, Mary-H{\'e}l{\`e}ne and Vaulot, Daniel and Eikrem, Wenche}
}
@article {Organelli2017,
	title = {On the discrimination of multiple phytoplankton groups from light absorption spectra of assemblages with mixed taxonomic composition and variable light conditions},
	journal = {Applied Optics},
	volume = {56},
	number = {14},
	year = {2017},
	note = {tex.mendeley-tags: RCC151,RCC322,RCC904},
	month = {may},
	pages = {3952},
	abstract = {According to recommendations of the international community of phytoplankton functional type algorithm devel- opers, a set of experiments on marine algal cultures was conducted to (1) investigate uncertainties and limits in phytoplankton group discrimination from hyperspectral light absorption properties of assemblages withmixed taxo- nomic composition, and (2) evaluate the extent to which modifications of the absorption spectral features due to variable light conditions affect the optical discrimination of phytoplankton. Results showed that spectral absorption signatures of multiple species can be extracted from mixed assemblages, even at low relative contributions. Errors in retrieved pigment abundances are, however, influenced by the co-occurrence of species with similar spectral features. Plasticity of absorption spectra due to changes in light conditions weakly affects interspecific differences, with errors {\textexclamdown}21\% for retrievals of pigment concentrations from mixed assemblages.},
	keywords = {RCC151, RCC322, RCC904},
	issn = {0003-6935},
	doi = {10.1364/AO.56.003952},
	url = {https://www.osapublishing.org/abstract.cfm?URI=ao-56-14-3952},
	author = {Organelli, Emanuele and Nuccio, Caterina and Lazzara, Luigi and Uitz, Julia and Bricaud, Annick and Massi, Luca}
}
@article {Moutier2017,
	title = {Evolution of the scattering properties of phytoplankton cells from flow cytometry measurements},
	journal = {PLoS ONE},
	volume = {12},
	number = {7},
	year = {2017},
	note = {ISBN: 1111111111 tex.mendeley-tags: RCC1,RCC950},
	abstract = {Combining a modern, data-analytic perspective with a focus on applications in the social sciences, the Second Edition of Applied Regression Analysis and Generalized Linear Models provides in-depth coverage of regression analysis, generalized linear models, and closely related methods. Although the text is largely accessible to readers with a modest background in statistics and mathematics, author John Fox also presents more advanced material throughout the book. Key Updates to the Second Edition:Provides greatly enhanced coverage of generalized linear models, with an emphasis on models for categorical and count data Offers new chapters on missing data in regression models and on methods of model selection Includes expanded treatment of robust regression, time-series regression, nonlinear regression, and nonparametric regression Incorporates new examples using larger data sets Includes an extensive Web site at http://www.sagepub.com/fox that presents appendixes, data sets used in the book and for data-analytic exercises, and the data-analytic exercises themselves Intended Audience: This core text will be a valuable resource for graduate students and researchers in the social sciences (particularly sociology, political science, and psychology) and other disciplines that employ linear and related models for data analysis. High Praise for the First Edition: Even though the book is written with social scientists as the target audience, the depth of material and how it is conveyed give it far broader appeal. Indeed, I recommend it as a useful learning text and resource for researchers and students in any field that applies regression or linear models (that is, most everyone), including courses for undergraduate statistics majors.... The author is to be commended for giving us this book, which I trust will find a wide and enduring readership.-JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION [T]his wonderfully comprehensive book focuses on regression analysis and linear models.... We enthusiastically recommend this book {\textemdash} having used it in class, we know that it is thorough and well liked by students. -CHANCE},
	keywords = {RCC1, RCC950},
	issn = {19326203},
	doi = {10.1371/journal.pone.0181180},
	author = {Moutier, William and Dufor{\^e}t-Gaurier, Lucile and Thyssen, M{\'e}lilotus and Loisel, Hubert and M{\'e}riaux, Xavier and Courcot, Lucie and Dessailly, David and R{\^e}ve, Anne H{\'e}l{\`e}ne and Gr{\'e}gori, Gerald and Alvain, S{\'e}verine and Barani, Aude and Brutier, Laurent and Dugenne, Mathilde}
}
@article {Degraeve-Guilbault2017,
	title = {Glycerolipid characterization and nutrient deprivation-associated changes in the green picoalga ostreococcus tauri},
	journal = {Plant Physiology},
	volume = {173},
	number = {4},
	year = {2017},
	note = {tex.mendeley-tags: RCC3401,RCC4222,RCC745,RCC788,RCC789,RCC802,RCC809,RCC834},
	pages = {2060{\textendash}2080},
	abstract = {The picoalga Ostreococcus tauri is a minimal photosynthetic eukaryote that has been used as a model system. O. tauri is known to efficiently produce docosahexaenoic acid (DHA). We provide a comprehensive study of the glycerolipidome of O. tauri and validate this species as model for related picoeukaryotes. O. tauri lipids displayed unique features that combined traits from the green and the chromalveolate lineages. The betaine lipid diacylglyceryl-hydroxymethyl-trimethyl-β-alanine and phosphatidyldimethylpropanethiol, both hallmarks of chromalveolates, were identified as presumed extraplastidial lipids. DHA was confined to these lipids, while plastidial lipids of prokaryotic type were characterized by the overwhelming presence of ω-3 C18 polyunsaturated fatty acids (FAs), 18:5 being restricted to galactolipids. C16:4, an FA typical of green microalgae galactolipids, also was a major component of O. tauri extraplastidial lipids, while the 16:4-coenzyme A (CoA) species was not detected. Triacylglycerols (TAGs) displayed the complete panel of FAs, and many species exhibited combinations of FAs diagnostic for plastidial and extraplastidial lipids. Importantly, under nutrient deprivation, 16:4 and ω-3 C18 polyunsaturated FAs accumulated into de novo synthesized TAGs while DHA-TAG species remained rather stable, indicating an increased contribution of FAs of plastidial origin to TAG synthesis. Nutrient deprivation further severely down-regulated the conversion of 18:3 to 18:4, resulting in obvious inversion of the 18:3/18:4 ratio in plastidial lipids, TAGs, as well as acyl-CoAs. The fine-tuned and dynamic regulation of the 18:3/18:4 ratio suggested an important physiological role of these FAs in photosynthetic membranes. Acyl position in structural and storage lipids together with acyl-CoA analysis further help to determine mechanisms possibly involved in glycerolipid synthesis.},
	keywords = {rcc3401, RCC4222, RCC745, RCC788, RCC789, RCC802, RCC809, RCC834},
	issn = {0032-0889},
	doi = {10.1104/pp.16.01467},
	url = {http://www.plantphysiol.org/lookup/doi/10.1104/pp.16.01467},
	author = {Degraeve-Guilbault, Charlotte and Br{\'e}h{\'e}lin, Claire and Haslam, Richard and Sayanova, Olga and Marie-Luce, Glawdys and Jouhet, Juliette and Corellou, Florence}
}
@article {Monier2017,
	title = {Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton},
	journal = {Proceedings of the National Academy of Sciences},
	year = {2017},
	note = {tex.mendeley-tags: RCC1107,RCC1621,RCC2573,RCC2593,RCC745,RCC809},
	pages = {201708097},
	keywords = {rcc1107, RCC1621, RCC2573, RCC2593, RCC745, RCC809},
	issn = {0027-8424},
	doi = {10.1073/pnas.1708097114},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1708097114},
	author = {Monier, Adam and Chambouvet, Aurelie and Milner, David S. and Attah, Victoria and Terrado, Ram{\'o}n and Lovejoy, Connie and Moreau, Herv{\'e} and Santoro, Alyson E. and Derelle, Evelyne and Richards, Thomas A.}
}
@article {Marie2017,
	title = {Improvement of phytoplankton culture isolation using single cell sorting by flow cytometry},
	journal = {Journal of Phycology},
	volume = {53},
	number = {2},
	year = {2017},
	note = {tex.mendeley-tags: 2016,RCC1008,RCC299,RCC350,RCC4108,RCC4548,RCC4549,RCC4550,RCC4551,RCC4552,RCC4553,RCC4554,RCC4555,RCC4556,RCC4557,RCC4558,RCC4559,RCC4560,RCC4561,RCC4562,RCC4563,RCC4564,RCC4565,RCC4566,RCC4567,RCC4568,RCC4569,RCC4570,RCC4571,RCC4572,RCC4573,RCC4574,RCC4575,RCC4576,RCC4577,RCC4578,RCC4579,RCC4657,RCC4658,RCC4659,RCC4660,RCC4661,RCC4662,RCC4663,RCC4664,RCC4665,RCC4666,RCC90},
	month = {apr},
	pages = {271{\textendash}282},
	keywords = {2016, RCC1008, RCC299, RCC350, RCC4108, RCC4548, RCC4549, RCC4550, RCC4551, RCC4552, RCC4553, RCC4554, RCC4555, RCC4556, RCC4557, RCC4558, RCC4559, RCC4560, RCC4561, RCC4562, RCC4563, RCC4564, RCC4565, RCC4566, RCC4567, RCC4568, RCC4569, RCC4570, RCC4571, RCC4572, RCC4573, RCC4574, RCC4575, RCC4576, RCC4577, RCC4578, RCC4579, RCC4657, RCC4658, RCC4659, RCC4660, RCC4661, RCC4662, RCC4663, RCC4664, RCC4665, RCC4666, RCC90},
	issn = {00223646},
	doi = {10.1111/jpy.12495},
	url = {http://doi.wiley.com/10.1111/jpy.12495},
	author = {Marie, Dominique and Le Gall, Florence and Edern, Roseline and Gourvil, Priscillia and Vaulot, Daniel},
	editor = {Valentin, K.}
}
@article {Balzano2017c,
	title = {Morphological and genetic diversity of Beaufort Sea diatoms with high contributions from the Chaetoceros neogracilis species complex},
	journal = {Journal of Phycology},
	volume = {53},
	number = {1},
	year = {2017},
	note = {tex.mendeley-tags: RCC1984,RCC1985,RCC1986,RCC1988,RCC1989,RCC1990,RCC1991,RCC1992,RCC1993,RCC1995,RCC1997,RCC1999,RCC2000,RCC2002,RCC2003,RCC2004,RCC2005,RCC2006,RCC2008,RCC2010,RCC2011,RCC2012,RCC2014,RCC2016,RCC2017,RCC2021,RCC2037,RCC2038,RCC2039,RCC2042,RCC2043,RCC2261,RCC2262,RCC2263,RCC2264,RCC2265,RCC2266,RCC2267,RCC2268,RCC2269,RCC2270,RCC2272,RCC2273,RCC2274,RCC2275,RCC2276,RCC2277,RCC2278,RCC2279,RCC2280,RCC2281,RCC2282,RCC2318,RCC2506,RCC2517,RCC2520,RCC2521,RCC2522},
	month = {feb},
	pages = {161{\textendash}187},
	abstract = {Seventy-five diatom strains isolated from the Beaufort Sea (Canadian Arctic) in the summer of 2009 were characterized by light and electron microscopy (SEM and TEM), as well as 18S and 28S rRNA gene sequencing. These strains group into 20 genotypes and 17 morphotypes and are affiliated with the genera Arcocellulus, Attheya, Chaetoceros, Cylindrotheca, Eucampia, Nitzschia, Porosira, Pseudo-nitzschia, Shionodiscus, Thalassiosira, and Synedropsis. Most of the species have a distribution confined to the northern/polar area. Chaetoceros neogracilis and Chaetoceros gelidus were the most represented taxa. Strains of C. neogracilis were morphologically similar and shared identical 18S rRNA gene sequences, but belonged to four distinct genetic clades based on 28S rRNA, ITS-1 and ITS-2 phylogenies. Secondary structure prediction revealed that these four clades differ in hemi-compensatory base changes (HCBCs) in paired positions of the ITS-2, suggesting their inability to interbreed. Reproductively isolated C. neogracilis genotypes can thus co-occur in summer phytoplankton communities in the Beaufort Sea. C. neogracilis generally occurred as single cells but also formed short colonies. It is phylogenetically distinct from an Antarctic species, erroneously identified in some previous studies as C. neogracilis, but named here as Chaetoceros sp. This work provides taxonomically validated sequences for 20 Arctic diatom taxa, which will facilitate future metabarcoding studies on phytoplankton in this region.},
	keywords = {RCC1984, RCC1985, RCC1986, RCC1988, RCC1989, RCC1990, RCC1991, RCC1992, RCC1993, RCC1995, RCC1997, RCC1999, RCC2000, RCC2002, RCC2003, RCC2004, RCC2005, RCC2006, RCC2008, RCC2010, RCC2011, RCC2012, RCC2014, RCC2016, RCC2017, RCC2021, RCC2037, RCC2038, RCC2039, RCC2042, RCC2043, RCC2261, RCC2262, RCC2263, RCC2264, RCC2265, RCC2266, RCC2267, RCC2268, RCC2269, RCC2270, RCC2272, RCC2273, RCC2274, RCC2275, RCC2276, RCC2277, RCC2278, RCC2279, RCC2280, RCC2281, RCC2282, RCC2318, RCC2506, RCC2517, RCC2520, RCC2521, RCC2522},
	issn = {00223646},
	doi = {10.1111/jpy.12489},
	url = {http://doi.wiley.com/10.1111/jpy.12489},
	author = {Balzano, Sergio and Percopo, Isabella and Siano, Raffaele and Gourvil, Priscillia and Chanoine, M{\'e}lanie and Marie, Dominique and Vaulot, Daniel and Sarno, Diana},
	editor = {Wood, M.}
}
@article {Mackey2017,
	title = {Physiological and proteomic characterization of light adaptations in marine Synechococcus},
	journal = {Environmental Microbiology},
	volume = {19},
	number = {6},
	year = {2017},
	note = {tex.mendeley-tags: rcc539,rcc752},
	month = {jun},
	pages = {2348{\textendash}2365},
	keywords = {rcc539, rcc752},
	issn = {14622912},
	doi = {10.1111/1462-2920.13744},
	url = {http://doi.wiley.com/10.1111/1462-2920.13744},
	author = {Mackey, Katherine R. M. and Post, Anton F and McIlvin, Matthew R and Saito, Mak A}
}
@article {Blanc-Mathieu2017,
	title = {Population genomics of picophytoplankton unveils novel chromosome hypervariability},
	journal = {Science Advances},
	volume = {3},
	number = {7},
	year = {2017},
	note = {tex.mendeley-tags: RCC1105,RCC1108,RCC1110,RCC1112,RCC1114,RCC1115,RCC1116,RCC1117,RCC1118,RCC1123,RCC1558,RCC1559,RCC1561,RCC299,RCC4221,RCC809},
	month = {jul},
	pages = {e1700239},
	keywords = {RCC1105, RCC1108, RCC1110, RCC1112, RCC1114, RCC1115, RCC1116, RCC1117, RCC1118, RCC1123, RCC1558, RCC1559, RCC1561, RCC299, RCC4221, RCC809},
	issn = {2375-2548},
	doi = {10.1126/sciadv.1700239},
	url = {http://advances.sciencemag.org/lookup/doi/10.1126/sciadv.1700239},
	author = {Blanc-Mathieu, Romain and Krasovec, Marc and Hebrard, Maxime and Yau, Sheree and Desgranges, Elodie and Martin, Joel and Schackwitz, Wendy and Kuo, Alan and Salin, Gerald and Donnadieu, Cecile and Desdevises, Yves and Sanchez-Ferandin, Sophie and Moreau, Herv{\'e} and Rivals, Eric and Grigoriev, Igor V. and Grimsley, Nigel and Eyre-Walker, Adam and Piganeau, Gwenael}
}
@article {Derelle2017,
	title = {Prasinovirus attack of ostreococcus is furtive by day but savage by night},
	journal = {Journal of Virology},
	volume = {92},
	number = {4},
	year = {2017},
	note = {tex.mendeley-tags: RCC4221},
	month = {nov},
	pages = {JVI.01703{\textendash}17},
	abstract = {Prasinoviruses are large DNA viruses that infect diverse genera of green microalgae worldwide in aquatic ecosystems, but molecular knowledge of their life-cycles is lacking. Several complete genomes of both these viruses and their marine algal hosts are now available and have been used to show the pervasive presence of these species in microbial metagenomes. We have analysed the life-cycle of OtV5, a lytic virus, using RNA-Seq from 12 time points of healthy or infected Ostreococcus tauri cells over a day/night cycle in culture. In the day, viral gene transcription remained low while host nitrogen metabolism gene transcription was initially strongly repressed for two successive time points before being induced for 8 hours, but in the night viral transcription increased steeply while host nitrogen metabolism genes were repressed and many host functions that are normally reduced in the night appeared to be compensated either by genes expressed from the virus or by increased expression of a subset of 4.4 \% of the host{\textquoteright}s genes. Some host cells lysed progressively during the night, but a larger proportion lysed the following morning. Our data suggest that the life-cycles of algal viruses mirror the diurnal rhythms of their hosts.},
	keywords = {accepted 9, mamiellophyceae, ncldv, Ostreococcus, phycodnaviridae, prasinophytes, RCC4221, received 28 september 2017},
	issn = {0022-538X},
	doi = {10.1128/JVI.01703-17},
	url = {http://jvi.asm.org/lookup/doi/10.1128/JVI.01703-17},
	author = {Derelle, Evelyne and Yau, Sheree and Moreau, Herv{\'e} and Grimsley, Nigel H.}
}
@article {Andersen2017,
	title = {Rediscovery of the Ochromonas type species Ochromonas triangulata (Chrysophyceae) from its type locality (Lake Veysove, Donetsk region, Ukraine)},
	journal = {Phycologia},
	volume = {56},
	number = {6},
	year = {2017},
	note = {tex.ids= Andersen2017a tex.mendeley-tags: 2017,RCC21},
	pages = {591{\textendash}604},
	abstract = {Ochromonas triangulata, the type species for a genus with over 125 taxa, was collected for only the second time, again from the type locality. Cell morphology, cell division, palmelloid stage and cyst structure generally agreed with the original description. Molecular phylogenetic analysis based on the 18S rRNA gene revealed 13 clades of Ochromonas-like flagellates as well as the clade represented by our O. triangulata strain and the nearly identical strain RCC-21/AC025. We also conducted a concatenated analysis using the 18S rRNA and the rbcL genes, and we recovered the same 14 clades. One clade, containing strains CCAP 933/27 and CCMP1861, previously named Ochromonas tuberculata, was re-identified as Chrysastrella paradoxa and Chrysastrella breviappendiculata, respectively. One clade included the Poterioochromonas strains but we were unable to convincingly connect species names to the strains because authentic strains were unknown or not examined. Organisms in the clade that included the well-known Ochromonas danica were assigned to Chlorochromonas. The generic name Melkoniania gen. nov. was proposed for one distinct clade of marine flagellates. These changes addressed some of the issues associated with the polyphyletic Ochromonas sensu lato but many problems remained.},
	keywords = {2017, RCC21},
	issn = {0031-8884},
	doi = {10.2216/17-15.1},
	url = {http://www.phycologia.org/doi/10.2216/17-15.1},
	author = {Andersen, Robert A. and Graf, Louis and Malakhov, Yuriy and Yoon, Hwan Su}
}
@article {Simon2017,
	title = {Revision of the genus micromonas manton et parke (chlorophyta, mamiellophyceae), of the type species m. pusilla (butcher) manton \& parke and of the species m. commoda van baren, bachy and worden and description of two new species based on the genetic},
	journal = {Protist},
	volume = {168},
	number = {5},
	year = {2017},
	note = {tex.mendeley-tags: 2017,RCC1109,RCC114,RCC2306,RCC2308,RCC299,RCC372,RCC373,RCC418,RCC434,RCC447,RCC448,RCC449,RCC450,RCC451,RCC461,RCC465,RCC472,RCC497,RCC498,RCC570,RCC629,RCC647,RCC658,RCC676,RCC692,RCC746,RCC803,RCC804,RCC805,RCC806,RCC807,RCC808,RCC828,RCC829,RCC830,RCC831,RCC833,RCC834,RCC835,RCC836,sbr?hyto$_\textrmd$ipo},
	month = {nov},
	pages = {612{\textendash}635},
	keywords = {2017, ASSEMBLE, rcc, RCC1109, RCC114, RCC2306, RCC2308, RCC299, RCC372, RCC373, RCC418, RCC434, RCC447, RCC448, RCC449, RCC450, RCC451, RCC461, RCC465, RCC472, RCC497, RCC498, RCC570, RCC629, RCC647, RCC658, RCC676, RCC692, RCC746, RCC803, RCC804, RCC805, RCC806, RCC807, RCC808, RCC828, RCC829, RCC830, RCC831, RCC833, RCC834, RCC835, RCC836, SBR$_\textrmP$hyto$_\textrmD$IPO, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto$_\textrmd$ipo},
	issn = {14344610},
	doi = {10.1016/j.protis.2017.09.002},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S1434461017300780},
	author = {Simon, Nathalie and Foulon, Elodie and Grulois, Daphne and Six, Christophe and Desdevises, Yves and Latimier, Marie and Le Gall, Florence and Tragin, Margot and Houdan, Aude and Derelle, Evelyne and Jouenne, Fabien and Marie, Dominique and Le Panse, Sophie and Vaulot, Daniel and Marin, Birger}
}
@article {Demory2017,
	title = {Temperature is a key factor in Micromonas{\textendash}virus interactions},
	journal = {The ISME Journal},
	volume = {11},
	number = {3},
	year = {2017},
	note = {Publisher: Nature Publishing Group tex.mendeley-tags: 2017,RCC4229,RCC4253,RCC4265,RCC451,RCC829,RCC834,sbr?hyto$_\textrmd$ipo,sbr?hyto?app},
	month = {mar},
	pages = {601{\textendash}612},
	abstract = {The genus Micromonas comprises phytoplankton that show among the widest latitudinal distributions on Earth, and members of this genus are recurrently infected by prasinoviruses in contrasted thermal ecosystems. In this study, we assessed how temperature influences the interplay between the main genetic clades of this prominent microalga and their viruses. The growth of three Micromonas strains (Mic-A, Mic-B, Mic-C) and the stability of their respective lytic viruses (MicV-A, MicV-B, MicV-C) were measured over a thermal range of 4{\textendash}32.5 {\textdegree}C. Similar growth temperature optima (Topt) were predicted for all three hosts but Mic-B exhibited a broader thermal tolerance than Mic-A and Mic-C, suggesting distinct thermoacclimation strategies. Similarly, the MicV-C virus displayed a remarkable thermal stability compared with MicV-A and MicV-B. Despite these divergences, infection dynamics showed that temperatures below Topt lengthened lytic cycle kinetics and reduced viral yield and, notably, that infection at temperatures above Topt did not usually result in cell lysis. Two mechanisms operated depending on the temperature and the biological system. Hosts either prevented the production of viral progeny or maintained their ability to produce virions with no apparent cell lysis, pointing to a possible switch in the viral life strategy. Hence, temperature changes critically affect the outcome of Micromonas infection and have implications for ocean biogeochemistry and evolution.},
	keywords = {2017, RCC4229, RCC4253, RCC4265, RCC451, RCC829, RCC834, sbr?hyto$_\textrmd$ipo, sbr?hyto?app},
	issn = {1751-7362},
	doi = {10.1038/ismej.2016.160},
	url = {http://dx.doi.org/10.1038/ismej.2016.160 http://www.nature.com/doifinder/10.1038/ismej.2016.160},
	author = {Demory, David and Arsenieff, Laure and Simon, Nathalie and Six, Christophe and Rigaut-jalabert, Fabienne and Marie, Dominique and Ge, Pei and Bigeard, Estelle and Jacquet, St{\'e}phan and Sciandra, Antoine and Bernard, Olivier and Rabouille, Sophie and Baudoux, Anne-claire}
}
@article {Simmons2016,
	title = {Abundance and biogeography of picoprasinophyte ecotypes and other phytoplankton in the eastern north pacific ocean},
	journal = {Applied and Environmental Microbiology},
	volume = {82},
	number = {6},
	year = {2016},
	note = {tex.mendeley-tags: 2016,rcc},
	month = {mar},
	pages = {1693{\textendash}1705},
