@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 {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}
}
@booklet {dennu_biological_2023,
	title = {Biological and genomic resources for the cosmopolitan phytoplankton Bathycoccus: Insights into genetic diversity and major structural variations},
	year = {2023},
	note = {Pages: 2023.10.16.562038 Section: New Results},
	month = {oct},
	publisher = {bioRxiv},
	abstract = {Population-scale sequencing has become a standard practice to explore the natural genetic diversity underlying adaptation, notably in land plants. However, current sequencing initiatives for eukaryotic phytoplankton primarily concentrate on creating reference genomes for model organisms and characterizing natural communities through metagenomics approaches. Consequently, few species have been thoroughly sequenced and intraspecific genetic diversity remains virtually undescribed, limiting our understanding of diversity and adaptation mechanisms. Here we report a biological and genomic resource to explore the genetic diversity of the cosmopolitan and ecologically important Bathycoccus genus. To span broad geographical and temporal scales, we selected available strains but also isolated and genotyped strains from both the Banyuls bay (Mediterranean sea) and the Baffin bay (Arctic ocean). By combining ONT long reads and Illumina short reads technologies, we produced and annotated 28 Bathycoccus sp. de novo assembled genomes of high quality, including 24 genomes of Bathycoccus prasinos strains along a latitudinal gradient between 40{\textdegree} and 78{\textdegree} North, one reference genome of the Bathycoccus calidus species and 3 genomes of a yet undescribed Bathycoccus species named Bathycoccus catiminus. We assessed the genetic diversity of this genus through phylogenomic analyses and highlighted the central role of this genomic resource in providing new insights into the diversity of outlier chromosomal structures. The Bathycoccus biological and genomic resources offer a robust framework for investigating the diversity and adaptation mechanisms of eukaryotic phytoplankton in the Ocean. Significance statement Comparative and functional approaches for the study of eukaryotic phytoplankton and their adaptation to latitudes and seasons that rely on extensive biological and genomic resources are currently lacking. Here we report such resources and describe the natural diversity of the cosmopolitan phytoplankton Bathycoccus, providing insights into its species and intraspecific diversity and establishing it as a robust model for functional and ecological studies.},
	keywords = {RCC1615, RCC1868, RCC4222, RCC4752, RCC5417, RCC685, RCC716},
	doi = {10.1101/2023.10.16.562038},
	url = {https://www.biorxiv.org/content/10.1101/2023.10.16.562038v1},
	author = {Dennu, Louis and Devic, Martine and Rigonato, Janaina and Falciatore, Angela and Lozano, Jean-Claude and Verg{\'e}, Val{\'e}rie and Mariac, C{\'e}dric and Jaillon, Olivier and Team, The Dark Edge genomics sampling and Sabot, Fran{\c c}ois and Bouget, Fran{\c c}ois-Yves}
}
@booklet {clark_coccolithophorids_2023,
	title = {Coccolithophorids precipitate carbonate in clumped isotope equilibrium with seawater},
	year = {2023},
	month = {nov},
	publisher = {EGUsphere},
	type = {preprint},
	abstract = {Numerous recent studies have tested the clumped isotope (Δ47) thermometer on a variety of biogenic carbonates such as foraminifera and bivalves and showed that all follow a common calibration. While the sample size requirements for a reliable Δ47 measurement have decreased over the years, the availability and preservation of many biogenic carbonates is still 10 limited and/or require substantial time to be extracted from sediments in sufficient amounts. We thus determined the Δ47temperature relationship for coccolith carbonate, which is abundant and often well-preserved in sediments. The carbon and oxygen isotopic compositions of coccolith calcite have limited use in palaeoenvironmental reconstructions due to physiological effects that cause variability in the carbon and oxygen isotopic values. However, the relatively limited data available suggest that clumped isotopes may not be influenced by these effects. We cultured three species of coccolithophores in well15 constrained carbonate system conditions with a CO2(aq) between 5 and 45 μM and temperatures between 6{\textdegree}C and 27{\textdegree}C.},
	keywords = {RCC1130, RCC1303, RCC3370},
	doi = {10.5194/egusphere-2023-2581},
	url = {https://egusphere.copernicus.org/preprints/2023/egusphere-2023-2581/},
	author = {Clark, Alexander J. and Torres-Romero, Ismael and Jaggi, Madalina and Bernasconi, Stefano M. and Stoll, Heather M.}
}
@article {veron_new_2023,
	title = {New species of Pavlovophyceae (Haptophyta) and revision of the genera Exanthemachrysis, Rebecca and Pavlova},
	journal = {European Journal of Taxonomy},
	volume = {861},
	year = {2023},
	month = {mar},
	pages = {21{\textendash}47},
	abstract = {The justification of the 4 genera that currently compose the class Pavlovophyceae is based on a low number of species and a relative paucity of available, traceable and referenced cultures. Previous integrative phylogeny work revealed strains that can refine and strengthen our knowledge of the genera in the class. The application of multiple light and electron microscopy techniques allowed us to prioritize the cytomorphological characters (pyrenoid, thylakoid, stigma, knob-scales, life stage / life cycle) used for the taxonomy of these algae and to describe two new species: Exanthemachrysis fresneliae V{\'e}ron sp.~nov. and Rebecca billardiae V{\'e}ron sp.~nov. Consequently, revisions of the two genera Exanthemachrysis Lepailleur emend. V{\'e}ron and Rebecca Green emend. V{\'e}ron were made. In addition, the genus Pavlova Butcher emend V{\'e}ron is revised in the light of these characters. Particular emphasis is placed on the life stages and habitat of the species.},
