@article {rihtman_coordinated_2024,
	title = {Coordinated transcriptional response to environmental stress by a \textit{Synechococcus virus},
	journal = {The ISME Journal},
	year = {2024},
	month = {mar},
	pages = {wrae032},
	abstract = {Viruses are a major control on populations of microbes. Often, their virulence is examined in controlled laboratory conditions. Yet, in nature, environmental conditions lead to changes in host physiology and fitness that may impart both costs and benefits on viral success.},
	keywords = {rcc752},
	issn = {1751-7362, 1751-7370},
	doi = {10.1093/ismejo/wrae032},
	url = {https://academic.oup.com/ismej/advance-article/doi/10.1093/ismejo/wrae032/7618445},
	author = {Rihtman, Branko and Torcello-Requena, Alberto and Mikhaylina, Alevtina and Puxty, Richard J and Clokie, Martha R J and Millard, Andrew D and Scanlan, David J}
}
@article {varga_cytotoxicity_2024,
	title = {Cytotoxicity of Prymnesium parvum extracts and prymnesin analogs on epithelial fish gill cells RTgill-W1 and the human colon cell line HCEC-1CT},
	journal = {Archives of Toxicology},
	year = {2024},
	month = {jan},
	abstract = {Harmful algal blooms kill fish populations worldwide, as exemplified by the haptophyte microalga Prymnesium~parvum. The suspected causative agents are prymnesins, categorized as A-, B-, and C-types based on backbone carbon atoms. Impacts of P.~parvum extracts and purified prymnesins were tested on the epithelial rainbow trout fish gill cell line RTgill-W1 and on the human colon epithelial cells HCEC-1CT. Cytotoxic potencies ranked A > C > B-type with concentrations spanning from low (A- and C-type) to middle (B-type) nM ranges. Although RTgill-W1 cells were about twofold more sensitive than HCEC-1CT, the cytotoxicity of prymnesins is not limited to fish gills. Both cell lines responded rapidly to prymnesins; with EC50 values for B-types in RTgill-W1 cells of 110 {\textpm} 11~nM and 41.5 {\textpm} 0.6~nM after incubations times of 3 and 24~h. Results of fluorescence imaging and measured lytic effects suggest plasma membrane interactions. Postulating an osmotic imbalance as mechanisms of toxicity, incubations with prymnesins in media lacking either Cl-, Na+, or Ca2+ were performed. Cl- removal reduced morphometric rearrangements observed in RTgill-W1 and cytotoxicity in HCEC-1CT cells. Ca2+-free medium in RTgill-W1 cells exacerbated effects on the cell nuclei. Prymnesin composition of different P.~parvum strains showed that analog composition within one type scarcely influenced the cytotoxic potential, while analog type potentially dictate potency. Overall, A-type prymnesins were the most potent ones in both cell lines followed by the C-types, and lastly B-types. Disturbance of Ca2+ and Cl- ionoregulation may be integral to prymnesin toxicity.},
	keywords = {Fluorescence microscopy, Ichthyotoxin, Ionoregulation, Microalgae, MS, RCC1436, RCC191, UHPLC},
	issn = {1432-0738},
	doi = {10.1007/s00204-023-03663-5},
	url = {https://doi.org/10.1007/s00204-023-03663-5},
	author = {Varga, Elisabeth and Prause, H{\'e}l{\`e}ne-Christine and Riepl, Matthias and Hochmayr, Nadine and Berk, Deniz and Attakpah, Eva and Kiss, Endre and Medi{\'c}, Nikola and Del Favero, Giorgia and Larsen, Thomas Ostenfeld and Hansen, Per Juel and Marko, Doris}
}
@article {dufour_differential_2024,
	title = {Differential acclimation kinetics of the two forms of type IV chromatic acclimaters occurring in marine Synechococcus cyanobacteria},
	journal = {Frontiers in Microbiology},
	volume = {15},
	year = {2024},
	pages = {1349322},
	abstract = {Synechococcus , the second most abundant marine phytoplanktonic organism, displays the widest variety of pigment content of all marine oxyphototrophs, explaining its ability to colonize all spectral niches occurring in the upper lit layer of oceans. Seven Synechococcus pigment types (PTs) have been described so far based on the phycobiliprotein composition and chromophorylation of their light-harvesting complexes, called phycobilisomes. The most elaborate and abundant PT (3d) in the open ocean consists of cells capable of type IV chromatic acclimation (CA4), i.e., to reversibly modify the ratio of the blue light-absorbing phycourobilin (PUB) to the green light-absorbing phycoerythrobilin (PEB) in phycobilisome rods to match the ambient light color. Two genetically distinct types of chromatic acclimaters, so-called PTs 3dA and 3dB, occur at similar global abundance in the ocean, but the precise physiological differences between these two types and the reasons for their complementary niche partitioning in the field remain obscure. Here, photoacclimation experiments in different mixes of blue and green light of representatives of these two PTs demonstrated that they differ by the ratio of blue-to-green light required to trigger the CA4 process. Furthermore, shift experiments between 100\% blue and 100\% green light, and vice-versa , revealed significant discrepancies between the acclimation pace of the two types of chromatic acclimaters. This study provides novel insights into the finely tuned adaptation mechanisms used by Synechococcus cells to colonize the whole underwater light field.},
	keywords = {RCC2319, RCC2369, RCC2374, RCC2533, RCC2553, RCC2571, RCC515, rcc555, RCC751},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2024.1349322},
	url = {https://www.frontiersin.org/articles/10.3389/fmicb.2024.1349322/full},
	author = {Dufour, Louison and Garczarek, Laurence and Gouriou, Bastian and Clairet, Julia and Ratin, Morgane and Partensky, Fr{\'e}d{\'e}ric}
}
@article {roux_ecophysiological_2024,
	title = {Ecophysiological response of the cupped oyster Crassostrea gigas exposed to the green dinoflagellate Lepidodinium chlorophorum},
	journal = {Aquaculture},
	year = {2024},
	month = {feb},
	pages = {740644},
	keywords = {RCC6911},
	issn = {00448486},
	doi = {10.1016/j.aquaculture.2024.740644},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0044848624001054},
	author = {Roux, Pauline and Garc{\'\i}a-Corona, Jos{\'e} Luis and Ragueneau, Stacy and Schapira, Mathilde and Siano, Raffaele and Pernet, Fabrice and Queau, Isabelle and Malestroit, Pascale and Tallec, Kevin and Fleury, Elodie}
}
@article {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 {azizah_2-homoectoine_2023,
	title = {2-Homoectoine: An Additional Member of the Ectoine Family from Phyto- and Bacterioplankton Involved in Osmoadaptation},
	journal = {Journal of Natural Products},
	year = {2023},
	note = {Publisher: American Chemical Society},
	month = {dec},
	abstract = {Ectoine is a central osmolyte in marine plankton due to its excellent cytoprotective traits and its multifunctional roles supporting the survival of microalgae and bacteria under unfavorable environmental conditions. The protective effect of ectoine toward several kinds of stresses stirred interest in biotechnology, pharmacy, and other fields including cosmetics. Also, its hydroxylated derivative, 5-hydroxyectoine, exhibits functions similar to ectoine. Here we introduce a molecular networking-based approach to expand the family of ectoine derivatives from phyto- and bacterioplankton. A ZIC-HILIC separation protocol coupled with HRMS/MS-based molecular networking allowed us to identify the new ectoine derivative 1,4,5,6-tetrahydro-2-ethyl-4-pyrimidinecarboxylic acid, or 2-homoectoine (1). 1 is found in many algae including dinoflagellates, chlorophytes, and haptophytes. In axenic strains, the content of 1 is substantially lower. In accordance, we found that marine bacteria are prolific producers of the compound as well. This suggests that the microalgae with their associated microbiome have to be considered as sources of the compound. Increasing concentrations of the compound under high salinity suggest a role as a protectant against osmotic stress.},
	keywords = {RCC131, RCC3579},
	issn = {0163-3864},
	doi = {10.1021/acs.jnatprod.3c00766},
	url = {https://doi.org/10.1021/acs.jnatprod.3c00766},
	author = {Azizah, Muhaiminatul and Pohnert, Georg}
}
@article {strauss_bay_2023,
	title = {The Bay of Bengal exposes abundant photosynthetic picoplankton and newfound diversity along salinity-driven gradients},
	journal = {Environmental Microbiology},
	year = {2023},
	abstract = {The Bay of Bengal (BoB) is a 2,600,000 km2 expanse in the Indian Ocean upon which many humans rely. However, the primary producers underpinning food chains here remain poorly characterized. We examined phytoplankton abundance and diversity along strong BoB latitudinal and vertical salinity gradients-which have low temperature variation (27-29{\textdegree}C) between the surface and subsurface chlorophyll maximum (SCM). In surface waters, Prochlorococcus averaged 11.7 {\textpm} 4.4 {\texttimes} 104  cells ml-1 , predominantly HLII, whereas LLII and {\textquoteright}rare{\textquoteright} ecotypes, HLVI and LLVII, dominated in the SCM. Synechococcus averaged 8.4 {\textpm} 2.3 {\texttimes} 104  cells ml-1 in the surface, declined rapidly with depth, and population structure of dominant Clade II differed between surface and SCM; Clade X was notable at both depths. Across all sites, Ostreococcus Clade OII dominated SCM eukaryotes whereas communities differentiated strongly moving from Arabian Sea-influenced high salinity (southerly; prasinophytes) to freshwater-influenced low salinity (northerly; stramenopiles, specifically, diatoms, pelagophytes, and dictyochophytes, plus the prasinophyte Micromonas) surface waters. Eukaryotic phytoplankton peaked in the south (1.9 {\texttimes} 104  cells ml-1 , surface) where a novel Ostreococcus was revealed, named here Ostreococcus bengalensis. We expose dominance of a single picoeukaryote and hitherto {\textquoteright}rare{\textquoteright} picocyanobacteria at depth in this complex ecosystem where studies suggest picoplankton are replacing larger phytoplankton due to climate change.},
	keywords = {RCC393, RCC809},
	issn = {1462-2920},
	doi = {10.1111/1462-2920.16431},
	author = {Strauss, Jan and Choi, Chang Jae and Grone, Jonathan and Wittmers, Fabian and Jimenez, Valeria and Makareviciute-Fichtner, Kriste and Bachy, Charles and Jaeger, Gualtiero Spiro and Poirier, Camille and Eckmann, Charlotte and Spezzano, Rachele and L{\"o}scher, Carolin R. and Sarma, V. V. S. S. and Mahadevan, Amala and Worden, Alexandra Z.}
}
@article {churakova_biogenic_2023,
	title = {Biogenic silica accumulation in picoeukaryotes: Novel players in the marine silica cycle},
	journal = {Environmental Microbiology Reports},
	volume = {n/a},
	number = {n/a},
	year = {2023},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1758-2229.13144},
	abstract = {It is well known that the biological control of oceanic silica cycling is dominated by diatoms, with sponges and radiolarians playing additional roles. Recent studies have revealed that some smaller marine organisms (e.g. the picocyanobacterium Synechococcus) also take up silicic acid (dissolved silica, dSi) and accumulate silica, despite not exhibiting silicon dependent cellular structures. Here, we show biogenic silica (bSi) accumulation in five strains of picoeukaryotes (<2{\textendash}3 μm), including three novel isolates from the Baltic Sea, and two marine species (Ostreococcus tauri and Micromonas commoda), in cultures grown with added dSi (100 μM). Average bSi accumulation in these novel biosilicifiers was between 30 and 92 amol Si cell-1. Growth rate and cell size of the picoeukaryotes were not affected by dSi addition. Still, the purpose of bSi accumulation in these smaller eukaryotic organisms lacking silicon dependent structures remains unclear. In line with the increasing recognition of picoeukaryotes in biogeochemical cycling, our findings suggest that they can also play a significant role in silica cycling.},
	keywords = {RCC4221, RCC827},
	issn = {1758-2229},
	doi = {10.1111/1758-2229.13144},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1758-2229.13144},
	author = {Churakova, Yelena and Aguilera, Anabella and Charalampous, Evangelia and Conley, Daniel J. and Lundin, Daniel and Pinhassi, Jarone and Farnelid, Hanna}
}
@article {cruz_bioprospecting_2023,
	title = {Bioprospecting for industrially relevant exopolysaccharide-producing cyanobacteria under Portuguese simulated climate},
	journal = {Scientific Reports},
	volume = {13},
	number = {1},
	year = {2023},
	note = {Number: 1 Publisher: Nature Publishing Group},
	pages = {13561},
	abstract = {Cyanobacterial exopolysaccharides (EPS) are potential candidates for the production of sustainable biopolymers. Although the bioactive and physicochemical properties of cyanobacterial-based EPS are attractive, their commercial exploitation is limited by the high production costs. Bioprospecting and characterizing novel EPS-producing strains for industrially relevant conditions is key to facilitate their implementation in various biotechnological applications and fields. In the present work, we selected twenty-five Portuguese cyanobacterial strains from a diverse taxonomic range (including some genera studied for the first time) to be grown in diel light and temperature, simulating the Portuguese climate conditions, and evaluated their growth performance and proximal composition of macronutrients. Synechocystis and Cyanobium genera, from marine and freshwater origin, were highlighted as fast-growing (0.1{\textendash}0.2~g~L-1~day-1) with distinct biomass composition. Synechocystis sp. LEGE 07367 and Chroococcales cyanobacterium LEGE 19970, showed a production of 0.3 and 0.4~g~L-1 of released polysaccharides (RPS). These were found to be glucan-based polymers with high molecular weight and a low number of monosaccharides than usually reported for cyanobacterial EPS. In addition, the absence of known cyanotoxins in these two RPS producers was also confirmed. This work provides the initial steps for the development of cyanobacterial EPS bioprocesses under the Portuguese climate.},
	keywords = {Biochemistry, Biotechnology, Microbiology, rcc2380},
	issn = {2045-2322},
	doi = {10.1038/s41598-023-40542-6},
	url = {https://www.nature.com/articles/s41598-023-40542-6},
	author = {Cruz, Jos{\'e} Diogo and Delattre, C{\'e}dric and Felpeto, Aldo Barreiro and Pereira, Hugo and Pierre, Guillaume and Morais, Jo{\~a}o and Petit, Emmanuel and Silva, Joana and Azevedo, Joana and Elboutachfaiti, Redouan and Maia, In{\^e}s B. and Dubessay, Pascal and Michaud, Philippe and Vasconcelos, Vitor}
}
@article {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 {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 {lopez-pacheco_growth_2023,
	title = {Growth Behavior, Biomass Composition and Fatty Acid Methyl Esters (FAMEs) Production Potential of Chlamydomonas reinhardtii, and Chlorella vulgaris Cultures},
	journal = {Marine Drugs},
	volume = {21},
	number = {8},
	year = {2023},
	month = {aug},
	pages = {450},
	abstract = {The production of biomolecules by microalgae has a wide range of applications in the development of various materials and products, such as biodiesel, food supplements, and cosmetics. Microalgae biomass can be produced using waste and in a smaller space than other types of crops (e.g., soja, corn), which shows microalgae{\textquoteright}s great potential as a source of biomass. Among the produced biomolecules of greatest interest are carbohydrates, proteins, lipids, and fatty acids. In this study, the production of these biomolecules was determined in two strains of microalgae (Chlamydomonas reinhardtii and Chlorella vulgaris) when exposed to different concentrations of nitrogen, phosphorus, and sulfur. Results show a significant microalgal growth (3.69 g L-1) and carbohydrates (163 mg g-1) increase in C. reinhardtii under low nitrogen concentration. Also, higher lipids content was produced under low sulfur concentration (246 mg g-1). It was observed that sulfur variation could affect in a negative way proteins production in C. reinhardtii culture. In the case of C. vulgaris, a higher biomass production was obtained in the standard culture medium (1.37 g L-1), and under a low-phosphorus condition, C. vulgaris produced a higher lipids concentration (248 mg g-1). It was observed that a low concentration of nitrogen had a better effect on the accumulation of fatty acid methyl esters (FAMEs) (C16-C18) in both microalgae. These results lead us to visualize the effects that the variation in macronutrients can have on the growth of microalgae and their possible utility for the production of microalgae-based subproducts.},
	keywords = {RCC2488},
	issn = {1660-3397},
	doi = {10.3390/md21080450},
	url = {https://www.mdpi.com/1660-3397/21/8/450},
	author = {L{\'o}pez-Pacheco, Itzel Y. and Ayala-Moreno, Victoria Guadalupe and Mejia-Melara, Catherinne Arlette and Rodr{\'\i}guez-Rodr{\'\i}guez, Jos{\'e} and Cuellar-Bermudez, Sara P. and Gonz{\'a}lez-Gonz{\'a}lez, Reyna Berenice and Coronado-Apodaca, Karina G. and Farfan-Cabrera, Leonardo I. and Gonz{\'a}lez-Meza, Georgia Mar{\'\i}a and Iqbal, Hafiz M. N. and Parra-Sald{\'\i}var, Roberto}
}
@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}
}
@article {cho_phylogenomic_2023,
	title = {Phylogenomic position of genetically diverse phagotrophic stramenopile flagellates in the sediment-associated MAST-6 lineage and a potentially halotolerant placididean},
	journal = {Molecular Phylogenetics and Evolution},
	year = {2023},
	month = {nov},
	pages = {107964},
	abstract = {Unlike morphologically conspicuous ochrophytes, many flagellates belonging to basally branching stramenopiles are small and often overlooked. As a result, many of these lineages are known only through molecular surveys and identified as MArine STramenopiles (MAST), and remain largely uncharacterized at the cellular or genomic level. These likely phagotrophic flagellates are not only phylogenetically diverse, but also extremely abundant in some environments, making their characterization all the more important. MAST-6 is one example of a phylogenetically distinct group that has been known to be associated with sediments, but little else is known about it. Indeed, until the present study, only a single species from this group, Pseudophyllomitus vesiculosus (Pseudophyllomitidae), has been both formally described and associated with genomic information. Here, we describe four new species including two new genera of sediment-dwelling MAST-6, Vomastramonas tehuelche gen. et sp. nov., Mastreximonas tlaamin gen. et sp. nov., one undescribed Pseudophyllomitus sp., BSC2, and a new species belonging to Placididea, the potentially halotolerant Haloplacidia sinai sp. nov. We also provide two additional bikosian transcriptomes from a public culture collection, to allow for better phylogenetic reconstructions of deep-branching stramenopiles. With the SSU rRNA sequences of the new MAST-6 species, we investigate the phylogenetic diversity of the MAST-6 group and show a high relative abundance of MAST-6 related to M. tlaamin in samples across various depths and geographical locations. Using the new MAST-6 species, we also update the phylogenomic tree of stramenopiles, particularly focusing on the paraphyly of Bigyra.},
	keywords = {benthic protists, Bigyra, MAST-6, phylogenomics, Placididea, RCC1078, RCC257, Stramenopile},
	issn = {1055-7903},
	doi = {10.1016/j.ympev.2023.107964},
	url = {https://www.sciencedirect.com/science/article/pii/S1055790323002646},
	author = {Cho, Anna and Tikhonenkov, Denis V. and Lax, Gordon and Prokina, Kristina I. and Keeling, Patrick J.}
}
@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 {alonso-saez_transcriptional_2023,
	title = {Transcriptional Mechanisms of Thermal Acclimation in \textit{Prochlorococcus},
	journal = {mBio},
	year = {2023},
	pages = {e03425{\textendash}22},
	abstract = {Low temperature limits the growth and the distribution of the key oceanic primary producer Prochlorococcus, which does not proliferate above a latitude of ca. 40{\textdegree}. Yet, the molecular basis of thermal acclimation in this cyanobacterium remains unexplored. We analyzed the transcriptional response of the Prochlorococcus marinus strain MIT9301 in long-term acclimations and in natural Prochlorococcus populations along a temperature range enabling its growth (17 to 30{\textdegree}C). MIT9301 upregulated mechanisms of the global stress response at the temperature minimum (17{\textdegree}C) but maintained the expression levels of genes involved in essential metabolic pathways (e.g., ATP synthesis and carbon fixation) along the whole thermal niche. Notably, the declining growth of MIT9301 from the optimum to the minimum temperature was coincident with a transcriptional suppression of the photosynthetic apparatus and a dampening of its circadian expression patterns, indicating a loss in their regulatory capacity under cold conditions. Under warm conditions, the cellular transcript inventory of MIT9301 was strongly streamlined, which may also induce regulatory imbalances due to stochasticity in gene expression. The daytime transcriptional suppression of photosynthetic genes at low temperature was also observed in metatranscriptomic reads mapping to MIT9301 across the global ocean, implying that this molecular mechanism may be associated with the restricted distribution of Prochlorococcus to temperate zones.},
	keywords = {RCC3377},
	issn = {2150-7511},
	doi = {10.1128/mbio.03425-22},
	url = {https://journals.asm.org/doi/10.1128/mbio.03425-22},
	author = {Alonso-S{\'a}ez, Laura and Palacio, Antonio S. and Cabello, Ana M. and Robaina-Est{\'e}vez, Semid{\'a}n and Gonz{\'a}lez, Jos{\'e} M. and Garczarek, Laurence and L{\'o}pez-Urrutia, {\'A}ngel},
	editor = {Martiny, Jennifer B. H.}
}
@article {syhapanha_transcriptomicsguided_2023,
	title = {Transcriptomics-guided identification of an algicidal protease of the marine bacterium Kordia algicida OT-1},
	journal = {MicrobiologyOpen},
	volume = {12},
	number = {5},
	year = {2023},
	pages = {e1387},
	abstract = {In recent years, interest in algicidal bacteria has risen due to their ecological importance and their potential as biotic regulators of harmful algal blooms. Algicidal bacteria shape the plankton communities of the oceans by inhibiting or lysing microalgae and by consuming the released nutrients. Kordia algicida strain OT-1 is a model marine algicidal bacterium that was isolated from a bloom of the diatom Skeletonema costatum. Previous work has suggested that algicidal activity is mediated by secreted proteases. Here, we utilize a transcriptomics-guided approach to identify the serine protease gene KAOT1_RS09515, hereby named alpA1 as a key element in the algicidal activity of K. algicida. The protease AlpA1 was expressed and purified from a heterologous host and used in in vitro bioassays to validate its activity. We also show that K. algicida is the only algicidal species within a group of four members of the Kordia genus. The identification of this algicidal protease opens the possibility of real-time monitoring of the ecological impact of algicidal bacteria in natural phytoplankton blooms., Algicidal bacteria shape the plankton communities of the oceans by lysing microalgae and consuming the released nutrients. Kordia algicida is an environmentally relevant marine bacterium whose algicidal activity is mediated by secreted proteases. In this study, we utilize a transcriptomics-guided approach to identify the secreted serine protease AlpA1 as a key factor in the algicidal process. This discovery offers new approaches for the real-time monitoring and manipulation of algicidal bacteria in algal blooms.},
	keywords = {RCC75},
	issn = {2045-8827},
	doi = {10.1002/mbo3.1387},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10565126/},
	author = {Syhapanha, Kristy S. and Russo, David A. and Deng, Yun and Meyer, Nils and Poulin, Remington X. and Pohnert, Georg}
}
@article {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 {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 {ferrieux_comparative_2022,
	title = {Comparative Thermophysiology of Marine Synechococcus CRD1 Strains Isolated From Different Thermal Niches in Iron-Depleted Areas},
	journal = {Frontiers in Microbiology},
	volume = {13},
	year = {2022},
	abstract = {Marine Synechococcus cyanobacteria are ubiquitous in the ocean, a feature likely related to their extensive genetic diversity. Amongst the major lineages, clades I and IV preferentially thrive in temperate and cold, nutrient-rich waters, whilst clades II and III prefer warm, nitrogen or phosphorus-depleted waters. The existence of such cold (I/IV) and warm (II/III) thermotypes is corroborated by physiological characterization of representative strains. A fifth clade, CRD1, was recently shown to dominate the Synechococcus community in iron-depleted areas of the world ocean and to encompass three distinct ecologically significant taxonomic units (ESTUs CRD1A-C) occupying different thermal niches, suggesting that distinct thermotypes could also occur within this clade. Here, using comparative thermophysiology of strains representative of these three CRD1 ESTUs we show that the CRD1A strain MITS9220 is a warm thermotype, the CRD1B strain BIOS-U3-1 a cold temperate thermotype, and the CRD1C strain BIOS-E4-1 a warm temperate stenotherm. Curiously, the CRD1B thermotype lacks traits and/or genomic features typical of cold thermotypes. In contrast, we found specific physiological traits of the CRD1 strains compared to their clade I, II, III, and IV counterparts, including a lower growth rate and photosystem II maximal quantum yield at most temperatures and a higher turnover rate of the D1 protein. Together, our data suggests that the CRD1 clade prioritizes adaptation to low-iron conditions over temperature adaptation, even though the occurrence of several CRD1 thermotypes likely explains why the CRD1 clade as a whole occupies most iron-limited waters.},
	keywords = {RCC2374, RCC2385, RCC2533, RCC2534, RCC2571, RCC515, rcc539, rcc791},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2022.893413},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2022.893413},
	author = {Ferrieux, Mathilde and Dufour, Louison and Dor{\'e}, Hugo and Ratin, Morgane and Gu{\'e}neugu{\`e}s, Audrey and Chasselin, L{\'e}o and Marie, Dominique and Rigaut-jalabert, Fabienne and Le Gall, Florence and Sciandra, Th{\'e}o and Monier, Garance and Hoebeke, Mark and Corre, Erwan and Xia, Xiaomin and Liu, Hongbin and Scanlan, David J. and Partensky, Fr{\'e}d{\'e}ric and Garczarek, Laurence}
}
@article {yung_diversity_2022,
	title = {Diversity and Evolution of Mamiellophyceae: Early-Diverging Phytoplanktonic Green Algae Containing Many Cosmopolitan Species},
	journal = {Journal of Marine Science and Engineering},
	volume = {10},
	number = {2},
	year = {2022},
	note = {Number: 2 Publisher: Multidisciplinary Digital Publishing Institute},
	month = {feb},
	pages = {240},
	abstract = {The genomic revolution has bridged a gap in our knowledge about the diversity, biology and evolution of unicellular photosynthetic eukaryotes, which bear very few discriminating morphological features among species from the same genus. The high-quality genome resources available in the class Mamiellophyceae (Chlorophyta) have been paramount to estimate species diversity and screen available metagenomic data to assess the biogeography and ecological niches of different species on a global scale. Here we review the current knowledge about the diversity, ecology and evolution of the Mamiellophyceae and the large double-stranded DNA prasinoviruses infecting them, brought by the combination of genomic and metagenomic analyses, including 26 metabarcoding environmental studies, as well as the pan-oceanic GOS and the Tara Oceans expeditions.},
	keywords = {Biogeography, evolution, genomics, mamiellophyceae, metagenomics, microalgae{\textendash}virus interactions, phycoDNAvirus, RCC809},
	issn = {2077-1312},
	doi = {10.3390/jmse10020240},
	url = {https://www.mdpi.com/2077-1312/10/2/240},
	author = {Yung, Charmaine C. M. and Rey Redondo, Elvira and Sanchez, Fr{\'e}d{\'e}ric and Yau, Sheree and Piganeau, Gwenael}
}
@article {grebert_diversity_2022,
	title = {Diversity and evolution of pigment types in marine \textit{Synechococcus cyanobacteria},
	journal = {Genome Biology and Evolution},
	year = {2022},
	pages = {evac035},
	abstract = {DNA integration and site-specific recombination, suggesting that their genomic variability relies D in part on a {\textquoteleft}tycheposon{\textquoteright}-like mechanism. Comparison of the phylogenies obtained for PBS and E core genes revealed that the evolutionary history of PBS rod genes differs from the core T genome and is characterized by the co-existence of different alleles and frequent allelic P exchange. We propose a scenario for the evolution of the different pigment types and highlight E the importance of incomplete lineage sorting in maintaining a wide diversity of pigment types in C different Synechococcus lineages despite multiple speciation events.},
	keywords = {RCC307, to add},
	issn = {1759-6653},
	doi = {10.1093/gbe/evac035},
	url = {https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evac035/6547267},
	author = {Gr{\'e}bert, Th{\'e}ophile and Garczarek, Laurence and Daubin, Vincent and Humily, Florian and Marie, Dominique and Ratin, Morgane and Devailly, Alban and Farrant, Gregory K. and Mary, Isabelle and Mella-Flores, Daniella and Tanguy, Gwenn and Labadie, Karine and Wincker, Patrick and Kehoe, David M. and Partensky, Fr{\'e}d{\'e}ric},
	editor = {Angert, Esther}
}
@article {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 {penot_genomic_2022,
	title = {Genomic and meta-genomic insights into the functions, diversity and global distribution of haptophyte algae},
	journal = {Applied Phycology},
	year = {2022},
	note = {Publisher: Taylor \& Francis _eprint: https://doi.org/10.1080/26388081.2022.2103732},
	pages = {1{\textendash}20},
	abstract = {Haptophytes are an environmentally important phylum of eukaryotic phytoplankton, forming the second most abundant algal group after diatoms in recent estimates of ocean biodiversity. Haptophytes are phylogenetically and functionally diverse, including globally distributed and bloom-forming calcifying species such as Emiliania and Coccolithus, and non-calcifying orders that may form important components of phytoplankton communities in polar (Phaeocystis, Chrysochromulina) through to sub-tropical latitudes (Pavlova). In this review, we synthesize available phylogenetic, genomic and environmental information concerning the diversity of haptophyte life, considering the origins and placement on the eukaryotic tree; the diversity of the five major orders (Pavlovophyceae, Phaeocystales, Prymnesiales, the CSZ clade, and Isochrysidales); and the contrasting biogeographical distributions of haptophyte groups across different Tara Oceans sampling stations and size fractions. We additionally consider outstanding questions within the fields of haptophyte diversity and biology, particularly in the context of newly discovered and largely uncultured major groups (DPL lineages and Rappemonads), and current gaps in our knowledge of genomic content and niche adaptation across the haptophyte tree.},
	keywords = {18S rDNA, coccolithophorid, dispersal, meta-genomics, niche adaptation, prymnesiophyte, RCC1129, RCC1187, RCC1387, RCC1480, RCC1532, RCC851, RCC914, systematics, to read},
	issn = {null},
	doi = {10.1080/26388081.2022.2103732},
	url = {https://doi.org/10.1080/26388081.2022.2103732},
	author = {Penot, Mathias and Dacks, Joel B. and Read, Betsy and Dorrell, Richard G.}
}
@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 {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 {nikitashina_metabolic_2022,
	title = {Metabolic adaptation of diatoms to hypersalinity},
	journal = {Phytochemistry},
	year = {2022},
	pages = {113267},
	abstract = {Microalgae are important primary producers and form the basis for the marine food web. As global climate changes, so do salinity levels that algae are exposed to. A metabolic response of algal cells partly alleviates the resulting osmotic stress. Some metabolites involved in the response are well studied, but the full metabolic implications of adaptation remain unclear. Improved analytical methodology provides an opportunity for additional insight. We can now follow responses to stress in major parts of the metabolome and derive comprehensive charts of the resulting metabolic re-wiring. In this study, we subjected three species of diatoms to high salinity conditions and compared their metabolome to controls in an untargeted manner. The three well-investigated species with sequenced genomes Phaeodactylum tricornutum, Thalassiosira pseudonana, and Skeletonema marinoi were selected for our survey. The microalgae react to salinity stress with common adaptations in the metabolome by amino acid up-regulation, production of saccharides, and inositols. But also species-specific dysregulation of metabolites is common. Several metabolites previously not connected with osmotic stress reactions are identified, including 4-hydroxyproline, pipecolinic acid, myo-inositol, threonic acid, and acylcarnitines. This expands our knowledge about osmoadaptation and calls for further functional characterization of metabolites and pathways in algal stress physiology.},