	abstract = {Eukaryotic algae within the picoplankton size class (<=2 ??m in diameter) are important marine primary producers, but their spatial and ecological distributions are not well characterized. Here, we studied three picoeukaryotic prasinophyte genera and their cyanobacterial counterparts, Prochlorococcus and Synechococcus , during two cruises along a North Pacific transect characterized by different ecological regimes. Picoeukaryotes and Synechococcus reached maximum abundances of 1.44 {\texttimes} 10 5 and 3.37 {\texttimes} 10 5 cells ? ml -1 , respectively, in mesotrophic waters, while Prochlorococcus reached 1.95 {\texttimes} 10 5 cells ? ml -1 in the oligotrophic ocean. Of the picoeukaryotes, Bathycoccus was present at all stations in both cruises, reaching 21,368 {\textpm} 327 18S rRNA gene copies ? ml -1 . Micromonas and Ostreococcus clade OI were detected only in mesotrophic and coastal waters and Ostreococcus clade OII only in the oligotrophic ocean. To resolve proposed Bathycoccus ecotypes, we established genetic distances for 1,104 marker genes using targeted metagenomes and the Bathycoccus prasinos genome. The analysis was anchored in comparative genome analysis of three Ostreococcus species for which physiological and environmental data are available to facilitate data interpretation. We established that two Bathycoccus ecotypes exist, named here BI (represented by coastal isolate Bathycoccus prasinos ) and BII. These share 82\% {\textpm} 6\% nucleotide identity across homologs, while the Ostreococcus spp. share 75\% {\textpm} 8\%. We developed and applied an analysis of ecomarkers to metatranscriptomes sequenced here and published -omics data from the same region. The results indicated that the Bathycoccus ecotypes cooccur more often than Ostreococcus clades OI and OII do. Exploratory analyses of relative transcript abundances suggest that Bathycoccus NRT2.1 and AMT2.2 are high-affinity NO 3 - and low-affinity NH 4 + transporters, respectively, with close homologs in multiple picoprasinophytes. Additionally, in the open ocean, where dissolved iron concentrations were low (0.08 nM), there appeared to be a shift to the use of nickel superoxide dismutases (SODs) from Mn/Fe/Cu SODs closer inshore. Our study documents the distribution of picophytoplankton along a North Pacific ecological gradient and offers new concepts and techniques for investigating their biogeography.},
	keywords = {2016, rcc},
	issn = {0099-2240},
	doi = {10.1128/AEM.02730-15},
	url = {http://aem.asm.org/lookup/doi/10.1128/AEM.02730-15},
	author = {Simmons, Melinda P. and Sudek, Sebastian and Monier, Adam and Limardo, Alexander J. and Jimenez, Valeria and Perle, Christopher R. and Elrod, Virginia A. and Pennington, J. Timothy and Worden, Alexandra Z.},
	editor = {Schloss, P. D.}
}
@article {Bolton2016,
	title = {Decrease in coccolithophore calcification and CO2 since the middle Miocene},
	journal = {Nature Communications},
	volume = {7},
	year = {2016},
	note = {tex.mendeley-tags: 2016,rcc},
	pages = {10284},
	abstract = {Marine algae are instrumental in carbon cycling and atmospheric carbon dioxide (CO2) regulation. One group, coccolithophores, uses carbon to photosynthesize and to calcify, covering their cells with chalk platelets (coccoliths). How ocean acidification influences coccolithophore calcification is strongly debated, and the effects of carbonate chemistry changes in the geological past are poorly understood. This paper relates degree of coccolith calcification to cellular calcification, and presents the first records of size-normalized coccolith thickness spanning the last 14 Myr from tropical oceans. Degree of calcification was highest in the low-pH, high-CO2 Miocene ocean, but decreased significantly between 6 and 4 Myr ago. Based on this and concurrent trends in a new alkenone ep record, we propose that decreasing CO2 partly drove the observed trend via reduced cellular bicarbonate allocation to calcification. This trend reversed in the late Pleistocene despite low CO2, suggesting an additional regulator of calcification such as alkalinity. 1},
	keywords = {2016, rcc},
	issn = {2041-1723},
	doi = {10.1038/ncomms10284},
	url = {http://www.nature.com/doifinder/10.1038/ncomms10284},
	author = {Bolton, Clara T. and Hern{\'a}ndez-S{\'a}nchez, Mar{\'\i}a T. and Fuertes, Miguel-{\'A}ngel and Gonz{\'a}lez-Lemos, Sa{\'u}l and Abrevaya, Lorena and M{\'e}ndez-Vicente, Ana and Flores, Jos{\'e}-Abel and Probert, Ian and Giosan, Liviu and Johnson, Joel and Stoll, Heather M.}
}
@article {Mincer2016,
	title = {Methanol production by a broad phylogenetic array of marine phytoplankton.},
	journal = {PloS one},
	volume = {11},
	number = {3},
	year = {2016},
	note = {Publisher: Public Library of Science tex.mendeley-tags: 2016},
	month = {jan},
	pages = {e0150820},
	abstract = {Methanol is a major volatile organic compound on Earth and serves as an important carbon and energy substrate for abundant methylotrophic microbes. Previous geochemical surveys coupled with predictive models suggest that the marine contributions are exceedingly large, rivaling terrestrial sources. Although well studied in terrestrial ecosystems, methanol sources are poorly understood in the marine environment and warrant further investigation. To this end, we adapted a Purge and Trap Gas Chromatography/Mass Spectrometry (P\&T-GC/MS) method which allowed reliable measurements of methanol in seawater and marine phytoplankton cultures with a method detection limit of 120 nanomolar. All phytoplankton tested (cyanobacteria: Synechococcus spp. 8102 and 8103, Trichodesmium erythraeum, and Prochlorococcus marinus), and Eukarya (heterokont diatom: Phaeodactylum tricornutum, coccolithophore: Emiliania huxleyi, cryptophyte: Rhodomonas salina, and non-diatom heterokont: Nannochloropsis oculata) produced methanol, ranging from 0.8-13.7 micromolar in culture and methanol per total cellular carbon were measured in the ranges of 0.09-0.3\%. Phytoplankton culture time-course measurements displayed a punctuated production pattern with maxima near early stationary phase. Stabile isotope labeled bicarbonate incorporation experiments confirmed that methanol was produced from phytoplankton biomass. Overall, our findings suggest that phytoplankton are a major source of methanol in the upper water column of the world{\textquoteright}s oceans.},
	keywords = {2016},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0150820},
	url = {http://dx.doi.org/10.1371/journal.pone.0150820},
	author = {Mincer, Tracy J and Aicher, Athena C}
}
@article {Amiraux2016,
	title = {Paradoxical effects of temperature and solar irradiance on the photodegradation state of killed phytoplankton},
	journal = {Journal of Phycology},
	volume = {52},
	number = {3},
	year = {2016},
	note = {tex.mendeley-tags: 2016,rcc2022},
	month = {jun},
	pages = {475{\textendash}485},
	abstract = {The aim of this paper was to study the effects of temperature and irradiance on the photodegradation state of killed phytoplankton cells. For this purpose, killed cells of the diatom Chaetoceros neogracilis RCC2022 were irradiated (PAR radiations) at 36 and 446 J. s(-1.) m(-2) (for a same cumulative dose of irradiation energy) and at two temperatures (7 and 17{\textdegree}C). Analyses of specific lipid tracers (fatty acids and sterols) revealed that low temperatures and irradiances increased photooxidative damages of monounsaturated lipids (i.e. palmitoleic acid, cholesterol and campesterol). The high efficiency of type II photosensitized degradation processes was attributed to: (i) the relative preservation of the sensitizer (chlorophyll) at low irradiances allowing a longer production of singlet oxygen and (ii) the slow diffusion rate of singlet oxygen through membranes at low temperatures inducing more damages. Conversely, high temperatures and irradiances induced (i) a rapid degradation of the photosensitizer and a loss of singlet oxygen by diffusion outside the membranes (limiting type II photosensitized oxidation), and (ii) intense autoxidation processes degrading unsaturated cell lipids and oxidation products used as photodegradation tracers. Our results may likely explain the paradoxical relationship observed in situ between latitude and photodegradation state of phytoplankton cells. This article is protected by copyright. All rights reserved.},
	keywords = {2016, rcc2022},
	issn = {00223646},
	doi = {10.1111/jpy.12410},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/26992328 http://doi.wiley.com/10.1111/jpy.12410},
	author = {Amiraux, Remi and Jeanthon, Christian and Vaultier, Fr{\'e}d{\'e}ric and Rontani, Jean-Fran{\c c}ois},
	editor = {Mock, T.}
}
@article {Blanco-Ameijeiras2016,
	title = {Phenotypic variability in the coccolithophore emiliania huxleyi.},
	journal = {PloS one},
	volume = {11},
	number = {6},
	year = {2016},
	note = {ISBN: 10.1371/journal.pone.0157697 Publisher: Public Library of Science tex.mendeley-tags: 2016,rcc1212,rcc1215,rcc1216,rcc1228,rcc1238,rcc1255,rcc1258,rcc1259,rcc1731,rcc3553},
	month = {jan},
	pages = {e0157697},
	abstract = {Coccolithophores are a vital part of oceanic phytoplankton assemblages that produce organic matter and calcium carbonate (CaCO3) containing traces of other elements (i.e. Sr and Mg). Their associated carbon export from the euphotic zone to the oceans{\textquoteright} interior plays a crucial role in CO2 feedback mechanisms and biogeochemical cycles. The coccolithophore Emiliania huxleyi has been widely studied as a model organism to understand physiological, biogeochemical, and ecological processes in marine sciences. Here, we show the inter-strain variability in physiological and biogeochemical traits in 13 strains of E. huxleyi from various biogeographical provinces obtained from culture collections commonly used in the literature. Our results demonstrate that inter-strain genetic variability has greater potential to induce larger phenotypic differences than the phenotypic plasticity of single strains cultured under a broad range of variable environmental conditions. The range of variation found in physiological parameters and calcite Sr:Ca highlights the need to reconsider phenotypic variability in paleoproxy calibrations and model parameterizations to adequately translate findings from single strain laboratory experiments to the real ocean.},
	keywords = {2016, rcc1212, RCC1215, RCC1216, RCC1228, rcc1238, RCC1255, rcc1258, RCC1259, rcc1731, rcc3553},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0157697},
	url = {http://dx.doi.org/10.1371/journal.pone.0157697},
	author = {Blanco-Ameijeiras, Sonia and Lebrato, Mario and Stoll, Heather M and Iglesias-Rodriguez, Debora and M{\"u}ller, Marius N and M{\'e}ndez-Vicente, Ana and Oschlies, Andreas}
}
@article {Percopo2016b,
	title = {Pseudo-nitzschia arctica sp. nov., a new cold-water cryptic Pseudo-nitzschia species within the P. pseudodelicatissima complex},
	journal = {Journal of Phycology},
	volume = {52},
	number = {2},
	year = {2016},
	note = {tex.mendeley-tags: RCC2002,RCC2004,RCC2005,RCC2517},
	month = {apr},
	pages = {184{\textendash}199},
	abstract = {A new nontoxic Pseudo-nitzschia species belonging to the P. pseudodelicatissima complex, P. arctica, was isolated from different areas of the Arctic. The erection of P. arctica is mainly supported by molecular data, since the species shares identical ultrastructure with another species in the complex, P. fryxelliana, and represents a new case of crypticity within the genus. Despite their morphological similarity, the two species are not closely related in phylogenies based on LSU, ITS and rbcL. Interestingly, P. arctica is phylogenetically most closely related to P. granii and P. subcurvata, from which the species is, however, morphologically different. P. granii and P. subcurvata lack the central larger interspace which is one of the defining features of the P. pseudodelicatissima complex. The close genetic relationship between P. arctica and the two species P. granii and P. subcurvata is demonstrated by analysis of the secondary structure of ITS2 which revealed no compensatory base changes, two hemi-compensatory base changes, and two deletions in P. arctica with respect to the other two species. These findings emphasize that rates of morphological differentiation, molecular evolution and speciation are often incongruent for Pseudo-nitzschia species, resulting in a restricted phylogenetic value for taxonomic characters used to discriminate species. The description of a new cryptic species, widely distributed in the Arctic and potentially representing an endemic component of the Arctic diatom flora, reinforces the idea of the existence of noncosmopolitan Pseudo-nitzschia species and highlights the need for combined morphological and molecular analyses to assess the distributional patterns of phytoplankton species.},
	keywords = {RCC2002, RCC2004, RCC2005, RCC2517},
	issn = {00223646},
	doi = {10.1111/jpy.12395},
	url = {http://doi.wiley.com/10.1111/jpy.12395},
	author = {Percopo, Isabella and Ruggiero, Maria Valeria and Balzano, Sergio and Gourvil, Priscillia and Lundholm, Nina and Siano, Raffaele and Tammilehto, Anna and Vaulot, Daniel and Sarno, Diana},
	editor = {Mock, T.}
}
@article {Vannier2016,
	title = {Survey of the green picoalga Bathycoccus genomes in the global ocean},
	journal = {Scientific Reports},
	volume = {6},
	number = {1},
	year = {2016},
	note = {tex.mendeley-tags: 2016,RCC1105,RCC715,RCC716,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo},
	month = {dec},
	pages = {37900},
	keywords = {2016, RCC1105, RCC715, RCC716, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo},
	issn = {2045-2322},
	doi = {10.1038/srep37900},
	url = {http://www.nature.com/articles/srep37900},
	author = {Vannier, Thomas and Leconte, Jade and Seeleuthner, Yoann and Mondy, Samuel and Pelletier, Eric and Aury, Jean-Marc and de Vargas, Colomban and Sieracki, Michael and Iudicone, Daniele and Vaulot, Daniel and Wincker, Patrick and Jaillon, Olivier}
}
@article {Yau2016,
	title = {A viral immunity chromosome in the marine picoeukaryote, ostreococcus tauri},
	journal = {PLOS Pathogens},
	volume = {12},
	number = {10},
	year = {2016},
	note = {tex.mendeley-tags: 2016,RCC299,RCC4221,RCC809},
	month = {oct},
	pages = {e1005965},
	keywords = {2016, RCC299, RCC4221, RCC809},
	issn = {1553-7374},
	doi = {10.1371/journal.ppat.1005965},
	url = {http://dx.plos.org/10.1371/journal.ppat.1005965},
	author = {Yau, Sheree and Hemon, Claire and Derelle, Evelyne and Moreau, Herv{\'e} and Piganeau, Gwenael and Grimsley, Nigel},
	editor = {Ding, Shou-Wei}
}
@article {Varkey2015,
	title = {Effects of low temperature on tropical and temperate isolates of marine Synechococcus},
	journal = {The ISME Journal},
	year = {2015},
	note = {Publisher: Nature Publishing Group tex.mendeley-tags: rcc},
	pages = {1{\textendash}12},
	keywords = {rcc},
	issn = {1751-7362},
	doi = {10.1038/ismej.2015.179},
	url = {http://www.nature.com/doifinder/10.1038/ismej.2015.179},
	author = {Varkey, Deepa and Mazard, Sophie and Ostrowski, Martin and Tetu, Sasha G and Haynes, Paul and Paulsen, Ian T}
}
@article {Baudoux2015,
	title = {Interplay between the genetic clades of {\textexclamdown}i{\textquestiondown}Micromonas{\textexclamdown}/i{\textquestiondown} and their viruses in the Western English Channel.},
	journal = {Environmental microbiology reports},
	year = {2015},
	note = {tex.mendeley-tags: 2015,rcc,sbr?hyto$_\textrmd$ipo},
	month = {jun},
	abstract = {The genus Micromonas comprises distinct genetic clades that commonly dominate eukaryotic phytoplankton community from polar to tropical waters. This phytoplankter is also recurrently infected by abundant and genetically diverse prasinoviruses. Here we report on the interplay between prasinoviruses and Micromonas with regards to the genetic diversity of this host. During one year, we monitored the abundance of 3 clades of Micromonas and their viruses in the Western English Channel both in the environment, using clade-specific probes and flow cytometry, and in the laboratory, using clonal strains of Micromonas clades to assay for their viruses by plaque-forming units. We showed that the seasonal fluctuations of Micromonas clades were closely mirrored by the abundances of their corresponding viruses, indicating that the members of Micromonas genus are susceptible to viral infection, regardless of their genetic affiliation. The characterization of 45 viral isolates revealed that Micromonas clades are attacked by specific virus populations, which exhibit distinctive clade specificity, life strategies, and genetic diversity. However, some viruses can also cross-infect different host clades suggesting a mechanism of horizontal gene transfer within Micromonas genus. This study provides novel insights into the impact of viral infection for the ecology and evolution of the prominent phytoplankter Micromonas.},
	keywords = {2015, rcc, RCC?o?dd, sbr?hyto$_\textrmd$ipo},
	issn = {1758-2229},
	doi = {10.1111/1758-2229.12309},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/26081716},
	author = {Baudoux, A-C and Lebredonchel, H and Dehmer, H and Latimier, M and Edern, R and Rigaut-Jalabert, F and Ge, P and Guillou, L and Foulon, E and Bozec, Y and Cariou, T and Desdevises, Y and Derelle, E and Grimsley, N and Moreau, H and Simon, N}
}
@article {Kamikawa2015,
	title = {Multiple losses of photosynthesis in Nitzschia (Bacillariophyceae)},
	journal = {Phycological Research},
	volume = {63},
	year = {2015},
	note = {tex.mendeley-tags: rcc},
	pages = {19{\textendash}28},
	abstract = {In order to obtain insights into the evolution of colorless (apochlorotic) diatoms, we investigated newly established apochlorotic strains of Nitzschia spp. using light and electron microscopy and molecular phylogenetic analyses. Fluores- cence microscopic observations demonstrated that the apochlorotic diatoms lack chlorophylls. Transmission electron microscopy of two apochlorotic strains also demonstrated that their plastids lacked thylakoids; instead, having four- membrane-bound organelles without thylakoids, similar to nonphotosynthetic plastid remnants. From the apochlorotic strains, we also found plastid small subunit rRNA genes that were unusually long branched in phylogenetic analyses, as observed in other nonphotosynthetic plastids. Molecular phylogenetic analysis of the nucleus-encoded large subunit rRNA genes showed eight distinct lineages for apochlo- rotic diatoms. The eight apochlorotic lineages were not monophyletic, suggesting that the loss of photosynthesis took place multiple times independently within Nitzschia. Several diatoms, including Nitzschia spp., are mixotrophic, which is an expected mode of nutrition that would help explain the evolutionary switch from a photosynthetic lifestyle to a heterotrophic lifestyle. Key},
	keywords = {apochlorotic diatoms, genetic diversity, large subunit rrna, molecular phylogenetic analysis, nonphotosynthetic plastids, plastid 16s rrna, rcc},
	issn = {13220829},
	doi = {10.1111/pre.12072},
	url = {http://doi.wiley.com/10.1111/pre.12072},
	author = {Kamikawa, Ryoma and Yubuki, Naoji and Yoshida, Masaki and Taira, Misaka and Nakamura, Noriaki and Ishida, Ken-ichiro and Leander, Brian S. and Miyashita, Hideaki and Hashimoto, Tetsuo and Mayama, Shigeki and Inagaki, Yuji}
}
@article {MartinezMartinez2015,
	title = {New lipid envelope-containing dsDNA virus isolates infecting Micromonas pusilla reveal a separate phylogenetic group},
	journal = {Aquatic Microbial Ecology},
	volume = {74},
	year = {2015},
	note = {tex.mendeley-tags: rcc},
	pages = {17{\textendash}28},
	abstract = {Viral infection of phytoplankton has major implications for biochemical and energy cycles, community dynamics, and microbial evolution in the marine environment. The non-bloom forming picoplankter Micromonas pusilla, a significant component of the plankton community worldwide, is known to be susceptible to infection by both dsDNA and dsRNA viruses. Logically, comprehensive knowledge of the ecology of M. pusilla requires a better understanding of the div - ersity and infection mechanisms of their viruses. Here, we investigated 19 new M. pusilla-specific viruses (MpVs) isolated from different locations and years. We performed partial characterization of those MpVs including structural characteristics, genome size, phylogenetic analysis based on partial DNA polymerase gene sequences, host range, and stability at different temperatures and upon exposure to chloroform. Combined, these characteristics allowed classification of the MpVs into 2 groups. Exposure to chloroform led to loss of infectivity by all MpVs in one group, which sug- gests the presence of an outer lipid envelope. In addition, all except one of the members in that group formed a monophylogenetic clade that was distinct from all other MpV isolates. The distinc- tive characteristics of the 2 MpV groups suggest different infection strategies, which may have im- portant implications for the ecology of both host and virus populations in the environment. Knowl- edge gained from our study adds value to the MpV isolates as a scientific resource as it will aid in developing and testing in the laboratory new hypotheses about the ecological and biogeochemical implications of M. pusilla viral infection in the environment},
	keywords = {characterization, micromonas pusilla, ncldv, phycodnaviridae, rcc, RCC?o?dd, virus diversity},
	issn = {0948-3055},
	doi = {10.3354/ame01723},
	url = {http://www.int-res.com/abstracts/ame/v74/n1/p17-28/},
	author = {Mart{\'\i}nez Mart{\'\i}nez, J and Boere, A and Gilg, I and van Lent, Jwm and Witte, Hj and van Bleijswijk, Jdl and Brussaard, Cpd}
}
@article {Chambouvet2014,
	title = {Diverse molecular signatures for ribosomally {\textquoteright}active{\textquoteright} Perkinsea in marine sediments},
	journal = {BMC Microbiology},
	volume = {14},
	number = {1},
	year = {2014},
	note = {tex.mendeley-tags: 2014,rcc,sbr?hyto?ppo},
	pages = {110},
	abstract = {BACKGROUND:Perkinsea are a parasitic lineage within the eukaryotic superphylum Alveolata. Recent studies making use of environmental small sub-unit ribosomal RNA gene (SSU rDNA) sequencing methodologies have detected a significant diversity and abundance of Perkinsea-like phylotypes in freshwater environments. In contrast only a few Perkinsea environmental sequences have been retrieved from marine samples. Only two groups of Perkinsea have been cultured and morphologically described and these are parasites of marine molluscs or marine protists. These two marine groups form separate and distantly related phylogenetic clusters, composed of closely related lineages on SSU rDNA trees. Here, we test the hypothesis that Perkinsea are a hitherto under-sampled group in marine environments. Using 454 diversity {\textquoteright}tag{\textquoteright} sequencing we investigate the diversity and distribution of these protists in marine sediments and water column samples taken from the Deep Chlorophyll Maximum (DCM) and sub-surface using both DNA and RNA as the source template and sampling four European offshore locations.RESULTS:We detected the presence of 265 sequences branching with known Perkinsea, the majority of them recovered from marine sediments. Moreover, 27\% of these sequences were sampled from RNA derived cDNA libraries. Phylogenetic analyses classify a large proportion of these sequences into 38 cluster groups (including 30 novel marine cluster groups), which share less than 97\% sequence similarity as to suggest this diversity encompasses a range of biologically and ecologically distinct organisms.CONCLUSIONS:These results demonstrate that the Perkinsea lineage is considerably more diverse than previously detected in marine environments. This wide diversity of Perkinsea-like protists is largely retrieved in marine sediment with a significant proportion detected in RNA derived libraries suggesting this diversity represents ribosomally {\textquoteright}active{\textquoteright} and intact cells. Given the phylogenetic range of hosts infected by known Perkinsea parasites, these data suggest that Perkinsea either play a significant but hitherto unrecognized role as parasites in marine sediments and/or members of this group are present in the marine sediment possibly as part of the {\textquoteright}seed bank{\textquoteright} microbial community.},