	keywords = {habitats, haptophytes, new species, phytoplankton, pyrenoid, RCC1528, RCC1541},
	issn = {2118-9773},
	doi = {10.5852/ejt.2023.861.2063},
	url = {https://europeanjournaloftaxonomy.eu/index.php/ejt/article/view/2063},
	author = {Veron, Benoit and Rougier, Etienne and Taylor, Anthony and Goux, Didier}
}
@booklet {wang_novel_2023,
	title = {Novel dimethylsulfoniopropionate biosynthesis enzymes in diverse marine bacteria, cyanobacteria and abundant algae},
	year = {2023},
	month = {mar},
	publisher = {In Review},
	type = {preprint},
	abstract = {Abstract Dimethylsulfoniopropionate (DMSP) is an abundant marine organosulfur compound[1] with roles in stress protection[2, 3], chemotaxis[4], nutrient and sulfur cycling[5] and, potentially, climate regulation[6, 7]. Marine algae and bacteria are considered significant DMSP producers, but many diverse representatives lack known DMSP synthesis genes/enzymes[8, 9]. Here, new DMSP biosynthesis enzymes were identified that considerably increase the number and diversity of potential DMSP-producing organisms, inferring new and significant global DMSP producers. A novel bifunctional DMSP biosynthesis enzyme, DsyGD, identified in the rhizobacterium Gynuella sunshinyii, produces DMSP at levels higher than any other bacterium from methylthiohydroxybutyrate (MTHB) via an N-terminal MTHB S-methyltransferase domain (termed DsyG) and a C-terminal dimethylsulfoniohydroxybutyrate (DMSHB) decarboxylase domain (termed DsyD, which is the first reported enzyme with this activity). DsyGD is also found in some filamentous cyanobacteria, not previously known to produce DMSP. Regulation of DMSP production and dsyGD transcription was consistent with their role in osmoprotection. Indeed, cloned dsyGD conferred osmotolerance to bacteria deficient in osmolyte production, something not previously demonstrated for any known DMSP synthesis gene, and which could be exploited for biotechnology e.g., engineering salt tolerance. DsyGD characterisation led to identification of phylogenetically distinct DsyG-like proteins, termed DSYE, with MTHB S-methyltransferase activity, in diverse and environmentally abundant Chlorophyta, Chlorachniophyta, Ochraphyta, Haptophyta and Bacillariophyta algae. These algae comprise a mix of low, high and previously unknown DMSP producers[10]. Algae containing DSYE, particularly bloom-forming Pelagophyceae species, which we showed to accumulate medium-high intracellular DMSP levels, were globally more abundant DMSP producers than Haptophyta, Dinophyta and Bacillariophyta with DSYB and/or TpMMT. This highlights the potential importance of Pelagophyceae and other DSYE containing algae in global DMSP production and sulfur cycling.},
	keywords = {RCC100, RCC2956, RCC4094, RCC4422, RCC6172},
	doi = {10.21203/rs.3.rs-2678769/v1},
	url = {https://www.researchsquare.com/article/rs-2678769/v1},
	author = {Wang, Jinyan and Zhou, Shun and Curson, Andrew and Vieira, Ana and Walsham, Keanu and Monaco, Serena and Li, Chun-Yang and Rivera, Peter Paolo and Wang, Xiao-Di and Hanwell, Libby and Zhu, Xiao-Yu and Le{\~a}o, Pedro and Lea-Smith, David J. and Zhang, Yuzhong and Zhang, Xiaohua and Todd, Jonathan}
}
@article {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 {storti_tailoring_2023,
	title = {Tailoring confocal microscopy for real-time analysis of photosynthesis at single-cell resolution},
	journal = {Cell Reports Methods},
	year = {2023},
	pages = {100568},
	abstract = {Photoautotrophs{\textquoteright} environmental responses have been extensively studied at the organism and ecosystem level. However, less is known about their photosynthesis at the single-cell level. This information is needed to understand photosynthetic acclimation processes, as light changes as it penetrates cells, layers of cells, or organs. Furthermore, cells within the same tissue may behave differently, being at different developmental/ physiological stages. Here, we describe an approach for single-cell and subcellular photophysiology based on the customization of confocal microscopy to assess chlorophyll fluorescence quenching by the saturation pulse method. We exploit this setup to (1) reassess the specialization of photosynthetic activities in developing tissues of non-vascular plants; (2) identify a specific subpopulation of phytoplankton cells in marine photosymbiosis, which consolidate energetic connections with their hosts; and (3) examine the link between light penetration and photoprotection responses inside the different tissues that constitute a plant leaf anatomy.},
	keywords = {rcc1383},
	issn = {26672375},
	doi = {10.1016/j.crmeth.2023.100568},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2667237523002126},
	author = {Storti, Mattia and Hsine, Haythem and Uwizeye, Clarisse and Bastien, Olivier and Yee, Daniel P. and Chevalier, Fabien and Decelle, Johan and Giustini, C{\'e}cile and B{\'e}al, Daniel and Curien, Gilles and Finazzi, Giovanni and Tolleter, Dimitri}
}
@article {barbeyron_zobellia_2023,
	title = {\textit{Zobellia alginiliquefaciens sp. nov., a novel member of the flavobacteria isolated from the epibiota of the brown alga Ericaria zosteroides (C. Agardh) Molinari \& Guiry 2020},
	journal = {International Journal of Systematic and Evolutionary Microbiology},
	volume = {73},
	number = {6},
	year = {2023},
	note = {Publisher: Microbiology Society,},
	pages = {005924},