	keywords = {Diatomic algae, Hypersalinity stress response, Osmolytes, Phaeodactylaceae, Phaeodactylum tricornutum, RCC75, Skeletonema marinoi, Skeletonemataceae, Thalassiosira pseudonana, Thalassiosiraceae, Untargeted metabolite profiling},
	issn = {0031-9422},
	doi = {10.1016/j.phytochem.2022.113267},
	url = {https://www.sciencedirect.com/science/article/pii/S0031942222001832},
	author = {Nikitashina, Vera and Stettin, Daniel and Pohnert, Georg}
}
@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 {haney_multiple_2022,
	title = {Multiple Photolyases Protect the Marine Cyanobacterium Synechococcus from Ultraviolet Radiation},
	journal = {mBio},
	volume = {13},
	number = {4},
	year = {2022},
	month = {aug},
	pages = {e01511{\textendash}22},
	abstract = {<p>Marine cyanobacteria depend on light for photosynthesis, restricting their growth to the photic zone. The upper part of this layer is exposed to strong UV radiation (UVR), a DNA mutagen that can harm these microorganisms. To thrive in UVR-rich waters, marine cyanobacteria employ photoprotection strategies that are still not well defined. Among these are photolyases, light-activated enzymes that repair DNA dimers generated by UVR. Our analysis of genomes of 81 strains of Synechococcus, Cyanobium, and Prochlorococcus isolated from the world{\textquoteright}s oceans shows that they possess up to five genes encoding different members of the photolyase/cryptochrome family, including a photolyase with a novel domain arrangement encoded by either one or two separate genes. We disrupted the putative photolyase-encoding genes in Synechococcus sp. strain RS9916 and discovered that each gene contributes to the overall capacity of this organism to survive UVR. Additionally, each conferred increased survival after UVR exposure when transformed into Escherichia coli lacking its photolyase and SOS response. Our results provide the first evidence that this large set of photolyases endows Synechococcus with UVR resistance that is far superior to that of E. coli, but that, unlike for E. coli, these photolyases provide Synechococcus with the vast majority of its UVR tolerance.</p>
},
	keywords = {rcc555},
	issn = {2150-7511},
	doi = {10.1128/mbio.01511-22},
	url = {https://journals.asm.org/doi/10.1128/mbio.01511-22},
	author = {Haney, Allissa M. and Sanfilippo, Joseph E. and Garczarek, Laurence and Partensky, Fr{\'e}d{\'e}ric and Kehoe, David M.},
	editor = {Ruby, Edward}
}
@article {johnson_nutritional_2022,
	title = {Nutritional response of a coccolithophore to changing pH and temperature},
	journal = {Limnology and Oceanography},
	volume = {n/a},
	number = {n/a},
	year = {2022},
	note = {_eprint: https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.1002/lno.12204},
	abstract = {Coccolithophores are a calcifying unicellular phytoplankton group that are at the base of the marine food web, and their lipid content provides a source of energy to consumers. Coccolithophores are vulnerable to ocean acidification and warming, therefore it is critical to establish the effects of climate change on these significant marine primary producers, and determine potential consequences that these changes can have on their consumers. Here, we quantified the impact of changes in pH and temperature on the nutritional condition (lipid content, particulate organic carbon/nitrogen), growth rate, and morphology of the most abundant living coccolithophore species, Emiliania huxleyi. We used a regression type approach with nine pH levels (ranging from 7.66 to 8.44) and two temperatures (15{\textdegree}C and 20{\textdegree}C). Lipid production was greater under reduced pH, and growth rates were distinctly lower at 15{\textdegree}C than at 20{\textdegree}C. The production potential of lipids, which estimates the availability of lipids to consumers, increased under 20{\textdegree}C, but decreased under low pH. The results indicate that, while consumers will benefit energetically under ocean warming, this benefit will be mitigated by ocean acidification. The carbon to nitrogen ratio was higher at 20{\textdegree}C and low pH, indicating that the nutritional quality of coccolithophores for consumers will decline under climate change. The impact of low pH on the structural integrity of the coccosphere may also mean that coccolithophores are easier to digest for consumers. Many responses suggest cellular stress, indicating that increases in temperature and reductions in pH may have a negative impact on the ecophysiology of coccolithophores.},
	keywords = {RCC1832},
	issn = {1939-5590},
	doi = {10.1002/lno.12204},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1002/lno.12204},
	author = {Johnson, Roberta and Langer, Gerald and Rossi, Sergio and Probert, Ian and Mammone, Marta and Ziveri, Patrizia}
}
@article {azizah_orchestrated_2022,
	title = {Orchestrated Response of Intracellular Zwitterionic Metabolites in Stress Adaptation of the Halophilic Heterotrophic Bacterium Pelagibaca bermudensis},
	journal = {Marine Drugs},
	volume = {20},
	number = {11},
	year = {2022},
	month = {nov},
	pages = {727},
	abstract = {Osmolytes are naturally occurring organic compounds that protect cells against various forms of stress. Highly polar, zwitterionic osmolytes are often used by marine algae and bacteria to counteract salinity or temperature stress. We investigated the effect of several stress conditions including different salinities, temperatures, and exposure to organic metabolites released by the alga Tetraselmis striata on the halophilic heterotrophic bacterium Pelagibaca bermudensis. Using ultrahigh-performance liquid chromatography (UHPLC) on a ZIC-HILIC column and high-resolution electrospray ionization mass spectrometry, we simultaneously detected and quantified the eleven highly polar compounds dimethylsulfoxonium propionate (DMSOP), dimethylsulfoniopropionate (DMSP), gonyol, cysteinolic acid, ectoine, glycine betaine (GBT), carnitine, sarcosine, choline, proline, and 4-hydroxyproline. All compounds are newly described in P. bermudensis and potentially involved in physiological functions essential for bacterial survival under variable environmental conditions. We report that adaptation to various forms of stress is accomplished by adjusting the pattern and amount of the zwitterionic metabolites.},
	keywords = {RCC131},
	issn = {1660-3397},
	doi = {10.3390/md20110727},
	url = {https://www.mdpi.com/1660-3397/20/11/727},
	author = {Azizah, Muhaiminatul and Pohnert, Georg}
}
@article {carrigee_phycoerythrobilin_2022,
	title = {The phycoerythrobilin isomerization activity of MpeV in Synechococcus sp. WH8020 is prevented by the presence of a histidine at position 141 within its phycoerythrin-I β-subunit substrate},
	journal = {Frontiers in Microbiology},
	volume = {13},
	year = {2022},
	pages = {1011189},
	abstract = {Marine Synechococcus efficiently harvest available light for photosynthesis using complex antenna systems, called phycobilisomes, composed of an allophycocyanin core surrounded by rods, which in the open ocean are always constituted of phycocyanin and two phycoerythrin (PE) types: PEI and PEII. These cyanobacteria display a wide pigment diversity primarily resulting from differences in the ratio of the two chromophores bound to PEs, the green-light absorbing phycoerythrobilin and the blue-light absorbing phycourobilin. Prior to phycobiliprotein assembly, bilin lyases post-translationally catalyze the ligation of phycoerythrobilin to conserved cysteine residues on α- or β-subunits, whereas the closely related lyase-isomerases isomerize phycoerythrobilin to phycourobilin during the attachment reaction. MpeV was recently shown in Synechococcus sp. RS9916 to be a lyase-isomerase which doubly links phycourobilin to two cysteine residues (C50 and C61; hereafter C50, 61) on the β-subunit of both PEI and PEII. Here we show that Synechococcus sp. WH8020, which belongs to the same pigment type as RS9916, contains MpeV that demonstrates lyase-isomerase activity on the PEII β-subunit but only lyase activity on the PEI β-subunit. We also demonstrate that occurrence of a histidine at position 141 of the PEI β-subunit from WH8020, instead of a leucine in its counterpart from RS9916, prevents the isomerization activity by WH8020 MpeV, showing for the first time that both the substrate and the enzyme play a role in the isomerization reaction. We propose a structural-based mechanism for the role of H141 in blocking isomerization. More generally, the knowledge of the amino acid present at position 141 of the β-subunits may be used to predict which phycobilin is bound at C50, 61 of both PEI and PEII from marine Synechococcus strains.},
	keywords = {RCC2437, RCC307, RCC751},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2022.1011189},
	url = {https://www.frontiersin.org/articles/10.3389/fmicb.2022.1011189/full},
	author = {Carrigee, Lyndsay A. and Frick, Jacob P. and Liu, Xindi and Karty, Jonathan A. and Trinidad, Jonathan C. and Tom, Irin P. and Yang, Xiaojing and Dufour, Louison and Partensky, Fr{\'e}d{\'e}ric and Schluchter, Wendy M.}
}
@article {meyer_pronounced_2022,
	title = {Pronounced Uptake and Metabolism of Organic Substrates by Diatoms Revealed by Pulse-Labeling Metabolomics},
	journal = {Frontiers in Marine Science},
	volume = {9},
	year = {2022},
	pages = {821167},
	abstract = {Diatoms contribute as a dominant group of microalgae to approximately 20\% of the global carbon fixation. In the plankton, these photosynthetic algae are exposed to a plethora of metabolites, especially when competing algae are lysed. It is well established that diatoms can take up specific metabolites, such as vitamins, amino acids as nitrogen source, or dimethylsulfoniopropoionate to compensate for changes in water salinity. It is, however, unclear to which extent diatoms take up other organic resources and if these are incorporated into the cell{\textasciiacute}s metabolism. Here, we explore the general scope of uptake of metabolites from competitors. Using labeled metabolites released during lysis of algae grown under a 13CO2 atmosphere, we show that the cosmopolitan diatom Chaetoceros didymus takes up even dilute organic substrates from these lysates with little bias for molecular weight or polarity. This is reflected by a high degree of labeling in the metabolome of the exposed cells. The newly developed pulse label/mass spectrometry metabolomics approach reveals that polarity and molecular weight has no detectable influence on uptake. We further show that the taken-up metabolites are partly maintained without metabolic modification within the cells, but also a substantial part is subject to catabolic and anabolic transformation. One of the most dominant phytoplankton groups thus has the potential to compete with heterotrophs, suggesting that the observed osmotrophy may substantially impact organic material fluxes in the oceans. Our findings call for the refinement of our understanding of competition in the plankton.},
	keywords = {RCC75},
	issn = {2296-7745},
	doi = {10.3389/fmars.2022.821167},
	url = {https://www.frontiersin.org/articles/10.3389/fmars.2022.821167/full},
	author = {Meyer, Nils and Rydzyk, Aljoscha and Pohnert, Georg}
}
@article {pilatova_revisiting_2022,
	title = {Revisiting biocrystallization: purine crystalline inclusions are widespread in eukaryotes},
	journal = {The ISME Journal},
	year = {2022},
	month = {jun},
	keywords = {RCC1350, RCC745},
	issn = {1751-7362, 1751-7370},
	doi = {10.1038/s41396-022-01264-1},
	url = {https://www.nature.com/articles/s41396-022-01264-1},
	author = {Pil{\'a}tov{\'a}, Jana and P{\'a}nek, Tom{\'a}{\v s} and Obornik, Miroslav and {\v C}epi{\v c}ka, Ivan and Mojze{\v s}, Peter}
}
@article {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 {Trefaut2020,
	title = {Annual phytoplankton dynamics in coastal waters from fildes bay, western antarctic peninsula},
	journal = {Scientific Reports},
	volume = {11},
	number = {1},
	year = {2021},
	note = {tex.mendeley-tags: RCC2265,RCC2289,RCC4582,RCC4586,RCC5152},
	month = {dec},
	pages = {1368},
	abstract = {Year-round reports of phytoplankton dynamics in the West Antarctic Peninsula are rare and mainly limited to microscopy and/or pigment-based studies. We analyzed the phytoplankton community from coastal waters of Fildes Bay in the West Antarctic Peninsula between January 2014 and 2015 using metabarcoding of the nuclear and plastidial 18/16S rRNA gene from both size-fractionated and flow cytometry sorted samples. Overall 14 classes of photosynthetic eukaryotes were present in our samples with the following dominating: Bacillariophyta (diatoms), Pelagophyceae and Dictyochophyceae for division Ochrophyta, Mamiellophyceae and Pyramimonadophyceae for division Chlorophyta, Haptophyta and Cryptophyta. Each metabarcoding approach yielded a different image of the phytoplankton community with for example Prymnesiophyceae more prevalent in plastidial metabarcodes and Mamiellophyceae in nuclear ones. Diatoms were dominant in the larger size fractions and during summer, while Prymnesiophyceae and Cryptophyceae were dominant in colder seasons. Pelagophyceae were particularly abundant towards the end of autumn (May). In addition of Micromonas polaris and Micromonas sp. clade B3, both previously reported in Arctic waters, we detected a new Micromonas 18S rRNA sequence signature, close to, but clearly distinct from M. polaris , which potentially represents a new clade specific of the Antarctic. These results highlight the need for complementary strategies as well as the importance of year-round monitoring for a comprehensive description of phytoplankton communities in Antarctic coastal waters.},
	keywords = {RCC2265, RCC2289, RCC4582, RCC4586, RCC5152},
	issn = {2045-2322},
	doi = {10.1038/s41598-020-80568-8},
	url = {http://biorxiv.org/content/early/2020/10/27/2020.10.27.356600.abstract http://www.nature.com/articles/s41598-020-80568-8},
	author = {Trefault, Nicole and de la Iglesia, Rodrigo and Moreno-Pino, Mario and Lopes dos Santos, Adriana and G{\'e}rikas Ribeiro, Catherine and Parada-Pozo, G{\'e}nesis and Cristi, Antonia and Marie, Dominique and Vaulot, Daniel}
}
@article {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 {park_bioluminescence_2021,
	title = {Bioluminescence capability and intensity in the dinoflagellate Alexandrium species},
	journal = {ALGAE},
	volume = {36},
	year = {2021},
	abstract = {Some species in the dinoflagellate genus Alexandrium are bioluminescent. Of the 33 formally described Alexandrium species, the bioluminescence capability of only nine species have been tested, and eight have been reported to be bioluminescent. The present study investigated the bioluminescence capability of seven Alexandrium species that had not been tested. Alexandrium mediterraneum, A. pohangense, and A. tamutum were bioluminescent, but A. andersonii, A. hiranoi, A. insuetum, and A. pseudogonyaulax were not. We also measured the bioluminescent intensity of A. affine, A. fraterculus, A. mediterraneum, A. ostenfeldii, A. pacificum, A. pohangense, A. tamarense, and A. tamutum. The mean 200-second-integrated bioluminescence intensity per cell ranged from 0.02 to 32.2 {\texttimes} 104 relative luminescence unit per cell (RLU cell-1), and the mean maximum bioluminescence intensity per cell per second (BLMax) ranged from 0.01 to 10.3 {\texttimes} 104 RLU cell-1 s-1. BLMax was significantly correlated with the maximum growth rates of Alexandrium species, except for A. tamarense. A phylogenetic tree based on large subunit ribosomal DNA (LSU rDNA), showed that the bioluminescent species A. affine, A. catenella, A. fraterculus, A. mediterraneum, A. pacificum, and A. tamarense formed a large clade. However, the toxicity or mixotrophic capability of these species was split. Thus, their bioluminescence capability in this clade was more consistent than their toxicity or mixotrophic capability. Phylogenetic trees based on LSU rDNA and the luciferase gene of Alexandrium were consistent except for A. pohangense. The results of the present study can provide a basis for understanding the interspecific diversity in bioluminescence of Alexandrium.},
	keywords = {RCC4104},
	doi = {10.4490/algae.2021.36.12.6},
	author = {Park, Sang Ah and Jeong, Hae Jin and Ok, Jin and Kang, Heechang and You, Jihyun and Eom, Se and Yoo, Yeong and Lee, Moo Joon}
}
@article {phelps_carbon_2021,
	title = {Carbon Isotope Fractionation in Noelaerhabdaceae Algae in Culture and a Critical Evaluation of the Alkenone Paleobarometer},
	journal = {Geochemistry, Geophysics, Geosystems},
	volume = {22},
	number = {7},
	year = {2021},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1029/2021GC009657},
	pages = {e2021GC009657},
	abstract = {The carbon isotope fractionation in algal organic matter ($\varepsilon$p), including the long-chain alkenones produced by the coccolithophorid family Noelaerhabdaceae, is used to reconstruct past atmospheric CO2 levels. The conventional proxy linearly relates $\varepsilon$p to changes in cellular carbon demand relative to diffusive CO2 supply, with larger $\varepsilon$p values occurring at lower carbon demand relative to supply (i.e., abundant CO2). However, the response of Gephyrocapsa oceanica, one of the dominant alkenone producers of the last few million years, has not been studied closely. Here, we subject G. oceanica to various CO2 levels by increasing pCO2 in the culture headspace, as opposed to increasing dissolved inorganic carbon (DIC) and alkalinity concentrations at constant pH. We note no substantial change in physiology, but observe an increase in $\varepsilon$p as carbon demand relative to supply decreases, consistent with DIC manipulations. We compile existing Noelaerhabdaceae $\varepsilon$p data and show that the diffusive model poorly describes the data. A meta-analysis of individual treatments (unique combinations of lab, strain, and light conditions) shows that the slope of the $\varepsilon$p response depends on the light conditions and range of carbon demand relative to CO2 supply in the treatment, which is incompatible with the diffusive model. We model $\varepsilon$p as a multilinear function of key physiological and environmental variables and find that both photoperiod duration and light intensity are critical parameters, in addition to CO2 and cell size. While alkenone carbon isotope ratios indeed record CO2 information, irradiance and other factors are also necessary to properly describe alkenone $\varepsilon$p.},
	keywords = {alkenone, carbon dioxide, carbon isotope, coccolithophore, irradiance, paleobarometry, rcc, RCC1303},
	issn = {1525-2027},
	doi = {10.1029/2021GC009657},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1029/2021GC009657},
	author = {Phelps, Samuel R. and Hennon, Gwenn M. M. and Dyhrman, Sonya T. and Hern{\'a}ndez Lim{\'o}n, Mar{\'\i}a D. and Williamson, Olivia M. and Polissar, Pratigya J.}
}
@booklet {thomy_combining_2021,
	title = {Combining Nanopore and Illumina Sequencing Permits Detailed Analysis of Insertion Mutations and Structural Variations Produced by PEG-Mediated Transformation in Ostreococcus tauri},
	year = {2021},
	month = {feb},
	publisher = {LIFE SCIENCES},
	type = {preprint},
	abstract = {Ostreococcus tauri is a simple unicellular green alga representing an ecologically important group of phytoplankton in oceans worldwide. Modern molecular techniques must be developed in order to understand the mechanisms that permit adaptation of microalgae to their environment. We present for the first time in O. tauri a detailed characterization of individual genomic integration events of foreign DNA of plasmid origin after PEG-mediated transformation. Vector integration appears to be random, occurring mainly at a single locus, and thus confirming the utility of this technique for insertional mutagenesis. While the mechanism of double-stranded DNA repair in the O. tauri model remains to be elucidated, we clearly demonstrate by genome resequencing that the integration of the vector leads to frequent structural variations (deletions/insertions and duplications) and some chromosomal rearrangements in the genome at the insertion loci, and often within the vector sequence itself. From these observations, we speculate that a non-homologous end joining-like mechanism is required during random insertion events, as described in plants and other freshwater algal models. PEG-mediated transformation is therefore a promising molecular biology tool, not only for functional genomic studies, but also for biotechnological research in ecologically important marine algae.},
	keywords = {RCC1115},
	doi = {10.20944/preprints202102.0506.v1},
	url = {https://www.preprints.org/manuscript/202102.0506/v1},
	author = {Thomy, Julie and Sanchez, Fr{\'e}d{\'e}ric and Gut, Marta and Cruz, Fernando and Alioto, Tyler and Piganeau, Gwenael and Grimsley, Nigel and Yau, Sheree}
}
@article {thomy_combining_2021,
	title = {Combining Nanopore and Illumina Sequencing Permits Detailed Analysis of Insertion Mutations and Structural Variations Produced by PEG-Mediated Transformation in Ostreococcus tauri},
	journal = {Cells},
	volume = {10},
	number = {3},
	year = {2021},
	pages = {664},
	abstract = {Ostreococcus tauri is a simple unicellular green alga representing an ecologically important group of phytoplankton in oceans worldwide. Modern molecular techniques must be developed in order to understand the mechanisms that permit adaptation of microalgae to their environment. We present for the first time in O. tauri a detailed characterization of individual genomic integration events of foreign DNA of plasmid origin after PEG-mediated transformation. Vector integration occurred randomly at a single locus in the genome and mainly as a single copy. Thus, we confirmed the utility of this technique for insertional mutagenesis. While the mechanism of double-stranded DNA repair in the O. tauri model remains to be elucidated, we clearly demonstrate by genome resequencing that the integration of the vector leads to frequent structural variations (deletions/insertions and duplications) and some chromosomal rearrangements in the genome at the insertion loci. Furthermore, we often observed variations in the vector sequence itself. From these observations, we speculate that a nonhomologous end-joining-like mechanism is employed during random insertion events, as described in plants and other freshwater algal models. PEG-mediated transformation is therefore a promising molecular biology tool, not only for functional genomic studies, but also for biotechnological research in this ecologically important marine alga.},
	keywords = {RCC1115, RCC7079, RCC7080, RCC7081, RCC7082, RCC7083, RCC7084, RCC7085},
	issn = {2073-4409},
	doi = {10.3390/cells10030664},
	url = {https://www.mdpi.com/2073-4409/10/3/664},
	author = {Thomy, Julie and Sanchez, Fr{\'e}d{\'e}ric and Gut, Marta and Cruz, Fernando and Alioto, Tyler and Piganeau, Gwenael and Grimsley, Nigel and Yau, Sheree}
}
@inbook {Paredes2021,
	title = {Cryopreservation of algae},
	booktitle = {Cryopreservation and freeze-drying protocols},
	volume = {2180},
	year = {2021},
	pages = {607{\textendash}621},
	publisher = {Springer Science+Business Media, LLC},
	organization = {Springer Science+Business Media, LLC},
	keywords = {cryopreservation, macroalgae, Microalgae},
	isbn = {978-1-07-160783-1},
	doi = {10.1007/978-1-0716-0783-1_32},
	url = {http://link.springer.com/10.1007/978-1-0716-0783-1_32},
	author = {Paredes, Estefania and Ward, Angela and Probert, Ian and Gouhier, L{\'e}na and Campbell, Christine N.},
	editor = {Wolkers, Willem F. and Oldenhof, Harriette}
}
@article {fenizia_cysteinolic_2021,
	title = {Cysteinolic Acid Is a Widely Distributed Compatible Solute of Marine Microalgae},
	journal = {Marine Drugs},
	volume = {19},
	number = {12},
	year = {2021},
	note = {Number: 12 Publisher: Multidisciplinary Digital Publishing Institute},
	month = {dec},
	pages = {683},
	abstract = {Phytoplankton rely on bioactive zwitterionic and highly polar small metabolites with osmoregulatory properties to compensate changes in the salinity of the surrounding seawater. Dimethylsulfoniopropionate (DMSP) is a main representative of this class of metabolites. Salinity-dependent DMSP biosynthesis and turnover contribute significantly to the global sulfur cycle. Using advanced chromatographic and mass spectrometric techniques that enable the detection of highly polar metabolites, we identified cysteinolic acid as an additional widely distributed polar metabolite in phytoplankton. Cysteinolic acid belongs to the class of marine sulfonates, metabolites that are commonly produced by algae and consumed by bacteria. It was detected in all dinoflagellates, haptophytes, diatoms and prymnesiophytes that were surveyed. We quantified the metabolite in different phytoplankton taxa and revealed that the cellular content can reach even higher concentrations than the ubiquitous DMSP. The cysteinolic acid concentration in the cells of the diatom Thalassiosira weissflogii increases significantly when grown in a medium with elevated salinity. In contrast to the compatible solute ectoine, cysteinolic acid is also found in high concentrations in axenic algae, indicating biosynthesis by the algae and not the associated bacteria. Therefore, we add this metabolite to the family of highly polar metabolites with osmoregulatory characteristics produced by phytoplankton.},
	keywords = {cysteinolic acid, diatoms, DMSP, ectoine, LC/MS analysis, osmoadaptation, osmoregulation, phytoplankton, RCC76, salinity},
	doi = {10.3390/md19120683},
	url = {https://www.mdpi.com/1660-3397/19/12/683},
	author = {Fenizia, Simona and Weissflog, Jerrit and Pohnert, Georg}
}
@article {pan_effects_2021,
	title = {Effects of Epibiotic Diatoms on the Productivity of the Calanoid Copepod Acartia tonsa (Dana) in Intensive Aquaculture Systems},
	journal = {Frontiers in Marine Science},
	volume = {8},
	year = {2021},
	pages = {1386},
	abstract = {We evaluated here the effects of the epibiotic diatom Tabularia sp. on the productivity of the calanoid copepod Acartia tonsa (Dana) for assessing their risk on copepod intensive aquaculture industry for the provision of live feed. In the first experiment, uninfested and intensively infested females were cultivated individually for the assessment of egg production. Intensively infested females appeared to have a significantly lower egg production (5.0{\textendash}9.0 eggs/female/d) than uninfested females (22.0{\textendash}26.0 eggs/female/d) during 5 consecutive days. In the second experiment, effects of culture densities on diatom epibiosis were investigated in 9 L cultures at three different densities (200, 400, and 600 ind. L{\textendash}1). Another culture at higher volume (250 L) and lowest density (200 ind. L{\textendash}1) was also carried out to test the effect of culture volume on diatom epibiosis. The infestation rate (\%), infestation intensity (ratio of surface diatom coverage levels, classified as levels 0{\textendash}3) and daily egg harvest rate (number of harvested eggs per day per liter) were evaluated among the four culture populations. The copepods had higher infestation rate (53.69{\textendash}60.14\%) and intensity rate (high ratios at level 2 and 3) when the densities were increased from 200 ind./L to 400 and 600 ind./L. Although egg harvest increased with increasing culture density, it seemed that the diatom-infested A. tonsa population reach a saturated egg production when the density was higher than 400 ind./L. Nevertheless, the differences of culture volumes (250 and 9 L) appeared to be not to have any effect when the copepods were cultivated at the same density (200 ind./L). This study reveals for the first time that the epibiosis of the diatom Tabularia sp. reduces the individual egg production, and egg harvest rate in high-density culture of the copepod A. tonsa. Our findings implicate that diatom epibiosis should be avoid in copepod intensive culture systems.},
	keywords = {rcc, RCC350},
	issn = {2296-7745},
	doi = {10.3389/fmars.2021.728779},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2021.728779},
	author = {Pan, Yen-Ju and Wang, Wei-Lung and Hwang, Jiang-Shiou and Souissi, Sami}
}
@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 {pinto_features_2021,
	title = {Features of the Opportunistic Behaviour of the Marine Bacterium Marinobacter algicola in the Microalga Ostreococcus tauri Phycosphere},
	journal = {Microorganisms},
	volume = {9},
	year = {2021},
	pages = {1777},
	abstract = {Although interactions between microalgae and bacteria are observed in both natural environment and the laboratory, the modalities of coexistence of bacteria inside microalgae phyco-spheres in laboratory cultures are mostly unknown. Here, we focused on well-controlled cultures of the model green picoalga Ostreococcus tauri and the most abundant member of its phycosphere, Marinobacter algicola. The prevalence of M. algicola in O. tauri cultures raises questions about how this bacterium maintains itself under laboratory conditions in the microalga culture. The results showed that M. algicola did not promote O. tauri growth in the absence of vitamin B12 while M. algicola depended on O. tauri to grow in synthetic medium, most likely to obtain organic carbon sources provided by the microalgae. M. algicola grew on a range of lipids, including triacylglycerols that are known to be produced by O. tauri in culture during abiotic stress. Genomic screening revealed the absence of genes of two particular modes of quorum-sensing in Marinobacter genomes which refutes the idea that these bacterial communication systems operate in this genus. To date, the {\textquoteright}opportunistic{\textquoteright} behaviour of M. algicola in the laboratory is limited to several phytoplanktonic species including Chlorophyta such as O. tauri. This would indicate a preferential occurrence of M. algicola in association with these specific microalgae under optimum laboratory conditions.},
	keywords = {RCC4221},
	doi = {10.3390/microorganisms9081777},
	author = {Pinto, Jordan and Lami, Rapha{\"e}l and Krasovec, Marc and Grimaud, R{\'e}gis and Urios, Laurent and Lupette, Josselin and Escande, Marie-Line and Sanchez, Fr{\'e}d{\'e}ric and Intertaglia, Laurent and Grimsley, Nigel and Piganeau, Gwenael and Sanchez, Sophie}
}
@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 {grebert_molecular_2021,
	title = {Molecular bases of an alternative dual-enzyme system for light color acclimation of marine \textit{Synechococcus cyanobacteria},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {118},
	number = {9},
	year = {2021},
	pages = {e2019715118},
	abstract = {<p>Marine Synechococcus cyanobacteria owe their ubiquity in part to the wide pigment diversity of their light-harvesting complexes. In open ocean waters, cells predominantly possess sophisticated antennae with rods composed of phycocyanin and two types of phycoerythrins (PEI and PEII). Some strains are specialized for harvesting either green or blue light, while others can dynamically modify their light absorption spectrum to match the dominant ambient color. This process, called type IV chromatic acclimation (CA4), has been linked to the presence of a small genomic island occurring in two configurations (CA4-A and CA4-B). While the CA4-A process has been partially characterized, the CA4-B process has remained an enigma. Here we characterize the function of two members of the phycobilin lyase E/F clan, MpeW and MpeQ, in Synechococcus sp. strain A15-62 and demonstrate their critical role in CA4-B. While MpeW, encoded in the CA4-B island and up-regulated in green light, attaches the green light-absorbing chromophore phycoerythrobilin to cysteine-83 of the PEII α-subunit in green light, MpeQ binds phycoerythrobilin and isomerizes it into the blue light-absorbing phycourobilin at the same site in blue light, reversing the relationship of MpeZ and MpeY in the CA4-A strain RS9916. Our data thus reveal key molecular differences between the two types of chromatic acclimaters, both highly abundant but occupying distinct complementary ecological niches in the ocean. They also support an evolutionary scenario whereby CA4-B island acquisition allowed former blue light specialists to become chromatic acclimaters, while former green light specialists would have acquired this capacity by gaining a CA4-A island.</p>