	keywords = {2014, Biomarks, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1186/1471-2180-14-110},
	url = {http://www.biomedcentral.com/1471-2180/14/110},
	author = {Chambouvet, Aurelie and Berney, Cedric and Romac, Sarah and Audic, St{\'e}phane and Maguire, Finlay and de Vargas, Colomban and Richards, Thomas}
}
@article {hamilton_exposure_2014,
	title = {Exposure to bloom-like concentrations of two marine Synechococcus cyanobacteria (strains CC9311 and CC9902) differentially alters fish behaviour},
	journal = {Conservation Physiology},
	volume = {2},
	number = {cou020},
	year = {2014},
	abstract = {Coastal California experiences large-scale blooms of Synechococcus cyanobacteria, which are predicted to become more prevalent by the end of the 21st century as a result of global climate change. This study investigated whether exposure to bloom-like concentrations of two Synechococcus strains, CC9311 and CC9902, alters fish behaviour. Black perch (Embiotoca jacksoni) were exposed to Synechococcus strain CC9311 or CC9902 (1.5 {\texttimes} 106 cells ml-1) or to control seawater in experimental aquaria for 3 days. Fish movement inside a testing arena was then recorded and analysed using video camera-based motion-tracking software. Compared with control fish, fish exposed to CC9311 demonstrated a significant preference for the dark zone of the tank in the light{\textendash}dark test, which is an indication of increased anxiety. Furthermore, fish exposed to CC9311 also had a statistically significant decrease in velocity and increase in immobility and they meandered more in comparison to control fish. There was a similar trend in velocity, immobility and meandering in fish exposed to CC9902, but there were no significant differences in behaviour or locomotion between this group and control fish. Identical results were obtained with a second batch of fish. Additionally, in this second trial we also investigated whether fish would recover after a 3 day period in seawater without cyanobacteria. Indeed, there were no longer any significant differences in behaviour among treatments, demonstrating that the sp. CC9311-induced alteration of behaviour is reversible. These results demonstrate that blooms of specific marine Synechococcus strains can induce differential sublethal effects in fish, namely alterations light{\textendash}dark preference behaviour and motility.},
	keywords = {RCC1086},
	issn = {2051-1434},
	doi = {10.1093/conphys/cou020},
	url = {https://doi.org/10.1093/conphys/cou020},
	author = {Hamilton, T. J. and Paz-Yepes, J. and Morrison, R. A. and Palenik, B. and Tresguerres, M.}
}
@article {Biller2014,
	title = {Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus},
	journal = {Scientific Data},
	volume = {1},
	year = {2014},
	note = {Publisher: Nature Publishing Group tex.mendeley-tags: rcc},
	month = {sep},
	pages = {1{\textendash}11},
	abstract = {The marine cyanobacterium Prochlorococcus is the numerically dominant photosynthetic organism in the oligotrophic oceans, and a model system in marine microbial ecology. Here we report 27 new whole genome sequences (2 complete and closed; 25 of draft quality) of cultured isolates, representing five major phylogenetic clades of Prochlorococcus. The sequenced strains were isolated from diverse regions of the oceans, facilitating studies of the drivers of microbial diversity{\textemdash}both in the lab and in the field. To improve the utility of these genomes for comparative genomics, we also define pre-computed clusters of orthologous groups of proteins (COGs), indicating how genes are distributed among these and other publicly available Prochlorococcus genomes. These data represent a significant expansion of Prochlorococcus reference genomes that are useful for numerous applications in microbial ecology, evolution and oceanography.},
	keywords = {Environmental microbiology, genomics, rcc, RCC?o?dd},
	issn = {2052-4463},
	doi = {10.1038/sdata.2014.34},
	url = {http://www.nature.com/articles/sdata201434},
	author = {Biller, Steven J. and Berube, Paul M. and Berta-Thompson, Jessie W. and Kelly, Libusha and Roggensack, Sara E. and Awad, Lana and Roache-Johnson, Kathryn H. and Ding, Huiming and Giovannoni, Stephen J. and Rocap, Gabrielle and Moore, Lisa R. and Chisholm, Sallie W. and H. and Ding, Huiming and Giovannoni, Stephen J. and Moore, Lisa R. and Chisholm, Sallie W.}
}
@article {Marie2014,
	title = {An improved protocol for flow cytometry analysis of phytoplankton cultures and natural samples},
	journal = {Cytometry},
	volume = {85},
	year = {2014},
	note = {tex.mendeley-tags: RCC100,RCC1085,RCC114,RCC156,RCC168,RCC174,RCC180,RCC190,RCC263,RCC365,RCC400,RCC432,RCC446,RCC475,RCC480,RCC504,RCC745,RCC91},
	pages = {962{\textendash}968},
	abstract = {Preservation of cells, choice of fixative, storage, and thawing conditions are recurrent issues for the analysis of phytoplankton by flow cytometry. We examined the effects of addition of the surfactant Pluronic F68 to glutaraldehyde-fixed photosynthetic organisms in cultures and natural samples. In particular, we examined cell losses and modifications of side scatter (a proxy of cell size) and fluorescence of natural pigments. We found that different marine phytoplankton species react differently to the action of Pluronic F68. In particular, photosynthetic prokaryotes are less sensitive than eukaryotes. Observed cell losses may result from cell lysis or from cell adhesion to the walls of plastic tubes that are commonly used for flow cytometry analysis. The addition of the surfactant, Pluronic F68, has a positive effect on cells for long-term storage. We recommend to modify current protocols for preservation of natural marine planktonic samples, by fixing them with glutaraldehyde 0.25\% (final concentration) and adding Pluronic F68 at a final concentration of 0.01\% in the samples before preservation. Pluronic F68 also appears effective for preserving samples without fixation for subsequent sorting, e.g. for molecular biology analyses. (c) 2014 International Society for Advancement of Cytometry},
	keywords = {ASSEMBLE, MACUMBA, RCC100, RCC1085, RCC114, RCC156, RCC168, rcc174, RCC180, RCC190, RCC263, RCC365, RCC400, RCC432, RCC446, RCC475, RCC480, RCC504, RCC745, RCC91, RCC?o?dd, SBR$_\textrmP$hyto$_\textrmD$PO},
	doi = {10.1002/cyto.a.22517},
	author = {Marie, D and Rigaut-Jalabert, F and Vaulot, D}
}
@article {Duanmu2014,
	title = {Marine algae and land plants share conserved phytochrome signaling systems},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {111},
	number = {44},
	year = {2014},
	note = {tex.mendeley-tags: Micromonas,RCC,rcc},
	pages = {15827{\textendash}15832},
	abstract = {Phytochrome photosensors control a vast gene network in streptophyte plants, acting as master regulators of diverse growth and developmental processes throughout the life cycle. In contrast with their absence in known chlorophyte algal genomes and most sequenced prasinophyte algal genomes, a phytochrome is found in Micromonas pusilla, a widely distributed marine picoprasinophyte ({\textexclamdown}2 {\textmu}m cell diameter). Together with phytochromes identified from other prasinophyte lineages, we establish that prasinophyte and streptophyte phytochromes share core light-input and signaling-output domain architectures except for the loss of C-terminal response regulator receiver domains in the streptophyte phytochrome lineage. Phylogenetic reconstructions robustly support the presence of phytochrome in the common progenitor of green algae and land plants. These analyses reveal a monophyletic clade containing streptophyte, prasinophyte, cryptophyte, and glaucophyte phytochromes implying an origin in the eukaryotic ancestor of the Archaeplastida. Transcriptomic measurements reveal diurnal regulation of phytochrome and bilin chromophore biosynthetic genes in Micromonas. Expression of these genes precedes both light-mediated phytochrome redistribution from the cytoplasm to the nucleus and increased expression of photosynthesis-associated genes. Prasinophyte phytochromes perceive wavelengths of light transmitted farther through seawater than the red/far-red light sensed by land plant phytochromes. Prasinophyte phytochromes also retain light-regulated histidine kinase activity lost in the streptophyte phytochrome lineage. Our studies demonstrate that light-mediated nuclear translocation of phytochrome predates the emergence of land plants and likely represents a widespread signaling mechanism in unicellular algae.},
	keywords = {Micromonas, rcc},
	doi = {10.1073/pnas.1416751111},
	url = {http://www.pnas.org/content/111/44/15827.abstract},
	author = {Duanmu, Deqiang and Bachy, Charles and Sudek, Sebastian and Wong, Chee-Hong and Jimenez, Valeria and Rockwell, Nathan C and Martin, Shelley S and Ngan, Chew Yee and Reistetter, Emily N and van Baren, Marijke J and Price, Dana C and Wei, Chia-Lin and Reyes-Prieto, Adrian and Lagarias, J Clark and Worden, Alexandra Z}
}
@article {Keeling2014,
	title = {The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing},
	journal = {PLoS biology},
	volume = {12},
	number = {6},
	year = {2014},
	note = {Publisher: Public Library of Science tex.mendeley-tags: 2014,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {e1001889},
	abstract = {Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world{\textquoteright}s oceans},
	keywords = {2014, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	doi = {10.1371/journal.pbio.1001889},
	url = {http://dx.doi.org/10.1371\%252Fjournal.pbio.1001889},
	author = {Keeling, Patrick J and Burki, Fabien and Wilcox, Heather M and Allam, Bassem and Allen, Eric E and Amaral-Zettler, Linda A and Armbrust, E Virginia and Archibald, John M and Bharti, Arvind K and Bell, Callum J and Beszteri, Bank and Bidle, Kay D and Cameron, Connor T and Campbell, Lisa and Caron, David A and Cattolico, Rose Ann and Collier, Jackie L and Coyne, Kathryn and Davy, Simon K and Deschamps, Phillipe and Dyhrman, Sonya T and Edvardsen, Bente and Gates, Ruth D and Gobler, Christopher J and Greenwood, Spencer J and Guida, Stephanie M and Jacobi, Jennifer L and Jakobsen, Kjetill S and James, Erick R and Jenkins, Bethany and John, Uwe and Johnson, Matthew D and Juhl, Andrew R and Kamp, Anja and Katz, Laura A and Kiene, Ronald and Kudryavtsev, Alexander and Leander, Brian S and Lin, Senjie and Lovejoy, Connie and Lynn, Denis and Marchetti, Adrian and McManus, George and Nedelcu, Aurora M and Menden-Deuer, Susanne and Miceli, Cristina and Mock, Thomas and Montresor, Marina and Moran, Mary Ann and Murray, Shauna and Nadathur, Govind and Nagai, Satoshi and Ngam, Peter B and Palenik, Brian and Pawlowski, Jan and Petroni, Giulio and Piganeau, Gwenael and Posewitz, Matthew C and Rengefors, Karin and Romano, Giovanna and Rumpho, Mary E and Rynearson, Tatiana and Schilling, Kelly B and Schroeder, Declan C and Simpson, Alastair G B and Slamovits, Claudio H and Smith, David R and Smith, G Jason and Smith, Sarah R and Sosik, Heidi M and Stief, Peter and Theriot, Edward and Twary, Scott N and Umale, Pooja E and Vaulot, Daniel and Wawrik, Boris and Wheeler, Glen L and Wilson, William H and Xu, Yan and Zingone, Adriana and Worden, Alexandra Z}
}
@article {Morrissey2014,
	title = {A novel protein, ubiquitous in marine phytoplankton, concentrates iron at the cell surface and facilitates uptake},
	journal = {Current Biology},
	volume = {25},
	number = {3},
	year = {2014},
	note = {tex.mendeley-tags: rcc},
	month = {dec},
	pages = {364{\textendash}371},
	abstract = {Numerous cellular functions including respiration require iron. Plants and phytoplankton must also maintain the iron-rich photosynthetic electron transport chain, which most likely evolved in the iron-replete reducing environments of the Proterozoic ocean [1]. Iron bioavailability has drastically decreased in the contemporary ocean [1], most likely selecting for the evolution of efficient iron acquisition mechanisms among modern phytoplankton. Mesoscale iron fertilization experiments often result in blooms dominated by diatoms [2], indicating that diatoms have adaptations that allow survival in iron-limited waters and rapid multiplication when iron becomes available. Yet the genetic and molecular bases are unclear, as very few iron uptake genes have been functionally characterized from marine eukaryotic phytoplankton, and large portions of diatom iron starvation transcriptomes are genes encoding unknown functions [3{\textendash}5]. Here we show that the marine diatom Phaeodactylum tricornutum utilizes ISIP2a to concentrate Fe(III) at the cell surface as part of a novel, copper-independent and thermodynamically controlled iron uptake system. ISIP2a is expressed in response to iron limitation several days prior to the induction of ferrireductase activity, and it facilitates significant Fe(III) uptake during the initial response to Fe limitation. ISIP2a is able to directly bind Fe(III) and increase iron uptake when heterologously expressed, whereas knockdown of ISIP2a in P. tricornutum decreases iron uptake, resulting in impaired growth and chlorosis during iron limitation. ISIP2a is expressed by diverse marine phytoplankton, indicating that it is an ecologically significant adaptation to the unique nutrient composition of marine environments.},
	keywords = {rcc},
	issn = {09609822},
	doi = {10.1016/j.cub.2014.12.004},
	url = {http://www.sciencedirect.com/science/article/pii/S0960982214015632},
	author = {Morrissey, Joe and Sutak, Robert and Paz-Yepes, Javier and Tanaka, Atsuko and Moustafa, Ahmed and Veluchamy, Alaguraj and Thomas, Yann and Botebol, Hugo and Bouget, Fran{\c c}ois-Yves and McQuaid, Jeffrey B. and Tirichine, Leila and Allen, Andrew E. and Lesuisse, Emmanuel and Bowler, Chris}
}
@article {DelCampo2014,
	title = {The others: our biased perspective of eukaryotic genomes},
	journal = {Trends in Ecology \& Evolution},
	volume = {29},
	number = {5},
	year = {2014},
	note = {Publisher: Elsevier tex.mendeley-tags: RCC,rcc},
	pages = {252{\textendash}259},
	abstract = {?There is an important bias in eukaryotic knowledge, affecting cultures and genomes.?Eukaryotic genomics are biased towards multicellular organisms and their parasites.?A phylogeny-driven initiative is needed to overcome the eukaryotic genomic bias.?We propose to sequence neglected cultures and increase culturing efforts.?Single-cell genomics should be embraced as a tool to explore eukaryotic diversity.},
	keywords = {rcc},
	doi = {10.1016/j.tree.2014.03.006},
	url = {http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(14)00064-0},
	author = {del Campo, Javier and Sieracki, Michael E and Molestina, Robert and Keeling, Patrick and Massana, Ramon and Ruiz-Trillo, I{\~n}aki}
}
@article {Kashtan2014,
	title = {Single-cell genomics reveals hundreds of coexisting subpopulations in wild prochlorococcus},
	journal = {Science},
	volume = {344},
	number = {6182},
	year = {2014},
	note = {tex.mendeley-tags: RCC278},
	pages = {416{\textendash}420},
	abstract = {Extensive genomic diversity within coexisting members of a microbial species has been revealed through selected cultured isolates and metagenomic assemblies. Yet, the cell-by-cell genomic composition of wild uncultured populations of co-occurring cells is largely unknown. In this work, we applied large-scale single-cell genomics to study populations of the globally abundant marine cyanobacterium Prochlorococcus. We show that they are composed of hundreds of subpopulations with distinct {\textquotedblleft}genomic backbones,{\textquotedblright} each backbone consisting of a different set of core gene alleles linked to a small distinctive set of flexible genes. These subpopulations are estimated to have diverged at least a few million years ago, suggesting ancient, stable niche partitioning. Such a large set of coexisting subpopulations may be a general feature of free-living bacterial species with huge populations in highly mixed habitats.},
	keywords = {RCC278},
	doi = {10.1126/science.1248575},
	url = {http://www.sciencemag.org/content/344/6182/416.abstract},
	author = {Kashtan, Nadav and Roggensack, Sara E and Rodrigue, S{\'e}bastien and Thompson, Jessie W and Biller, Steven J and Coe, Allison and Ding, Huiming and Marttinen, Pekka and Malmstrom, Rex R and Stocker, Roman and Follows, Michael J and Stepanauskas, Ramunas and Chisholm, Sallie W}
}
@article {Dia2014,
	title = {Spatiotemporal changes in the genetic diversity of harmful algal blooms caused by the toxic dinoflagellate Alexandrium minutum},
	journal = {Molecular Ecology},
	volume = {23},
	number = {3},
	year = {2014},
	note = {tex.mendeley-tags: 2014,macumba,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {549{\textendash}560},
	abstract = {Organisms with sexual and asexual reproductive systems benefit from both types of reproduction. Sexual recombination generates new combinations of alleles, whereas clonality favours the spread of the fittest genotype through the entire population. Therefore, the rate of sexual vs. clonal reproduction has a major influence on the demography and genetic structure of natural populations. We addressed the effect of reproductive system on populations of the dinoflagellate Alexandrium minutum. More specifically, we monitored the spatiotemporal genetic diversity during and between bloom events in two estuaries separated by 150 km for two consecutive years. An analysis of population genetic patterns using microsatellite markers revealed surprisingly high genotypic and genetic diversity. Moreover, there was significant spatial and temporal genetic differentiation during and between bloom events. Our results demonstrate that (i) interannual genetic differentiation can be very high, (ii) estuaries are partially isolated during bloom events and (iii) genetic diversity can change rapidly during a bloom event. This rapid genetic change may reflect selective effects that are nevertheless not strong enough to reduce allelic diversity. Thus, sexual reproduction and/or migration may regularly erase any genetic structure produced within estuaries during a bloom event.},
	keywords = {2014, bloom dynamics, clonality, linkage disequilibrium, MACUMBA, population genetics, rcc, RCC?o?dd, resting cyst, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, sexual reproduction},
	doi = {10.1111/mec.12617},
	url = {http://dx.doi.org/10.1111/mec.12617},
	author = {Dia, A and Guillou, L and Mauger, S and Bigeard, E and Marie, D and Valero, M and Destombe, C}
}
@article {Monier2013,
	title = {Gene invasion in distant eukaryotic lineages: discovery of mutually exclusive genetic elements reveals marine biodiversity},
	journal = {The ISME journal},
	volume = {7},
	year = {2013},
	note = {Publisher: International Society for Microbial Ecology tex.mendeley-tags: Micromonas,RCC,rcc},
	pages = {1764{\textendash}1774},
	keywords = {horizontal transfer, inteins, invasive elements, metagenomics, Micromonas, polymorphic introns, rcc, viridiplantae},
	doi = {10.1038/ismej.2013.70},
	url = {http://dx.doi.org/10.1038/ismej.2013.70 10.1038/ismej.2013.70},
	author = {Monier, Adam and Sudek, Sebastian and Fast, Naomi M and Worden, Alexandra Z}
}
@article {Humily2013,
	title = {A gene island with two possible configurations is involved in chromatic acclimation in marine synechococcus},
	journal = {PLoS ONE},
	volume = {8},
	number = {12},
	year = {2013},
	note = {Publisher: Public Library of Science tex.mendeley-tags: 2013,macumba,rcc,sbr?hyto?app},
	pages = {e84459},
	abstract = {{\textexclamdown}p{\textquestiondown}{\textexclamdown}italic{\textquestiondown}Synechococcus{\textexclamdown}/italic{\textquestiondown}, the second most abundant oxygenic phototroph in the marine environment, harbors the largest pigment diversity known within a single genus of cyanobacteria, allowing it to exploit a wide range of light niches. Some strains are capable of Type IV chromatic acclimation (CA4), a process by which cells can match the phycobilin content of their phycobilisomes to the ambient light quality. Here, we performed extensive genomic comparisons to explore the diversity of this process within the marine {\textexclamdown}italic{\textquestiondown}Synechococcus{\textexclamdown}/italic{\textquestiondown} radiation. A specific gene island was identified in all CA4-performing strains, containing two genes ({\textexclamdown}italic{\textquestiondown}fciA{\textexclamdown}/italic{\textquestiondown}/b) coding for possible transcriptional regulators and one gene coding for a phycobilin lyase. However, two distinct configurations of this cluster were observed, depending on the lineage. CA4-A islands contain the {\textexclamdown}italic{\textquestiondown}mpeZ{\textexclamdown}/italic{\textquestiondown} gene, encoding a recently characterized phycoerythrobilin lyase-isomerase, and a third, small, possible regulator called {\textexclamdown}italic{\textquestiondown}fciC{\textexclamdown}/italic{\textquestiondown}. In CA4-B islands, the lyase gene encodes an uncharacterized relative of MpeZ, called MpeW. While {\textexclamdown}italic{\textquestiondown}mpeZ{\textexclamdown}/italic{\textquestiondown} is expressed more in blue light than green light, this is the reverse for {\textexclamdown}italic{\textquestiondown}mpeW{\textexclamdown}/italic{\textquestiondown}, although only small phenotypic differences were found among chromatic acclimaters possessing either CA4 island type. This study provides novel insights into understanding both diversity and evolution of the CA4 process.{\textexclamdown}/p{\textquestiondown}},
	keywords = {2013, MACUMBA, MicroB3, rcc, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto?app},
	doi = {10.1371/journal.pone.0084459},
	url = {http://dx.doi.org/10.1371/journal.pone.0084459},
	author = {Humily, Florian and Partensky, Fr{\'e}d{\'e}ric and Six, Christophe and Farrant, Gregory K and Ratin, Morgane and Marie, Dominique and Garczarek, Laurence}
}
@article {Collen2013,
	title = {Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {110},
	number = {13},
	year = {2013},
	note = {tex.mendeley-tags: RCC299},
	pages = {5247{\textendash}5252},
