@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 {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 {novak_vanclova_new_2024,
	title = {New plastids, old proteins: repeated endosymbiotic acquisitions in kareniacean dinoflagellates},
	journal = {EMBO Reports},
	year = {2024},
	abstract = {Abstract Dinoflagellates are a diverse group of ecologically significant micro-eukaryotes that can serve as a~model system for plastid symbiogenesis due to their susceptibility to plastid loss and replacement via serial endosymbiosis. Kareniaceae harbor fucoxanthin-pigmented plastids instead of the ancestral peridinin-pigmented ones and support them with a diverse range of nucleus-encoded plastid-targeted proteins originating from the haptophyte endosymbiont, dinoflagellate host, and/or lateral gene transfers (LGT). Here, we present predicted plastid proteomes from seven distantly related kareniaceans in three genera ( Karenia , Karlodinium , and Takayama ) and analyze their evolutionary patterns using automated tree building and sorting. We project a~relatively limited ( \textasciitilde 10\%) haptophyte signal pointing towards a shared origin in the family Chrysochromulinaceae. Our data establish significant variations in the functional distributions of these signals, emphasizing the importance of micro-evolutionary processes in shaping the chimeric proteomes. Analysis of plastid genome sequences recontextualizes these results by a striking finding the extant kareniacean plastids are in fact not all of the same origin, as two of the studied species ( Karlodinium armiger , Takayama helix ) possess plastids from different haptophyte orders than the rest.},
	keywords = {RCC1513, RCC3446, RCC6516},
	issn = {1469-3178},
	doi = {10.1038/s44319-024-00103-y},
	url = {https://www.embopress.org/doi/full/10.1038/s44319-024-00103-y},
	author = {Nov{\'a}k Vanclov{\'a}, Anna Mg and Nef, Charlotte and F{\"u}ssy, Zolt{\'a}n and Vancl, Ad{\'e}l and Liu, Fuhai and Bowler, Chris and Dorrell, Richard G}
}
@booklet {sheward_short-term_2024,
	title = {Short-term response of Emiliania huxleyi growth and morphology to abrupt salinity stress},
	year = {2024},
	month = {feb},
	publisher = {Biogeochemistry: Open Ocean},
	type = {preprint},
	abstract = {Abstract. The marine coccolithophore species Emiliania huxleyi tolerates a broad range of salinity conditions over its near-global distribution, including the relatively stable physiochemical conditions of open ocean environments and nearshore environments with dynamic and extreme short-term salinity fluctuations. Previous studies show that salinity impacts the physiology and morphology of E. huxleyi, suggesting that salinity stress influences the calcification of this globally important species. However, it remains unclear how rapidly E. huxleyi responds to salinity changes and therefore whether E. huxleyi morphology is sensitive to short-term, transient salinity events (such as occur on meteorological timescales) in addition longer duration salinity changes. Here, we investigate the real-time growth and calcification response of two E. huxleyi strains isolated from shelf-sea environments to the abrupt onset of hyposaline and hypersaline conditions over a time periods of 156 h (6.5 days). Morphological responses in the size of the cellular exoskeleton (coccosphere) and the calcium carbonate plates (coccoliths) that form the coccosphere occurred as rapidly as 24{\textendash}48 h following the abrupt onset of salinity 25 (hyposaline) and salinity 45 (hypersaline) conditions. Generally, cells tended towards smaller coccospheres (-24 \%) with smaller coccoliths (-7 to -11 \%) and reduced calcification under hyposaline conditions whereas cells growing under hypersaline conditions had either relatively stable coccosphere and coccolith sizes (Mediterranean strain RCC1232) or larger coccospheres (+35 \%) with larger coccoliths (+13 \%) and increased calcification (Norwegian strain PLYB11). This short-term response is consistent with reported coccolith size trends with salinity over longer durations of low and high salinity exposure in culture and under natural salinity gradients. The coccosphere size response of PLYB11 to salinity stress was greater in magnitude than observed in RCC1232 but occurred after a longer duration of exposure (ca. 96{\textendash}128 h) to the new salinity conditions compared to RCC1232. In both strains, coccosphere size changes were larger and occurred more rapidly than changes in coccolith size, which tended to occur more gradually over the course of the experiments. Variability in the magnitude and timing of rapid morphological responses to short-term salinity stress between these two strains supports previous suggestions that the response of E. huxleyi to salinity stress is strain specific. At the start of the experiments, the light condition was also switched from a light: dark cycle to continuous light with the aim of desynchronising cell division. As cell density and mean cell size data sampled every 4 h showed regular periodicity under all salinity conditions, the cell division cycle retained its entrainment to pre-experiment light: dark conditions for the entire experiment duration. Extended acclimation periods to continuous light are therefore advisable for E. huxleyi to ensure successful desynchronisation of the cell division cycle. When working with phased or synchronised populations, data should be compared between samples taken from the same phase of the cell division cycle to avoid artificially distorting the magnitude or even direction of physiological or (bio)geochemical response to the environmental stressor.},
	keywords = {RCC1232},
	doi = {10.5194/egusphere-2024-349},
	url = {https://egusphere.copernicus.org/preprints/2024/egusphere-2024-349/},
	author = {Sheward, Rosie M. and Geb{\"u}hr, Christina and Bollmann, J{\"o}rg and Herrle, Jens O.}
}
@article {kamakura_transcriptional_2024,
	title = {Transcriptional responses to salinity-induced changes in cell wall morphology of the euryhaline diatom Pleurosira laevis},
	journal = {Journal of Phycology},
	volume = {n/a},
	number = {n/a},
	year = {2024},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jpy.13437},
	abstract = {Diatoms are unicellular algae with morphologically diverse silica cell walls, which are called frustules. The mechanism of frustule morphogenesis has attracted attention in biology and nanomaterials engineering. However, the genetic regulation of the morphology remains unclear. We therefore used transcriptome sequencing to search for genes involved in frustule morphology in the centric diatom Pleurosira laevis, which exhibits morphological plasticity between flat and domed valve faces in salinity 2 and 7, respectively. We observed differential expression of transposable elements (TEs) and transporters, likely due to osmotic response. Up-regulation of mechanosensitive ion channels and down-regulation of Ca2+-ATPases in cells with flat valves suggested that cytosolic Ca2+ levels were changed between the morphologies. Calcium signaling could be a mechanism for detecting osmotic pressure changes and triggering morphological shifts. We also observed an up-regulation of ARPC1 and annexin, involved in the regulation of actin filament dynamics known to affect frustule morphology, as well as the up-regulation of genes encoding frustule-related proteins such as BacSETs and frustulin. Taken together, we propose a model in which salinity-induced morphogenetic changes are driven by upstream responses, such as the regulation of cytosolic Ca2+ levels, and downstream responses, such as Ca2+-dependent regulation of actin dynamics and frustule-related proteins. This study highlights the sensitivity of euryhaline diatoms to environmental salinity and the role of active cellular processes in controlling gross valve morphology under different osmotic pressures.},
	keywords = {cytoskeletal element, morphological plasticity, osmotic pressure, polymorphism, RNA-Seq, transporter, valve morphogenesis},
	issn = {1529-8817},
	doi = {10.1111/jpy.13437},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.13437},
	author = {Kamakura, Shiho and Bilcke, Gust and Sato, Shinya}
}
@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 {das_assessing_2023,
	title = {Assessing indicators of arsenic toxicity using variable fluorescence in a commercially valuable microalgae: physiological and toxicological aspects},
	journal = {Journal of Hazardous Materials},
	year = {2023},
	month = {mar},
	pages = {131215},
	abstract = {Indicators signaling Arsenic (As) stress through physiology of microalgae using non-destructive methods like variable fluorescence are rare but requisite. This study reports stress markers indicating arsenic (As) toxicity (in two concentrations 11.25{\textmu}g/L and 22.5{\textmu}g/L compared to a control) exposed to a microalga (Diacronema lutheri), using fast repetition rate fluorometry (FRRf). Growth and physiological parameters such as cell density, chl a and the maximum quantum yield Fv/Fm showed coherence and impeded after the exponential phase (day 9 - day 12) in As treatments compared to the control (p < 0.05). On contrary photo-physiological constants were elevated showing higher optical (aLHII) and functional [Sigma (σPSII)] absorption cross-section for the As treatments (p < 0.05) further implying the lack of biomass production yet an increase in light absorption. In addition, As exposure increased the energy dissipation by heat (NPQ-NSV) showing a strong relationship with the de-epoxidation ratio (DR) involving photoprotective pigments. Total As bioaccumulation by D. lutheri showed a strong affinity with Fe adsorption throughout the algal growth curve. This study suggests some prompt photo-physiological proxies signaling As contamination and endorsing its usefulness in risk assessments, given the high toxicity and ubiquitous presence of As in the ecosystem.},
	keywords = {Arsenic bioaccumulation, de-epoxidation ratio (DR), Optical absorption cross section, pigment concentrations, RCC1537},
	issn = {0304-3894},
	doi = {10.1016/j.jhazmat.2023.131215},
	url = {https://www.sciencedirect.com/science/article/pii/S0304389423004971},
	author = {Das, Shagnika and Lizon, Fabrice and Gevaert, Fran{\c c}ois and Bialais, Capucine and Duong, Gwendoline and Ouddane, Baghdad and Souissi, Sami}
}
@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.}
}
@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 {florenza_choice_2023,
	title = {Choice of methodology and surrogate prey are decisive for the quality of protistan bacterivory rate estimates},
	journal = {Aquatic Microbial Ecology},
	volume = {89},
	year = {2023},
	month = {mar},
	pages = {43{\textendash}53},
	abstract = {Microeukaryote predation on bacteria is a fundamental phenomenon to understand energy and nutrient dynamics at the base of the aquatic food web. To date, the most prevalent way to estimate grazing rates is by using epifluorescence microscopy to enumerate ingestion events of fluorescently labelled tracers (FLTs) after short-term incubation experiments. However, this approach can be sensitive to the type of FLT, requires skillful preparation of the samples and is limited to small sample sizes. We tested the susceptibility of rate estimates to the choice of prey and made a side-by-side comparison between microscopy and flow cytometry when recording ingestion by a bacterivorous flagellate. Short-term uptake experiments were established using 5 types of FLTs differing in quality (living, dead or inert) and size (large or small), with Ochromonas triangulata as a model flagellate. The experiments showed that (1) each of the different prey types yielded different clearing rates, ranging from 0.5 to 3.6 nl cell-1 h-1, with the largest differences (3fold or higher) between small prey (lower rates) and large prey (higher rates); (2) the cytometry estimate differed significantly from the microscopy estimate in 3 out of 4 experimental configurations; and (3) the precision of the cytometric analysis was greater, with > 3-fold higher uncertainty associated with microscopy counting. Our results validate that flow cytometry provides a more precise bacterivory estimate, and that the choice of FLT influences the grazing rate estimate to a high extent regardless of the analytical method used.},
	keywords = {RCC21},
	issn = {0948-3055, 1616-1564},
	doi = {10.3354/ame01996},
	url = {https://www.int-res.com/abstracts/ame/v89/p43-53/},
	author = {Florenza, J and Bertilsson, S}
}
@booklet {clark_coccolithophorids_2023,
	title = {Coccolithophorids precipitate carbonate in clumped isotope equilibrium with seawater},
	year = {2023},
	month = {nov},
	publisher = {EGUsphere},
	type = {preprint},
	abstract = {Numerous recent studies have tested the clumped isotope (Δ47) thermometer on a variety of biogenic carbonates such as foraminifera and bivalves and showed that all follow a common calibration. While the sample size requirements for a reliable Δ47 measurement have decreased over the years, the availability and preservation of many biogenic carbonates is still 10 limited and/or require substantial time to be extracted from sediments in sufficient amounts. We thus determined the Δ47temperature relationship for coccolith carbonate, which is abundant and often well-preserved in sediments. The carbon and oxygen isotopic compositions of coccolith calcite have limited use in palaeoenvironmental reconstructions due to physiological effects that cause variability in the carbon and oxygen isotopic values. However, the relatively limited data available suggest that clumped isotopes may not be influenced by these effects. We cultured three species of coccolithophores in well15 constrained carbonate system conditions with a CO2(aq) between 5 and 45 μM and temperatures between 6{\textdegree}C and 27{\textdegree}C.},
	keywords = {RCC1130, RCC1303, RCC3370},
	doi = {10.5194/egusphere-2023-2581},
	url = {https://egusphere.copernicus.org/preprints/2023/egusphere-2023-2581/},
	author = {Clark, Alexander J. and Torres-Romero, Ismael and Jaggi, Madalina and Bernasconi, Stefano M. and Stoll, Heather M.}
}
@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 {ben-joseph_crystallization_2023,
	title = {Crystallization of Coccolith Calcite at Different Life-Cycle Phases Exhibits Distinct Degrees of Cellular Confinement},
	journal = {Small Structures},
	volume = {n/a},
	number = {n/a},
	year = {2023},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/sstr.202200353},
	pages = {2200353},
	abstract = {Coccolithophores are a group of unicellular marine algae that shape global geochemical cycles via the production of calcium carbonate crystals. Interestingly, different life-cycle phases of the same coccolithophore species produce very different calcitic scales, called coccoliths. In the widely studied diploid phase, the crystals have anisotropic and complex morphologies, while haploid cells produce coccoliths consisting solely of calcite crystals with simple rhombohedral morphology. Understanding how these two life-cycle phases control crystallization is a highly sought-after goal, yet, haploid phase crystallization has rarely been studied, and the process by which they form is unknown. Herein, advanced electron microscopy is employed to elucidate the cellular architecture of the calcification process in haploid cells. The results show that in contrast to diploid-phase calcification, the coccolith-forming vesicle of haploid-phase cells is voluminous. In this solution-like environment, the crystals nucleate and grow asynchronously in a process that resembles calcite growth in bulk solution, leading to the simple morphologies of the crystals. The two distinct mineralization regimes of coccolithophore life-cycle phases suggest that cellular architecture, and specifically confinement of the crystallization process, is a pivotal determinant of biomineral morphology and assembly.},
	keywords = {biomineralization, calcites, Coccoliths, crystal growths, haploid{\textendash}diploid life cycles, RCC1181, RCC3777},
	issn = {2688-4062},
	doi = {10.1002/sstr.202200353},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/sstr.202200353},
	author = {Ben-Joseph, Oz and de Haan, Diede and Rechav, Katya and Shimoni, Eyal and Levin-Zaidman, Smadar and Langer, Gerald and Probert, Ian and Wheeler, Glen L. and Gal, Assaf}
}
@article {yu_does_2023,
	title = {Does the life cycle stage matter for distinguishing phytoplankton via fluoro-electrochemical microscopy?},
	journal = {Cell Reports Physical Science},
	year = {2023},
	pages = {101223},
	abstract = {Phytoplankton have species-specific responses toward electrogenerated oxidants, allowing high-throughput species analysis. Herein, a fluoro-electrochemical method is used to expose single Chlamydomonas concordia vegetative cells at different points within their life cycle to electro-generated oxidants from seawater. The resulting decay in fluorescence from chlorophyll-a is measured as a function of time and drops to zero for phytoplankton adjacent to the electrode over a period of a few seconds. The chlorophyll-a transient timescale allows mother cells, which are distinctively larger and require a larger quantity of oxidants, to be distinguished from either zoospores or {\textquotedblleft}growing{\textquotedblright} cells, while all the cells show the same intrinsic susceptibility modulated only by the size of the phytoplankton. These observations are essential for the future automated characterization of the speciation of phytoplankton populations as they show that there is no need to manually identify the life cycle stage.},
	keywords = {electrogenerated radicals, fluoro-electrochemistry, Green algae, life cycle, marine phytoplankton, oxidative damage, RCC1, remote sensing, susceptibility library},
	issn = {2666-3864},
	doi = {10.1016/j.xcrp.2022.101223},
	url = {https://www.sciencedirect.com/science/article/pii/S2666386422005410},
	author = {Yu, Jiahao and Yang, Minjun and Batchelor-McAuley, Christopher and Barton, Samuel and Rickaby, Rosalind E. M. and Bouman, Heather A. and Compton, Richard G.}
}
@article {sands_genetic_2023,
	title = {Genetic and physiological responses to light quality in a deep ocean ecotype of Ostreococcus, an ecologically important photosynthetic picoeukaryote},
	journal = {Journal of Experimental Botany},
	year = {2023},
	pages = {erad347},
	abstract = {Abstract Phytoplankton are exposed to dramatic variations in light quality when cells are carried by upwelling or downwelling currents or encounter sediment. We investigated the potential impact of light quality changes in Ostreococcus, a key marine photosynthetic picoeukaryote, by analysing changes in its transcriptome, pigment content and photophysiology after acclimation to monochromatic red, green or blue light. The clade B species RCC809, isolated from the deep euphotic zone of the tropical Atlantic Ocean, responded to blue light by accelerating cell division at the expense of storage reserves and by increasing the relative level of blue-light absorbing pigments. RCC809 responded to red and green light by increasing its potential for photoprotection. In contrast, the clade A species OTTH0595, which originates from a shallow water environment, showed no difference in photosynthetic properties and minor differences in carotenoid contents between light qualities. This was associated with the loss of candidate lightquality responsive promoter motifs identified in RCC809 genes. These results demonstrate that light quality can have a major influence on the physiology of eukaryotic phytoplankton and suggest that different light quality environments can drive selection for diverse patterns of responsiveness and environmental niche partitioning.},
	keywords = {Rcc141, RCC4221, RCC745, RCC809},
	issn = {0022-0957, 1460-2431},
	doi = {10.1093/jxb/erad347},
	url = {https://academic.oup.com/jxb/advance-article/doi/10.1093/jxb/erad347/7258950},
	author = {Sands, Elizabeth and Davies, Sian and Puxty, Richard John and Verg{\'e}, Val{\'e}rie and Bouget, Fran{\c c}ois-Yves and Scanlan, David John and Carr{\'e}, Isabelle Alice}
}
@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.}
}
@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 {groussman_marferret_2023,
	title = {MarFERReT, an open-source, version-controlled reference library of marine microbial eukaryote functional genes},
	journal = {Scientific Data},
	volume = {10},
	number = {1},
	year = {2023},
	note = {Number: 1 Publisher: Nature Publishing Group},
	pages = {926},
	abstract = {Metatranscriptomics generates large volumes of sequence data about transcribed genes in natural environments. Taxonomic annotation of these datasets depends on availability of curated reference sequences. For marine microbial eukaryotes, current reference libraries are limited by gaps in sequenced organism diversity and barriers to updating libraries with new sequence data, resulting in taxonomic annotation of about half of eukaryotic environmental transcripts. Here, we introduce Marine Functional EukaRyotic Reference Taxa (MarFERReT), a marine microbial eukaryotic sequence library designed for use with taxonomic annotation of eukaryotic metatranscriptomes. We gathered 902 publicly accessible marine eukaryote genomes and transcriptomes and assessed their sequence quality and cross-contamination issues, selecting 800 validated entries for inclusion in MarFERReT. Version 1.1 of MarFERReT contains reference sequences from 800 marine eukaryotic genomes and transcriptomes, covering 453 species- and strain-level taxa, totaling nearly 28 million protein sequences with associated NCBI and PR2 Taxonomy identifiers and Pfam functional annotations. The MarFERReT project repository hosts containerized build scripts, documentation on installation and use case examples, and information on new versions of MarFERReT.},
	keywords = {Classification and taxonomy, Microbial genetics, transcriptomics},
	issn = {2052-4463},
	doi = {10.1038/s41597-023-02842-4},
	url = {https://www.nature.com/articles/s41597-023-02842-4},
	author = {Groussman, R. D. and Blaskowski, S. and Coesel, S. N. and Armbrust, E. V.}
}
@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 {barton_novel_2023,
	title = {A novel fluoro-electrochemical technique for classifying diverse marine nanophytoplankton},
	year = {2023},
	month = {apr},
	publisher = {Life Sciences},
	type = {preprint},
	abstract = {<p>To broaden our understanding of pelagic ecosystem responses to environmental change, it is essential that we improve the spatio-temporal resolution of in situ monitoring of phytoplankton communities. A key challenge for existing methods is in classifying and quantifying cells within the nanophytoplankton size range (2-20{\textmu}m). This is particularly difficult when there are similarities in morphology, making visual differentiation difficult for both trained taxonomists and machine learning based approaches. Here we present a rapid fluoro-electrochemical technique for classifying nanophytoplankton, and using a library of 52 diverse strains of nanophytoplankton we assess the accuracy of this technique based on two measurements at the individual level: charge required to reduce per cell chlorophyll a fluorescence by 50\%, and cell radius. We demonstrate a high degree of accuracy overall (\&gt;90\%) in categorising cells belonging to widely recognised key functional groups, however this is reduced when we consider the broader diversity of {\textquotedblleft}nano-phytoflagellates{\textquotedblright}. Notably, we observe that some groups, for example calcifying Isochrysidales, have much greater resilience to electrochemically driven oxidative conditions relative to others of a similar size, making them more easily categorised by the technique. The findings of this study present a promising step forward in advancing our toolkit for monitoring phytoplankton communities. We highlight that, for improved categorisation accuracy, future iterations of the method can be enhanced by measuring additional predictor variables with minimal adjustments to the set-up. In doing so, we foresee this technique being highly applicable, and potentially invaluable, for in situ classification and enumeration of the nanophytoplankton size fraction.</p>
},
	keywords = {RCC1, rcc1084, RCC1130, RCC1150, RCC1178, RCC1185, RCC1198, RCC1216, rcc1217, RCC1242, RCC1314, RCC1346, RCC1489, RCC1511, RCC1546, RCC1557, RCC1614, rcc1731, RCC191, RCC2570, RCC3598, RCC3696, RCC3776, RCC3780, RCC4207, RCC4221, RCC4273, RCC4657, RCC4660, RCC6, RCC623, RCC6516, RCC656, RCC678, RCC69, RCC74, RCC76, RCC8, RCC80, RCC81, RCC88, RCC911, RCC950},
	doi = {10.1002/lom3.10572},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/10.1002/lom3.10572},
	author = {Barton, Samuel and Yang, Minjun and Chen, Haotian and Batchelor-McAuley, Christopher and Compton, Richard and Bouman, Heather and Rickaby, Rosalind}
}
@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 {bendif_rapid_2023,
	title = {Rapid diversification underlying the global dominance of a cosmopolitan phytoplankton},
	journal = {The ISME Journal},
	year = {2023},
	note = {Publisher: Nature Publishing Group},
	pages = {1{\textendash}11},
	abstract = {Marine phytoplankton play important roles in the global ecosystem, with a limited number of cosmopolitan keystone species driving their biomass. Recent studies have revealed that many of these phytoplankton are complexes composed of sibling species, but little is known about the evolutionary processes underlying their formation. Gephyrocapsa huxleyi, a widely distributed and abundant unicellular marine planktonic algae, produces calcified scales (coccoliths), thereby significantly affects global biogeochemical cycles via sequestration of inorganic carbon. This species is composed of morphotypes defined by differing degrees of coccolith calcification, the evolutionary ecology of which remains unclear. Here, we report an integrated morphological, ecological and genomic survey across globally distributed G. huxleyi strains to reconstruct evolutionary relationships between morphotypes in relation to their habitats. While G. huxleyi has been considered a single cosmopolitan species, our analyses demonstrate that it has evolved to comprise at least three distinct species, which led us to formally revise the taxonomy of the G. huxleyi complex. Moreover, the first speciation event occurred before the onset of the last interglacial period (\textasciitilde140 ka), while the second followed during this interglacial. Then, further rapid diversifications occurred during the most recent ice-sheet expansion of the last glacial period and established morphotypes as dominant populations across environmental clines. These results suggest that glacial-cycle dynamics contributed to the isolation of ocean basins and the segregations of oceans fronts as extrinsic drivers of micro-evolutionary radiations in extant marine phytoplankton.},
	keywords = {Microbial biooceanography, phylogenomics, population genetics, rcc1212, RCC1216, rcc1220, RCC1239, RCC1240, RCC1242, RCC1245, rcc1252, RCC1253, RCC1266, RCC1304, rcc1731, RCC1754, RCC1813, RCC1823, rcc1824, RCC1830, RCC1838, RCC1840, RCC1853, RCC1856, RCC3746, RCC4027, RCC4028, RCC4030, RCC5134, RCC5137, RCC5141, RCC6381, RCC6421, RCC6427, RCC6566, RCC6660, RCC6666, RCC911, RCC963},
	issn = {1751-7370},
	doi = {10.1038/s41396-023-01365-5},
	url = {https://www.nature.com/articles/s41396-023-01365-5},
	author = {Bendif, El Mahdi and Probert, Ian and Archontikis, Odysseas A. and Young, Jeremy R. and Beaufort, Luc and Rickaby, Rosalind E. and Filatov, Dmitry}
}
@article {parsy_selection_2023,
	title = {Selection of photosynthetic microorganisms grown in artificial saline industrial effluents with liquid digestate: From screening to consortium cultures},
	journal = {Algal Research},
	year = {2023},
	month = {mar},
	pages = {103061},
	abstract = {The objective of this study was to determine the feasibility of using saline industrial streams as a culture medium to grow microalgae and cyanobacteria. Experiments were performed to determine the extent of the growth in artificial saline produced water and aquifer water supplemented with liquid digestate. Tests were performed in 96-wells microplates. Media were composed with different proportion of saline artificial produced water or aquifer water supplemented with 5\% v/v liquid digestate (final concentrations: 149{\textendash}195 mgN{\textperiodcentered}L-1, 1.5{\textendash}2.7 mgP{\textperiodcentered}L-1). Media were completed to 100 \% with artificial seawater, corresponding to final salinities of 40, 70 and 100 g{\textperiodcentered}L-1. D. salina, N. oceanica and T. suecica showed the best growth rates. They were selected to perform mixed cultures in 80 mL tubes in the same culture media. Population evolutions were followed for 19 days. Depending on salinity and industrial effluent used, different species became predominant over the two others (N. oceanica, T. suecica and D. salina. at 40, 70 and 100 g{\textperiodcentered}L-1, respectively). It appears that mixed culture is a good solution to have a biomass production during a culture process where the culture media will evolve in terms of salinity and composition.},