},
	keywords = {RCC2374, to add},
	issn = {0027-8424, 1091-6490},
	doi = {10.1073/pnas.2019715118},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.2019715118},
	author = {Gr{\'e}bert, Th{\'e}ophile and Nguyen, Adam A. and Pokhrel, Suman and Joseph, Kes Lynn and Ratin, Morgane and Dufour, Louison and Chen, Bo and Haney, Allissa M. and Karty, Jonathan A. and Trinidad, Jonathan C. and Garczarek, Laurence and Schluchter, Wendy M. and Kehoe, David M. and Partensky, Fr{\'e}d{\'e}ric}
}
@article {decamp_new_2021,
	title = {A New, Quick, and Simple Protocol to Evaluate Microalgae Polysaccharide Composition},
	journal = {Marine Drugs},
	volume = {19},
	number = {2},
	year = {2021},
	pages = {101},
	abstract = {In this work, a new methodological approach, relying on the high specificity of enzymes in a complex mixture, was developed to estimate the composition of bioactive polysaccharides produced by microalgae, directly in algal cultures. The objective was to set up a protocol to target oligomers commonly known to be associated with exopolysaccharides{\textquoteright} (EPS) nutraceutical and pharmaceutical activities (i.e., rhamnose, fucose, acidic sugars, etc.) without the constraints classically associated with chromatographic methods, while maintaining a resolution sufficiently high to enable their monitoring in the culture system. Determination of the monosaccharide content required the application of acid hydrolysis (2 M trifluoroacetic acid) followed by NaOH (2 M) neutralization. Quantification was then carried out directly on the fresh hydrolysate using enzyme kits corresponding to the main monosaccharides in a pre-determined composition of the polysaccharides under analysis. Initial results showed that the enzymes were not sensitive to the presence of TFA and NaOH, so the methodology could be carried out on fresh hydrolysate. The limits of quantification of the method were estimated as being in the order of the log of nanograms of monosaccharides per well, thus positioning it among the chromatographic methods in terms of analytical performance. A comparative analysis of the results obtained by the enzymatic method with a reference method (high-performance anion-exchange chromatography) confirmed good recovery rates, thus validating the closeness of the protocol. Finally, analyses of raw culture media were carried out and compared to the results obtained in miliQ water; no differences were observed. The new approach is a quick, functional analysis method allowing routine monitoring of the quality of bioactive polysaccharides in algal cultures grown in photobioreactors.},
	keywords = {rcc2380, RCC3438},
	issn = {1660-3397},
	doi = {10.3390/md19020101},
	url = {https://www.mdpi.com/1660-3397/19/2/101},
	author = {Decamp, Antoine and Michelo, Orane and Rabbat, Christelle and Laroche, C{\'e}line and Grizeau, Dominique and Pruvost, J{\'e}r{\'e}my and Gon{\c c}alves, Olivier}
}
@article {Farhat2021,
	title = {Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp.},
	journal = {BMC Biology},
	year = {2021},
	note = {Publisher: BMC Biology tex.mendeley-tags: RCC4383,RCC4398},
	pages = {1{\textendash}21},
	keywords = {Dinoflagellate, genome, Introner elements, Non-canonical introns, parasite, RCC4383, RCC4398},
	doi = {10.1186/s12915-020-00927-9},
	author = {Farhat, Sarah and Le, Phuong and Kayal, Ehsan and Noel, Benjamin and Bigeard, Estelle and Corre, Erwan and Maumus, Florian and Florent, Isabelle and Alberti, Adriana and Aury, Jean-Marc and Barbeyron, Tristan and Cai, Ruibo and Silva, Corinne Da and Istace, Benjamin and Labadie, Karine and Marie, Dominique and Mercier, Jonathan and Rukwavu, Tsinda and Szymczak, Jeremy and Tonon, Thierry and Alves-de-Souza, Catharina and Rouze, Pierre and de Peer, Yves Van and Wincker, Patrick and Rombauts, Stephane and Porcel, Betina M and Guillou, Laure}
}
@article {kawachi_rappemonads_2021,
	title = {Rappemonads are haptophyte phytoplankton},
	journal = {Current Biology},
	year = {2021},
	month = {mar},
	abstract = {Rapidly accumulating genetic data from environmental sequencing approaches have revealed an extraordinary level of unsuspected diversity within marine phytoplankton,1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 which is responsible for around 50\% of global net primary production.12,13 However, the phenotypic identity of many of the organisms distinguished by environmental DNA sequences remains unclear. The rappemonads represent a plastid-bearing protistan lineage that to date has only been identified by environmental plastid 16S rRNA sequences.14, 15, 16, 17 The phenotypic identity of this group, which does not confidently cluster in any known algal clades in 16S rRNA phylogenetic reconstructions,15 has remained unknown since the first report of environmental sequences over two decades ago. We show that rappemonads are closely related to a haptophyte microalga, Pavlomulina ranunculiformis gen. nov. et sp. nov., and belong to a new haptophyte class, the Rappephyceae. Organellar phylogenomic analyses provide strong evidence for the inclusion of this lineage within the Haptophyta as a sister group to the Prymnesiophyceae. Members of this new class have a cosmopolitan distribution in coastal and oceanic regions. The relative read abundance of Rappephyceae in a large environmental barcoding dataset was comparable to, or greater than, those of major haptophyte species, such as the bloom-forming Gephyrocapsa huxleyi and Prymnesium parvum, and this result indicates that they likely have a significant impact as primary producers. Detailed characterization of Pavlomulina allowed for reconstruction of the ancient evolutionary history of the Haptophyta, a group that is one of the most important components of extant marine phytoplankton communities.},
	keywords = {environmental DNA sequences, morphological evolution, organellar phylogenomics, phytoplankton diversity, RCC3430, transmission electron microscopy},
	issn = {0960-9822},
	doi = {10.1016/j.cub.2021.03.012},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982221003511},
	author = {Kawachi, Masanobu and Nakayama, Takuro and Kayama, Motoki and Nomura, Mami and Miyashita, Hideaki and Bojo, Othman and Rhodes, Lesley and Sym, Stuart and Pienaar, Richard N. and Probert, Ian and Inouye, Isao and Kamikawa, Ryoma}
}
@article {langer_role_2021,
	title = {Role of silicon in the development of complex crystal shapes in coccolithophores},
	journal = {New Phytologist},
	volume = {231},
	number = {5},
	year = {2021},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.17230},
	pages = {1845{\textendash}1857},
	abstract = {The development of calcification by the coccolithophores had a profound impact on ocean carbon cycling, but the evolutionary steps leading to the formation of these complex biomineralized structures are not clear. Heterococcoliths consisting of intricately shaped calcite crystals are formed intracellularly by the diploid life cycle phase. Holococcoliths consisting of simple rhombic crystals can be produced by the haploid life cycle stage but are thought to be formed extracellularly, representing an independent evolutionary origin of calcification. We use advanced microscopy techniques to determine the nature of coccolith formation and complex crystal formation in coccolithophore life cycle stages. We find that holococcoliths are formed in intracellular compartments in a similar manner to heterococcoliths. However, we show that silicon is not required for holococcolith formation and that the requirement for silicon in certain coccolithophore species relates specifically to the process of crystal morphogenesis in heterococcoliths. We therefore propose an evolutionary scheme in which the lower complexity holococcoliths represent an ancestral form of calcification in coccolithophores. The subsequent recruitment of a silicon-dependent mechanism for crystal morphogenesis in the diploid life cycle stage led to the emergence of the intricately shaped heterococcoliths, enabling the formation of the elaborate coccospheres that underpin the ecological success of coccolithophores.},
	keywords = {biomineralization, Calcification, coccolith, coccolithophore, evolution, rcc, RCC1178, RCC1181, RCC1456, RCC1460, RCC1461, RCC1477, RCC1800, RCC1801, RCC3777, RCC6506, silicon},
	issn = {1469-8137},
	doi = {10.1111/nph.17230},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.17230},
	author = {Langer, Gerald and Taylor, Alison R. and Walker, Charlotte E. and Meyer, Erin M. and Ben Joseph, Oz and Gal, Assaf and Harper, Glenn M. and Probert, Ian and Brownlee, Colin and Wheeler, Glen L.}
}
@article {labban_temperature_2021,
	title = {Temperature Responses of Heterotrophic Bacteria in Co-culture With a Red Sea Synechococcus Strain},
	journal = {Frontiers in Microbiology},
	volume = {12},
	year = {2021},
	pages = {612732},
	abstract = {Interactions between autotrophic and heterotrophic bacteria are fundamental for marine biogeochemical cycling. How global warming will affect the dynamics of these essential microbial players is not fully understood. The aims of this study were to identify the major groups of heterotrophic bacteria present in a Synechococcus culture originally isolated from the Red Sea and assess their joint responses to experimental warming within the metabolic ecology framework. A co-culture of Synechococcus sp. RS9907 and their associated heterotrophic bacteria, after determining their taxonomic affiliation by 16S rRNA gene sequencing, was acclimated and maintained in the lab at different temperatures (24{\textendash}34{\textdegree}C). The abundance and cellular properties of Synechococcus and the three dominant heterotrophic bacterial groups (pertaining to the genera Paracoccus, Marinobacter, and Muricauda) were monitored by flow cytometry. The activation energy of Synechococcus, which grew at 0.94{\textendash}1.38 d{\textendash}1, was very similar (0.34 {\textpm} 0.02 eV) to the value hypothesized by the metabolic theory of ecology (MTE) for autotrophs (0.32 eV), while the values of the three heterotrophic bacteria ranged from 0.16 to 1.15 eV and were negatively correlated with their corresponding specific growth rates (2.38{\textendash}24.4 d{\textendash}1). The corresponding carrying capacities did not always follow the inverse relationship with temperature predicted by MTE, nor did we observe a consistent response of bacterial cell size and temperature. Our results show that the responses to future ocean warming of autotrophic and heterotrophic bacteria in microbial consortia might not be well described by theoretical universal rules.},
	keywords = {rcc, RCC546},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2021.612732},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8141594/},
	author = {Labban, Abbrar and Palacio, Antonio S. and Garc{\'\i}a, Francisca C. and Hadaidi, Ghaida and Ansari, Mohd I. and L{\'o}pez-Urrutia, {\'A}ngel and Alonso-S{\'a}ez, Laura and Hong, Pei-Ying and Mor{\'a}n, Xos{\'e} Anxelu G.}
}
@article {Nissimov2020,
	title = {Aquatic virus culture collection: an absent (but necessary) safety net for environmental microbiologists},
	journal = {Applied Phycology},
	volume = {00},
	number = {00},
	year = {2020},
	note = {Publisher: Taylor \& Francis},
	pages = {1{\textendash}15},
	keywords = {algae, Aquatic viruses, bacteria, biological preservation, community resource, culture collection, genetic and metabolic diversity},
	issn = {2638-8081},
	doi = {10.1080/26388081.2020.1770123},
	url = {https://doi.org/10.1080/26388081.2020.1770123 https://www.tandfonline.com/doi/full/10.1080/26388081.2020.1770123},
	author = {Nissimov, Jozef I and Campbell, Christine N and Probert, Ian and Wilson, William H}
}
@article {Pan2020,
	title = {Assessments of first feeding protocols on the larviculture of California grunion Leuresthes tenuis (Osteichthyes: Atherinopsidae)},
	journal = {Aquaculture Research},
	volume = {51},
	number = {7},
	year = {2020},
	note = {Publisher: Blackwell Publishing Ltd tex.mendeley-tags: RCC350},
	month = {jul},
	pages = {3054{\textendash}3058},
	keywords = {California grunion, Copepod, larval rearing, live feed, quiescent egg, RCC350},
	issn = {13652109},
	doi = {10.1111/are.14637},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/are.14637},
	author = {Pan, Yen Ju and D{\'e}pos{\'e}, Emilien and Souissi, Anissa and H{\'e}nard, St{\'e}phane and Schaadt, Mike and Mastro, Ed and Souissi, Sami}
}
@article {Palacio2020,
	title = {Changes in population age-structure obscure the temperature-size rule in marine cyanobacteria},
	journal = {Frontiers in Microbiology},
	volume = {11},
	year = {2020},
	note = {Publisher: Frontiers Media S.A. tex.mendeley-tags: RCC2382,RCC3377},
	month = {aug},
	pages = {2059},
	abstract = {The temperature-size Rule (TSR) states that there is a negative relationship between ambient temperature and body size. This rule has been independently evaluated for different phases of the life cycle in multicellular eukaryotes, but mostly for the average population in unicellular organisms. We acclimated two model marine cyanobacterial strains (Prochlorococcus marinus MIT9301 and Synechococcus sp. RS9907) to a gradient of temperatures and measured the changes in population age-structure and cell size along their division cycle. Both strains displayed temperature-dependent diel changes in cell size, and as a result, the relationship between temperature and average cell size varied along the day. We computed the mean cell size of new-born cells in order to test the prediction of the TSR on a single-growth stage. Our work reconciles previous inconsistent results when testing the TSR on unicellular organisms, and shows that when a single-growth stage is considered the predicted negative response to temperature is revealed.},
	keywords = {cell cycle, Cell Division, cell size, Prochlorococcus, rcc2382, RCC3377, Synechococcus, temperature, temperature-size rule},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2020.02059},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2020.02059/full},
	author = {Palacio, Antonio S. and Cabello, Ana Mar{\'\i}a and Garc{\'\i}a, Francisca C. and Labban, Abbrar and Mor{\'a}n, Xos{\'e} Anxelu G. and Garczarek, Laurence and Alonso-S{\'a}ez, Laura and L{\'o}pez-Urrutia, {\'A}ngel}
}
@article {Mucko2020,
	title = {Characterization of a lipid-producing thermotolerant marine photosynthetic pico-alga in the genus Picochlorum (Trebouxiophyceae)},
	journal = {European Journal of Phycology},
	volume = {00},
	number = {00},
	year = {2020},
	note = {Publisher: Taylor \& Francis tex.mendeley-tags: RCC1034,RCC13,RCC14,RCC289,RCC475,RCC6905,RCC846,RCC9,RCC945},
	month = {aug},
	pages = {1{\textendash}16},
	keywords = {morphology, photosynthetic picoeukaryotes, phylogeny, physiology, Picochlorum, RCC1034, RCC13, RCC14, rcc289, RCC475, RCC6905, RCC846, RCC9, RCC945},
	issn = {0967-0262},
	doi = {10.1080/09670262.2020.1757763},
	url = {https://doi.org/10.1080/09670262.2020.1757763 https://www.tandfonline.com/doi/full/10.1080/09670262.2020.1757763},
	author = {Mucko, Maja and Padis{\'a}k, Judit and Gligora Udovi{\v c}, Marija and P{\'a}lmai, Tam{\'a}s and Novak, Tihana and Medi{\'c}, Nikola and Ga{\v s}parovi{\'c}, Bla{\v z}enka and Peharec {\v S}tefani{\'c}, Petra and Orli{\'c}, Sandi and Ljube{\v s}i{\'c}, Zrinka}
}
@article {Cai2020,
	title = {Cryptic species in the parasitic Amoebophrya species complex revealed by a polyphasic approach},
	journal = {Scientific Reports},
	volume = {10},
	number = {1},
	year = {2020},
	note = {Publisher: Springer US tex.mendeley-tags: RCC1627,RCC1720,RCC3018,RCC3043,RCC3044,RCC3047,RCC3048,RCC3049,RCC3145,RCC3278,RCC3596,RCC4381,RCC4382,RCC4383,RCC4384,RCC4385,RCC4386,RCC4387,RCC4388,RCC4389,RCC4390,RCC4391,RCC4392,RCC4393,RCC4394,RCC4395,RCC4396,RCC4397,RCC4398,RCC4399,RCC4400,RCC4401,RCC4402,RCC4403,RCC4404,RCC4405,RCC4406,RCC4407,RCC4408,RCC4409,RCC4410,RCC4411,RCC4412,RCC4413,RCC4414,RCC4415,RCC4416,RCC4711,RCC4712,RCC4713,RCC4715,RCC4716,RCC4722,RCC4723,RCC4726,RCC4728,RCC4729,RCC4732,RCC4733,RCC4734,RCC5984,RCC5985,RCC5986,RCC5987,RCC5988,RCC5989,RCC5990,RCC5991,RCC5992,RCC5993,RCC5994,RCC5995,RCC5997,RCC5998,RCC5999,RCC6000,RCC6001,RCC6002,RCC6003,RCC6004,RCC6005,RCC6006,RCC6007,RCC6008,RCC6009,RCC6010,RCC6079,RCC6080,RCC6081,RCC6082,RCC6083,RCC6084,RCC6085,RCC6087,RCC6088,RCC6094,RCC6096,RCC6100,RCC6101,RCC6102,RCC6103,RCC6104,RCC6105,RCC6106,RCC6107,RCC6108,RCC6109,RCC6110,RCC6111,RCC6112,RCC6113,RCC6115,RCC6116,RCC6117,RCC6118,RCC6119,RCC6120,RCC6121},
	month = {dec},
	pages = {2531},
	keywords = {RCC1627, RCC1720, RCC3018, RCC3043, RCC3044, RCC3047, RCC3048, RCC3049, RCC3145, RCC3278, RCC3596, RCC4381, RCC4382, RCC4383, RCC4384, RCC4385, RCC4386, RCC4387, RCC4388, RCC4389, RCC4390, RCC4391, RCC4392, RCC4393, RCC4394, RCC4395, RCC4396, RCC4397, RCC4398, RCC4399, RCC4400, RCC4401, RCC4402, RCC4403, RCC4404, RCC4405, RCC4406, RCC4407, RCC4408, RCC4409, RCC4410, RCC4411, RCC4412, RCC4413, RCC4414, RCC4415, RCC4416, RCC4711, RCC4712, RCC4713, RCC4715, RCC4716, RCC4722, RCC4723, RCC4726, RCC4728, RCC4729, RCC4732, RCC4733, RCC4734, RCC5984, RCC5985, RCC5986, RCC5987, RCC5988, RCC5989, RCC5990, RCC5991, RCC5992, RCC5993, RCC5994, RCC5995, RCC5997, RCC5998, RCC5999, RCC6000, RCC6001, RCC6002, RCC6003, RCC6004, RCC6005, RCC6006, RCC6007, RCC6008, RCC6009, RCC6010, RCC6079, RCC6080, RCC6081, RCC6082, RCC6083, RCC6084, RCC6085, RCC6087, RCC6088, RCC6094, RCC6096, RCC6100, RCC6101, RCC6102, RCC6103, RCC6104, RCC6105, RCC6106, RCC6107, RCC6108, RCC6109, RCC6110, RCC6111, RCC6112, RCC6113, RCC6115, RCC6116, RCC6117, RCC6118, RCC6119, RCC6120, RCC6121},
	issn = {2045-2322},
	doi = {10.1038/s41598-020-59524-z},
	url = {http://dx.doi.org/10.1038/s41598-020-59524-z http://www.nature.com/articles/s41598-020-59524-z},
	author = {Cai, Ruibo and Kayal, Ehsan and Alves-de-Souza, Catharina and Bigeard, Estelle and Corre, Erwan and Jeanthon, Christian and Marie, Dominique and Porcel, Betina M and Siano, Raffaele and Szymczak, Jeremy and Wolf, Matthias and Guillou, Laure}
}
@article {Ribeiro2020,
	title = {Culturable diversity of Arctic phytoplankton during pack ice melting},
	journal = {Elementa: Science of the Anthropocene},
	volume = {8},
	number = {1},
	year = {2020},
	note = {tex.mendeley-tags: RCC5197,RCC5198,RCC5199,RCC5200,RCC5201,RCC5202,RCC5203,RCC5204,RCC5205,RCC5206,RCC5207,RCC5208,RCC5209,RCC5210,RCC5211,RCC5212,RCC5213,RCC5214,RCC5215,RCC5216,RCC5217,RCC5218,RCC5219,RCC5220,RCC5221,RCC5222,RCC5223,RCC5224,RCC5225,RCC5226,RCC5227,RCC5228,RCC5229,RCC5230,RCC5231,RCC5232,RCC5233,RCC5234,RCC5235,RCC5236,RCC5237,RCC5238,RCC5239,RCC5240,RCC5241,RCC5242,RCC5243,RCC5244,RCC5245,RCC5246,RCC5247,RCC5248,RCC5249,RCC5250,RCC5251,RCC5252,RCC5253,RCC5254,RCC5255,RCC5256,RCC5257,RCC5258,RCC5259,RCC5260,RCC5261,RCC5262,RCC5263,RCC5264,RCC5265,RCC5266,RCC5267,RCC5268,RCC5269,RCC5270,RCC5271,RCC5272,RCC5273,RCC5274,RCC5275,RCC5276,RCC5277,RCC5278,RCC5279,RCC5280,RCC5281,RCC5282,RCC5283,RCC5284,RCC5285,RCC5286,RCC5287,RCC5288,RCC5289,RCC5290,RCC5291,RCC5292,RCC5293,RCC5294,RCC5295,RCC5296,RCC5297,RCC5298,RCC5299,RCC5300,RCC5301,RCC5302,RCC5303,RCC5304,RCC5305,RCC5306,RCC5307,RCC5308,RCC5309,RCC5310,RCC5311,RCC5312,RCC5313,RCC5314,RCC5315,RCC5316,RCC5317,RCC5318,RCC5319,RCC5320,RCC5321,RCC5322,RCC5323,RCC5324,RCC5325,RCC5326,RCC5327,RCC5328,RCC5329,RCC5330,RCC5331,RCC5332,RCC5333,RCC5334,RCC5335,RCC5336,RCC5337,RCC5338,RCC5339,RCC5340,RCC5341,RCC5342,RCC5343,RCC5344,RCC5345,RCC5346,RCC5347,RCC5348,RCC5349,RCC5350,RCC5351,RCC5352,RCC5353,RCC5354,RCC5355,RCC5356,RCC5357,RCC5358,RCC5359,RCC5360,RCC5361,RCC5362,RCC5363,RCC5364,RCC5365,RCC5366,RCC5367,RCC5368,RCC5369,RCC5370,RCC5371,RCC5372,RCC5373,RCC5374,RCC5375,RCC5376,RCC5377,RCC5378,RCC5379,RCC5380,RCC5381,RCC5382,RCC5383,RCC5384,RCC5385,RCC5386,RCC5387,RCC5388,RCC5389,RCC5390,RCC5391,RCC5392,RCC5393,RCC5394,RCC5395,RCC5396,RCC5397,RCC5398,RCC5399,RCC5400,RCC5401,RCC5402,RCC5403,RCC5404,RCC5405,RCC5406,RCC5407,RCC5408,RCC5409,RCC5410,RCC5411,RCC5412,RCC5413,RCC5414,RCC5415,RCC5416,RCC5417,RCC5418,RCC5419,RCC5420,RCC5421,RCC5422,RCC5423,RCC5424,RCC5425,RCC5426,RCC5427,RCC5428,RCC5429,RCC5430,RCC5431,RCC5432,RCC5433,RCC5434,RCC5435,RCC5436,RCC5437,RCC5438,RCC5439,RCC5440,RCC5441,RCC5442,RCC5443,RCC5444,RCC5445,RCC5446,RCC5447,RCC5448,RCC5449,RCC5450,RCC5451,RCC5452,RCC5453,RCC5454,RCC5455,RCC5456,RCC5457,RCC5458,RCC5459,RCC5460,RCC5461,RCC5462,RCC5463,RCC5464,RCC5465,RCC5466,RCC5467,RCC5468,RCC5469,RCC5470,RCC5471,RCC5472,RCC5473,RCC5474,RCC5475,RCC5476,RCC5477,RCC5478,RCC5479,RCC5480,RCC5481,RCC5482,RCC5483,RCC5484,RCC5485,RCC5486,RCC5487,RCC5488,RCC5489,RCC5490,RCC5491,RCC5492,RCC5493,RCC5494,RCC5495,RCC5496,RCC5497,RCC5498,RCC5499,RCC5500,RCC5501,RCC5502,RCC5503,RCC5504,RCC5505,RCC5506,RCC5507,RCC5508,RCC5509,RCC5510,RCC5511,RCC5512,RCC5513,RCC5514,RCC5515,RCC5516,RCC5517,RCC5518,RCC5519,RCC5520,RCC5521,RCC5522,RCC5523,RCC5524,RCC5525,RCC5526,RCC5527,RCC5528,RCC5529,RCC5530,RCC5531,RCC5532,RCC5533,RCC5534,RCC5535,RCC5536,RCC5537,RCC5538,RCC5539,RCC5540,RCC5541,RCC5542,RCC5543,RCC5544,RCC5545,RCC5546,RCC5547,RCC5548,RCC5549,RCC5550,RCC5551,RCC5552,RCC5553,RCC5554,RCC5555,RCC5556,RCC5557,RCC5558,RCC5559,RCC5560,RCC5561,RCC5562,RCC5563,RCC5564,RCC5565,RCC5566,RCC5567,RCC5568,RCC5569,RCC5570,RCC5571,RCC5572,RCC5573,RCC5574,RCC5575,RCC5576,RCC5577,RCC5578,RCC5579,RCC5580,RCC5581,RCC5582,RCC5583,RCC5584,RCC5585,RCC5586,RCC5587,RCC5588,RCC5589,RCC5590,RCC5591,RCC5592,RCC5593,RCC5594,RCC5595,RCC5596,RCC5597,RCC5598,RCC5599,RCC5600,RCC5601,RCC5602,RCC5603,RCC5604,RCC5605,RCC5606,RCC5607,RCC5608,RCC5609,RCC5610,RCC5611,RCC5612},
	month = {feb},
	pages = {6},
	abstract = {Massive phytoplankton blooms develop at the Arctic ice edge, sometimes extending far under the pack ice. An extensive culturing effort was conducted before and during a phytoplankton bloom in Baffin Bay between April and July 2016. Different isolation strategies were applied, including flow cytometry cell sorting, manual single cell pipetting and serial dilution. Although all three techniques yielded the most common organisms, each technique retrieved specific taxa, highlighting the importance of using several methods to maximize the number and diversity of isolated strains. More than 1,000 cultures were obtained, characterized by 18S rRNA sequencing and optical microscopy and de-replicated to a subset of 276 strains presented in this work. Strains grouped into 57 genotypes defined by 100\% 18S rRNA sequence similarity. These genotypes spread across five divisions: Heterokontophyta, Chlorophyta, Cryptophyta, Haptophyta and Dinophyta. Diatoms were the most abundant group (193 strains), mostly represented by the genera Chaetoceros and Attheya. The genera Rhodomonas and Pyramimonas were the most abundant non-diatom nanoplankton strains, while Micromonas polaris dominated the picoplankton. Diversity at the class level was higher during the peak of the bloom. Potentially new species were isolated, in particular within the genera Navicula, Nitzschia, Coscinodiscus, Thalassiosira, Pyramimonas, Mantoniella and Isochrysis.},
	keywords = {RCC5197, RCC5198, RCC5199, RCC5200, RCC5201, RCC5202, RCC5203, RCC5204, RCC5205, RCC5206, RCC5207, RCC5208, RCC5209, RCC5210, RCC5211, RCC5212, RCC5213, RCC5214, RCC5215, RCC5216, RCC5217, RCC5218, RCC5219, RCC5220, RCC5221, RCC5222, RCC5223, RCC5224, RCC5225, RCC5226, RCC5227, RCC5228, RCC5229, RCC5230, RCC5231, RCC5232, RCC5233, RCC5234, RCC5235, RCC5236, RCC5237, RCC5238, RCC5239, RCC5240, RCC5241, RCC5242, RCC5243, RCC5244, RCC5245, RCC5246, RCC5247, RCC5248, RCC5249, RCC5250, RCC5251, RCC5252, RCC5253, RCC5254, RCC5255, RCC5256, RCC5257, RCC5258, RCC5259, RCC5260, RCC5261, RCC5262, RCC5263, RCC5264, RCC5265, RCC5266, RCC5267, RCC5268, RCC5269, RCC5270, RCC5271, RCC5272, RCC5273, RCC5274, RCC5275, RCC5276, RCC5277, RCC5278, RCC5279, RCC5280, RCC5281, RCC5282, RCC5283, RCC5284, RCC5285, RCC5286, RCC5287, RCC5288, RCC5289, RCC5290, RCC5291, RCC5292, RCC5293, RCC5294, RCC5295, RCC5296, RCC5297, RCC5298, RCC5299, RCC5300, RCC5301, RCC5302, RCC5303, RCC5304, RCC5305, RCC5306, RCC5307, RCC5308, RCC5309, RCC5310, RCC5311, RCC5312, RCC5313, RCC5314, RCC5315, RCC5316, RCC5317, RCC5318, RCC5319, RCC5320, RCC5321, RCC5322, RCC5323, RCC5324, RCC5325, RCC5326, RCC5327, RCC5328, RCC5329, RCC5330, RCC5331, RCC5332, RCC5333, RCC5334, RCC5335, RCC5336, RCC5337, RCC5338, RCC5339, RCC5340, RCC5341, RCC5342, RCC5343, RCC5344, RCC5345, RCC5346, RCC5347, RCC5348, RCC5349, RCC5350, RCC5351, RCC5352, RCC5353, RCC5354, RCC5355, RCC5356, RCC5357, RCC5358, RCC5359, RCC5360, RCC5361, RCC5362, RCC5363, RCC5364, RCC5365, RCC5366, RCC5367, RCC5368, RCC5369, RCC5370, RCC5371, RCC5372, RCC5373, RCC5374, RCC5375, RCC5376, RCC5377, RCC5378, RCC5379, RCC5380, RCC5381, RCC5382, RCC5383, RCC5384, RCC5385, RCC5386, RCC5387, RCC5388, RCC5389, RCC5390, RCC5391, RCC5392, RCC5393, RCC5394, RCC5395, RCC5396, RCC5397, RCC5398, RCC5399, RCC5400, RCC5401, RCC5402, RCC5403, RCC5404, RCC5405, RCC5406, RCC5407, RCC5408, RCC5409, RCC5410, RCC5411, RCC5412, RCC5413, RCC5414, RCC5415, RCC5416, RCC5417, RCC5418, RCC5419, RCC5420, RCC5421, RCC5422, RCC5423, RCC5424, RCC5425, RCC5426, RCC5427, RCC5428, RCC5429, RCC5430, RCC5431, RCC5432, RCC5433, RCC5434, RCC5435, RCC5436, RCC5437, RCC5438, RCC5439, RCC5440, RCC5441, RCC5442, RCC5443, RCC5444, RCC5445, RCC5446, RCC5447, RCC5448, RCC5449, RCC5450, RCC5451, RCC5452, RCC5453, RCC5454, RCC5455, RCC5456, RCC5457, RCC5458, RCC5459, RCC5460, RCC5461, RCC5462, RCC5463, RCC5464, RCC5465, RCC5466, RCC5467, RCC5468, RCC5469, RCC5470, RCC5471, RCC5472, RCC5473, RCC5474, RCC5475, RCC5476, RCC5477, RCC5478, RCC5479, RCC5480, RCC5481, RCC5482, RCC5483, RCC5484, RCC5485, RCC5486, RCC5487, RCC5488, RCC5489, RCC5490, RCC5491, RCC5492, RCC5493, RCC5494, RCC5495, RCC5496, RCC5497, RCC5498, RCC5499, RCC5500, RCC5501, RCC5502, RCC5503, RCC5504, RCC5505, RCC5506, RCC5507, RCC5508, RCC5509, RCC5510, RCC5511, RCC5512, RCC5513, RCC5514, RCC5515, RCC5516, RCC5517, RCC5518, RCC5519, RCC5520, RCC5521, RCC5522, RCC5523, RCC5524, RCC5525, RCC5526, RCC5527, RCC5528, RCC5529, RCC5530, RCC5531, RCC5532, RCC5533, RCC5534, RCC5535, RCC5536, RCC5537, RCC5538, RCC5539, RCC5540, RCC5541, RCC5542, RCC5543, RCC5544, RCC5545, RCC5546, RCC5547, RCC5548, RCC5549, RCC5550, RCC5551, RCC5552, RCC5553, RCC5554, RCC5555, RCC5556, RCC5557, RCC5558, RCC5559, RCC5560, RCC5561, RCC5562, RCC5563, RCC5564, RCC5565, RCC5566, RCC5567, RCC5568, RCC5569, RCC5570, RCC5571, RCC5572, RCC5573, RCC5574, RCC5575, RCC5576, RCC5577, RCC5578, RCC5579, RCC5580, RCC5581, RCC5582, RCC5583, RCC5584, RCC5585, RCC5586, RCC5587, RCC5588, RCC5589, RCC5590, RCC5591, RCC5592, RCC5593, RCC5594, RCC5595, RCC5596, RCC5597, RCC5598, RCC5599, RCC5600, RCC5601, RCC5602, RCC5603, RCC5604, RCC5605, RCC5606, RCC5607, RCC5608, RCC5609, RCC5610, RCC5611, RCC5612},
	issn = {2325-1026},
	doi = {10.1525/elementa.401},
	url = {https://www.biorxiv.org/content/10.1101/642264v1 https://www.elementascience.org/article/10.1525/elementa.401/},
	author = {Ribeiro, Catherine G{\'e}rikas and dos Santos, Adriana Lopes and Gourvil, Priscillia and Le Gall, Florence and Marie, Dominique and Tragin, Margot and Probert, Ian and Vaulot, Daniel}
}
@article {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 {Fitzsimons2020,
	title = {Dissolved organic phosphorus uptake by marine phytoplankton is enhanced by the presence of dissolved organic nitrogen},
	journal = {Journal of Experimental Marine Biology and Ecology},
	volume = {530-531},
	number = {July},
	year = {2020},
	note = {Publisher: Elsevier tex.mendeley-tags: RC2563,RCC2565},
	month = {sep},
	pages = {151434},
	abstract = {Organic nutrients can constitute the major fractions (up to 70\%) of aquatic nitrogen (N) and phosphorus (P), but their cycling is poorly understood relative to the inorganic pools. Some phytoplankton species access P from the dissolved organic phosphorus (DOP) pool through expression of alkaline phosphatase (AP), which hydrolyses orthophosphate from organic molecules, and is thought to occur either at low concentrations of dissolved inorganic P (DIP), or elevated ratios of dissolved inorganic N (DIN) to DIP. Three algal strains native to the North-East Atlantic Ocean (coccolithophore, dinoflagellate and diatom species) were grown under representative, temperate conditions, and the dissolved N and P components amended to include dissolved organic N (DON) and DOP. The activity of AP was measured to determine the rate of DOP uptake by each algal species. The addition of DON and DOP enhanced the growth of the algal species, regardless of DIN and DIP concentrations. In cultures where the total concentrations and absolute N: P ratio was unchanged but the N pool included both DON and DIN, an increase in alkaline phosphatase activity (APA) was measured. This suggested that the presence of DON triggered the selective uptake of DOP. The uptake of organic P was confirmed by detection of adenosine in DOP-amended culture media, indicating that P had been cleaved from ADP and ATP added to the media as DOP, and cellular P concentration in these cultures exceeded the calculated concentration based on uptake of DIP only. Our data demonstrates that organic nutrients can enhance and sustain marine algal productivity. The findings have implications for marine ecosystem function and health, since climate change scenarios predict variable riverine inputs to coastal areas, altered N: P ratios, and changes in the inorganic to organic balance of the nutrient pools.},
	keywords = {Alkaline phosphatase, COASTAL WATERS, Dissolved organic nitrogen, Dissolved organic phosphorus, Marine algae, P-limitation, RCC2563, RCC2565},
	issn = {00220981},
	doi = {10.1016/j.jembe.2020.151434},
	url = {https://doi.org/10.1016/j.jembe.2020.151434 https://linkinghub.elsevier.com/retrieve/pii/S0022098119304666},
	author = {Fitzsimons, Mark F. and Probert, Ian and Gaillard, Fanny and Rees, Andrew P.}
}
@article {Coelho2020,
	title = {Ectocarpus: an evo-devo model for the brown algae},
	journal = {EvoDevo},
	volume = {11},
	number = {1},
	year = {2020},
	note = {ISBN: 1322702000164 Publisher: BioMed Central},
	month = {dec},
	pages = {19},
	keywords = {Brown algae, complex, Complex multicellularity, cycle, Ectocarpus, ectocarpus is a genus, filamentous, Gametophyte, life-cycle, Marine, multicellu-, multicellularity, natural habitat and life, of small, Phaeoviruses, Sex determination, Sporophyte},
	issn = {2041-9139},
	doi = {10.1186/s13227-020-00164-9},
	url = {https://doi.org/10.1186/s13227-020-00164-9 https://evodevojournal.biomedcentral.com/articles/10.1186/s13227-020-00164-9},
	author = {Coelho, Susana M and Peters, Akira F and M{\"u}ller, Dieter and Cock, J Mark}
}
@article {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 {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 {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 {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 {Langer2020,
	title = {Li partitioning into coccoliths of Emiliania huxleyi : evaluating the general role of {\textquotedblleft}vital effects{\textquotedblright} in explaining element partitioning in biogenic carbonates},
	journal = {Geochemistry, Geophysics, Geosystems},
	year = {2020},
	note = {ISBN: 0000000272 tex.mendeley-tags: RCC3652},
	month = {jun},
	pages = {0{\textendash}2},
	abstract = {Abstract Emiliania huxleyi cells were grown in artificial seawater of different Li and Ca concentrations and coccolith Li/Ca ratios determined. Coccolith Li/Ca ratios were positively correlated to seawater Li/Ca ratios only if the seawater Li concentration was changed, not if the seawater Ca concentration was changed. This Li partitioning pattern of E. huxleyi was previously also observed in the benthic foraminifer Amphistegina lessonii and inorganically precipitated calcite. We argue that Li partitioning in both E. huxleyi and A. lessonii is dominated by a coupled transmembrane transport of Li and Ca from seawater to the site of calcification. We present a refined version of a recently proposed transmembrane transport model for Li and Ca. The model assumes that Li and Ca enter the cell via Ca channels, the Li flux being dependent on the Ca flux. While the original model features a linear function to describe the experimental data, our refined version uses a power function, changing the stoichiometry of Li and Ca. The version presented here accurately predicts the observed dependence of DLi on seawater Li/Ca ratios. Our data demonstrate that minor element partitioning in calcifying organisms is partly mediated by biological processes even if the partitioning behaviour of the calcifying organism is indistinguishable from that of inorganically precipitated calcium carbonate.},