	abstract = {Red seaweeds are key components of coastal ecosystems and are economically important as food and as a source of gelling agents, but their genes and genomes have received little attention. Here we report the sequencing of the 105-Mbp genome of the florideophyte Chondrus crispus (Irish moss) and the annotation of the 9,606 genes. The genome features an unusual structure characterized by gene-dense regions surrounded by repeat-rich regions dominated by transposable elements. Despite its fairly large size, this genome shows features typical of compact genomes, e.g., on average only 0.3 introns per gene, short introns, low median distance between genes, small gene families, and no indication of large-scale genome duplication. The genome also gives insights into the metabolism of marine red algae and adaptations to the marine environment, including genes related to halogen metabolism, oxylipins, and multicellularity (microRNA processing and transcription factors). Particularly interesting are features related to carbohydrate metabolism, which include a minimalistic gene set for starch biosynthesis, the presence of cellulose synthases acquired before the primary endosymbiosis showing the polyphyly of cellulose synthesis in Archaeplastida, and cellulases absent in terrestrial plants as well as the occurrence of a mannosylglycerate synthase potentially originating from a marine bacterium. To explain the observations on genome structure and gene content, we propose an evolutionary scenario involving an ancestral red alga that was driven by early ecological forces to lose genes, introns, and intergenetic DNA; this loss was followed by an expansion of genome size as a consequence of activity of transposable elements.},
	keywords = {RCC299},
	doi = {10.1073/pnas.1221259110},
	url = {http://www.pnas.org/content/110/13/5247.abstract},
	author = {Collen, Jonas and Porcel, Betina and Carr{\'e}, Wilfrid and Ball, Steven G and Chaparro, Cristian and Tonon, Thierry and Barbeyron, Tristan and Michel, Gurvan and Noel, Benjamin and Valentin, Klaus and Elias, Marek and Artiguenave, Fran{\c c}ois and Arun, Alok and Aury, Jean-Marc and Barbosa-Neto, Jos{\'e} F and Bothwell, John H and Bouget, Fran{\c c}ois-Yves and Brillet, Loraine and Cabello-Hurtado, Francisco and Capella-Guti{\'e}rrez, Salvador and Charrier, B{\'e}n{\'e}dicte and Cladi{\`e}re, Lionel and Cock, J Mark and Coelho, Susana M and Colleoni, Christophe and Czjzek, Mirjam and Da Silva, Corinne and Delage, Ludovic and Denoeud, France and Deschamps, Philippe and Dittami, Simon M and Gabald{\'o}n, Toni and Gachon, Claire M M and Groisillier, Agn{\`e}s and Herv{\'e}, C{\'e}cile and Jabbari, Kamel and Katinka, Michael and Kloareg, Bernard and Kowalczyk, Nathalie and Labadie, Karine and Leblanc, Catherine and Lopez, Pascal J and McLachlan, Deirdre H and Meslet-Cladiere, Laurence and Moustafa, Ahmed and Nehr, Zofia and Nyvall Coll{\'e}n, Pi and Panaud, Olivier and Partensky, Fr{\'e}d{\'e}ric and Poulain, Julie and Rensing, Stefan A and Rousvoal, Sylvie and Samson, Gaelle and Symeonidi, Aikaterini and Weissenbach, Jean and Zambounis, Antonios and Wincker, Patrick and Boyen, Catherine}
}
@article {Chamnansinp2013,
	title = {Global diversity of two widespread, colony-forming diatoms of the marine plankton, Chaetoceros socialis (syn. C. radians ) and Chaetoceros gelidus sp. nov.},
	journal = {Journal of Phycology},
	volume = {49},
	number = {6},
	year = {2013},
	note = {ISBN: 1529-8817 tex.mendeley-tags: RCC3007},
	month = {dec},
	pages = {1128{\textendash}1141},
	keywords = {Arctic, Biogeography, Chaetoceros gelidus sp. nov., Chaetoceros radians, Chaetoceros socialis, Diatom, Distribution, Global, phylogeny, RCC3007},
	issn = {00223646},
	doi = {10.1111/jpy.12121},
	url = {http://doi.wiley.com/10.1111/jpy.12121},
	author = {Chamnansinp, Atchaneey and Li, Yang and Lundholm, Nina and Moestrup, {\O}jvind},
	editor = {Bowler, C.}
}
@article {Subirana2013,
	title = {Morphology, genome plasticity, and phylogeny in the genus ostreococcus reveal a cryptic species, o. mediterraneus sp. nov. (mamiellales, mamiellophyceae)},
	journal = {Protist},
	volume = {164},
	number = {5},
	year = {2013},
	note = {tex.mendeley-tags: RCC1112,RCC1114,RCC1117,RCC143,RCC1620,RCC1621,RCC1623,RCC1624,RCC2572,RCC2573,RCC2574,RCC2575,RCC2577,RCC2578,RCC2579,RCC2582,RCC2583,RCC2584,RCC2585,RCC2587,RCC2590,RCC344,RCC356,RCC393,RCC501,RCC745,RCC809},
	pages = {643{\textendash}659},
	abstract = {Coastal marine waters in many regions worldwide support abundant populations of extremely small (1-3 ??m diameter) unicellular eukaryotic green algae, dominant taxa including several species in the class Mamiellophyceae. Their diminutive size conceals surprising levels of genetic diversity and defies classical species{\textquoteright} descriptions. We present a detailed analysis within the genus Ostreococcus and show that morphological characteristics cannot be used to describe diversity within this group. Karyotypic analyses of the best-characterized species O. tauri show it to carry two chromosomes that vary in size between individual clonal lines, probably an evolutionarily ancient feature that emerged before species{\textquoteright} divergences within the Mamiellales. By using a culturing technique specifically adapted to members of the genus Ostreococcus, we purified {\textquestiondown}30 clonal lines of a new species, Ostreococcus mediterraneus sp. nov., previously known as Ostreococcus clade D, that has been overlooked in several studies based on PCR-amplification of genetic markers from environment-extracted DNA. Phylogenetic analyses of the S-adenosylmethionine synthetase gene, and of the complete small subunit ribosomal RNA gene, including detailed comparisons of predicted ITS2 (internal transcribed spacer 2) secondary structures, clearly support that this is a separate species. In addition, karyotypic analyses reveal that the chromosomal location of its ribosomal RNA gene cluster differs from other Ostreococcus clades.},
	keywords = {barcode, Chromosome, culture, ITS2, karyotype, picoeukaryote, rcc, RCC1112, RCC1114, RCC1117, RCC143, RCC1620, RCC1621, RCC1623, RCC1624, RCC2572, RCC2573, RCC2574, RCC2575, RCC2577, RCC2578, RCC2579, RCC2582, RCC2583, RCC2584, RCC2585, RCC2587, RCC2590, RCC344, RCC356, RCC393, rcc501, RCC745, RCC809, ribosomal gene},
	doi = {10.1016/j.protis.2013.06.002},
	url = {http://www.sciencedirect.com/science/article/pii/S1434461013000497},
	author = {Subirana, Lucie and P{\'e}quin, B{\'e}rang{\`e}re and Michely, St{\'e}phanie and Escande, Marie-Line and Meilland, Julie and Derelle, Evelyne and Marin, Birger and Piganeau, Gwenael and Desdevises, Yves and Moreau, Herv{\'e} and Grimsley, Nigel H}
}
@article {Vandepoele2013,
	title = {pico-PLAZA, a genome database of microbial photosynthetic eukaryotes},
	journal = {Environmental Microbiology},
	volume = {15},
	number = {8},
	year = {2013},
	note = {tex.mendeley-tags: Micromonas,rcc},
	pages = {2147{\textendash}2153},
	abstract = {With the advent of next generation genome sequencing, the number of sequenced algal genomes and transcriptomes is rapidly growing. Although a few genome portals exist to browse individual genome sequences, exploring complete genome information from multiple species for the analysis of user-defined sequences or gene lists remains a major challenge. pico-PLAZA is a web-based resource (http://bioinformatics.psb.ugent.be/pico-plaza/) for algal genomics that combines different data types with intuitive tools to explore genomic diversity, perform integrative evolutionary sequence analysis and study gene functions. Apart from homologous gene families, multiple sequence alignments, phylogenetic trees, Gene Ontology, InterPro and text-mining functional annotations, different interactive viewers are available to study genome organization using gene collinearity and synteny information. Different search functions, documentation pages, export functions and an extensive glossary are available to guide non-expert scientists. To illustrate the versatility of the platform, different case studies are presented demonstrating how pico-PLAZA can be used to functionally characterize large-scale EST/RNA-Seq data sets and to perform environmental genomics. Functional enrichments analysis of 16 Phaeodactylum tricornutum transcriptome libraries offers a molecular view on diatom adaptation to different environments of ecological relevance. Furthermore, we show how complementary genomic data sources can easily be combined to identify marker genes to study the diversity and distribution of algal species, for example in metagenomes, or to quantify intraspecific diversity from environmental strains.},
	keywords = {Micromonas, rcc},
	doi = {10.1111/1462-2920.12174},
	url = {http://dx.doi.org/10.1111/1462-2920.12174},
	author = {Vandepoele, Klaas and Van Bel, Michiel and Richard, Guilhem and Van Landeghem, Sofie and Verhelst, Bram and Moreau, Herv{\'e} and Van de Peer, Yves and Grimsley, Nigel and Piganeau, Gwenael}
}
@article {Guillou2013,
	title = {The protist ribosomal reference database (PR2): a catalog of unicellular eukaryote small SubUnit rRNA sequences with curated taxonomy},
	journal = {Nucleic Acids Research},
	volume = {41},
	year = {2013},
	note = {tex.mendeley-tags: 2013,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo},
	pages = {D597{\textendash}D604},
	keywords = {2013, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo},
	doi = {10.1093/nar/gks1160},
	author = {Guillou, Laure and Bachar, Dipankar and Audic, St{\'e}phane and Bass, David and Berney, Cedric and Bittner, Lucie and Boutte, Christophe and Burgaud, Gaetan and de Vargas, Colomban and Decelle, Johan and del Campo, Javier and Dolan, John and Dunthorn, Micah and Bente, Edvardsen and Holzmann, Maria and Kooistra, Wiebe H C F and Lara, Enrique and Lebescot, Noan and Logares, Ramiro and Mah{\'e}, Fr{\'e}d{\'e}ric and Massana, Ramon and Montresor, Marina and Morard, Raphael and Not, Fabrice and Pawlowski, Jan and Probert, Ian and Sauvadet, Anne-Laure and Siano, Raffaele and Stoeck, Thorsten and Vaulot, Daniel and Zimmermann, Pascal and Christen, Richard}
}
@article {Balzano2012,
	title = {Composition of the summer photosynthetic pico and nanoplankton communities in the Beaufort Sea assessed by T-RFLP and sequences of the 18S rRNA gene from flow cytometry sorted samples},
	journal = {The ISME journal},
	volume = {6},
	number = {8},
	year = {2012},
	note = {ISBN: 1751-7362 tex.mendeley-tags: 2012,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {1480{\textendash}1498},
	abstract = {The composition of photosynthetic pico and nanoeukaryotes was investigated in the North East Pacific and the Arctic Ocean with special emphasis on the Beaufort Sea during the MALINA cruise in summer 2009. Photosynthetic populations were sorted using flow cytometry based on their size and pigment fluorescence. Diversity of the sorted photosynthetic eukaryotes was determined using terminal-restriction fragment length polymorphism analysis and cloning/sequencing of the 18S ribosomal RNA gene. Picoplankton was dominated by Mamiellophyceae, a class of small green algae previously included in the prasinophytes: in the North East Pacific, the contribution of an Arctic Micromonas ecotype increased steadily northward becoming the only taxon occurring at most stations throughout the Beaufort Sea. In contrast, nanoplankton was more diverse: North Pacific stations were dominated by Pseudo-nitzschia sp. whereas those in the Beaufort Sea were dominated by two distinct Chaetoceros species as well as by Chrysophyceae, Pelagophyceae and Chrysochromulina spp.. This study confirms the importance of Arctic Micromonas within picoplankton throughout the Beaufort Sea and demonstrates that the photosynthetic picoeukaryote community in the Arctic is much less diverse than at lower latitudes. Moreover, in contrast to what occurs in warmer waters, most of the key pico- and nanoplankton species found in the Beaufort Sea could be successfully established in culture.},
	keywords = {2012, ASSEMBLE, Chaetoceros, MALINA, Pyramimonas, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, Souchotheque},
	issn = {1751-7362},
	doi = {10.1038/ismej.2011.213},
	author = {Balzano, Sergio and Marie, Dominique and Gourvil, Priscillia and Vaulot, Daniel}
}
@article {Balzano2012a,
	title = {Diversity of cultured photosynthetic flagellates in the North East Pacific and Arctic Oceans in summer},
	journal = {Biogeosciences},
	volume = {9},
	year = {2012},
	note = {tex.mendeley-tags: 2012,macumba,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {4553{\textendash}4571},
	keywords = {2012, ASSEMBLE, MACUMBA, MALINA, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	doi = {10.5194/bg-9-4553-2012},
	author = {Balzano, Sergio and Gourvil, Priscillia and Siano, Raffaele and Chanoine, M{\'e}lanie and Marie, Dominique and Lessard, Sylvie and Sarno, Diana and Vaulot, Daniel}
}
@article {Monier2012,
	title = {Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges},
	journal = {Environmental Microbiology},
	volume = {14},
	number = {1},
	year = {2012},
	note = {Publisher: Blackwell Publishing Ltd tex.mendeley-tags: Micromonas,RCC,rcc},
	pages = {162{\textendash}176},
	abstract = {Phosphate (PO4) is an important limiting nutrient in marine environments. Marine cyanobacteria scavenge PO4 using the high-affinity periplasmic phosphate binding protein PstS. The pstS gene has recently been identified in genomes of cyanobacterial viruses as well. Here, we analyse genes encoding transporters in genomes from viruses that infect eukaryotic phytoplankton. We identified inorganic PO4 transporter-encoding genes from the PHO4 superfamily in several virus genomes, along with other transporter-encoding genes. Homologues of the viral pho4 genes were also identified in genome sequences from the genera that these viruses infect. Genome sequences were available from host genera of all the phytoplankton viruses analysed except the host genus Bathycoccus. Pho4 was recovered from Bathycoccus by sequencing a targeted metagenome from an uncultured Atlantic Ocean population. Phylogenetic reconstruction showed that pho4 genes from pelagophytes, haptophytes and infecting viruses were more closely related to homologues in prasinophytes than to those in what, at the species level, are considered to be closer relatives (e.g. diatoms). We also identified PHO4 superfamily members in ocean metagenomes, including new metagenomes from the Pacific Ocean. The environmental sequences grouped with pelagophytes, haptophytes, prasinophytes and viruses as well as bacteria. The analyses suggest that multiple independent pho4 gene transfer events have occurred between marine viruses and both eukaryotic and bacterial hosts. Additionally, pho4 genes were identified in available genomes from viruses that infect marine eukaryotes but not those that infect terrestrial hosts. Commonalities in marine host-virus gene exchanges indicate that manipulation of host-PO4 uptake is an important adaptation for viral proliferation in marine systems. Our findings suggest that PO4-availability may not serve as a simple bottom-up control of marine phytoplankton.},
	keywords = {Micromonas, rcc},
	doi = {10.1111/j.1462-2920.2011.02576.x},
	url = {http://dx.doi.org/10.1111/j.1462-2920.2011.02576.x},
	author = {Monier, Adam and Welsh, Rory M and Gentemann, Chelle and Weinstock, George and Sodergren, Erica and Armbrust, E Virginia and Eisen, Jonathan A and Worden, Alexandra Z}
}
@article {Baines2012,
	title = {Significant silicon accumulation by marine picocyanobacteria},
	journal = {Nature Geoscience},
	volume = {5},
	number = {12},
	year = {2012},
	note = {arXiv: 9605103 [cs] ISBN: 1752-08941?752-0908 Publisher: Nature Publishing Group tex.arxivid: cs/9605103 tex.mendeley-tags: rcc1084,rcc1086,rcc752},
	pages = {886{\textendash}891},
	abstract = {The marine silicon cycle is thought to be intimately tied to the carbon cycle through its effect on the growth of diatoms. These unicellular algae form substantial blooms in cold, nutrient-rich waters. Their dense, siliceous cell walls promote the sinking of particulate matter, and all the carbon and nutrients contained therein1. As such, diatoms are thought to be the primary organisms responsible for the low levels of dissolved silicon observed in the surface ocean and the export of mineral silica to depth. Here, we use synchrotron X-ray fluorescence microscopy to determine the elemental composition of individual diatoms and cyanobacterial cells from the eastern equatorial Pacific and the Sargasso Sea.We show that cells of Synechococcus, a small unicellular marine cyanobacterium that dominates in nutrient-depleted waters2, can exhibit cellular ratios of silicon to sulphur, and silicon to phosphorus, approaching those detected in diatoms in the same location. Silicon accumulation was also observed in cultured Synechococcus strains. We estimate that the water column inventory of silicon in Synechococcus can exceed that of diatomsinsomecases.We suggest that picocyanobacteriamay exert a previously unrecognized influence on the oceanic silicon cycle, especially in nutrient-poorwaters.},
	keywords = {rcc1084, RCC1086, rcc752},
	issn = {1752-0894},
	doi = {10.1038/ngeo1641},
	url = {http://www.nature.com/doifinder/10.1038/ngeo1641},
	author = {Baines, Stephen B. and Twining, Benjamin S. and Brzezinski, Mark a. and Krause, Jeffrey W. and Vogt, Stefan and Assael, Dylan and McDaniel, Hannah}
}
@article {Thompson2012,
	title = {Unicellular cyanobacterium symbiotic with a single-celled eukaryotic alga},
	journal = {Science},
	volume = {337},
	number = {6101},
	year = {2012},
	note = {tex.mendeley-tags: 2012,microb3,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {1546{\textendash}1550},
	abstract = {Symbioses between nitrogen (N)2{\textendash}fixing prokaryotes and photosynthetic eukaryotes are important for nitrogen acquisition in N-limited environments. Recently, a widely distributed planktonic uncultured nitrogen-fixing cyanobacterium (UCYN-A) was found to have unprecedented genome reduction, including the lack of oxygen-evolving photosystem II and the tricarboxylic acid cycle, which suggested partnership in a symbiosis. We showed that UCYN-A has a symbiotic association with a unicellular prymnesiophyte, closely related to calcifying taxa present in the fossil record. The partnership is mutualistic, because the prymnesiophyte receives fixed N in exchange for transferring fixed carbon to UCYN-A. This unusual partnership between a cyanobacterium and a unicellular alga is a model for symbiosis and is analogous to plastid and organismal evolution, and if calcifying, may have important implications for past and present oceanic N2 fixation.},
	keywords = {2012, MicroB3, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	doi = {10.1126/science.1222700},
	url = {http://www.sciencemag.org/content/337/6101/1546.abstract},
	author = {Thompson, Anne W and Foster, Rachel A and Krupke, Andreas and Carter, Brandon J and Musat, Niculina and Vaulot, Daniel and Kuypers, Marcel M M and Zehr, Jonathan P}
}
@article {Karpowicz2011,
	title = {The GreenCut2 resource, a phylogenomically derived inventory of proteins specific to the plant lineage},
	journal = {Journal of Biological Chemistry},
	volume = {286},
	number = {24},
	year = {2011},
	note = {ISBN: 1083-351X (Electronic)0?021-9258 (Linking) tex.mendeley-tags: rcc745,rcc809},
	month = {jun},
	pages = {21427{\textendash}21439},
	abstract = {The plastid is a defining structure of photosynthetic eukaryotes and houses many plant-specific processes, including the light reactions, carbon fixation, pigment synthesis, and other primary metabolic processes. Identifying proteins associated with catalytic, structural, and regulatory functions that are unique to plastid-containing organisms is necessary to fully define the scope of plant biochemistry. Here, we performed phylogenomics on 20 genomes to compile a new inventory of 597 nucleus-encoded proteins conserved in plants and green algae but not in non-photosynthetic organisms. 286 of these proteins are of known function, whereas 311 are not characterized. This inventory was validated as applicable and relevant to diverse photosynthetic eukaryotes using an additional eight genomes from distantly related plants (including Micromonas, Selaginella, and soybean). Manual curation of the known proteins in the inventory established its importance to plastid biochemistry. To predict functions for the 52\% of proteins of unknown function, we used sequence motifs, subcellular localization, co-expression analysis, and RNA abundance data. We demonstrate that 18\% of the proteins in the inventory have functions outside the plastid and/or beyond green tissues. Although 32\% of proteins in the inventory have homologs in all cyanobacteria, unexpectedly, 30\% are eukaryote-specific. Finally, 8\% of the proteins of unknown function share no similarity to any characterized protein and are plant lineage-specific. We present this annotated inventory of 597 proteins as a resource for functional analyses of plant-specific biochemistry.},
	keywords = {RCC745, RCC809},
	issn = {0021-9258},
	doi = {10.1074/jbc.M111.233734},
	url = {http://www.jbc.org/cgi/doi/10.1074/jbc.M111.233734},
	author = {Karpowicz, Steven J. and Prochnik, Simon E. and Grossman, Arthur R. and Merchant, Sabeeha S.}
}
@article {Blot2011,
	title = {Light history influences the response of the marine cyanobacterium Synechococcus sp. WH7803 to oxidative stress},
	journal = {Plant Physiology},
	volume = {156},
	year = {2011},
	note = {ISBN: 1532-2548 (Electronic) 0032-0889 (Linking) tex.mendeley-tags: 2011,rcc,sbr?hyto?app},
	pages = {1934{\textendash}1954},
	abstract = {Marine Synechococcus undergo a wide range of environmental stressors, especially high and variable irradiance, which may induce oxidative stress through the generation of reactive oxygen species (ROS). While light and ROS could act synergistically on the impairment of photosynthesis, inducing photodamage and inhibiting photosystem II repair, acclimation to high irradiance is also thought to confer resistance to other stressors. To identify the respective roles of light and ROS in the photoinhibition process and detect a possible light-driven tolerance to oxidative stress, we compared the photophysiological and transcriptomic responses of Synechococcus sp. WH7803 acclimated to low (LL) or high light (HL) to oxidative stress, induced by hydrogen peroxide (H2O2) or methylviologen. While photosynthetic activity was much more affected in HL than in LL cells, only HL cells were able to recover growth and photosynthesis after addition of 25 microM H2O2. Depending upon light conditions and H2O2 concentration, the latter oxidizing agent induced photosystem II inactivation through both direct damages to the reaction centres and inhibition of its repair cycle. Although the global transcriptome response appeared similar in LL and HL cells, some processes were specifically induced in HL cells that seemingly helped them withstand oxidative stress, including enhancement of photoprotection and ROS detoxification, repair of ROS-driven damages and regulation of redox state. Detection of putative LexA binding sites allowed the identification of the putative LexA regulon, which was down-regulated in HL compared to LL cells, but up-regulated by oxidative stress under both growth irradiances.},