	keywords = {Aquifer water, cyanobacteria, Liquid digestate, Microalgae, Produced water, RCC4223, RCC537, rcc752},
	issn = {2211-9264},
	doi = {10.1016/j.algal.2023.103061},
	url = {https://www.sciencedirect.com/science/article/pii/S2211926423000942},
	author = {Parsy, Aur{\'e}lien and Sambusiti, Cecilia and Baldoni-Andrey, Patrick and P{\'e}ri{\'e}, Fr{\'e}d{\'e}ric and Guyoneaud, R{\'e}my}
}
@article {dedman_shotgun_2023,
	title = {Shotgun proteomics reveals temperature-dependent regulation of major nutrient metabolism in coastal Synechococcus sp. WH5701},
	journal = {Algal Research},
	year = {2023},
	month = {oct},
	pages = {103279},
	abstract = {Marine cyanobacteria are major contributors to the oceanic carbon sink and are predicted to increase in numbers in the future warmed ocean. As a result, the influence of marine cyanobacteria on marine biogeochemical cycling will likely be enhanced. Associated with elevations in temperature the ocean will undergo increased stratification, reducing supply of essential nutrients to upper phototrophic layers. It is therefore critical that we resolve the manners by which cyanobacteria respond to variations in temperature, and consequences for major nutrient metabolism which may ultimately direct global biogeochemistry and trophic transfer. In this study we use the coastal Synechococcus sp. WH5701 to examine proteomic alterations in major nutrient (C, N and P) metabolic pathways following exposure to varying temperature. In response to temperature treatments, Synechococcus displayed higher rates of growth and photosynthetic efficiency when temperatures were raised from 17 {\textdegree}C to 23 {\textdegree}C and 28 {\textdegree}C, associated with a significant \textasciitilde30{\textendash}40 \% alteration in the cellular proteome. As temperatures increased, proteomic investment towards photosynthetic machinery appeared up-regulated, whilst abundance of RuBisCO was reduced, associated with an apparent alteration in CCM composition and carbon metabolism. N demand appeared to increase in-line with temperature, associated with alterations in the GS-GOGAT pathway, likely due to increased demand for and efficiency of protein synthesis. In contrast, P demand at the highest temperature appeared reduced as investment in the ribosome declines due to improved translation efficiency, whilst luxury P-storage appeared a feature of growth at low temperature. It appears likely that as seawater temperatures rise under ocean warming, the biochemical composition of cyanobacteria will be altered, increasing cellular C- and N- to P ratios, ultimately impacting upon their contribution to oceanic biogeochemical cycling.},
	keywords = {climate change, Ocean warming, phytoplankton, Proteomics: Marine biogeochemistry, rcc1084},
	issn = {2211-9264},
	doi = {10.1016/j.algal.2023.103279},
	url = {https://www.sciencedirect.com/science/article/pii/S2211926423003120},
	author = {Dedman, Craig J. and Barton, Samuel and Fournier, Marjorie and Rickaby, Rosalind E. M.}
}
@article {klintzsch_stable_2023,
	title = {Stable Carbon Isotope Signature of Methane Released from Phytoplankton},
	journal = {Geophysical Research Letters},
	year = {2023},
	month = {feb},
	abstract = {Aquatic ecosystems play an important role in global methane cycling and many field studies have reported methane supersaturation in the oxic surface mixed layer (SML) of the ocean and in the epilimnion of lakes. The origin of methane formed under oxic condition is hotly debated and several pathways have recently been offered to explain the {\textquoteleft}methane paradox{\textquoteright}. In this context, stable isotope measurements have been applied to constrain methane sources in supersaturated oxygenated waters. Here we present stable carbon isotope signatures for six widespread marine phytoplankton species, three haptophyte algae and three cyanobacteria, incubated under laboratory conditions. The observed isotopic patterns implicate that methane formed by phytoplankton might be clearly distinguished from methane produced by methanogenic archaea. Comparing results from phytoplankton experiments with isotopic data from field measurements, suggests that algal and cyanobacterial populations may contribute substantially to methane formation observed in the SML of oceans and lakes.},
	keywords = {RCC1216, ⛔ No DOI found},
	doi = {10.22541/essoar.167689993.32180072/v1},
	url = {https://essopenarchive.org/users/587513/articles/625160-stable-carbon-isotope-signature-of-methane-released-from-phytoplankton?commit=633a121ee07c48e6c59ffeca06fd5d5ebe1df4d4},
	author = {Klintzsch, Thomas and Geisinger, Hannah and Wieland, Anna and Langer, Gerald and Nehrke, Gernot and Bizic, Mina and Greule, Markus and Lenhart, Katharina and Borsch, Christian and Schroll, Moritz and Keppler, Frank}
}
@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 {storti_tailoring_2023,
	title = {Tailoring confocal microscopy for real-time analysis of photosynthesis at single-cell resolution},
	journal = {Cell Reports Methods},
	year = {2023},
	pages = {100568},
	abstract = {Photoautotrophs{\textquoteright} environmental responses have been extensively studied at the organism and ecosystem level. However, less is known about their photosynthesis at the single-cell level. This information is needed to understand photosynthetic acclimation processes, as light changes as it penetrates cells, layers of cells, or organs. Furthermore, cells within the same tissue may behave differently, being at different developmental/ physiological stages. Here, we describe an approach for single-cell and subcellular photophysiology based on the customization of confocal microscopy to assess chlorophyll fluorescence quenching by the saturation pulse method. We exploit this setup to (1) reassess the specialization of photosynthetic activities in developing tissues of non-vascular plants; (2) identify a specific subpopulation of phytoplankton cells in marine photosymbiosis, which consolidate energetic connections with their hosts; and (3) examine the link between light penetration and photoprotection responses inside the different tissues that constitute a plant leaf anatomy.},
	keywords = {rcc1383},
	issn = {26672375},
	doi = {10.1016/j.crmeth.2023.100568},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2667237523002126},
	author = {Storti, Mattia and Hsine, Haythem and Uwizeye, Clarisse and Bastien, Olivier and Yee, Daniel P. and Chevalier, Fabien and Decelle, Johan and Giustini, C{\'e}cile and B{\'e}al, Daniel and Curien, Gilles and Finazzi, Giovanni and Tolleter, Dimitri}
}
@booklet {blocka_taxonomic_2023,
	title = {Taxonomic profling of microbes co-cultured with protists in the Roscoff Culture Collection},
	year = {2023},
	publisher = {ETH Z{\"u}rich},
	type = {Semester Project Report},
	abstract = {The ocean hosts an enormous diversity of microorganisms. However, most of these are notat present available for culture, which makes them difcult to study. We know that manymarine organisms rely on complex nutrient cycles which are difcult to unravel. Microalgaeproduces soluble carbon-, sulfur-, and nitrogen-containing compounds which are taken up byheterotrophic bacteria. The photosynthesizers, on the other hand, often rely on co-factors ofbacterial origin, such as vitamin B12. Since many ocean bacteria may rely on algal organicproducts to obtain essential nutrients, searching for microbes of interest in algal strain culturescan help pinpoint the method of cultivation. In this study, 16S meta-barcoding was performedon bacteria associated to sixty strains from the Roscoff Culture Collection. The bacterial taxonomic composition differed between the algal divisions. Hierarchical clustering revealed interand intra-division differences. The microbiota of the samples mostly belonged to Bacteroidota,Alpha- and Gammaproteobacteria. This is consistent with previous studies on the cycling ofnutrients in the ocean, as these groups are metabolically flexible and ubiquitous heterotrophs.Among the sequenced reads, there appear members of poorly described or undescribed prokaryotic lineages at high taxonomic levels, which could be subject to further study and cultivationefforts. Obtaining these organisms in pure culture could allow the description of new lineagesand their unique metabolisms, and potentially, the production of their bio-products of interest.},
	author = {Blocka, Zuzanna}
}
@article {barbeyron_zobellia_2023,
	title = {\textit{Zobellia alginiliquefaciens sp. nov., a novel member of the flavobacteria isolated from the epibiota of the brown alga Ericaria zosteroides (C. Agardh) Molinari \& Guiry 2020},
	journal = {International Journal of Systematic and Evolutionary Microbiology},
	volume = {73},
	number = {6},
	year = {2023},
	note = {Publisher: Microbiology Society,},
	pages = {005924},
	abstract = {Strain LLG6346-3.1T, isolated from the thallus of the brown alga Ericaria zosteroides collected from the Mediterranean Sea near Bastia in Corsica, France, was characterised using a polyphasic method. Cells were Gram-stain-negative, strictly aerobic, non-flagellated, motile by gliding, rod-shaped and grew optimally at 30{\textendash}33 {\textdegree}C, at pH 8{\textendash}8.5 and with 4{\textendash}5 \% NaCl. LLG6346-3.1T used the seaweed polysaccharide alginic acid as a sole carbon source which was vigorously liquefied. The results of phylogenetic analyses indicated that the bacterium is affiliated to the genus Zobellia (family Flavobacteriaceae , class Flavobacteriia ). LLG6346-3.1T exhibited 16S rRNA gene sequence similarity values of 98.6 and 98.3 \% to the type strains of Zobellia russellii and Zobellia roscoffensis , respectively, and of 97.4{\textendash}98.5 \% to members of other species of the genus Zobellia . The DNA G+C content of LLG6346-3.1T was determined to be 38.3 mol\%. Digital DNA{\textendash}DNA hybridisation predictions by the average nucleotide identity (ANI) and genome to genome distance calculator (GGDC) methods between LLG6346-3.1T and other members of the genus Zobellia showed values of 76{\textendash}88 \% and below 37 \%, respectively. The results of phenotypic, phylogenetic and genomic analyses indicate that LLG6346-3.1T is distinct from species of the genus Zobellia with validly published names and that it represents a novel species of the genus Zobellia , for which the name Zobellia alginiliquefaciens sp. nov. is proposed. The type strain is LLG6346-3.1T (= RCC7657T = LMG 32918T).},
	keywords = {RCC7657},
	issn = {1466-5034},
	doi = {10.1099/ijsem.0.005924},
	url = {https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.005924},
	author = {Barbeyron, Tristan and Le Duff, Nolwen and Duchaud, Eric and Thomas, Fran{\c c}ois}
}
@article {bordiga_unexpected_2023,
	title = {Unexpected silicon localization in calcium carbonate exoskeleton of cultured and fossil coccolithophores},
	journal = {Scientific Reports},
	volume = {13},
	number = {1},
	year = {2023},
	note = {Number: 1 Publisher: Nature Publishing Group},
	month = {may},
	pages = {7417},
	abstract = {Coccolithophores, marine calcifying phytoplankton, are important primary producers impacting the global carbon cycle at different timescales. Their biomineral structures, the calcite containing coccoliths, are among the most elaborate hard parts of any organism. Understanding the morphogenesis of coccoliths is not only relevant in the context of coccolithophore eco-physiology but will also inform biomineralization and crystal design research more generally. The recent discovery of a silicon (Si) requirement for crystal shaping in some coccolithophores has opened up a new avenue of biomineralization research. In order to develop a mechanistic understanding of the role of Si, the presence and localization of this chemical element in coccoliths needs to be known. Here, we document for the first time the uneven Si distribution in Helicosphaera carteri coccoliths through three synchrotron-based techniques employing X-ray Fluorescence and Infrared Spectromicroscopy. The enrichment of Si in specific areas of the coccoliths point to a targeted role of this element in the coccolith formation. Our findings mark a key step in biomineralization research because it opens the door for a detailed mechanistic understanding of the role Si plays in shaping coccolith crystals.},
	keywords = {Biogeochemistry, Marine biology, Palaeontology, RCC1323},
	issn = {2045-2322},
	doi = {10.1038/s41598-023-34003-3},
	url = {https://www.nature.com/articles/s41598-023-34003-3},
	author = {Bordiga, M. and Lupi, C. and Langer, G. and Gianoncelli, A. and Birarda, G. and Pollastri, S. and Bonanni, V. and Bedolla, D. E. and Vaccari, L. and Gariani, G. and Cerino, F. and Cabrini, M. and Beran, A. and Zuccotti, M. and Fiorentino, G. and Zanoni, M. and Garagna, S. and Cobianchi, M. and Di Giulio, A.}
}
@article {walde_viral_2023,
	title = {Viral infection impacts the 3D subcellular structure of the abundant marine diatom Guinardia delicatula},
	journal = {Frontiers in Marine Science},
	volume = {9},
	year = {2023},
	abstract = {Viruses are key players in marine ecosystems where they infect abundant marine microbes. RNA viruses are emerging as key members of the marine virosphere. They have recently been identified as a potential source of mortality in diatoms, a group of microalgae that accounts for roughly 40\% of the primary production in the ocean. Despite their likely importance, their impacts on host populations and ecosystems remain difficult to assess. In this study, we introduce an innovative approach that combines automated 3D confocal microscopy with quantitative image analysis and physiological measurements to expand our understanding of viral infection. We followed different stages of infection of the bloom-forming diatom Guinardia delicatula by the RNA virus GdelRNAV-04 until the complete lysis of the host. From 20h after infection, we observed quantifiable changes in subcellular host morphology and biomass. Our microscopy monitoring also showed that viral infection of G. delicatula induced the formation of auxospores as a probable defense strategy against viruses. Our method enables the detection of discriminative morphological features on the subcellular scale and at high throughput for comparing populations, making it a promising approach for the quantification of viral infections in the field in the future.},
	keywords = {RCC3083, RCC5812},
	issn = {2296-7745},
	doi = {10.3389/fmars.2022.1034235},
	url = {https://www.frontiersin.org/articles/10.3389/fmars.2022.1034235},
	author = {Walde, Marie and Camplong, Cyprien and de Vargas, Colomban and Baudoux, Anne-claire and Simon, Nathalie}
}
@article {sucheras-marx_coccolith_2022,
	title = {Coccolith size rules {\textendash} What controls the size of coccoliths during coccolithogenesis?},
	journal = {Marine Micropaleontology},
	volume = {170},
	year = {2022},
	pages = {102080},
	abstract = {Heterococcoliths are calcite platelets produced inside diploid coccolithophore cells and extruded to form a covering on the cell surface called a coccosphere. The size of coccoliths is an important parameter sometimes used to identify species, and it is observed to be influenced in extant species by abiotic parameters (e.g., CO2, light). However, the variable distribution of coccolith sizes occurring within a single coccosphere questions the mechanisms controlling coccolith size. A relationship between cell/coccosphere size and mean coccolith size was previously identified, called the {\textquotedblleft}coccolithophore size rules{\textquotedblright}. In this study, we query the mechanisms controlling the size of a coccolith during coccolithogenesis. A culture experiment on Gephyrocapsa huxleyi strain RCC1216 shows that coccolithogenesis occurs during the cell growth G1 interphase and newly produced coccoliths get bigger as the cell grows. These observations provide parameters for the development of two numerical models used to simulate the coccolith size distribution within a coccolithophore population. Neither model can accurately reproduce an empirical monoclonal coccolith size distribution, indicating that additional factors influence coccolith size. According to our results, coccolith size is only clearly related to cell size at the time of its formation. We confirm that application of the coccolithophore size rules model should be limited to inferring average cell dimensions from (fossil) coccolith biometry, and that comparisons are valid only in multipopulational studies. The coccolith size rule model {\textendash} the constraining effect of coccolith production during G1 interphase cell growth on coccolith size {\textendash} proposed here is applicable only for some placolith-forming species.},
	keywords = {Biometry, coccolith, coccolithophore, life cycle, RCC1216, Size variation},
	issn = {0377-8398},
	doi = {10.1016/j.marmicro.2021.102080},
	url = {https://www.sciencedirect.com/science/article/pii/S0377839821001213},
	author = {Such{\'e}ras-Marx, Baptiste and Viseur, Sophie and Walker, Charlotte E. and Beaufort, Luc and Probert, Ian and Bolton, Clara}
}
@article {sorokina_draft_2022,
	title = {Draft genome assembly and sequencing dataset of the marine diatom Skeletonema costatum RCC75},
	journal = {Data in Brief},
	year = {2022},
	month = {feb},
	pages = {107931},
	abstract = {Diatoms (Bacillariophyceae) are a major constituent of the phytoplankton and have a universally recognized ecological importance. Between 1,000 and 1,300 diatom genera have been described in the literature, but only 10 nuclear genomes have been published and made available to the public up to date. Skeletonema costatum is a cosmopolitan marine diatom, principally occurring in coastal regions, and is one of the most abundant members of the Skeletonema genus. Here we present a draft assembly of the Skeletonema costatum RCC75 genome, obtained from PacBio and Illumina NovaSeq data. This dataset will expand the knowledge of the Bacillariophyceae genetics and contribute to the global understanding of phytoplankton{\textquoteright}s physiological, ecological, and environmental functioning.},
	keywords = {Algal genome, BACILLARIOPHYCEAE, diatoms, genome sequencing, Illumina sequencing, PacBio sequencing, RCC75},
	issn = {2352-3409},
	doi = {10.1016/j.dib.2022.107931},
	url = {https://www.sciencedirect.com/science/article/pii/S2352340922001433},
	author = {Sorokina, Maria and Barth, Emanuel and Zulfiqar, Mahnoor and Kwantes, Michiel and Pohnert, Georg and Steinbeck, Christoph}
}
@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 {dore_global_2022,
	title = {Global Phylogeography of Marine Synechococcus in Coastal Areas Reveals Strong Community Shifts},
	journal = {mSystems},
	year = {2022},
	note = {Publisher: American Society for Microbiology},
	pages = {e00656{\textendash}22},
	abstract = {Marine Synechococcus comprise a numerically and ecologically prominent phytoplankton group, playing a major role in both carbon cycling and trophic networks in all oceanic regions except in the polar oceans. Despite their high abundance in coastal areas, our knowledge of Synechococcus communities in these environments is based on only a few local studies. Here, we use the global metagenome data set of the Ocean Sampling Day (June 21st, 2014) to get a snapshot of the taxonomic composition of coastal Synechococcus communities worldwide, by recruitment on a reference database of 141 picocyanobacterial genomes, representative of the whole Prochlorococcus, Synechococcus, and Cyanobium diversity. This allowed us to unravel drastic community shifts over small to medium scale gradients of environmental factors, in particular along European coasts. The combined analysis of the phylogeography of natural populations and the thermophysiological characterization of eight strains, representative of the four major Synechococcus lineages (clades I to IV), also brought novel insights about the differential niche partitioning of clades I and IV, which most often co-dominate the Synechococcus community in cold and temperate coastal areas. Altogether, this study reveals several important characteristics and specificities of the coastal communities of Synechococcus worldwide. IMPORTANCE Synechococcus is the second most abundant phytoplanktonic organism on Earth, and its wide genetic diversity allowed it to colonize all the oceans except for polar waters, with different clades colonizing distinct oceanic niches. In recent years, the use of global metagenomics data sets has greatly improved our knowledge of {\textquotedblleft}who is where{\textquotedblright} by describing the distribution of Synechococcus clades or ecotypes in the open ocean. However, little is known about the global distribution of Synechococcus ecotypes in coastal areas, where Synechococcus is often the dominant phytoplanktonic organism. Here, we leverage the global Ocean Sampling Day metagenomics data set to describe Synechococcus community composition in coastal areas worldwide, revealing striking community shifts, in particular along the coasts of Europe. As temperature appears as an important driver of the community composition, we also characterize the thermal preferenda of 8 Synechococcus strains, bringing new insights into the adaptation to temperature of the dominant Synechococcus clades.},
	keywords = {RCC1086, RCC1695, RCC2369, rcc2380, RCC2553, RCC2556, RCC2570, rcc791},
	doi = {10.1128/msystems.00656-22},
	url = {https://journals.asm.org/doi/full/10.1128/msystems.00656-22},
	author = {Dor{\'e}, Hugo and Leconte, Jade and Guyet, Ulysse and Breton, Sol{\`e}ne and Farrant, Gregory K. and Demory, David and Ratin, Morgane and Hoebeke, Mark and Corre, Erwan and Pitt, Frances D. and Ostrowski, Martin and Scanlan, David J. and Partensky, Fr{\'e}d{\'e}ric and Six, Christophe and Garczarek, Laurence}
}
@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 {parsy_impact_2022,
	title = {Impact of salinities, metals and organic compounds found in saline oil \& gas produced water on microalgae and cyanobacteria},
	journal = {Ecotoxicology and Environmental Safety},
	volume = {234},
	year = {2022},
	pages = {113351},
	abstract = {This work evaluates the impact of salinity and the toxicity of some metals and organic compounds commonly found in produced waters on the growth of model photosynthetic organisms. Five strains of marine microalgae and one cyanobacteria (i.e. Dunaliella salina, Nannochloropsis oceanica, Tetraselmis suecica, Picochlorum cos- tavermella, Coccomyxa simplex and Synechococcus rubescens) were tested in microplates as well as the freshwater Chlorella vulgaris selected as reference. Results revealed that D.salina was able to growth at high salinity (up to 135 g.L- 1). Copper was the most toxic metal for all strains (half maximal effective concentration between 0.1 and 10 mg.L- 1) except for D.salina and C.simplex. These two strains were the most resistant to all metals tested. All organic compounds presented half maximal effective concentration above 10 mg.L- 1, none of them being very toxic for the studied microorganisms. P.costavermella and C.simplex were the most resistant strains to organic compounds. Looking at tolerance to salinity, metals and organic compounds, D.salina appeared to be the best choice for biomass production in produced waters. In addition, growths in 80\% artificial produced water sup- plemented with f medium confirm the feasibility to use this medium to produce biomass.},
	keywords = {RCC4223, RCC537, rcc752},
	issn = {01476513},
	doi = {10.1016/j.ecoenv.2022.113351},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0147651322001919},
	author = {Parsy, Aur{\'e}lien and Guyoneaud, R{\'e}my and Lot, Marie-Claire and Baldoni-Andrey, Patrick and P{\'e}ri{\'e}, Fr{\'e}d{\'e}ric and Sambusiti, Cecilia}
}
@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 {falciatore_light-driven_2022,
	title = {Light-driven processes: key players of the functional biodiversity in microalgae},
	journal = {Comptes Rendus. Biologies},
	volume = {345},
	number = {2},
	year = {2022},
	pages = {1{\textendash}24},
	doi = {10.5802/crbiol.80},
	url = {https://comptes-rendus.academie-sciences.fr/biologies/articles/10.5802/crbiol.80/},
	author = {Falciatore, Angela and Bailleul, Benjamin and Boulouis, Alix and Bouly, Jean-Pierre and Bujaldon, Sandrine and Cheminant-Navarro, Soizic and Choquet, Yves and Vitry, Catherine de and Eberhard, Stephan and Jaubert, Marianne and Kuras, Richard and Lafontaine, Ingrid and Landier, Sophie and Selles, Julien and Vallon, Olivier and Wostrikoff, Katia}
}
@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 {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 {fan_quantifying_2022,
	title = {Quantifying the Extent of Calcification of a Coccolithophore Using a Coulter Counter},
	journal = {Analytical Chemistry},
	year = {2022},
	month = {sep},
	pages = {acs.analchem.2c01971},
	abstract = {Although, in principle, the Coulter Counter technique yields an absolute measure of particle volume, in practice, calibration is nearuniversally employed. For regularly shaped and non-biological samples, the use of latex beads for calibration can provide sufficient accuracy. However, this is not the case with particles encased in biogenically formed calcite. To date, there has been no effective route by which a Coulter Counter can be calibrated to enable the calcification of coccolithophores�single cells encrusted with biogenic calcite�to be quantified. Consequently, herein, we seek to answer the following question: to what extent can a Coulter Counter be used to provide accurate information regarding the calcite content of a singlespecies coccolithophore population? Through the development of a new calibration methodology, based on the measurement and dynamic tracking of the acid-driven calcite dissolution reaction, a route by which the cellular calcite content can be determined is presented. This new method allows, for the first time, a Coulter Counter to be used to yield an absolute measurement of the amount of calcite per cell.},
	keywords = {RCC1198, RCC1216, RCC1314},
	issn = {0003-2700, 1520-6882},
	doi = {10.1021/acs.analchem.2c01971},
	url = {https://pubs.acs.org/doi/10.1021/acs.analchem.2c01971},
	author = {Fan, Xinmeng and Batchelor-McAuley, Christopher and Yang, Minjun and Barton, Samuel and Rickaby, Rosalind E. M. and Bouman, Heather A. and Compton, Richard G.}
}
@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 {schmitt_temperature_2022,
	title = {Temperature Affects the Biological Control of Dinoflagellates by the Generalist Parasitoid Parvilucifera rostrata},
	journal = {Microorganisms},
	volume = {10},
	number = {2},
	year = {2022},
	note = {Number: 2 Publisher: Multidisciplinary Digital Publishing Institute},
	pages = {385},
	abstract = {The increase in emerging harmful algal blooms in the last decades has led to an extensive concern in understanding the mechanisms behind these events. In this paper, we assessed the growth of two blooming dinoflagellates (Alexandrium minutum and Heterocapsa triquetra) and their susceptibility to infection by the generalist parasitoid Parvilucifera rostrata under a temperature gradient. The growth of the two dinoflagellates differed across a range of temperatures representative of the Penz{\'e} Estuary (13 to 22 {\textdegree}C) in early summer. A. minutum growth increased across this range and was the highest at 19 and 22 {\textdegree}C, whereas H. triquetra growth was maximal at intermediate temperatures (15{\textendash}18 {\textdegree}C). Interestingly, the effect of temperature on the parasitoid infectivity changed depending on which host dinoflagellate was infected with the dinoflagellate responses to temperature following a positive trend in A. minutum (higher infections at 20{\textendash}22 {\textdegree}C) and a unimodal trend in H. triquetra (higher infections at 18 {\textdegree}C). Low temperatures negatively affected parasitoid infections in both hosts (i.e., {\textquotedblleft}thermal refuge{\textquotedblright}). These results demonstrate how temperature shifts may not only affect bloom development in microalgal species but also their control by parasitoids.},