	keywords = {RCC3652},
	issn = {1525-2027},
	doi = {10.1029/2020GC009129},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1029/2020GC009129},
	author = {Langer, Gerald and Sadekov, Aleksey and Greaves, Mervyn and Nehrke, Gernot and Probert, Ian and Misra, Sambuddha and Thoms, Silke}
}
@article {Stettin2020,
	title = {Metabolomics benefits from orbitrap GC{\textendash}MS{\textemdash}Comparison of low- and high-resolution GC{\textendash}MS},
	journal = {Metabolites},
	volume = {10},
	number = {4},
	year = {2020},
	note = {tex.mendeley-tags: RCC75},
	month = {apr},
	pages = {143},
	abstract = {The development of improved mass spectrometers and supporting computational tools is expected to enable the rapid annotation of whole metabolomes. Essential for the progress is the identification of strengths and weaknesses of novel instrumentation in direct comparison to previous instruments. Orbitrap liquid chromatography (LC){\textendash}mass spectrometry (MS) technology is now widely in use, while Orbitrap gas chromatography (GC){\textendash}MS introduced in 2015 has remained fairly unexplored in its potential for metabolomics research. This study aims to evaluate the additional knowledge gained in a metabolomics experiment when using the high-resolution Orbitrap GC{\textendash}MS in comparison to a commonly used unit-mass resolution single-quadrupole GC{\textendash}MS. Samples from an osmotic stress treatment of a non-model organism, the microalga Skeletonema costatum, were investigated using comparative metabolomics with low- and high-resolution methods. Resulting datasets were compared on a statistical level and on the level of individual compound annotation. Both MS approaches resulted in successful classification of stressed vs. non-stressed microalgae but did so using different sets of significantly dysregulated metabolites. High-resolution data only slightly improved conventional library matching but enabled the correct annotation of an unknown. While computational support that utilizes high-resolution GC{\textendash}MS data is still underdeveloped, clear benefits in terms of sensitivity, metabolic coverage, and support in structure elucidation of the Orbitrap GC{\textendash}MS technology for metabolomics studies are shown here.},
	keywords = {Comparative metabolomics, Diatom, High-resolution mass spectrometry (HRMS), Instrument comparison, Mass Spectrometry (Orbitrap GC-MS), Metabolite identification, Orbitrap Gas Chromatography, Osmotic stress, RCC75},
	issn = {2218-1989},
	doi = {10.3390/metabo10040143},
	url = {https://www.mdpi.com/2218-1989/10/4/143},
	author = {Stettin, Daniel and Poulin, Remington X. and Pohnert, Georg}
}
@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 {Gebser2020,
	title = {Phytoplankton-derived zwitterionic gonyol and dimethylsulfonioacetate interfere with microbial dimethylsulfoniopropionate sulfur cycling},
	journal = {MicrobiologyOpen},
	number = {February},
	year = {2020},
	note = {tex.mendeley-tags: RCC1731,RCC75,RCC76RCC1217,RCC841},
	month = {feb},
	pages = {e1014},
	keywords = {rcc1217, rcc1731, RCC75, RCC76, RCC841, school of life sciences, university of essex},
	issn = {20458827},
	doi = {10.1002/mbo3.1014},
	url = {http://doi.wiley.com/10.1002/mbo3.1014},
	author = {Gebser, Bj{\"o}rn and Thume, Kathleen and Steinke, Michael and Pohnert, Georg}
}
@article {Aveiro2020,
	title = {The polar lipidome of cultured emiliania huxleyi: A source of bioactive lipids with relevance for biotechnological applications},
	journal = {Biomolecules},
	volume = {10},
	number = {10},
	year = {2020},
	note = {tex.ids= Aveiro2020a tex.mendeley-tags: RCC1250 publisher: Multidisciplinary Digital Publishing Institute},
	pages = {1434},
	abstract = {Polar lipids from microalgae have aroused greater interest as a natural source of omega-3 (n-3) polyunsaturated fatty acids (PUFA), an alternative to fish, but also as bioactive compounds with multiple applications. The present study aims to characterize the polar lipid profile of cultured microalga Emiliania huxleyi using hydrophilic interaction liquid chromatography coupled with high-resolution mass spectrometry (HILIC{\textendash}MS) and fatty acids (FA) analysis by gas chromatography (GC{\textendash}MS). The lipidome of E. huxleyi revealed the presence of distinct n-3 PUFA (40\% of total FA), namely docosahexaenoic acid (22:6n-3) and stearidonic acid (18:4n-3), which give this microalga an increased commercial value as a source of n-3 PUFA present in the form of polar lipids. A total of 134 species of polar lipids were identified and some of these species, particularly glycolipids, have already been reported for their bioactive properties. Among betaine lipids, the diacylglyceryl carboxyhydroxymethylcholine (DGCC) class is the least reported in microalgae. For the first time, monomethylphosphatidylethanolamine (MMPE) has been found in the lipidome of E. huxleyi. Overall, this study highlights the potential of E. huxleyi as a sustainable source of high-value polar lipids that can be exploited for different applications, namely human and animal nutrition, cosmetics, and pharmaceuticals.},
	keywords = {Emiliania huxleyi, haptophyta, Lipidomics, Mass spectrometry, Microalgae, RCC1250},
	issn = {2218-273X},
	doi = {10.3390/biom10101434},
	url = {https://www.mdpi.com/2218-273X/10/10/1434},
	author = {Aveiro, Susana S. and Melo, T{\^a}nia and Figueiredo, Ana and Domingues, Pedro and Pereira, Hugo and Maia, In{\^e}s B. and Silva, Joana and Domingues, M. Ros{\'a}rio and Nunes, Cl{\'a}udia and Moreira, Ana S. P.}
}
@article {Avilan2020,
	title = {ppGpp influences protein protection, growth and photosynthesis in Phaeodactylum tricornutum},
	journal = {bioRxiv},
	year = {2020},
	note = {Publisher: Cold Spring Harbor Laboratory tex.mendeley-tags: RCC2967},
	month = {mar},
	pages = {2020.03.05.978130},
	abstract = {{\textbullet} Chloroplasts retain elements of a bacterial stress response pathway that is mediated by the signalling nucleotides guanosine penta-and tetraphosphate, or (p)ppGpp. In the model flowering plant Arabidopsis, ppGpp acts as a potent regulator of plastid gene expression and influences photosynthesis, plant growth and development. However, little is known about ppGpp metabolism or its evolution in other photosynthetic eukaryotes. {\textbullet} Here, we studied the function of ppGpp in the diatom P. tricornutum using transgenic lines containing an inducible system for ppGpp accumulation. We used these lines to investigate the effects of ppGpp on growth, photosynthesis, lipid metabolism and protein expression. {\textbullet} We demonstrate that ppGpp accumulation reduces photosynthetic capacity and promotes a quiescent-like state with reduced proliferation and ageing. Strikingly, using non-targeted proteomics, we discovered that ppGpp accumulation also leads to the coordinated upregulation of a protein protection response in multiple cellular compartments. {\textbullet} Our findings highlight the importance of ppGpp as a fundamental regulator of chloroplast function across different domains of life, and lead to new questions about the molecular mechanisms and roles of (p)ppGpp signalling in photosynthetic eukaryotes.},
	keywords = {chloroplast, diatoms, lipid droplets, Phaeodactylum tricornutum, Photosynthesis, ppGpp, proteome, RCC2967},
	doi = {10.1101/2020.03.05.978130},
	url = {https://doi.org/10.1101/2020.03.05.978130},
	author = {Avilan, Luisana and Lebrun, Regine and Puppo, Carine and Citerne, Sylvie and Cuin{\'e}, Stephane and Li-Beisson, Yonghua and Menand, Benoit and Field, Ben and Gontero, Brigitte}
}
@article {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 {Derilus2020,
	title = {Synergism between the Black Queen effect and the proteomic constraint on genome size reduction in the photosynthetic picoeukaryotes},
	journal = {Scientific Reports},
	volume = {10},
	number = {1},
	year = {2020},
	note = {Publisher: Springer US tex.mendeley-tags: RCC1110,RCC1116,RCC809},
	pages = {8918},
	keywords = {RCC1110, RCC1116, RCC809},
	issn = {2045-2322},
	doi = {10.1038/s41598-020-65476-1},
	url = {http://dx.doi.org/10.1038/s41598-020-65476-1 http://www.nature.com/articles/s41598-020-65476-1},
	author = {Derilus, D and Rahman, M Z and Pinero, F and Massey, S E}
}
@article {GerikasRibeiro2020,
	title = {Taxonomic reassignment of \textit{Pseudohaptolina birgeri comb. nov . (Haptophyta)},
	journal = {Phycologia},
	volume = {in press},
	year = {2020},
	note = {tex.mendeley-tags: RCC5268,RCC5270},
	month = {oct},
	pages = {1{\textendash}10},
	keywords = {RCC5268, RCC5270},
	issn = {0031-8884},
	doi = {10.1080/00318884.2020.1830255},
	url = {https://www.biorxiv.org/content/10.1101/2020.05.06.081489v1 https://www.tandfonline.com/doi/full/10.1080/00318884.2020.1830255},
	author = {G{\'e}rikas Ribeiro, Catherine and Lopes dos Santos, Adriana and Probert, Ian and Vaulot, Daniel and Edvardsen, Bente}
}
@article {Pollard2020,
	title = {A tunable 3D printed microfluidic resistive pulse sensor for the characterisation of algae and microplastics},
	journal = {ChemRxiv},
	year = {2020},
	note = {tex.mendeley-tags: RCC5374,RCC893},
	abstract = {Technologies that can detect and characterise particulates in liquids have applications in health, food and environmental monitoring. Here we present a low-cost and high-throughput multiuse counter that classifies a particle{\textquoteright}s size, concentration, porosity and shape. Using an additive manufacturing process, we have assembled a reusable flow resistive pulse sensor. The device remains stable for several days with repeat measurements. We demonstrate its use for characterising algae with spherical and rod structures as well as microplastics shed from teabags. We present a methodology that results in a specific signal for microplastics, namely a conductive pulse, in contrast to particles with smooth surfaces such as calibration particles or algae, allowing the presence of microplastics to be easily confirmed and quantified. In addition, the shape of the signal and particle are correlated, giving an extra physical property to characterise suspended particulates. The technology can rapidly screen volumes of liquid, 1 mL/ min, for the presence of microplastics and algae.},
	keywords = {RCC5374, RCC893},
	issn = {2187-4247},
	doi = {10.26434/chemrxiv.12249833.v1},
	author = {Pollard, M. and Hunsicker, E. and Platt, M.}
}
@article {Tisserand2020,
	title = {Use of organic exudates from two polar diatoms by bacterial isolates from the Arctic Ocean},
	journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences},
	volume = {378},
	number = {2181},
	year = {2020},
	note = {Publisher: NLM (Medline) tex.mendeley-tags: RCC2278,RCC4289},
	month = {oct},
	pages = {20190356},
	abstract = {Global warming affects primary producers in the Arctic, with potential consequences for the bacterial community composition through the consumption of microalgae-derived dissolved organic matter (DOM). To determine the degree of specificity in the use of an exudate by bacterial taxa, we used simple microalgae-bacteria model systems. We isolated 92 bacterial strains from the sea ice bottom and the water column in spring-summer in the Baffin Bay (Arctic Ocean). The isolates were grouped into 42 species belonging to Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes. Forty strains were tested for their capacity to grow on the exudate from two Arctic diatoms. Most of the strains tested (78\%) were able to grow on the exudate from the pelagic diatom Chaetoceros neogracilis, and 33\% were able to use the exudate from the sea ice diatom Fragilariopsis cylindrus. 17.5\% of the strains were not able to grow with any exudate, while 27.5\% of the strains were able to use both types of exudates. All strains belonging to Flavobacteriia (n = 10) were able to use the DOM provided by C. neogracilis, and this exudate sustained a growth capacity of up to 100 times higher than diluted Marine Broth medium, of two Pseudomonas sp. strains and one Sulfitobacter strain. The variable bioavailability of exudates to bacterial strains highlights the potential role of microalgae in shaping the bacterial community composition. This article is part of the theme issue {\textquoteright}The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystem functioning{\textquoteright}.},
	keywords = {Arctic Ocean, bacterial diversity, bacterial isolation, biodegradation, diatoms, dissolved organic exudates, RCC2278, RCC4289},
	issn = {14712962},
	doi = {10.1098/rsta.2019.0356},
	url = {https://royalsocietypublishing.org/doi/10.1098/rsta.2019.0356},
	author = {Tisserand, Lucas and Dadaglio, La{\"e}titia and Intertaglia, Laurent and Catala, Philippe and Panagiotopoulos, Christos and Obernosterer, Ingrid and Joux, Fabien}
}
@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 {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 {Sanfilippo2019,
	title = {Interplay between differentially expressed enzymes contributes to light color acclimation in marine Synechococcus},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {116},
	number = {13},
	year = {2019},
	note = {tex.mendeley-tags: RCC1086,RCC2035,RCC2380,RCC2382,RCC2385,RCC2433,RCC2437,RCC2528,RCC2533,RCC2534,RCC2535,RCC2571,RCC2673,RCC28,RCC307,RCC328,RCC515,RCC555,RCC791},
	month = {mar},
	pages = {6457{\textendash}6462},
	abstract = {Marine Synechococcus , a globally important group of cyanobacteria, thrives in various light niches in part due to its varied photosynthetic light-harvesting pigments. Many Synechococcus strains use a process known as chromatic acclimation to optimize the ratio of two chromophores, green-light{\textendash}absorbing phycoerythrobilin (PEB) and blue-light{\textendash}absorbing phycourobilin (PUB), within their light-harvesting complexes. A full mechanistic understanding of how Synechococcus cells tune their PEB to PUB ratio during chromatic acclimation has not yet been obtained. Here, we show that interplay between two enzymes named MpeY and MpeZ controls differential PEB and PUB covalent attachment to the same cysteine residue. MpeY attaches PEB to the light-harvesting protein MpeA in green light, while MpeZ attaches PUB to MpeA in blue light. We demonstrate that the ratio of mpeY to mpeZ mRNA determines if PEB or PUB is attached. Additionally, strains encoding only MpeY or MpeZ do not acclimate. Examination of strains of Synechococcus isolated from across the globe indicates that the interplay between MpeY and MpeZ uncovered here is a critical feature of chromatic acclimation for marine Synechococcus worldwide.},
	keywords = {RCC1086, RCC2035, rcc2380, rcc2382, RCC2385, RCC2433, RCC2437, RCC2528, RCC2533, RCC2534, RCC2535, RCC2571, RCC2673, RCC28, RCC307, RCC328, RCC515, rcc555, rcc791},
	issn = {0027-8424},
	doi = {10.1073/pnas.1810491116},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1810491116},
	author = {Sanfilippo, Joseph E. and Nguyen, Adam A. and Garczarek, Laurence and Karty, Jonathan A. and Pokhrel, Suman and Strnat, Johann A. and Partensky, Fr{\'e}d{\'e}ric and Schluchter, Wendy M. and Kehoe, David M.}
}
@article {Iglesias2019,
	title = {NMR characterization and evaluation of antibacterial and antiobiofilm activity of organic extracts from stationary phase batch cultures of five marine microalgae (Dunaliella sp., D. salina, Chaetoceros calcitrans, C. gracilis and Tisochrysis lutea)},
	journal = {Phytochemistry},
	volume = {164},
	number = {April},
	year = {2019},
	note = {Publisher: Elsevier tex.mendeley-tags: RCC1349,RCC1811,RCC3579,RCC5,RCC5953},
	month = {aug},
	pages = {192{\textendash}205},
	keywords = {Antibacterial, Antibiofilm, Chaetoceros, Dunaliella, Metabolite identification, NMR, RCC1349, RCC1811, RCC3579, RCC5, RCC5953, Tisochrysis},
	issn = {00319422},
	doi = {10.1016/j.phytochem.2019.05.001},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0031942219300184},
	author = {Iglesias, Ma Jos{\'e} and Soengas, Raquel and Probert, Ian and Guilloud, Emilie and Gourvil, Priscillia and Mehiri, Mohamed and L{\'o}pez, Yuly and Cepas, Virginio and Guti{\'e}rrez-del-R{\'\i}o, Ignacio and Redondo-Blanco, Sa{\'u}l and Villar, Claudio J. and Lomb{\'o}, Felipe and Soto, Sara and Ortiz, Fernando L{\'o}pez}
}
@article {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 {Gaignard2019,
	title = {Screening of marine microalgae: Investigation of new exopolysaccharide producers},
	journal = {Algal Research},
	volume = {44},
	year = {2019},
	note = {tex.ids= Gaignard2019a tex.mendeley-tags: RCC1084,RCC1196,RCC1504,RCC1714,RCC1774,RCC1786,RCC1863,RCC1978,RCC1983,RCC2035,RCC232,RCC2350,RCC2352,RCC2368,RCC2380,RCC2381,RCC2383,RCC2436,RCC2558,RCC2598,RCC2608,RCC2614,RCC2624,RCC2638,RCC269,RCC2696,RCC2703,RCC2932,RCC3069,RCC3072,RCC3092,RCC3093,RCC3436,RCC3649,RCC377,RCC4094,RCC4438,RCC4555,RCC4621,RCC4631,RCC4657,RCC76,RCC775,RCC821,RCC97 publisher: Elsevier},
	month = {dec},
	pages = {101711},
	abstract = {Biopolymers, such as exopolysaccharides are widely exploited by industry as hydrocolloids (gelling, thickening agents) and biological agents (anti-inflammatory, anti-parasitic, antioxidant, etc.). In this study, 166 marine microalgae and cyanobacteria species have been screened in order to identify strains producing original exopolysaccharides. This screening allowed the highlighting of 45 positive strains. In a second time, the monosaccharide compositions from 20 EPS of them were determined by GC/MS and HPAEC-PAD. The results led to a discovery of 8 new genera of microalgae producing EPS, including polymers with a very original composition like richness in GlcA. Finally, a phylogenic tree has been contructed in order to assess the link between the phylogeny of microalgae and the global composition of their exopolymers, based on data obtained in this study and from the literature.},
	keywords = {rcc1084, RCC1196, RCC1504, RCC1714, RCC1774, RCC1786, RCC1863, RCC1978, RCC1983, RCC2035, RCC232, RCC2350, RCC2352, RCC2368, rcc2380, RCC2381, RCC2383, RCC2436, RCC2558, RCC2598, RCC2608, RCC2614, RCC2624, RCC2638, RCC269, RCC2696, RCC2703, RCC2932, RCC3069, RCC3072, RCC3092, RCC3093, RCC3436, RCC3649, RCC377, RCC4094, RCC4438, RCC4555, RCC4621, RCC4631, RCC4657, RCC76, RCC775, RCC821, RCC97},
	issn = {22119264},
	doi = {10.1016/j.algal.2019.101711},
	url = {https://www.sciencedirect.com/science/article/pii/S2211926419303261 https://linkinghub.elsevier.com/retrieve/pii/S2211926419303261},
	author = {Gaignard, C. and Laroche, C. and Pierre, G. and Dubessay, P. and Delattre, C. and Gardarin, C. and Gourvil, P. and Probert, I. and Dubuffet, A. and Michaud, P.}
}
@article {Breton2019,
	title = {Unveiling membrane thermoregulation strategies in marine picocyanobacteria},
	journal = {New Phytologist},
	number = {July},
	year = {2019},
	note = {ISBN: 0000000244022 tex.mendeley-tags: RCC2374,RCC2385,RCC515,RCC539},
	month = {oct},
	pages = {nph.16239},
	keywords = {RCC2374, RCC2385, RCC515, rcc539},
	issn = {0028-646X},
	doi = {10.1111/nph.16239},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.16239},
	author = {Breton, Sol{\`e}ne and Jouhet, Juliette and Guyet, Ulysse and Gros, Val{\'e}rie and Pittera, Justine and Demory, David and Partensky, Fr{\'e}d{\'e}ric and Dor{\'e}, Hugo and Ratin, Morgane and Mar{\'e}chal, {\'E}ric and Nguyen, Ngoc An and Garczarek, Laurence and Six, Christophe}
}
@article {Pierre2019,
	title = {What is in store for EPS microalgae in the next decade?},
	journal = {Molecules},
	volume = {24},
	number = {23},
	year = {2019},
	month = {nov},
	pages = {4296},
	abstract = {Microalgae and their metabolites have been an El Dorado since the turn of the 21st century. Many scientific works and industrial exploitations have thus been set up. These developments have often highlighted the need to intensify the processes for biomass production in photo-autotrophy and exploit all the microalgae value including ExoPolySaccharides (EPS). Indeed, the bottlenecks limiting the development of low value products from microalgae are not only linked to biology but also to biological engineering problems including harvesting, recycling of culture media, photoproduction, and biorefinery. Even respecting the so-called {\textquotedblleft}Biorefinery Concept{\textquotedblright}, few applications had a chance to emerge and survive on the market. Thus, exploiting EPS from microalgae for industrial applications in some low-value markets such as food is probably not a mature proposition considering the competitiveness of polysaccharides from terrestrial plants, macroalgae, and bacteria. However, it does not imply drawing a line on their uses but rather {\textquotedblleft}thinking them{\textquotedblright} differently. This review provides insights into microalgae, EPS, and their exploitation. Perspectives on issues affecting the future of EPS microalgae are also addressed with a critical point of view.},
	keywords = {application, eps, exopolysaccharides, market, Microalgae},
	issn = {1420-3049},
	doi = {10.3390/molecules24234296},
	url = {https://www.mdpi.com/1420-3049/24/23/4296},
	author = {Pierre, Guillaume and Delattre, C{\'e}dric and Dubessay, Pascal and Jubeau, S{\'e}bastien and Vialleix, Carole and Cadoret, Jean-Paul and Probert, Ian and Michaud, Philippe}
}
@article {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 {Meng2018,
	title = {Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network},
	journal = {Molecular Ecology},
	year = {2018},
	note = {tex.mendeley-tags: RCC1491,RCC1516,RCC3387,RCC3468,RCC3507},
	pages = {0{\textendash}2},
	abstract = {Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and used a sequence similarity network (SSN) to compare the underlying genomic basis of functional features within the group. This approach constitutes the most comprehensive picture to date of the genomic potential of dinoflagellates. A core predicted proteome composed of 252 connected components (CCs) of putative conserved protein domains (pCDs) was identified. Of these, 206 were novel and 16 lacked any functional annotation in public databases. Integration of functional information in our network analyses allowed investigation of pCDs specifically associated to functional traits. With respect to toxicity, sequences homologous to those of proteins found in species with toxicity potential (e.g. sxtA4 and sxtG) were not specific to known toxin-producing species. Although not fully specific to symbiosis, the most represented functions associated with proteins involved in the symbiotic trait were related to membrane processes and ion transport. Overall, our SSN approach led to identification of 45,207 and 90,794 specific and constitutive pCDs of respectively the toxic and symbiotic species represented in our analyses. Of these, 56\% and 57\% respectively (i.e. 25,393 and 52,193 pCDs) completely lacked annotation in public databases. This stresses the extent of our lack of knowledge, while emphasizing the potential of SSNs to identify candidate pCDs for further functional genomic characterization. This article is protected by copyright. All rights reserved.},
	keywords = {Genomics/Proteomics, Microbial Biology, Molecular Evolution, Protists, rcc1491, RCC1516, RCC3387, rcc3468, rcc3507, transcriptomics},
	issn = {09621083},
	doi = {10.1111/mec.14579},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/29624751\%0Ahttp://doi.wiley.com/10.1111/mec.14579},
	author = {Meng, Arnaud and Corre, Erwan and Probert, Ian and Gutierrez-Rodriguez, Andres and Siano, Raffaele and Annamale, Anita and Alberti, Adriana and Da Silva, Corinne and Wincker, Patrick and Le Crom, St{\'e}phane and Not, Fabrice and Bittner, Lucie}
}
@article {Fox2018,
	title = {Calcein staining as a tool to investigate coccolithophore calcification},
	journal = {Frontiers in Marine Science},
	volume = {5},
	number = {September},
	year = {2018},
	note = {tex.mendeley-tags: RCC 1461,RCC 3777,RCC1130,RCC1303,RCC1456},
	abstract = {This brief paper summarizes the literature on academic accommodations for students with psychiatric disabilities. A definition of psychiatric disability precedes a brief summary of the following specific psychiatric diagnoses: depression, bipolar affective disorder; borderline personality disorder; schizophrenia; and anxiety disorders. Also noted are behavior or personality disorders specifically excluded from coverage under the Americans with Disabilities Act. Functional limitations of this population that may affect academic performance are then listed and defined. Among these are medication side effects, sustaining concentration, maintaining stamina, interacting with others, responding to negative feedback, responding to change, and severe test anxiety. Examples of appropriate instructional strategies are followed by a discussion of reasonable accommodations to provide these students with equal access to the curriculum. Examples are then given of classroom accommodations, examination accommodations, and assignment accommodations. Characteristics of accommodations that are not reasonable are also listed. The paper concludes with a resource list including Web site and contact information for the DO-IT (Disabilities, Opportunities, Internetworking, and Technology) Project. (DB)},
	keywords = {bet hedging, calcein, Calcification, coccolith, coccolithophore, flow cytometry, haptophyte, RCC1130, RCC1303, RCC1456, RCC1461, RCC3777, secretion},
	issn = {2296-7745},
	doi = {10.3389/fmars.2018.00326},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2018.00326/full},
	author = {Fox, Emily and Meyer, Erin and Panasiak, Natalie and Taylor, Alison R.}
}
@article {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 {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 {Partensky2018,
	title = {Comparison of photosynthetic performances of marine picocyanobacteria with different configurations of the oxygen-evolving complex},
	journal = {Photosynthesis Research},
	volume = {138},
	number = {1},
	year = {2018},
	note = {tex.mendeley-tags: RCC752},
	pages = {57{\textendash}71},
	abstract = {The extrinsic PsbU and PsbV proteins are known to play a critical role in stabilizing the Mn4CaO5 cluster of the PSII oxygen-evolving complex (OEC). However, most isolates of the marine cyanobacterium Prochlorococcus naturally miss these proteins, even though they have kept the main OEC protein, PsbO. A structural homology model of the PSII of such a natural deletion mutant strain (P. marinus MED4) did not reveal any obvious compensation mechanism for this lack. To assess the physiological consequences of this unusual OEC, we compared oxygen evolution between Prochlorococcus strains missing psbU and psbV (PCC 9511 and SS120) and two marine strains possessing these genes (Prochlorococcus sp. MIT9313 and Synechococcus sp. WH7803). While the low light-adapted strain SS120 exhibited the lowest maximal O2 evolution rates (Pmax per divinyl-chlorophyll a, per cell or per photosystem II) of all four strains, the high light-adapted strain PCC 9511 displayed even higher PChlmax and PPSIImax at high irradiance than Synechococcus sp. WH7803. Furthermore, thermoluminescence glow curves did not show any alteration in the B-band shape or peak position that could be related to the lack of these extrinsic proteins. This suggests an efficient functional adaptation of the OEC in these natural deletion mutants, in which PsbO alone is seemingly sufficient to ensure proper oxygen evolution. Our study also showed that Prochlorococcus strains exhibit negative net O2 evolution rates at the low irradiances encountered in minimum oxygen zones, possibly explaining the very low O2 concentrations measured in these environments, where Prochlorococcus is the dominant oxyphototroph.},
	keywords = {rcc752},
	issn = {1573-5079},
	doi = {10.1007/s11120-018-0539-3},
	url = {https://doi.org/10.1007/s11120-018-0539-3},
	author = {Partensky, Fr{\'e}d{\'e}ric and Mella-Flores, Daniella and Six, Christophe and Garczarek, Laurence and Czjzek, Mirjam and Marie, Dominique and Kotabov{\'a}, Eva and Felcmanov{\'a}, Kristina and Pr{\'a}{\v s}il, Ond{\v r}ej}
}
@article {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 {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 {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 {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 {EMI4:EMI412614,
	title = {Relative stability of ploidy in a marine Synechococcus across various growth conditions},
	journal = {Environmental Microbiology Reports},
	year = {2018},
	note = {tex.mendeley-tags: RCC752},
	month = {feb},
	pages = {in press},
	abstract = {Marine picocyanobacteria of the genus Synechococcus are ubiquitous phototrophs in oceanic systems. Consistent with these organisms occupying vast tracts of the nutrient impoverished ocean, most marine Synechococcus so far studied are monoploid i.e. contain a single chromosome copy. The exception is the oligoploid strain Synechococcus sp. WH7803, which on average possesses around 4 chromosome copies. Here, we set out to understand the role of resource availability (through nutrient deplete growth) and physical stressors (UV, exposure to low and high temperature) in regulating ploidy level in this strain. Using qPCR to assay ploidy status we demonstrate the relative stability of chromosome copy number in Synechococcus sp. WH7803. Such robustness in maintaining an oligoploid status even under nutrient and physical stress is indicative of a fundamental role, perhaps facilitating recombination of damaged DNA regions as a result of prolonged exposure to oxidative stress, or allowing added flexibility in gene expression via possessing multiple alleles. This article is protected by copyright. All rights reserved.},
	keywords = {rcc752},
	issn = {17582229},
	doi = {10.1111/1758-2229.12614},
	url = {http://dx.doi.org/10.1111/1758-2229.12614 http://doi.wiley.com/10.1111/1758-2229.12614},
	author = {Perez-Sepulveda, Blanca and Pitt, Frances and N{\textquoteright}Guyen, An Ngoc and Ratin, Morgane and Garczarek, Laurence and Millard, Andrew and Scanlan, David J}
}
@article {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 {Mahmoud2017,
	title = {Adaptation to blue light in marine synechococcus requires MpeU, an enzyme with similarity to phycoerythrobilin lyase isomerases},
	journal = {Frontiers in Microbiology},
	volume = {8},
	number = {February},
	year = {2017},
	note = {tex.mendeley-tags: 2017,rcc555,sbr?hyto?app},
	month = {feb},
	pages = {243},
	abstract = {Marine Synechococcus cyanobacteria have successfully adapted to environments with different light colors, which likely contributes to this genus being the second most abundant photosynthetic microorganism worldwide. Populations of Synechococcus that grow in deep, blue ocean waters contain large amounts of the blue-light absorbing chromophore phycourobilin (PUB) in their light harvesting complexes (phycobilisomes). Here we show that all Synechococcus strains adapted to blue light possess a gene called mpeU. MpeU is structurally similar to phycobilin lyases, enzymes that ligate chromophores to phycobiliproteins. Interruption of mpeU caused a reduction in PUB content, produced impaired phycobilisomes and reduced growth rate more strongly in blue than green light. When mpeU was reintroduced in the mpeU mutant background, the mpeU-less phenotype was complemented in terms of PUB content and phycobilisome content. Fluorescence spectra of mpeU mutant cells and purified phycobilisomes revealed red-shifted phycoerythrin emission peaks, likely indicating a defect in chromophore ligation to phycoerythrin-I (PE-I) or phycoerythrin-II (PE-II). Our results suggest that MpeU is a lyase-isomerase that attaches a phycoerythrobilin to a PEI or PEII subunit and isomerizes it to PUB. MpeU is therefore an important determinant in adaptation of Synechococcus spp. to capture photons in blue light environments throughout the world{\textquoteright}s oceans.},