	keywords = {2011, rcc, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto?app},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=21670225},
	author = {Blot, N and Mella-Flores, D and Six, C and Lecorguille, G and Boutte, C and Peyrat, A and Monnier, A and Ratin, M and Gourvil, P and Campbell, D A and Garczarek, L}
}
@article {Gobler2011,
	title = {Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {108},
	number = {11},
	year = {2011},
	note = {ISBN: 0027-8424 tex.mendeley-tags: RCC,rcc},
	pages = {4352{\textendash}4357},
	abstract = {Harmful algal blooms (HABs) cause significant economic and ecological damage worldwide. Despite considerable efforts, a comprehensive understanding of the factors that promote these blooms has been lacking, because the biochemical pathways that facilitate their dominance relative to other phytoplankton within specific environments have not been identified. Here, biogeochemical measurements showed that the harmful alga Aureococcus anophagefferens outcompeted co-occurring phytoplankton in estuaries with elevated levels of dissolved organic matter and turbidity and low levels of dissolved inorganic nitrogen. We subsequently sequenced the genome of A. anophagefferens and compared its gene complement with those of six competing phytoplankton species identified through metaproteomics. Using an ecogenomic approach, we specifically focused on gene sets that may facilitate dominance within the environmental conditions present during blooms. A. anophagefferens possesses a larger genome (56 Mbp) and has more genes involved in light harvesting, organic carbon and nitrogen use, and encoding selenium-and metal-requiring enzymes than competing phytoplankton. Genes for the synthesis of microbial deterrents likely permit the proliferation of this species, with reduced mortality losses during blooms. Collectively, these findings suggest that anthropogenic activities resulting in elevated levels of turbidity, organic matter, and metals have opened a niche within coastal ecosystems that ideally suits the unique genetic capacity of A. anophagefferens and thus, has facilitated the proliferation of this and potentially other HABs.},
	keywords = {brown-tide blooms, comparative genomics, eutrophication, evolution, genome, genomics, long-island, marine-phytoplankton, multidrug, proteins, proteome, rcc, repeat, responses, san-francisco bay, signal-transduction, transporters},
	doi = {10.1073/pnas.1016106108},
	author = {Gobler, C J and Berry, D L and Dyhrman, S T and Wilhelm, S W and Salamov, A and Lobanov, A V and Zhang, Y and Collier, J L and Wurch, L L and Kustka, A B and Dill, B D and Shah, M and VerBerkmoes, N C and Kuo, A and Terry, A and Pangilinan, J and Lindquist, E A and Lucas, S and Paulsen, I T and Hattenrath-Lehmann, T K and Talmage, S C and Walker, E A and Koch, F and Burson, A M and Marcoval, M A and Tang, Y Z and LeCleir, G R and Coyne, K J and Berg, G M and Bertrand, E M and Saito, M A and Gladyshev, V N and Grigoriev, I V}
}
@article {Edvardsen2011,
	title = {Ribosomal DNA phylogenies and a morphological revision privide the basis for a new taxonomy of Prymnesiales (Haptophyta)},
	journal = {European Journal of Phycology},
	volume = {46},
	year = {2011},
	note = {tex.mendeley-tags: 2011,RCC1185,RCC1187,RCC1189,RCC1385,RCC1387,RCC1388,RCC1390,RCC1432,RCC1438,RCC1440,RCC1441,RCC1448,RCC1453,RCC2056,RCC2057,RCC2059,RCC2060,RCC2061,RCC2063,RCC2064,RCC305,RCC339,RCC3417,RCC3421,RCC3422,RCC3424,RCC3425,RCC3429,RCC406,rcc},
	pages = {202{\textendash}228},
	keywords = {2011, ASSEMBLE, rcc, RCC1185, RCC1187, RCC1189, RCC1385, RCC1387, RCC1388, RCC1390, RCC1432, RCC1438, RCC1440, RCC1441, RCC1448, RCC1453, RCC2056, RCC2057, RCC2059, RCC2060, RCC2061, RCC2063, RCC2064, RCC305, RCC339, RCC3417, RCC3421, RCC3422, RCC3424, RCC3425, RCC3429, RCC406, SBR$_\textrmP$hyto$_\textrmE$PPO},
	doi = {10.1080/09670262.2011.594095},
	author = {Edvardsen, B and Eikrem, W and Throndsen, J and A., Saez and Probert, I and Medlin, L}
}
@article {Beaufort2011,
	title = {Sensitivity of coccolithophores to carbonate chemistry and ocean acidification},
	journal = {Nature},
	volume = {476},
	year = {2011},
	note = {tex.mendeley-tags: 2011,rcc,sbr?hyto?ppo},
	pages = {80{\textendash}83},
	abstract = {Coccolithophores produce the major fraction of pelagic carbonate, a key component of the carbon cycle. The effect of elevated CO2 on their calcification is poorly understood. Culture experiments have yielded varied calcification responses to increased pCO2 between and within coccolithophore taxa. We used a novel automated method for pattern recognition and morphometric analysis to quantify the calcite mass of coccolithophores from {\textquestiondown}700 samples from present past (last 40-Kyr) oceans. Comparison of morphological data with ocean carbonate chemistry reconstructed in both space and time indicate decreasing calcification with increasing pCO2, and decreasing CO32. At pH {\textexclamdown}8.0, delicate Emiliania huxleyi are strongly affected by decalcification. However, highly calcified E. huxleyi morphotypes predominate in waters with lowest pH. This suggests that coccolithophore strains pre-adapted to future, more acidic oceans already populate regions of contemporary oceans. The future carbon feedback from coccolithophore calcification will depend on the genetic diversity and adaptability of coccolithophore populations.},
	keywords = {2011, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1038/nature10295},
	author = {Beaufort, L and Probert, I and de Garidel-Thoron, T and Bendif, E M and Ruiz-Pino, D and Metzl, N and Goyet, C and Buchet, N and Coupel, P and Grelaud, M and Rost, B and Rickaby, R E M and de Vargas, C}
}
@article {Franklin2010,
	title = {Dimethylsulphoniopropionate (DMSP), DMSP-lyase activity (DLA) and dimethylsulphide (DMS) in 10 species of coccolithophore},
	journal = {Marine Ecology-Progress Series},
	volume = {410},
	year = {2010},
	note = {ISBN: 0171-8630 tex.mendeley-tags: 2010,rcc},
	pages = {13{\textendash}23},
	abstract = {We investigated dimethylsulphoniopropionate (DMSP) quota (pg DMSP cell(-1)), intracellular DMSP concentration (mM), in vitro and in vivo DMSP-lyase activity (DLA) and dimethylsulphide (DMS) concentration in batch cultures of 10 species of coccolithophore. Species were chosen to span the phylogenetic and size range that exists within the coccolithophores. Our overall objective was to examine if Emiliania huxleyi, considered a {\textquoteright}model{\textquoteright} coccolithophore species, is representative in terms of DMSP, DLA and DMS, because other coccolithophores contribute substantially to phyto-plankton biomass and carbon fluxes in temperate and tropical waters. DMSP was found in all species, and DMSP quotas correlated significantly with cell volume, reflecting the fundamental physiological role of DMSP as a compatible solute in this group. This DMSP quota-cell volume relationship can be used to calculate the relative contribution of different species to total DMSP. Lowered nutrient availability (batch growth at a 10-fold lower nutrient concentration) did not significantly affect DMSP quota. In contrast to DMSP, DLA and DMS concentration were variable between the subset of species investigated. Coccolithophore DLA is known only in E. huxleyi and Gephyrocapsa oceanica, and we found DLA to be restricted to these closely related species. If DLA is restricted to a subset of coccolithophores, then those species are more likely to emit DMS directly in the sea. Our results indicate that in ecosystems where coccolithophores form stable populations, species other than E. huxleyi can make significant contributions to the particulate DMSP pool and hence to the amount of DMSP potentially available to the microbial loop.},
	keywords = {2010, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO},
	doi = {10.3354/meps08596},
	author = {Franklin, D J and Steinke, M and Young, J and Probert, I and Malin, G}
}
@article {Frada2010,
	title = {A guide to extant coccolithophores (Calcihaptophycidae, Haptophyta) using light microscopy.},
	journal = {Journal of Nannoplankton Research},
	volume = {31},
	year = {2010},
	note = {tex.mendeley-tags: 2010,rcc,sbr?hyto?ppo},
	pages = {58{\textendash}112},
	keywords = {2010, ? No DOI found, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	author = {Frada, Miguel and Young, Jeremy and Cach{\~a}o, M{\'a}rio and Lino, S{\'\i}lvia and Martins, Ana and Narciso, {\'A}urea and Probert, Ian and de Vargas, Colomban}
}
@article {Moreau2010,
	title = {Marine Prasinovirus genomes show low evolutionary divergence and acquisition of protein metabolism genes by horizontal gene transfer},
	journal = {Journal of Virology},
	volume = {84},
	number = {24},
	year = {2010},
	note = {ISBN: 0022-538X tex.mendeley-tags: RCC1105,RCC745},
	pages = {12555{\textendash}12563},
	abstract = {Although marine picophytoplankton are at the base of the global food chain, accounting for half of the planetary primary production, they are outnumbered 10 to 1 and are largely controlled by hugely diverse populations of viruses. Eukaryotic microalgae form a ubiquitous and particularly dynamic fraction of such plankton, with environmental clone libraries from coastal regions sometimes being dominated by one or more of the three genera Bathycoccus, Micromonas, and Ostreococcus (class Prasinophyceae). The complete sequences of two double-stranded (dsDNA) Bathycoccus, one dsDNA Micromonas, and one new dsDNA Ostreococcus virus genomes are described. Genome comparison of these giant viruses revealed a high degree of conservation, both for orthologous genes and for synteny, except for one 36-kb inversion in the Ostreococcus lucimarinus virus and two very large predicted proteins in Bathycoccus prasinos viruses. These viruses encode a gene repertoire of certain amino acid biosynthesis pathways never previously observed in viruses that are likely to have been acquired from lateral gene transfer from their host or from bacteria. Pairwise comparisons of whole genomes using all coding sequences with homologous counterparts, either between viruses or between their corresponding hosts, revealed that the evolutionary divergences between viruses are lower than those between their hosts, suggesting either multiple recent host transfers or lower viral evolution rates.},
	keywords = {RCC1105, RCC745},
	doi = {10.1128/jvi.01123-10},
	author = {Moreau, Herv{\'e} and Piganeau, Gwenael and Desdevises, Yves and Cooke, Richard and Derelle, Evelyne and Grimsley, Nigel}
}
@article {McDonald2010,
	title = {The mixed lineage nature of nitrogen transport and assimilation in marine eukaryotic phytoplankton: a case study of Micromonas},
	journal = {Molecular Biology and Evolution},
	volume = {27},
	number = {10},
	year = {2010},
	note = {tex.mendeley-tags: RCC299},
	pages = {2268{\textendash}2283},
	abstract = {The prasinophyte order Mamiellales contains several widespread marine picophytoplankton (<=2 ??m diameter) taxa, including Micromonas and Ostreococcus. Complete genome sequences are available for two Micromonas isolates, CCMP1545 and RCC299. We performed in silico analyses of nitrogen transporters and related assimilation genes in CCMP1545 and RCC299 and compared these with other green lineage organisms as well as Chromalveolata, fungi, bacteria, and archaea. Phylogenetic reconstructions of ammonium transporter (AMT) genes revealed divergent types contained within each Mamiellales genome. Some were affiliated with plant and green algal AMT1 genes and others with bacterial AMT2 genes. Land plant AMT2 genes were phylogenetically closer to archaeal transporters than to Mamiellales AMT2 genes. The Mamiellales represent the first green algal genomes to harbor AMT2 genes, which are not found in Chlorella and Chlamydomonas or the chromalveolate algae analyzed but are present in oomycetes. Fewer nitrate transporter (NRT) than AMT genes were identified in the Mamiellales. NRT1 was found in all but CCMP1545 and showed highest similarity to Mamiellales and proteobacterial NRTs. NRT2 genes formed a bootstrap-supported clade basal to other green lineage organisms. Several nitrogen-related genes were colocated, forming a nitrogen gene cluster. Overall, RCC299 showed the most divergent suite of nitrogen transporters within the various Mamiellales genomes, and we developed TaqMan quantitative polymerase chain reaction primer{\textendash}probes targeting a subset of these, as well as housekeeping genes, in RCC299. All those investigated showed expression either under standard growth conditions or under nitrogen depletion. Like other recent publications, our findings show a higher degree of {\textquotedblleft}mixed lineage gene affiliations{\textquotedblright} among eukaryotes than anticipated, and even the most phylogenetically anomalous versions appear to be functional. Nitrogen is often considered a regulating factor for phytoplankton populations. This study provides a springboard for exploring the use and functional diversification of inorganic nitrogen transporters and related genes in eukaryotic phytoplankton.},
	keywords = {rcc, RCC299},
	doi = {10.1093/molbev/msq113},
	url = {http://mbe.oxfordjournals.org/content/27/10/2268.abstract},
	author = {McDonald, Sarah M and Plant, Joshua N and Worden, Alexandra Z}
}
@article {Marin2010,
	title = {Molecular phylogeny and classification of the Mamiellophyceae class. nov. (Chlorophyta) based on sequence comparisons of the nuclear- and plastid-encoded rRNA operons},
	journal = {Protist},
	volume = {161},
	number = {2},
	year = {2010},
	note = {ISBN: 1618-0941 tex.mendeley-tags: Micromonas,rcc},
	pages = {304{\textendash}336},
	abstract = {Molecular phylogenetic analyses of the Mamiellophyceae classis nova, a ubiquitous group of largely picoplanktonic green algae comprising scaly and non-scaly prasinophyte unicells, were performed using single and concatenated gene sequence comparisons of the nuclear- and plastid-encoded rRNA operons. The study resolved all major clades within the class, identified molecular signature sequences for most clades through an exhaustive search for non-homoplasious synapomorphies [Marin et al. (2003): Protist 154: 99-145] and incorporated these signatures into the diagnoses of two novel orders, Monomastigales ord nov., Dolichomastigales ord. nov., and four novel families, Monomastigaceae fam. nov., Dolichomastigaceae fam. nov., Crustomastigaceae fam. nov., and Bathycoccaceae fam. nov., within a revised classification of the class. A database search for the presence of environmental rDNA sequences in the Monomastigales and Dolichomastigales identified an unexpectedly large genetic diversity of Monomastigales confined to freshwater, a novel clade (Dolicho$_\textrmB$) in the Dolichomastigaceae from deep sea sediments and a novel freshwater clade in the Crustomastigaceae. The Mamiellophyceae represent one of the ecologically most successful groups of eukaryotic, photosynthetic picoplankters in marine and likely also freshwater environments. Copyright 2009 Elsevier GmbH. All rights reserved.},
	keywords = {Index Medicus, Micromonas, rcc},
	doi = {10.1016/j.protis.2009.10.002},
	author = {Marin, Birger and Melkonian, Michael}
}
@article {Mohr2010,
	title = {A new chlorophyll d -containing cyanobacterium : evidence for niche adaptation in the genus Acaryochloris},
	journal = {The ISME journal},
	year = {2010},
	note = {tex.mendeley-tags: RCC,RCC1983,rcc},
	pages = {1456{\textendash}1469},
	abstract = {Chlorophyll d is a photosynthetic pigment that, based on chemical analyses, has only recently been recognized to be widespread in oceanic and lacustrine environments. However, the diversity of organisms harbouring this pigment is not known. Until now, the unicellular cyanobacterium Acaryochloris marina is the only characterized organism that uses chlorophyll d as a major photopigment. In this study we describe a new cyanobacterium possessing a high amount of chlorophyll d, which was isolated from waters around Heron Island, Great Barrier Reef (231 260 31.200 S, 1511 540 50.400 E). The 16S ribosomal RNA is 2\% divergent from the two previously described isolates of A. marina, which were isolated from waters around the Palau islands (Pacific Ocean) and the Salton Sea lake (California), suggesting that it belongs to a different clade within the genus Acaryochloris. An overview sequence analysis of its genome based on Illumina technology yielded 871 contigs with an accumulated length of 8 371965nt. Their analysis revealed typical features associated with Acaryochloris, such as an extended gene family for chlorophyll-binding proteins. However, compared with A. marina MBIC11017, distinct genetic, morphological and physiological differences were observed. Light saturation is reached at lower light intensities, Chl d/a ratios are less variable with light intensity and the phycobiliprotein phycocyanin is lacking, suggesting that cyanobacteria of the genus Acaryochloris occur in distinct ecotypes. These data characterize Acaryochloris as a niche-adapted cyanobacterium and show that more rigorous attempts are worthwhile to isolate, cultivate and analyse chlorophyll d-containing cyanobacteria for understanding the ecophysiology of these organisms. The},
	keywords = {acaryochloris, chlorophyll d, coral reef, cyanobacteria, microbial diversity, overview, rcc, RCC1983},
	doi = {10.1038/ismej.2010.67},
	author = {Mohr, Remus and Schliep, Martin and Kurz, Thorsten and Maldener, Iris and Adams, David G and Larkum, Anthony D W and Chen, Min and Hess, Wolfgang R}
}
@article {Siano2010,
	title = {Pelagodinium gen. nov. and P. beii comb. nov., a dinoflagellate symbiont of planktonic foraminifera},
	journal = {Protist},
	volume = {161},
	year = {2010},
	note = {tex.mendeley-tags: 2010,rcc,rcc1491,sbr?hyto?ppo},
	pages = {385{\textendash}399},
	abstract = {The taxonomic status of the free-living stage of the dinoflagellate Gymnodinium b{\'e}ii, symbiont of the foraminifer Orbulina universa, was reassessed on the basis of detailed morpho-genetic analyses. Electron microscopy observations revealed previously undescribed morphological features of the cell that are important for species recognition. The presence of a single elongated apical vesicle (EAV) ornamented with a row of small knobs, absent in species of the genus Gymnodinium, calls into question the current taxonomic position of the symbiont. The presence of a type E extraplastidial eyespot, the arrangement of the amphiesmal vesicles in series and the absence of trichocysts confirm the affiliation with other symbiotic dinoflagellates and certain genetically related non-symbiotic genera, all belonging to the order Suessiales. The arrangement of the series of vesicles of the analyzed strain is unique within the Suessiales, and the ultrastructure of the pyrenoid is different from other symbiotic dinoflagellates. A large subunit (LSU) rDNA phylogenetic analysis confirmed that the analyzed pelagic symbiont clusters in an independent, well-supported clade within the Suessiales with other sequences of symbiotic dinoflagellates extracted from planktonic foraminifera. Hence a novel genus, Pelagodinium gen. nov., is erected for this pelagic, symbiotic dinoflagellate, and Gymnodinium b{\'e}ii is reclassified as Pelagodinium b{\'e}ii.},
	keywords = {2010, ASSEMBLE, rcc, rcc1491, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1016/j.protis.2010.01.002},
	author = {Siano, R and Montresor, M and Probert, I and Not, F and de Vargas, C}
}
@article {Minge2010,
	title = {A phylogenetic mosaic plastid proteome and unusual plastid-targeting signals in the green-colored dinoflagellate Lepidodinium chlorophorum},
	journal = {BMC Evolutionary Biology},
	volume = {10},
	year = {2010},
	note = {ISBN: 1471-2148 tex.mendeley-tags: 2010,rcc},
	pages = {191},
	abstract = {Background: Plastid replacements through secondary endosymbioses include massive transfer of genes from the endosymbiont to the host nucleus and require a new targeting system to enable transport of the plastid-targeted proteins across 3-4 plastid membranes. The dinoflagellates are the only eukaryotic lineage that has been shown to have undergone several plastid replacement events, and this group is thus highly relevant for studying the processes involved in plastid evolution. In this study, we analyzed the phylogenetic origin and N-terminal extensions of plastid-targeted proteins from Lepidodinium chlorophorum, a member of the only dinoflagellate genus that harbors a green secondary plastid rather than the red algal-derived, peridinin-containing plastid usually found in photosynthetic dinoflagellates. Results: We sequenced 4,746 randomly picked clones from a L. chlorophorum cDNA library. 22 of the assembled genes were identified as genes encoding proteins functioning in plastids. Some of these were of green algal origin. This confirms that genes have been transferred from the plastid to the host nucleus of L. chlorophorum and indicates that the plastid is fully integrated as an organelle in the host. Other nuclear-encoded plastid-targeted protein genes, however, are clearly not of green algal origin, but have been derived from a number of different algal groups, including dinoflagellates, streptophytes, heterokonts, and red algae. The characteristics of N-terminal plastid-targeting peptides of all of these genes are substantially different from those found in peridinin-containing dinoflagellates and green algae. Conclusions: L. chlorophorum expresses plastid-targeted proteins with a range of different origins, which probably arose through endosymbiotic gene transfer (EGT) and horizontal gene transfer (HGT). The N-terminal extension of the genes is different from the extensions found in green alga and other dinoflagellates (peridinin- and haptophyte plastids). These modifications have likely enabled the mosaic proteome of L. chlorophorum.},
	keywords = {2010, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO},
	doi = {10.1186/1471-2148-10-191},
	author = {Minge, M A and Shalchian-Tabrizi, K and Torresen, O K and Takishita, K and Probert, I and Inagaki, Y and Klaveness, D and Jakobsen, K S}
}
@conference {Meusnier2009,
	title = {DNA barcoding of protists in culture collections},
	booktitle = {Third international barcode of life conference},
	year = {2009},
	note = {tex.mendeley-tags: RCC,rcc},
	address = {Mexico City},
	keywords = {? No DOI found, rcc, SBR$_\textrmP$hyto$_\textrmD$PO},
	author = {Meusnier, Isabelle and Andersen, Robert A and Stern, Rowena and Bertrand, C and Kuepper, Frithjof and Brand, Jerry and Friedl, Thomas and Blackburn, Susan and Dinh, Donna and Acreman, Judy and Sedl{\'a}{\v c}ek, Ivo and P{\v r}ibyl, Pavel and Jutson, Maria and Phang, Siew Moi and Melkonian, M and Karpov, S and Hajibabaei, Mehrdad}