	keywords = {dinoflagellate blooms, functional response, parasitic control, RCC2800, RCC2823, RCC2982, RCC3018, RCC4398, temperature effect},
	issn = {2076-2607},
	doi = {10.3390/microorganisms10020385},
	url = {https://www.mdpi.com/2076-2607/10/2/385},
	author = {Schmitt, Matthew and Telusma, Aaron and Bigeard, Estelle and Guillou, Laure and Alves-de-Souza, Catharina}
}
@article {eyal_variability_2022,
	title = {The variability in the structural and functional properties of coccolith base plates},
	journal = {Acta Biomaterialia},
	volume = {148},
	year = {2022},
	pages = {336{\textendash}344},
	abstract = {Biomineralization processes exert varying levels of control over crystallization, ranging from poorly ordered polycrystalline arrays to intricately shaped single crystals. Coccoliths, calcified scales formed by unicellular algae, are a model for a highly controlled crystallization process. The coccolith crystals nucleate next to an organic oval structure that was termed the base plate, leading to the assumption that it is responsible for the oriented nucleation of the crystals via stereochemical interactions. In recent years, several works focusing on a well-characterized model species demonstrated a fundamental role for indirect interactions that facilitate coccolith crystallization. Here, we developed the tools to extract the base plates from five different species, giving the opportunity to systematically explore the relations between base plate and coccolith properties. We used multiple imaging techniques to evaluate the structural and chemical features of the base plates under native hydrated conditions. The results show a wide range of properties, overlaid on a common rudimentary scaffold that lacks any detectable structural or chemical motifs that can explain direct nucleation control. This work emphasizes that it is the combination between the base plate and the chemical environment inside the cell that cooperatively facilitate the exquisite control over the crystallization process. Statement of significance Biological organic scaffolds can serve as functional surfaces that guide the formation of inorganic materials. However, in many cases the specific interactions that facilitate such tight regulation are complex and not fully understood. In this work, we elucidate the architecture of such amodel biological template, an organic scale that directs the assembly of exquisite crystalline arrays of marine microalgae. By using cryo electron microscopy, we reveal the native state organization of these scales from several species. The observed similarities and differences allow us to propose that the chemical microenvironment, rather than stereochemical matching, is the pivotal regulator of the process.},
	keywords = {biomineralization, Calcite, Coccoliths, Cryo electron tomography, Crystallization, RCC1130, RCC1181, RCC190, RCC3777},
	issn = {1742-7061},
	doi = {10.1016/j.actbio.2022.06.027},
	url = {https://www.sciencedirect.com/science/article/pii/S174270612200366X},
	author = {Eyal, Zohar and Krounbi, Leilah and Ben Joseph, Oz and Avrahami, Emanuel M. and Pinkas, Iddo and Peled-Zehavi, Hadas and Gal, Assaf}
}
@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 {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 {croteau_contrasting_2021,
	title = {Contrasting nonphotochemical quenching patterns under high light and darkness aligns with light niche occupancy in Arctic diatoms},
	journal = {Limnology and Oceanography},
	volume = {66},
	number = {S1},
	year = {2021},
	note = {_eprint: https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.1002/lno.11587},
	pages = {S231{\textendash}S245},
	abstract = {Over the seasons, Arctic diatom species occupy shifting habitats defined by contrasting light climates, constrained by snow and ice cover dynamics interacting with extreme photoperiod and solar angle variations. How Arctic diatom photoadaptation strategies differ across their heterogeneous light niches remains a poorly documented but crucial missing link to anticipate Arctic Ocean responses to shrinking sea-ice and increasing light. To address this question, we selected five Arctic diatom species with diverse life traits, representative of distinct light niches across the seasonal light environment continuum: from snow-covered dimly lit bottom ice to summer stratified waters. We studied their photoacclimation plasticity to two growth light levels and the subsequent responses of their nonphotochemical quenching (NPQ) and xanthophyll cycle to both dark incubations and light shifts. We deciphered NPQ and xanthophyll cycle tuning in darkness and their light-dependent induction kinetics, which aligned with species{\textquoteright} light niche occupancy. In ice-related species, NPQ was sustained in darkness and its induction was more reactive to moderate light shifts. Open-water species triggered strong NPQ induction in darkness and reached higher maximal NPQ under high light. Marginal ice zone species showed strong adaptation to light fluctuations with a dark response fine-tuned depending upon light history. We argue these traits are anchored in diverging photoadaption strategies fostering Arctic diatom success in their respective light niches.},
	keywords = {RCC2046, RCC2278, RCC5318},
	issn = {1939-5590},
	doi = {10.1002/lno.11587},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lno.11587},
	author = {Croteau, Dany and Gu{\'e}rin, S{\'e}bastien and Bruyant, Flavienne and Ferland, Joannie and Campbell, Douglas A. and Babin, Marcel and Lavaud, Johann}
}
@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 {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}
}
@article {benites_evolutionary_2021,
	title = {Evolutionary Genomics of Sex-Related Chromosomes at the Base of the Green Lineage},
	journal = {Genome Biology and Evolution},
	volume = {13},
	number = {10},
	year = {2021},
	pages = {evab216},
	abstract = {Although sex is now accepted as a ubiquitous and ancestral feature of eukaryotes, direct observation of sex is still lacking in most unicellular eukaryotic lineages. Evidence of sex is frequently indirect and inferred from the identification of genes involved in meiosis from whole genome data and/or the detection of recombination signatures from genetic diversity in natural populations. In haploid unicellular eukaryotes, sex-related chromosomes are named mating-type (MTs) chromosomes and generally carry large genomic regions where recombination is suppressed. These regions have been characterized in Fungi and Chlorophyta and determine gamete compatibility and fusion. Two candidate MT{\th} and MT{\`A} alleles, spanning 450{\textendash}650 kb, have recently been described in Ostreococcus tauri, a marine phytoplanktonic alga from the Mamiellophyceae class, an early diverging branch in the green lineage. Here, we investigate the architecture and evolution of these candidate MT{\th} and MT{\`A} alleles. We analyzed the phylogenetic profile and GC content of MT gene families in eight different genomes whose divergence has been previously estimated at up to 640 Myr, and found evidence that the divergence of the two MT alleles predates speciation in the Ostreococcus genus. Phylogenetic profiles of MT transspecific polymorphisms in gametologs disclosed candidate MTs in two additional species, and possibly a third. These Mamiellales MT candidates are likely to be the oldest mating-type loci described to date, which makes them fascinating models to investigate the evolutionary mechanisms of haploid sex determination in eukaryotes.},
	keywords = {RCC1105, RCC1115, RCC2590, RCC299, rcc3401, RCC4221, RCC809, RCC834},
	issn = {1759-6653},
	doi = {10.1093/gbe/evab216},
	url = {https://academic.oup.com/gbe/article/doi/10.1093/gbe/evab216/6380139},
	author = {Benites, Luis Felipe and Bucchini, Fran{\c c}ois and Sanchez-Brosseau, Sophie and Grimsley, Nigel and Vandepoele, Klaas and Piganeau, Gwenael},
	editor = {Wolfe, Kenneth}
}
@article {bock_experimental_2021,
	title = {Experimental identification and in silico prediction of bacterivory in green algae},
	journal = {The ISME Journal},
	year = {2021},
	note = {Publisher: Nature Publishing Group},
	month = {mar},
	pages = {1{\textendash}14},
	abstract = {While algal phago-mixotrophs play a major role in aquatic microbial food webs, their diversity remains poorly understood. Recent studies have indicated several species of prasinophytes, early diverging green algae, to be able to consume bacteria for nutrition. To further explore the occurrence of phago-mixotrophy in green algae, we conducted feeding experiments with live fluorescently labeled bacteria stained with CellTracker Green CMFDA, heat-killed bacteria stained with 5-(4,6-dichlorotriazin-2-yl) aminofluorescein (DTAF), and magnetic beads. Feeding was detected via microscopy and/or flow cytometry in five strains of prasinophytes when provided with live bacteria: Pterosperma cristatum NIES626, Pyramimonas parkeae CCMP726, Pyramimonas parkeae NIES254, Nephroselmis pyriformis RCC618, and Dolichomastix tenuilepis CCMP3274. No feeding was detected when heat-killed bacteria or magnetic beads were provided, suggesting a strong preference for live prey in the strains tested. In parallel to experimental assays, green algal bacterivory was investigated using a gene-based prediction model. The predictions agreed with the experimental results and suggested bacterivory potential in additional green algae. Our observations underline the likelihood of widespread occurrence of phago-mixotrophy among green algae, while additionally highlighting potential biases introduced when using prey proxy to evaluate bacterial ingestion by algal cells.},
	keywords = {RCC180, RCC3375, RCC369, RCC618},
	issn = {1751-7370},
	doi = {10.1038/s41396-021-00899-w},
	url = {http://www.nature.com/articles/s41396-021-00899-w},
	author = {Bock, Nicholas A. and Charvet, Sophie and Burns, John and Gyaltshen, Yangtsho and Rozenberg, Andrey and Duhamel, Solange and Kim, Eunsoo}
}
@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 {Henry2021,
	title = {The influences of phytoplankton species, mineral particles and concentrations of dispersed oil on the formation and fate of marine oil-related aggregates},
	journal = {Science of the Total Environment},
	volume = {752},
	year = {2021},
	note = {Publisher: Elsevier B.V. tex.mendeley-tags: RCC1698,RCC1719,RCC290},
	month = {jan},
	pages = {141786},
	abstract = {The formation and fallout of oil-related marine snow have been associated with interactions between dispersed oil and small marine particles, like phytoplankton and mineral particles. In these studies, the influences of phytoplankton species, mineral particle concentration, and oil concentration on the aggregation of oil in seawater (SW) were investigated. The experiments were performed in a low-turbidity carousel incubation system, using natural SW at 13 {\textdegree}C. Aggregation was measured by silhouette camera analyses, and oil compound group distribution and depletion by gas chromatography (GC-FID or GC{\textendash}MS). Aggregates with median sizes larger than 500 ??m in diameter were measured in the presence of dispersed oil and the phytoplankton species Thalassiosira rotula, Phaeocystis globosa, Skeletonema pseudocostatum, but not with the microalgae Micromonas pusilla. When mineral particles (diatomaceous earth) were incubated at different concentrations (5{\textendash}30 mg/L) with dispersed oil and S. pseudocostatum, the largest aggregates were measured at the lower mineral particle concentration (5 mg/L). Since dispersed oil rapidly dilutes in the marine water column, experiments were performed with oil concentrations of from 10 mg/L to 0.01 mg/L in the presence of S. pseudocostatum and diatomaceous earth. Aggregates larger than 500 ??m was measured only at the highest oil concentrations (10 mg/L). However, oil attachment to the marine particles were also measured at low oil concentrations (<=1 mg/L). Depletion of oil compound groups (n-alkanes, naphthalenes, PAHs, decalins) were measured at all oil concentrations, both in aggregate and water phases, with biodegradation as the expected main depletion process. These results showed that oil concentration may be important for oil-related marine snow formation, but that even oil droplets at low concentrations may attach to the particles and be transported by prevailing currents.},
	keywords = {Aggregation, Dispersed oil, Marine snow, Mineral particles, phytoplankton, RCC1698, RCC1719, RCC290},
	issn = {18791026},
	doi = {10.1016/j.scitotenv.2020.141786},
	author = {Henry, Ingrid A. and Netzer, Roman and Davies, Emlyn and Brakstad, Odd Gunnar}
}
@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 {dayras_microalgal_2021,
	title = {Microalgal Diet Influences the Nutritive Quality and Reproductive Investment of the Cyclopoid Copepod Paracyclopina nana},
	journal = {Frontiers in Marine Science},
	volume = {8},
	year = {2021},
	pages = {1147},
	abstract = {Copepods represent an interesting alternative or a complement live food to brine shrimps and rotifers commonly used in aquaculture. They constitute the natural prey of many fish species and therefore do not require a potential nutritional enrichment. But an optimization of the microalgal diets used to feed copepods is essential to improve their mass culture. This study examined the effects of seven microalgal diets, namely single-species diets of Rhodomonas salina (R), Tisochrysis lutea (T), and Pavlova lutheri (=Diacronema lutheri) (P), two-species diets (R + T, T + P, and R + P), and a three-species diet (R + T + P), on the fatty acid and monosaccharide composition of the cyclopoid copepod Paracyclopina nana as well as its reproductive investment. Experiments were run during 15 days in 10-L beakers; starting with nauplii collected from a large 300-L batch culture. Copepods fatty acid contents were studied, particularly the relative amounts of docosahexaenoic acid (DHA) and eicosa-pentaenoic acid (EPA). The R + T, R, and T diets induced the highest total fatty acid amount in copepods. R + T and R also generated the lowest DHA/EPA ratios in copepods due to high EPA contents. The highest value of total monosaccharides was found in copepods fed with R + T + P. Diets R + T and R induced the greatest prosome volumes and clutch volumes in ovigerous females. Both prosome volume and clutch volume in P. nana ovigerous females were correlated to the individual EPA amount. The results demonstrated that all diets including R. salina enhanced the productivity of P. nana in mass culture, particularly when combined with T. lutea. R. salina, and T. lutea induced complementary fatty acid and monosaccharide profiles, confirming that R + T represents the best microalgae combination for productive culture of P. nana. Conversely, P. lutheri did not enhance the nutritional profile nor the fecundity of P. nana in the culture. This study is the first to demonstrate that R. salina is a suitable microalga for productive mass culture of P. nana for use as live food in aquaculture.},
	keywords = {rcc, RCC1349, RCC1537, RCC20},
	issn = {2296-7745},
	doi = {10.3389/fmars.2021.697561},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2021.697561},
	author = {Dayras, Paul and Bialais, Capucine and Sadovskaya, Irina and Lee, Min-Chul and Lee, Jae-Seong and Souissi, Sami}
}
@mastersthesis {busse_mixotrophy_2021,
	title = {Mixotrophy by Phytoflagellates in the Northern Gulf of Alaska: Impacts of Physico-Chemical Characteristics and Prey Concentration on Feeding by Photosynthetic Nano- and Dinoflagellates},
	year = {2021},
	school = {Western Washington University},
	type = {masters},
	keywords = {? No DOI found, RCC3010},
	author = {Busse, Hana}
}
@article {filatov_mode_2021,
	title = {The mode of speciation during a recent radiation in open-ocean phytoplankton},
	journal = {Current Biology},
	year = {2021},
	month = {oct},
	abstract = {Despite the enormous ecological importance of marine phytoplankton, surprisingly little is known about how new phytoplankton species originate and evolve in the open ocean, in the absence of apparent geographic barriers that typically act as isolation mechanisms in speciation. To investigate the mechanism of open-ocean speciation, we combined fossil and climatic records from the late Quaternary with genome-wide evolutionary genetic analyses of speciation in the ubiquitous and abundant pelagic coccolithophore genus Gephyrocapsa (including G. huxleyi, formerly known as Emiliania huxleyi). Based on the analysis of 43 sequenced genomes, we report that the best-fitting scenario for all speciation events analyzed included an extended period of complete isolation followed by recent (Holocene) secondary contact, supporting the role of geographic or oceanographic barriers in population divergence and speciation. Consistent with this, fossil data reveal considerable diachroneity of species first occurrence. The timing of all speciation events coincided with glacial phases of glacial-interglacial cycles, suggesting that stronger isolation between the ocean basins and increased segregation of ecological niches during glaciations are important drivers of speciation in marine phytoplankton. The similarity across multiple speciation events implies the generality of this inferred speciation scenario for marine phytoplankton.},
	keywords = {phytoplankton, population genetic modeling, rcc1212, rcc1238, RCC1239, RCC1253, RCC1281, RCC1296, RCC1310, RCC1314, RCC1562, RCC1836, RCC3370, RCC3711, RCC3733, RCC3862, RCC3898, RCC4002, RCC4028, RCC4030, RCC4032, RCC4033, RCC4034, RCC4035, RCC4036, RCC5119, RCC5134, RCC5137, RCC5141, RCC6566, RCC6730, secondary contact, sequence polymorphism, speciation},
	issn = {0960-9822},
	doi = {10.1016/j.cub.2021.09.073},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982221013415},
	author = {Filatov, Dmitry A. and Bendif, El Mahdi and Archontikis, Odysseas A. and Hagino, Kyoko and Rickaby, Rosalind E. M.}
}
@article {jimenez_no_2021,
	title = {No evidence of Phago-mixotropy in Micromonas polaris (Mamiellophyceae), the Dominant Picophytoplankton Species in the Arctic},
	journal = {Journal of Phycology},
	volume = {57},
	number = {2},
	year = {2021},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jpy.13125},
	pages = {435{\textendash}446},
	abstract = {In the Arctic Ocean, the small green alga Micromonas polaris dominates picophytoplankton during the summer months but is also present in winter. It has been previously hypothesized to be phago-mixotrophic (capable of bacteria ingestion) based on laboratory and field experiments. Prey uptake was analyzed in several M. polaris strains isolated from different regions and depths of the Arctic Ocean and in Ochromonas triangulata, a known phago-mixotroph used as a control. Measuring ingestion of either fluorescent beads or fluorescently labeled bacteria by flow cytometry, we found no evidence of phago-mixotrophy in any M. polaris strain while O. triangulata was ingesting both beads and bacteria. In addition, in silico predictions revealed that members of the genus Micromonas lack a genetic signature of phagocytotic capacity.},
	keywords = {Arctic, Micromonas, phago-mixotrophy, phytoplankton, rcc, RCC21, RCC2288, RCC2306, RCC4298},
	issn = {1529-8817},
	doi = {10.1111/jpy.13125},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.13125},
	author = {Jimenez, Valeria and Burns, John A. and Le Gall, Florence and Not, Fabrice and Vaulot, Daniel}
}
@article {yang_opto-electrochemical_2021,
	title = {Opto-Electrochemical Dissolution Reveals Coccolith Calcium Carbonate Content},
	journal = {Angewandte Chemie International Edition},
	volume = {60},
	number = {38},
	year = {2021},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/anie.202108435},
	pages = {20999{\textendash}21006},
	abstract = {Coccoliths are plates of biogenic calcium carbonate secreted by calcifying marine phytoplankton; annually these phytoplankton are responsible for exporting >1 billion tonnes (1015 g) of calcite to the deep ocean. Rapid and reliable methods for assessing the degree of calcification are technically challenging because the coccoliths are micron sized and contain picograms (pg) of calcite. Here we pioneer an opto-eletrochemical acid titration of individual coccoliths which allows 3D reconstruction of each individual coccolith via in situ optical imaging enabling direct inference of the coccolith mass. Coccolith mass ranging from 2 to 400 pg are reported herein, evidencing both inter- and intra-species variation over four different species. We foresee this scientific breakthrough, which is independent of knowledge regarding the species and calibration-free, will allow continuous monitoring and reporting of the degree of coccolith calcification in the changing marine environment.},
	keywords = {analytical methods, calcite dissolution, electrochemistry, global carbonate cycle, marine phytoplankton, RCC1130, RCC1198, RCC1216, RCC1314},
	issn = {1521-3773},
	doi = {10.1002/anie.202108435},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.202108435},
	author = {Yang, Minjun and Batchelor-McAuley, Christopher and Barton, Samuel and Rickaby, Rosalind E. M. and Bouman, Heather A. and Compton, Richard G.}
}
@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 {royer_response_2021,
	title = {Response of dimethylsulfoniopropionate (DMSP) and dimethylsulfoxide (DMSO) cell quotas to oxidative stress in three phytoplankton species},
	journal = {Journal of Plankton Research},
	volume = {43},
	number = {5},
	year = {2021},
	month = {sep},
	pages = {673{\textendash}690},
	abstract = {Several phytoplankton species produce the metabolites dimethylsulfoniopropionate (DMSP) and dimethylsulfoxide (DMSO) but their intracellular roles need to be better understood. To improve the understanding of the DMSP antioxidant function suggested by Sunda et al. (2002), we exposed the diatom Skeletonema costatum, the Prymnesiophyceae Phaeocystis globosa and the dinoflagellate Heterocapsa triquetra to experimental treatments known to cause potential oxidative stress (high light intensities (HL); HL with 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU); menadione sodium bisulfite (MSB)). DMSP and DMSO concentrations decreased after 6 h in all treatments indicating an interaction with Reactive Oxygen Species (ROS) produced. DMSP and DMSO-to-cell ratios in control conditions were higher for H. triquetra, while being unable to grow under HL. DMSP and DMSO-to-cell carbon were the highest for P. globosa, while the other species had similar values. During long-term treatment, these ratios were not increased in high-light grown cells of P. globosa and S. costatum. Overall, this illustrates that (1) the DMSP- and DMSO-to-cell or carbon seems to be not indicative of the capability of the species to tolerate an oxidative stress, (2) these molecules could react with ROS and lower their cellular concentration, but no clues demonstrated that these molecules are part of the antioxidant response of the cell.},
	keywords = {rcc, RCC1719, RCC4800},
	issn = {0142-7873},
	doi = {10.1093/plankt/fbab052},
	url = {https://doi.org/10.1093/plankt/fbab052},
	author = {Royer, C and Gypens, N and Cardol, P and Borges, A V and Roberty, S}
}
@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 {gebuhr_strain-specific_2021,
	title = {Strain-specific morphological response of the dominant calcifying phytoplankton species Emiliania huxleyi to salinity change},
	journal = {PLOS ONE},
	volume = {16},
	number = {2},
	year = {2021},
	note = {Publisher: Public Library of Science},
	month = {feb},
	pages = {e0246745},
	abstract = {The future physiology of marine phytoplankton will be impacted by a range of changes in global ocean conditions, including salinity regimes that vary spatially and on a range of short- to geological timescales. Coccolithophores have global ecological and biogeochemical significance as the most important calcifying marine phytoplankton group. Previous research has shown that the morphology of their exoskeletal calcified plates (coccoliths) responds to changing salinity in the most abundant coccolithophore species, Emiliania huxleyi. However, the extent to which these responses may be strain-specific is not well established. Here we investigated the growth response of six strains of E. huxleyi under low (ca. 25) and high (ca. 45) salinity batch culture conditions and found substantial variability in the magnitude and direction of response to salinity change across strains. Growth rates declined under low and high salinity conditions in four of the six strains but increased under both low and high salinity in strain RCC1232 and were higher under low salinity and lower under high salinity in strain PLYB11. When detailed changes in coccolith and coccosphere size were quantified in two of these strains that were isolated from contrasting salinity regimes (coastal Norwegian low salinity of ca. 30 and Mediterranean high salinity of ca. 37), the Norwegian strain showed an average 26\% larger mean coccolith size at high salinities compared to low salinities. In contrast, coccolith size in the Mediterranean strain showed a smaller size trend (11\% increase) but severely impeded coccolith formation in the low salinity treatment. Coccosphere size similarly increased with salinity in the Norwegian strain but this trend was not observed in the Mediterranean strain. Coccolith size changes with salinity compiled for other strains also show variability, strongly suggesting that the effect of salinity change on coccolithophore morphology is likely to be strain specific. We propose that physiological adaptation to local conditions, in particular strategies for plasticity under stress, has an important role in determining ecotype responses to salinity.},
	keywords = {Calcification, Carbonates, Ecophysiology, Marine ecology, Marine geology, Morphometry, Paleoclimatology, rcc1210, RCC1232, rcc1824, rcc868, RCC904, salinity},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0246745},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0246745},
	author = {Geb{\"u}hr, Christina and Sheward, Rosie M. and Herrle, Jens O. and Bollmann, J{\"o}rg}
}
@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 {bachy_viruses_2021,
	title = {Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts},
	journal = {The ISME Journal},
	year = {2021},
	note = {Publisher: Nature Publishing Group},
	month = {may},
	pages = {1{\textendash}19},
	abstract = {The marine picoeukaryote Bathycoccus prasinos has been considered a cosmopolitan alga, although recent studies indicate two ecotypes exist, Clade BI (B. prasinos) and Clade BII. Viruses that infect Bathycoccus Clade BI are known (BpVs), but not that infect BII. We isolated three dsDNA prasinoviruses from the Sargasso Sea against Clade BII isolate RCC716. The BII-Vs do not infect BI, and two (BII-V2 and BII-V3) have larger genomes (\textasciitilde210 kb) than BI-Viruses and BII-V1. BII-Vs share \textasciitilde90\% of their proteins, and between 65\% to 83\% of their proteins with sequenced BpVs. Phylogenomic reconstructions and PolB analyses establish close-relatedness of BII-V2 and BII-V3, yet BII-V2 has 10-fold higher infectivity and induces greater mortality on host isolate RCC716. BII-V1 is more distant, has a shorter latent period, and infects both available BII isolates, RCC716 and RCC715, while BII-V2 and BII-V3 do not exhibit productive infection of the latter in our experiments. Global metagenome analyses show Clade BI and BII algal relative abundances correlate positively with their respective viruses. The distributions delineate BI/BpVs as occupying lower temperature mesotrophic and coastal systems, whereas BII/BII-Vs occupy warmer temperature, higher salinity ecosystems. Accordingly, with molecular diagnostic support, we name Clade BII Bathycoccus calidus sp. nov. and propose that molecular diversity within this new species likely connects to the differentiated host-virus dynamics observed in our time course experiments. Overall, the tightly linked biogeography of Bathycoccus host and virus clades observed herein supports species-level host specificity, with strain-level variations in infection parameters.},
	keywords = {RCC715, RCC716},
	issn = {1751-7370},
	doi = {10.1038/s41396-021-00989-9},
	url = {https://www.nature.com/articles/s41396-021-00989-9},
	author = {Bachy, Charles and Yung, Charmaine C. M. and Needham, David M. and Gazit{\'u}a, Maria Consuelo and Roux, Simon and Limardo, Alexander J. and Choi, Chang Jae and Jorgens, Danielle M. and Sullivan, Matthew B. and Worden, Alexandra Z.}