	abstract = {Strain LLG6346-3.1T, isolated from the thallus of the brown alga Ericaria zosteroides collected from the Mediterranean Sea near Bastia in Corsica, France, was characterised using a polyphasic method. Cells were Gram-stain-negative, strictly aerobic, non-flagellated, motile by gliding, rod-shaped and grew optimally at 30{\textendash}33 {\textdegree}C, at pH 8{\textendash}8.5 and with 4{\textendash}5 \% NaCl. LLG6346-3.1T used the seaweed polysaccharide alginic acid as a sole carbon source which was vigorously liquefied. The results of phylogenetic analyses indicated that the bacterium is affiliated to the genus Zobellia (family Flavobacteriaceae , class Flavobacteriia ). LLG6346-3.1T exhibited 16S rRNA gene sequence similarity values of 98.6 and 98.3 \% to the type strains of Zobellia russellii and Zobellia roscoffensis , respectively, and of 97.4{\textendash}98.5 \% to members of other species of the genus Zobellia . The DNA G+C content of LLG6346-3.1T was determined to be 38.3 mol\%. Digital DNA{\textendash}DNA hybridisation predictions by the average nucleotide identity (ANI) and genome to genome distance calculator (GGDC) methods between LLG6346-3.1T and other members of the genus Zobellia showed values of 76{\textendash}88 \% and below 37 \%, respectively. The results of phenotypic, phylogenetic and genomic analyses indicate that LLG6346-3.1T is distinct from species of the genus Zobellia with validly published names and that it represents a novel species of the genus Zobellia , for which the name Zobellia alginiliquefaciens sp. nov. is proposed. The type strain is LLG6346-3.1T (= RCC7657T = LMG 32918T).},
	keywords = {RCC7657},
	issn = {1466-5034},
	doi = {10.1099/ijsem.0.005924},
	url = {https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.005924},
	author = {Barbeyron, Tristan and Le Duff, Nolwen and Duchaud, Eric and Thomas, Fran{\c c}ois}
}
@article {yee_v-type_2023,
	title = {The V-type ATPase enhances photosynthesis in marine phytoplankton and further links phagocytosis to symbiogenesis},
	journal = {Current Biology},
	year = {2023},
	month = {may},
	pages = {S0960982223006152},
	abstract = {Diatoms, dinoflagellates, and coccolithophores are dominant groups of marine eukaryotic phytoplankton that are collectively responsible for the majority of primary production in the ocean.1 These phytoplankton contain additional intracellular membranes around their chloroplasts, which are derived from ancestral engulfment of red microalgae by unicellular heterotrophic eukaryotes that led to secondary and tertiary endosymbiosis.2 However, the selectable evolutionary advantage of these membranes and the physiological significance for extant phytoplankton remain poorly understood. Since intracellular digestive vacuoles are ubiquitously acidified by V-type H+-ATPase (VHA),3 proton pumps were proposed to acidify the microenvironment around secondary chloroplasts to promote the dehydration of dissolved inorganic carbon (DIC) into CO2, thus enhancing photosynthesis.4,5 We report that VHA is localized around the chloroplasts of centric diatoms and that VHA significantly contributes to their photosynthesis across a wide range of oceanic irradiances. Similar results in a pennate diatom, dinoflagellate, and coccolithophore, but not green or red microalgae, imply the co-option of phagocytic VHA activity into a carbon-concentrating mechanism (CCM) is common to secondary endosymbiotic phytoplankton. Furthermore, analogous mechanisms in extant photosymbiotic marine invertebrates6{\textendash}8 provide functional evidence for an adaptive advantage throughout the transition from endosymbiosis to symbiogenesis. Based on the contribution of diatoms to ocean biogeochemical cycles, VHA-mediated enhancement of photosynthesis contributes at least 3.5 Gtons of fixed carbon per year (or 7\% of primary production in the ocean), providing an example of a symbiosis-derived evolutionary innovation with global environmental implications.},
	keywords = {RCC3387},
	issn = {09609822},
	doi = {10.1016/j.cub.2023.05.020},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982223006152},
	author = {Yee, Daniel P. and Samo, Ty J. and Abbriano, Raffaela M. and Shimasaki, Bethany and Vernet, Maria and Mayali, Xavier and Weber, Peter K. and Mitchell, B. Greg and Hildebrand, Mark and Decelle, Johan and Tresguerres, Martin}
}
@article {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 {biller_isolation_2022,
	title = {Isolation and Characterization of Cyanobacterial Extracellular Vesicles},
	journal = {Journal of Visualized Experiments},
	year = {2022},
	month = {feb},
	abstract = {Cyanobacteria are a diverse group of photosynthetic, Gram-negative bacteria that play critical roles in global ecosystems and serve as essential biotechnology models. Recent work has demonstrated that both marine and freshwater cyanobacteria produce extracellular vesicles - small membrane-bound structures released from the outer surface of the microbes. While vesicles likely contribute to diverse biological processes, their specific functional roles in cyanobacterial biology remain largely unknown. To encourage and advance research in this area, a detailed protocol is presented for isolating, concentrating, and purifying cyanobacterial extracellular vesicles. The current work discusses methodologies that have successfully isolated vesicles from large cultures of Prochlorococcus, Synechococcus, and Synechocystis. Methods for quantifying and characterizing vesicle samples from these strains are presented. Approaches for isolating vesicles from aquatic field samples are also described. Finally, typical challenges encountered with cyanobacterial vesicle purification, methodological considerations for different downstream applications, and the trade-offs between approaches are also discussed.},
	doi = {10.3791/63481},
	author = {Biller, Steven and Mu{\~n}oz Marin, Maria and Lima, Steeve and Matinha-Cardoso, Jorge and Tamagnini, Paula and Oliveira, Paulo}
}
@article {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 {liu_phycosphere_2022,
	title = {Phycosphere pH of unicellular nano- and micro- phytoplankton cells and consequences for iron speciation},
	journal = {The ISME Journal},
	volume = {16},
	number = {10},
	year = {2022},