	keywords = {2017, Blue light, light harvesting complex, Lyase isomerase, marine cyanobacteria, Marine Synechococcus, phycobilin, Phycobilisome, Phycoerythrin, Phycourobilin, rcc555, sbr?hyto?app},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2017.00243},
	url = {http://journal.frontiersin.org/article/10.3389/fmicb.2017.00243/full},
	author = {Mahmoud, Rania M. and Sanfilippo, Joseph E. and Nguyen, Adam A. and Strnat, Johann A. and Partensky, Fr{\'e}d{\'e}ric and Garczarek, Laurence and Abo El Kassem, Nabil and Kehoe, David M. and Schluchter, Wendy M.}
}
@article {Pittera2016,
	title = {Adaptive thermostability of light-harvesting complexes in marine picocyanobacteria},
	journal = {The ISME Journal},
	volume = {11},
	number = {1},
	year = {2017},
	note = {tex.mendeley-tags: 2016,rcc1594,rcc1682,rcc2380,rcc2382,rcc752,rcc791},
	pages = {112{\textendash}124},
	keywords = {2016, rcc1594, rcc1682, rcc2380, rcc2382, rcc752, rcc791},
	issn = {1751-7362},
	doi = {10.1038/ismej.2016.102},
	url = {http://www.nature.com/doifinder/10.1038/ismej.2016.102},
	author = {Pittera, Justine and Partensky, Fr{\'e}d{\'e}ric and Six, Christophe}
}
@article {LopesdosSantos2017,
	title = {Chloropicophyceae, a new class of picophytoplanktonic prasinophytes},
	journal = {Scientific Reports},
	volume = {7},
	number = {1},
	year = {2017},
	note = {tex.mendeley-tags: 2017,RCC1019,RCC1021,RCC1032,RCC1043,RCC1124,RCC138,RCC15,RCC1871,RCC19,RCC227,RCC2335,RCC2337,RCC2339,RCC287,RCC297,RCC3368,RCC3373,RCC3374,RCC3375,RCC3376,RCC3402,RCC4429,RCC4430,RCC4434,RCC4572,RCC4656,RCC696,RCC700,RCC701,RCC712,RCC713,RCC717,RCC719,RCC722,RCC726,RCC856,RCC857,RCC887,RCC917,RCC996,RCC997,RCC998,RCC999,sbr?hyto$_\textrmd$ipo},
	month = {dec},
	pages = {14019},
	keywords = {2017, RCC1019, RCC1021, RCC1032, RCC1043, RCC1124, RCC138, RCC15, RCC1871, RCC19, RCC227, RCC2335, RCC2337, RCC2339, RCC287, RCC297, RCC3368, RCC3373, RCC3374, RCC3375, RCC3376, RCC3402, RCC4429, RCC4430, RCC4434, RCC4572, RCC4656, RCC696, RCC700, RCC701, RCC712, RCC713, RCC717, RCC719, RCC722, RCC726, RCC856, RCC857, RCC887, RCC917, RCC996, RCC997, RCC998, RCC999, sbr?hyto$_\textrmd$ipo},
	issn = {2045-2322},
	doi = {10.1038/s41598-017-12412-5},
	url = {http://www.nature.com/articles/s41598-017-12412-5},
	author = {Lopes dos Santos, Adriana and Pollina, Thibaut and Gourvil, Priscillia and Corre, Erwan and Marie, Dominique and Garrido, Jos{\'e} Luis and Rodr{\'\i}guez, Francisco and No{\"e}l, Mary-H{\'e}l{\`e}ne and Vaulot, Daniel and Eikrem, Wenche}
}
@article {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 {Ruiz2017,
	title = {Emerging interaction patterns in the emiliania huxleyi-EhV system},
	journal = {Viruses},
	volume = {9},
	number = {3},
	year = {2017},
	note = {tex.mendeley-tags: RCC1211,RCC1213,RCC1215,RCC1216,RCC1218,RCC1228,RCC1231,RCC1235,RCC1239,RCC1241,RCC1242,RCC1246,RCC1249,RCC1250,RCC1253,RCC1255,RCC1256,RCC1257,RCC1259,RCC1268,RCC1269,RCC1272,RCC1276,RCC1322,RCC1744,RCC1745,RCC1857,RCC3548,RCC3856,RCC3923,RCC3956},
	month = {mar},
	pages = {61},
	abstract = {Viruses are thought to be fundamental in driving microbial diversity in the oceanic planktonic realm. That role and associated emerging infection patterns remain particularly elusive for eukaryotic phytoplankton and their viruses. Here we used a vast number of strains from the model system Emiliania huxleyi/Emiliania huxleyi Virus to quantify parameters such as growth rate ({\textmu}), resistance (R), and viral production (Vp) capacities. Algal and viral abundances were monitored by flow cytometry during 72-h incubation experiments. The results pointed out higher viral production capacity in generalist EhV strains, and the virus-host infection network showed a strong co-evolution pattern between E. huxleyi and EhV populations. The existence of a trade-off between resistance and growth capacities was not confirme},
	keywords = {algae virus, coccolithophore, coccolithovirus, cost of, haptophyta, infectivity trade-offs, killing-the-winner, marine viral ecology, phycodnaviridae, RCC1211, RCC1213, RCC1215, RCC1216, RCC1218, RCC1228, RCC1231, RCC1235, RCC1239, RCC1241, RCC1242, RCC1246, RCC1249, RCC1250, RCC1253, RCC1255, rcc1256, RCC1257, RCC1259, RCC1268, RCC1269, RCC1272, RCC1276, RCC1322, RCC1744, RCC1745, RCC1857, RCC3548, RCC3856, RCC3923, RCC3956, resistance, viral-host interactions},
	issn = {1999-4915},
	doi = {10.3390/v9030061},
	url = {http://www.mdpi.com/1999-4915/9/3/61},
	author = {Ruiz, Eliana and Oosterhof, Monique and Sandaa, Ruth-Anne and Larsen, Aud and Pagarete, Ant{\'o}nio}
}
@article {Kuhlisch2017,
	title = {A fast and direct liquid chromatography-mass spectrometry method to detect and quantify polyunsaturated aldehydes and polar oxylipins in diatoms},
	journal = {Limnology and Oceanography: Methods},
	volume = {15},
	number = {1},
	year = {2017},
	note = {Publisher: John Wiley \& Sons, Ltd tex.mendeley-tags: RCC75,RCC776},
	month = {jan},
	pages = {70{\textendash}79},
	abstract = {Abstract Polyunsaturated aldehydes (PUAs) are a group of microalgal metabolites that have attracted a lot of attention due to their biological activity. Determination of PUAs has become an important routine procedure in plankton and biofilm investigations, especially those that deal with chemically mediated interactions. Here we introduce a fast and direct derivatization free method that allows quantifying PUAs in the nanomolar range, sufficient to undertake the analysis from cultures and field samples. The sample preparation requires one simple filtration step and the initiation of PUA formation by cell disruption. After centrifugation the samples are ready for measurement without any further handling. Within one chromatographic run this method additionally allows us to monitor the formation of the polar oxylipins arising from the cleavage of precursor fatty acids. The robust method is based on analyte separation and detection using ultra high performance liquid chromatography-atmospheric pressure chemical ionization mass spectrometry (UHPLC-APCI MS) and enables high throughput investigations by employing an analysis time of only 5 min. Our protocol thus provides an alternative and extension to existing PUA determinations based on gas chromatography-mass spectrometry (GC-MS) with shorter run times and without any chemical derivatization. It also enables researchers with widely available LC-MS analytical platforms to monitor PUAs. Additionally, non-volatile oxylipins such as ?-oxo-acids and related compounds can be elucidated and monitored.},
	keywords = {RCC75, RCC776},
	issn = {1541-5856},
	doi = {10.1002/lom3.10143},
	url = {https://doi.org/10.1002/lom3.10143},
	author = {Kuhlisch, Constanze and Deicke, Michael and Ueberschaar, Nico and Wichard, Thomas and Pohnert, Georg}
}
@article {Fischer2017,
	title = {Identity of the limiting nutrient (N vs. P) affects the competitive success of mixotrophs},
	journal = {Marine Ecology Progress Series},
	volume = {563},
	year = {2017},
	note = {tex.mendeley-tags: RCC744},
	pages = {51{\textendash}63},
	abstract = {ABSTRACT: Empirical and theoretical evidence predicts that mixotrophic bacterivores dominate over specialized heterotrophic bacterivores and specialist photoautotrophs under conditions of high light and low loss rates. Here we extend this concept towards nutrient limitation and ask whether the identity of the limiting nutrient affects the competition of mixotrophs with their specialist competitors. Due to their photosynthetic machinery, mixotrophs should have higher cellular N contents than heterotrophs and, following this assumption, a higher demand for N. Conversely, heterotrophs, with their potential high growth rates compared to mixotrophs, may have a higher demand for P (?growth rate hypothesis?). Simplified, mixotrophs should be more prone to N-limitation, while heterotrophs should be more prone to P-limitation. We tested these predictions in artificial food webs studying the competitive success of mixotrophic bacterivores under a range of light intensities and loss rates and under either P- or N-limitation. Under low-light conditions, mixotrophs were more successful than heterotrophs under P-limitation, whereas the heterotrophs were more successful under N-limitation. At higher light intensity, mixotrophs had an advantage over photoautotrophs, due to the acquisition of nutrients ingested with prey. Overall, the effects of the limiting nutrient on the competitive success of mixotrophs were stronger under conditions already unfavorable for mixotrophs (low light). Further, our results suggest that communities dominated by mixotrophs might have low and relatively stable seston C:nutrient ratios. The results presented here supplement existing data well and help to define the ecological niche of mixotrophic protists.},
	keywords = {RCC744},
	doi = {10.3354/meps11968},
	url = {https://www.int-res.com/abstracts/meps/v563/p51-63},
	author = {Fischer, R and HA, Giebel and Ptacnik, R}
}
@article {Fischer2017a,
	title = {Importance of mixotrophic bacterivory can be predicted by light and loss rates},
	journal = {Oikos},
	volume = {126},
	number = {5},
	year = {2017},
	note = {Publisher: John Wiley \& Sons, Ltd (10.1111) tex.mendeley-tags: RCC744},
	month = {may},
	pages = {713{\textendash}722},
	abstract = {Recent observational studies form oligotrophic waters provide ample evidence that mixotrophic flagellates often account for the bulk of bacterivory. However, we lack a general framework that allows a mechanistic understanding of success of mixotrophs in the competition with heterotrophic bacterivores. This is especially needed for integrating mixotrophy in models of the microbial loop. Based on general tradeoffs linked to the combined resource use in mixotrophs (generalist versus specialist), we propose a concept where mixotrophs are favored by conditions of high light ? low losses, corresponding to the situation found in the surface waters of oligotrophic oceans. Under such conditions, they can achieve positive net growth at very low resource levels, allowing simultaneous competition with specialized protists. Conversely, heterotrophic bacterivores and photoautotrophs should be especially favored in more productive and low-light conditions. We show experimentally that the combined effect of light and loss rates (dilution) predicts the success of mixotrophic bacterivorous flagellates. Moreover, our results suggest that total bacterivory, contrary as seen in the traditional microbial loop concept, has a more intricate coupling to light.},
	keywords = {RCC744},
	issn = {0030-1299},
	doi = {10.1111/oik.03539},
	url = {https://doi.org/10.1111/oik.03539},
	author = {Fischer, Robert and Giebel, Helge-Ansgar and Hillebrand, Helmut and Ptacnik, Robert}
}
@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 {Mackey2017,
	title = {Physiological and proteomic characterization of light adaptations in marine Synechococcus},
	journal = {Environmental Microbiology},
	volume = {19},
	number = {6},
	year = {2017},
	note = {tex.mendeley-tags: rcc539,rcc752},
	month = {jun},
	pages = {2348{\textendash}2365},
	keywords = {rcc539, rcc752},
	issn = {14622912},
	doi = {10.1111/1462-2920.13744},
	url = {http://doi.wiley.com/10.1111/1462-2920.13744},
	author = {Mackey, Katherine R. M. and Post, Anton F and McIlvin, Matthew R and Saito, Mak A}
}
@article {Blanc-Mathieu2017,
	title = {Population genomics of picophytoplankton unveils novel chromosome hypervariability},
	journal = {Science Advances},
	volume = {3},
	number = {7},
	year = {2017},
	note = {tex.mendeley-tags: RCC1105,RCC1108,RCC1110,RCC1112,RCC1114,RCC1115,RCC1116,RCC1117,RCC1118,RCC1123,RCC1558,RCC1559,RCC1561,RCC299,RCC4221,RCC809},
	month = {jul},
	pages = {e1700239},
	keywords = {RCC1105, RCC1108, RCC1110, RCC1112, RCC1114, RCC1115, RCC1116, RCC1117, RCC1118, RCC1123, RCC1558, RCC1559, RCC1561, RCC299, RCC4221, RCC809},
	issn = {2375-2548},
	doi = {10.1126/sciadv.1700239},
	url = {http://advances.sciencemag.org/lookup/doi/10.1126/sciadv.1700239},
	author = {Blanc-Mathieu, Romain and Krasovec, Marc and Hebrard, Maxime and Yau, Sheree and Desgranges, Elodie and Martin, Joel and Schackwitz, Wendy and Kuo, Alan and Salin, Gerald and Donnadieu, Cecile and Desdevises, Yves and Sanchez-Ferandin, Sophie and Moreau, Herv{\'e} and Rivals, Eric and Grigoriev, Igor V. and Grimsley, Nigel and Eyre-Walker, Adam and Piganeau, Gwenael}
}
@article {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 {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 {Cuvelier2017,
	title = {Responses of the picoprasinophyte Micromonas commoda to light and ultraviolet stress},
	journal = {PLOS ONE},
	volume = {12},
	number = {3},
	year = {2017},
	note = {ISBN: 1111111111 tex.mendeley-tags: RCC299},
	month = {mar},
	pages = {e0172135},
	keywords = {RCC299},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0172135},
	url = {http://dx.plos.org/10.1371/journal.pone.0172135},
	author = {Cuvelier, Marie L and Guo, Jian and Ortiz, Alejandra C. and van Baren, Marijke J. and Tariq, Muhammad Akram and Partensky, Fr{\'e}d{\'e}ric and Worden, Alexandra Z},
	editor = {Cockshutt, Amanda M.}
}
@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 {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 {Simmons2016,
	title = {Abundance and biogeography of picoprasinophyte ecotypes and other phytoplankton in the eastern north pacific ocean},
	journal = {Applied and Environmental Microbiology},
	volume = {82},
	number = {6},
	year = {2016},
	note = {tex.mendeley-tags: 2016,rcc},
	month = {mar},
	pages = {1693{\textendash}1705},
	abstract = {Eukaryotic algae within the picoplankton size class (<=2 ??m in diameter) are important marine primary producers, but their spatial and ecological distributions are not well characterized. Here, we studied three picoeukaryotic prasinophyte genera and their cyanobacterial counterparts, Prochlorococcus and Synechococcus , during two cruises along a North Pacific transect characterized by different ecological regimes. Picoeukaryotes and Synechococcus reached maximum abundances of 1.44 {\texttimes} 10 5 and 3.37 {\texttimes} 10 5 cells ? ml -1 , respectively, in mesotrophic waters, while Prochlorococcus reached 1.95 {\texttimes} 10 5 cells ? ml -1 in the oligotrophic ocean. Of the picoeukaryotes, Bathycoccus was present at all stations in both cruises, reaching 21,368 {\textpm} 327 18S rRNA gene copies ? ml -1 . Micromonas and Ostreococcus clade OI were detected only in mesotrophic and coastal waters and Ostreococcus clade OII only in the oligotrophic ocean. To resolve proposed Bathycoccus ecotypes, we established genetic distances for 1,104 marker genes using targeted metagenomes and the Bathycoccus prasinos genome. The analysis was anchored in comparative genome analysis of three Ostreococcus species for which physiological and environmental data are available to facilitate data interpretation. We established that two Bathycoccus ecotypes exist, named here BI (represented by coastal isolate Bathycoccus prasinos ) and BII. These share 82\% {\textpm} 6\% nucleotide identity across homologs, while the Ostreococcus spp. share 75\% {\textpm} 8\%. We developed and applied an analysis of ecomarkers to metatranscriptomes sequenced here and published -omics data from the same region. The results indicated that the Bathycoccus ecotypes cooccur more often than Ostreococcus clades OI and OII do. Exploratory analyses of relative transcript abundances suggest that Bathycoccus NRT2.1 and AMT2.2 are high-affinity NO 3 - and low-affinity NH 4 + transporters, respectively, with close homologs in multiple picoprasinophytes. Additionally, in the open ocean, where dissolved iron concentrations were low (0.08 nM), there appeared to be a shift to the use of nickel superoxide dismutases (SODs) from Mn/Fe/Cu SODs closer inshore. Our study documents the distribution of picophytoplankton along a North Pacific ecological gradient and offers new concepts and techniques for investigating their biogeography.},
	keywords = {2016, rcc},
	issn = {0099-2240},
	doi = {10.1128/AEM.02730-15},
	url = {http://aem.asm.org/lookup/doi/10.1128/AEM.02730-15},
	author = {Simmons, Melinda P. and Sudek, Sebastian and Monier, Adam and Limardo, Alexander J. and Jimenez, Valeria and Perle, Christopher R. and Elrod, Virginia A. and Pennington, J. Timothy and Worden, Alexandra Z.},
	editor = {Schloss, P. D.}
}
@article {Bolton2016,
	title = {Decrease in coccolithophore calcification and CO2 since the middle Miocene},
	journal = {Nature Communications},
	volume = {7},
	year = {2016},
	note = {tex.mendeley-tags: 2016,rcc},
	pages = {10284},
	abstract = {Marine algae are instrumental in carbon cycling and atmospheric carbon dioxide (CO2) regulation. One group, coccolithophores, uses carbon to photosynthesize and to calcify, covering their cells with chalk platelets (coccoliths). How ocean acidification influences coccolithophore calcification is strongly debated, and the effects of carbonate chemistry changes in the geological past are poorly understood. This paper relates degree of coccolith calcification to cellular calcification, and presents the first records of size-normalized coccolith thickness spanning the last 14 Myr from tropical oceans. Degree of calcification was highest in the low-pH, high-CO2 Miocene ocean, but decreased significantly between 6 and 4 Myr ago. Based on this and concurrent trends in a new alkenone ep record, we propose that decreasing CO2 partly drove the observed trend via reduced cellular bicarbonate allocation to calcification. This trend reversed in the late Pleistocene despite low CO2, suggesting an additional regulator of calcification such as alkalinity. 1},
	keywords = {2016, rcc},
	issn = {2041-1723},
	doi = {10.1038/ncomms10284},
	url = {http://www.nature.com/doifinder/10.1038/ncomms10284},
	author = {Bolton, Clara T. and Hern{\'a}ndez-S{\'a}nchez, Mar{\'\i}a T. and Fuertes, Miguel-{\'A}ngel and Gonz{\'a}lez-Lemos, Sa{\'u}l and Abrevaya, Lorena and M{\'e}ndez-Vicente, Ana and Flores, Jos{\'e}-Abel and Probert, Ian and Giosan, Liviu and Johnson, Joel and Stoll, Heather M.}
}
@article {Waltman2016,
	title = {Identifying aspects of the post-transcriptional program governing the proteome of the green alga micromonas pusilla.},
	journal = {PloS one},
	volume = {11},
	number = {7},
	year = {2016},
	note = {ISBN: 10.1371/journal.pone.0155839 Publisher: Public Library of Science tex.mendeley-tags: 2016,RCC,rcc834},
	month = {jan},
	pages = {e0155839},
	abstract = {Micromonas is a unicellular motile alga within the Prasinophyceae, a green algal group that is related to land plants. This picoeukaryote ({\textexclamdown}2 ??m diameter) is widespread in the marine environment but is not well understood at the cellular level. Here, we examine shifts in mRNA and protein expression over the course of the day-night cycle using triplicated mid-exponential, nutrient replete cultures of Micromonas pusilla CCMP1545. Samples were collected at key transition points during the diel cycle for evaluation using high-throughput LC-MS proteomics. In conjunction, matched mRNA samples from the same time points were sequenced using pair-ended directional Illumina RNA-Seq to investigate the dynamics and relationship between the mRNA and protein expression programs of M. pusilla. Similar to a prior study of the marine cyanobacterium Prochlorococcus, we found significant divergence in the mRNA and proteomics expression dynamics in response to the light:dark cycle. Additionally, expressional responses of genes and the proteins they encoded could also be variable within the same metabolic pathway, such as we observed in the oxygenic photosynthesis pathway. A regression framework was used to predict protein levels from both mRNA expression and gene-specific sequence-based features. Several features in the genome sequence were found to influence protein abundance including codon usage as well as 3{\textquoteright} UTR length and structure. Collectively, our studies provide insights into the regulation of the proteome over a diel cycle as well as the relationships between transcriptional and translational programs in the widespread marine green alga Micromonas.},
	keywords = {2016, rcc, RCC834},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0155839},
	url = {http://dx.doi.org/10.1371/journal.pone.0155839},
	author = {Waltman, Peter H and Guo, Jian and Reistetter, Emily Nahas and Purvine, Samuel and Ansong, Charles K and van Baren, Marijke J and Wong, Chee-Hong and Wei, Chia-Lin and Smith, Richard D and Callister, Stephen J and Stuart, Joshua M and Worden, Alexandra Z}
}
@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 {Vannier2016,
	title = {Survey of the green picoalga Bathycoccus genomes in the global ocean},
	journal = {Scientific Reports},
	volume = {6},
	number = {1},
	year = {2016},
	note = {tex.mendeley-tags: 2016,RCC1105,RCC715,RCC716,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo},
	month = {dec},
	pages = {37900},
	keywords = {2016, RCC1105, RCC715, RCC716, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo},
	issn = {2045-2322},
	doi = {10.1038/srep37900},
	url = {http://www.nature.com/articles/srep37900},
	author = {Vannier, Thomas and Leconte, Jade and Seeleuthner, Yoann and Mondy, Samuel and Pelletier, Eric and Aury, Jean-Marc and de Vargas, Colomban and Sieracki, Michael and Iudicone, Daniele and Vaulot, Daniel and Wincker, Patrick and Jaillon, Olivier}
}
@article {Yau2016,
	title = {A viral immunity chromosome in the marine picoeukaryote, ostreococcus tauri},
	journal = {PLOS Pathogens},
	volume = {12},
	number = {10},
	year = {2016},
	note = {tex.mendeley-tags: 2016,RCC299,RCC4221,RCC809},
	month = {oct},
	pages = {e1005965},
	keywords = {2016, RCC299, RCC4221, RCC809},
	issn = {1553-7374},
	doi = {10.1371/journal.ppat.1005965},
	url = {http://dx.plos.org/10.1371/journal.ppat.1005965},
	author = {Yau, Sheree and Hemon, Claire and Derelle, Evelyne and Moreau, Herv{\'e} and Piganeau, Gwenael and Grimsley, Nigel},
	editor = {Ding, Shou-Wei}
}
@article {Supraha2015,
	title = {Eco-physiological adaptation shapes the response of calcifying algae to nutrient limitation},
	journal = {Scientific Reports},
	volume = {5},
	number = {November},
	year = {2015},
	note = {Publisher: Nature Publishing Group tex.mendeley-tags: 2015,RCC1323,RCC1334},
	pages = {16499},
	keywords = {2015, RCC1323, RCC1334},
	issn = {2045-2322},
	doi = {10.1038/srep16499},
	url = {http://www.nature.com/articles/srep16499},
	author = {{\v S}upraha, Luka and Gerecht, Andrea C. and Probert, Ian and Henderiks, Jorijntje}
}
@article {Varkey2015,
	title = {Effects of low temperature on tropical and temperate isolates of marine Synechococcus},
	journal = {The ISME Journal},
	year = {2015},
	note = {Publisher: Nature Publishing Group tex.mendeley-tags: rcc},
	pages = {1{\textendash}12},
	keywords = {rcc},
	issn = {1751-7362},
	doi = {10.1038/ismej.2015.179},
	url = {http://www.nature.com/doifinder/10.1038/ismej.2015.179},
	author = {Varkey, Deepa and Mazard, Sophie and Ostrowski, Martin and Tetu, Sasha G and Haynes, Paul and Paulsen, Ian T}
}
@article {Wheeler2015,
	title = {Evolution of alternative biosynthetic pathways for vitamin C following plastid acquisition in photosynthetic eukaryotes},
	journal = {eLife},
	volume = {4},
	year = {2015},
	note = {ISBN: 8196242115 tex.mendeley-tags: RCC299},
	pages = {1{\textendash}25},
	abstract = {Ascorbic acid (vitamin C) is an enzyme co-factor in eukaryotes that also plays a critical role in protecting photosynthetic eukaryotes against damaging reactive oxygen species derived from the chloroplast. Many animal lineages, including primates, have become ascorbate auxotrophs due to the loss of the terminal enzyme in their biosynthetic pathway, L-gulonolactone oxidase (GULO). The alternative pathways found in land plants and Euglena use a different terminal enzyme, L-galactonolactone dehydrogenase (GLDH). The evolutionary processes leading to these differing pathways and their contribution to the cellular roles of ascorbate remain unclear. Here we present molecular and biochemical evidence demonstrating that GULO was functionally replaced with GLDH in photosynthetic eukaryote lineages following plastid acquisition. GULO has therefore been lost repeatedly throughout eukaryote evolution. The formation of the alternative biosynthetic pathways in photosynthetic eukaryotes uncoupled ascorbate synthesis from hydrogen peroxide production and likely contributed to the rise of ascorbate as a major photoprotective antioxidant.},
	keywords = {ascorbate, evolutionary biology, Galdieria, genomics, L-gulonolactone oxidase, plant biology, Porphyra, RCC299, vitamin C},
	issn = {2050084X},
	doi = {10.7554/eLife.06369},
	author = {Wheeler, Glen and Ishikawa, Takahiro and Pornsaksit, Varissa and Smirnoff, Nicholas}
}
@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 {Potvin2015,
	title = {Morphology , molecular phylogeny , and pigment characterization of a novel phenotype of the dinoflagellate genus Pelagodinium from Korean waters},
	journal = {Algae},
	volume = {30},
	number = {3},
	year = {2015},
	note = {tex.mendeley-tags: rcc},
	pages = {183{\textendash}195},
	abstract = {The dinoflagellate genus Pelagodinium is genetically classified in distinct sub-clades and subgroups. However, it is dif- ficult to determine whether this genetic diversity represents intra- or interspecific divergence within the genus since only the morphology of the type strain of the genus Pelagodinium, Pelagodinium bei, is available. An isolate associated with the genus Pelagodinium from Shiwha Bay, Korea, was recently cultured. This isolate formed a subgroup with 3 to 4 strains from the Atlantic Ocean, Mediterranean Sea, and Indian Ocean. This subgroup was distinct from the subgroup contain- ing P. bei. The morphology of the isolate was analyzed using optical and scanning electron microscopy and was almost identical to that of P. bei except that this isolate had two series of amphiesmal vesicles (AVs) in the cingulum, unlike P. bei that has one series. When the pigment compositions of the isolate and P. bei were analyzed using high-performance liquid chromatography, these two strains had peridinin as a major accessory pigment and their pigment compositions were almost identical. In addition, the swimming behaviors of these two strains were very similar. The re-examination of the type culture of P. bei revealed two series in the cingulum as for the isolate. The new findings on the number of series of AVs in the cingulum, the pigment composition, and the swimming behaviors suggest that P. bei and the isolate may be conspecific despite their association to genetically different subgroups. This study provides a basis to further understand the molecular classification within Pelagodinium combining genetic, morphological, pigment, and behavioral data.},
	keywords = {foraminifera, gymnodinium bei, pelagic symbiont, rcc, suessiaceae, suessiales},
	doi = {10.4490/algae.2015.30.3.183},
	author = {Potvin, {\'E}ric and Jeong, Hae Jin and Kang, Nam Seon and Noh, Jae Hoon and Yang, Eun Jin}
}
@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 {Abby2014,
	title = {Bacteria in Ostreococcus tauri cultures - friends, foes or hitchhikers?},
	journal = {Frontiers in microbiology},
	volume = {5},
	year = {2014},
	note = {Publisher: Frontiers tex.mendeley-tags: rcc},
	month = {jan},
	pages = {505},
	abstract = {Marine phytoplankton produce half of the oxygen we breathe and their astounding diversity is just starting to be unraveled. Many microbial phytoplankton are thought to be phototrophic, depending solely on inorganic sources of carbon and minerals for growth rather than preying on other planktonic cells. However, there is increasing evidence that symbiotic associations, to a large extent with bacteria, are required for vitamin or nutrient uptake for many eukaryotic microalgae. Here, we use in silico approaches to look for putative symbiotic interactions by analysing the gene content of microbial communities associated with 13 different Ostreococcus tauri (Chlorophyta, Mamilleophyceae) cultures sampled from the Mediterranean Sea. While we find evidence for bacteria in all cultures, there is no ubiquitous bacterial group, and the most prevalent group, Flavobacteria, is present in 10 out of 13 cultures. Among seven of the microbiomes, we detected genes predicted to encode type 3 secretion systems (T3SS, in 6/7 microbiomes) and/or putative type 6 secretion systems (T6SS, in 4/7 microbiomes). Phylogenetic analyses show that the corresponding genes are closely related to genes of systems identified in bacterial-plant interactions, suggesting that these T3SS might be involved in cell-to-cell interactions with O. tauri.},
	keywords = {bacterial diversity, Bacterial symbiosis, Illumina sequencing, microbiome, Ostreococcus, phycosphere, phytoplankton, picoeukaryote, rcc, RCC?o?dd, secretion system},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2014.00505},
	url = {http://journal.frontiersin.org/Journal/10.3389/fmicb.2014.00505/abstract},
	author = {Abby, Sophie S and Touchon, Marie and De Jode, Aurelien and Grimsley, Nigel and Piganeau, Gwenael}
}
@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 {Pittera2014,
	title = {Connecting thermal physiology and latitudinal niche partitioning in marine Synechococcus},
	journal = {The ISME journal},
	volume = {8},
	number = {6},
	year = {2014},
	note = {Publisher: International Society for Microbial Ecology tex.mendeley-tags: 2014,macumba,microb3,rcc,sbr?hyto?app},
	pages = {1221{\textendash}1236},
	abstract = {Marine Synechococcus cyanobacteria constitute a monophyletic group that displays a wide latitudinal distribution, ranging from the equator to the polar fronts. Whether these organisms are all physiologically adapted to stand a large temperature gradient or stenotherms with narrow growth temperature ranges has so far remained unexplored. We submitted a panel of six strains, isolated along a gradient of latitude in the North Atlantic Ocean, to long- and short-term variations of temperature. Upon a downward shift of temperature, the strains showed strikingly distinct resistance, seemingly related to their latitude of isolation, with tropical strains collapsing while northern strains were capable of growing. This behaviour was associated to differential photosynthetic performances. In the tropical strains, the rapid photosystem II inactivation and the decrease of the antioxydant [beta]-carotene relative to chl a suggested a strong induction of oxidative stress. These different responses were related to the thermal preferenda of the strains. The northern strains could grow at 10[thinsp][deg]C while the other strains preferred higher temperatures. In addition, we pointed out a correspondence between strain isolation temperature and phylogeny. In particular, clades I and IV laboratory strains were all collected in the coldest waters of the distribution area of marine Synechococus. We, however, show that clade I Synechococcus exhibit different levels of adaptation, which apparently reflect their location on the latitudinal temperature gradient. This study reveals the existence of lineages of marine Synechococcus physiologically specialised in different thermal niches, therefore suggesting the existence of temperature ecotypes within the marine Synechococcus radiation.},
	keywords = {2014, adaptation, ecotype, MACUMBA, marine cyanobacteria, MicroB3, rcc, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto?app, Synechococcus, temperature},
	doi = {10.1038/ismej.2013.228},
	url = {http://dx.doi.org/10.1038/ismej.2013.228 10.1038/ismej.2013.228},
	author = {Pittera, Justine and Humily, Florian and Thorel, Maxine and Grulois, Daphne and Garczarek, Laurence and Six, Christophe}
}
@article {hamilton_exposure_2014,
	title = {Exposure to bloom-like concentrations of two marine Synechococcus cyanobacteria (strains CC9311 and CC9902) differentially alters fish behaviour},
	journal = {Conservation Physiology},
	volume = {2},
	number = {cou020},
	year = {2014},