}
@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 {Bestion2020,
	title = {Abrupt declines in marine phytoplankton production driven by warming and biodiversity loss in a microcosm experiment},
	journal = {Ecology Letters},
	volume = {23},
	number = {3},
	year = {2020},
	note = {tex.mendeley-tags: RCC1303,RCC1512,RCC4221,RCC623,RCC626,RCC652,RCC80,RCC834},
	month = {mar},
	pages = {457{\textendash}466},
	abstract = {Rising sea surface temperatures are expected to lead to the loss of phytoplankton biodiversity. However, we currently understand very little about the interactions between warming, loss of phytoplankton diversity and its impact on the oceans{\textquoteright} primary production. We experimentally manipulated the species richness of marine phytoplankton communities under a range of warming scenarios, and found that ecosystem production declined more abruptly with species loss in communities exposed to higher temperatures. Species contributing positively to ecosystem production in the warmed treatments were those that had the highest optimal temperatures for photosynthesis, implying that the synergistic impacts of warming and biodiversity loss on ecosystem functioning were mediated by thermal trait variability. As species were lost from the communities, the probability of taxa remaining that could tolerate warming diminished, resulting in abrupt declines in ecosystem production. Our results highlight the potential for synergistic effects of warming and biodiversity loss on marine primary production.},
	keywords = {biodiversity, biodiversity loss, climate change, ecosystem functioning, phytoplankton, RCC1303, rcc1512, RCC4221, RCC623, RCC626, RCC652, RCC80, RCC834, thermal per-},
	issn = {1461-023X},
	doi = {10.1111/ele.13444},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ele.13444},
	author = {Bestion, Elvire and Barton, Samuel and Garc{\'\i}a, Francisca C. and Warfield, Ruth and Yvon-Durocher, Gabriel},
	editor = {Hillebrand, Helmut}
}
@article {Androuin2020,
	title = {Better off alone? New insights in the symbiotic relationship between the flatworm Symsagittifera roscoffensis and the microalgae Tetraselmis convolutae},
	journal = {Symbiosis},
	number = {Keebles 1910},
	year = {2020},
	note = {tex.mendeley-tags: RCC1563},
	month = {jun},
	abstract = {The acoel flatworm Symsagittifera roscoffensis lives in obligatory symbiosis with the microalgal chlorophyte Tetraselmis convolutae. Although this interaction has been studied for more than a century, little is known on the potential reciprocal benefits of both partners, a subject that is still controversial. In order to provide new insights into this question, we have compared the photophysiology of the free-living microalgae to the symbiotic form in the flatworm, both acclimated at different light irradiances. Photosynthesis {\textendash} Irradiance curves showed that the free-living T. convolutae had greater photosynthetic performance (i.e., oxygen production rates, ability to harvest light) than their symbiotic form, regardless of the light acclimation. However, they were affected by photoinhibition under high irradiances, which did not happen for the symbiotic form. The resistance of symbiotic microalgae to photoinhibition were corroborated by pigment analyses, which evidenced the induction of photoprotective mechanisms such as xanthophyll cycle as well as lutein and β-carotene accumulation. These processes were induced even under low light acclimation and exacerbated upon high light acclimation, suggesting a global stress situation for the symbiotic microalgae. We hypothesize that the internal conditions in the sub-epidermal zone of the flatworm (e.g., osmotic and pH), as well as the phototaxis toward high light imposed by the worm in its environment, would be major reasons for this chronic stress situation. Overall, our study suggests that the relationship between S. roscoffensis and T. convolutae may be a farming strategy in favor of the flatworm rather than a symbiosis with mutual benefits.},
	keywords = {Animal-plant, Photobiology, RCC1563, symbiosis, Symsagittifera roscoffensis, Tetraselmis convolutae},
	issn = {0334-5114},
	doi = {10.1007/s13199-020-00691-y},
	url = {http://link.springer.com/10.1007/s13199-020-00691-y},
	author = {Androuin, Thibault and Six, Christophe and Bordeyne, Fran{\c c}ois and de Bettignies, Florian and Noisette, Fanny and Davoult, Dominique}
}
@article {Benner2019,
	title = {Capacity of the common Arctic picoeukaryote Micromonas to adapt to a warming ocean},
	journal = {Limnology and Oceanography Letters},
	volume = {5},
	number = {2},
	year = {2020},
	note = {tex.mendeley-tags: RCC807},
	month = {apr},
	pages = {221{\textendash}227},
	keywords = {RCC807},
	issn = {2378-2242},
	doi = {10.1002/lol2.10133},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/lol2.10133},
	author = {Benner, Ina and Irwin, Andrew J and Finkel, Zoe V}
}
@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 {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 {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 {Dore2020,
	title = {Evolutionary mechanisms of long-term genome diversification associated with niche partitioning in marine picocyanobacteria},
	journal = {Frontiers in Microbiology},
	volume = {11},
	number = {September},
	year = {2020},
	note = {tex.mendeley-tags: RCC1084,RCC1085,RCC1086,RCC1087,RCC156,RCC158,RCC162,RCC2033,RCC2035,RCC2319,RCC2366,RCC2368,RCC2369,RCC2374,RCC2376,RCC2378,RCC2379,RCC2380,RCC2381,RCC2382,RCC2383,RCC2385,RCC2433,RCC2436,RCC2438,RCC2527,RCC2528,RCC2533,RCC2534,RCC2535,RCC2553,RCC2554,RCC2555,RCC2556,RCC2571,RCC2673,RCC278,RCC296,RCC307,RCC328,RCC3377,RCC407,RCC515,RCC539,RCC555,RCC556,RCC752,RCC753,RCC791},
	month = {sep},
	pages = {1{\textendash}23},
	keywords = {amino-acid substitutions, comparative genomics, evolution, genomic islands, marine cyanobacteria, niche adaptation, Prochlorococcus, rcc1084, RCC1085, RCC1086, RCC1087, RCC156, RCC158, rcc162, RCC2033, RCC2035, RCC2319, RCC2366, RCC2368, RCC2369, RCC2374, RCC2376, RCC2378, RCC2379, rcc2380, RCC2381, rcc2382, RCC2383, RCC2385, RCC2433, RCC2436, RCC2438, RCC2527, RCC2528, RCC2533, RCC2534, RCC2535, RCC2553, RCC2554, RCC2555, RCC2556, RCC2571, RCC2673, RCC278, rcc296, RCC307, RCC328, RCC3377, RCC407, RCC515, rcc539, rcc555, RCC556, rcc752, RCC753, rcc791, Synechococcus},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2020.567431},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2020.567431/full},
	author = {Dor{\'e}, Hugo and Farrant, Gregory K. and Guyet, Ulysse and Haguait, Julie and Humily, Florian and Ratin, Morgane and Pitt, Frances D. and Ostrowski, Martin and Six, Christophe and Brillet-Gu{\'e}guen, Loraine and Hoebeke, Mark and Bisch, Antoine and Le Corguill{\'e}, Gildas and Corre, Erwan and Labadie, Karine and Aury, Jean-Marc and Wincker, Patrick and Choi, Dong Han and Noh, Jae Hoon and Eveillard, Damien and Scanlan, David J. and Partensky, Fr{\'e}d{\'e}ric and Garczarek, Laurence}
}
@article {Barton2020,
	title = {Evolutionary temperature compensation of carbon fixation in marine phytoplankton},
	journal = {Ecology Letters},
	year = {2020},
	note = {tex.mendeley-tags: RCC1303,RCC1512,RCC1773,RCC4221,RCC623,RCC626,RCC652,RCC80,RCC834},
	month = {feb},
	pages = {ele.13469},
	abstract = {The efficiency of carbon sequestration by the biological pump could decline in the coming decades because respiration tends to increase more with temperature than photosynthesis. Despite these differences in the short-term temperature sensitivities of photosynthesis and respiration, it remains unknown whether the long-term impacts of global warming on metabolic rates of phytoplankton can be modulated by evolutionary adaptation. We found that respiration was consistently more temperature dependent than photosynthesis across 18 diverse marine phytoplankton, resulting in universal declines in the rate of carbon fixation with short-term increases in temperature. Long-term experimental evolution under high temperature reversed the short-term stimulation of metabolic rates, resulting in increased rates of carbon fixation. Our findings suggest that thermal adaptation may therefore have an ameliorating impact on the efficiency of phytoplankton as primary mediators of the biological carbon pump.},
	keywords = {climate change, evolutionary ecology, metabolism, phytoplankton physiology, RCC1303, rcc1512, RCC1773, RCC4221, RCC623, RCC626, RCC652, RCC80, RCC834, thermal performance curves},
	issn = {1461-023X},
	doi = {10.1111/ele.13469},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ele.13469},
	author = {Barton, Samuel and Jenkins, James and Buckling, Angus and Schaum, C.-Elisa and Smirnoff, Nicholas and Raven, John A. and Yvon-Durocher, Gabriel},
	editor = {Ezenwa, Vanessa}
}
@article {Henry2020,
	title = {Formation and fate of oil-related aggregates (ORAs) in seawater at different temperatures},
	journal = {Marine Pollution Bulletin},
	volume = {159},
	number = {July},
	year = {2020},
	note = {Publisher: Elsevier tex.mendeley-tags: RCC4289},
	month = {oct},
	pages = {111483},
	abstract = {In this study, the formation and fate of oil-related aggregates (ORAs) from chemically dispersed oil in seawater (SW) were investigated at different temperatures (5 {\textdegree}C, 13 {\textdegree}C, 20 {\textdegree}C). Experiments in natural SW alone, and in SW amended with typical marine snow constituents (phytoplankton and mineral particles), showed that the presence of algae stimulated the formation of large ORAs, while high SW temperature resulted in faster aggregate formation. The ORAs formed at 5 {\textdegree}C and 13 {\textdegree}C required mineral particles for sinking, while the aggregates also sank in the absence of mineral particles at 20{\textdegree}. Early in the experimental periods, oil compound accumulation in ORAs was faster than biodegradation, particularly in aggregates with algae, followed by rapid biodegradation. High abundances of bacteria associated with hydrocarbon biodegradation were determined in the ORAs, together with algae-associated bacteria, while clustering analyses showed separation between bacterial communities in experiments with oil alone and oil with algae/mineral particles.},
	keywords = {Aggregation, biodegradation, Dispersed oil, Marine snow, Microbial communities, RCC4289, Sinking},
	issn = {0025326X},
	doi = {10.1016/j.marpolbul.2020.111483},
	url = {https://doi.org/10.1016/j.marpolbul.2020.111483 https://linkinghub.elsevier.com/retrieve/pii/S0025326X20306019},
	author = {Henry, Ingrid A. and Netzer, Roman and Davies, Emlyn J. and Brakstad, Odd Gunnar}
}
@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 {Leconte2020,
	title = {Genome resolved biogeography of mamiellales},
	journal = {Genes},
	volume = {11},
	number = {1},
	year = {2020},
	note = {tex.mendeley-tags: RCC1105,RCC299,RCC4221: RCC2590,RCC809},
	month = {jan},
	pages = {66},
	abstract = {Among marine phytoplankton, Mamiellales encompass several species from the genera Micromonas, Ostreococcus and Bathycoccus, which are important contributors to primary production. Previous studies based on single gene markers described their wide geographical distribution but led to discussion because of the uneven taxonomic resolution of the method. Here, we leverage genome sequences for six Mamiellales species, two from each genus Micromonas, Ostreococcus and Bathycoccus, to investigate their distribution across 133 stations sampled during the Tara Oceans expedition. Our study confirms the cosmopolitan distribution of Mamiellales and further suggests non-random distribution of species, with two triplets of co-occurring genomes associated with different temperatures: Ostreococcus lucimarinus, Bathycoccus prasinos and Micromonas pusilla were found in colder waters, whereas Ostreococcus spp. RCC809, Bathycoccus spp. TOSAG39-1 and Micromonas commoda were more abundant in warmer conditions. We also report the distribution of the two candidate mating-types of Ostreococcus for which the frequency of sexual reproduction was previously assumed to be very low. Indeed, both mating types were systematically detected together in agreement with either frequent sexual reproduction or the high prevalence of a diploid stage. Altogether, these analyses provide novel insights into Mamiellales{\textquoteright} biogeography and raise novel testable hypotheses about their life cycle and ecology.},
	keywords = {Biogeography, mamiellales, mating-type, RCC1105, RCC2590, RCC299, RCC4221, RCC809, sexual reproduction, tara oceans},
	issn = {2073-4425},
	doi = {10.3390/genes11010066},
	url = {https://www.mdpi.com/2073-4425/11/1/66},
	author = {Leconte and Benites and Vannier and Wincker and Piganeau and Jaillon}
}
@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 {Schiffrine2020,
	title = {Growth and elemental stoichiometry of the ecologically-relevant arctic diatom chaetoceros gelidus: A mix of polar and temperate},
	journal = {Frontiers in Marine Science},
	volume = {6},
	number = {January},
	year = {2020},
	note = {tex.mendeley-tags: RCC2046},
	month = {jan},
	keywords = {ammonium, Arctic diatom, ele, Light, nitrate, RCC2046, urea},
	issn = {2296-7745},
	doi = {10.3389/fmars.2019.00790},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2019.00790/full},
	author = {Schiffrine, Nicolas and Tremblay, Jean-{\'e}ric and Babin, Marcel}
}
@article {bottini_high_2020,
	title = {High resolution spatial analyses of trace elements in coccoliths reveal new insights into element incorporation in coccolithophore calcite},
	journal = {Scientific Reports},
	volume = {10},
	number = {1},
	year = {2020},
	note = {Number: 1 Publisher: Nature Publishing Group},
	pages = {9825},
	abstract = {Coccolithophores are phytoplanktonic algae which produce an exoskeleton made of single platelets of calcite named coccoliths. They are widespread in all oceans and directly impact the short- and long-term C cycle. The study of coccolith size, morphology and elemental composition reveals important information regarding the ability of the cell to calcify and on the factors that influence this process. In this regard, very little is known about coccolith composition and its changes under altered environmental conditions. Here, we present high resolution (50 {\texttimes} 50 nm) elemental spatial distribution in pristine coccoliths of Coccolithus pelagicus and Gephyrocapsa oceanica reconstructed via X-ray fluorescence analyses at synchrotron. The studied specimens are from control culture and metal-enriched (V, Ni, Zn and Pb) experiments. The analysed specimens produced under stress conditions, display an irregular shape and are thinner, especially in the external rim, with ca. 1/3 lower Ca concentrations compared to specimens from the control. The same specimens also have higher Sr/Ca ratio with highest values in the coccolith external rim, suggesting that difficulty in calcification is additionally reflected in increased Sr/Ca ratios. Selenium is found in the coccolith as possible substitute of carbonate in the calcite. V and Pb apparently did not interact with the coccoliths while Zn and Ni were deposited on the coccolith surface.},
	keywords = {Environmental chemistry, Environmental impact, Marine chemistry, Pollution remediation, RCC1198, RCC1303},
	issn = {2045-2322},
	doi = {10.1038/s41598-020-66503-x},
	url = {http://www.nature.com/articles/s41598-020-66503-x},
	author = {Bottini, Cinzia and Dapiaggi, Monica and Erba, Elisabetta and Faucher, Giulia and Rotiroti, Nicola}
}
@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 {Baumeister2020,
	title = {Identification to species level of live single microalgal cells from plankton samples with matrix-free laser/desorption ionization mass spectrometry},
	journal = {Metabolomics},
	volume = {16},
	number = {3},
	year = {2020},
	note = {ISBN: 0123456789 Publisher: Springer US tex.mendeley-tags: RCC 4667,RCC1717,RCC2561,RCC2562,RCC3008,RCC5791,RCC6807,RCC6808,RCC6809,RCC6810,RCC6811,RCC6812,RCC6813,RCC6814,RCC6815,RCC6816,RCC6817,RCC6818,RCC6819,RCC6820,RCC6821},
	month = {mar},
	pages = {28},
	keywords = {ionization high-, Live single-cell mass spectrometry, matrix-free laser desorption, Matrix-free laser desorption/ionization high-resol, Metabolic fingerprinting, Microalgal identification, RCC1717, RCC2561, RCC2562, RCC3008, RCC4667, RCC5791, RCC6807, RCC6808, RCC6809, RCC6810, RCC6811, RCC6812, RCC6813, RCC6814, RCC6815, RCC6816, RCC6817, RCC6818, RCC6819, RCC6820, RCC6821, resolution mass spectrometry, Spectral pattern matching, Spectrum similarity},
	issn = {1573-3882},
	doi = {10.1007/s11306-020-1646-7},
	url = {https://doi.org/10.1007/s11306-020-1646-7 http://link.springer.com/10.1007/s11306-020-1646-7},
	author = {Baumeister, Tim U H and Vallet, Marine and Kaftan, Filip and Guillou, Laure and Svato{\v s}, Ale{\v s} and Pohnert, Georg}
}
@article {BlancoAmeijeiras2020,
	title = {Influence of temperature and CO 2 on Plasma-membrane permeability to CO 2 and HCO 3 - in the marine haptophytes emiliania huxleyi and calcidiscus leptoporus (prymnesiophyceae)},
	journal = {Journal of Phycology},
	year = {2020},
	note = {tex.mendeley-tags: RCC1130,RCC1258},
	month = {jun},
	pages = {jpy.13017},
	abstract = {Membrane permeabilities to CO2 and HCO3- constrain the function of CO2 concentrating mechanisms that algae use to supply inorganic carbon for photosynthesis. In diatoms and green algae, plasma membranes are moderately to highly permeable to CO2 but effectively impermeable to HCO3-. Here, CO2 and HCO3- membrane permeabilities were measured using an 18O-exchange technique on two species of haptophyte algae, Emiliania huxleyi and Calcidiscus leptoporus, which showed that the plasma membranes of these species are also highly permeable to CO2 (0.006{\textendash}0.02 cm ? s-1) but minimally permeable to HCO3-. Increased temperature and CO2 generally increased CO2 membrane permeabilities in both species, possibly due to changes in lipid composition or CO2 channel proteins. Changes in CO2 membrane permeabilities showed no association with the density of calcium carbonate coccoliths surrounding the cell, which could potentially impede passage of compounds. Haptophyte plasma-membrane permeabilities to CO2 were somewhat lower than those of diatoms but generally higher than membrane permeabilities of green algae. One caveat of these measurements is that the model used to interpret 18O-exchange data assumes that carbonic anhydrase, which catalyzes 18O-exchange, is homogeneously distributed in the cell. The implications of this assumption were tested using a two-compartment model with an inhomogeneous distribution of carbonic anhydrase to simulate 18O-exchange data and then inferring plasma-membrane CO2 permeabilities from the simulated data. This analysis showed that the inferred plasma-membrane CO2 permeabilities are minimal estimates but should be quite accurate under most conditions.},
	keywords = {carbon concentrating mechanism, CO2, haptophyte, membrane, PERMEABILITY, RCC1130, rcc1258},
	issn = {0022-3646},
	doi = {10.1111/jpy.13017},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.13017},
	author = {Blanco-Ameijeiras, Sonia and Stoll, Heather M. and Zhang, Hongrui and Hopkinson, Brian M.},
	editor = {Raven, J.}
}
@article {Vigor2020,
	title = {Isoprostanoid profiling of marine microalgae},
	journal = {Biomolecules},
	volume = {10},
	number = {7},
	year = {2020},
	note = {Publisher: MDPI AG tex.mendeley-tags: RCC1349,RCC20,RCC69},
	month = {jul},
	pages = {1073},
	abstract = {{\textexclamdown}p{\textquestiondown}Algae result from a complex evolutionary history that shapes their metabolic network. For example, these organisms can synthesize different polyunsaturated fatty acids, such as those found in land plants and oily fish. Due to the presence of numerous double-bonds, such molecules can be oxidized nonenzymatically, and this results in the biosynthesis of high-value bioactive metabolites named isoprostanoids. So far, there have been only a few studies reporting isoprostanoid productions in algae. To fill this gap, the current investigation aimed at profiling isoprostanoids by liquid chromatography -mass spectrometry/mass spectrometry (LC-MS/MS) in four marine microalgae. A good correlation was observed between the most abundant polyunsaturated fatty acids (PUFAs) produced by the investigated microalgal species and their isoprostanoid profiles. No significant variations in the content of oxidized derivatives were observed for Rhodomonas salina and Chaetoceros gracilis under copper stress, whereas increases in the production of C18-, C20- and C22-derived isoprostanoids were monitored in Tisochrysis lutea and Phaeodactylum tricornutum. In the presence of hydrogen peroxide, no significant changes were observed for C. gracilis and for T. lutea, while variations were monitored for the other two algae. This study paves the way to further studying the physiological roles of isoprostanoids in marine microalgae and exploring these organisms as bioresources for isoprostanoid production.{\textexclamdown}/p{\textquestiondown}},
	keywords = {Isoprostanoids, Micro-LC-MS/MS, Microalgae, Oxidative stress, PUFAs, RCC1349, RCC20, RCC69},
	issn = {2218-273X},
	doi = {10.3390/biom10071073},
	url = {https://www.mdpi.com/2218-273X/10/7/1073},
	author = {Vigor, Claire and Oger, Camille and Reversat, Guillaume and Rocher, Amandine and Zhou, Bingqing and Linares-Maurizi, Amandyne and Guy, Alexandre and Bultel-Ponc{\'e}, Val{\'e}rie and Galano, Jean-Marie and Vercauteren, Joseph and Durand, Thierry and Potin, Philippe and Tonon, Thierry and Leblanc, Catherine}
}
@article {Helliwell2020,
	title = {A novel single-domain Na +-selective voltage-gated channel in photosynthetic eukaryotes},
	journal = {bioRxiv},
	year = {2020},
	note = {Publisher: Cold Spring Harbor Laboratory tex.mendeley-tags: RCC1456},
	month = {apr},
	pages = {2020.04.29.068528},
	abstract = {The evolution of Na+-selective four-domain voltage-gated channels (4D-Navs) in animals allowed rapid Na+-dependent electrical excitability, and enabled the development of sophisticated systems for rapid and long-range signalling. Whilst bacteria encode single-domain Na+-selective voltage-gated channels (BacNav), they typically exhibit much slower kinetics than 4D-Navs, and are not thought to have crossed the prokaryote-eukaryote boundary. As such, the capacity for rapid Na+-selective signalling is considered to be confined to certain animal taxa, and absent from photosynthetic eukaryotes. Certainly, in land plants, such as the Venus Flytrap where fast electrical excitability has been described, this is most likely based on fast anion channels. Here, we report a unique class of eukaryotic Na+-selective single-domain channels (EukCatBs) that are present primarily in haptophyte algae, including the ecologically important calcifying coccolithophores. The EukCatB channels exhibit very rapid voltage-dependent activation and inactivation kinetics, and sensitivity to the highly selective 4D-Nav blocker tetrodotoxin. The results demonstrate that the capacity for rapid Na+-based signalling in eukaryotes is not restricted to animals or to the presence of 4D-Navs. The EukCatB channels therefore represent an independent evolution of fast Na+-based electrical signalling in eukaryotes that likely contribute to sophisticated cellular control mechanisms operating on very short time scales in unicellular algae. One Sentence Summary The capacity for rapid Na+-based signalling has evolved in ecologically important coccolithophore species via a novel class of voltage-gated Na+ channels, EukCatBs.},
	keywords = {RCC1456},
	doi = {10.1101/2020.04.29.068528},
	url = {https://doi.org/10.1101/2020.04.29.068528},
	author = {Helliwell, Katherine E and Chrachri, Abdul and Koester, Julie and Wharam, Susan and Wheeler, Glen L and Brownlee, Colin}
}
@article {Calmes2020,
	title = {Parallelisable non-invasive biomass, fitness and growth measurement of macroalgae and other protists with nephelometry},
	journal = {Algal Research},
	volume = {46},
	number = {November 2019},
	year = {2020},
	note = {Publisher: Elsevier tex.mendeley-tags: RCC149,RCC3088,RCC3510,RCC3553},
	pages = {101762},
	abstract = {With the exponential development of algal aquaculture and blue biotechnology, there is a strong demand for simple, inexpensive, high-throughput, quantitative phenotyping assays to measure the biomass, growth and fertility of algae and other marine protists. Here, we validate nephelometry, a method that relies on measuring the scattering of light by particles in suspension, as a non-invasive tool to measure in real-time the biomass of aquatic micro-organisms, such as microalgae, filamentous algae, as well as non-photosynthetic protists. Nephelometry is equally applicable to optic density and chlorophyll fluorescence measurements for the quantification of some microalgae, but outperforms other spectroscopy methods to quantify the biomass of biofilm-forming and filamentous algae, highly pigmented species and non-photosynthetic eukaryotes. Thanks to its insensitivity to the sample{\textquoteright}s pigmentation, nephelometry is also the method of choice when chlorophyll content varies between samples or time points, for example due to abiotic stress or pathogen infection. As examples, we illustrate how nephelometry can be combined with fluorometry or image analysis to monitor the quantity and time-course of spore release in fertile kelps or the progression of symptoms in diseased algal cultures.},
	keywords = {Algal cultivation, Biomass, Biotechnology, Nephelometry, Phenotyping, RCC149, RCC3088, RCC3510, rcc3553},
	issn = {22119264},
	doi = {10.1016/j.algal.2019.101762},
	url = {https://doi.org/10.1016/j.algal.2019.101762},
	author = {Calmes, Beno{\^\i}t and Strittmatter, Martina and Jacquemin, Bertrand and Perrineau, Marie Mathilde and Rousseau, C{\'e}line and Badis, Yacine and Cock, J. Mark and Destombe, Christophe and Valero, Myriam and Gachon, Claire M.M.}
}
@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 {Guyet2020,
	title = {Synergic effects of temperature and irradiance on the physiology of the marine synechococcus strain WH7803},
	journal = {Frontiers in Microbiology},
	volume = {11},
	year = {2020},
	note = {Publisher: Frontiers Media S.A. tex.mendeley-tags: RCC752},
	month = {jul},
	pages = {1707},
	abstract = {Understanding how microorganisms adjust their metabolism to maintain their ability to cope with short-term environmental variations constitutes one of the major current challenges in microbial ecology. Here, the best physiologically characterized marine Synechococcus strain, WH7803, was exposed to modulated light/dark cycles or acclimated to continuous high-light (HL) or low-light (LL), then shifted to various stress conditions, including low (LT) or high temperature (HT), HL and ultraviolet (UV) radiations. Physiological responses were analyzed by measuring time courses of photosystem (PS) II quantum yield, PSII repair rate, pigment ratios and global changes in gene expression. Previously published membrane lipid composition were also used for correlation analyses. These data revealed that cells previously acclimated to HL are better prepared than LL-acclimated cells to sustain an additional light or UV stress, but not a LT stress. Indeed, LT seems to induce a synergic effect with the HL treatment, as previously observed with oxidative stress. While all tested shift conditions induced the downregulation of many photosynthetic genes, notably those encoding PSI, cytochrome b6/f and phycobilisomes, UV stress proved to be more deleterious for PSII than the other treatments, and full recovery of damaged PSII from UV stress seemed to involve the neo-synthesis of a fairly large number of PSII subunits and not just the reassembly of pre-existing subunits after D1 replacement. In contrast, genes involved in glycogen degradation and carotenoid biosynthesis pathways were more particularly upregulated in response to LT. Altogether, these experiments allowed us to identify responses common to all stresses and those more specific to a given stress, thus highlighting genes potentially involved in niche acclimation of a key member of marine ecosystems. Our data also revealed important specific features of the stress responses compared to model freshwater cyanobacteria.},
	keywords = {light stress, marine cyanobacteria, rcc752, Synechococcus, temperature stress, transcriptomics, UV radiations},
	issn = {1664302X},
	doi = {10.3389/fmicb.2020.01707},
	url = {www.frontiersin.org},