}
@article {Scanlan2009,
	title = {Ecological genomics of marine picocyanobacteria},
	journal = {Microbiology and Molecular Biology Reviews},
	volume = {73},
	year = {2009},
	note = {tex.mendeley-tags: 2009,rcc,sbr?hyto?app},
	pages = {249{\textendash}299},
	keywords = {2009, rcc, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto?app},
	doi = {10.1128/MMBR.00035-08},
	author = {Scanlan, D J and Ostrowski, M and Mazard, S and Dufresne, A and Garczarek, L and Hess, W R and Post, A F and Hagemann, M and Paulsen, I and Partensky, F}
}
@article {Worden2009,
	title = {Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas},
	journal = {Science},
	volume = {324},
	year = {2009},
	note = {tex.mendeley-tags: RCC299,RCC827},
	pages = {268{\textendash}272},
	abstract = {The photosynthetic picoeukaryote Micromonas thrives from tropical to polar marine ecosystems and belongs to an anciently diverged sister clade to land plants. We sequenced genomes from two Micromonas isolates (22 Mb, CCMP1545; 21 Mb, RCC299) and the results improve understanding of their ecology and green-lineage evolution. Despite high 18S rDNA sequence identity, only 90\% of their predicted genes were shared. Novel intronic repeat elements in CCMP1545, otherwise found only in metagenomic data, and unique riboswitch arrangements emphasized their independent evolutionary paths. Phylogenomic profiles revealed putative ancestral features, but also indicated selection/acquisition processes are actively shaping a {\textquoteleft}unique{\textquoteright} gene pool in each differently than {\textquoteleft}core{\textquoteright} genes. Current climate-change trajectories are predicted to produce conditions favoring picophytoplankton, making Micromonas potential indicators of biological change in ocean ecosystems.},
	keywords = {rcc, RCC299, RCC827, SBR$_\textrmP$hyto$_\textrmD$PO, SBR$_\textrmP$hyto$_\textrmE$PPO},
	doi = {10.1126/science.1167222},
	author = {Worden, A Z and Lee, J.- H and Mock, T and Rouz{\'e}, P and Simmons, M P and Aerts, A L and Allen, A E and Cuvelier, M L and Derelle, E and Everett, M V and Foulon, E and Grimwood, J and Gundlach, H and Henrissat, B and Napoli, C and McDonald, S M and Parker, M S and Rombauts, S and Salamov, A and Von Dassow, P and Badger, J H and Coutinho, P M and Demir, E and Dubchak, I and Gentemann, C and Eikrem, W and Gready, J E and John, U and Lanier, W and Lindquist, E A and Lucas, S and Mayer, K F X and Moreau, H and Not, F and Otillar, R and Panaud, O and Pangilinan, J and Paulsen, I and Piegu, B and Poliakov, A and Robbens, S and Schmutz, J and Toulza, E and Wyss, T and Zelensky, A and Zhou, K and Armbrust, E V and Bhattacharya, D and Goodenough, U W and Van de Peer, Y and Grigoriev, I V}
}
@article {Wolhowe2009,
	title = {Growth phase dependent hydrogen isotopic fractionation in alkenone-producing haptophytes},
	journal = {Biogeosciences},
	volume = {6},
	number = {8},
	year = {2009},
	note = {ISBN: 1726-4170 tex.mendeley-tags: 2009,rcc},
	pages = {1681{\textendash}1694},
	abstract = {Recent works have investigated use of the hydrogen isotopic composition Of C-37 alkenones (delta D-K37s), lipid biomarkers of certain haptophyte microalgae, as an independent paleosalinity proxy. We discuss herein the factors impeding the success of such an application and identify the potential alternative use of delta D-K37s measurements as a proxy for non-thermal, physiological stress impacts on the U-37(K{\textquoteright}) paleotemperature index. Batch-culture experiments with the haptophyte Emiliania huxleyi (CCMP 1742) were conducted to determine the magnitude and variability of the isotopic contrasts between individual C-37 alkenones. Further experiments were conducted with Emiliania huxleyi (CCMP 1742) and Gephyrocapsa oceanica (PZ3-1) to determine whether, and to what extent, delta D-K37s varies between the physiological extremes of nutrient-replete exponential growth and nutrient-depleted senescence. Emiliania huxleyi was observed to exhibit an isotopic contrast between di- and tri-unsaturated C-37 alkenones (alpha(K37:3-K37:2)approximate to 0.97) that is nearly identical to that reported recently by others for environmental samples. Furthermore, this contrast appears to be constant with growth stage. The consistency of the offset across different growth stages suggests that a single, well-defined value for alpha(K37:3-K37:2) may exist and that its use in an isotope mass-balance will allow accurate determination of delta D values for individual alkenones without having to rely on time- and labor-intensive chemical separations. The isotopic fractionation between growth medium and C-37 alkenones was observed to increase dramatically upon the onset of nutrient-depletion-induced senescence, suggesting that delta D-K37s, may serve as an objective tool for recognizing and potentially correcting, at least semi-quantitatively, for the effects of nutrient stress on U-37(K{\textquoteright}) temperature records.},
	keywords = {2009, rcc, RCC1300, SBR$_\textrmP$hyto$_\textrmE$PPO},
	doi = {10.5194/bg-6-1681-2009},
	author = {Wolhowe, M D and Prahl, F G and Probert, I and Maldonado, M}
}
@article {Monier2009,
	title = {Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus},
	journal = {Genome Research},
	volume = {19},
	year = {2009},
	note = {tex.mendeley-tags: 2009,rcc,sbr?hyto?ppo},
	pages = {1441{\textendash}1449},
	keywords = {2009, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1101/gr.091686.109},
	author = {Monier, A and Pagarete, A and Allen, M J and Read, B A and de Vargas, C and Claverie, J M and Ogata, H}
}
@article {Jancek2008,
	title = {Clues about the genetic basis of adaptation emerge from comparing the proteomes of two Ostreococcus ecotypes (Chlorophyta, Prasinophyceae)},
	journal = {Molecular Biology and Evolution},
	volume = {25},
	number = {11},
	year = {2008},
	note = {Edition: 2008/08/06 ISBN: 1537-1719 (Electronic) 0737-4038 (Linking) tex.mendeley-tags: RCC,rcc},
	pages = {2293{\textendash}2300},
	abstract = {We compared the proteomes of two picoplanktonic Ostreococcus unicellular green algal ecotypes to analyze the genetic basis of their adaptation with their ecological niches. We first investigated the function of the species-specific genes using Gene Ontology databases and similarity searches. Although most species-specific genes had no known function, we identified several species-specific functions involved in various cellular processes, which could be critical for environmental adaptations. Additionally, we investigated the rate of evolution of orthologous genes and its distribution across chromosomes. We show that faster evolving genes encode significantly more membrane or excreted proteins, consistent with the notion that selection acts on cell surface modifications that is driven by selection for resistance to viruses and grazers, keystone actors of phytoplankton evolution. The relationship between GC content and chromosome length also suggests that both strains have experienced recombination since their divergence and that lack of recombination on the two outlier chromosomes could explain part of their peculiar genomic features, including higher rates of evolution.},
	keywords = {adaptation, Base Composition, Chlorophyta/*genetics, Ecosystem, Physiological/*genetics, Phytoplankton/genetics, Proteome/*genetics, rcc, Species Specificity},
	doi = {10.1093/molbev/msn168},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=18678753},
	author = {Jancek, S and Gourbiere, S and Moreau, H and Piganeau, G}
}
@article {Six2008,
	title = {Contrasting photoacclimation strategies in ecotypes of the eukayotic picoplankter {\textexclamdown}i{\textquestiondown}Ostreococcus{\textexclamdown}/i{\textquestiondown}},
	journal = {Limnology and Oceanography},
	volume = {53},
	year = {2008},
	note = {tex.mendeley-tags: 2008,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?app},
	pages = {255{\textendash}265},
	abstract = {Ostreococcus, the smallest known marine picoeukaryote, includes low- and high-light ecotypes. To determine the basis for niche partitioning between Ostreococcus sp. RCC809, isolated from the bottom of the tropical Atlantic euphotic zone, and the lagoon strain Ostreococcus tauri, we studied their photophysiologies under growth irradiances from 15 mmol photons m22 s21 to 800 mmol photons m22 s21 with a common nutrient replete regime. With increasing growth irradiance, both strains down-regulated cellular chlorophyll a and chlorophyll b (Chl a and Chl b) content, increased xanthophyll de-epoxidation correlated with nonphotochemical excitation quenching, and accumulated lutein. Ribulose-1,5-bisphosphate carboxylase/oxygenase content remained fairly stable. Under low-growth irradiances of 15{\textendash}80 mmol photons m22 s21, O. sp. RCC809 had equivalent or slightly higher growth rates, lower Chl a, a higher Chl b : Chl a ratio, and a larger photosystem II (PSII) antenna than O. tauri. O. tauri was more phenotypically plastic in response to growth irradiance, with a larger dynamic range in growth rate, Chl a, photosystem cell content, and cellular absorption cross-section of PSII. Estimating the amino acid and nitrogen costs for photoacclimation showed that the deep-sea oceanic O. sp. RCC809 relies largely on lower nitrogen cost changes in PSII antenna size to achieve a limited range of s-type light acclimation. O. sp. RCC809, however, suffers photoinhibition under higher light. This limited capacity for photoacclimation is compatible with the stable low-light and nutrient conditions at the base of the euphotic layer of the tropical Atlantic Ocean. In the more variable, high-nutrient, lagoon environment, O. tauri can afford to use a higher cost n-type acclimation of photosystem contents to exploit a wider range of light.},
	keywords = {2008, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, sbr?hyto?app},
	doi = {10.4319/lo.2008.53.1.0255},
	author = {Six, C and Finkel, Z V and Rodriguez, F and Marie, D and Partensky, F and Campbell, D A}
}
@article {Vaulot2008,
	title = {The diversity of small eukaryotic phytoplankton ({\textexclamdown}3 {\textmu}m) in marine ecosystems},
	volume = {32},
	number = {5},
	year = {2008},
	note = {Publication Title: FEMS microbiology reviews tex.mendeley-tags: 2008,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {795{\textendash}820},
	abstract = {Small cells dominate photosynthetic biomass and primary production in many marine ecosystems. Traditionally, picoplankton refers to cells {\textexclamdown} or =2 microm. Here we extend the size range of the organisms considered to 3 microm, a threshold often used operationally in field studies. While the prokaryotic component of picophytoplankton is dominated by two genera, Prochlorococcus and Synechococcus, the eukaryotic fraction is much more diverse. Since the discovery of the ubiquitous Micromonas pusilla in the early 1950s, just over 70 species that can be {\textexclamdown}3 microm have been described. In fact, most algal classes contain such species. Less than a decade ago, culture-independent approaches (in particular, cloning and sequencing, denaturing gradient gel electrophoresis, FISH) have demonstrated that the diversity of eukaryotic picoplankton is much more extensive than could be assumed from described taxa alone. These approaches revealed the importance of certain classes such as the Prasinophyceae but also unearthed novel divisions such as the recently described picobiliphytes. In the last couple of years, the first genomes of photosynthetic picoplankton have become available, providing key information on their physiological capabilities. In this paper, we discuss the range of methods that can be used to assess small phytoplankton diversity, present the species described to date, review the existing molecular data obtained on field populations, and end up by looking at the promises offered by genomics.},
	keywords = {2008, diversity, genomics, Marine ecosystems, Micro-algae, picoplankton, rcc, sbr?hyto$_\textrmd$ipo, taxonomy},
	author = {Vaulot, Daniel and Eikrem, Wenche and Viprey, Manon and Moreau, Herv{\'e}}
}
@article {Foulon2008,
	title = {Ecological niche partitioning in the picoplanktonic green alga Micromonas pusilla: evidence from environmental surveys using phylogenetic probes},
	journal = {Environmental Microbiology},
	volume = {10},
	year = {2008},
	note = {tex.mendeley-tags: 2008,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {2433{\textendash}2443},
	keywords = {2008, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	doi = {10.1111/j.1462-2920.2008.01673.x},
	author = {Foulon, E and Not, F and Jalabert, F and Cariou, T and Massana, R and Simon, N}
}
@article {Misumi2008,
	title = {Genome analysis and its significance in four unicellular algae, Cyanidioshyzon merolae, Ostreococcus tauri, Chlamydomonas reinhardtii, and Thalassiosira pseudonana},
	journal = {Journal of Plant Research},
	volume = {121},
	number = {1},
	year = {2008},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {3{\textendash}17},
	abstract = {Algae play a more important role than land plants in the maintenance of the global environment and productivity. Progress in genome analyses of these organisms means that we can now obtain information on algal genomes, global annotation and gene expression. The full genome information for several algae has already been analyzed. Whole genomes of the red alga Cyanidioshyzon merolae, the green algae Ostreococcus tauri and Chlamydomonas reinhardtii, and the diatom Thalassiosira pseudonana have been sequenced. Genome composition and the features of cells among the four algae were compared. Each alga maintains basic genes as photosynthetic eukaryotes and possesses additional gene groups to represent their particular characteristics. This review discusses and introduces the latest research that makes the best use of the particular features of each organism and the significance of genome analysis to study biological phenomena. In particular, examples of post-genome studies of organelle multiplication in C. merolae based on analyzed genome information are presented.},
	keywords = {rcc},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=18074102},
	author = {Misumi, O and Yoshida, Y and Nishida, K and Fujiwara, T and Sakajiri, T and Hirooka, S and Nishimura, Y and Kuroiwa, T}
}
@article {Derelle2008,
	title = {Life-cycle and genome of OtV5, a large DNA virus of the pelagic marine unicellular green alga {\textexclamdown}i{\textquestiondown}Ostreococcus tauri{\textexclamdown}/i{\textquestiondown}},
	journal = {PLoS ONE},
	volume = {3},
	number = {5},
	year = {2008},
	note = {Publisher: Public Library of Science tex.mendeley-tags: RCC,rcc},
	pages = {e2250},
	abstract = {Large DNA viruses are ubiquitous, infecting diverse organisms ranging from algae to man, and have probably evolved from an ancient common ancestor. In aquatic environments, such algal viruses control blooms and shape the evolution of biodiversity in phytoplankton, but little is known about their biological functions. We show that Ostreococcus tauri, the smallest known marine photosynthetic eukaryote, whose genome is completely characterized, is a host for large DNA viruses, and present an analysis of the life-cycle and 186,234 bp long linear genome of OtV5. OtV5 is a lytic phycodnavirus which unexpectedly does not degrade its host chromosomes before the host cell bursts. Analysis of its complete genome sequence confirmed that it lacks expected site-specific endonucleases, and revealed the presence of 16 genes whose predicted functions are novel to this group of viruses. OtV5 carries at least one predicted gene whose protein closely resembles its host counterpart and several other host-like sequences, suggesting that horizontal gene transfers between host and viral genomes may occur frequently on an evolutionary scale. Fifty seven percent of the 268 predicted proteins present no similarities with any known protein in Genbank, underlining the wealth of undiscovered biological diversity present in oceanic viruses, which are estimated to harbour 200Mt of carbon.},
	keywords = {rcc},
	doi = {10.1371/journal.pone.0002250},
	url = {http://dx.doi.org/10.1371/journal.pone.0002250},
	author = {Derelle, Evelyne and Ferraz, Conchita and Escande, Marie-Line and Eycheni{\'e}, Sophie and Cooke, Richard and Piganeau, Gwenael and Desdevises, Yves and Bellec, Laure and Moreau, Herv{\'e} and Grimsley, Nigel}
}
@article {Cardol2008,
	title = {An original adaptation of photosynthesis in the marine green alga Ostreococcus},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {105},
	number = {22},
	year = {2008},
	note = {tex.mendeley-tags: RCC745,RCC809},
	pages = {7881{\textendash}7886},
	abstract = {Adaptation of photosynthesis in marine environment has been examined in two strains of the green, picoeukaryote : OTH95, a surface/high-light strain, and RCC809, a deep-sea/low-light strain. Differences between the two strains include changes in the light-harvesting capacity, which is lower in OTH95, and in the photoprotection capacity, which is enhanced in OTH95. Furthermore, RCC809 has a reduced maximum rate of O evolution, which is limited by its decreased photosystem I (PSI) level, a possible adaptation to Fe limitation in the open oceans. This decrease is, however, accompanied by a substantial rerouting of the electron flow to establish an HO-to-HO cycle, involving PSII and a potential plastid plastoquinol terminal oxidase. This pathway bypasses electron transfer through the cytochrome complex and allows the pumping of {\^a}{\texteuro}{\oe}extra{\^a}{\texteuro} protons into the thylakoid lumen. By promoting the generation of a large {\^I}{\textquotedblright}pH, it facilitates ATP synthesis and nonphotochemical quenching when RCC809 cells are exposed to excess excitation energy. We propose that the diversion of electrons to oxygen downstream of PSII, but before PSI, reflects a common and compulsory strategy in marine phytoplankton to bypass the constraints imposed by light and/or nutrient limitation and allow successful colonization of the open-ocean marine environment.},
	keywords = {rcc, RCC745, RCC809},
	doi = {10.1073/pnas.0802762105},
	url = {http://www.pnas.org/content/105/22/7881.abstract},
	author = {Cardol, Pierre and Bailleul, Benjamin and Rappaport, Fabrice and Derelle, Evelyne and Baal, Daniel and Breyton, C{\'e}cile and Bailey, Shaun and Wollman, Francis Andr{\'e} and Grossman, Arthur and Moreau, Herv{\'e} and Finazzi, Giovanni}
}
@article {Bowler2008,
	title = {The Phaeodactylum genome reveals the evolutionary history of diatom genomes},
	journal = {Nature},
	volume = {456},
	number = {7219},
	year = {2008},
	note = {Publisher: Macmillan Publishers Limited. All rights reserved tex.mendeley-tags: 2008,rcc,sbr?hyto?ppo},
	pages = {239{\textendash}244},
	keywords = {2008, rcc, SBR$_\textrmP$hyto$_\textrmE$PPOdipo, sbr?hyto?ppo},
	doi = {10.1038/nature07410},
	url = {http://dx.doi.org/10.1038/nature07410 http://www.nature.com/nature/journal/v456/n7219/suppinfo/nature07410_S1.html},
	author = {Bowler, Chris and Allen, Andrew E and Badger, Jonathan H and Grimwood, Jane and Jabbari, Kamel and Kuo, Alan and Maheswari, Uma and Martens, Cindy and Maumus, Florian and Otillar, Robert P and Rayko, Edda and Salamov, Asaf and Vandepoele, Klaas and Beszteri, Bank and Gruber, Ansgar and Heijde, Marc and Katinka, Michael and Mock, Thomas and Valentin, Klaus and Verret, Frederic and Berges, John A and Brownlee, Colin and Cadoret, Jean-Paul and Chiovitti, Anthony and Choi, Chang Jae and Coesel, Sacha and De Martino, Alessandra and Detter, J Chris and Durkin, Colleen and Falciatore, Angela and Fournet, Jerome and Haruta, Miyoshi and Huysman, Marie J J and Jenkins, Bethany D and Jiroutova, Katerina and Jorgensen, Richard E and Joubert, Yolaine and Kaplan, Aaron and Kroger, Nils and Kroth, Peter G and La Roche, Julie and Lindquist, Erica and Lommer, Markus and Martin-Jezequel, Veronique and Lopez, Pascal J and Lucas, Susan and Mangogna, Manuela and McGinnis, Karen and Medlin, Linda K and Montsant, Anton and Secq, Marie-Pierre Oudot-Le and Napoli, Carolyn and Obornik, Miroslav and Parker, Micaela Schnitzler and Petit, Jean-Louis and Porcel, Betina M and Poulsen, Nicole and Robison, Matthew and Rychlewski, Leszek and Rynearson, Tatiana A and Schmutz, Jeremy and Shapiro, Harris and Siaut, Magali and Stanley, Michele and Sussman, Michael R and Taylor, Alison R and Vardi, Assaf and von Dassow, Peter and Vyverman, Wim and Willis, Anusuya and Wyrwicz, Lucjan S and Rokhsar, Daniel S and Weissenbach, Jean and Armbrust, E Virginia and Green, Beverley R and Van de Peer, Yves and Grigoriev, Igor V}
}
@article {Rodriguez2008,
	title = {Phylogenetic and morphological characterization of the green algae infesting blue mussel Mytilus edulis in the North and South Atlantic},
	journal = {Diseases of Aquatic Organisms},
	volume = {81},
	year = {2008},
	note = {tex.mendeley-tags: RCC894},
	pages = {231{\textendash}240},
	keywords = {rcc, RCC894, SBR$_\textrmP$hyto$_\textrmD$PO},
	doi = {10.3354/dao01956},
	author = {Rodriguez, F and Feist, S W and Guillou, L and Harkestad, L S and Bateman, K and Renault, T and Mortensen, S}
}
@article {LeGall2008,
	title = {Picoplankton diversity in the south-east pacific ocean from cultures},
	journal = {Biogeosciences},
	volume = {5},
	year = {2008},
	note = {tex.mendeley-tags: 2008,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?app},
	pages = {203{\textendash}214},
	keywords = {2008, PICOFUNPAC, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, sbr?hyto?app},
	doi = {10.5194/bg-5-203-2008},
	author = {Le Gall, F and Rigaut-Jalabert, F and Marie, D and Garczareck, L and Viprey, M and Godet, A and Vaulot, D}
}
@article {Robbens2007,
	title = {The complete chloroplast and mitochondrial DNA sequence of Ostreococcus tauri: organelle genomes of the smallest eukaryote are examples of compaction},
	journal = {Molecular Biology and Evolution},
	volume = {24},
	number = {4},
	year = {2007},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {956{\textendash}968},
	abstract = {The complete nucleotide sequence of the mt (mitochondrial) and cp (chloroplast) genomes of the unicellular green alga Ostreococcus tauri has been determined. The mt genome assembles as a circle of 44,237 bp and contains 65 genes. With an overall average length of only 42 bp for the intergenic regions, this is the most gene-dense mt genome of all Chlorophyta. Furthermore, it is characterized by a unique segmental duplication, encompassing 22 genes and covering 44\% of the genome. Such a duplication has not been observed before in green algae, although it is also present in the mt genomes of higher plants. The quadripartite cp genome forms a circle of 71,666 bp, containing 86 genes divided over a larger and a smaller single-copy region, separated by 2 inverted repeat sequences. Based on genome size and number of genes, the Ostreococcus cp genome is the smallest known among the green algae. Phylogenetic analyses based on a concatenated alignment of cp, mt, and nuclear genes confirm the position of O. tauri within the Prasinophyceae, an early branch of the Chlorophyta.},