	note = {Number: 10 Publisher: Nature Publishing Group},
	month = {oct},
	pages = {2329{\textendash}2336},
	abstract = {Surface ocean pH is declining due to anthropogenic atmospheric CO2 uptake with a global decline of \textasciitilde0.3 possible by 2100. Extracellular pH influences a range of biological processes, including nutrient uptake, calcification and silicification. However, there are poor constraints on how pH levels in the extracellular microenvironment surrounding phytoplankton cells (the phycosphere) differ from bulk seawater. This adds uncertainty to biological impacts of environmental change. Furthermore, previous modelling work suggests that phycosphere pH of small cells is close to bulk seawater, and this has not been experimentally verified. Here we observe under 140 μmol photons{\textperiodcentered}m-2{\textperiodcentered}s-1 the phycosphere pH of Chlamydomonas concordia (5 {\textmu}m diameter), Emiliania huxleyi (5 {\textmu}m), Coscinodiscus radiatus (50 {\textmu}m) and C. wailesii (100 {\textmu}m) are 0.11 {\textpm} 0.07, 0.20 {\textpm} 0.09, 0.41 {\textpm} 0.04 and 0.15 {\textpm} 0.20 (mean {\textpm} SD) higher than bulk seawater (pH 8.00), respectively. Thickness of the pH boundary layer of C. wailesii increases from 18 {\textpm} 4 to 122 {\textpm} 17 {\textmu}m when bulk seawater pH decreases from 8.00 to 7.78. Phycosphere pH is regulated by photosynthesis and extracellular enzymatic transformation of bicarbonate, as well as being influenced by light intensity and seawater pH and buffering capacity. The pH change alters Fe speciation in the phycosphere, and hence Fe availability to phytoplankton is likely better predicted by the phycosphere, rather than bulk seawater. Overall, the precise quantification of chemical conditions in the phycosphere is crucial for assessing the sensitivity of marine phytoplankton to ongoing ocean acidification and Fe limitation in surface oceans.},
	keywords = {Biogeochemistry, Microbial biooceanography, RCC1, rcc1731, Water microbiology},
	issn = {1751-7370},
	doi = {10.1038/s41396-022-01280-1},
	url = {https://www.nature.com/articles/s41396-022-01280-1},
	author = {Liu, Fengjie and Gledhill, Martha and Tan, Qiao-Guo and Zhu, Kechen and Zhang, Qiong and Sala{\"u}n, Pascal and Tagliabue, Alessandro and Zhang, Yanjun and Weiss, Dominik and Achterberg, Eric P. and Korchev, Yuri}
}
@article {croteau_shifts_2022,
	title = {Shifts in growth light optima among diatom species support their succession during the spring bloom in the Arctic},
	journal = {Journal of Ecology},
	volume = {n/a},
	number = {n/a},
	year = {2022},
	note = {_eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2745.13874},
	abstract = {1. Diatoms of the Arctic Ocean annually experience extreme changes of light environment linked to photoperiodic cycles and seasonal variations of the snow and sea-ice cover extent and thickness which attenuate light penetration in the water column. Arctic diatom communities exploit this complex seasonal dynamic through a well-documented species succession during spring, beginning in sea-ice and culminating in massive phytoplankton blooms underneath sea-ice and in the marginal ice zone. The pattern of diatom taxa sequentially dominating this succession is relatively well conserved interannually, and taxonomic shifts seem to align with habitat transitions. 2. To understand whether differential photoadaptation strategies among diatom taxa explain these recurring succession sequences, we coupled lab experiments with field work in Baffin Bay at 67.5{\textdegree}N. Based on field data, we selected five diatom species typical of different ecological niches and measured their growth rates under light intensity ranges representative of their natural habitats. To characterize their photoacclimative responses, we sampled pigments and total particulate carbon, and conducted 14C-uptake photosynthesis response curves and variable fluorescence measurements. 3. We documented a gradient in species respective light intensity for maximal growth suggesting divergent light response plasticity, which for the most part align with species sequential dominance. Other photophysiological parameters supported this ecophysiological framing, although contrasts were always clear only between succession endmembers, Nitzschia frigida and Chaetoceros neogracilis. To validate that these photoacclimative responses are representative of in situ dynamics, we compared them to the chlorophyll a-specific light-limited slope (α*) and saturated rate of photosynthesis (P*M), monitored in Baffin Bay on sea-ice and planktonic communities. This complementary approach confirmed that unusual responses in α* and P*M as a function of light history intensity are similar between sentinel sympagic species N. frigida and natural ice-core communities. While no light-history-dependent trends were observed in planktonic communities, their α* and P*M values were in the range of measurements from our monospecific cultures. 4. Synthesis. Our results suggest that Arctic diatoms species photoadaptation strategy is tuned to the light environment of the habitats in which they dominate and indeed drives the seasonal taxonomic succession.},
	keywords = {Arctic Ocean, diatoms, Ecophysiology, photoacclimation, photoadaptation, primary production, RCC2046, RCC2278, seasonal species succession, spring bloom},
	issn = {1365-2745},
	doi = {10.1111/1365-2745.13874},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/1365-2745.13874},
	author = {Croteau, D. and Lacour, T. and Schiffrine, N. and Morin, P.-I. and Forget, M.-H. and Bruyant, F. and Ferland, J. and Lafond, A. and Campbell, D. A. and Tremblay, J.-E. and Babin, M. and Lavaud, J.}
}
@article {schmitt_temperature_2022,
	title = {Temperature Affects the Biological Control of Dinoflagellates by the Generalist Parasitoid Parvilucifera rostrata},
	journal = {Microorganisms},
	volume = {10},