	author = {Guyet, Ulysse and Nguyen, Ngoc A. and Dor{\'e}, Hugo and Haguait, Julie and Pittera, Justine and Conan, Ma{\"e}l and Ratin, Morgane and Corre, Erwan and Le Corguill{\'e}, Gildas and Brillet-Gu{\'e}guen, Loraine and Hoebeke, Mark and Six, Christophe and Steglich, Claudia and Siegel, Anne and Eveillard, Damien and Partensky, Fr{\'e}d{\'e}ric and Garczarek, Laurence}
}
@article {Demory2020,
	title = {A thermal trade-off between viral production and degradation drives phytoplankton-virus population dynamics},
	journal = {bioRxiv},
	year = {2020},
	note = {Publisher: Cold Spring Harbor Laboratory tex.mendeley-tags: RCC4229,RCC4265,RCC451,RCC4523,RCC829,RCC834},
	month = {aug},
	pages = {2020.08.18.256156},
	abstract = {Marine viruses interact with their microbial hosts in dynamic environments shaped by variations in abiotic factors, including temperature. However, the impacts of temperature on viral infection of phytoplankton are not well understood. Here we coupled mathematical modeling with experimental datasets to explore the effect of temperature on three Micromonas-prasinovirus pairs. Our model shows the negative consequences of high temperatures on infection and suggests a temperature-dependent threshold between viral production and degradation. Modeling long-term dynamics in environments with different average temperatures revealed the potential for long-term host-virus coexistence, epidemic free, or habitat loss states. Hence, we generalized our model to global sea surface temperature of present and future seas and show that climate change may influence virus-host dynamics differently depending on the virus-host pair. Our study suggests that temperature-dependent changes in the infectivity of virus particles may lead to shifts in virus-host habitats in warmer oceans, analogous to projected changes in the habitats of macro-and microorganisms .},
	keywords = {RCC4229, RCC4265, RCC451, RCC4523, RCC829, RCC834},
	doi = {10.1101/2020.08.18.256156},
	url = {https://doi.org/10.1101/2020.08.18.256156},
	author = {Demory, David and Weitz, Joshua S and Baudoux, Anne-claire and Touzeau, Suzanne and Simon, Natalie and Rabouille, Sophie and Sciandra, Antoine and Bernard, Olivier}
}
@article {Bretherton2020,
	title = {Trait-dependent variability of the response of marine phytoplankton to oil and dispersant exposure},
	journal = {Marine Pollution Bulletin},
	volume = {153},
	number = {January},
	year = {2020},
	note = {Publisher: Elsevier tex.mendeley-tags: RCC1614},
	pages = {110906},
	abstract = {The Deepwater Horizon oil spill released millions of barrels of crude oil into the Gulf of Mexico, and saw widespread use of the chemical dispersant Corexit. We assessed the role of traits, such as cell size, cell wall, motility, and mixotrophy on the growth and photosynthetic response of 15 phytoplankton taxa to oil and Corexit. We collected growth and photosynthetic data on five algal cultures. These responses could be separated into resistant (Tetraselmis astigmatica, Ochromonas sp., Heterocapsa pygmaea) and sensitive (Micromonas pusilla, Prorocentrum minimum). We combined this data with 10 species previously studied and found that cell size is most important in determining the biomass response to oil, whereas motility/mixotrophy is more important in the dispersed oil. Our analysis accounted for a third of the variance observed, so further work is needed to identify other factors that contribute to oil resistance.},
	keywords = {Chemical dispersants, Chlorophyll, crude oil, Photosynthesis, phytoplankton, RCC1614, Trait-based analysis},
	issn = {18793363},
	doi = {10.1016/j.marpolbul.2020.110906},
	url = {https://doi.org/10.1016/j.marpolbul.2020.110906},
	author = {Bretherton, Laura and Hillhouse, Jessica and Kamalanathan, Manoj and Finkel, Zoe V. and Irwin, Andrew J. and Quigg, Antonietta}
}
@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 {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 {Helliwell2019,
	title = {Alternative mechanisms for fast na + /ca 2+ signaling in eukaryotes via a novel class of single-domain voltage-gated channels},
	journal = {Current Biology},
	volume = {29},
	number = {9},
	year = {2019},
	note = {tex.mendeley-tags: RCC299},
	pages = {1503{\textendash}1511.e6},
	abstract = {Rapid Na + /Ca 2+ -based action potentials govern essential cellular functions in eukaryotes, from the motile responses of unicellular protists, such as Paramecium [1, 2], to complex animal neuromuscular activity [3]. A key innovation underpinning this fundamental signaling process has been the evolution of four-domain voltage-gated Na + /Ca 2+ channels (4D-Ca v s/Na v s). These channels are widely distributed across eukaryote diversity [4], albeit several eukaryotes, including land plants and fungi, have lost voltage-sensitive 4D-Ca v /Na v s [5{\textendash}7]. Because these lineages appear to lack rapid Na + /Ca 2+ -based action potentials, 4D-Ca v /Na v s are generally considered necessary for fast Na + /Ca 2+ -based signaling [7]. However, the cellular mechanisms underpinning the membrane physiology of many eukaryotes remain unexamined. Eukaryotic phytoplankton critically influence our climate as major primary producers. Several taxa, including the globally abundant diatoms, exhibit membrane excitability [8{\textendash}10]. We previously demonstrated that certain diatom genomes encode 4D-Ca v /Na v s [4] but also proteins of unknown function, resembling prokaryote single-domain, voltage-gated Na + channels (BacNa v s) [4]. Here, we show that single-domain channels are actually broadly distributed across major eukaryote phytoplankton lineages and represent three novel classes of single-domain channels, which we refer collectively to as EukCats. Functional characterization of diatom EukCatAs indicates that they are voltage-gated Na + - and Ca 2+ -permeable channels, with rapid kinetics resembling metazoan 4D-Ca v s/Na v s. In Phaeodactylum tricornutum, which lacks 4D-Ca v /Na v s, EukCatAs underpin voltage-activated Ca 2+ signaling important for membrane excitability, and mutants exhibit impaired motility. EukCatAs therefore provide alternative mechanisms for rapid Na + /Ca 2+ signaling in eukaryotes and may functionally replace 4D-Ca v s/Na v s in pennate diatoms. Marine phytoplankton thus possess unique signaling mechanisms that may be key to environmental sensing in the oceans. Diatoms exhibit fast animal-like action potentials, but many species lack 4D-Ca v /Na v channels that underpin membrane excitability in animals. Diatoms do encode novel 1D voltage-gated channels (EukCatAs). Helliwell, Chrachri et al. show that EukCatAs are fast Na + and Ca 2+ channels that provide alternative mechanisms for rapid signaling in eukaryotes.},
	keywords = {action potentials, BacNa v, calcium channel, diatoms, EukCats, gliding motility, ion selectivity, RCC299, signaling, single-domain channel, voltage-gated channel},
	issn = {09609822},
	doi = {10.1016/j.cub.2019.03.041},
	author = {Helliwell, Katherine E. and Chrachri, Abdul and Koester, Julie A. and Wharam, Susan and Verret, Frederic and Taylor, Alison R. and Wheeler, Glen L. and Brownlee, Colin}
}
@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 {Lorenzo2019,
	title = {Effects of elevated co 2 on growth, calcification and spectral dependence of photoinhibition in the coccolithophore Emiliania huxleyi (Prymnesiophyceae)},
	journal = {Journal of Phycology},
	year = {2019},
	note = {tex.mendeley-tags: RCC1226},
	month = {may},
	pages = {jpy.12885},
	keywords = {rcc1226},
	issn = {0022-3646},
	doi = {10.1111/jpy.12885},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.12885},
	author = {Lorenzo, M. Rosario and Neale, Patrick J. and Sobrino, Cristina and Le{\'o}n, Pablo and V{\'a}zquez, V{\'\i}ctor and Bresnan, Eileen and Segovia, Mar{\'\i}a}
}
@article {Krasovec2019,
	title = {First estimation of the spontaneous mutation rate in Diatoms},
	journal = {Genome Biology and Evolution},
	volume = {1},
	year = {2019},
	note = {tex.mendeley-tags: RCC2967},
	pages = {1{\textendash}23},
	keywords = {diatoms, Mutation accumulation, mutation rate in phaeodactylum, mutation spectrum, phaeodactylum, RCC2967, running title, spontaneous mutation rate, tricornutum},
	issn = {1759-6653},
	doi = {10.1093/gbe/evz130},
	url = {https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evz130/5520952},
	author = {Krasovec, Marc and Sanchez-Brosseau, Sophie and Piganeau, Gwenael},
	editor = {Baer, Charles}
}
@article {Arsenieff2019,
	title = {First viruses infecting the marine diatom guinardia delicatula},
	journal = {Frontiers in Microbiology},
	volume = {9},
	number = {January},
	year = {2019},
	note = {tex.mendeley-tags: RCC1000,RCC2023,RCC3046,RCC3083,RCC3093,RCC3101,RCC4657,RCC4659,RCC4660,RCC4667,RCC4834,RCC5154,RCC5777,RCC5778,RCC5779,RCC5780,RCC5781,RCC5782,RCC5783,RCC5784,RCC5785,RCC5787,RCC5788,RCC5789,RCC5790,RCC5792,RCC5793,RCC5794,RCC80},
	month = {jan},
	keywords = {diatoms, genomics, host-virus dynamics, RCC1000, RCC2023, RCC3046, RCC3083, RCC3093, RCC3101, RCC4657, RCC4659, RCC4660, RCC4667, RCC4834, RCC5154, RCC5777, RCC5778, RCC5779, RCC5780, RCC5781, RCC5782, RCC5783, RCC5784, RCC5785, RCC5787, RCC5788, RCC5789, RCC5790, RCC5792, RCC5793, RCC5794, RCC80, single-stranded RNA viruses, Western English Channel},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2018.03235},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2018.03235/full},
	author = {Arsenieff, Laure and Simon, Nathalie and Rigaut-jalabert, Fabienne and Le Gall, Florence and Chaffron, Samuel and Corre, Erwan and Com, Emmanuelle and Bigeard, Estelle and Baudoux, Anne-claire}
}
@article {bramucci_phaeobacter_2019,
	title = {Phaeobacter inhibens induces apoptosis-like programmed cell death in calcifying Emiliania huxleyi},
	journal = {Scientific Reports},
	volume = {9},
	number = {1},
	year = {2019},
	note = {Number: 1 Publisher: Nature Publishing Group},
	month = {mar},
	pages = {1{\textendash}12},
	abstract = {The model coccolithophore, Emiliania huxleyi, forms expansive blooms dominated by the calcifying cell type, which produce calcite scales called coccoliths. Blooms last several weeks, after which the calcified algal cells rapidly die, descending into the deep ocean. E. huxleyi bloom collapse is attributed to E. huxleyi viruses (EhVs) that infect and kill calcifying cells, while other E. huxleyi pathogens, such as bacteria belonging to the roseobacter clade, are overlooked. EhVs kill calcifying E. huxleyi by inducing production of bioactive viral-glycosphingolipids (vGSLs), which trigger algal programmed cell death (PCD). The roseobacter Phaeobacter inhibens was recently shown to interact with and kill the calcifying cell type of E. huxleyi, but the mechanism of algal death remains unelucidated. Here we demonstrate that P. inhibens kills calcifying E. huxleyi by inducing a highly specific type of PCD called apoptosis-like-PCD (AL-PCD). Host death can successfully be abolished in the presence of a pan-caspase inhibitor, which prevents the activation of caspase-like molecules. This finding differentiates P. inhibens and EhV pathogenesis of E. huxleyi, by demonstrating that bacterial-induced AL-PCD requires active caspase-like molecules, while the viral pathogen does not. This is the first demonstration of a bacterium inducing AL-PCD in an algal host as a killing mechanism.},
	keywords = {RCC1216},
	issn = {2045-2322},
	doi = {10.1038/s41598-018-36847-6},
	url = {http://www.nature.com/articles/s41598-018-36847-6},
	author = {Bramucci, Anna R. and Case, Rebecca J.}
}
@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 {Barton2019,
	title = {Quantifying the temperature dependence of growth rate in marine phytoplankton within and across species},
	journal = {Limnology and Oceanography},
	year = {2019},
	note = {tex.mendeley-tags: RCC1303,RCC1512,RCC1731,RCC1773,RCC4221,RCC539,RCC6,RCC623,RCC626,RCC652,RCC653,RCC655,RCC834,RCC88},
	abstract = {Abstract Models of marine biogeochemistry capture the effects of temperature on phytoplankton growth via the monotonic, exponential Eppley coefficient, without considering the physiological or evolutionary processes that underpin this emergent, across-species temperature response. Here, we investigated both the within- and across-species temperature dependence of growth rate for 18 species of marine phytoplankton. We found that the temperature dependence of growth rate derived across species was lower than the average temperature response within species. This finding supports a {\textquotedblleft}partial compensation{\textquotedblright} model of thermal adaptation and suggests that adaptation can partially compensate for the underlying thermodynamic effects of temperature on physiological rates observed within species. We also found that thermal tolerance traits (e.g. the optimum temperature for growth) systematically covaried with a host of key functional traits (e.g. cell size, elemental composition). Consequently, turnover in species composition in a warmer ocean, linked to interspecific variability in thermal tolerance traits, could be associated with major shifts in the functional trait composition of marine phytoplankton communities with far reaching implications for ecosystem functioning.},
	keywords = {RCC1303, rcc1512, rcc1731, RCC1773, RCC4221, rcc539, RCC6, RCC623, RCC626, RCC652, RCC653, RCC655, RCC834, RCC88},
	issn = {0024-3590},
	doi = {10.1002/lno.11170},
	author = {Barton, Samuel and Yvon-Durocher, Gabriel}
}
@article {LingeJohnsen2019,
	title = {Relationship between coccolith length and thickness in the coccolithophore species Emiliania huxleyi and Gephyrocapsa oceanica},
	journal = {PLOS ONE},
	volume = {14},
	number = {8},
	year = {2019},
	note = {tex.mendeley-tags: RCC1210,RCC1223,RCC1232,RCC1824,RCC1843,RCC868},
	month = {aug},
	pages = {e0220725},
	keywords = {rcc1210, RCC1223, RCC1232, rcc1824, rcc1843, rcc868},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0220725},
	url = {http://dx.plos.org/10.1371/journal.pone.0220725},
	author = {Linge Johnsen, Simen Alexander and Bollmann, J{\"o}rg and Gebuehr, Christina and Herrle, Jens O.},
	editor = {Keller, David Peter}
}
@article {bendif_repeated_2019,
	title = {Repeated species radiations in the recent evolution of the key marine phytoplankton lineage Gephyrocapsa},
	journal = {Nature Communications},
	volume = {10},
	number = {1},
	year = {2019},
	pages = {4234},
	abstract = {Abstract Phytoplankton account for nearly half of global primary productivity and strongly affect the global carbon cycle, yet little is known about the forces that drive the evolution of these keystone microscopic organisms. Here we combine morphometric data from the fossil record of the ubiquitous coccolithophore genus Gephyrocapsa with genomic analyses of extant species to assess the genetic processes underlying Pleistocene palaeontological patterns. We demonstrate that all modern diversity in Gephyrocapsa (including Emiliania huxleyi ) originated in a rapid species radiation during the last 0.6 Ma, coincident with the latest of the three pulses of Gephyrocapsa diversification and extinction documented in the fossil record. Our evolutionary genetic analyses indicate that new species in this genus have formed in sympatry or parapatry, with occasional hybridisation between species. This sheds light on the mode of speciation during evolutionary radiation of marine phytoplankton and provides a model of how new plankton species form.},
	keywords = {RCC1253, RCC1296, RCC3370, RCC3711, RCC4028, RCC4030, RCC4032, RCC4033, RCC4034},
	issn = {2041-1723},
	doi = {10.1038/s41467-019-12169-7},
	url = {https://www.nature.com/articles/s41467-019-12169-7},
	author = {Bendif, El Mahdi and Nevado, Bruno and Wong, Edgar L. Y. and Hagino, Kyoko and Probert, Ian and Young, Jeremy R. and Rickaby, Rosalind E. M. and Filatov, Dmitry A.}
}
@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 {Bouget2019,
	title = {Transient transformation of ostreococcus species (OTTH595, RCC809 and RCC802) and bathycoccus},
	year = {2019},
	note = {Publication Title: protocols.io tex.mendeley-tags: RCC802,RCC809},
	keywords = {RCC802, RCC809},
	doi = {10.17504/protocols.io.83uhynw},
	url = {https://www.protocols.io/view/transient-transformation-of-ostreococcus-species-o-83uhynw},
	author = {Bouget, Fran{\c c}ois Yves}
}
@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 {Beuvier2019,
	title = {X-ray nanotomography of coccolithophores reveals that coccolith mass and segment number correlate with grid size},
	journal = {Nature Communications},
	volume = {10},
	number = {1},
	year = {2019},
	note = {Publisher: Springer US tex.mendeley-tags: RCC1212,RCC1216,RCC1314,RCC3370,RCC4032,RCC4036},
	month = {dec},
	pages = {751},
	abstract = {Coccolithophores of the No{\"e}laerhabdaceae family are covered by imbricated coccoliths, each composed of multiple calcite crystals radially distributed around the periphery of a grid. The factors that determine coccolith size remain obscure. Here, we used synchrotron-based three-dimensional Coherent X-ray Diffraction Imaging to study coccoliths of 7 species of Gephyrocapsa, Emiliania and Reticulofenestra with a resolution close to 30 nm. Segmentation of 45 coccoliths revealed remarkable size, mass and segment number variations, even within single coccospheres. In particular, we observed that coccolith mass correlates with grid perimeter which scales linearly with crystal number. Our results indirectly support the idea that coccolith mass is determined in the coccolith vesicle by the size of the organic base plate scale (OBPS) around which R-unit nucleation occurs every 110{\textendash}120 nm. The curvation of coccoliths allows inference of a positive correlation between cell nucleus, OBPS and coccolith sizes.},
	keywords = {Biomaterials, Marine biology, rcc1212, RCC1216, RCC1314, RCC3370, RCC4032, RCC4036},
	issn = {2041-1723},
	doi = {10.1038/s41467-019-08635-x},
	url = {http://www.nature.com/articles/s41467-019-08635-x},
	author = {Beuvier, T. and Probert, I. and Beaufort, L. and Such{\'e}ras-Marx, B. and Chushkin, Y. and Zontone, F. and Gibaud, A.}
}
@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 {Annunziata2018,
	title = {A bHLH-PAS protein regulates light-dependent rhythmic processes in the marine diatom Phaeodactylum tricornutum},
	journal = {bioRxiv},
	year = {2018},
	note = {tex.mendeley-tags: RCC2967},
	pages = {271445},
	abstract = {Periodic light dark cycles govern the timing of basic biological processes in organisms inhabiting land as well as the sea, where life evolved. Although prominent marine phytoplanktonic organisms such as diatoms show robust diurnal rhythms in growth, cell cycle and gene expression, the molecular bases controlling these processes are still obscure. By exploring the regulatory landscape of diatom diurnal rhythms, we here unveil the key function of a Phaeodactylum tricornutum bHLH-PAS protein, named Pt bHLH1a, in the regulation of light-dependent rhythms. Peak expression of Pt bHLH1a mRNA occurs at the end of the light period and it is adjusted to photoperiod changes. Ectopic over-expression of Pt bHLH1a results in lines with altered cell division and gene expression and showing a phase shift in diurnal responses, compared to the wild-type cells. Reduced oscillations in gene expression are also observed in continuous darkness, showing that the regulation of rhythmicity by Pt bHLH1a is not directly dependent on light inputs and cell division. Pt bHLH1a orthologs are widespread in both pennate and centric diatom genomes, hinting at a common function in many species. This study adds new elements to understand diatom biology and ecology and offers new perspectives to elucidate timekeeping mechanisms in marine organisms belonging to a major, but still underinvestigated branch of the tree of life.},
	keywords = {RCC2967},
	doi = {10.1101/271445},
	url = {https://www.biorxiv.org/content/early/2018/02/25/271445},
	author = {Annunziata, Rossella and Ritter, Andr{\'e}s and Fortunato, Antonio Emidio and Cheminant-Navarro, Soizic and Agier, Nicolas and Huysman, Marie J. J. and Winge, Per and Bones, Atle and Bouget, Fran{\c c}ois-Yves and Lagomarsino, Marco Cosentino and Bouly, Jean Pierre and Falciatore, Angela}
}
@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 {Guyon2018,
	title = {Comparative analysis of culture conditions for the optimization of carotenoid production in several strains of the picoeukaryote ostreococcus},
	journal = {Marine Drugs},
	volume = {16},
	number = {3},
	year = {2018},
	note = {tex.mendeley-tags: 2018,RCC745,RCC802,RCC809,rcc},
	pages = {76},
	abstract = {Microalgae are promising sources for the sustainable production of compounds of interest for biotechnologies. Compared to higher plants, microalgae have a faster growth rate and can be grown in industrial photobioreactors. The microalgae biomass contains specific metabolites of high added value for biotechnology such as lipids, polysaccharides or carotenoid pigments. Studying carotenogenesis is important for deciphering the mechanisms of adaptation to stress tolerance as well as for biotechnological production. In recent years, the picoeukaryote Ostreococcus tauri has emerged as a model organism thanks to the development of powerful genetic tools. Several strains of Ostreococcus isolated from different environments have been characterized with respect to light response or iron requirement. We have compared the carotenoid contents and growth rates of strains of Ostreococcus (OTTH595, RCC802 and RCC809) under a wide range of light, salinity and temperature conditions. Carotenoid profiles and productivities varied in a strain-specific and stress-dependent manner. Our results also illustrate that phylogenetically related microalgal strains originating from different ecological niches present specific interests for the production of specific molecules under controlled culture conditions.},
	keywords = {2018, carotenoids, GROWTH RATE, Light, Ostreococcus, rcc, RCC745, RCC802, RCC809, salinity, temperature},
	issn = {1660-3397},
	doi = {10.3390/md16030076},
	url = {http://www.mdpi.com/1660-3397/16/3/76},
	author = {Guyon, Jean-baptiste and Schatt, Philippe and Lozano, Jean-Claude and Liennard, Marion and Bouget, Fran{\c c}ois-Yves}
}
@article {Farhat2018,
	title = {Comparative time-scale gene expression analysis highlights the infection processes of two amoebophrya strains},
	journal = {Frontiers in Microbiology},
	volume = {9},
	number = {October},
	year = {2018},
	note = {tex.mendeley-tags: RCC1627,RCC3596,RCC4383,RCC4398},
	month = {oct},
	pages = {1{\textendash}19},
	keywords = {amoebophrya, Dinoflagellates, Gene Expression, infection, oxidative stress response, parasite, plankton, RCC1627, RCC3596, RCC4383, RCC4398, syndiniales},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2018.02251},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2018.02251/full},
	author = {Farhat, Sarah and Florent, Isabelle and Noel, Benjamin and Kayal, Ehsan and Da Silva, Corinne and Bigeard, Estelle and Alberti, Adriana and Labadie, Karine and Corre, Erwan and Aury, Jean-Marc and Rombauts, Stephane and Wincker, Patrick and Guillou, Laure and Porcel, Betina M.}
}
@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 {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 {Grebert2018,
	title = {Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {in press},
	year = {2018},
	note = {tex.mendeley-tags: 2018,RCC1016,RCC1017,RCC1018,RCC1020,RCC1023,RCC1027,RCC1030,RCC1031,RCC1084,RCC1085,RCC1086,RCC1087,RCC1096,RCC1097,RCC1649,RCC1661,RCC1688,RCC2032,RCC2033,RCC2035,RCC2319,RCC2366,RCC2368,RCC2369,RCC2370,RCC2372,RCC2373,RCC2374,RCC2375,RCC2376,RCC2378,RCC2379,RCC2380,RCC2381,RCC2382,RCC2383,RCC2384,RCC2385,RCC2415,RCC2432,RCC2433,RCC2434,RCC2435,RCC2436,RCC2437,RCC2438,RCC2457,RCC2525,RCC2526,RCC2527,RCC2528,RCC2529,RCC2530,RCC2532,RCC2533,RCC2534,RCC2536,RCC2553,RCC2554,RCC2555,RCC2556,RCC2567,RCC2568,RCC2569,RCC2570,RCC2571,RCC2673,RCC30,RCC3010,RCC3012,RCC3014,RCC307,RCC316,RCC318,RCC325,RCC326,RCC328,RCC37,RCC44,RCC46,RCC47,RCC515,RCC539,RCC542,RCC543,RCC550,RCC552,RCC553,RCC555,RCC556,RCC557,RCC558,RCC559,RCC62,RCC650,RCC66,RCC752,RCC753,RCC790,RCC791,RCC792,RCC793,RCC794,sbr?hyto?app},
	month = {feb},
	pages = {201717069},
	abstract = {Marine Synechococcus cyanobacteria are major contributors to global oceanic primary production and exhibit a unique diversity of photosynthetic pigments, allowing them to exploit a wide range of light niches. However, the relationship between pigment content and niche partitioning has remained largely undetermined so far due to the lack of a single-genetic marker resolving all pigment types (PT). Here, we developed a novel and robust method based on three distinct marker genes to estimate the relative abundance of all Synechococcus PTs from metagenomes. Analysis of the Tara Oceans dataset allowed us to unveil for the first time the global distribution of Synechococcus PTs and to decipher their realized environmental niches. Green-light specialists (PT 3a) dominated in warm, green equatorial waters, whereas blue-light specialists (PT 3c) were particularly abundant in oligotrophic areas. Type IV chromatic acclimaters (CA4-A/B), which are able to dynamically modify their light absorption properties to maximally absorb green or blue light, were unexpectedly the most abundant PT in our dataset and predominated at depth and high latitudes. We also identified local populations in which CA4 might be inactive due to the lack of specific CA4 genes, notably in warm high nutrient low chlorophyll areas. Major ecotypes within clades I-IV and CRD1 were preferentially associated with a particular PT, while others exhibited a wide range of PTs. Altogether, this study brings unprecedented insights into the ecology of Synechococcus PTs and highlights the complex interactions between vertical phylogeny, pigmentation and environmental parameters that shape Synechococcus populations and evolution.},
	keywords = {2018, RCC1016, RCC1017, RCC1018, RCC1020, RCC1023, RCC1027, RCC1030, RCC1031, rcc1084, RCC1085, RCC1086, RCC1087, RCC1096, RCC1097, RCC1649, RCC1661, RCC1688, RCC2032, RCC2033, RCC2035, RCC2319, RCC2366, RCC2368, RCC2369, RCC2370, RCC2372, RCC2373, RCC2374, RCC2375, RCC2376, RCC2378, RCC2379, rcc2380, RCC2381, rcc2382, RCC2383, RCC2384, RCC2385, RCC2415, RCC2432, RCC2433, RCC2434, RCC2435, RCC2436, RCC2437, RCC2438, RCC2457, RCC2525, RCC2526, RCC2527, RCC2528, RCC2529, RCC2530, RCC2532, RCC2533, RCC2534, RCC2536, RCC2553, RCC2554, RCC2555, RCC2556, RCC2567, RCC2568, RCC2569, RCC2570, RCC2571, RCC2673, rcc30, RCC3010, RCC3012, RCC3014, RCC307, RCC316, RCC318, RCC325, RCC326, RCC328, RCC37, RCC44, RCC46, RCC47, RCC515, rcc539, RCC542, RCC543, RCC550, RCC552, RCC553, rcc555, RCC556, RCC557, RCC558, RCC559, RCC62, RCC650, RCC66, rcc752, RCC753, RCC790, rcc791, RCC792, RCC793, RCC794, sbr?hyto?app},
	issn = {0027-8424},
	doi = {10.1073/pnas.1717069115},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1717069115},
	author = {Gr{\'e}bert, Th{\'e}ophile and Dor{\'e}, Hugo and Partensky, Fr{\'e}d{\'e}ric and Farrant, Gregory K. and Boss, Emmanuel S. and Picheral, Marc and Guidi, Lionel and Pesant, St{\'e}phane and Scanlan, David J. and Wincker, Patrick and Acinas, Silvia G. and Kehoe, David M. and Garczarek, Laurence}
}
@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 {Klinger2018,
	title = {Plastid transcript editing across dinoflagellate lineages shows lineage-specific application but conserved trends},
	journal = {Genome Biology and Evolution},
	volume = {10},
	number = {April},
	year = {2018},
	note = {tex.mendeley-tags: RCC1513},
	pages = {1019{\textendash}1038},
	abstract = {Dinoflagellates are a group of unicellular protists with immense ecological and evolutionary significance and cell biological diversity. Of the photosynthetic dinoflagellates, the majority possess a plastid containing the pigment peridinin, whereas some lineages have replaced this plastid by serial endosymbiosis with plastids of distinct evolutionary affiliations, including a fucoxanthin pigment-containing plastid of haptophyte origin. Previous studies have described the presence of widespread substitutional RNA editing in peridinin and fucoxanthin plastid genes. Because reports of this process have been limited to manual assessment of individual lineages, global trends concerning this RNA editing and its effect on the biological function of the plastid are largely unknown. Using novel bioinformatic methods, we examine the dynamics and evolution of RNA editing over a large multispecies data set of dinoflagellates, including novel sequence data from the peridinin dinoflagellate Pyrocystis lunula and the fucoxanthin dinoflagellate Karenia mikimotoi. We demonstrate that while most individual RNA editing events in dinoflagellate plastids are restricted to single species, global patterns, and functional consequences of editing are broadly conserved. We find that editing is biased toward specific codon positions and regions of genes, and generally corrects otherwise deleterious changes in the genome prior to translation, though this effect is more prevalent in peridinin than fucoxanthin lineages. Our results support a model for promiscuous editing application subsequently shaped by purifying selection, and suggest the presence of an underlying editing mechanism transferred from the peridinin-containing ancestor into fucoxanthin plastids postendosymbiosis, with remarkably conserved functional consequences in the new lineage.},