	keywords = {rcc},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17251180},
	author = {Robbens, S and Derelle, E and Ferraz, C and Wuyts, J and Moreau, H and Van de Peer, Y}
}
@article {Kettler2007,
	title = {Patterns and implications of gene gain and loss in the evolution of Prochlorococcus},
	journal = {PLoS genetics},
	volume = {3},
	year = {2007},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {e231},
	keywords = {rcc},
	doi = {10.1371/journal.pgen.0030231},
	author = {Kettler, G and Martiny, A C and Huang, K and Zucker, J and Coleman, M L and Rodrigue, S and Chen, F and Lapidus, A and Ferriera, S and Johnson, J and Steglich, C and Church, G and Richardson, P and Chisholm, S W}
}
@article {Piganeau2007,
	title = {Screening the Sargasso Sea metagenome for data to investigate genome evolution in Ostreococcus (Prasinophyceae, Chlorophyta)},
	journal = {Gene},
	volume = {406},
	year = {2007},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {184{\textendash}190},
	abstract = {The Sargasso Sea water shotgun sequencing unveiled an unprecedented glimpse of marine prokaryotic diversity and gene content. The sequence data was gathered from 0.8 ??m filtered surface water extracts, and revealed picoeukaryotic (cell size {\textexclamdown} 2 ??m) sequences alongside the prokaryotic data. We used the available genome sequence of the picoeukaryote Ostreococcus tauri (Prasinophyceae, Chlorophyta) as a benchmark for the eukaryotic sequence content of the Sargasso Sea metagenome. Sequence data from at least two new Ostreococcus strains were identified and analyzed, and showed a bias towards higher coverage of the AT-rich organellar genomes. The Ostreococcus nuclear sequence data retrieved from the Sargasso metagenome is divided onto 731 scaffolds of average size 3917 bp, and covers 23\% of the complete nuclear genome and 14\% of the total number of protein coding genes in O. tauri. We used this environmental Ostreococcus sequence data to estimate the level of constraint on intronic and intergenic sequences in this compact genome.},
	keywords = {rcc},
	doi = {10.1016/j.gene.2007.09.015},
	author = {Piganeau, G and Moreau, H}
}
@article {Medlin2007,
	title = {A taxonomic review of the genus Phaeocystis},
	journal = {Biogeochemistry},
	volume = {83},
	number = {1-3},
	year = {2007},
	note = {ISBN: 0085-4417 tex.mendeley-tags: rcc3541},
	pages = {3{\textendash}18},
	abstract = {Phaeocystis is recognized both as a nuisance and as an ecologicallyphytoplankton species. Its polymorphic life cycle with bothand flagellated cells causes many taxonomic problems. Sequenceamong 22 isolates representing a global distribution of thehas been compared using three molecular markers. The-1,5-bisphosphate carboxylase/oxygenase (RUBISCO) spacer is tooto resolve species. The most conserved 18S ribosomalacid (rDNA) analysis suggests that an undescribedPhaeocystis sp. (isolate PLY559) is a sister taxon to theunicellular Phaeocystis jahnii; this clade branched priorthe divergence of all other Phaeocystis species, including theones. The internal transcribed spacer (ITS) region showsvariation that some spatial population structure can be, at least in P. antarctica. P. globosa and P. pouchetii havedifferent ITS copies, suggestive of cryptic species that areable to hybridize. A molecular clock has been constructed thatthe divergence of the cold water colonial forms from the-water colonial forms to be about 30 Ma and the divergence of P.and P. pouchetii to be about 15 Ma. A short description ofcolonial stage and the flagellated stage for each formallyspecies is provided. Morphological information is alsoon a number of undescribed species. These include the strain559, consisting of non-colonial cells with peculiar tubular, a second non-colonial species from the north westernSea producing a lot of mucus, and a colonial species with-less flagellates found in Italian waters. In addition, threemorphotypes with scales different from those of P.were reported in the literature from Antarctic waters. Theemerging from both molecular and morphological data is that theof species in the genus is still underestimated and that crypticpseudocryptic diversity requires a sound assessment in futureof this genus. Based on all published observations, an emendedof the genus is provided.},
	keywords = {Molecular clock, P. cordata, P. globosa, P. jahnii, P. pouchetii, P. scrobiculata, Phaeocystis antarctica, rcc3541, rDNA analysis},
	issn = {01682563},
	doi = {10.1007/s10533-007-9087-1},
	author = {Medlin, Linda and Zingone, Adriana}
}
@article {Palenik2007,
	title = {The tiny eukaryote \textit{Ostreococcus provides genomic insights into the paradox of plankton speciation},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {104},
	number = {18},
	year = {2007},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {7705{\textendash}7710},
	abstract = {The smallest known eukaryotes, at approximately 1-mum diameter, are Ostreococcus tauri and related species of marine phytoplankton. The genome of Ostreococcus lucimarinus has been completed and compared with that of O. tauri. This comparison reveals surprising differences across orthologous chromosomes in the two species from highly syntenic chromosomes in most cases to chromosomes with almost no similarity. Species divergence in these phytoplankton is occurring through multiple mechanisms acting differently on different chromosomes and likely including acquisition of new genes through horizontal gene transfer. We speculate that this latter process may be involved in altering the cell-surface characteristics of each species. In addition, the genome of O. lucimarinus provides insights into the unique metal metabolism of these organisms, which are predicted to have a large number of selenocysteine-containing proteins. Selenoenzymes are more catalytically active than similar enzymes lacking selenium, and thus the cell may require less of that protein. As reported here, selenoenzymes, novel fusion proteins, and loss of some major protein families including ones associated with chromatin are likely important adaptations for achieving a small cell size.},
	keywords = {rcc},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17460045},
	author = {Palenik, B and Grimwood, J and Aerts, A and Rouz{\'e}, P and Salamov, A and Putnam, N and Dupont, C and Jorgensen, R and Derelle, E and Rombauts, S and Zhou, K and Otillar, R and Merchant, S S and Podell, S and Gaasterland, T and Napoli, C and Gendler, K and Manuell, A and Tai, V and Vallon, O and Piganeau, G and Jancek, S and Heijde, M and Jabbari, K and Bowler, C and Lohr, M and Robbens, S and Werner, G and Dubchak, I and Pazour, G J and Ren, Q and Paulsen, I and Delwiche, C and Schmutz, J and Rokhsar, D and Van de Peer, Y and Moreau, H and Grigoriev, I V}
}
@article {Derelle2006,
	title = {Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {103},
	number = {31},
	year = {2006},
	note = {tex.mendeley-tags: RCC745},
	pages = {11647{\textendash}11652},
	abstract = {The green lineage is reportedly 1,500 million years old, evolving shortly after the endosymbiosis event that gave rise to early photosynthetic eukaryotes. In this study, we unveil the complete genome sequence of an ancient member of this lineage, the unicellular green alga Ostreococcus tauri (Prasinophyceae). This cosmopolitan marine primary producer is the world{\textquoteright}s smallest free-living eukaryote known to date. Features likely reflecting optimization of environmentally relevant pathways, including resource acquisition, unusual photosynthesis apparatus, and genes potentially involved in C4 photosynthesis, were observed, as was downsizing of many gene families. Overall, the 12.56-Mb nuclear genome has an extremely high gene density, in part because of extensive reduction of intergenic regions and other forms of compaction such as gene fusion. However, the genome is structurally complex. It exhibits previously unobserved levels of heterogeneity for a eukaryote. Two chromosomes differ structurally from the other eighteen. Both have a significantly biased G+C content, and, remarkably, they contain the majority of transposable elements. Many chromosome 2 genes also have unique codon usage and splicing, but phylogenetic analysis and composition do not support alien gene origin. In contrast, most chromosome 19 genes show no similarity to green lineage genes and a large number of them are specialized in cell surface processes. Taken together, the complete genome sequence, unusual features, and downsized gene families, make O. tauri an ideal model system for research on eukaryotic genome evolution, including chromosome specialization and green lineage ancestry.},
	keywords = {rcc, RCC745, SBR$_\textrmP$hyto},
	doi = {10.1073/pnas.0604795103},
	url = {http://www.pnas.org/cgi/content/abstract/103/31/11647},
	author = {Derelle, Evelyne and Ferraz, Conchita and Rombauts, Stephane and Rouze, Pierre and Worden, Alexandra Z and Robbens, Steven and Partensky, Fr{\'e}d{\'e}ric and Degroeve, Sven and Echeynie, Sophie and Cooke, Richard and Saeys, Yvan and Wuyts, Jan and Jabbari, Kamel and Bowler, Chris and Panaud, Olivier and Piegu, Benoit and Ball, Steven G and Ral, Jean-Philippe and Bouget, Fran{\c c}ois-Yves and Piganeau, Gwenael and De Baets, Bernard and Picard, Andr{\'e} and Delseny, Michel and Demaille, Jacques and Van de Peer, Yves and Moreau, Herv{\'e}}
}
@article {Palenik2006,
	title = {Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {103},
	number = {36},
	year = {2006},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {13555{\textendash}13559},
	abstract = {Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus are important primary producers in both types of ecosystems. We have found that the genome of a coastal cyanobacterium, Synechococcus sp. strain CC9311, has significant differences from an open ocean strain, Synechococcus sp. strain WH8102, and these are consistent with the differences between their respective environments. CC9311 has a greater capacity to sense and respond to changes in its (coastal) environment. It has a much larger capacity to transport, store, use, or export metals, especially iron and copper. In contrast, phosphate acquisition seems less important, consistent with the higher concentration of phosphate in coastal environments. CC9311 is predicted to have differences in its outer membrane lipopolysaccharide, and this may be characteristic of the speciation of some cyanobacterial groups. In addition, the types of potentially horizontally transferred genes are markedly different between the coastal and open ocean genomes and suggest a more prominent role for phages in horizontal gene transfer in oligotrophic environments.},
	keywords = {rcc},
	doi = {10.1073/pnas.0602963103},
	url = {http://www.pnas.org/cgi/content/abstract/103/36/13555},
	author = {Palenik, Brian and Ren, Qinghu and Dupont, Chris L and Myers, Garry S and Heidelberg, John F and Badger, Jonathan H and Madupu, Ramana and Nelson, William C and Brinkac, Lauren M and Dodson, Robert J and Durkin, A Scott and Daugherty, Sean C and Sullivan, Stephen A and Khouri, Hoda and Mohamoud, Yasmin and Halpin, Rebecca and Paulsen, Ian T}
}
@article {palenik_genome_2006,
	title = {Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {103},
	number = {36},
	year = {2006},
	note = {Publisher: National Academy of Sciences Section: Biological Sciences},
	pages = {13555{\textendash}13559},
	abstract = {Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus are important primary producers in both types of ecosystems. We have found that the genome of a coastal cyanobacterium, Synechococcus sp. strain CC9311, has significant differences from an open ocean strain, Synechococcus sp. strain WH8102, and these are consistent with the differences between their respective environments. CC9311 has a greater capacity to sense and respond to changes in its (coastal) environment. It has a much larger capacity to transport, store, use, or export metals, especially iron and copper. In contrast, phosphate acquisition seems less important, consistent with the higher concentration of phosphate in coastal environments. CC9311 is predicted to have differences in its outer membrane lipopolysaccharide, and this may be characteristic of the speciation of some cyanobacterial groups. In addition, the types of potentially horizontally transferred genes are markedly different between the coastal and open ocean genomes and suggest a more prominent role for phages in horizontal gene transfer in oligotrophic environments.},
	keywords = {cyanobacteria, genomics, Marine, RCC1086},
	issn = {0027-8424, 1091-6490},
	doi = {10.1073/pnas.0602963103},
	url = {https://www.pnas.org/content/103/36/13555},
	author = {Palenik, Brian and Ren, Qinghu and Dupont, Chris L. and Myers, Garry S. and Heidelberg, John F. and Badger, Jonathan H. and Madupu, Ramana and Nelson, William C. and Brinkac, Lauren M. and Dodson, Robert J. and Durkin, A. Scott and Daugherty, Sean C. and Sullivan, Stephen A. and Khouri, Hoda and Mohamoud, Yasmin and Halpin, Rebecca and Paulsen, Ian T.}
}
@article {Slapeta2006,
	title = {Global dispersal and ancient cryptic species in the smallest marine eukaryotes},
	journal = {Molecular Biology and Evolution},
	volume = {23},
	number = {1},
	year = {2006},
	note = {tex.mendeley-tags: Micromonas,RCC,rcc},
	pages = {23{\textendash}29},
	abstract = {Small eukaryotic species ({\textexclamdown}1 mm) are thought to behave as prokaryotes in that, lacking geographical barriers to their dispersal due to their tiny size, they are ubiquitous. Accordingly, the absence of geographical insulation would imply the existence of a relatively small number of microeukaryotic species. To test these ideas, we sequenced and compared several nuclear, mitochondrial, and chloroplast genes from the isolates of a marine picoeukaryotic alga ([\~]2 microm), Micromonas pusilla, collected worldwide. Independent and combined phylogenetic analyses demonstrate that this traditional single morphospecies actually comprises several independent lineages, some of which are shown to be ubiquitous in oceans. However, while some lineages group closely related strains, others form distant clusters, revealing the existence of cryptic species. Moreover, molecular dating using a relaxed clock suggests that their first diversification may have started as early as during the Late Cretaceous ([\~]65 MYA), implying that "M. pusilla" is the oldest group of cryptic species known to date. Our results illustrate that global dispersal of a picoeukaryote is possible in oceans, but this does not imply a reduced species number. On the contrary, we show that the morphospecies concept is untenable because it overlooks a large genetic and species diversity and may lead to incorrect biological assumptions.},
	keywords = {Micromonas, rcc},
	doi = {10.1093/molbev/msj001},
	url = {http://mbe.oxfordjournals.org/cgi/content/abstract/23/1/23},
	author = {Slapeta, Jan and L{\'o}pez-Garc{\'\i}a, P and Moreira, David}
}
@article {Farinas2006,
	title = {Natural synchronisation for the study of cell division in the green unicellular alga Ostreococcus tauri},
	journal = {Plant Molecular Biology},
	volume = {60},
	number = {2},
	year = {2006},
	note = {tex.mendeley-tags: RCC745},
	pages = {277{\textendash}292},
	abstract = {Ostreococcus tauri (Prasinophyceae) is a marine unicellular green alga which diverged early in the green lineage. The interest of O. tauri as a potential model to study plant cell division is based on its key phylogenetic position, its simple binary division, a very simple cellular organisation and now the availability of the full genome sequence. In addition O. tauri has a minimal yet complete set of cell cycle control genes. Here we show that division can be naturally synchronised by light/dark cycles and that organelles divide before the nucleus. This natural synchronisation, although being only partial, enables the study of the expression of CDKs throughout the cell cycle. The expression patterns of OtCDKA and OtCDKB were determined both at the mRNA and protein levels. The single OtCDKA gene is constantly expressed throughout the cell cycle, whereas OtCDKB is highly regulated and expressed only in S/G2/M phases. More surprisingly, OtCDKA is not phosphorylated at the tyrosine residue, in contrast to OtCDKB which is strongly phosphorylated during cell division. OtCDKA kinase activity appears before the S phase, indicating a possible role of this protein in the G1/S transition. OtCDKB kinase activity occurs later than OtCDKA, and its tyrosine phosphorylation is correlated to G2/M, suggesting a possible control of the mitotic activity. To our knowledge this is the first organism in the green lineage which showed CDKB tyrosine phosphorylation during cell cycle progression.},
	keywords = {Cyclin-dependent kinases, Green alga, Histone H1 kinase activity, Ostreococcus tauri, Phosphorylation, RCC745, Synchronisation of the cell division},
	issn = {01674412},
	doi = {10.1007/s11103-005-4066-1},
	author = {Farinas, Beno{\^\i}t and Mary, Camille and De O Manes, Carmem Lara and Bhaud, Yvonne and Peaucellier, G{\'e}rard and Moreau, Herv{\'e}}
}
@article {Rodriguez2005h,
	title = {Ecotype diversity in the marine picoeukaryote Ostreococcus (Chlorophyta, Prasinophyceae).},
	journal = {Environmental Microbiology},
	volume = {7},
	year = {2005},
	note = {tex.mendeley-tags: RCC113,RCC143,RCC343,RCC356,RCC371,RCC393,RCC410,RCC420,RCC434,RCC501,RCC658,RCC745,Rcc141},
	pages = {853{\textendash}859},
	keywords = {rcc, RCC113, Rcc141, RCC143, RCC343, RCC356, RCC371, RCC393, rcc410, RCC420, RCC434, rcc501, RCC658, RCC745, SBR$_\textrmP$hyto$_\textrmD$PO},
	doi = {10.1111/j.1462-2920.2005.00758.x},
	author = {Rodriguez, F and Derelle, E and Guillou, L and Le Gall, F and Vaulot, D and Moreau, H}
}
@article {Robbens2005,
	title = {Genome-wide analysis of core cell cycle genes in the unicellular green alga Ostreococcus tauri},
	journal = {Molecular Biology and Evolution},
	volume = {22},
	number = {3},
	year = {2005},
	note = {tex.mendeley-tags: RCC745},
	pages = {589{\textendash}597},
	abstract = {The cell cycle has been extensively studied in various organisms, and the recent access to an overwhelming amount of genomic data has given birth to a new integrated approach called comparative genomics. Comparing the cell cycle across species shows that its regulation is evolutionarily conserved; the best-known example is the pivotal role of cyclin-dependent kinases in all the eukaryotic lineages hitherto investigated. Interestingly, the molecular network associated with the activity of the CDK-cyclin complexes is also evolutionarily conserved, thus, defining a core cell cycle set of genes together with lineage-specific adaptations. In this paper, we describe the core cell cycle genes of Ostreococcus tauri, the smallest free-living eukaryotic cell having a minimal cellular organization with a nucleus, a single chloroplast, and only one mitochondrion. This unicellular marine green alga, which has diverged at the base of the green lineage, shows the minimal yet complete set of core cell cycle genes described to date. It has only one homolog of CDKA, CDKB, CDKD, cyclin A, cyclin B, cyclin D, cyclin H, Cks, Rb, E2F, DP, DEL, Cdc25, and Wee L We have also added the APC and SCF E3 ligases to the core cell cycle gene set. We discuss the potential of genome-wide analysis in the identification of divergent orthologs of cell cycle genes in different lineages by mining the genomes of evolutionarily important and strategic organisms.},
	keywords = {Anaphase Promoting Complex, Arabidopsis Thaliana, Cdk Activity, cell division cycle, Chlorophyta, cyclin, cyclin dependant kinase, Green alga, Kinase, Ostreococcus tauri, Plant, Prasinophyceae, rcc, RCC745, Retinoblastoma Protein, Saccharomyces Cerevisiae, Yeast},
	doi = {10.1093/molbev/msi044},
	author = {Robbens, S and Khadaroo, B and Camasses, A and Derelle, E and Ferraz, C and Inze, D and Van, de Peer Y and Moreau, H}
}
@article {Zhu2005,
	title = {Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene},
	journal = {FEMS Microbiology Ecology},
	volume = {52},
	number = {1},
	year = {2005},
	note = {tex.mendeley-tags: Micromonas,RCC,rcc},
	pages = {79{\textendash}92},
	abstract = {A quantitative PCR (QPCR) assay based on the use of SYBR Green I was developed to assess the abundance of specific groups of picoeukaryotes in marine waters. Six primer sets were designed targeting four different taxonomic levels: domain (Eukaryota), division (Chlorophyta), order (Mamiellales) and genus (Bathycoccus, Micromonas, and Ostreococcus). Reaction conditions were optimized for each primer set which was validated in silico, on agarose gels, and by QPCR against a variety of target and non-target cultures. The approach was tested by estimating gene copy numbers for Micromonas, Bathycoccus, and Ostreococcus in seawater samples to which cultured cells were added in various concentrations. QPCR was then used to determine that rRNA gene (rDNA) copy number varied from one to more than 12,000 in 18 strains of phytoplankton. Finally, QPCR was applied to environmental samples from a Mediterranean Sea coastal site and the results were compared to those obtained by Fluorescent in situ hybridization (FISH). The data obtained demonstrate that Chlorophyta and more specifically Mamiellales were important in these waters, especially during the winter picoplankton bloom. The timing of major abundance peaks of the targeted species was similar by QPCR and FISH. When used in conjunction with other techniques such as FISH or gene clone libraries, QPCR appears as very promising to quickly obtain data on the ecological distribution of important phytoplankton groups. Data interpretation must take into account primer specificity and the varying rRNA gene copy number among eukaryotes. ?? 2004 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.},
	keywords = {Coastal ecosystems, Ecology, Fluorescent in situ hybridization, Micromonas, picoplankton, prasinophytes, Quantitative PCR, rcc},
	author = {Zhu, Fei and Massana, Ramon and Not, Fabrice and Marie, Dominique and Vaulot, Daniel}
}
@article {Six2005a,
	title = {New insights into the nature and phylogeny of prasinophyte antenna proteins: Ostreococcus tauri, a case study},
	journal = {Molecular Biology and Evolution},
	volume = {22},
	number = {11},
	year = {2005},
	note = {tex.mendeley-tags: RCC113,RCC114,RCC745: RCC417},
	pages = {2217{\textendash}2230},