	abstract = {Coastal California experiences large-scale blooms of Synechococcus cyanobacteria, which are predicted to become more prevalent by the end of the 21st century as a result of global climate change. This study investigated whether exposure to bloom-like concentrations of two Synechococcus strains, CC9311 and CC9902, alters fish behaviour. Black perch (Embiotoca jacksoni) were exposed to Synechococcus strain CC9311 or CC9902 (1.5 {\texttimes} 106 cells ml-1) or to control seawater in experimental aquaria for 3 days. Fish movement inside a testing arena was then recorded and analysed using video camera-based motion-tracking software. Compared with control fish, fish exposed to CC9311 demonstrated a significant preference for the dark zone of the tank in the light{\textendash}dark test, which is an indication of increased anxiety. Furthermore, fish exposed to CC9311 also had a statistically significant decrease in velocity and increase in immobility and they meandered more in comparison to control fish. There was a similar trend in velocity, immobility and meandering in fish exposed to CC9902, but there were no significant differences in behaviour or locomotion between this group and control fish. Identical results were obtained with a second batch of fish. Additionally, in this second trial we also investigated whether fish would recover after a 3 day period in seawater without cyanobacteria. Indeed, there were no longer any significant differences in behaviour among treatments, demonstrating that the sp. CC9311-induced alteration of behaviour is reversible. These results demonstrate that blooms of specific marine Synechococcus strains can induce differential sublethal effects in fish, namely alterations light{\textendash}dark preference behaviour and motility.},
	keywords = {RCC1086},
	issn = {2051-1434},
	doi = {10.1093/conphys/cou020},
	url = {https://doi.org/10.1093/conphys/cou020},
	author = {Hamilton, T. J. and Paz-Yepes, J. and Morrison, R. A. and Palenik, B. and Tresguerres, M.}
}
@article {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 {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 {Clerissi2014,
	title = {Unveiling of the diversity of prasinoviruses (phycodnaviridae) in marine samples by using high-throughput sequencing analyses of PCR-Amplified DNA polymerase and major capsid protein genes},
	journal = {Applied and Environmental Microbiology},
	volume = {80},
	number = {10},
	year = {2014},
	note = {tex.mendeley-tags: Micromonas,rcc},
	pages = {3150{\textendash}3160},
	abstract = {Viruses strongly influence the ecology and evolution of their eukaryotic hosts in the marine environment, but little is known about their diversity and distribution. Prasinoviruses infect an abundant and widespread class of phytoplankton, the Mamiellophyceae, and thereby exert a specific and important role in microbial ecosystems. However, molecular tools to specifically identify this viral genus in environmental samples are still lacking. We developed two primer sets, designed for use with polymerase chain reactions and 454 pyrosequencing technologies, to target two conserved genes, encoding the DNA polymerase (PolB gene) and the major capsid protein (MCP gene). While only one copy of the PolB gene is present in Prasinovirus genomes, there are at least seven paralogs for MCP, the copy we named number 6 being shared with other eukaryotic alga-infecting viruses. Primer sets for PolB and MCP6 were thus designed and tested on 6 samples from the Tara Oceans project. The results suggest that the MCP6 amplicons show greater richness but that PolB gave a wider coverage of Prasinovirus diversity. As a consequence, we recommend use of the PolB primer set, which will certainly reveal exciting new insights about the diversity and distribution of prasinoviruses at the community scale.},
	keywords = {Micromonas, rcc, TARA-Oceans},
	doi = {10.1128/aem.00123-14},
	url = {http://aem.asm.org/content/80/10/3150.abstract},
	author = {Clerissi, Camille and Grimsley, Nigel and Ogata, Hiroyuki and Hingamp, Pascal and Poulain, Julie and Desdevises, Yves}
}
@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 {Humily2013,
	title = {A gene island with two possible configurations is involved in chromatic acclimation in marine synechococcus},
	journal = {PLoS ONE},
	volume = {8},
	number = {12},
	year = {2013},
	note = {Publisher: Public Library of Science tex.mendeley-tags: 2013,macumba,rcc,sbr?hyto?app},
	pages = {e84459},
	abstract = {{\textexclamdown}p{\textquestiondown}{\textexclamdown}italic{\textquestiondown}Synechococcus{\textexclamdown}/italic{\textquestiondown}, the second most abundant oxygenic phototroph in the marine environment, harbors the largest pigment diversity known within a single genus of cyanobacteria, allowing it to exploit a wide range of light niches. Some strains are capable of Type IV chromatic acclimation (CA4), a process by which cells can match the phycobilin content of their phycobilisomes to the ambient light quality. Here, we performed extensive genomic comparisons to explore the diversity of this process within the marine {\textexclamdown}italic{\textquestiondown}Synechococcus{\textexclamdown}/italic{\textquestiondown} radiation. A specific gene island was identified in all CA4-performing strains, containing two genes ({\textexclamdown}italic{\textquestiondown}fciA{\textexclamdown}/italic{\textquestiondown}/b) coding for possible transcriptional regulators and one gene coding for a phycobilin lyase. However, two distinct configurations of this cluster were observed, depending on the lineage. CA4-A islands contain the {\textexclamdown}italic{\textquestiondown}mpeZ{\textexclamdown}/italic{\textquestiondown} gene, encoding a recently characterized phycoerythrobilin lyase-isomerase, and a third, small, possible regulator called {\textexclamdown}italic{\textquestiondown}fciC{\textexclamdown}/italic{\textquestiondown}. In CA4-B islands, the lyase gene encodes an uncharacterized relative of MpeZ, called MpeW. While {\textexclamdown}italic{\textquestiondown}mpeZ{\textexclamdown}/italic{\textquestiondown} is expressed more in blue light than green light, this is the reverse for {\textexclamdown}italic{\textquestiondown}mpeW{\textexclamdown}/italic{\textquestiondown}, although only small phenotypic differences were found among chromatic acclimaters possessing either CA4 island type. This study provides novel insights into understanding both diversity and evolution of the CA4 process.{\textexclamdown}/p{\textquestiondown}},
	keywords = {2013, MACUMBA, MicroB3, rcc, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto?app},
	doi = {10.1371/journal.pone.0084459},
	url = {http://dx.doi.org/10.1371/journal.pone.0084459},
	author = {Humily, Florian and Partensky, Fr{\'e}d{\'e}ric and Six, Christophe and Farrant, Gregory K and Ratin, Morgane and Marie, Dominique and Garczarek, Laurence}
}
@article {Collen2013,
	title = {Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {110},
	number = {13},
	year = {2013},
	note = {tex.mendeley-tags: RCC299},
	pages = {5247{\textendash}5252},
	abstract = {Red seaweeds are key components of coastal ecosystems and are economically important as food and as a source of gelling agents, but their genes and genomes have received little attention. Here we report the sequencing of the 105-Mbp genome of the florideophyte Chondrus crispus (Irish moss) and the annotation of the 9,606 genes. The genome features an unusual structure characterized by gene-dense regions surrounded by repeat-rich regions dominated by transposable elements. Despite its fairly large size, this genome shows features typical of compact genomes, e.g., on average only 0.3 introns per gene, short introns, low median distance between genes, small gene families, and no indication of large-scale genome duplication. The genome also gives insights into the metabolism of marine red algae and adaptations to the marine environment, including genes related to halogen metabolism, oxylipins, and multicellularity (microRNA processing and transcription factors). Particularly interesting are features related to carbohydrate metabolism, which include a minimalistic gene set for starch biosynthesis, the presence of cellulose synthases acquired before the primary endosymbiosis showing the polyphyly of cellulose synthesis in Archaeplastida, and cellulases absent in terrestrial plants as well as the occurrence of a mannosylglycerate synthase potentially originating from a marine bacterium. To explain the observations on genome structure and gene content, we propose an evolutionary scenario involving an ancestral red alga that was driven by early ecological forces to lose genes, introns, and intergenetic DNA; this loss was followed by an expansion of genome size as a consequence of activity of transposable elements.},
	keywords = {RCC299},
	doi = {10.1073/pnas.1221259110},
	url = {http://www.pnas.org/content/110/13/5247.abstract},
	author = {Collen, Jonas and Porcel, Betina and Carr{\'e}, Wilfrid and Ball, Steven G and Chaparro, Cristian and Tonon, Thierry and Barbeyron, Tristan and Michel, Gurvan and Noel, Benjamin and Valentin, Klaus and Elias, Marek and Artiguenave, Fran{\c c}ois and Arun, Alok and Aury, Jean-Marc and Barbosa-Neto, Jos{\'e} F and Bothwell, John H and Bouget, Fran{\c c}ois-Yves and Brillet, Loraine and Cabello-Hurtado, Francisco and Capella-Guti{\'e}rrez, Salvador and Charrier, B{\'e}n{\'e}dicte and Cladi{\`e}re, Lionel and Cock, J Mark and Coelho, Susana M and Colleoni, Christophe and Czjzek, Mirjam and Da Silva, Corinne and Delage, Ludovic and Denoeud, France and Deschamps, Philippe and Dittami, Simon M and Gabald{\'o}n, Toni and Gachon, Claire M M and Groisillier, Agn{\`e}s and Herv{\'e}, C{\'e}cile and Jabbari, Kamel and Katinka, Michael and Kloareg, Bernard and Kowalczyk, Nathalie and Labadie, Karine and Leblanc, Catherine and Lopez, Pascal J and McLachlan, Deirdre H and Meslet-Cladiere, Laurence and Moustafa, Ahmed and Nehr, Zofia and Nyvall Coll{\'e}n, Pi and Panaud, Olivier and Partensky, Fr{\'e}d{\'e}ric and Poulain, Julie and Rensing, Stefan A and Rousvoal, Sylvie and Samson, Gaelle and Symeonidi, Aikaterini and Weissenbach, Jean and Zambounis, Antonios and Wincker, Patrick and Boyen, Catherine}
}
@article {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 {Subirana2013,
	title = {Morphology, genome plasticity, and phylogeny in the genus ostreococcus reveal a cryptic species, o. mediterraneus sp. nov. (mamiellales, mamiellophyceae)},
	journal = {Protist},
	volume = {164},
	number = {5},
	year = {2013},
	note = {tex.mendeley-tags: RCC1112,RCC1114,RCC1117,RCC143,RCC1620,RCC1621,RCC1623,RCC1624,RCC2572,RCC2573,RCC2574,RCC2575,RCC2577,RCC2578,RCC2579,RCC2582,RCC2583,RCC2584,RCC2585,RCC2587,RCC2590,RCC344,RCC356,RCC393,RCC501,RCC745,RCC809},
	pages = {643{\textendash}659},
	abstract = {Coastal marine waters in many regions worldwide support abundant populations of extremely small (1-3 ??m diameter) unicellular eukaryotic green algae, dominant taxa including several species in the class Mamiellophyceae. Their diminutive size conceals surprising levels of genetic diversity and defies classical species{\textquoteright} descriptions. We present a detailed analysis within the genus Ostreococcus and show that morphological characteristics cannot be used to describe diversity within this group. Karyotypic analyses of the best-characterized species O. tauri show it to carry two chromosomes that vary in size between individual clonal lines, probably an evolutionarily ancient feature that emerged before species{\textquoteright} divergences within the Mamiellales. By using a culturing technique specifically adapted to members of the genus Ostreococcus, we purified {\textquestiondown}30 clonal lines of a new species, Ostreococcus mediterraneus sp. nov., previously known as Ostreococcus clade D, that has been overlooked in several studies based on PCR-amplification of genetic markers from environment-extracted DNA. Phylogenetic analyses of the S-adenosylmethionine synthetase gene, and of the complete small subunit ribosomal RNA gene, including detailed comparisons of predicted ITS2 (internal transcribed spacer 2) secondary structures, clearly support that this is a separate species. In addition, karyotypic analyses reveal that the chromosomal location of its ribosomal RNA gene cluster differs from other Ostreococcus clades.},
	keywords = {barcode, Chromosome, culture, ITS2, karyotype, picoeukaryote, rcc, RCC1112, RCC1114, RCC1117, RCC143, RCC1620, RCC1621, RCC1623, RCC1624, RCC2572, RCC2573, RCC2574, RCC2575, RCC2577, RCC2578, RCC2579, RCC2582, RCC2583, RCC2584, RCC2585, RCC2587, RCC2590, RCC344, RCC356, RCC393, rcc501, RCC745, RCC809, ribosomal gene},
	doi = {10.1016/j.protis.2013.06.002},
	url = {http://www.sciencedirect.com/science/article/pii/S1434461013000497},
	author = {Subirana, Lucie and P{\'e}quin, B{\'e}rang{\`e}re and Michely, St{\'e}phanie and Escande, Marie-Line and Meilland, Julie and Derelle, Evelyne and Marin, Birger and Piganeau, Gwenael and Desdevises, Yves and Moreau, Herv{\'e} and Grimsley, Nigel H}
}
@article {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 {Vandepoele2013,
	title = {pico-PLAZA, a genome database of microbial photosynthetic eukaryotes},
	journal = {Environmental Microbiology},
	volume = {15},
	number = {8},
	year = {2013},
	note = {tex.mendeley-tags: Micromonas,rcc},
	pages = {2147{\textendash}2153},
	abstract = {With the advent of next generation genome sequencing, the number of sequenced algal genomes and transcriptomes is rapidly growing. Although a few genome portals exist to browse individual genome sequences, exploring complete genome information from multiple species for the analysis of user-defined sequences or gene lists remains a major challenge. pico-PLAZA is a web-based resource (http://bioinformatics.psb.ugent.be/pico-plaza/) for algal genomics that combines different data types with intuitive tools to explore genomic diversity, perform integrative evolutionary sequence analysis and study gene functions. Apart from homologous gene families, multiple sequence alignments, phylogenetic trees, Gene Ontology, InterPro and text-mining functional annotations, different interactive viewers are available to study genome organization using gene collinearity and synteny information. Different search functions, documentation pages, export functions and an extensive glossary are available to guide non-expert scientists. To illustrate the versatility of the platform, different case studies are presented demonstrating how pico-PLAZA can be used to functionally characterize large-scale EST/RNA-Seq data sets and to perform environmental genomics. Functional enrichments analysis of 16 Phaeodactylum tricornutum transcriptome libraries offers a molecular view on diatom adaptation to different environments of ecological relevance. Furthermore, we show how complementary genomic data sources can easily be combined to identify marker genes to study the diversity and distribution of algal species, for example in metagenomes, or to quantify intraspecific diversity from environmental strains.},
	keywords = {Micromonas, rcc},
	doi = {10.1111/1462-2920.12174},
	url = {http://dx.doi.org/10.1111/1462-2920.12174},
	author = {Vandepoele, Klaas and Van Bel, Michiel and Richard, Guilhem and Van Landeghem, Sofie and Verhelst, Bram and Moreau, Herv{\'e} and Van de Peer, Yves and Grimsley, Nigel and Piganeau, Gwenael}
}
@article {Guillou2013,
	title = {The protist ribosomal reference database (PR2): a catalog of unicellular eukaryote small SubUnit rRNA sequences with curated taxonomy},
	journal = {Nucleic Acids Research},
	volume = {41},
	year = {2013},
	note = {tex.mendeley-tags: 2013,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo},
	pages = {D597{\textendash}D604},
	keywords = {2013, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo},
	doi = {10.1093/nar/gks1160},
	author = {Guillou, Laure and Bachar, Dipankar and Audic, St{\'e}phane and Bass, David and Berney, Cedric and Bittner, Lucie and Boutte, Christophe and Burgaud, Gaetan and de Vargas, Colomban and Decelle, Johan and del Campo, Javier and Dolan, John and Dunthorn, Micah and Bente, Edvardsen and Holzmann, Maria and Kooistra, Wiebe H C F and Lara, Enrique and Lebescot, Noan and Logares, Ramiro and Mah{\'e}, Fr{\'e}d{\'e}ric and Massana, Ramon and Montresor, Marina and Morard, Raphael and Not, Fabrice and Pawlowski, Jan and Probert, Ian and Sauvadet, Anne-Laure and Siano, Raffaele and Stoeck, Thorsten and Vaulot, Daniel and Zimmermann, Pascal and Christen, Richard}
}
@article {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 {Kirkham2011,
	title = {Basin-scale distribution patterns of photosynthetic picoeukaryotes along an Atlantic Meridional Transect},
	journal = {Environmental Microbiology},
	volume = {13},
	number = {4},
	year = {2011},
	note = {Publisher: Blackwell Publishing Ltd tex.mendeley-tags: Micromonas,RCC,rcc},
	pages = {975{\textendash}990},
	abstract = {Summary Photosynthetic picoeukaryotes (PPEs) of a size {\textexclamdown} 3 {\textmu}m play a crucial role in oceanic primary production. However, little is known of the structure of the PPE community over large spatial scales. Here, we investigated the distribution of various PPE classes along an Atlantic Meridional Transect sampled in boreal autumn 2004 that encompasses a range of ocean provinces (gyres, upwelling, temperate regions), using dot blot hybridization technology targeting plastid 16S rRNA gene amplicons. Two algal classes, Prymnesiophyceae and Chrysophyceae, dominated the PPE community throughout the Atlantic Ocean, over a range of water masses presenting different trophic profiles. However, these classes showed strongly complementary distributions with Chrysophyceae dominating northern temperate waters, the southern gyre and equatorial regions, while prymnesiophytes dominated the northern gyre. Phylogenetic analyses using both plastid and nuclear rRNA genes revealed a high diversity among members of both classes, including sequences contained in lineages with no close cultured counterpart. Other PPE classes were less prevalent along the transect, with members of the Cryptophyceae, Pelagophyceae and Eustigmatophyceae essentially restricted to specific regions. Multivariate statistical analyses revealed strong relationships between the distribution patterns of some of these latter PPE classes and temperature, light intensity and nutrient concentrations. Cryptophyceae, for example, were mostly found in the upwelling region and associated with higher nutrient concentrations. However, the key classes of Prymnesiophyceae and Chrysophyceae were not strongly influenced by the variables measured. Although there appeared to be a positive relationship between Chrysophyceae distribution and light intensity, the complementary distributions of these classes could not be explained by the variables recorded and this requires further explanation.},
	keywords = {Micromonas, rcc},
	doi = {10.1111/j.1462-2920.2010.02403.x},
	url = {http://dx.doi.org/10.1111/j.1462-2920.2010.02403.x},
	author = {Kirkham, Amy R and Jardillier, Ludwig E and Tiganescu, Ana and Pearman, John and Zubkov, Mikhail V and Scanlan, David J}
}
@article {Reid2011,
	title = {Coccolithophores: Functional biodiversity, enzymes and bioprospecting},
	journal = {Marine Drugs},
	volume = {9},
	number = {4},
	year = {2011},
	note = {tex.mendeley-tags: 2011,rcc},
	pages = {586{\textendash}602},
	keywords = {2011, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO},
	doi = {10.3390/md9040586},
	url = {http://www.mdpi.com/1660-3397/9/4/586/},
	author = {Reid, Emma L and Worthy, Charlotte A and Probert, Ian and Ali, Sohail T and Love, John and Napier, Johnathan and Littlechild, Jenny A and Somerfield, Paul J and Allen, Michael J}
}
@article {Karpowicz2011,
	title = {The GreenCut2 resource, a phylogenomically derived inventory of proteins specific to the plant lineage},
	journal = {Journal of Biological Chemistry},
	volume = {286},
	number = {24},
	year = {2011},
	note = {ISBN: 1083-351X (Electronic)0?021-9258 (Linking) tex.mendeley-tags: rcc745,rcc809},
	month = {jun},
	pages = {21427{\textendash}21439},
	abstract = {The plastid is a defining structure of photosynthetic eukaryotes and houses many plant-specific processes, including the light reactions, carbon fixation, pigment synthesis, and other primary metabolic processes. Identifying proteins associated with catalytic, structural, and regulatory functions that are unique to plastid-containing organisms is necessary to fully define the scope of plant biochemistry. Here, we performed phylogenomics on 20 genomes to compile a new inventory of 597 nucleus-encoded proteins conserved in plants and green algae but not in non-photosynthetic organisms. 286 of these proteins are of known function, whereas 311 are not characterized. This inventory was validated as applicable and relevant to diverse photosynthetic eukaryotes using an additional eight genomes from distantly related plants (including Micromonas, Selaginella, and soybean). Manual curation of the known proteins in the inventory established its importance to plastid biochemistry. To predict functions for the 52\% of proteins of unknown function, we used sequence motifs, subcellular localization, co-expression analysis, and RNA abundance data. We demonstrate that 18\% of the proteins in the inventory have functions outside the plastid and/or beyond green tissues. Although 32\% of proteins in the inventory have homologs in all cyanobacteria, unexpectedly, 30\% are eukaryote-specific. Finally, 8\% of the proteins of unknown function share no similarity to any characterized protein and are plant lineage-specific. We present this annotated inventory of 597 proteins as a resource for functional analyses of plant-specific biochemistry.},
	keywords = {RCC745, RCC809},
	issn = {0021-9258},
	doi = {10.1074/jbc.M111.233734},
	url = {http://www.jbc.org/cgi/doi/10.1074/jbc.M111.233734},
	author = {Karpowicz, Steven J. and Prochnik, Simon E. and Grossman, Arthur R. and Merchant, Sabeeha S.}
}
@article {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 {Edvardsen2011,
	title = {Ribosomal DNA phylogenies and a morphological revision privide the basis for a new taxonomy of Prymnesiales (Haptophyta)},
	journal = {European Journal of Phycology},
	volume = {46},
	year = {2011},
	note = {tex.mendeley-tags: 2011,RCC1185,RCC1187,RCC1189,RCC1385,RCC1387,RCC1388,RCC1390,RCC1432,RCC1438,RCC1440,RCC1441,RCC1448,RCC1453,RCC2056,RCC2057,RCC2059,RCC2060,RCC2061,RCC2063,RCC2064,RCC305,RCC339,RCC3417,RCC3421,RCC3422,RCC3424,RCC3425,RCC3429,RCC406,rcc},
	pages = {202{\textendash}228},
	keywords = {2011, ASSEMBLE, rcc, RCC1185, RCC1187, RCC1189, RCC1385, RCC1387, RCC1388, RCC1390, RCC1432, RCC1438, RCC1440, RCC1441, RCC1448, RCC1453, RCC2056, RCC2057, RCC2059, RCC2060, RCC2061, RCC2063, RCC2064, RCC305, RCC339, RCC3417, RCC3421, RCC3422, RCC3424, RCC3425, RCC3429, RCC406, SBR$_\textrmP$hyto$_\textrmE$PPO},
	doi = {10.1080/09670262.2011.594095},
	author = {Edvardsen, B and Eikrem, W and Throndsen, J and A., Saez and Probert, I and Medlin, L}
}
@article {Beaufort2011,
	title = {Sensitivity of coccolithophores to carbonate chemistry and ocean acidification},
	journal = {Nature},
	volume = {476},
	year = {2011},
	note = {tex.mendeley-tags: 2011,rcc,sbr?hyto?ppo},
	pages = {80{\textendash}83},
	abstract = {Coccolithophores produce the major fraction of pelagic carbonate, a key component of the carbon cycle. The effect of elevated CO2 on their calcification is poorly understood. Culture experiments have yielded varied calcification responses to increased pCO2 between and within coccolithophore taxa. We used a novel automated method for pattern recognition and morphometric analysis to quantify the calcite mass of coccolithophores from {\textquestiondown}700 samples from present past (last 40-Kyr) oceans. Comparison of morphological data with ocean carbonate chemistry reconstructed in both space and time indicate decreasing calcification with increasing pCO2, and decreasing CO32. At pH {\textexclamdown}8.0, delicate Emiliania huxleyi are strongly affected by decalcification. However, highly calcified E. huxleyi morphotypes predominate in waters with lowest pH. This suggests that coccolithophore strains pre-adapted to future, more acidic oceans already populate regions of contemporary oceans. The future carbon feedback from coccolithophore calcification will depend on the genetic diversity and adaptability of coccolithophore populations.},
	keywords = {2011, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1038/nature10295},
	author = {Beaufort, L and Probert, I and de Garidel-Thoron, T and Bendif, E M and Ruiz-Pino, D and Metzl, N and Goyet, C and Buchet, N and Coupel, P and Grelaud, M and Rost, B and Rickaby, R E M and de Vargas, C}
}
@article {Lepere2011,
	title = {Whole Genome Amplification (WGA) of marine photosynthetic eukaryote populations},
	journal = {FEMS Microbiology Ecology},
	volume = {76},
	year = {2011},
	note = {tex.mendeley-tags: 2011,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo},
	pages = {516{\textendash}523},
	keywords = {2011, PICOFUNPAC, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo},
	doi = {10.1111/j.1574-6941.2011.01072.x},
	author = {Lepere, Cecile and Demura, M and Kawachi, M and Romac, S and Probert, I and Vaulot, D}
}
@article {Foresi2010,
	title = {Characterization of a nitric oxide synthase from the plant kingdom: NO generation from the green alga Ostreococcus tauri is light irradiance and growth phase dependent},
	journal = {The Plant Cell},
	volume = {22},
	number = {11},
	year = {2010},
	note = {Edition: 2010/12/02 ISBN: 1532-298X (Electronic) 1040-4651 (Linking) tex.mendeley-tags: RCC745},
	pages = {3816{\textendash}3830},
	abstract = {The search for a nitric oxide synthase (NOS) sequence in the plant kingdom yielded two sequences from the recently published genomes of two green algae species of the Ostreococcus genus, O. tauri and O. lucimarinus. In this study, we characterized the sequence, protein structure, phylogeny, biochemistry, and expression of NOS from O. tauri. The amino acid sequence of O. tauri NOS was found to be 45\% similar to that of human NOS. Folding assignment methods showed that O. tauri NOS can fold as the human endothelial NOS isoform. Phylogenetic analysis revealed that O. tauri NOS clusters together with putative NOS sequences of a Synechoccocus sp strain and Physarum polycephalum. This cluster appears as an outgroup of NOS representatives from metazoa. Purified recombinant O. tauri NOS has a K(m) for the substrate l-Arg of 12 +/- 5 muM. Escherichia coli cells expressing recombinant O. tauri NOS have increased levels of NO and cell viability. O. tauri cultures in the exponential growth phase produce 3-fold more NOS-dependent NO than do those in the stationary phase. In O. tauri, NO production increases in high intensity light irradiation and upon addition of l-Arg, suggesting a link between NOS activity and microalgal physiology.},
	keywords = {*Light, Amino Acid Sequence, Animals, Base Sequence, Chlorophyta/*enzymology/*growth \& development/phys, Humans, Isoenzymes/chemistry/genetics/metabolism, Models, Molecular, Molecular Sequence Data, Nitric Oxide Synthase/chemistry/genetics/*metaboli, Nitric Oxide/*biosynthesis, phylogeny, Plant Proteins/genetics/*metabolism, Protein Structure, rcc, RCC745, Sequence Alignment, Tertiary},
	doi = {10.1105/tpc.109.073510},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=21119059},
	author = {Foresi, N and Correa-Aragunde, N and Parisi, G and Calo, G and Salerno, G and Lamattina, L}
}
@article {Franklin2010,
	title = {Dimethylsulphoniopropionate (DMSP), DMSP-lyase activity (DLA) and dimethylsulphide (DMS) in 10 species of coccolithophore},
	journal = {Marine Ecology-Progress Series},
	volume = {410},
	year = {2010},
	note = {ISBN: 0171-8630 tex.mendeley-tags: 2010,rcc},
	pages = {13{\textendash}23},
	abstract = {We investigated dimethylsulphoniopropionate (DMSP) quota (pg DMSP cell(-1)), intracellular DMSP concentration (mM), in vitro and in vivo DMSP-lyase activity (DLA) and dimethylsulphide (DMS) concentration in batch cultures of 10 species of coccolithophore. Species were chosen to span the phylogenetic and size range that exists within the coccolithophores. Our overall objective was to examine if Emiliania huxleyi, considered a {\textquoteright}model{\textquoteright} coccolithophore species, is representative in terms of DMSP, DLA and DMS, because other coccolithophores contribute substantially to phyto-plankton biomass and carbon fluxes in temperate and tropical waters. DMSP was found in all species, and DMSP quotas correlated significantly with cell volume, reflecting the fundamental physiological role of DMSP as a compatible solute in this group. This DMSP quota-cell volume relationship can be used to calculate the relative contribution of different species to total DMSP. Lowered nutrient availability (batch growth at a 10-fold lower nutrient concentration) did not significantly affect DMSP quota. In contrast to DMSP, DLA and DMS concentration were variable between the subset of species investigated. Coccolithophore DLA is known only in E. huxleyi and Gephyrocapsa oceanica, and we found DLA to be restricted to these closely related species. If DLA is restricted to a subset of coccolithophores, then those species are more likely to emit DMS directly in the sea. Our results indicate that in ecosystems where coccolithophores form stable populations, species other than E. huxleyi can make significant contributions to the particulate DMSP pool and hence to the amount of DMSP potentially available to the microbial loop.},
	keywords = {2010, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO},
	doi = {10.3354/meps08596},
	author = {Franklin, D J and Steinke, M and Young, J and Probert, I and Malin, G}
}
@article {Frada2010,
	title = {A guide to extant coccolithophores (Calcihaptophycidae, Haptophyta) using light microscopy.},
	journal = {Journal of Nannoplankton Research},
	volume = {31},
	year = {2010},
	note = {tex.mendeley-tags: 2010,rcc,sbr?hyto?ppo},
	pages = {58{\textendash}112},
	keywords = {2010, ? No DOI found, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	author = {Frada, Miguel and Young, Jeremy and Cach{\~a}o, M{\'a}rio and Lino, S{\'\i}lvia and Martins, Ana and Narciso, {\'A}urea and Probert, Ian and de Vargas, Colomban}
}
@article {Moreau2010,
	title = {Marine Prasinovirus genomes show low evolutionary divergence and acquisition of protein metabolism genes by horizontal gene transfer},
	journal = {Journal of Virology},
	volume = {84},
	number = {24},
	year = {2010},
	note = {ISBN: 0022-538X tex.mendeley-tags: RCC1105,RCC745},
	pages = {12555{\textendash}12563},
	abstract = {Although marine picophytoplankton are at the base of the global food chain, accounting for half of the planetary primary production, they are outnumbered 10 to 1 and are largely controlled by hugely diverse populations of viruses. Eukaryotic microalgae form a ubiquitous and particularly dynamic fraction of such plankton, with environmental clone libraries from coastal regions sometimes being dominated by one or more of the three genera Bathycoccus, Micromonas, and Ostreococcus (class Prasinophyceae). The complete sequences of two double-stranded (dsDNA) Bathycoccus, one dsDNA Micromonas, and one new dsDNA Ostreococcus virus genomes are described. Genome comparison of these giant viruses revealed a high degree of conservation, both for orthologous genes and for synteny, except for one 36-kb inversion in the Ostreococcus lucimarinus virus and two very large predicted proteins in Bathycoccus prasinos viruses. These viruses encode a gene repertoire of certain amino acid biosynthesis pathways never previously observed in viruses that are likely to have been acquired from lateral gene transfer from their host or from bacteria. Pairwise comparisons of whole genomes using all coding sequences with homologous counterparts, either between viruses or between their corresponding hosts, revealed that the evolutionary divergences between viruses are lower than those between their hosts, suggesting either multiple recent host transfers or lower viral evolution rates.},
	keywords = {RCC1105, RCC745},
	doi = {10.1128/jvi.01123-10},
	author = {Moreau, Herv{\'e} and Piganeau, Gwenael and Desdevises, Yves and Cooke, Richard and Derelle, Evelyne and Grimsley, Nigel}
}
@article {McDonald2010,
	title = {The mixed lineage nature of nitrogen transport and assimilation in marine eukaryotic phytoplankton: a case study of Micromonas},
	journal = {Molecular Biology and Evolution},
	volume = {27},
	number = {10},
	year = {2010},
	note = {tex.mendeley-tags: RCC299},
	pages = {2268{\textendash}2283},