	keywords = {constructive neutral evolution, Dinoflagellate, plastid, RCC1513, serial endosymbiosis, transcript editing},
	issn = {1759-6653},
	doi = {10.1093/gbe/evy057},
	url = {https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evy057/4935245},
	author = {Klinger, Christen M and Paoli, Lucas and Newby, Robert J and Wang, Matthew Yu-Wei and Carroll, Hyrum D and Leblond, Jeffrey D and Howe, Christopher J and Dacks, Joel B and Bowler, Chris and Cahoon, A Bruce and Dorrell, Richard G and Richardson, Elisabeth}
}
@article {Walker2018,
	title = {The requirement for calcification differs between ecologically important coccolithophore species},
	journal = {New Phytologist},
	volume = {in press},
	year = {2018},
	note = {tex.mendeley-tags: RCC1731},
	month = {jun},
	keywords = {Calcification, coccolithophore, Coccolithus braarudii, Emiliania huxleyi, phytoplankton, rcc1731},
	issn = {0028646X},
	doi = {10.1111/nph.15272},
	url = {http://doi.wiley.com/10.1111/nph.15272},
	author = {Walker, Charlotte E. and Taylor, Alison R. and Langer, Gerald and Durak, Gra{\.z}yna M. and Heath, Sarah and Probert, Ian and Tyrrell, Toby and Brownlee, Colin and Wheeler, Glen L.}
}
@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 {Gu2017,
	title = {Adenoides sinensis , a new sand-dwelling dinoflagellate species from China and reexamination of A. eludens from an Atlantic strain},
	journal = {Phycologia},
	volume = {57},
	number = {October},
	year = {2017},
	note = {tex.mendeley-tags: 2017,RCC1982,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {1{\textendash}13},
	abstract = {The sand-dwelling?1dinoflagellate generaAdenoidesandPseudadenoidesare morphologically very close butdistinct in their molecular phylogeny. We established three cultures by isolating single cells from sand samples collected inintertidal zones of Qingdao (Yellow Sea), Dongshan (South China Sea) and Brittany (English Channel, North Atlantic,France). Strain morphology was examined with light and scanning electron microscopy, and both large subunitribosomal DNA (LSU rDNA) and small subunit ribosomal DNA (SSU rDNA) sequences were amplified. Molecularphylogeny, corroborated by morphological examination showing the existence of a ventral pore, confirmed theidentification of the French strain (RCC1982) asAdenoides eludens. The Chinese strains differed fromAdenoides eludensin two additional posterior intercalary plates and differed fromPseudadenoidesin one additional apical plate having theplate formula of Po, Cp, X, 50,600, 4S, 5000, 5p, 10000or alternatively Po, Cp, X, 50,600, 5S, 5000, 3p, 20000. Maximumlikelihood and Bayesian inference carried out with concatenated LSU and SSU sequences demonstrated that the Chinesestrains were closely related but different fromA. eludensand, in corroboration with morphological evidence, supportedtheir classification as a distinct species,Adenoides sinensis sp. nov. Morphological and molecular results confirmed theclose relationship between the two generaAdenoidesandPseudadenoides.},
	keywords = {2017, rcc, RCC1982, sbr?hyto$_\textrmd$ipo},
	doi = {10.2216/17-76.1},
	author = {Gu, Haifeng and Li, Xintian and Chom{\'e}rat, Nicolas and Luo, Zhaohe and Sarno, Diana and Gourvil, Priscillia and Balzano, Sergio and Siano, Raffaele}
}
@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 {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 {Stuart2016,
	title = {Copper toxicity response influences mesotrophic S ynechococcus community structure},
	journal = {Environmental Microbiology},
	volume = {19},
	number = {2},
	year = {2017},
	note = {ISBN: 3907122046 tex.mendeley-tags: 2016,RCC1086,RCC2673},
	month = {feb},
	pages = {756{\textendash}769},
	abstract = {Picocyanobacteria from the genus Synechococcus are ubiquitous in ocean waters. Their phylogenetic and genomic diversity suggests ecological niche differentiation, but the selective forces influencing this are not well defined. Marine picocyanobacteria are sensitive to Cu toxicity, so adaptations to this stress could represent a selective force within, and between, {\textquotedblleft}species{\textquotedblright} also known as clades. We compared Cu stress responses in cultures and natural populations of marine Synechococcus from two co-occurring major mesotrophic clades (I and IV). Using custom microarrays and proteomics to characterize expression responses to Cu in the lab and field, we found evidence for a general stress regulon in marine Synechococcus. However, the two clades also exhibited distinct responses to copper. The Clade I representative induced expression of genomic island genes in cultures and Southern California Bight populations, while the Clade IV representative downregulated Fe-limitation proteins. Copper incubation experiments suggest that Clade IV populations may harbor stress-tolerant subgroups, and thus fitness tradeoffs may govern Cu-tolerant strain distributions. This work demonstrates that Synechococcus has distinct adaptive strategies to deal with Cu toxicity at both the clade and subclade level, implying that metal toxicity and stress response adaptations represent an important selective force for influencing diversity within marine Synechococcus populations. This},
	keywords = {2016, alkylsuccinate, methanogenic, n -alkane, paraffin, RCC1086, RCC2673, smithella, syntrophy},
	issn = {14622912},
	doi = {10.1111/1462-2920.13630},
	url = {http://doi.wiley.com/10.1111/1462-2920.13630},
	author = {Stuart, Rhona K. and Bundy, Randelle and Buck, Kristen and Ghassemain, Majid and Barbeau, Kathy and Palenik, Brian}
}
@article {Gutierrez-Rodriguez2017,
	title = {Dimethylated sulfur compounds in symbiotic protists: A potentially significant source for marine DMS(P)},
	journal = {Limnology and Oceanography},
	number = {February},
	year = {2017},
	note = {tex.mendeley-tags: 2017,rcc1383,rcc1491,rcc3468,rcc3507,sbr?hyto$_\textrmd$ipo},
	month = {feb},
	keywords = {2017, rcc1383, rcc1491, rcc3468, rcc3507, sbr?hyto$_\textrmd$ipo},
	issn = {00243590},
	doi = {10.1002/lno.10491},
	url = {http://doi.wiley.com/10.1002/lno.10491},
	author = {Gutierrez-Rodriguez, Andres and Pillet, Loic and Biard, Tristan and Said-Ahmad, Ward and Amrani, Alon and Sim{\'o}, Rafel and Not, Fabrice}
}
@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 {faucher_impact_2017,
	title = {Impact of trace metal concentrations on coccolithophore growth and morphology: laboratory simulations of Cretaceous stress},
	journal = {Biogeosciences},
	volume = {14},
	number = {14},
	year = {2017},
	note = {Publisher: Copernicus GmbH},
	month = {jul},
	pages = {3603{\textendash}3613},
	abstract = {<p><strong class="journal-contentHeaderColor">Abstract.</strong> The Cretaceous ocean witnessed intervals of profound perturbations such as volcanic input of large amounts of CO$_\textrm2$, anoxia, eutrophication and introduction of biologically relevant metals. Some of these extreme events were characterized by size reduction and/or morphological changes of a few calcareous nannofossil species. The correspondence between intervals of high trace metal concentrations and coccolith dwarfism suggests a negative effect of these elements on nannoplankton biocalcification processes in past oceans. In order to test this hypothesis, we explored the potential effect of a mixture of trace metals on growth and morphology of four living coccolithophore species, namely \textitEmiliania huxleyi, Gephyrocapsa oceanica, Pleurochrysis carterae and \textitCoccolithus pelagicus. The phylogenetic history of coccolithophores shows that the selected living species are linked to Mesozoic species showing dwarfism under excess metal concentrations. The trace metals tested were chosen to simulate the environmental stress identified in the geological record and upon known trace metal interactions with living coccolithophore algae.<br><br>Our laboratory experiments demonstrated that elevated trace metal concentrations, similarly to the fossil record, affect coccolithophore algae size and/or weight. Smaller coccoliths were detected in \textitE. huxleyi and \textitC. pelagicus, while coccoliths of \textitG. oceanica showed a decrease in size only at the highest trace metal concentrations. \textitP. carterae coccolith size was unresponsive to changing trace metal concentrations. These differences among species allow discriminating the most- (\textitP. carterae), intermediate- (\textitE. huxleyi and \textitG. oceanica) and least-tolerant (\textitC. pelagicus) taxa. The fossil record and the experimental results converge on a selective response of coccolithophores to metal availability.<br><br>These species-specific differences must be considered before morphological features of coccoliths are used to reconstruct paleo-chemical conditions.</p>},
	keywords = {RCC1198, RCC1216, RCC1303},
	issn = {1726-4170},
	doi = {10.5194/bg-14-3603-2017},
	url = {https://bg.copernicus.org/articles/14/3603/2017/},
	author = {Faucher, Giulia and Hoffmann, Linn and Bach, Lennart T. and Bottini, Cinzia and Erba, Elisabetta and Riebesell, Ulf}
}
@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 {Parks2017,
	title = {Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta)},
	journal = {American Journal of Botany},
	volume = {105},
	number = {3},
	year = {2017},
	note = {tex.mendeley-tags: RCC205,RCC80},
	pages = {1{\textendash}18},
	keywords = {and, b, c, citation, diatoms, e, gene tree, genome duplication, j, n, nakov, paleopolyploidy, parks m, polyploidy, RCC205, RCC80, ruck, synonymous divergence, t, these authors contributed equally, to this work, wickett},
	doi = {10.1101/181115},
	author = {Parks, Matthew and Nakov, Teofil and Ruck, Elizabeth and Wickett, Norman J and Alverson, Andrew J and Rice, Ada L and Conservation, Plant and Botanic, Chicago and Glencoe, Garden}
}
@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 {Limardo2017,
	title = {Quantitative biogeography of picoprasinophytes establishes ecotype distributions and significant contributions to marine phytoplankton},
	journal = {Environmental Microbiology},
	year = {2017},
	note = {tex.mendeley-tags: RCC1105,RCC715,RCC716,RCC809},
	month = {jun},
	keywords = {RCC1105, RCC715, RCC716, RCC809},
	issn = {14622912},
	doi = {10.1111/1462-2920.13812},
	url = {http://doi.wiley.com/10.1111/1462-2920.13812},
	author = {Limardo, Alexander J. and Sudek, Sebastian and Choi, Chang Jae and Poirier, Camille and Rii, Yoshimi M. and Blum, Marguerite and Roth, Robyn and Goodenough, Ursula and Church, Matthew J. and Worden, Alexandra Z.}
}
@article {Dominguez-Martin2017,
	title = {Quantitative proteomics shows extensive remodeling induced by nitrogen limitation in prochlorococcus marinus SS120},
	journal = {mSystems},
	volume = {2},
	number = {3},
	year = {2017},
	note = {tex.mendeley-tags: RCC156},
	month = {jun},
	pages = {e00008{\textendash}17},
	abstract = {Prochlorococcus requires the capability to accommodate to environmental changes in order to proliferate in oligotrophic oceans, in particular regarding nitrogen availability. A precise knowledge of the composition and changes in the proteome can yield fundamental insights into such a response. Here we report a detailed proteome analysis of the important model cyanobacterium Prochlorococcus marinus SS120 after treatment with azaserine, an inhibitor of ferredoxin-dependent glutamate synthase (GOGAT), to simulate extreme nitrogen starvation. In total, 1,072 proteins, corresponding to 57\% of the theoretical proteome, were identified{\textemdash}the maximum proteome coverage obtained for any Prochlorococcus strain thus far. Spectral intensity, calibrated quantification by the Hi3 method, was obtained for 1,007 proteins. Statistically significant changes ( P value of {\textexclamdown}0.05) were observed for 408 proteins, with the majority of proteins (92.4\%) downregulated after 8 h of treatment. There was a strong decrease in ribosomal proteins upon azaserine addition, while many transporters were increased. The regulatory proteins P II and PipX were decreased, and the global nitrogen regulator NtcA was upregulated. Furthermore, our data for Prochlorococcus indicate that NtcA also participates in the regulation of photosynthesis. Prochlorococcus responds to the lack of nitrogen by slowing down translation, while inducing photosynthetic cyclic electron flow and biosynthesis of proteins involved in nitrogen uptake and assimilation.},
	keywords = {RCC156},
	issn = {2379-5077},
	doi = {10.1128/mSystems.00008-17},
	url = {http://msystems.asm.org/lookup/doi/10.1128/mSystems.00008-17},
	author = {Dom{\'\i}nguez-Mart{\'\i}n, Maria Agustina and G{\'o}mez-Baena, Guadalupe and D{\'\i}ez, Jes{\'u}s and L{\'o}pez-Grueso, Maria Jos{\'e} and Beynon, Robert J. and Garc{\'\i}a-Fern{\'a}ndez, Jos{\'e} Manuel},
	editor = {Huber, Julie A.}
}
@article {Roesler2017,
	title = {Recommendations for obtaining unbiased chlorophyll estimates from in situ chlorophyll fluorometers: A global analysis of WET Labs ECO sensors},
	journal = {Limnology and Oceanography: Methods},
	volume = {15},
	number = {6},
	year = {2017},
	note = {tex.mendeley-tags: RCC233,RCC42,RCC834},
	pages = {572{\textendash}585},
	abstract = {Chlorophyll fluorometers provide the largest in situ global data set for estimating phytoplankton biomass because of their ease of use, size, power consumption, and relatively low price. While in situ chlorophyll a (Chl) fluorescence is proxy for Chl a concentration, and hence phytoplankton biomass, there exist large natural variations in the relationship between in situ fluorescence and extracted Chl a concentration. Despite this large natural variability, we present here a global validation data set for the WET Labs Environmental Characterization Optics (ECO) series chlorophyll fluorometers that suggests a factor of 2 overestimation in the factory calibrated Chl a estimates for this specific manufacturer and series of sensors. We base these results on paired High Pressure Liquid Chromatography (HPLC) and in situ fluorescence match ups for which non-photochemically quenched fluorescence observations were removed. Additionally, we examined matchups between the factory-calibrated in situ fluorescence and estimates of chlorophyll concentration determined from in situ radiometry, absorption line height, NASA{\textquoteright}s standard ocean color algorithm as well as laboratory calibrations with phytoplankton monocultures spanning diverse species that support the factor of 2 bias. We therefore recommend the factor of 2 global bias correction be applied for the WET Labs ECO sensors, at the user level, to improve the global accuracy of chlorophyll concentration estimates and products derived from them. We recommend that other fluorometer makes and models should likewise undergo global analyses to identify potential bias in factory calibration.},
	keywords = {RCC233, RCC42, RCC834},
	issn = {15415856},
	doi = {10.1002/lom3.10185},
	author = {Roesler, Collin and Uitz, Julia and Claustre, Herv{\'e} and Boss, Emmanuel and Xing, Xiaogang and Organelli, Emanuele and Briggs, Nathan and Bricaud, Annick and Schmechtig, Catherine and Poteau, Antoine and D{\textquoteright}Ortenzio, Fabrizio and Ras, Josephine and Drapeau, Susan and Ha{\"e}ntjens, Nils and Barbieux, Marie}
}
@article {Riou2017,
	title = {Specificity re-evaluation of oligonucleotide probes for the detection of marine picoplankton by tyramide signal amplification-fluorescent in situ hybridization},
	journal = {Frontiers in Microbiology},
	volume = {8},
	number = {May},
	year = {2017},
	note = {tex.mendeley-tags: RCC257},
	month = {may},
	pages = {854},
	abstract = {Oligonucleotide probes are increasingly being used to characterize natural microbial assemblages by Tyramide Signal Amplification-Fluorescent in situ Hybridization (TSA-FISH, or CAtalysed Reporter Deposition CARD-FISH). In view of the fast-growing rRNA databases, we re-evaluated the in silico specificity of eleven bacterial and eukaryotic probes and competitor frequently used for the quantification of marine picoplankton. We performed tests on cell cultures to decrease the risk for non-specific hybridization, before they are used on environmental samples. The probes were confronted to recent databases and hybridization conditions were tested against target strains matching perfectly with the probes, and against the closest non-target strains presenting one to four mismatches. We increased the hybridization stringency from 55\% to 65\% formamide for the Eub338+EubII+EubIII probe mix to be specific to the Eubacteria domain. In addition, we found that recent changes in the Gammaproteobacteria classification decreased the specificity of Gam42a probe, and that the Roseo536R and Ros537 probes were not specific to, and missed part of the Roseobacter clade. Changes in stringency conditions were important for bacterial probes; these induced respectively a significant increase, in Eubacteria and Roseobacter and no significant changes in Gammaproteobacteria concentrations from the investigated natural environment. We confirmed the eukaryotic probes original conditions, and propose the Euk1209+NChlo01+Chlo02 probe mix to target the largest picoeukaryotic diversity. Experiences acquired through these investigations leads us to propose the use of seven steps protocol for complete FISH probe specificity check-up to improve data quality in environmental studies.},
	keywords = {CARD-FISH, Eukaryota, oligonucleotide, PROBES, Prokaryote, RCC257, specificity, TSA-FISH},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2017.00854},
	url = {http://journal.frontiersin.org/article/10.3389/fmicb.2017.00854/full},
	author = {Riou, Virginie and P{\'e}riot, Marine and Biegala, Isabelle C.}
}
@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 {Paerl2016,
	title = {Use of plankton-derived vitamin B1 precursors, especially thiazole-related precursor, by key marine picoeukaryotic phytoplankton},
	journal = {The ISME Journal},
	volume = {11},
	number = {3},
	year = {2017},
	note = {Publisher: Nature Publishing Group tex.mendeley-tags: rcc3401,rcc745},
	month = {mar},
	pages = {753{\textendash}765},
	keywords = {rcc3401, RCC745},
	issn = {1751-7362},
	doi = {10.1038/ismej.2016.145},
	url = {http://www.nature.com/doifinder/10.1038/ismej.2016.145},
	author = {Paerl, Ryan W and Bouget, Fran{\c c}ois-Yves and Lozano, Jean-Claude and Verg{\'e}, Val{\'e}rie and Schatt, Philippe and Allen, Eric E and Palenik, Brian and Azam, Farooq}
}
@article {Leliaert2016,
	title = {Chloroplast phylogenomic analyses reveal the deepest-branching lineage of the Chlorophyta, Palmophyllophyceae class. nov.},
	journal = {Scientific Reports},
	volume = {6},
	year = {2016},
	note = {tex.mendeley-tags: 2016,RCC15,RCC299},
	month = {may},
	pages = {25367},
	keywords = {2016, RCC15, RCC299},
	issn = {2045-2322},
	doi = {10.1038/srep25367},
	url = {http://www.nature.com/articles/srep25367},
	author = {Leliaert, Frederik and Tronholm, Ana and Lemieux, Claude and Turmel, Monique and DePriest, Michael S. and Bhattacharya, Debashish and Karol, Kenneth G. and Fredericq, Suzanne and Zechman, Frederick W. and Lopez-Bautista, Juan M.}
}
@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 {Klouch2016,
	title = {Historical records from dated sediment cores reveal the multidecadal dynamic of the toxic dinoflagellate Alexandrium minutum in the Bay of Brest (France)},
	journal = {FEMS Microbiology Ecology},
	volume = {92},
	number = {7},
	year = {2016},
	note = {tex.mendeley-tags: 2016,rcc,sbr?hyto$_\textrmd$ipo},
	month = {jul},
	pages = {fiw101},
	abstract = {The multiannual dynamic of the cyst-forming and toxic marine dinoflagellate Alexandrium minutum was studied over a time scale of about 150 years by a paleoecological approach based on ancient DNA (aDNA) quantification and cyst revivification data obtained from two dated sediment cores of the Bay of Brest (Brittany, France). The first genetic traces of the species presence in the study area dated back to 1873 {\textpm} 6. Specific aDNA could be quantified by a newly-developed real-time PCR assay in the upper core layers, in which the germination of the species (in up to 17-19 year-old sediments) was also obtained. In both cores studied, our quantitative paleogenetic data showed a statistically significant increasing trend in the abundance of A. minutum ITS1 rDNA copies over time, corroborating three decades of local plankton data that have documented an increasing trend in the species cell abundance. By comparison, paleogenetic data of the dinoflagellate Scrippsiella donghaienis did not show a coherent trend between the cores studied, supporting the hypothesis of the existence of a species-specific dynamic of A. minutum in the study area. This work contributes to the development of paleoecological research, further showing its potential for biogeographical, ecological and evolutionary studies on marine microbes.},
	keywords = {2016, rcc, sbr?hyto$_\textrmd$ipo},
	issn = {1574-6941},
	doi = {10.1093/femsec/fiw101},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/27162179 https://academic.oup.com/femsec/article-lookup/doi/10.1093/femsec/fiw101},
	author = {Klouch, Khadidja Z and Schmidt, Sabine and Andrieux-Loyer, Fran{\c c}oise and Le Gac, Micka{\"e}l and Hervio-Heath, Dominique and Qui-Minet, Zujaila N and Qu{\'e}r{\'e}, Julien and Bigeard, Estelle and Guillou, Laure and Siano, Raffaele},
	editor = {Laanbroek, Riks}
}
@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 {Stawiarski2016,
	title = {The physiological response of picophytoplankton to temperature and its model representation},
	journal = {Fronitiers in Marine Science},
	volume = {3},
	number = {164},
	year = {2016},
	note = {tex.mendeley-tags: rcc162,rcc1677,rcc212,rcc289,rcc296,rcc30,rcc361,rcc438,rcc503},
	pages = {1{\textendash}13},
	keywords = {chlorophyll a to carbon, chlorophyll a to carbon ratio, Eppley, frontiers in marine science, frontiersin, org, physiological parameterization, phytoplankton growth rates, phytoplankton size scaling, picoeukaryotes, picophytoplankton, ratio, rcc162, rcc1677, rcc212, rcc289, rcc296, rcc30, rcc361, rcc438, rcc503, temperature tolerance, www},
	issn = {2296-7745},
	doi = {10.3389/fmars.2016.00164},
	author = {Stawiarski, Beate and Buitenhuis, Erik T and Qu{\'e}r{\'e}, Corinne Le}
}
@article {Garrido2016,
	title = {Pigment variations in Emiliania huxleyi (CCMP370) as a response to changes in light intensity or quality},
	journal = {Environmental Microbiology},
	volume = {18},
	number = {12},
	year = {2016},
	note = {tex.mendeley-tags: 2016,rcc1255},
	month = {dec},
	pages = {4412{\textendash}4425},
	keywords = {2016, RCC1255},
	issn = {14622912},
	doi = {10.1111/1462-2920.13373},
	url = {http://doi.wiley.com/10.1111/1462-2920.13373},
	author = {Garrido, Jos{\'e} L. and Brunet, Christophe and Rodr{\'\i}guez, Francisco}
}
@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 {Bendif2016,
	title = {Recent reticulate evolution in the ecologically dominant lineage of coccolithophores},
	journal = {Frontiers in Microbiology},
	volume = {7},
	number = {May},
	year = {2016},
	note = {tex.mendeley-tags: 2016,RCC4032,RCC4033,RCC4034,RCC4035,RCC4036,rcc,sbr?hyto},
	month = {may},
	keywords = {2016, coccolithophores, cyto-nuclear discordance, diversity, Emiliania, evolution, Gephyrocapsa, introgressive hybridization, rcc, RCC4032, RCC4033, RCC4034, RCC4035, RCC4036, Reticulofenestra, sbr?hyto},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2016.00784},
	url = {http://journal.frontiersin.org/article/10.3389/fmicb.2016.00784 http://journal.frontiersin.org/Article/10.3389/fmicb.2016.00784/abstract},
	author = {Bendif, El Mahdi and Probert, Ian and D{\'\i}az-Rosas, Francisco and Thomas, Daniela and van den Engh, Ger and Young, Jeremy R. and von Dassow, Peter}
}
@article {Durak2016,
	title = {A role for diatom-like silicon transporters in calcifying coccolithophores},
	journal = {Nature Communications},
	volume = {7},
	number = {February},
	year = {2016},
	note = {tex.mendeley-tags: 2016,RCC1130,RCC1303,RCC1453,RCC1456,RCC3432},
	pages = {10543},
	abstract = {Biomineralisation by marine phytoplankton, such as the silicifying diatoms and calcifying coccolithophores, plays an important role in carbon and nutrient cycling in the oceans. Silicification and calcification are distinct cellular processes with no known common mechanisms. As a result, it is thought that coccolithophores are able to outcompete diatoms in Si-depleted waters, which can contribute to the formation of coccolithophore blooms. Here, we show that an expanded family of diatom-like silicon transporters (SITs) are present in both silicifying and calcifying haptophyte phytoplankton, including some coccolithophores of global ecological importance. We find an essential role for Si in calcification in these coccolithophores, indicating that Si uptake contributes to the very different forms of biomineralisation in diatoms and coccolithophores. However, SITs and the requirement for Si are significantly absent from the highly abundant bloom-forming coccolithophores, such as Emiliania huxleyi. These very different requirements for Si in coccolithophores are likely to have major influence on their competitive interactions with diatoms and other siliceous phytoplankton.},
	keywords = {(RCC1130, (RCC1456), 2016, biomineralisation, coccolithophores, Gephyrocapsa oceanica (RCC1303) and Scyphosphaera, haptophytes, RCC1130, RCC1303, RCC1453, RCC1456, RCC3432, silica, TMR5 (RCC3432{\textemdash}Sea of Japan) and PZ241 (RCC1453{\textemdash}Med},
	issn = {2041-1723},
	doi = {10.1038/ncomms10543},
	author = {Durak, Grazyna M and Taylor, Alison R and Probert, Ian and de Vargas, Colomban and Audic, St{\'e}phane and Schroeder, Declan C and Brownlee, Colin and Wheeler, Glen L}
}
@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 {Simmons2015,
	title = {Intron invasions trace algal speciation and reveal nearly identical Arctic and Antarctic Micromonas populations.},
	journal = {Molecular biology and evolution},
	year = {2015},
	note = {tex.mendeley-tags: rcc},
	month = {may},
	abstract = {Spliceosomal introns are a hallmark of eukaryotic genes that are hypothesized to play important roles in genome evolution but have poorly understood origins. Although most introns lack sequence homology to each other, recently new families of spliceosomal introns that are repeated hundreds of times in individual genomes have been discovered in a few organisms. The prevalence and conservation of these introner elements (IEs) or introner-like elements (ILEs) in other taxa, as well as their evolutionary relationships to regular spliceosomal introns, are still unknown. Here, we systematically investigate introns in the widespread marine green alga Micromonas and report new families of IEs, numerous intron presence-absence polymorphisms, and potential intron insertion hot-spots. The new families enabled identification of conserved IE secondary structure features and establishment of a novel general model for repetitive intron proliferation across genomes. Despite shared secondary structure, the IE families from each Micromonas lineage bear no obvious sequence similarity to those in the other lineages, suggesting their appearance is intimately linked with the process of speciation. Two of the new IE families come from an Arctic culture (Micromonas Clade E2) isolated from a polar region where this alga is increasing in abundance due to climate change. The same two families were detected in metagenomic data from Antarctica - a system where Micromonas has never before been reported. Strikingly high identity between the Arctic isolate and Antarctic coding sequences that flank the IEs suggests connectivity between populations in the two polar systems that we postulate occurs through deep-sea currents. Recovery of Clade E2 sequences in North Atlantic Deep Waters beneath the Gulf Stream supports this hypothesis. Our work illuminates the dynamic relationships between an unusual class of repetitive introns, genome evolution, speciation and global distribution of this sentinel marine alga.},