	abstract = {The basal position of the Mamiellales (Prasinophyceae) within the green lineage makes these unicellular organisms key to elucidating early stages in the evolution of chlorophyll a/b{\textendash}binding light-harvesting complexes (LHCs). Here, we unveil the complete and unexpected diversity of Lhc proteins in Ostreococcus tauri, a member of the Mamiellales order, based on results from complete genome sequencing. Like Mantoniella squamata, O. tauri possesses a number of genes encoding an unusual prasinophyte-specific Lhc protein type herein designated "Lhcp". Biochemical characterization of the complexes revealed that these polypeptides, which bind chlorophylls a, b, and a chlorophyll c{\textendash}like pigment (Mg-2,4-divinyl-phaeoporphyrin a5 monomethyl ester) as well as a number of unusual carotenoids, are likely predominant. They are retrieved to some extent in both reaction center I (RCI){\textendash} and RCII-enriched fractions, suggesting a possible association to both photosystems. However, in sharp contrast to previous reports on LHCs of M. squamata, O. tauri also possesses other LHC subpopulations, including LHCI proteins (encoded by five distinct Lhca genes) and the minor LHCII polypeptides, CP26 and CP29. Using an antibody against plant Lhca2, we unambiguously show that LHCI proteins are present not only in O. tauri, in which they are likely associated to RCI, but also in other Mamiellales, including M. squamata. With the exception of Lhcp genes, all the identified Lhc genes are present in single copy only. Overall, the discovery of LHCI proteins in these prasinophytes, combined with the lack of the major LHCII polypeptides found in higher plants or other green algae, supports the hypothesis that the latter proteins appeared subsequent to LHCI proteins. The major LHC of prasinophytes might have arisen prior to the LHCII of other chlorophyll a/b{\textendash}containing organisms, possibly by divergence of a LHCI gene precursor. However, the discovery in O. tauri of CP26-like proteins, phylogenetically placed at the base of the major LHCII protein clades, yields new insight to the origin of these antenna proteins, which have evolved separately in higher plants and green algae. Its diverse but numerically limited suite of Lhc genes renders O. tauri an exceptional model system for future research on the evolution and function of LHC components.},
	keywords = {rcc, RCC113, RCC114, RCC417, RCC745, SBR$_\textrmP$hyto$_\textrmD$PO},
	doi = {10.1093/molbev/msi220},
	author = {Six, C and Worden, A Z and Rodriguez, F and Moreau, H and Partensky, F}
}
@inbook {Marie2005,
	title = {Phytoplankton cell counting by flow cytometry},
	booktitle = {Algal culturing techniques},
	year = {2005},
	note = {tex.mendeley-tags: 2005,rcc,sbr?hyto},
	pages = {253{\textendash}267},
	publisher = {Academic Press},
	organization = {Academic Press},
	keywords = {2005, PICODIV, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto},
	author = {Marie, D and Simon, N and Vaulot, D},
	editor = {Andersen, R A}
}
@article {Guillou2004,
	title = {Diversity of picoplanktonic prasinophytes assessed by direct nuclear SSU rDNA sequencing of environmental samples and novel isolates retrieved from oceanic and coastal marine ecosystems},
	journal = {Protist},
	volume = {155},
	year = {2004},
	note = {tex.mendeley-tags: 2004,rcc,sbr?hyto},
	pages = {193{\textendash}214},
	keywords = {2004, PICODIV, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto, SOMLIT},
	doi = {10.1078/143446104774199592},
	author = {Guillou, Laure and Eikrem, W and Chr{\'e}tiennot-Dinet, M.-J. and Le Gall, F and Massana, R and Romari, K and Pedr{\'o}s-Ali{\'o}, C and Vaulot, D}
}
@article {Vaulot2004,
	title = {The roscoff culture collection (RCC): a collection dedicated to marine picoplankton},
	journal = {Nova Hedwigia},
	volume = {79},
	number = {1/2},
	year = {2004},
	note = {tex.mendeley-tags: 2004,rcc,sbr?hyto},
	pages = {49{\textendash}70},
	keywords = {10$_\textrmb$est, 2004, PICODIV, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto},
	doi = {10.1127/0029-5035/2004/0079-0049},
	author = {Vaulot, D and Le Gall, F and Marie, D and Guillou, L and Partensky, F}
}
@article {Ral2004,
	title = {Starch division and partitioning. A mechanism for granule propagation and maintenance in the picophytoplanktonic green alga Ostreococcus tauri},
	journal = {Plant Physiology},
	volume = {136},
	number = {2},
	year = {2004},
	note = {tex.mendeley-tags: RCC745},
	pages = {3333{\textendash}3340},
	abstract = {Whereas Glc is stored in small-sized hydrosoluble glycogen particles in archaea, eubacteria, fungi, and animal cells, photosynthetic eukaryotes have resorted to building starch, which is composed of several distinct polysaccharide fractions packed into a highly organized semicrystalline granule. In plants, both the initiation of polysaccharide synthesis and the nucleation mechanism leading to formation of new starch granules are currently not understood. Ostreococcus tauri, a unicellular green alga of the Prasinophyceae family, defines the tiniest eukaryote with one of the smallest genomes. We show that it accumulates a single starch granule at the chloroplast center by using the same pathway as higher plants. At the time of plastid division, we observe elongation of the starch and division into two daughter structures that are partitioned in each newly formed chloroplast. These observations suggest that in this system the information required to initiate crystalline polysaccharide growth of a new granule is contained within the preexisting polysaccharide structure and the design of the plastid division machinery.},
	keywords = {Adp Glucose Pyrophosphorylase, Amylopectin, Arabidopsis, Bacterial Glycogen, Biogenesis, Biosynthesis, Chlamydomonas Reinhardtii, Enzyme, Prasinophyceae, rcc, RCC745, Synthase},
	doi = {10.1104/pp.104.044131},
	author = {Ral, J P and Derelle, E and Ferraz, C and Wattebled, F and Farinas, B and Corellou, F and Buleon, A and Slomianny, M C and Delvalle, D and D, Hulst C and Rombauts, S and Moreau, H and Ball, S}
}
@article {Fuller2003,
	title = {Clade-specific 16S ribosomal DNA oligonucleotides reveal the predominance of a single marine Synechococcus clade throughout a stratified water column in the Red Sea},
	journal = {Applied and Environmental Microbiology},
	volume = {69},
	number = {5},
	year = {2003},
	note = {tex.mendeley-tags: 2003,rcc,sbr?hyto},
	pages = {2430{\textendash}2443},
	abstract = {Phylogenetic relationships among members of the marine Synechococcus genus were determined following sequencing of the 16S ribosomal DNA (rDNA) from 31 novel cultured isolates from the Red Sea and several other oceanic environments. This revealed a large genetic diversity within the marine Synechococcus cluster consistent with earlier work but also identified three novel clades not previously recognized. Phylogenetic analyses showed one clade, containing halotolerant isolates lacking phycoerythrin (PE) and including strains capable, or not, of utilizing nitrate as the sole N source, which clustered within the MC-A (Synechococcus subcluster 5.1) lineage. Two copies of the 16S rRNA gene are present in marine Synechococcus genomes, and cloning and sequencing of these copies from Synechococcus sp. strain WH 7803 and genomic information from Synechococcus sp. strain WH 8102 reveal these to be identical. Based on the 16S rDNA sequence information, clade-specific oligonucleotides for the marine Synechococcus genus were designed and their specificity was optimized. Using dot blot hybridization technology, these probes were used to determine the in situ community structure of marine Synechococcus populations in the Red Sea at the time of a Synechococcus maximum during April 1999. A predominance of genotypes representative of a single clade was found, and these genotypes were common among strains isolated into culture. Conversely, strains lacking PE, which were also relatively easily isolated into culture, represented only a minor component of the Synechococcus population. Genotypes corresponding to well-studied laboratory strains also appeared to be poorly represented in this stratified water column in the Red Sea.},
	keywords = {2003, PICODIV, rcc, SBR$_\textrmP$hyto, sbr?hyto},
	issn = {0099-2240},
	doi = {10.1128/AEM.69.5.2430-2443.2003},
	url = {http://aem.asm.org/cgi/content/abstract/69/5/2430},
	author = {Fuller, Nicholas J and Marie, Dominique and Partensky, Fr{\'e}d{\'e}ric and Vaulot, Daniel and Post, Anton F and Scanlan, David J}
}
@article {Palenik2003,
	title = {The genome of a motile marine Synechococcus},
	journal = {Nature},
	volume = {424},
	number = {6952},
	year = {2003},
	note = {tex.mendeley-tags: 2003,rcc,sbr?hyto},
	pages = {1037{\textendash}1042},
	abstract = {Marine unicellular cyanobacteria are responsible for an estimated 20-40\% of chlorophyll biomass and carbon fixation in the oceans(1). Here we have sequenced and analysed the 2.4-megabase genome of Synechococcus sp. strain WH8102, revealing some of the ways that these organisms have adapted to their largely oligotrophic environment. WH8102 uses organic nitrogen and phosphorus sources and more sodium-dependent transporters than a model freshwater cyanobacterium. Furthermore, it seems to have adopted strategies for conserving limited iron stores by using nickel and cobalt in some enzymes, has reduced its regulatory machinery (consistent with the fact that the open ocean constitutes a far more constant and buffered environment than fresh water), and has evolved a unique type of swimming motility. The genome of WH8102 seems to have been greatly influenced by horizontal gene transfer, partially through phages. The genetic material contributed by horizontal gene transfer includes genes involved in the modification of the cell surface and in swimming motility. On the basis of its genome, WH8102 is more of a generalist than two related marine cyanobacteria(2).},
	keywords = {2003, Cyanobacterium Synechococcus, Degradation, Ecology, Gene, IDENTIFICATION, Polypeptide, Prochlorococcus, rcc, SBR$_\textrmP$hyto, sbr?hyto, SEQUENCE, Sp Pcc7942, Strains},
	doi = {10.1038/nature01943},
	author = {Palenik, B and Brahamsha, B and Larimer, F W and Land, M and Hauser, L and Chain, P and Lamerdin, J and Regala, W and Allen, E E and McCarren, J and Paulsen, I and Dufresne, A and Partensky, F and Webb, E A and Waterbury, J}
}
@article {Derelle2002,
	title = {DNA libraries for sequencing the genome of Ostreococcus tauri (Chlorophyta, Prasinophyceae): The smallest free-living eukaryotic cell},
	journal = {Journal of Phycology},
	volume = {38},
	number = {6},
	year = {2002},
	note = {tex.mendeley-tags: RCC745},
	pages = {1150{\textendash}1156},
	abstract = {Ostreococcus tauri is a marine photosynthetic picoeukaryote presenting a minimal cellular organization with one nucleus, one chloroplast, and one mitochondrion. It has the smallest genome described among free-living eukaryotic cells, and we showed by pulsed-field gel electrophoresis (PFGE) that it is divided between 15 bands ranging from 1.2 to 0.15 Mb, giving a total size of 9.7 Mb. A Bacterial Artificial Chromosome (BAC) library was prepared from genomic DNA extracted from a culture of O. tauri. A total of 2457 clones was obtained with an average insert size of around 70 kb, representing an 18-fold coverage of the genome. The library was spotted on high density filters, and several probes of coding sequences were hybridized to both the high density BAC library filters and directly to the dried PFGE gels of the O. tauri genomic DNA. These hybridizations allowed a preliminary organization of the library and the localization of several markers on the chromosomes. Randomly selected fragments were also sequenced, representing 12\% of the O. tauri genome. Many sequences showed significant similarities in data banks, mainly with plant and algae sequences. About 1000 coding sequences could be identified. These data confirmed the position of O. tauri in the green lineage and the hypothesis of a very compact organization of its genome.},
	keywords = {Pico$_\textrmR$eview, rcc, RCC745},
	doi = {10.1046/j.1529-8817.2002.02021.x},
	url = {c:\%5CDV\%5CPapers reprints\%5CPhytoplankton Physiology\%5CDerelle Ostreococcus DNA libraries JPhycol 02.pdf},
	author = {Derelle, E and Ferraz, C and Lagoda, P and Eychenie, S and Cooke, R and Regad, F and Sabau, X and Courties, C and Delseny, M and Demaille, J and Picard, A and Moreau, H}
}
@article {Jacquet2001,
	title = {Cell cycle regulation by light in Prochlorococcus strains},
	journal = {Applied and Environmental Microbiology},
	volume = {67},
	number = {2},
	year = {2001},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {782{\textendash}790},
	abstract = {<p>The effect of light on the synchronization of cell cycling was investigated in several strains of the oceanic photosynthetic prokaryote Prochlorococcus using flow cytometry. When exposed to a light-dark (L-D) cycle with an irradiance of 25 mu mol of quanta m(-2) s(-1), the low-light-adapted strain SS 120 appeared to be better synchronized than the high-light-adapted strain PCC 9511. Submitting LD-entrained populations to shifts (advances or delays) in the timing of the "light on" signal translated to corresponding shifts in the initiation of the S phase, suggesting that this signal is a key parameter for the synchronization of population cell cycles. Cultures that were shifted from an L-D cycle to continuous irradiance showed persistent diel oscillations of flow-cytometric signals (light scatter and chlorophyll fluorescence) but with significantly reduced amplitudes and a phase shift. Complete darkness arrested most of the cells in the G(1), phase of the cell cycle, indicating that light is required to trigger the initiation of DNA replication and cell division. However, some cells also arrested in the S phase, suggesting that cell cycle controls in Prochlorococcus spp. are not as strict as in marine Synechococcus spp. Shifting Prochlorococcus cells from low to high irradiance translated quasi-instantaneously into an increase of cells in both the S and G(2) phases of the cell cycle and then into faster growth, whereas the inverse shift induced rapid slowing of the population growth rate. These data suggest a close coupling between irradiance levels and cell cycling in Prochloroeoccus spp.</p>
},
	keywords = {cyanobacteria, Equatorial Pacific, Gene Expression, Growth, Mediterranean Sea, North Atlantic, Photosynthetic Prokaryote, picoplankton, Populations, rcc, Synechococcus},
	doi = {10.1128/AEM.67.2.782-790.2001},
	author = {Jacquet, S and Partensky, F and Marie, D and Casotti, R and Vaulot, D}
}
@article {Dupuy2000,
	title = {Feeding rate of the oyster Crassostrea gigas in a natural planktonic community of the Mediterranean Thau Lagoon},
	journal = {Marine Ecology - Progress Series},
	volume = {205},
	year = {2000},
	note = {ISBN: 0171-8630 Publisher: Inter-Research tex.address: Nordbunte 23, D-21385 Oldendorf Luhe, Germany tex.mendeley-tags: RCC,rcc},
	pages = {171{\textendash}184},
	abstract = {The Mediterranean Thau Lagoon is an important oyster farming area in Europe. Oyster growth rates are among the highest in France, although chlorophyll a concentration is low. Previous studies have demonstrated that picophytoplankton, nano-microphytoplankton, dinoflagellates and loricate ciliates such as tintinnids are abundant. However, heterotrophic flagellates and aloricate ciliates have not been investigated. The aim of this study was to assess picophytoplankton, protist and zooplankton abundances in the Lagoon and to investigate the particular structure of the microbial food web, which may explain such paradoxical oyster growth. In oligotrophic waters in the Thau Lagoon, the picoeukaryote Ostreococcus tauri is the dominant autotrophic picoplankter, with an abundance maximum in summer. On 17 August 1998, following a rainfall event, pico- and nanophytoplankton abundances were not as high as expected and we observed a high abundance of large diatoms. At this time, the available carbon resources were produced by microphytoplankton (84.5\%), and picoplank-tonic cells represented only 1.27 \% in terms of carbon. Heterotrophic cells were low in abundance and constituted {\textexclamdown}14\% of carbon resources. In order to evaluate the importance of the {\textquoteright}protozoan trophic link{\textquoteright} for energy transfer from the microbial food web to large benthic suspension feeders, the oyster Crassostrea gigas was offered a planktonic community as potential prey. In the grazing experiment, all {\textquestiondown}5 mum flagellates, microphytoplankton, dinoflagellates, ciliates and large zooplankton were retained by the oyster gills. Only flagellates {\textexclamdown}5 pm and O. Tauri were not very well retained (45 and 2\% respectively). The high clearance rates of C. Gigas found in this experiment can be explained by a low concentration of suspended particulate matter (0.65 mg l(-1)). The oysters adapted their retention mechanism when they Lived in oligotrophic waters. These results indicate that, under the given experimental conditions, picophytoplankton did not represent a valuable trophic resource for farmed oysters because (1) C. Gigas cannot retain picoparticles and (2) the picoplankton represented a poor carbon resource capable of being transferred via a weak heterotrophic protist community. In the oyster pens of the Thau Lagoon during this study, microphytoplanktonic primary producers, in particular diatoms, were the main food sources for bivalve suspension feeders.},
	keywords = {ABUNDANCE, bivalve, carbon, COASTAL WATERS, EPIFLUORESCENCE MICROSCOPY, FILTRATION-RATE, food source, FOOD-CHAINS, GEUKENSIA-DEMISSA, heterotrophic protist, microbial food web, MYTILUS-EDULIS, oyster, PARTICLE SELECTION, picophytoplankton, rcc, RETENTION, Thau Lagoon, trophic link},
	doi = {10.3354/meps205171},
	author = {Dupuy, C and Vaquer, A and LamHoai, T and Rougier, C and Mazouni, N and Lautier, J and Collos, Y and LeGall, S}
}
@article {Guillou1999,
	title = {Bolidomonas: a new genus with two species belonging to a new algal class, the Bolidophyceae (Heterokonta)},
	journal = {Journal of Phycology},
	volume = {35},
	year = {1999},
	note = {tex.mendeley-tags: 1999,rcc,sbr?hyto},
	pages = {368{\textendash}381},
	abstract = {A new algal class, the Bolidophyceae (Heterokonta), is described from one genus, Bolidomonas, gen, nov., and two species, Bolidomonas pacifica, sp, nov and Bolidomonas mediterranea, sp, nov., isolated from the equatorial Pacific Ocean and the Mediterranean Sea, respectively. Both species are approximately 1.2 mu m in diameter and have two unequal flagella; the longer flagellum bears tubular hairs, whereas the shorter is smooth. The flagellar basal apparatus is restricted to two basal bodies, and there is no transitional helix. Cells are naked, devoid of walls or siliceous structures. The internal cellular organization is simple with a single plastid containing a ring genophore and a girdle lamella, one mitochondrion with tubular cristae, and one Golgi apparatus close to the basal bodies. The Mediterranean and the Pacific species differ in the insertion angle between their flagella and their pattern of swimming, these differences possibly being linked to each other. Analyses of the SSU rDNA gene place the two strains as a sister group to the diatoms, Moreover, pigment analyses confirm this position, as fucoxanthin is found as the major carotenoid in both lineages. These data strongly suggest that the ancestral heterokont that gave rise to the diatom lineage was probably a biflagellated unicell.},
	keywords = {10$_\textrmb$est, 1999, Bolidophyceae, CELL-CYCLE, CHRYSOPHYCEAE, diatoms, DIVINYL-CHLOROPHYLL, FINE-STRUCTURE, FLAGELLAR APPARATUS, Heterokonta, Marine, marine picoeukaryotes, oligotrophic ocean, rcc, RNA, SBR$_\textrmP$hyto, sbr?hyto, SEQUENCE, sp-nov, stramenopiles, ultrastructure},
	doi = {10.1046/j.1529-8817.1999.3520368.x},
	author = {Guillou, L and Chr{\'e}tiennot-Dinet, M.-J. and Medlin, L K and Claustre, H and Loiseaux-de Go{\"e}r, S and Vaulot, D}
}
@article {Shimada1996,
	title = {Vertical distributions and photosynthetic action spectra of two oceanic picophytoplankers, Prochlorococcus marinus and Synechococcus sp},
	journal = {Marine Biology},
	volume = {127},
	year = {1996},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {15{\textendash}23},
	keywords = {OPTICAL-PROPERTIES, Photosynthesis, rcc, \#PROCHLOROCOCCUS},
	doi = {10.1007/BF00993639},
	author = {Shimada, A and Maruyama, T and Miyachi, S}
}
@article {Moore1995,
	title = {Comparative physiology of Synechococcus and Prochlorococcus: influence of light and temperature on growth, pigments, fluorescence and absorptive properties},
	journal = {Marine Ecology - Progress Series},
	volume = {116},
	year = {1995},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {259{\textendash}275},
	keywords = {GROWTH RATE, Light, MARINE OPTICS, rcc, Synechococcus, temperature, \#PROCHLOROPHYTE},
	doi = {10.3354/meps116259},
	author = {Moore, L R and Goericke, R and Chisholm, S W}
}
@article {Chretiennot-Dinet1995,
	title = {A new marine picoeucaryote: Ostreococcus tauri gen. et sp. nov. (Chlorophyta, Prasinophyceae)},
	journal = {Phycologia},
	volume = {34},
	number = {4},
	year = {1995},
	note = {tex.mendeley-tags: RCC745},
	pages = {285{\textendash}292},
	keywords = {FRESH-WATER ECOSYSTEMS, morphology, picoplankton, pigments, PROCHLOROCOCCUS-MARINUS, Prokaryote, rcc, RCC745, Size},
	doi = {10.2216/i0031-8884-34-4-285.1},
	author = {Chr{\'e}tiennot-Dinet, M.-J. and Courties, C and Vaquer, A and Neveux, J and Claustre, H and Lautier, J and Machado, M C}
}
@article {Simon1994,
	title = {Characterization of oceanic photosynthetic picoeukaryotes by flow cytometry analysis},
	journal = {Journal of Phycology},
	volume = {30},
	year = {1994},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {922{\textendash}935},
	keywords = {flow cytometry, hplc, pigments, rcc, RCC SBR$_\textrmP$hyto, \#PICOPLANKTON},
	doi = {10.1111/j.0022-3646.1994.00922.x},
	author = {Simon, N and Barlow, R G and Marie, D and Partensky, F and Vaulot, D}
}
@article {Vaulot1994,
	title = {Phaeocystis spp.: morphology, ploidy, pigment composition and genome size of cultured strains},
	journal = {Journal of Phycology},
	volume = {30},
	year = {1994},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {1022{\textendash}1035},
	keywords = {rcc, RCC SBR$_\textrmP$hyto},
	doi = {10.1111/j.0022-3646.1994.01022.x},
	author = {Vaulot, D and Birrien, J.-L. and Marie, D and Casotti, R and Veldhuis, M J W and Kraay, G W and Chr{\'e}tiennot-Dinet, M.-J.}
}
@article {Morel1993,
	title = {Prochlorococcus and Synechococcus: a comparative study of their size, pigmentation and related optical properties},
	journal = {Journal of Marine Research},
	volume = {51},
	year = {1993},
	note = {tex.mendeley-tags: 1993,rcc,sbr?hyto},
	pages = {617{\textendash}649},
	keywords = {1993, hplc, OPTICS, Pigment, rcc, SBR$_\textrmP$hyto, sbr?hyto, Synechococcus, \#PROCHLOROPHYTE},
	doi = {10.1357/0022240933223963},
	author = {Morel, A and Ahn, Y.-W. and Partensky, F and Vaulot, Daniel and Claustre, H}
}