	number = {2},
	year = {2022},
	note = {Number: 2 Publisher: Multidisciplinary Digital Publishing Institute},
	pages = {385},
	abstract = {The increase in emerging harmful algal blooms in the last decades has led to an extensive concern in understanding the mechanisms behind these events. In this paper, we assessed the growth of two blooming dinoflagellates (Alexandrium minutum and Heterocapsa triquetra) and their susceptibility to infection by the generalist parasitoid Parvilucifera rostrata under a temperature gradient. The growth of the two dinoflagellates differed across a range of temperatures representative of the Penz{\'e} Estuary (13 to 22 {\textdegree}C) in early summer. A. minutum growth increased across this range and was the highest at 19 and 22 {\textdegree}C, whereas H. triquetra growth was maximal at intermediate temperatures (15{\textendash}18 {\textdegree}C). Interestingly, the effect of temperature on the parasitoid infectivity changed depending on which host dinoflagellate was infected with the dinoflagellate responses to temperature following a positive trend in A. minutum (higher infections at 20{\textendash}22 {\textdegree}C) and a unimodal trend in H. triquetra (higher infections at 18 {\textdegree}C). Low temperatures negatively affected parasitoid infections in both hosts (i.e., {\textquotedblleft}thermal refuge{\textquotedblright}). These results demonstrate how temperature shifts may not only affect bloom development in microalgal species but also their control by parasitoids.},
	keywords = {dinoflagellate blooms, functional response, parasitic control, RCC2800, RCC2823, RCC2982, RCC3018, RCC4398, temperature effect},
	issn = {2076-2607},
	doi = {10.3390/microorganisms10020385},
	url = {https://www.mdpi.com/2076-2607/10/2/385},
	author = {Schmitt, Matthew and Telusma, Aaron and Bigeard, Estelle and Guillou, Laure and Alves-de-Souza, Catharina}
}
@article {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}
}
@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}
}
@article {long_dinophyceae_2021,
	title = {Dinophyceae can use exudates as weapons against the parasite Amoebophrya sp. (Syndiniales)},
	journal = {ISME Communications},
	volume = {1},
	number = {1},
	year = {2021},
	note = {Bandiera_abtest: a Cg_type: Nature Research Journals Number: 1 Primary_atype: Research Publisher: Nature Publishing Group Subject_term: Microbial ecology;Plant ecology;Water microbiology Subject_term_id: microbial-ecology;plant-ecology;water-microbiology},
	pages = {1{\textendash}10},
	abstract = {Parasites in the genus Amoebophrya sp. infest dinoflagellate hosts in marine ecosystems and can be determining factors in the demise of blooms, including toxic red tides. These parasitic protists, however, rarely cause the total collapse of Dinophyceae blooms. Experimental addition of parasite-resistant Dinophyceae (Alexandrium minutum or Scrippsiella donghaienis) or exudates into a well-established host-parasite coculture (Scrippsiella acuminata-Amoebophrya sp.) mitigated parasite success and increased the survival of the sensitive host. This effect was mediated by waterborne molecules without the need for a physical contact. The strength of the parasite defenses varied between dinoflagellate species, and strains of A. minutum and was enhanced with increasing resistant host cell concentrations. The addition of resistant strains or exudates never prevented the parasite transmission entirely. Survival time of Amoebophrya sp. free-living stages (dinospores) decreased in presence of A. minutum but not of S. donghaienis. Parasite progeny drastically decreased with both species. Integrity of the dinospore membrane was altered by A. minutum, providing a first indication on the mode of action of anti-parasitic molecules. These results demonstrate that extracellular defenses can be an effective strategy against parasites that protects not only the resistant cells producing them, but also the surrounding community.},
	keywords = {microbial ecology, Plant ecology, rcc, RCC1627, RCC4383, RCC4714, RCC749, Water microbiology},
	issn = {2730-6151},
	doi = {10.1038/s43705-021-00035-x},
	url = {http://www.nature.com/articles/s43705-021-00035-x},
	author = {Long, Marc and Marie, Dominique and Szymczak, Jeremy and Toullec, Jordan and Bigeard, Estelle and Sourisseau, Marc and Le Gac, Micka{\"e}l and Guillou, Laure and Jauzein, C{\'e}cile}
}
@article {tostevin_influence_2021,
	title = {The influence of elevated SiO2(aq) on intracellular silica uptake and microbial metabolism},
	journal = {Geobiology},
	volume = {n/a},
	number = {n/a},
	year = {2021},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/gbi.12442},
	abstract = {Microbes are known to accumulate intracellular SiO2(aq) up to 100s of mmol/l from modern seawater (SiO2(aq) <100 {\textmu}mol/l), despite having no known nutrient requirement for Si. Before the evolution of siliceous skeletons, marine silica concentrations were likely an order of magnitude higher than the modern ocean, raising the possibility that intracellular SiO2(aq) accumulation interfered with normal cellular function in non-silicifying algae. Yet, because few culturing studies have isolated the effects of SiO2(aq) at high concentration, the potential impact of elevated marine silica on early microbial evolution is unknown. Here, we test the influence of elevated SiO2(aq) on eukaryotic algae, as well as a prokaryote species. Our results demonstrate that under SiO2(aq) concentrations relevant to ancient seawater, intracellular Si accumulates to concentrations comparable to those found in siliceous algae such as diatoms. In addition, all eukaryotic algae showed a statistically significant response to the high-Si treatment, including reduced average cell sizes and/or a reduction in the maximum growth rate. In contrast, there was no consistent response to the high-Si treatment by the prokaryote species. Our results highlight the possibility that elevated marine SiO2(aq) may have been an environmental stressor during early eukaryotic evolution.},