	keywords = {rcc},
	issn = {1537-1719},
	doi = {10.1093/molbev/msv122},
	url = {http://mbe.oxfordjournals.org/cgi/content/long/msv122v1},
	author = {Simmons, Melinda P and Bachy, Charles and Sudek, Sebastian and van Baren, Marijke J and Sudek, Lisa and Ares, Manuel and Worden, Alexandra Z}
}
@article {Bendif2015,
	title = {Morphological and phylogenetic characterization of new gephyrocapsa isolates suggests introgressive hybridization in the Emiliania/Gephyrocapsa complex (haptophyta)},
	journal = {Protist},
	volume = {166},
	number = {3},
	year = {2015},
	note = {tex.mendeley-tags: 2015,RCC1281,RCC1282,RCC1284,RCC1286,RCC1292,RCC1300,RCC1305,RCC1307,RCC1316,RCC1317,RCC1318,RCC1319,RCC1320,RCC1562,RCC1839,RCC3370,RCC3862,RCC3898,rcc},
	pages = {323{\textendash}336},
	abstract = {The coccolithophore genus Gephyrocapsa contains a cosmopolitan assemblage of pelagic species, including the bloom-forming Gephyrocapsa oceanica, and is closely related to the emblematic coccolithophore Emiliania huxleyi within the No{\"e}laerhabdaceae. These two species have been extensively studied and are well represented in culture collections, whereas cultures of other species of this family are lacking. We report on three new strains of Gephyrocapsa isolated into culture from samples from the Chilean coastal upwelling zone using a novel flow cytometric single-cell sorting technique. The strains were characterized by morphological analysis using scanning electron microscopy and phylogenetic analysis of 6 genes (nuclear 18S and 28S rDNA, plastidial 16S and tufA, and mitochondrial cox1 and cox3 genes). Morphometric features of the coccoliths indicate that these isolates are distinct from G. oceanica and best correspond to G. muellerae. Surprisingly, both plastidial and mitochondrial gene phylogenies placed these strains within the E. huxleyi clade and well separated from G. oceanica isolates, making Emiliania appear polyphyletic. The only nuclear sequence difference, 1bp in the 28S rDNA region, also grouped E. huxleyi with the new Gephyrocapsa isolates and apart from G. oceanica. Specifically, the G. muellerae morphotype strains clustered with the mitochondrial β clade of E. huxleyi, which, like G. muellerae, has been associated with cold (temperate and sub-polar) waters. Among putative evolutionary scenarios that could explain these results we discuss the possibility that E. huxleyi is not a valid taxonomic unit, or, alternatively the possibility of past hybridization and introgression between each E. huxleyi clade and older Gephyrocapsa clades. In either case, the results support the transfer of Emiliania to Gephyrocapsa. These results have important implications for relating morphological species concepts to ecological and evolutionary units of diversity.},
	keywords = {2015, coccolithophores, Emiliania huxleyi, Gephyrocapsa muellerae, Gephyrocapsa oceanica, hybridization, phylogeny., rcc, RCC1281, RCC1282, RCC1284, RCC1286, RCC1292, RCC1300, RCC1305, RCC1307, RCC1316, RCC1317, RCC1318, RCC1319, RCC1320, RCC1562, RCC1839, RCC3370, RCC3862, RCC3898, species concept},
	issn = {14344610},
	doi = {10.1016/j.protis.2015.05.003},
	url = {http://www.sciencedirect.com/science/article/pii/S1434461015000243},
	author = {Bendif, El Mahdi and Probert, Ian and Young, Jeremy R. and von Dassow, Peter}
}
@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 {Andersen2015,
	title = {Phaeocystis rex sp. nov. (Phaeocystales, Prymnesiophyceae): a new solitary species that produces a multilayered scale cell covering},
	journal = {European Journal of Phycology},
	volume = {50},
	number = {2},
	year = {2015},
	note = {Publisher: Taylor \& Francis tex.mendeley-tags: 2015,RCC 4025,rcc},
	pages = {207{\textendash}222},
	abstract = {A morphologically distinct marine species, Phaeocystis rex sp. nov., was described on the basis of light microscopy, transmission electron microscopy and DNA sequence comparisons. Non-motile cells were solitary (non-colonial), 6{\textendash}10 {\textmu}m in diameter and 8{\textendash}15 {\textmu}m long, and possessed chloroplasts with distinctive finger-like lobes. TEM observations demonstrated the presence of two short flagella and a very short haptonema that arose from an invagination of the protoplast. Non-motile cells were surrounded by one to several dense layers composed of scales, presumably unmineralized, and an amorphous material. Phylogenetic analyses based upon combined partial nucleotide sequences for five nuclear-or plastid-encoded genes (18S rRNA, 28S rRNA, 16S rRNA, psbA and rbcL) from cultured strains and from uncharacterized acantharian symbionts confirmed that P. rex was a distinct species. These analyses implied that P. rex occupies an intermediate evolutionary position between solitary and colonial Phaeocystis species.},
	keywords = {2015, algae, organic scales, Phaeocystales, Phaeocystis rex, Prymnesiophyceae, rcc, RCC4025, RCC?o?dd, SBR$_\textrmP$hyto$_\textrmE$PPO, systematics, ultrastructure},
	issn = {0967-0262},
	doi = {10.1080/09670262.2015.1024287},
	url = {http://www.tandfonline.com/doi/full/10.1080/09670262.2015.1024287},
	author = {Andersen, Robert A. and Bailey, J. Craig and Decelle, Johan and Probert, Ian}
}
@article {Decelle2015,
	title = {PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy},
	journal = {Molecular Ecology Resources},
	volume = {15},
	number = {6},
	year = {2015},
	note = {tex.mendeley-tags: 2015,macumba,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo},
	pages = {1435{\textendash}1445},
	abstract = {Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongo- ing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF data- base that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classifica- tion were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing.},
	keywords = {2015, MACUMBA, rcc, RCC?o?dd, SBR$_\textrmP$hyto$_\textrmD$IPO, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo},
	issn = {1755098X},
	doi = {10.1111/1755-0998.12401},
	url = {http://doi.wiley.com/10.1111/1755-0998.12401},
	author = {Decelle, Johan and Romac, Sarah and Stern, Rowena F. and Bendif, El Mahdi and Zingone, Adriana and Audic, St{\'e}phane and Guiry, Michael D. and Guillou, Laure and Tessier, D{\'e}sir{\'e} and Le Gall, Florence and Gourvil, Priscillia and dos Santos, Adriana Lopes and Probert, Ian and Vaulot, Daniel and de Vargas, Colomban and Christen, Richard}
}
@article {Probert2014a,
	title = {Brandtodinium gen. nov. and B. nutricula comb. Nov. (Dinophyceae), a dinoflagellate commonly found in symbiosis with polycystine radiolarians},
	journal = {Journal of Phycology},
	volume = {50},
	number = {2},
	year = {2014},
	note = {tex.mendeley-tags: RCC3378,RCC3379,RCC3380,RCC3381,RCC3382,RCC3383,RCC3384,RCC3385,RCC3386,RCC3387,RCC3388},
	pages = {388{\textendash}399},
	abstract = {Symbiotic interactions between pelagic hosts and microalgae have received little attention, although they are widespread in the photic layer of the world ocean, where they play a fundamental role in the ecology of the planktonic ecosystem. Polycystine radiolarians (including the orders Spumellaria, Collodaria and Nassellaria) are planktonic heterotrophic protists that are widely distributed and often abundant in the ocean. Many polycystines host symbiotic microalgae within their cytoplasm, mostly thought to be the dinoflagellate Scrippsiella nutricula, a species originally described by Karl Brandt in the late nineteenth century as Zooxanthella nutricula. The free-living stage of this dinoflagellate has never been characterized in terms of morphology and thecal plate tabulation. We examined morphological characters and sequenced conservative ribosomal markers of clonal cultures of the free-living stage of symbiotic dinoflagellates isolated from radiolarian hosts from the three polycystine orders. In addition, we sequenced symbiont genes directly from several polycystine-symbiont holobiont specimens from different oceanic regions. Thecal plate arrangement of the free-living stage does not match that of Scrippsiella or related genera, and LSU and SSU rDNA-based molecular phylogenies place these symbionts in a distinct clade within the Peridiniales. Both phylogenetic analyses and the comparison of morphological features of culture strains with those reported for other closely related species support the erection of a new genus that we name Brandtodinium gen. nov. and the recombination of S. nutricula as B. nutricula comb. nov.},
	keywords = {Dinoflagellate, MACUMBA, Peridiniales, polycystines, Radiolaria, rcc, RCC3378, RCC3379, RCC3380, RCC3381, RCC3382, RCC3383, RCC3384, RCC3385, RCC3386, RCC3387, RCC3388, SBR$_\textrmP$hyto$_\textrmD$PO, Scrippsiella, symbiosis, taxonomy, Zooxanthella},
	doi = {10.1111/jpy.12174},
	url = {http://dx.doi.org/10.1111/jpy.12174},
	author = {Probert, Ian and Siano, Raffaele and Poirier, Camille and Decelle, Johan and Biard, Tristan and Tuji, Akihiro and Suzuki, Noritoshi and Not, Fabrice}
}
@article {Bombar2014,
	title = {Comparative genomics reveals surprising divergence of two closely related strains of uncultivated UCYN-A cyanobacteria},
	journal = {The ISME Journal},
	volume = {8},
	number = {12},
	year = {2014},
	note = {Publisher: Nature Publishing Group tex.mendeley-tags: rcc},
	pages = {2530{\textendash}2542},
	keywords = {rcc},
	issn = {1751-7362},
	doi = {10.1038/ismej.2014.167},
	url = {http://www.nature.com/doifinder/10.1038/ismej.2014.167},
	author = {Bombar, Deniz and Heller, Philip and Sanchez-Baracaldo, Patricia and Carter, Brandon J and Zehr, Jonathan P}
}
@article {Bellec2014,
	title = {Cophylogenetic interactions between marine viruses and eukaryotic picophytoplankton},
	journal = {BMC Evolutionary Biology},
	volume = {14},
	number = {1},
	year = {2014},
	note = {tex.mendeley-tags: RCC1105,RCC1107,RCC1108,RCC1109,RCC114,RCC2482,RCC2483,RCC2484,RCC2485,RCC344,RCC356,RCC373,RCC418,RCC461,RCC464,RCC465,RCC629,RCC658,RCC745,RCC789,RCC834},
	pages = {59},
	abstract = {BACKGROUND:Numerous studies have investigated cospeciation (or cophylogeny) in various host-symbiont systems, and different patterns were inferred, from strict cospeciation where symbiont phylogeny mirrors host phylogeny, to complete absence of correspondence between trees. The degree of cospeciation is generally linked to the level of host specificity in the symbiont species and the opportunity they have to switch hosts. In this study, we investigated cophylogeny for the first time in a microalgae-virus association in the open sea, where symbionts are believed to be highly host-specific but have wide opportunities to switch hosts. We studied prasinovirus-Mamiellales associations using 51 different viral strains infecting 22 host strains, selected from the characterisation and experimental testing of the specificities of 313 virus strains on 26 host strains.RESULTS:All virus strains were restricted to their host genus, and most were species-specific, but some of them were able to infect different host species within a genus. Phylogenetic trees were reconstructed for viruses and their hosts, and their congruence was assessed based on these trees and the specificity data using different cophylogenetic methods, a topology-based approach, Jane, and a global congruence method, ParaFit. We found significant congruence between virus and host trees, but with a putatively complex evolutionary history.CONCLUSIONS:Mechanisms other than true cospeciation, such as host-switching, might explain a part of the data. It has been observed in a previous study on the same taxa that the genomic divergence between host pairs is larger than between their viruses. It implies that if cospeciation predominates in this algae-virus system, this would support the hypothesis that prasinoviruses evolve more slowly than their microalgal hosts, whereas host switching would imply that these viruses speciated more recently than the divergence of their host genera.},
	keywords = {rcc, RCC1105, rcc1107, RCC1108, RCC1109, RCC114, RCC2482, RCC2483, RCC2484, RCC2485, RCC344, RCC356, RCC373, RCC418, RCC461, RCC464, RCC465, RCC629, RCC658, RCC745, RCC789, RCC834, SBR$_\textrmP$hyto$_\textrmD$PO},
	doi = {10.1186/1471-2148-14-59},
	url = {http://www.biomedcentral.com/1471-2148/14/59},
	author = {Bellec, Laure and Clerissi, Camille and Edern, Roseline and Foulon, Elodie and Simon, Nathalie and Grimsley, Nigel and Desdevises, Yves}
}
@article {Lepelletier2014a,
	title = {Dinomyces arenysensis gen. et sp. nov. (rhizophydiales, dinomycetaceae fam. nov.), a chytrid infecting marine dinoflagellates},
	journal = {Protist},
	volume = {165},
	number = {2},
	year = {2014},
	note = {tex.mendeley-tags: 2014,macumba,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?app},
	pages = {230{\textendash}244},
	abstract = {Environmental 18S rRNA gene surveys of microbial eukaryotes have recently revealed the diversity of major parasitic agents in pelagic freshwater systems, consisting primarily of chytrid fungi. To date, only a few studies have reported the presence of chydrids in the marine environment and a limited number of marine chytrids have been properly identified and characterized. Here, we report the isolation and cultivation of a marine chytrid from samples taken during a bloom of the toxic dinoflagellate Alexandrium minutum in the Arenys de Mar harbour (Mediterranean Sea, Spain). Cross-infections using cultures and natural phytoplankton communities revealed that this chytrid is only able to infect certain species of dinoflagellates, with a rather wide host range but with a relative preference for Alexandrium species. Phylogenetic analyses showed that it belongs to the order Rhizophydiales, but cannot be included in any of the existing families within this order. Several ultrastructural characters confirmed the placement of this taxon within the Rhizophydiales as well its novelty notably in terms of zoospore structure. This marine chytridial parasitoid is described as a new genus and species, Dinomyces arenysensis, within the Dinomycetaceae fam. nov.},
	keywords = {2014, chytrid, Dinoflagellates, Dinomyces arenysensis, Fungi, MACUMBA, microbial parasitoids, rcc, RCC?o?dd, Rhizophydiales., SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, sbr?hyto?app},
	doi = {10.1016/j.protis.2014.02.004},
	url = {http://www.sciencedirect.com/science/article/pii/S1434461014000170},
	author = {Lepelletier, Fr{\'e}d{\'e}ric and Karpov, Sergey A and Alacid, Elisabet and Le Panse, Sophie and Bigeard, Estelle and Garc{\'e}s, Esther and Jeanthon, Christian and Guillou, Laure}
}
@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 {Bendif2014,
	title = {Genetic delineation between and within the widespread coccolithophore morpho-species Emiliania huxleyi and Gephyrocapsa oceanica (Haptophyta)},
	journal = {Journal of Phycology},
	volume = {50},
	year = {2014},
	note = {tex.mendeley-tags: 2014,cc3549,rcc,rcc1210,rcc1213,rcc1220,rcc1227,rcc1229,rcc1242,rcc1252,rcc1253,rcc1258,rcc1259,rcc1260,rcc1271,rcc1281,rcc1288,rcc1292,rcc1297,rcc1300,rcc1303,rcc1305,rcc1316,rcc1562,rcc174,rcc1839,rcc3545,rrcc1247,sbr?hyto?ppo},
	pages = {140{\textendash}148},
	keywords = {2014, cc3549, rcc, rcc1210, RCC1213, rcc1220, rcc1227, rcc1229, RCC1242, rcc1252, RCC1253, rcc1258, RCC1259, rcc1260, rcc1271, RCC1281, rcc1288, RCC1292, rcc1297, RCC1300, RCC1303, RCC1305, RCC1316, RCC1562, rcc174, RCC1839, rcc3545, rrcc1247, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1111/jpy.12147},
	author = {Bendif, El Mahdi and Probert, Ian and Carmichael, Margaux and Romac, Sarah and Hagino, Kyoko and de Vargas, Colomban}
}
@article {Nezan2014,
	title = {Genetic diversity of the harmful family Kareniaceae (Gymnodiniales, Dinophyceae) in France, with the description of {\textexclamdown}i{\textquestiondown}Karlodinium gentienii{\textexclamdown}/i{\textquestiondown} sp. nov.: A new potentially toxic dinoflagellate},
	journal = {Harmful Algae},
	volume = {40},
	year = {2014},
	note = {tex.mendeley-tags: 2014,rcc,sbr?hyto?app},
	pages = {75{\textendash}91},
	abstract = {A B S T R A C T The family Kareniaceae is mostly known in France for recurrent blooms of Karenia mikimotoi in the Atlantic, English Channel, and Mediterranean Sea and for the unusual green discoloration in the saltwater lagoon of Diana (Corsica) caused by Karlodinium corsicum in April 1994. In terms of diversity, this taxonomic group was long overlooked owing to the difficult identification of these small unarmored dinoflagellates. In this study, thanks to the molecular characterization performed on single cells from field samples and cultures, twelve taxonomic units were assigned to the known genera Karenia, Karlodinium and Takayama, whereas one could not be affiliated to any described genus. The molecular phylogeny inferred from the D1{\textendash}D2 region of the LSU rDNA showed that five of them formed a sister taxon of a known species, and could not be identified at species-level, on the basis of molecular analysis only. Among these latter taxa, one Karlodinium which was successfully cultured was investigated by studying the external morphological features (using two procedures for cells fixation), ultrastructure, pigment composition, and haemolytic activity. The results of our analyses corroborate the genetic results in favour of the erection of Karlodinium gentienii sp. nov., which possesses an internal complex system of trichocysts connected to external micro-processes particularly abundant in the epicone, and a peculiar pigment composition. In addition, preliminary assays showed a haemolytic activity.},
	keywords = {2014, rcc, sbr?hyto?app},
	issn = {15689883},
	doi = {10.1016/j.hal.2014.10.006},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S1568988314001863},
	author = {N{\'e}zan, Elisabeth and Siano, Raffaele and Boulben, Sylviane and Six, Christophe and Bilien, Gwenael and Ch{\`e}ze, Karine and Duval, Audrey and Le Panse, Sophie and Qu{\'e}r{\'e}, Julien and Chom{\'e}rat, Nicolas}
}
@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 {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 {Lepelletier2014,
	title = {Parvilucifera rostrata sp. nov., a novel parasite in the phylum Perkinsozoa that infects the toxic dinoflagellate Alexandrium minutum (Dinophyceae)},
	journal = {Protist},
	volume = {165},
	year = {2014},
	note = {tex.mendeley-tags: 2014,macumba,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?app},
	pages = {31{\textendash}49},
	keywords = {2014, MACUMBA, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto$_\textrmd$ipo, sbr?hyto?app},
	doi = {10.1016/j.protis.2013.09.005},
	author = {Lepelletier, F and Karpov, S A and Le Panse, S and Bigeard, E and Skovgaard, A and Jeanthon, C and Guillou, L}
}
@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 {Abida2013,
	title = {Bioprospecting marine plankton},
	journal = {Marine Drugs},
	volume = {11},
	number = {11},
	year = {2013},
	note = {tex.mendeley-tags: 2013,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo},
	pages = {4594{\textendash}4611},
	keywords = {2013, MicroB3, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo},
	doi = {10.3390/md11114594},
	url = {http://www.mdpi.com/1660-3397/11/11/4594},
	author = {Abida, Heni and Ruchaud, Sandrine and Rios, Laurent and Humeau, Anne and Probert, Ian and de Vargas, Colomban and Bach, St{\'e}phane and Bowler, Chris}
}
@article {Bendif2013,
	title = {On the description of Tisochrysis lutea gen . nov . sp . nov . and Isochrysis nuda sp. nov. in the Isochrysidales, and the transfer of Dicrateria to the Prymnesiales (Haptophyta)},
	journal = {Journal of Applied Phycology},
	volume = {25},
	year = {2013},
	note = {tex.mendeley-tags: 2013,RCC1195,RCC1207,RCC1281,RCC1286,RCC1344,RCC1346,RCC1347,RCC1348,RCC1349,RCC1350,RCC1353,RCC2477,RCC3681,RCC3684,RCC3686,RCC3687,RCC3690,RCC3691,RCC3692,RCC3693,RCC3694,RCC3695,RCC3696,RCC3699,RCC3701,RCC3707,rcc,sbr?hyto?ppo},
	pages = {1763{\textendash}1776},
	keywords = {2013, dicrateria, imantonia, isochrysidaceae, isochrysis galbana, phylogeny, rcc, RCC1195, RCC1207, RCC1281, RCC1286, RCC1344, RCC1346, RCC1347, RCC1348, RCC1349, RCC1350, RCC1353, RCC2477, RCC3681, RCC3684, RCC3686, RCC3687, RCC3690, RCC3691, RCC3692, RCC3693, RCC3694, RCC3695, RCC3696, RCC3699, RCC3701, RCC3707, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo, taxonomy, ultrastructure},
	doi = {10.1007/s10811-013-0037-0},
	author = {Bendif, El Mahdi and Probert, Ian and Schroeder, Declan C and de Vargas, Colomban}
}
@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 {stuart_genomic_2013,
	title = {Genomic island genes in a coastal marine Synechococcus strain confer enhanced tolerance to copper and oxidative stress},
	journal = {The ISME Journal},
	volume = {7},
	number = {6},
	year = {2013},
	note = {Number: 6 Publisher: Nature Publishing Group},
	pages = {1139{\textendash}1149},
	abstract = {Highly variable regions called genomic islands are found in the genomes of marine picocyanobacteria, and have been predicted to be involved in niche adaptation and the ecological success of these microbes. These picocyanobacteria are typically highly sensitive to copper stress and thus, increased copper tolerance could confer a selective advantage under some conditions seen in the marine environment. Through targeted gene inactivation of genomic island genes that were known to be upregulated in response to copper stress in Synechococcus sp. strain CC9311, we found two genes (sync_1495 and sync_1217) conferred tolerance to both methyl viologen and copper stress in culture. The prevalence of one gene, sync_1495, was then investigated in natural samples, and had a predictable temporal variability in abundance at a coastal monitoring site with higher abundance in winter months. Together, this shows that genomic island genes can confer an adaptive advantage to specific stresses in marine Synechococcus, and may help structure their population diversity.},
	keywords = {RCC1086},
	issn = {1751-7370},
	doi = {10.1038/ismej.2012.175},
	url = {http://www.nature.com/articles/ismej2012175},
	author = {Stuart, Rhona K. and Brahamsha, Bianca and Busby, Kayla and Palenik, Brian}
}
@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 {Blanc-Mathieu2013,
	title = {Organellar inheritance in the green lineage: Insights from ostreococcus tauri},
	journal = {Genome Biology and Evolution},
	volume = {5},
	number = {8},
	year = {2013},
	note = {tex.mendeley-tags: RCC1108,RCC1110,RCC1112,RCC1114,RCC1115,RCC1116,RCC1117,RCC1118,RCC1123,RCC1558,RCC1559,RCC1561,RCC745},
	pages = {1503{\textendash}1511},
	abstract = {Along the green lineage (Chlorophyta and Streptophyta), mitochondria and chloroplast are mainly uniparentally transmitted and their evolution is thus clonal. The mode of organellar inheritance in their ancestor is less certain. The inability to make clear phylogenetic inference is partly due to a lack of information for deep branching organisms in this lineage. Here, we investigate organellar evolution in the early branching green alga Ostreococcus tauri using population genomics data from the complete mitochondrial and chloroplast genomes. The haplotype structure is consistent with clonal evolution in mitochondria, while we find evidence for recombination in the chloroplast genome. The number of recombination events in the genealogy of the chloroplast suggests that recombination, and thus biparental inheritance, is not rare. Consistent with the evidence of recombination, we find that the ratio of the number of nonsynonymous to the synonymous polymorphisms per site is lower in chloroplast than in the mitochondria genome. We also find evidence for the segregation of two selfish genetic elements in the chloroplast. These results shed light on the role of recombination and the evolutionary history of organellar inheritance in the green lineage.},
	keywords = {rcc, RCC1108, RCC1110, RCC1112, RCC1114, RCC1115, RCC1116, RCC1117, RCC1118, RCC1123, RCC1558, RCC1559, RCC1561, RCC745},
	doi = {10.1093/gbe/evt106},
	url = {http://gbe.oxfordjournals.org/content/5/8/1503.abstract},
	author = {Blanc-Mathieu, Romain and Sanchez-Ferandin, Sophie and Eyre-Walker, Adam and Piganeau, Gwenael}
}
@article {Shukla2013,
	title = {Phycoerythrin-specific bilin lyase{\textendash}isomerase controls blue-green chromatic acclimation in marine Synechococcus},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {109},
	year = {2013},
	note = {tex.mendeley-tags: 2013,rcc,sbr?hyto?app},
	pages = {20136{\textendash}20141},
	keywords = {2013, rcc, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto?app},
	doi = {10.1073/pnas.1211777109},
	author = {Shukla, A and Biswas, A and Blot, N and Partensky, F and Karty, J A and Hammad, L A and Garczarek, L and Gutu, A and Schluchter, W M and Kehoe, D M}
}
@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 {Stern2012,
	title = {Evaluating the ribosomal internal transcribed spacer (ITS) as a candidate dinoflagellate barcode marker},
	journal = {PLoS ONE},
	volume = {7},
	year = {2012},
	note = {tex.mendeley-tags: 2012,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {e42780},
	keywords = {2012, ASSEMBLE, Barcoding, ITS, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	doi = {10.1371/journal.pone.0042780},
	url = {http://www.plosone.org/article/info\%253Adoi\%252F10.1371\%252Fjournal.pone.0042780},
	author = {Stern, Rowena F and Andersen, Robert A and Jameson, Ian and K{\"u}pper, Frithjof C and Coffroth, Mary-Alice and Vaulot, Daniel and Gall, Florence Le and Veron, Benoit and Brand, Jerry J and Skelton, Hayley and Kasai, Fumai and Lilly, Emily L and Keeling, Patrick J}
}
@article {Giovagnetti2012,
	title = {Growth and photophysiological responses of two picoplanktonic {\textexclamdown}i{\textquestiondown}Minutocellus species{\textexclamdown}/i{\textquestiondown}, strains RCC967 and RCC703 (Bacillariophyceae)},
	journal = {European Journal of Phycology},
	volume = {47},
	number = {4},
	year = {2012},
	note = {ISBN: 0967-0262 tex.mendeley-tags: rcc703,rcc967},
	pages = {408{\textendash}420},
	abstract = {Reaching up to 50\% of the total biomass in oligotrophic waters and armed with a set of ecological and biological properties related to their small size, picophytoplankton ({\textexclamdown}3.0 mm) are a good model to address ecophysiological questions regarding phytoplankton biodiversity. Two picoplanktonic diatoms, one isolated from an upwelling ecosystem in the Pacific Ocean (Minutocellus sp., strain RCC967), and another from oceanic waters in the Indian Ocean (Minutocellus sp., strain RCC703) were used to test hypotheses on the functional relation between ecological niche adaptation and photosynthetic regulation capacity and efficiency. Cultures were subjected to five sine light climates, each one set to peak at a different photon flux density, respectively 10, 50, 100, 250 and 500 mmol photons m(-2) s(-1). Growth rate, photosynthesis, non-photochemical fluorescence quenching, pigment composition, and particulate organic carbon and nitrogen content were followed daily for 5 days. Growth rate and physiological response curves were different in the two species, in agreement with their distinct habitats of origin. Such differences could be related to the diverse photoacclimative strategies displayed by the two species, revealing a clear adaptive divergence despite their close taxonomic relationship. Photoacclimative strategies of the two picoplanktonic diatoms are discussed in the light of functional diversity and ecosystem adaptation.},
	keywords = {carbon, diatoms, elemental stoichiometry, fluctuating light, marine-phytoplankton, non-photochemical fluorescence quenching, phaeodactylum-tricornutum, photoacclimation, photoprotection, photoregulation, Photosynthesis, picoeukaryotes, planktonic diatoms, rcc703, rcc967, RCC?o?dd, violaxanthin cycle, Xanthophyll cycle, xanthophyll-cycle activity},
	doi = {10.1080/09670262.2012.733030},
	author = {Giovagnetti, V and Cataldo, M L and Conversano, F and Brunet, C}
}
@article {Frada2012,
	title = {In situ survey of life cycle phases of the coccolithophore Emiliania huxleyi (Haptophyta)},
	journal = {Environmental Microbiology},
	volume = {14},
	number = {6},
	year = {2012},
	note = {Publisher: Blackwell Publishing Ltd tex.mendeley-tags: 2012,rcc,sbr?hyto?ppo},
	pages = {1558{\textendash}1569},