	abstract = {The prasinophyte order Mamiellales contains several widespread marine picophytoplankton (<=2 ??m diameter) taxa, including Micromonas and Ostreococcus. Complete genome sequences are available for two Micromonas isolates, CCMP1545 and RCC299. We performed in silico analyses of nitrogen transporters and related assimilation genes in CCMP1545 and RCC299 and compared these with other green lineage organisms as well as Chromalveolata, fungi, bacteria, and archaea. Phylogenetic reconstructions of ammonium transporter (AMT) genes revealed divergent types contained within each Mamiellales genome. Some were affiliated with plant and green algal AMT1 genes and others with bacterial AMT2 genes. Land plant AMT2 genes were phylogenetically closer to archaeal transporters than to Mamiellales AMT2 genes. The Mamiellales represent the first green algal genomes to harbor AMT2 genes, which are not found in Chlorella and Chlamydomonas or the chromalveolate algae analyzed but are present in oomycetes. Fewer nitrate transporter (NRT) than AMT genes were identified in the Mamiellales. NRT1 was found in all but CCMP1545 and showed highest similarity to Mamiellales and proteobacterial NRTs. NRT2 genes formed a bootstrap-supported clade basal to other green lineage organisms. Several nitrogen-related genes were colocated, forming a nitrogen gene cluster. Overall, RCC299 showed the most divergent suite of nitrogen transporters within the various Mamiellales genomes, and we developed TaqMan quantitative polymerase chain reaction primer{\textendash}probes targeting a subset of these, as well as housekeeping genes, in RCC299. All those investigated showed expression either under standard growth conditions or under nitrogen depletion. Like other recent publications, our findings show a higher degree of {\textquotedblleft}mixed lineage gene affiliations{\textquotedblright} among eukaryotes than anticipated, and even the most phylogenetically anomalous versions appear to be functional. Nitrogen is often considered a regulating factor for phytoplankton populations. This study provides a springboard for exploring the use and functional diversification of inorganic nitrogen transporters and related genes in eukaryotic phytoplankton.},
	keywords = {rcc, RCC299},
	doi = {10.1093/molbev/msq113},
	url = {http://mbe.oxfordjournals.org/content/27/10/2268.abstract},
	author = {McDonald, Sarah M and Plant, Joshua N and Worden, Alexandra Z}
}
@article {Siano2010,
	title = {Pelagodinium gen. nov. and P. beii comb. nov., a dinoflagellate symbiont of planktonic foraminifera},
	journal = {Protist},
	volume = {161},
	year = {2010},
	note = {tex.mendeley-tags: 2010,rcc,rcc1491,sbr?hyto?ppo},
	pages = {385{\textendash}399},
	abstract = {The taxonomic status of the free-living stage of the dinoflagellate Gymnodinium b{\'e}ii, symbiont of the foraminifer Orbulina universa, was reassessed on the basis of detailed morpho-genetic analyses. Electron microscopy observations revealed previously undescribed morphological features of the cell that are important for species recognition. The presence of a single elongated apical vesicle (EAV) ornamented with a row of small knobs, absent in species of the genus Gymnodinium, calls into question the current taxonomic position of the symbiont. The presence of a type E extraplastidial eyespot, the arrangement of the amphiesmal vesicles in series and the absence of trichocysts confirm the affiliation with other symbiotic dinoflagellates and certain genetically related non-symbiotic genera, all belonging to the order Suessiales. The arrangement of the series of vesicles of the analyzed strain is unique within the Suessiales, and the ultrastructure of the pyrenoid is different from other symbiotic dinoflagellates. A large subunit (LSU) rDNA phylogenetic analysis confirmed that the analyzed pelagic symbiont clusters in an independent, well-supported clade within the Suessiales with other sequences of symbiotic dinoflagellates extracted from planktonic foraminifera. Hence a novel genus, Pelagodinium gen. nov., is erected for this pelagic, symbiotic dinoflagellate, and Gymnodinium b{\'e}ii is reclassified as Pelagodinium b{\'e}ii.},
	keywords = {2010, ASSEMBLE, rcc, rcc1491, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1016/j.protis.2010.01.002},
	author = {Siano, R and Montresor, M and Probert, I and Not, F and de Vargas, C}
}
@article {Minge2010,
	title = {A phylogenetic mosaic plastid proteome and unusual plastid-targeting signals in the green-colored dinoflagellate Lepidodinium chlorophorum},
	journal = {BMC Evolutionary Biology},
	volume = {10},
	year = {2010},
	note = {ISBN: 1471-2148 tex.mendeley-tags: 2010,rcc},
	pages = {191},
	abstract = {Background: Plastid replacements through secondary endosymbioses include massive transfer of genes from the endosymbiont to the host nucleus and require a new targeting system to enable transport of the plastid-targeted proteins across 3-4 plastid membranes. The dinoflagellates are the only eukaryotic lineage that has been shown to have undergone several plastid replacement events, and this group is thus highly relevant for studying the processes involved in plastid evolution. In this study, we analyzed the phylogenetic origin and N-terminal extensions of plastid-targeted proteins from Lepidodinium chlorophorum, a member of the only dinoflagellate genus that harbors a green secondary plastid rather than the red algal-derived, peridinin-containing plastid usually found in photosynthetic dinoflagellates. Results: We sequenced 4,746 randomly picked clones from a L. chlorophorum cDNA library. 22 of the assembled genes were identified as genes encoding proteins functioning in plastids. Some of these were of green algal origin. This confirms that genes have been transferred from the plastid to the host nucleus of L. chlorophorum and indicates that the plastid is fully integrated as an organelle in the host. Other nuclear-encoded plastid-targeted protein genes, however, are clearly not of green algal origin, but have been derived from a number of different algal groups, including dinoflagellates, streptophytes, heterokonts, and red algae. The characteristics of N-terminal plastid-targeting peptides of all of these genes are substantially different from those found in peridinin-containing dinoflagellates and green algae. Conclusions: L. chlorophorum expresses plastid-targeted proteins with a range of different origins, which probably arose through endosymbiotic gene transfer (EGT) and horizontal gene transfer (HGT). The N-terminal extension of the genes is different from the extensions found in green alga and other dinoflagellates (peridinin- and haptophyte plastids). These modifications have likely enabled the mosaic proteome of L. chlorophorum.},
	keywords = {2010, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO},
	doi = {10.1186/1471-2148-10-191},
	author = {Minge, M A and Shalchian-Tabrizi, K and Torresen, O K and Takishita, K and Probert, I and Inagaki, Y and Klaveness, D and Jakobsen, K S}
}
@article {Jardillier2010,
	title = {Significant CO2 fixation by small prymnesiophytes in the subtropical and tropical northeast Atlantic Ocean},
	journal = {The ISME Journal},
	volume = {4},
	year = {2010},
	note = {Publisher: International Society for Microbial Ecology tex.mendeley-tags: Micromonas,rcc},
	pages = {1180{\textendash}1192},
	keywords = {Micromonas, rcc},
	doi = {10.1038/ismej.2010.36},
	url = {http://dx.doi.org/10.1038/ismej.2010.36 http://www.nature.com/ismej/journal/vaop/ncurrent/suppinfo/ismej201036s1.html},
	author = {Jardillier, Ludwig and Zubkov, Mikhail V and Pearman, John and Scanlan, David J}
}
@article {Liu2010,
	title = {A timeline of the environmental genetics of the haptophytes},
	journal = {Molecular Biology and Evolution},
	volume = {27},
	year = {2010},
	note = {tex.mendeley-tags: 2010,rcc,sbr?hyto?ppo},
	pages = {171{\textendash}176},
	abstract = {The use of genomic data and the rise of phylogenomics have radically changed our view of the eukaryotic tree of life at a high taxonomic level by identifying four to six "supergroups". Yet our understanding of the evolution of key innovations within each of these supergroups is limited because of poor species sampling relative to the massive diversity encompassed by each supergroup. Here we apply a multigene approach that incorporates a wide taxonomic diversity to infer the timeline of the emergence of strategic evolutionary transitions in the haptophytes, a group of ecologically and biogeochemically significant marine protists that belong to the Chromalveolata supergroup. Four genes (SSU, LSU, tufA and rbcL) were extensively analyzed under several Bayesian models to assess the robustness of the phylogeny, particularly with respect to (i) data partitioning, (ii) the origin of the genes (host vs. endosymbiont), (iii) across-site rate variation and (iv) across-lineage rate variation. We show with a relaxed clock analysis that the origin of haptophytes dates back to 824 MYA (95\% highest probability density 1031-637 MYA). Our dating results show that the ability to calcify evolved earlier than previously thought, between 329-291 MYA, in the Carboniferous period, and that the transition from mixotrophy to autotrophy occurred during the same time period. Although these two transitions precede a habitat change of major diversities from coastal / neritic waters to the pelagic realm (291-243 MYA, around the P/Tr boundary event), the emergence of calcification, full autotrophy and oceanic lifestyle seem mutually independent.},
	keywords = {2010, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1093/molbev/msp222},
	url = {http://mbe.oxfordjournals.org/cgi/content/abstract/msp222v1},
	author = {Liu, Hui and Aris-Brosou, Stephane and Probert, Ian and de Vargas, Colomban}
}
@conference {Meusnier2009,
	title = {DNA barcoding of protists in culture collections},
	booktitle = {Third international barcode of life conference},
	year = {2009},
	note = {tex.mendeley-tags: RCC,rcc},
	address = {Mexico City},
	keywords = {? No DOI found, rcc, SBR$_\textrmP$hyto$_\textrmD$PO},
	author = {Meusnier, Isabelle and Andersen, Robert A and Stern, Rowena and Bertrand, C and Kuepper, Frithjof and Brand, Jerry and Friedl, Thomas and Blackburn, Susan and Dinh, Donna and Acreman, Judy and Sedl{\'a}{\v c}ek, Ivo and P{\v r}ibyl, Pavel and Jutson, Maria and Phang, Siew Moi and Melkonian, M and Karpov, S and Hajibabaei, Mehrdad}
}
@article {Scanlan2009,
	title = {Ecological genomics of marine picocyanobacteria},
	journal = {Microbiology and Molecular Biology Reviews},
	volume = {73},
	year = {2009},
	note = {tex.mendeley-tags: 2009,rcc,sbr?hyto?app},
	pages = {249{\textendash}299},
	keywords = {2009, rcc, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto?app},
	doi = {10.1128/MMBR.00035-08},
	author = {Scanlan, D J and Ostrowski, M and Mazard, S and Dufresne, A and Garczarek, L and Hess, W R and Post, A F and Hagemann, M and Paulsen, I and Partensky, F}
}
@article {Liu2009,
	title = {Extreme diversity in noncalcifying haptophytes explains a major pigment paradox in open oceans},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {106},
	year = {2009},
	note = {tex.mendeley-tags: 2009,rcc,sbr?hyto?ppo},
	pages = {12803{\textendash}12808},
	keywords = {2009, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1073/pnas.0905841106},
	author = {Liu, H and Probert, I and Uitz, J and Claustre, H and Aris-Brossou, S and Frada, M and Not, F and de Vargas, C}
}
@article {Worden2009,
	title = {Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas},
	journal = {Science},
	volume = {324},
	year = {2009},
	note = {tex.mendeley-tags: RCC299,RCC827},
	pages = {268{\textendash}272},
	abstract = {The photosynthetic picoeukaryote Micromonas thrives from tropical to polar marine ecosystems and belongs to an anciently diverged sister clade to land plants. We sequenced genomes from two Micromonas isolates (22 Mb, CCMP1545; 21 Mb, RCC299) and the results improve understanding of their ecology and green-lineage evolution. Despite high 18S rDNA sequence identity, only 90\% of their predicted genes were shared. Novel intronic repeat elements in CCMP1545, otherwise found only in metagenomic data, and unique riboswitch arrangements emphasized their independent evolutionary paths. Phylogenomic profiles revealed putative ancestral features, but also indicated selection/acquisition processes are actively shaping a {\textquoteleft}unique{\textquoteright} gene pool in each differently than {\textquoteleft}core{\textquoteright} genes. Current climate-change trajectories are predicted to produce conditions favoring picophytoplankton, making Micromonas potential indicators of biological change in ocean ecosystems.},
	keywords = {rcc, RCC299, RCC827, SBR$_\textrmP$hyto$_\textrmD$PO, SBR$_\textrmP$hyto$_\textrmE$PPO},
	doi = {10.1126/science.1167222},
	author = {Worden, A Z and Lee, J.- H and Mock, T and Rouz{\'e}, P and Simmons, M P and Aerts, A L and Allen, A E and Cuvelier, M L and Derelle, E and Everett, M V and Foulon, E and Grimwood, J and Gundlach, H and Henrissat, B and Napoli, C and McDonald, S M and Parker, M S and Rombauts, S and Salamov, A and Von Dassow, P and Badger, J H and Coutinho, P M and Demir, E and Dubchak, I and Gentemann, C and Eikrem, W and Gready, J E and John, U and Lanier, W and Lindquist, E A and Lucas, S and Mayer, K F X and Moreau, H and Not, F and Otillar, R and Panaud, O and Pangilinan, J and Paulsen, I and Piegu, B and Poliakov, A and Robbens, S and Schmutz, J and Toulza, E and Wyss, T and Zelensky, A and Zhou, K and Armbrust, E V and Bhattacharya, D and Goodenough, U W and Van de Peer, Y and Grigoriev, I V}
}
@article {Wolhowe2009,
	title = {Growth phase dependent hydrogen isotopic fractionation in alkenone-producing haptophytes},
	journal = {Biogeosciences},
	volume = {6},
	number = {8},
	year = {2009},
	note = {ISBN: 1726-4170 tex.mendeley-tags: 2009,rcc},
	pages = {1681{\textendash}1694},
	abstract = {Recent works have investigated use of the hydrogen isotopic composition Of C-37 alkenones (delta D-K37s), lipid biomarkers of certain haptophyte microalgae, as an independent paleosalinity proxy. We discuss herein the factors impeding the success of such an application and identify the potential alternative use of delta D-K37s measurements as a proxy for non-thermal, physiological stress impacts on the U-37(K{\textquoteright}) paleotemperature index. Batch-culture experiments with the haptophyte Emiliania huxleyi (CCMP 1742) were conducted to determine the magnitude and variability of the isotopic contrasts between individual C-37 alkenones. Further experiments were conducted with Emiliania huxleyi (CCMP 1742) and Gephyrocapsa oceanica (PZ3-1) to determine whether, and to what extent, delta D-K37s varies between the physiological extremes of nutrient-replete exponential growth and nutrient-depleted senescence. Emiliania huxleyi was observed to exhibit an isotopic contrast between di- and tri-unsaturated C-37 alkenones (alpha(K37:3-K37:2)approximate to 0.97) that is nearly identical to that reported recently by others for environmental samples. Furthermore, this contrast appears to be constant with growth stage. The consistency of the offset across different growth stages suggests that a single, well-defined value for alpha(K37:3-K37:2) may exist and that its use in an isotope mass-balance will allow accurate determination of delta D values for individual alkenones without having to rely on time- and labor-intensive chemical separations. The isotopic fractionation between growth medium and C-37 alkenones was observed to increase dramatically upon the onset of nutrient-depletion-induced senescence, suggesting that delta D-K37s, may serve as an objective tool for recognizing and potentially correcting, at least semi-quantitatively, for the effects of nutrient stress on U-37(K{\textquoteright}) temperature records.},
	keywords = {2009, rcc, RCC1300, SBR$_\textrmP$hyto$_\textrmE$PPO},
	doi = {10.5194/bg-6-1681-2009},
	author = {Wolhowe, M D and Prahl, F G and Probert, I and Maldonado, M}
}
@article {Monier2009,
	title = {Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus},
	journal = {Genome Research},
	volume = {19},
	year = {2009},
	note = {tex.mendeley-tags: 2009,rcc,sbr?hyto?ppo},
	pages = {1441{\textendash}1449},
	keywords = {2009, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1101/gr.091686.109},
	author = {Monier, A and Pagarete, A and Allen, M J and Read, B A and de Vargas, C and Claverie, J M and Ogata, H}
}
@article {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 {Langer2009,
	title = {Strain-specific responses of Emiliania huxleyi to changing seawater carbonate chemistry},
	journal = {Biogeosciences},
	volume = {6},
	number = {11},
	year = {2009},
	note = {ISBN: 1726-4170 tex.mendeley-tags: 2009,rcc},
	pages = {2637{\textendash}2646},
	abstract = {Four strains of the coccolithophore E. huxleyi (RCC1212, RCC1216, RCC1238, RCC1256) were grown in dilute batch culture at four CO2 levels ranging from similar to 200 mu atm to similar to 1200 mu atm. Growth rate, particulate organic carbon content, and particulate inorganic carbon content were measured, and organic and inorganic carbon production calculated. The four strains did not show a uniform response to carbonate chemistry changes in any of the analysed parameters and none of the four strains displayed a response pattern previously described for this species. We conclude that the sensitivity of different strains of E. huxleyi to acidification differs substantially and that this likely has a genetic basis. We propose that this can explain apparently contradictory results reported in the literature.},
	keywords = {2009, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO},
	doi = {10.5194/bg-6-2637-2009},
	author = {Langer, G and Nehrke, G and Probert, I and Ly, J and Ziveri, P}
}
@article {VonDassow2009,
	title = {Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell},
	journal = {Genome Biology},
	volume = {10},
	number = {10},
	year = {2009},
	note = {tex.mendeley-tags: 2009,rcc,rcc1216,rcc1217,sbr?hyto?ppo},
	pages = {R114},
	abstract = {BACKGROUND:Eukaryotes are classified as either haplontic, diplontic, or haplo-diplontic, depending on which ploidy levels undergo mitotic cell division in the life cycle. Emiliania huxleyi is one of the most abundant phytoplankton species in the ocean, playing an important role in global carbon fluxes, and represents haptophytes, an enigmatic group of unicellular organisms that diverged early in eukaryotic evolution. This species is haplo-diplontic. Little is known about the haploid cells, but they have been hypothesized to allow persistence of the species between the yearly blooms of diploid cells. We sequenced over 38000 Expressed Sequence Tags (ESTs) from haploid and diploid E. huxleyi normalized cDNA libraries to identify genes involved in important processes specific to each life phase (2N calcification or 1N motility), and to better understand the haploid phase of this prominent haplo-diplontic organism.RESULTS:The haploid and diploid transcriptomes showed a dramatic differentiation, with [almost equal to]20\% greater transcriptome richness in diploid cells than in haploid cells and only [less than or equal to]50\% of transcripts estimated to be common between the two phases. The major functional category of transcripts differentiating haploids included signal transduction and motility genes. Diploid-specific transcripts included Ca2+, H+, and HCO3- pumps. Potential factors differentiating the transcriptomes included haploid-specific Myb transcription factor homologs and an unusual diploid-specific histone H4 homolog.CONCLUSIONS:This study permitted the identification of genes likely involved in diploid-specific biomineralization, haploid-specific motility, and transcriptional control. Greater transcriptome richness in diploid cells suggests they may be more versatile for exploiting a diversity of rich environments whereas haploid cells are intrinsically more streamlined.},
	keywords = {2009, rcc, RCC1216, rcc1217, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1186/gb-2009-10-10-r114},
	url = {http://genomebiology.com/2009/10/10/R114},
	author = {von Dassow, Peter and Ogata, Hiroyuki and Probert, Ian and Wincker, Patrick and Da Silva, Corinne and Audic, St{\'e}phane and Claverie, Jean-Michel and de Vargas, Colomban}
}
@article {Frada2008,
	title = {The {\textquotedblleft}Cheshire Cat{\textquotedblright} escape strategy of the coccolithophore Emiliania huxleyi in response to viral infection},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {105},
	year = {2008},
	note = {tex.mendeley-tags: 2008,rcc,sbr?hyto?ppo},
	pages = {15944{\textendash}15949},
	abstract = {The coccolithophore is one of the most successful eukaryotes in modern oceans. The two phases in its haplodiploid life cycle exhibit radically different phenotypes. The diploid calcified phase forms extensive blooms, which profoundly impact global biogeochemical equilibria. By contrast, the ecological role of the noncalcified haploid phase has been completely overlooked. Giant phycodnaviruses ( viruses, EhVs) have been shown to infect and lyse diploid-phase cells and to be heavily implicated in the regulation of populations and the termination of blooms. Here, we demonstrate that the haploid phase of is unrecognizable and therefore resistant to EhVs that kill the diploid phase. We further show that exposure of diploid to EhVs induces transition to the haploid phase. Thus we have clearly demonstrated a drastic difference in viral susceptibility between life cycle stages with different ploidy levels in a unicellular eukaryote. Resistance of the haploid phase of provides an escape mechanism that involves separation of meiosis from sexual fusion in time, thus ensuring that genes of dominant diploid clones are passed on to the next generation in a virus-free environment. These {\^a}{\texteuro}{\oe}Cheshire Cat{\^a}{\texteuro} ecological dynamics release host evolution from pathogen pressure and thus can be seen as an opposite force to a classic {\^a}{\texteuro}{\oe}Red Queen{\^a}{\texteuro} coevolutionary arms race. In , this phenomenon can account for the fact that the selective balance is tilted toward the boom-and-bust scenario of optimization of both growth rates of calcifying cells and infectivity of EhVs.},
	keywords = {2008, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1073/pnas.0807707105},
	author = {Frada, Miguel and Probert, Ian and Allen, Michael J and Wilson, William H and de Vargas, Colomban}
}
@article {Jancek2008,
	title = {Clues about the genetic basis of adaptation emerge from comparing the proteomes of two Ostreococcus ecotypes (Chlorophyta, Prasinophyceae)},
	journal = {Molecular Biology and Evolution},
	volume = {25},
	number = {11},
	year = {2008},
	note = {Edition: 2008/08/06 ISBN: 1537-1719 (Electronic) 0737-4038 (Linking) tex.mendeley-tags: RCC,rcc},
	pages = {2293{\textendash}2300},
	abstract = {We compared the proteomes of two picoplanktonic Ostreococcus unicellular green algal ecotypes to analyze the genetic basis of their adaptation with their ecological niches. We first investigated the function of the species-specific genes using Gene Ontology databases and similarity searches. Although most species-specific genes had no known function, we identified several species-specific functions involved in various cellular processes, which could be critical for environmental adaptations. Additionally, we investigated the rate of evolution of orthologous genes and its distribution across chromosomes. We show that faster evolving genes encode significantly more membrane or excreted proteins, consistent with the notion that selection acts on cell surface modifications that is driven by selection for resistance to viruses and grazers, keystone actors of phytoplankton evolution. The relationship between GC content and chromosome length also suggests that both strains have experienced recombination since their divergence and that lack of recombination on the two outlier chromosomes could explain part of their peculiar genomic features, including higher rates of evolution.},
	keywords = {adaptation, Base Composition, Chlorophyta/*genetics, Ecosystem, Physiological/*genetics, Phytoplankton/genetics, Proteome/*genetics, rcc, Species Specificity},
	doi = {10.1093/molbev/msn168},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=18678753},
	author = {Jancek, S and Gourbiere, S and Moreau, H and Piganeau, G}
}
@article {Six2008,
	title = {Contrasting photoacclimation strategies in ecotypes of the eukayotic picoplankter {\textexclamdown}i{\textquestiondown}Ostreococcus{\textexclamdown}/i{\textquestiondown}},
	journal = {Limnology and Oceanography},
	volume = {53},
	year = {2008},
	note = {tex.mendeley-tags: 2008,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?app},
	pages = {255{\textendash}265},
	abstract = {Ostreococcus, the smallest known marine picoeukaryote, includes low- and high-light ecotypes. To determine the basis for niche partitioning between Ostreococcus sp. RCC809, isolated from the bottom of the tropical Atlantic euphotic zone, and the lagoon strain Ostreococcus tauri, we studied their photophysiologies under growth irradiances from 15 mmol photons m22 s21 to 800 mmol photons m22 s21 with a common nutrient replete regime. With increasing growth irradiance, both strains down-regulated cellular chlorophyll a and chlorophyll b (Chl a and Chl b) content, increased xanthophyll de-epoxidation correlated with nonphotochemical excitation quenching, and accumulated lutein. Ribulose-1,5-bisphosphate carboxylase/oxygenase content remained fairly stable. Under low-growth irradiances of 15{\textendash}80 mmol photons m22 s21, O. sp. RCC809 had equivalent or slightly higher growth rates, lower Chl a, a higher Chl b : Chl a ratio, and a larger photosystem II (PSII) antenna than O. tauri. O. tauri was more phenotypically plastic in response to growth irradiance, with a larger dynamic range in growth rate, Chl a, photosystem cell content, and cellular absorption cross-section of PSII. Estimating the amino acid and nitrogen costs for photoacclimation showed that the deep-sea oceanic O. sp. RCC809 relies largely on lower nitrogen cost changes in PSII antenna size to achieve a limited range of s-type light acclimation. O. sp. RCC809, however, suffers photoinhibition under higher light. This limited capacity for photoacclimation is compatible with the stable low-light and nutrient conditions at the base of the euphotic layer of the tropical Atlantic Ocean. In the more variable, high-nutrient, lagoon environment, O. tauri can afford to use a higher cost n-type acclimation of photosystem contents to exploit a wider range of light.},
	keywords = {2008, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, sbr?hyto?app},
	doi = {10.4319/lo.2008.53.1.0255},
	author = {Six, C and Finkel, Z V and Rodriguez, F and Marie, D and Partensky, F and Campbell, D A}
}
@article {Claquin2008,
	title = {Effects of temperature on photosynthetic parameters and TEP production in eight species of marine microalgae},
	journal = {Aquatic Microbial Ecology},
	volume = {51},
	year = {2008},
	note = {tex.mendeley-tags: 2008,rcc},
	pages = {1{\textendash}11},
	keywords = {2008, rcc, SBR$_\textrmP$hyto},
	doi = {10.3354/ame01187},
	author = {Claquin, Pascal and Probert, Ian and Lefebvre, S{\'e}bastien and Veron, Benoit}
}
@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 {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 {Jouenne2008,
	title = {Plankton taxonomy in the computer age},
	journal = {Cahiers de Biologie Marine},
	volume = {49},
	year = {2008},
	note = {tex.mendeley-tags: 2008,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {355{\textendash}367},
	abstract = {<p>Preservation of biodiversity starts with knowledge of biodiversity. Based on this principle, numerous projects combining taxonomy and web-based technologies have developed over the last fifteen years, often with the aim of listing all living organisms described to date. Individual lists have been progressively incorporated into federative projects, such as Species 2000 or the Global Biodiversity Information Facility (GBIF). Nowadays, modern taxonomy is splited up between traditionalism and pragmatism. The Internet can provide new advantages to taxonomy (accessibility and efficiency) without reducing quality. In the future, it would be highly desirable to ba able to publish species descriptions and revisions on permanent web-sites on the model of GENBANK. Biodiversity inventory projects should converge to a very limited number of portals (e.g. Encyclopedia of Life). We illustrate these concepts by presenting Plankton*Net an interactive web site dedicated to the taxonomy and images of plankton.</p>
},
	keywords = {2008, ? No DOI found, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	author = {Jouenne, F and Probert, I and Vaulot, D}
}
@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 {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 {Piganeau2007,
	title = {Screening the Sargasso Sea metagenome for data to investigate genome evolution in Ostreococcus (Prasinophyceae, Chlorophyta)},
	journal = {Gene},
	volume = {406},
	year = {2007},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {184{\textendash}190},
	abstract = {The Sargasso Sea water shotgun sequencing unveiled an unprecedented glimpse of marine prokaryotic diversity and gene content. The sequence data was gathered from 0.8 ??m filtered surface water extracts, and revealed picoeukaryotic (cell size {\textexclamdown} 2 ??m) sequences alongside the prokaryotic data. We used the available genome sequence of the picoeukaryote Ostreococcus tauri (Prasinophyceae, Chlorophyta) as a benchmark for the eukaryotic sequence content of the Sargasso Sea metagenome. Sequence data from at least two new Ostreococcus strains were identified and analyzed, and showed a bias towards higher coverage of the AT-rich organellar genomes. The Ostreococcus nuclear sequence data retrieved from the Sargasso metagenome is divided onto 731 scaffolds of average size 3917 bp, and covers 23\% of the complete nuclear genome and 14\% of the total number of protein coding genes in O. tauri. We used this environmental Ostreococcus sequence data to estimate the level of constraint on intronic and intergenic sequences in this compact genome.},
	keywords = {rcc},
	doi = {10.1016/j.gene.2007.09.015},
	author = {Piganeau, G and Moreau, H}
}
@article {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 {Fuller2006,
	title = {Analysis of photosynthetic picoeukaryote diversity at open ocean sites in the Arabian Sea using a PCR biased towards marine algal plastids},
	journal = {Aquatic Microbial Ecology},
	volume = {43},
	year = {2006},
	note = {tex.mendeley-tags: 2006,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {79{\textendash}93},
	keywords = {2006, PICOCEAN, PICODIV, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	doi = {10.3354/ame043079},
	author = {Fuller, Nicholas J and Campbell, Colin and Allen, David J and Pitt, Frances D and Le Gall, F and Vaulot, Daniel and Scanlan, David J}
}
@article {Everroad2006,
	title = {Biochemical bases of Type IV chromatic adaptation in marine Synechococcus spp.},
	journal = {Journal of Bacteriology},
	volume = {188},
	year = {2006},
	note = {tex.mendeley-tags: 2006,rcc,sbr?hyto?app},
	pages = {3345{\textendash}3356},
	keywords = {2006, rcc, SBR$_\textrmP$hyto, sbr?hyto?app},
	doi = {10.1128/JB.188.9.3345-3356.2006},
	author = {Everroad, C and Six, C and Partensky, F and Thomas, J C and Holtzendorff, J and Wood, A M}
}
@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 {Robbens2005,
	title = {Genome-wide analysis of core cell cycle genes in the unicellular green alga Ostreococcus tauri},
	journal = {Molecular Biology and Evolution},
	volume = {22},
	number = {3},
	year = {2005},
	note = {tex.mendeley-tags: RCC745},
	pages = {589{\textendash}597},
	abstract = {The cell cycle has been extensively studied in various organisms, and the recent access to an overwhelming amount of genomic data has given birth to a new integrated approach called comparative genomics. Comparing the cell cycle across species shows that its regulation is evolutionarily conserved; the best-known example is the pivotal role of cyclin-dependent kinases in all the eukaryotic lineages hitherto investigated. Interestingly, the molecular network associated with the activity of the CDK-cyclin complexes is also evolutionarily conserved, thus, defining a core cell cycle set of genes together with lineage-specific adaptations. In this paper, we describe the core cell cycle genes of Ostreococcus tauri, the smallest free-living eukaryotic cell having a minimal cellular organization with a nucleus, a single chloroplast, and only one mitochondrion. This unicellular marine green alga, which has diverged at the base of the green lineage, shows the minimal yet complete set of core cell cycle genes described to date. It has only one homolog of CDKA, CDKB, CDKD, cyclin A, cyclin B, cyclin D, cyclin H, Cks, Rb, E2F, DP, DEL, Cdc25, and Wee L We have also added the APC and SCF E3 ligases to the core cell cycle gene set. We discuss the potential of genome-wide analysis in the identification of divergent orthologs of cell cycle genes in different lineages by mining the genomes of evolutionarily important and strategic organisms.},