	keywords = {Archaean, culturing, microbial metabolism, Proterozoic, RCC1, RCC1216, rcc1512, RCC1547, rcc539, silica},
	issn = {1472-4669},
	doi = {10.1111/gbi.12442},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/gbi.12442},
	author = {Tostevin, Rosalie and Snow, Joseph T. and Zhang, Qiong and Tosca, Nicholas J. and Rickaby, Rosalind E. M.}
}
@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}
}
@inbook {reddy_marine_2021,
	title = {Marine Biodiscovery in a Changing World},
	booktitle = {Progress in the Chemistry of Organic Natural Products 116},
	series = {Progress in the Chemistry of Organic Natural Products},
	year = {2021},
	pages = {1{\textendash}36},
	publisher = {Springer International Publishing},
	organization = {Springer International Publishing},
	address = {Cham},
	abstract = {The term {\textquotedblleft}marine biodiscovery{\textquotedblright} has been recently been adopted to describe the area of marine natural products dedicated to the search of new drugs. Several maritime countries such as Australia, New Zealand, South Korea, and Japan as well as some European countries have invested significantly in this area of research over the last 50 years. In the late 2000s, research in this field has received significant interest and support in Ireland for exploring new marine bioresources from the nutrient-rich waters of the Northeastern Atlantic Ocean. Despite undeniable success exemplified by the marketing of new drugs, especially in oncology, the integration of new technical but also environmental aspects should be considered. Indeed, global change, particularly in our oceans, such as climate change, biodiversity loss, and the emergence of microbial pathogens, not only affects the environment but ultimately contributes to social inequalities. In this contribution, new avenues and best practices are proposed, such as the development of biorepositories and shared data for the future of marine biodiscovery research. The extension of this type of scientific work will allow humanity to finally make the optimum use of marine bioresources.},
	keywords = {Bioprospecting, Biorepositories, Data management system, Marine biodiscovery, Marine natural products, Screenings, taxonomy},
	isbn = {978-3-030-80560-9},
	doi = {10.1007/978-3-030-80560-9_1},
	url = {https://doi.org/10.1007/978-3-030-80560-9_1},
	author = {Reddy, Maggie M. and Jennings, Laurence and Thomas, Olivier P.},
	editor = {Kinghorn, A. Douglas and Falk, Heinz and Gibbons, Simon and Asakawa, Yoshinori and Liu, Ji-Kai and Dirsch, Verena M.}
}
@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 {uwizeye_morphological_2021,
	title = {Morphological bases of phytoplankton energy management and physiological responses unveiled by 3D subcellular imaging},
	journal = {Nature Communications},
	volume = {12},
	number = {1},
	year = {2021},
	note = {Number: 1 Publisher: Nature Publishing Group},
	month = {feb},
	pages = {1{\textendash}12},
	abstract = {Phytoplankton account for a large proportion of global primary production and comprise a number of phylogenetically distinct lineages. Here, Uwizeye et al. use FIB-SEM to study ultrastructural plasticity of 7 distinct taxa and describe how subcellular organisation is linked to energy metabolism.},
	keywords = {RCC100, RCC4014, RCC827, RCC909},
	issn = {2041-1723},
	doi = {10.1038/s41467-021-21314-0},
	url = {http://www.nature.com/articles/s41467-021-21314-0},
	author = {Uwizeye, Clarisse and Decelle, Johan and Jouneau, Pierre-Henri and Flori, Serena and Gallet, Benoit and Keck, Jean-baptiste and Bo, Davide Dal and Moriscot, Christine and Seydoux, Claire and Chevalier, Fabien and Schieber, Nicole L. and Templin, Rachel and Allorent, Guillaume and Courtois, Florence and Curien, Gilles and Schwab, Yannick and Schoehn, Guy and Zeeman, Samuel C. and Falconet, Denis and Finazzi, Giovanni}
}
@article {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 {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 {decelle_subcellular_2021,
	title = {Subcellular architecture and metabolic connection in the planktonic photosymbiosis between Collodaria (radiolarians) and their microalgae},
	journal = {bioRxiv},
	year = {2021},
	note = {Company: Cold Spring Harbor Laboratory Distributor: Cold Spring Harbor Laboratory Label: Cold Spring Harbor Laboratory Section: New Results Type: article},
	pages = {2021.03.13.435225},
	abstract = {Photosymbiosis is widespread and ecologically important in the oceanic plankton but remains poorly studied. Here, we used multimodal subcellular imaging to investigate the photosymbiosis between colonial Collodaria and their microalga dinoflagellate (Brandtodinium) collected in surface seawaters. We showed that this symbiosis is a very dynamic system whereby symbionts interact with different host cells via extracellular vesicles within the {\textquotedblleft}greenhouse-like{\textquotedblright} colony. 3D electron microscopy revealed that the volume of the photosynthetic apparatus (plastid and pyrenoid) of the microalgae increased in symbiosis compared to free-living while the mitochondria volume was similar. Stable isotope probing coupled with NanoSIMS showed that carbon and nitrogen were assimilated and stored in the symbiotic microalga in starch granules and purine crystals, respectively. Nitrogen was also allocated to the algal nucleus (nucleolus). After 3 hours, low 13C and 15N transfer was detected in the host Golgi. Metal mapping revealed that intracellular iron concentration was similar in free-living and symbiotic microalgae (ca 40 ppm) and two-fold higher in the host, whereas copper concentration increased in symbiotic microalgae (up to 6900 ppm) and was detected in the host cell and extracellular vesicles. Sulfur mapping also pinpointed the importance of this nutrient for the algal metabolism. This study, which revealed subcellular changes of the morphology and nutrient homeostasis in symbiotic microalgae, improves our understanding on the metabolism of this widespread and abundant oceanic symbiosis and paves the way for more studies to investigate the metabolites exchanged.},