	abstract = {The cosmopolitan coccolithophore Emiliania huxleyi is characterized by a strongly differentiated haplodiplontic life cycle consisting of a diploid phase, generally bearing coccoliths (calcified) but that can be also non-calcified, and a non-calcified biflagellated haploid phase. Given most studies have focused on the bloom-producing calcified phase, there is little-to-no information about non-calcified cells in nature. Using field mesocoms as experimental platforms, we quantitatively surveyed calcified and non-calcified cells using the combined calcareous detection fluorescent in situ hybridization (COD-FISH) method and qualitatively screened for haploid specific transcripts using reverse transcription-PCR during E. huxleyi bloom successions. Diploid, calcified cells formed dense blooms that were followed by the massive proliferation of E. huxleyi viruses (EhVs), which caused bloom demise. Non-calcified cells were also detected throughout the experiment, accounting for a minor fraction of the population but becoming progressively more abundant during mid-late bloom periods concomitant with EhV burst. Non-calcified cell growth also paralleled a distinct window of haploid-specific transcripts and the appearance of autotrophic flagellates morphologically similar to haploid cells, both of which are suggestive of meiosis and sexual life cycling during natural blooms of this prominent marine phytoplankton species.},
	keywords = {2012, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1111/j.1462-2920.2012.02745.x},
	url = {http://dx.doi.org/10.1111/j.1462-2920.2012.02745.x},
	author = {Frada, Miguel J and Bidle, Kay D and Probert, Ian and de Vargas, Colomban}
}
@article {Decelle2012,
	title = {An original mode of symbiosis in open ocean plankton},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {109},
	year = {2012},
	note = {tex.mendeley-tags: 2012,rcc,sbr?hyto?ppo},
	pages = {18000{\textendash}18005},
	keywords = {2012, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1073/pnas.1212303109},
	author = {Decelle, J and Probert, I and Bittner, L and Desdevises, Y and Colin, S and de Vargas, C and Gali, M and Simo, R and Not, F}
}
@article {Treusch2012,
	title = {Phytoplankton distribution patterns in the northwestern Sargasso Sea revealed by small subunit rRNA genes from plastids},
	journal = {The ISME journal},
	volume = {6},
	year = {2012},
	note = {Publisher: International Society for Microbial Ecology tex.mendeley-tags: Micromonas,RCC,rcc},
	pages = {481{\textendash}492},
	keywords = {Bathycoccus, CHRYSOPHYCEAE, key?aper, Micromonas, Ostreococcus, pelagophyceae, Prasinophyceae, Prymnesiophyceae, QPCR, rcc, TRFLP},
	doi = {10.1038/ismej.2011.117},
	url = {http://dx.doi.org/10.1038/ismej.2011.117 http://www.nature.com/ismej/journal/vaop/ncurrent/suppinfo/ismej2011117s1.html},
	author = {Treusch, Alexander H and Demir-Hilton, Elif and Vergin, Kevin L and Worden, Alexandra Z and Carlson, Craig A and Donatz, Michael G and Burton, Robert M and Giovannoni, Stephen J}
}
@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 {Kulk2012,
	title = {Temperature-dependent growth and photophysiology of prokaryotic and eukaryotic oceanic picophytoplankton},
	journal = {Marine Ecology Progress Series},
	volume = {466},
	year = {2012},
	note = {tex.mendeley-tags: RCC407,RCC410,RCC879},
	pages = {43{\textendash}55},
	abstract = {ABSTRACT: It is expected that climate change will expand the open oligotrophic oceans by enhanced thermal stratification. Because temperature defines the geographic distribution of picophytoplankton in open-ocean ecosystems and regulates photophysiological responses, it is important to understand how temperature affects picophytoplankton growth and photophysiology. Two prokaryotic and 2 eukaryotic picophytoplankton strains were acclimated to 3 different temperatures, ranging from 16 to 24{\textdegree}C. Temperature-dependent growth and photophysiology were assessed by measurements of specific growth rates, cell size, pigment composition, absorption and electron transport rates. Growth of Prochlorococcus marinus (eMED4), Prochlorococcus sp. (eMIT9313), Ostreococcus sp. (clade B) and Pelagomonas calceolata was positively related to temperature, especially in the prokaryotic strains. Changes in photophysiology included increased light harvesting, increased electron transport and reduced photoinhibition at elevated temperatures. However, the changes related to light harvesting and electron transport could not fully explain the observed difference in growth. This suggests that other processes, such as Calvin cycle activity, are likely to limit growth at sub-optimal temperatures in these picophytoplankton strains. The overall changes in photophysiology during temperature acclimation will possibly allow photosynthesis at higher irradiance intensities, but the genetically defined low temperature tolerances and photosynthetic characteristics of the different ecotypes will likely be more important in determining picophytoplankton (depth) distribution and community composition.},
	keywords = {Absorption, Electron transport rate, Eukaryotic picophytoplankton, Growth, Pigment, Prochlorococcus, rcc, RCC407, rcc410, RCC879, temperature},
	issn = {01718630},
	doi = {10.3354/meps09898},
	url = {http://www.int-res.com/abstracts/meps/v466/p43-55/},
	author = {Kulk, Gemma and De Vries, Pablo and Van De Poll, Willem H. and Visser, Ronald J W and Buma, Anita G J}
}
@article {Langer2011a,
	title = {CO2 mediation of adverse effects of seawater acidification in Calcidiscus leptoporus},
	journal = {Geochemistry Geophysics Geosystems},
	volume = {12},
	number = {5},
	year = {2011},
	note = {ISBN: 1525-2027 tex.mendeley-tags: 2011,RCC1135,rcc},
	pages = {1{\textendash}8},
	abstract = {The coccolithophore Calcidiscus leptoporus (strain RCC1135) was grown in dilute batch culture at CO2 levels ranging from \~200 to \~1600 matm. Increasing CO2 concentration led to an increased percentage of malformed coccoliths and eventually (at \~1500 matm CO2) to aggregation of cells. Carbonate chemistry of natural seawater was manipulated in three ways: first, addition of acid; second, addition of a HCO3 -/CO3 2- solution; and third, addition of both acid and HCO3 -/CO32- solution. The data set allowed the disentangling of putative effects of the different parameters of the carbonate system. It is concluded that CO2 is the parameter of the carbonate system which causes both aberrant coccolithogenesis and aggregation of cells.},
	keywords = {2011, Calcification, coccolithophores, morphology, ocean acidification., rcc, RCC1135},
	issn = {1525-2027},
	doi = {10.1029/2010GC003393},
	url = {http://www.agu.org/pubs/crossref/2011/2010GC003393.shtml},
	author = {Langer, Gerald and Bode, Maya}
}
@article {Jeanthon2011,
	title = {Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea},
	journal = {Biogeosciences},
	volume = {8},
	year = {2011},
	note = {tex.mendeley-tags: 2011,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?app},
	pages = {1955{\textendash}1970},
	keywords = {2011, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, SBR$_\textrmP$hyto$_\textrmE$PPO, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto$_\textrmd$ipo, sbr?hyto?app},
	doi = {10.5194/bg-8-1955-2011},
	author = {Jeanthon, Christian and Boeuf, Dominique and Dahan, Oc{\'e}ane and Le Gall, F and Garczarek, Laurence and Bendif, El Mahdi and Lehours, Anne-Catherine}
}
@article {Bendif2011,
	title = {Integrative taxonomy of the pavlovophyceae (haptophyta) : a reassessment},
	journal = {Protist},
	volume = {162},
	year = {2011},
	note = {tex.mendeley-tags: 2011,RCC1526,RCC1527,RCC1528,RCC1529,RCC1530,RCC1531,RCC1532,RCC1533,RCC1534,RCC1535,RCC1536,RCC1537,RCC1538,RCC1539,RCC1540,RCC1541,RCC1542,RCC1543,RCC1544,RCC1545,RCC1546,RCC1548,RCC1549,RCC1551,RCC1552,RCC1553,RCC1554,RCC1557,rcc,rcc1523,rcc1524,rcc1525},
	pages = {738{\textendash}761},
	abstract = {The Pavlovophyceae (Haptophyta) contains four genera (Pavlova, Diacronema, Exanthemachrysis and Rebecca) and only thirteen characterised species. Considering the importance of members of this class, we constructed molecular phylogenies inferred from sequencing of ribosomal gene markers with comprehensive coverage of the described diversity and using type strains when available add on culture strains. Moreover, the morphology and ultrastructure of 12 of the described species was re-examined and the pigment signatures of many culture strains were determined. The molecular analysis revealed that sequences of all described species differed, although those of Pavlova gyrans and P. pinguis were nearly identical, these potentially forming a single cryptic species complex. Four well-delineated genetic clades were identified, one of which included species of both Pavlova andDiacronema. Unique combinations of morphological/ultrastructural characters were identified foreach of these clades. The ancestral pigment signature of the Pavlovophyceae consisted of a basic set of pigments plus MV chl cPAV, the latter being entirely absent in the Pavlova + Diacronema clade and supplemented by DV chl cPAV in part of the Exanthemachrysis clade. Based on this combination of characters, we propose a taxonomic revision of the class, with transfer of several Pavlova species to an emended Diacronema genus. The evolution of the class is discussed in the context of the phylogenetic reconstruction presented.},
	keywords = {2011, ASSEMBLE, rcc, RCC1523, rcc1524, rcc1525, RCC1526, RCC1527, RCC1528, RCC1529, RCC1530, RCC1531, RCC1532, RCC1533, RCC1534, RCC1535, RCC1536, RCC1537, RCC1538, RCC1539, RCC1540, RCC1541, RCC1542, RCC1543, RCC1544, RCC1545, RCC1546, RCC1548, RCC1549, RCC1551, RCC1552, RCC1553, RCC1554, RCC1557, SBR$_\textrmP$hyto$_\textrmE$PPO},
	doi = {10.1016/j.protis.2011.05.001},
	author = {Bendif, E M and Probert, I and Herv{\'e}, A and Billard, C and Goux, D and Lelong, C and Cadoret, J P and V{\'e}ron, B}
}
@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 {Hagino2011,
	title = {New evidence for morphological and genetic variation in the cosmopolitan coccolithophore Emiliana huxleyi (prymnesiophyceae) from the cox1b-ATP4 genes},
	journal = {Journal of Phycology},
	volume = {47},
	year = {2011},
	note = {tex.mendeley-tags: 2011,rcc,sbr?hyto?ppo},
	pages = {1164{\textendash}1176},
	abstract = {Emiliania huxleyi (Lohmann) Hay et Mohler is a cosmopolitan coccolithophore occurring from tropical to subpolar waters and exhibiting variations in morphology of coccoliths possibly related to environmental conditions. We examined morphological characters of coccoliths and partial mitochondrial sequences of the cytochrome oxidase 1b (cox1b) through adenosine triphosphate synthase 4 (atp4) genes of thirty-nine clonal E. huxleyi strains from the Atlantic and Pacific Oceans, Mediterranean Sea and their adjacent seas. Based on the morphological study of culture strains by SEM, Type O, a new morphotype characterized by coccoliths with an open central area, was separated from existing morphotypes A, B, B/C, C, R and var. corona, characterized by coccoliths with central area elements. Molecular phylogenetic studies revealed that E. huxleyi consists of at least two mitochondrial sequence groups with different temperature preferences/tolerances: a cool water group occurring in subarctic North Atlantic and Pacific and a warm water group occurring in the sub-tropical Atlantic and Pacific and in the Mediterranean Sea.},
	keywords = {2011, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1111/j.1529-8817.2011.01053.x},
	author = {Hagino, K and Bendif, El Mahdi and Young, J and Kogame, K and Takano, Y and Probert, I and Horiguchi, T and de Vargas, C and Okada, H}
}
@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 {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}
}
@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 {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 {Sharon2009,
	title = {Photosystem I gene cassettes are present in marine virus genomes},
	journal = {Nature},
	volume = {461},
	number = {7261},
	year = {2009},
	note = {Publisher: Macmillan Publishers Limited. All rights reserved tex.mendeley-tags: RCC307},
	pages = {258{\textendash}262},
	keywords = {RCC307, SBR$_\textrmP$hyto$_\textrmP$PM},
	doi = {10.1038/nature08284},
	url = {http://dx.doi.org/10.1038/nature08284 http://www.nature.com/nature/journal/v461/n7261/suppinfo/nature08284_S1.html},
	author = {Sharon, Itai and Alperovitch, Ariella and Rohwer, Forest and Haynes, Matthew and Glaser, Fabian and Atamna-Ismaeel, Nof and Pinter, Ron Y and Partensky, Fr{\'e}d{\'e}ric and Koonin, Eugene V and Wolf, Yuri I and Nelson, Nathan and B{\'e}j{\`a}, Oded}
}
@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 {Descles2008,
	title = {New tools for labeling silica in living diatoms},
	journal = {New Phytologist},
	volume = {177},
	number = {3},
	year = {2008},
	note = {ISBN: 0028-646X tex.mendeley-tags: rcc},
	pages = {822{\textendash}829},
	abstract = {Silicon biomineralization is a widespread mechanism found in several kingdoms that concerns both unicellular and multicellular organisms. As a result of genomic and molecular tools, diatoms have emerged as a good model for biomineralization studies and have provided most of the current knowledge on this process. However, the number of techniques available to study its dynamics at the cellular level is still rather limited. Here, new probes were developed specifically to label the pre-existing or the newly synthesized silica frustule of several diatoms species. It is shown that the LysoTracker Yellow HCK-123, which can be used to visualize silica frustules with common filter sets, presents an enhanced signal-to-noise ratio and allows details of the frustules to be imaged without of the use of ionophores. It is also demonstrated that methoxysilane derivatives can be coupled to fluorescein-5-isothiocyanate (FITC) to preferentially label the silica components of living cells. The coupling of labeling procedures might help to address the challenging question of the process of frustule exocytosis.},
	keywords = {3D-imaging, BACILLARIOPHYCEAE, BIOLOGY, biomineralization, DEPOSITION, diatoms, exocytosis, FLUORESCENT, nanopattern, pH, phaeodactylum-tricornutum, PLANTS, rcc, THALASSIOSIRA-PSEUDONANA, ultrastructure, VESICLE},
	doi = {10.1111/j.1469-8137.2007.02303.x},
	author = {Descles, J and Vartanian, M and El Harrak, A and Quinet, M and Bremond, N and Sapriel, G and Bibette, J and Lopez, P J}
}
@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 {Six2007,
	title = {Diversity and evolution of phycobilisomes in marine Synechococcus spp. - a comparative genomics study},
	journal = {Genome Biology},
	volume = {8},
	year = {2007},
	note = {tex.mendeley-tags: 2007,rcc,sbr?hyto?app},
	pages = {R259},
	keywords = {2007, rcc, SBR$_\textrmP$hyto, sbr?hyto?app},
	doi = {10.1186/gb-2007-8-12-r259},
	author = {Six, C and Thomas, J.-C. and Garczarek, L and Ostrowski, M and Dufresne, A and Blot, N and Scanlan, D J and Partensky, F}
}
@article {Probert2007a,
	title = {Light and electron microscope observations of Algirosphaera robusta (Prymnesiophyceae)},
	journal = {Journal of Phycology},
	volume = {43},
	year = {2007},
	note = {tex.mendeley-tags: 2007,rcc},
	pages = {319{\textendash}332},
	keywords = {2007, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO},
	doi = {10.1111/j.1529-8817.2007.00324.x},
	author = {Probert, I and Fresnel, J and Billard, C and Geisen, Markus and Young, J R}
}
@article {Dimier2007,
	title = {Photophysiological properties of the marine picoeukaryote Picochlorum RCC 237 (Trebouxiophyceae, Chlorophyta)},
	journal = {Journal of Phycology},
	volume = {43},
	number = {2},
	year = {2007},
	note = {ISBN: 0022-3646 tex.mendeley-tags: RCC,rcc},
	pages = {275{\textendash}283},
	abstract = {The photophysiological properties of strain RCC 237 belonging to the marine picoplanktonic genus Picochlorum, first described by Henley et al., were investigated under different photon flux densities (PFD), ranging from 40 to 400 mu mol photons. m(-2).s(-1), mainly focusing on the development of the xanthophyll cycle and its relationship with the nonphotochemical quenching of fluorescence (NPQ). The functioning of the xanthophyll cycle and its photoprotective role was investigated by applying a progressive increase of PFD and using dithiotreitol and norflurazon to block specific enzymatic reactions in order to study in depth the relationship between xanthophyll cycle and NPQ. These two processes were significantly related only during the gradually increasing light periods and not during stable light periods, where NPQ and zeaxanthin were decoupled. This result reveals that NPQ is a photoprotective process developed by algae only when cells are experiencing increasing PFD or in response to stressful light variations, for instance after a sudden light shift. Results showed that the photobiological properties of Picochlorum strain RCC 237 seem to be well related to the surface water characteristics, as it is able to maintain its photosynthetic characteristics under different PFDs and to quickly activate the xanthophyll cycle under high light.},
	keywords = {A FLUORESCENCE, CHLAMYDOMONAS-REINHARDTII, DIATOM PHAEODACTYLUM-TRICORNUTUM, ENERGY-DISSIPATION, fluctuating light, fluorescence quantum yield, MANTONIELLA-SQUAMATA, nonphotochemical quenching of fluorescence, photoacclimation, PHOTOSYNTHETIC APPARATUS, picoplankton, POOL SIZE, rcc, VIOLAXANTHIN DE-EPOXIDASE, Xanthophyll cycle, XANTHOPHYLL-CYCLE, zeaxanthin},
	doi = {10.1111/j.1529-8817.2007.00327.x},
	author = {Dimier, C and Corato, F and Saviello, G and Brunet, C}
}
@article {Khan2007,
	title = {Plastid genome sequence of the cryptophyte alga Rhodomonas salina CCMP1319: lateral transfer of putative DNA replication machinery and a test of chromist plastid phylogeny},
	journal = {Molecular Biology and Evolution},
	volume = {24},
	number = {8},
	year = {2007},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {1832{\textendash}1842},
	abstract = {Cryptophytes are a group of unicellular algae with chlorophyll c-containing plastids derived from the uptake of a secondary (i.e., eukaryotic) endosymbiont. Biochemical and molecular data indicate that cryptophyte plastids are derived from red algae, yet the question of whether or not cryptophytes acquired their red algal plastids independent of those in heterokont, haptophyte, and dinoflagellate algae is of long-standing debate. To better understand the origin and evolution of the cryptophyte plastid, we have sequenced the plastid genome of Rhodomonas salina CCMP1319: at 135,854 bp, it is the largest secondary plastid genome characterized thus far. It also possesses interesting features not seen in the distantly related cryptophyte Guillardia theta or in other red secondary plastids, including pseudogenes, introns, and a bacterial-derived gene for the tau/gamma subunit of DNA polymerase III (dnaX), the first time putative DNA replication machinery has been found encoded in any plastid genome. Phylogenetic analyses indicate that dnaX was acquired by lateral gene transfer (LGT) in an ancestor of Rhodomonas, most likely from a firmicute bacterium. A phylogenomic survey revealed no additional cases of LGT, beyond a noncyanobacterial type rpl36 gene similar to that recently characterized in other cryptophytes and haptophytes. Rigorous concatenated analysis of 45 proteins encoded in 15 complete plastid genomes produced trees in which the heterokont, haptophyte, and cryptophyte (i.e., chromist) plastids were monophyletic, and heterokonts and haptophytes were each other{\textquoteright}s closest relatives. However, statistical support for chromist monophyly disappears when amino acids are recoded according to their chemical properties in order to minimize the impact of composition bias, and a significant fraction of the concatenate appears consistent with a sister-group relationship between cryptophyte and haptophyte plastids.},
	keywords = {*DNA Replication, *Gene Transfer, *Genome, Bacteria/*genetics, Cryptophyta/*genetics, DNA, evolution, genes, Horizontal, Molecular, phylogeny, Plant, Plastids/*genetics, rcc, Sequence Analysis, symbiosis},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17522086},
	author = {Khan, H and Parks, N and Kozera, C and Curtis, B A and Parsons, B J and Bowman, S and Archibald, J M}
}
@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 {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 {Bruyant2005,
	title = {Diel variations in the photosynthetic parameters of Prochlorococcus strain PCC 9511: combined effects of light and cell cycle},
	journal = {Limnology and Oceanography},
	volume = {50},
	year = {2005},
	note = {tex.mendeley-tags: 2005,rcc,sbr?hyto},
	pages = {850{\textendash}863},
	keywords = {2005, rcc, SBR$_\textrmP$hyto, sbr?hyto},
	doi = {10.4319/lo.2005.50.3.0850},
	author = {Bruyant, F and Babin, M and Genty, B and Prasil, O and Behrenfeld, M J and Claustre, H and Bricaud, A and Holtzendorff, J and Koblizek, M and Garczareck, L and Partensky, F}
}
@article {Henley2004,
	title = {Phylogenetic analysis of the Nannochloris-like{\textquoteright} algae and diagnoses of Picochlorum oklahomensis gen. et sp nov (Trebouxiophyceae, Chlorophyta)},
	journal = {Phycologia},
	volume = {43},
	number = {6},
	year = {2004},
	note = {tex.mendeley-tags: 2004,rcc,sbr?hyto},
	pages = {641{\textendash}652},
	abstract = {A broadly halotolerant new isolate of a small asexual coccoid chlorophyte and six new, related freshwater isolates provided the impetus for a phylogenetic analysis of the so-called {\textquoteright}Nannochloris-like{\textquoteright} algae within the Trebouxiophyceae. Previous taxonomic disagreements concerning this group had not been rigorously tested with molecular phylogenetic analyses. We show with 18S ribosomal DNA (rDNA) sequence phylogeny that 19 of 22 isolates previously assigned to either Nannochloris or Nanochlorum fall within a diverse sister clade to a clade including the four {\textquoteright}true{\textquoteright} Chlorella species sensu loto. In addition, Marvania geminata, Gloeotila contorta, Chlorella sp. Yanaqocha RA1, Koliella spiculiformis, {\textquoteright}Chlorella minutissima{\textquoteright} C-1.1.9. and new Koliella, Gloeotila and Marvania isolates were included in the Nannochloris-like clade. Distinct freshwater and marine or saline lineages comprise at least three major subclades, generally corresponding to cell division pattern. Seven of 14 marine or saline isolates are known (and the others presumed) to divide by autosporulation. Eight freshwater isolates divide by binary fission, including two Koliella, two Gloeotila, N. bacillaris, Chlorella sp. Yanaqocha RA1, and two new unassigned isolates. Four freshwater isolates divide by budding or autosporulation (three Marvania, including CCAP 251/1b. previously assigned to N. coccoides). The autosporic taxa N. eucaryotum UTEX 2502 (marine) and C. minutissima C-1.1.9 (freshwater), which have nearly identical 18S rDNA sequences, are deeper-branching than the freshwater and marine or saline lineages. We propose including the 13 marine or saline, autosporic taxa (excluding N. eucaryotum UTEX 2502) in the new genus Picochlorum until distinctive morphological or biochemical characters are identified that would indicate multiple genera corresponding to subclades. Such characters exist in the freshwater lineages, supporting retention of Koliella, Gloeotila, Marvania and Nannochloris as distinct genera, although each is currently represented by few isolates. Nannochloris at this time may be restricted to N. bacillaris and Chlorella sp. Yanaqocha RA1. We also describe halotolerant P. oklahomensis Hironaka sp. nov. Based on 18S rDNA sequence and lack of chlorophyll b, Nannochloris sp. UTEX 2379 should be reassigned to the Eustigmatophyceae.},
	keywords = {18s-, 2004, Aquatic-sciences, cell-wall, chlorella-, green-alga, life-cycle, marvania-geminata, morphology-, Nanochlorum-eucaryotum, position-, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto, SEQUENCES},
	doi = {10.2216/i0031-8884-43-6-641.1},
	author = {Henley, W J and Hironaka, J L and Guillou, L and Buchheim, M A and Buchheim, J A and Fawley, M W and Fawley, K P}
}
@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 {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 {Biegala2003,
	title = {Quantitative assessment of picoeucaryotes in the natural environment using taxon specific oligonucleotide probes in association with TSA-FISH (Tyramide Signal Amplification - Fluorescent In Situ Hybridization) and flow cytometry},
	journal = {Applied and Environmental Microbiology},
	volume = {69},
	year = {2003},
	note = {tex.mendeley-tags: 2003,rcc,sbr?hyto},
	pages = {5519{\textendash}5529},
	keywords = {2003, PICODIV, rcc, SBR$_\textrmP$hyto, sbr?hyto, SOMLIT},
	doi = {10.1128/AEM.69.9.5519-5529.2003},
	author = {Biegala, I C and Not, F and Vaulot, D and Simon, N}
}
@article {Not2002,
	title = {Application of fluorescent in situ hybridization coupled with tyramide signal amplification (FISH-TSA) to assess eukaryotic picoplankton composition},
	volume = {28},
	year = {2002},
	note = {Publication Title: Aquatic microbial ecology tex.mendeley-tags: RCC,rcc},
	pages = {157{\textendash}166},
	abstract = {Photosynthetic picoeukaryotes (phytoplankton cells with a diameter smaller than 2 to 3 ??m) contribute significantly to both biomass and primary production in the oligotrophic open ocean and coastal waters, at certain times of the year. The identification of these organisms is difficult because of their small size and simple morphology, therefore hindering detailed ecological studies of their distribution and role. In this paper, we demonstrate the use of oligonucleotide probes specific to algal classes or to lower order taxa in combination with fluorescent in situ hybridization and tyramide signal amplification (FISH-TSA) to determine eukaryotic picophytoplankton diversity. Target cells were detected and enumerated using epifluorescence microscopy. The sensitivity of the technique and the specificity of the probes were tested on pure and mixed picoplanktonic strains, as well as on natural samples from the English Channel. In these samples, the community was dominated by cells belonging to the division Chlorophyta. Haptophyta, Bolidophyceae and Pelagophyceae were also detected at low abundance. The FISH-TSA method is readily applicable to the study of picoplankton diversity in natural communities.},
	keywords = {rcc},
	issn = {0948-3055},
	doi = {10.3354/ame028157},
	author = {Not, F and Simon, N and Biegala, IC and Vaulot, D}
}
@article {Guillou1999b,
	title = {Symbiomonas scintillans gen. et sp nov and Picophagus flagellatus gen. et sp nov (Heterokonta): Two new heterotrophic flagellates of picoplanktonic size},
	journal = {Protist},
	volume = {150},
	number = {4},
	year = {1999},
	note = {ISBN: 1434-4610 Publisher: Urban \& Fischer Verlag tex.address: Branch Office Jena, P O Box No.100 537, D-07705 Jena, Germany tex.mendeley-tags: 1999,rcc,sbr?hyto},
	pages = {383{\textendash}398},
	abstract = {Two new oceanic free-living heterotrophic Heterokonta species with picoplanktonic size ({\textexclamdown} 2 mu m) are described, Symbiomonas scintillans Guillou et Chretiennot-Dinet gen. Ef sp. Nov, was isolated from samples collected both in the equatorial Pacific Ocean and the Mediterranean Sea. This new species possesses ultrastructural features of the bicosoecids, such as the absence of a helix in the flagellar transitional region (found in Cafeteria roenbergensis and in a few bicosoecids), and a flagellar root system very similar to that of C. Roenbergensis, Acronema sippewissettensis, and Bicosoeca maris. This new species is characterized by a single flagellum with mastigonemes, the presence of endosymbiotic bacteria located close to the nucleus, the absence of a lorica and a R3 root composed of a 6+3+x microtubular structure. Phylogenetical analyses of nuclear-encoded SSU rDNA gene sequences indicate that this species is close to the bicosoecids C. Roenbergensis and Siluania monomastiga. Picophagus flagellatus Guillou et Chretiennot-Dinet gen. Et sp. Nov. Was collected in the equatorial Pacific Ocean, Cells are naked and possess two flagella, This species is characterized by the lack of a transitional helix and lateral filaments on the flagellar tubular hairs, the absence of siliceous scales, two unequal flagella, R1 + R3 roots, and the absence of a rhizoplast. SSU rDNA analyses place this strain at the base of the Chrysophyceae/Synurophyceae lineages.},
	keywords = {1999, APPARATUS, DEVELOPAYELLA-ELEGANS, EMPHASIS, MOLECULAR PHYLOGENY, picophytoplankton, PLASTIDS, rcc, RDNA, SBR$_\textrmP$hyto, sbr?hyto, SEQUENCES},
	doi = {10.1016/S1434-4610(99)70040-4},
	author = {Guillou, L and Chr{\'e}tiennot-Dinet, M.-J. and Boulben, S and Moon-van der Staay, S Y and Vaulot, D}
}
@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.}
}