	keywords = {Anaphase Promoting Complex, Arabidopsis Thaliana, Cdk Activity, cell division cycle, Chlorophyta, cyclin, cyclin dependant kinase, Green alga, Kinase, Ostreococcus tauri, Plant, Prasinophyceae, rcc, RCC745, Retinoblastoma Protein, Saccharomyces Cerevisiae, Yeast},
	doi = {10.1093/molbev/msi044},
	author = {Robbens, S and Khadaroo, B and Camasses, A and Derelle, E and Ferraz, C and Inze, D and Van, de Peer Y and Moreau, H}
}
@article {Six2005a,
	title = {New insights into the nature and phylogeny of prasinophyte antenna proteins: Ostreococcus tauri, a case study},
	journal = {Molecular Biology and Evolution},
	volume = {22},
	number = {11},
	year = {2005},
	note = {tex.mendeley-tags: RCC113,RCC114,RCC745: RCC417},
	pages = {2217{\textendash}2230},
	abstract = {The basal position of the Mamiellales (Prasinophyceae) within the green lineage makes these unicellular organisms key to elucidating early stages in the evolution of chlorophyll a/b{\textendash}binding light-harvesting complexes (LHCs). Here, we unveil the complete and unexpected diversity of Lhc proteins in Ostreococcus tauri, a member of the Mamiellales order, based on results from complete genome sequencing. Like Mantoniella squamata, O. tauri possesses a number of genes encoding an unusual prasinophyte-specific Lhc protein type herein designated "Lhcp". Biochemical characterization of the complexes revealed that these polypeptides, which bind chlorophylls a, b, and a chlorophyll c{\textendash}like pigment (Mg-2,4-divinyl-phaeoporphyrin a5 monomethyl ester) as well as a number of unusual carotenoids, are likely predominant. They are retrieved to some extent in both reaction center I (RCI){\textendash} and RCII-enriched fractions, suggesting a possible association to both photosystems. However, in sharp contrast to previous reports on LHCs of M. squamata, O. tauri also possesses other LHC subpopulations, including LHCI proteins (encoded by five distinct Lhca genes) and the minor LHCII polypeptides, CP26 and CP29. Using an antibody against plant Lhca2, we unambiguously show that LHCI proteins are present not only in O. tauri, in which they are likely associated to RCI, but also in other Mamiellales, including M. squamata. With the exception of Lhcp genes, all the identified Lhc genes are present in single copy only. Overall, the discovery of LHCI proteins in these prasinophytes, combined with the lack of the major LHCII polypeptides found in higher plants or other green algae, supports the hypothesis that the latter proteins appeared subsequent to LHCI proteins. The major LHC of prasinophytes might have arisen prior to the LHCII of other chlorophyll a/b{\textendash}containing organisms, possibly by divergence of a LHCI gene precursor. However, the discovery in O. tauri of CP26-like proteins, phylogenetically placed at the base of the major LHCII protein clades, yields new insight to the origin of these antenna proteins, which have evolved separately in higher plants and green algae. Its diverse but numerically limited suite of Lhc genes renders O. tauri an exceptional model system for future research on the evolution and function of LHC components.},
	keywords = {rcc, RCC113, RCC114, RCC417, RCC745, SBR$_\textrmP$hyto$_\textrmD$PO},
	doi = {10.1093/molbev/msi220},
	author = {Six, C and Worden, A Z and Rodriguez, F and Moreau, H and Partensky, F}
}
@article {Six2005,
	title = {Two novel phycoerythrin-associated linker proteins in the marine cyanobacterium synechococcus sp. Strain WH8102},
	journal = {Journal of Bacteriology},
	volume = {187},
	number = {5},
	year = {2005},
	note = {tex.mendeley-tags: 2005,rcc,sbr?hyto},
	pages = {1685{\textendash}1694},
	abstract = {The recent availability of the whole genome of Synechococcus sp. strain WH8102 allows us to have a global view of the complex structure of the phycobilisomes of this marine picocyanobacterium. Genomic analyses revealed several new characteristics of these phycobilisomes, consisting of an allophycocyanin core and rods made of one type of phycocyanin and two types of phycoerythrins (I and II). Although the allophycocyanin appears to be similar to that found commonly in freshwater cyanobacteria, the phycocyanin is simpler since it possesses only one complete set of alpha and beta subunits and two rod-core linkers (CpcG1 and CpcG2). It is therefore probably made of a single hexameric disk per rod. In contrast, we have found two novel putative phycoerythrin-associated linker polypeptides that appear to be specific for marine Synechococcus spp. The first one (SYNW2000) is unusually long (548 residues) and apparently results from the fusion of a paralog of MpeC, a phycoerythrin II linker, and of CpeD, a phycoerythrin-I linker. The second one (SYNW1989) has a more classical size (300 residues) and is also an MpeC paralog. A biochemical analysis revealed that, like MpeC, these two novel linkers were both chromophorylated with phycourobilin. Our data suggest that they are both associated (partly or totally) with phycoerythrin II, and we propose to name SYNW2000 and SYNW1989 MpeD and MpeE, respectively. We further show that acclimation of phycobilisomes to high light leads to a dramatic reduction of MpeC, whereas the two novel linkers are not significantly affected. Models for the organization of the rods are proposed.},
	keywords = {2005, rcc, SBR$_\textrmP$hyto, sbr?hyto},
	doi = {10.1128/JB.187.5.1685-1694.2005},
	url = {http://jb.asm.org/cgi/content/abstract/187/5/1685},
	author = {Six, Christophe and Thomas, Jean-Claude and Thion, Laurent and Lemoine, Yves and Zal, Frank and Partensky, Fr{\'e}d{\'e}ric}
}
@article {Guillou2004,
	title = {Diversity of picoplanktonic prasinophytes assessed by direct nuclear SSU rDNA sequencing of environmental samples and novel isolates retrieved from oceanic and coastal marine ecosystems},
	journal = {Protist},
	volume = {155},
	year = {2004},
	note = {tex.mendeley-tags: 2004,rcc,sbr?hyto},
	pages = {193{\textendash}214},
	keywords = {2004, PICODIV, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto, SOMLIT},
	doi = {10.1078/143446104774199592},
	author = {Guillou, Laure and Eikrem, W and Chr{\'e}tiennot-Dinet, M.-J. and Le Gall, F and Massana, R and Romari, K and Pedr{\'o}s-Ali{\'o}, C and Vaulot, D}
}
@article {Vaulot2004,
	title = {The roscoff culture collection (RCC): a collection dedicated to marine picoplankton},
	journal = {Nova Hedwigia},
	volume = {79},
	number = {1/2},
	year = {2004},
	note = {tex.mendeley-tags: 2004,rcc,sbr?hyto},
	pages = {49{\textendash}70},
	keywords = {10$_\textrmb$est, 2004, PICODIV, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto},
	doi = {10.1127/0029-5035/2004/0079-0049},
	author = {Vaulot, D and Le Gall, F and Marie, D and Guillou, L and Partensky, F}
}
@article {Fuller2003,
	title = {Clade-specific 16S ribosomal DNA oligonucleotides reveal the predominance of a single marine Synechococcus clade throughout a stratified water column in the Red Sea},
	journal = {Applied and Environmental Microbiology},
	volume = {69},
	number = {5},
	year = {2003},
	note = {tex.mendeley-tags: 2003,rcc,sbr?hyto},
	pages = {2430{\textendash}2443},
	abstract = {Phylogenetic relationships among members of the marine Synechococcus genus were determined following sequencing of the 16S ribosomal DNA (rDNA) from 31 novel cultured isolates from the Red Sea and several other oceanic environments. This revealed a large genetic diversity within the marine Synechococcus cluster consistent with earlier work but also identified three novel clades not previously recognized. Phylogenetic analyses showed one clade, containing halotolerant isolates lacking phycoerythrin (PE) and including strains capable, or not, of utilizing nitrate as the sole N source, which clustered within the MC-A (Synechococcus subcluster 5.1) lineage. Two copies of the 16S rRNA gene are present in marine Synechococcus genomes, and cloning and sequencing of these copies from Synechococcus sp. strain WH 7803 and genomic information from Synechococcus sp. strain WH 8102 reveal these to be identical. Based on the 16S rDNA sequence information, clade-specific oligonucleotides for the marine Synechococcus genus were designed and their specificity was optimized. Using dot blot hybridization technology, these probes were used to determine the in situ community structure of marine Synechococcus populations in the Red Sea at the time of a Synechococcus maximum during April 1999. A predominance of genotypes representative of a single clade was found, and these genotypes were common among strains isolated into culture. Conversely, strains lacking PE, which were also relatively easily isolated into culture, represented only a minor component of the Synechococcus population. Genotypes corresponding to well-studied laboratory strains also appeared to be poorly represented in this stratified water column in the Red Sea.},
	keywords = {2003, PICODIV, rcc, SBR$_\textrmP$hyto, sbr?hyto},
	issn = {0099-2240},
	doi = {10.1128/AEM.69.5.2430-2443.2003},
	url = {http://aem.asm.org/cgi/content/abstract/69/5/2430},
	author = {Fuller, Nicholas J and Marie, Dominique and Partensky, Fr{\'e}d{\'e}ric and Vaulot, Daniel and Post, Anton F and Scanlan, David J}
}
@article {Palenik2003,
	title = {The genome of a motile marine Synechococcus},
	journal = {Nature},
	volume = {424},
	number = {6952},
	year = {2003},
	note = {tex.mendeley-tags: 2003,rcc,sbr?hyto},
	pages = {1037{\textendash}1042},
	abstract = {Marine unicellular cyanobacteria are responsible for an estimated 20-40\% of chlorophyll biomass and carbon fixation in the oceans(1). Here we have sequenced and analysed the 2.4-megabase genome of Synechococcus sp. strain WH8102, revealing some of the ways that these organisms have adapted to their largely oligotrophic environment. WH8102 uses organic nitrogen and phosphorus sources and more sodium-dependent transporters than a model freshwater cyanobacterium. Furthermore, it seems to have adopted strategies for conserving limited iron stores by using nickel and cobalt in some enzymes, has reduced its regulatory machinery (consistent with the fact that the open ocean constitutes a far more constant and buffered environment than fresh water), and has evolved a unique type of swimming motility. The genome of WH8102 seems to have been greatly influenced by horizontal gene transfer, partially through phages. The genetic material contributed by horizontal gene transfer includes genes involved in the modification of the cell surface and in swimming motility. On the basis of its genome, WH8102 is more of a generalist than two related marine cyanobacteria(2).},
	keywords = {2003, Cyanobacterium Synechococcus, Degradation, Ecology, Gene, IDENTIFICATION, Polypeptide, Prochlorococcus, rcc, SBR$_\textrmP$hyto, sbr?hyto, SEQUENCE, Sp Pcc7942, Strains},
	doi = {10.1038/nature01943},
	author = {Palenik, B and Brahamsha, B and Larimer, F W and Land, M and Hauser, L and Chain, P and Lamerdin, J and Regala, W and Allen, E E and McCarren, J and Paulsen, I and Dufresne, A and Partensky, F and Webb, E A and Waterbury, J}
}
@article {Toledo2003,
	title = {A Synechococcus serotype is found preferentially in surface marine waters},
	journal = {Limnology and Oceanography},
	volume = {48},
	number = {5},
	year = {2003},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {1744{\textendash}1755},
	abstract = {In marine ecosystems, gradients of light, temperature, and nutrients occur horizontally (coastal to offshore) and vertically. The extent to which microorganisms acclimate or speciate in response to these gradients is under active investigation. Strain isolation data (e.g., site or depth), environmental DNA clone libraries, and preliminary physiology experiments have indicated that marine Synechococcus strain CC9605 might be adapted to the surface oligotrophic ocean. In the present work, we used an immunofluorescent approach to detect the CC9605 serotype in the California Current during September 1998. At two offshore stations, samples were collected along vertical profiles. The relative abundance of the CC9605 serotype was significantly higher in shallow depths within the mixed layer than in deeper depths at the two stations, with maximum values (+/- standard deviation) of 10.3\% +/- 6.4 and 28.7\% +/- 9.5. Surface samples along an offshore-inshore transect showed higher abundance in the most oligotrophic site (8\% +/- 3), compared with almost 1\% inshore, but one coastal site also had high relative abundance of the CC9605 serotype (7\% +/- 0.5). These data indicate that Synechococcus strains are not uniformly distributed and that some strains, such as CC9605, are more abundant in the mixed layer of the euphotic zone than below the mixed layer.},
	keywords = {Aquatic-sciences, california-current, cyanobacteria-, diversity-, flow-cytometry, immunofluorescence-, North-atlantic-ocean, phytoplankton-, prochlorococcus-populations, rcc, sargasso-sea, strains-},
	doi = {10.4319/lo.2003.48.5.1744},
	author = {Toledo, G and Palenik, B}
}
@article {Derelle2002,
	title = {DNA libraries for sequencing the genome of Ostreococcus tauri (Chlorophyta, Prasinophyceae): The smallest free-living eukaryotic cell},
	journal = {Journal of Phycology},
	volume = {38},
	number = {6},
	year = {2002},
	note = {tex.mendeley-tags: RCC745},
	pages = {1150{\textendash}1156},
	abstract = {Ostreococcus tauri is a marine photosynthetic picoeukaryote presenting a minimal cellular organization with one nucleus, one chloroplast, and one mitochondrion. It has the smallest genome described among free-living eukaryotic cells, and we showed by pulsed-field gel electrophoresis (PFGE) that it is divided between 15 bands ranging from 1.2 to 0.15 Mb, giving a total size of 9.7 Mb. A Bacterial Artificial Chromosome (BAC) library was prepared from genomic DNA extracted from a culture of O. tauri. A total of 2457 clones was obtained with an average insert size of around 70 kb, representing an 18-fold coverage of the genome. The library was spotted on high density filters, and several probes of coding sequences were hybridized to both the high density BAC library filters and directly to the dried PFGE gels of the O. tauri genomic DNA. These hybridizations allowed a preliminary organization of the library and the localization of several markers on the chromosomes. Randomly selected fragments were also sequenced, representing 12\% of the O. tauri genome. Many sequences showed significant similarities in data banks, mainly with plant and algae sequences. About 1000 coding sequences could be identified. These data confirmed the position of O. tauri in the green lineage and the hypothesis of a very compact organization of its genome.},
	keywords = {Pico$_\textrmR$eview, rcc, RCC745},
	doi = {10.1046/j.1529-8817.2002.02021.x},
	url = {c:\%5CDV\%5CPapers reprints\%5CPhytoplankton Physiology\%5CDerelle Ostreococcus DNA libraries JPhycol 02.pdf},
	author = {Derelle, E and Ferraz, C and Lagoda, P and Eychenie, S and Cooke, R and Regad, F and Sabau, X and Courties, C and Delseny, M and Demaille, J and Picard, A and Moreau, H}
}
@article {Laloui2002,
	title = {Genotyping of axenic and non-axenic isolates of the genus Prochlorococcus and the OMF-{\textquoteright}Synechococcus{\textquoteright} clade by size, sequence analysis or RFLP of the Internal Transcribed Spacer of the ribosomal operon},
	journal = {Microbiology},
	volume = {148},
	number = {2},
	year = {2002},
	note = {tex.mendeley-tags: 2002,rcc,sbr?hyto},
	pages = {453{\textendash}465},
	abstract = {PCR amplicons of the Internal Transcribed Spacer (ITS) of the rrn operon of three axenic OMF (oceanic, marine and freshwater) strains of {\textquoteright}Synechococcus{\textquoteright} (wH7803, PCC 7001 and PCC 6307, respectively) differ greatly in length from that of the axenic Prochlorococcus marinus subsp. pastoris PCC 9511(T), although these four cyanobacteria cluster relatively closely in phylogenetic trees inferred from 165 rRNA gene sequences. The ITSs of three strains (PCC 9511(T), PCC 6307 and PCC 7001) were sequenced and compared with those available for strains Prochlorococcus MED4 (CCMP 1378) and MIT9313 from genome sequencing projects. In spite of large differences in length, sequence and mean DNA base composition, conserved domains important for transcriptional antitermination and folding of the rRNA transcripts were identified in all ITSs. A new group-specific primer permitted ITS amplification even with non-axenic isolates of Prochlorococcus and one OMF-{\textquoteright}Synechococcus{\textquoteright} strain. Prochlorococcus isolates of the high-light-adapted clade (HL) differed from representatives of the low-light-adapted Glade (LL) by the length of their ITS. Restriction fragment length polymorphism (RFLP) of the ITS amplicons revealed three subclusters among the HL strains. Size, sequence data and RFLP of the ITS amplicons will therefore be valuable markers for the identification of different Prochlorococcus genotypes and for their discrimination from other cyanobacterial relatives with which they often co-exist in oceanic ecosystems.},
	keywords = {2002, Blue Green Alga, Chlorophyll B, community structure, cyanobacteria, Escherichia Coli, Marine Prokaryote, Multiple Evolutionary Origins, North Atlantic Ocean, Pacific Ocean, rcc, Rna Operon, SBR$_\textrmP$hyto, sbr?hyto},
	doi = {10.1099/00221287-148-2-453},
	author = {Laloui, W and Palinska, K A and Rippka, R and Partensky, F and de Marsac, N T and Herdman, M and Iteman, I}
}
@article {Jacquet2001,
	title = {Cell cycle regulation by light in Prochlorococcus strains},
	journal = {Applied and Environmental Microbiology},
	volume = {67},
	number = {2},
	year = {2001},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {782{\textendash}790},
	abstract = {<p>The effect of light on the synchronization of cell cycling was investigated in several strains of the oceanic photosynthetic prokaryote Prochlorococcus using flow cytometry. When exposed to a light-dark (L-D) cycle with an irradiance of 25 mu mol of quanta m(-2) s(-1), the low-light-adapted strain SS 120 appeared to be better synchronized than the high-light-adapted strain PCC 9511. Submitting LD-entrained populations to shifts (advances or delays) in the timing of the "light on" signal translated to corresponding shifts in the initiation of the S phase, suggesting that this signal is a key parameter for the synchronization of population cell cycles. Cultures that were shifted from an L-D cycle to continuous irradiance showed persistent diel oscillations of flow-cytometric signals (light scatter and chlorophyll fluorescence) but with significantly reduced amplitudes and a phase shift. Complete darkness arrested most of the cells in the G(1), phase of the cell cycle, indicating that light is required to trigger the initiation of DNA replication and cell division. However, some cells also arrested in the S phase, suggesting that cell cycle controls in Prochlorococcus spp. are not as strict as in marine Synechococcus spp. Shifting Prochlorococcus cells from low to high irradiance translated quasi-instantaneously into an increase of cells in both the S and G(2) phases of the cell cycle and then into faster growth, whereas the inverse shift induced rapid slowing of the population growth rate. These data suggest a close coupling between irradiance levels and cell cycling in Prochloroeoccus spp.</p>
},
	keywords = {cyanobacteria, Equatorial Pacific, Gene Expression, Growth, Mediterranean Sea, North Atlantic, Photosynthetic Prokaryote, picoplankton, Populations, rcc, Synechococcus},
	doi = {10.1128/AEM.67.2.782-790.2001},
	author = {Jacquet, S and Partensky, F and Marie, D and Casotti, R and Vaulot, D}
}
@article {West2001,
	title = {Closely related Prochlorococcus genotypes show remarkably different depth distributions in two oceanic regions as revealed by in situ hybridization using 16S rRNA-targeted oligonucleotides},
	journal = {Microbiology - UK},
	volume = {147},
	number = {7},
	year = {2001},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {1731{\textendash}1744},
	abstract = {An in situ hybridization method was applied to the identification of marine cyanobacteria assignable to the genus Procholorococcus using harseradish-peroxidase-labelled 16S rRNA-targeted oligonucleotide probes in combination with tyramide signal amplification (TSA). With this method very bright signals were obtained, in contrast to hybridizations with oligonucleotides monolabelled with fluorochromes, which failed to give positive signals. Genotype-specific oligonucleotides for high light (HL)- and low light (LL)adapted members of this genus were identified by 16S rRNA sequence analyses and their specificities confirmed in whole-cell hybridizations with cultured strains of Prochlorococcus marinus Chisholm et al., 1992, Prochlorococcus sp. and Synechococcus sp. In situ hybridization of these genotype-specific probes to field samples from stratified water bodies collected in the North Atlantic Ocean and the Red Sea allowed a rapid assessment of the abundance and spatial distribution of HL- and LL-adapted Prochlorococcus. In both oceanic regions the LL-adapted Prochlorococcus populations were localized in deeper water whereas the HL-adapted Prochlorococcus populations were not only distinct in each region but also exhibited strikingly different depth distributions, HLI being confined to shallow wafer in the North Atlantic, in contrast to HLII, which was present throughout the water column in the Red Sea.},
	keywords = {Escherichia Coli, IDENTIFICATION, Marine Cyanobacterium, Nucleic Acid Probes, Photosynthetic Prokaryote, PICODIV, Populations, rcc, Ribosomal Rna, SEQUENCES, Tyramide Signal Amplification, Whole Cell Hybridization},
	doi = {10.1099/00221287-147-7-1731},
	author = {West, N J and Schonhuber, W A and Fuller, N J and Amann, R I and Rippka, R and Post, A F and Scanlan, D J}
}
@article {Jacquet2001a,
	title = {Diel patterns of growth and division in marine picoplankton in culture},
	journal = {Journal of Phycology},
	volume = {37},
	number = {3},
	year = {2001},
	note = {tex.mendeley-tags: 2001,rcc,sbr?hyto},
	pages = {357{\textendash}369},
	abstract = {{The effect of a 12:12-h light:dark (LD) cycle on the phasing of several cell parameters was explored in a variety of marine picophytoplanktonic strains. These included the photosynthetic prokaryotes Pro-chlorococcus (strains MED 4, PCC 9511, and SS 120) and Synechococcus (strains ALMO 03, ROS 04, WH 7803, and WH 8103) and five picoeukaryotes (Bathycoccus prasinos Eikrem et Throndsen, Bolidomonas pacifica Guillou et Chretiennot-Dinet, Micromonas pusilla Manton et Parke, Pelagomonas calceolata Andersen et Saunders, and Pycnococcus provasolii Guillard et al.). Flow cytometric analysis was used to determine the relationship between cell light scatter, pigment fluorescence, DNA (when possible), and the LD cycle in these organisms. Asexpected, growth and division were tightly coupled to the LD cycle for all of these strains. For both Prochlorococcus and picoeukaryotes, chi and intracellular carbon increased throughout the light period as estimated by chi fluorescence and light scatter, respectively. In response to cell division, these parameters decreased regularly during the early part of the dark period, a decrease that either continued throughout the dark period or stopped for the second half of the dark period. For Synechococcus, the decrease of chi and scatter occurred earlier (in the middle of the light period), and for some strains these cellular parameters remained constant throughout the dark period. The timing of division was very similar for all picoeukaryotes and occurred just before the subjective dusk, whereas it was more variable between the different Prochlorococcus and Synechococcus strains. The burst of division for Prochlorococcus SS 120 and PCC 9511 was recorded at the subjective dusk, whereas the MED 4 strain divided later at night. Synechococcus ALMO 03, ROS 04, and WH 7803, which have a low phycourobilin to phycoerythrobilin (PUB:PEB) ratio, divided earlier, and their division was restricted to the light period. In contrast, the high PUB:PEB Synechococcus strain WH 8103 divided preferentially at night. There was a weak linear relationship between the FALS(max):FALS(min) ratio and growth rate calculated from cell counts (r = 0.83},
	keywords = {2001, Cell Division, Cyanobacteria Synechococcus, Dividing Cells, Equatorial Pacific, flow cytometry, Mediterranean Sea, Natural Populations, North Pacific Ocean, Photosynthetic Picoplankton, Picophytoplankton Dynamics, rcc, SBR$_\textrmP$hyto, sbr?hyto},
	doi = {10.1046/j.1529-8817.2001.037003357.x},
	author = {Jacquet, S and Partensky, F and Lennon, J F and Vaulot, D}
}
@article {Guillou1999a,
	title = {Diversity and abundance of Bolidophyceae (Heterokonta) in two oceanic regions},
	journal = {Applied and Environmental Microbiology},
	volume = {65},
	number = {10},
	year = {1999},
	note = {ISBN: 0099-2240 Publisher: Amer Soc Microbiology tex.address: 1325 Massachusetts Avenue, NW, Washington, DC 20005-4171, USA tex.mendeley-tags: 1999,rcc,sbr?hyto},
	pages = {4528{\textendash}4536},
	abstract = {The diversity and abundance of the Bolidophyceae (Heterokonta), a newly described picoplanktonic algal class which is a sister group to the diatoms, was assessed in the equatorial Pacific Ocean and in the Mediterranean Sea by culture isolation, molecular biology techniques, and pigment analyses. Eight strains of Bolidophyceae were isolated in culture from different mesotrophic and oligotrophic areas. The corresponding small subunit (SSU) rRNA gene sequences allowed us to design two probes specific for the Bolidophyceae. These probes have been used in natural samples (i) to selectively amplify and detect Bolidophyceae sequences and (ii) to quantify the relative abundance of Bolidophyceae within the picoeukaryote community. Sequences available to date indicate that the class Bolidophyceae comprises at least three different clades, two corresponding to the previously described species Bolidomonas pacifica and Bolidomonas mediterranea and the third one corresponding to a subspecies of B. Pacifica. Amplification of the SSU rRNA gene from natural samples with universal primers and hybridization using a Bolidomonas-specific probe followed by a eukaryote-specific probe allowed us to estimate the contribution of the Bolidophyceae to the eukaryotic DNA in both Pacific and Mediterranean waters to be lower than 1\%. Similarly, high-performance liquid chromatography analyses of fucoxanthin, the major carotenoid present in Bolidophyceae, indicated that less than 4\% of the total chlorophyll a in the picoplanktonic fraction in the equatorial Pacific was due to Bolidophyceae. Consequently, although strains of Bolidophyceae have been isolated from samples collected at several stations, this new class seems to have been a minor component of the natural picoeukaryotic populations in the ecosystems investigated, at least during the periods sampled.},
	keywords = {1999, ATLANTIC, BACTERIOPLANKTON, community structure, flow-cytometry, MOLECULAR PHYLOGENY, PACIFIC, phytoplankton, PIGMENT SIGNATURES, rcc, RNA GENE SEQUENCE, SBR$_\textrmP$hyto, sbr?hyto, ULTRAPHYTOPLANKTON},
	doi = {10.1128/AEM.65.10.4528-4536.1999},
	author = {Guillou, L and Moon-van der Staay, S Y and Claustre, H and Partensky, F and Vaulot, D}
}
@article {Courties1998,
	title = {Phylogenetic analysis and genome size of Ostreococcus tauri (Chlorophyta, Prasinophyceae)},
	journal = {Journal of Phycology},
	volume = {34},
	number = {5},
	year = {1998},
	note = {tex.mendeley-tags: RCC745},
	pages = {844{\textendash}849},
	abstract = {Ostreococcus tauri Courties et Chretiennot-Dinet is the smallest described autotrophic eukaryote dominating the phytoplanktonic assemblage of the marine Mediterranean Thau lagoon (France). Its taxonomic position was partly elucidated from ultrastructure and high-pressure liquid chromatography (HLPC) pigment analysis. The sequence analysis of the 18S rDNA gene of O. Tauri measured here is available in EMBL Nucleotide Sequence Database (accession number: Y15814) and allowed to clarify its phylogenetic position. O. Tauri belongs to the Prasinophyceae and appears very close to Mantoniella, a typical scaly Prasinophyceae, morphologically very different from the naked and coccoid Ostreococcus. An electrophoretic analysis of O. Tauri shows that the nucleus contains 10.20 mbp. This small genome fragmented into 14 chromosomes ranging in size from 300 to 1500 kbp, confirms the minimalist characteristics of Ostreococcus tauri.},
	keywords = {rcc, RCC745, SBR$_\textrmP$hyto},
	doi = {10.1046/j.1529-8817.1998.340844.x},
	author = {Courties, C and Perasso, R and Chr{\'e}tiennot-Dinet, M.-J. and Gouy, M and Guillou, L and Troussellier, M}
}
@article {toledo_synechococcus_1997,
	title = {Synechococcus diversity in the California current as seen by RNA polymerase (rpoC1) gene sequences of isolated strains.},
	journal = {Applied and environmental microbiology},
	volume = {63},
	number = {11},
	year = {1997},
	pages = {4298{\textendash}4303},
	keywords = {RCC1086},
	issn = {0099-2240},
	doi = {10.1128/AEM.63.11.4298-4303.1997},
	url = {https://AEM.asm.org/content/63/11/4298},
	author = {Toledo, G and Palenik, B}
}
@article {Scanlan1996,
	title = {High degree of genetic variation in Prochlorococcus (Prochlorophyta) revealed by RFLP analysis},
	journal = {European Journal of Phycology},
	volume = {31},
	number = {1},
	year = {1996},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {1{\textendash}9},
	keywords = {DIVINYL CHLOROPHYLL-A, FAMILY, Marine Synechococcus, Mediterranean Sea, Multiple Evolutionary Origins, north-atlantic, NUCLEOTIDE-SEQUENCE, picoplankton, Prokaryote, rcc, RCC SBR$_\textrmP$hyto, UNICELLULAR CYANOBACTERIUM},
	doi = {10.1080/09670269600651131},
	author = {Scanlan, D J and Hess, W R and Partensky, F and Newman, J 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 {Partensky1993,
	title = {Photoacclimation of Prochlorococcus sp. (Prochlorophyta) strains isolated from the North Atlantic and the Mediterranean Sea},
	journal = {Plant Physiology},
	volume = {101},
	year = {1993},
	note = {tex.mendeley-tags: RCC,rcc,sbr?hyto},
	pages = {295{\textendash}296},
	keywords = {hplc, Photosynthesis, Pigment, rcc, RCC SBR$_\textrmP$hyto, sbr?hyto, \#PROCHLOROPHYTE},
	doi = {10.1104/pp.101.1.285},
	author = {Partensky, F and Hoepffner, N and Li, W K W and Ulloa, O and Vaulot, D}
}
@article {Morel1993,
	title = {Prochlorococcus and Synechococcus: a comparative study of their size, pigmentation and related optical properties},
	journal = {Journal of Marine Research},
	volume = {51},
	year = {1993},
	note = {tex.mendeley-tags: 1993,rcc,sbr?hyto},
	pages = {617{\textendash}649},
	keywords = {1993, hplc, OPTICS, Pigment, rcc, SBR$_\textrmP$hyto, sbr?hyto, Synechococcus, \#PROCHLOROPHYTE},
	doi = {10.1357/0022240933223963},
	author = {Morel, A and Ahn, Y.-W. and Partensky, F and Vaulot, Daniel and Claustre, H}
}
@article {Chisholm1992,
	title = {\textit{Prochlorococcus marinus nov. gen. nov. sp.: an oxyphototrophic marine prokaryote containing divinyl chlorophyll a and b},
	journal = {Archives of Microbiology},
	volume = {157},
	year = {1992},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {297{\textendash}300},
	keywords = {rcc, systematics, \#PROCHLOROPHYTE},
	doi = {10.1007/BF00245165},
	author = {Chisholm, S W and Frankel, S L and Goericke, R and Olson, R J and Palenik, B and Waterbury, J B and West-Johnsrud, L and Zettler, E R}
}
@inbook {Waterbury1986,
	title = {Biological and ecological characterization of the marine unicellular cyanobacterium Synechococcus},
	booktitle = {Photosynthetic picoplankton},
	volume = {214},
	year = {1986},
	note = {tex.mendeley-tags: Canad. Bull. Fish. Aquatic Sci.,RCC,rcc},
	pages = {71{\textendash}120},
	keywords = {Canad. Bull. Fish. Aquatic Sci., phytoplankton, rcc, Synechococcus},
	author = {Waterbury, J B and Watson, S W and Valois, F W and Franks, D G},
	editor = {Platt, T and Li, W K W}
}