	doi = {10.1101/2021.03.13.435225},
	url = {https://www.biorxiv.org/content/10.1101/2021.03.13.435225v1},
	author = {Decelle, Johan and Veronesi, Giulia and LeKieffre, Charlotte and Gallet, Benoit and Chevalier, Fabien and Stryhanyuk, Hryhoriy and Marro, Sophie and Ravanel, St{\'e}phane and Tucoulou, R{\'e}mi and Schieber, Nicole and Finazzi, Giovanni and Schwab, Yannick and Musat, Niculina}
}
@article {barbeyron_zobellia_2021,
	title = {Zobellia roscoffensis sp. nov. and Zobellia nedashkovskayae sp. nov., two flavobacteria from the epiphytic microbiota of the brown alga Ascophyllum nodosum, and emended description of the genus Zobellia},
	journal = {International Journal of Systematic and Evolutionary Microbiology},
	volume = {71},
	number = {8},
	year = {2021},
	abstract = {Four marine bacterial strains were isolated from a thallus of the brown alga Ascophyllum nodosum collected in Roscoff, France. Cells were Gram-s- tain--negative, strictly aerobic, non-f-lagellated, gliding, rod--shaped and grew optimally at 25{\textendash}30 {\textdegree}C, at pH 7{\textendash}8 and with 2{\textendash}4 \% NaCl. Phylogenetic analyses of their 16S rRNA gene sequences showed that the bacteria were affiliated to the genus Zobellia (family Flavobacteriaceae, phylum Bacteroidetes). The four strains exhibited 97.8{\textendash}100 \% 16S rRNA gene sequence similarity values among themselves, 97.9{\textendash}99.1 \% to the type strains of Zobellia amurskyensis KMM 3526T and Zobellia laminariae KMM 3676T, and less than 99 \% to other species of the genus Zobellia. The DNA G+C content of the four strains ranged from 36.7 to 37.7 mol\%. Average nucleotide identity and digital DNA{\textendash}DNA hybridization calculations between the new strains and other members of the genus Zobellia resulted in values of 76.4{\textendash}88.9 \% and below 38.5 \%, respectively. Phenotypic, phylogenetic and genomic analyses showed that the four strains are distinct from species of the genus Zobellia with validly published names. They represent two novel species of the genus Zobellia, for which the names Zobellia roscoffensis sp. nov. and Zobellia nedashkovskayae sp. nov. are proposed with Asnod1--F08T (RCC6906T=KMM 6823T=CIP 111902T) and Asnod2--B07--BT (RCC6908T=KMM 6825T=CIP 111904T), respectively, as the type strains.},
	keywords = {RCC6906, RCC6907, RCC6908, RCC6909},
	issn = {1466-5026, 1466-5034},
	doi = {10.1099/ijsem.0.004913},
	url = {https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.004913},
	author = {Barbeyron, Tristan and Thi{\'e}baud, Manon and Le Duff, Nolwen and Martin, Marjolaine and Corre, Erwan and Tanguy, Gwenn and Vandenbol, Micheline and Thomas, Fran{\c c}ois}
}
@article {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 {Wittek2020,
	title = {Dimethylsulfoniopropionate (DMSP) and dimethylsulfoxide (DMSO) cell quotas variations arising from sea ice shifts of salinity and temperature in the Prymnesiophyceae Phaeocystis antarctica},
	journal = {Environmental Chemistry},
	year = {2020},
	note = {tex.mendeley-tags: RCC4023},
	abstract = {Environmental context. Dimethylsulfoniopropionate and dimethylsulfoxide could have a climatic influence especially in the polar areas. We investigate the effect of sea ice salinity and temperature on the production of these two sulfur metabolites by a polar microalga, and suggest their potential roles of osmoregulator and cryoprotectant. These results bring new information about the sulfur cycle in sea ice that is useful for climate models.. The Southern Ocean, which includes the seasonal ice zone (SIZ), is a source of large sea-air fluxes of dimethylsulfide (DMS), a climate active gas involved in Earth cooling processes. In this area, the prymnesiophyte Phaeocystis antarctica (P. antarctica) is one of the main producers of dimethylsulfoniopropionate (DMSP) and dimethylsulfoxide (DMSO), two metabolites that are precursors of DMS. These algae are also present in sea ice and contribute substantially to the high DMSP and DMSO concentrations observed in this habitat. DMSP and DMSO production in sea ice by P. antarctica is proposed to be promoted by its ability to live in extreme environmental conditions. We designed cell culture experiments to test that hypothesis, focusing on the impact of shifts of temperature and salinity on the DMSP and DMSO cell quotas. Our experiments show an increase in DMSP and DMSO cell quotas following shifts in salinity (34 to 75, at 4 {\textdegree}C), which suggests a potential osmoregulator function for both DMSP and DMSO. Stronger salinity shifts (up to 100) directly impact cell growth and induce a crash of the cultures. Combining the salinity (34 to 75) and temperature (4 {\textdegree}C to {\textendash}2.3 {\textdegree}C) shifts induces higher increases of DMSP and DMSO cell quotas that also suggests an implication of both metabolites in a cryoprotectant system. Experimental cell quotas (including diatom Fragilariopsis cylindrus quotas from a previous study) are then used to reconstruct DMSP and DMSO profiles in sea ice based on the biomass and taxonomy. Finally, the complexity of the transposition of rates obtained in the experimental domain to the real world is discussed.},
	keywords = {RCC4023},
	doi = {10.1071/EN19302},
	url = {https://doi.org/10.1071/EN19302},
	author = {Wittek, Boris and Carnat, Gauthier and Delille, Bruno and Tison, Jean-Louis and Gypens, Nathalie}
}
@article {Thorel2020,
	title = {Effect of 10 UV filters on the brine shrimp Artemia salina and themarinemicroalga Tetraselmis sp.},
	journal = {Toxics},
	volume = {8},
	number = {2},
	year = {2020},
	note = {Publisher: MDPI AG tex.mendeley-tags: RCC500},
	month = {jun},
	pages = {29},
	abstract = {The presence of pharmaceutical and personal care product (PPCP) residues in the aquatic environment is an emerging issue due to their uncontrolled release through gray water, and accumulation in the environment that may affect living organisms, ecosystems and public health. The aim of this study is to assess the toxicity of benzophenone-3 (BP-3), bis-ethylhexyloxyphenol methoxyphenyl triazine (BEMT), butyl methoxydibenzoylmethane (BM), methylene bis-benzotriazolyl tetramethylbutylphenol (MBBT), 2-ethylhexyl salicylate (ES), diethylaminohydroxybenzoyl hexyl benzoate (DHHB), diethylhexyl butamido triazone (DBT), ethylhexyl triazone (ET), homosalate (HS) and octocrylene (OC) on marine organisms from two major trophic levels, including autotrophs (Tetraselmis sp.) and heterotrophs (Artemia salina). In general, results showed that both HS and OC were the most toxic UV filters for our tested species, followed by a significant effect of BM on Artemia salina due to BM-but only at high concentrations (1 mg/L). ES, BP3 and DHHB affected the metabolic activity of the microalgae at 100 ??g/L. BEMT, DBT, ET, MBBT had no effect on the tested organisms, even at high concentrations (2 mg/L). OC toxicity represents a risk for those species, since concentrations used in this study are 15-90 times greater than those reported in occurrence studies for aquatic environments. For the first time in the literature, we report HS toxicity on a microalgae species at concentrations complementing those found in aquatic environments. These preliminary results could represent a risk in the future if concentrations of OC and HS continue to increase.},
	keywords = {Artemia salina, marine environment, Marine microalgae, RCC500, Toxicity tests, UV-filters},
	issn = {23056304},
	doi = {10.3390/TOXICS8020029},
	url = {www.mdpi.com/journal/toxics},
	author = {Thorel, Evane and Clergeaud, Fanny and Jaugeon, Lucie and Rodrigues, Alice M.S. and Lucas, Julie and Stien, Didier and Lebaron, Philippe}
}
@article {Belisle2020,
	title = {Genome sequences of synechococcus sp. Strain MIT S9220 and cocultured cyanophage SynMITS9220M01},
	journal = {Microbiology Resource Announcements},
	volume = {9},
	number = {30},
	year = {2020},
	note = {tex.mendeley-tags: RCC2571},
	month = {jul},
	pages = {28{\textendash}30},
	abstract = {Synechococcus bacteria are unicellular cyanobacteria that contribute significantly to global marine primary production. We report the nearly complete genome sequence of Synechococcus sp. strain MIT S9220, which lacks the nitrate utilization genes present in most marine Synechococcus genomes. Assembly also produced the complete genome sequence of a cyanophage present in the MIT S9220 culture.},
	keywords = {RCC2571},
	issn = {2576-098X},
	doi = {10.1128/MRA.00481-20},
	url = {https://mra.asm.org/content/9/30/e00481-20},
	author = {Belisle, B. Shafer and Avila Paz, Andres A. and Carpenter, Angelina R. and Cormier, Tayla C. and Lewis, Adam J. and Menin, Linnea S. and Oliveira, Daniel R and Song, Bukyung and Szeto, Amy and Tchantouridze, Elizabeth I and Watson, Kayleigh A and Yohannes, Mary T and Ahlgren, Nathan A},
	editor = {Putonti, Catherine}
}
@article {Schiffrine2020,
	title = {Growth and elemental stoichiometry of the ecologically-relevant arctic diatom chaetoceros gelidus: A mix of polar and temperate},
	journal = {Frontiers in Marine Science},
	volume = {6},
	number = {January},
	year = {2020},
	note = {tex.mendeley-tags: RCC2046},
	month = {jan},
	keywords = {ammonium, Arctic diatom, ele, Light, nitrate, RCC2046, urea},
	issn = {2296-7745},
	doi = {10.3389/fmars.2019.00790},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2019.00790/full},
	author = {Schiffrine, Nicolas and Tremblay, Jean-{\'e}ric and Babin, Marcel}
}
@article {Carrillo2020,
	title = {Identification and characterization of ChlreSEX4, a novel glucan phosphatase from Chlamydomonas reinhardtii green alga},
	journal = {Archives of Biochemistry and Biophysics},
	volume = {680},
	year = {2020},
	note = {Publisher: Academic Press Inc.},
	month = {feb},
	pages = {108235},
	abstract = {Chlamydomonas reinhardtii is the best known unicellular green alga model which has long been used to investigate all kinds of cellular processes, including starch metabolism. Here we identified and characterized a novel enzyme, ChlreSEX4, orthologous to glucan phosphatase SEX4 from Arabidopsis thaliana, that is capable of binding and dephosphorylating amylopectin in vitro. We also reported that cysteine 224 and tryptophan 305 residues are critical for enzyme catalysis and substrate binding. Furthermore, we verified that ChlreSEX4 gene is expressed in vivo and that glucan phosphatase activity is measurable in Chlamydomonas protein extracts. In view of the results presented, we suggest ChlreSEX4 as a functional phosphoglucan phosphatase from C. reinhardtii. Our data obtained so far contribute to understanding the phosphoglucan phosphatases evolutionary process in the green lineage and their role in starch reversible phosphorylation. In addition, this allows to position Chlamydomonas as a potential tool to obtain starches with different degrees of phosphorylation for industrial or biotechnological purposes.},
	keywords = {Chlamydomonas Reinhardtii, ChlreSEX4, Glucan phosphatase, SEX4, Starch phosphorylation},
	issn = {10960384},
	doi = {10.1016/j.abb.2019.108235},
	author = {Carrillo, Julieta B. and Torresi, Florencia and Morales, Luisina L. and Ricordi, Micaela and Gomez-Casati, Diego F. and Busi, Maria V. and Mart{\'\i}n, Mariana}
}
@article {Uwizeye2020,
	title = {In-cell quantitative structural imaging of phytoplankton using 3D electron microscopy},
	journal = {bioRxiv},
	year = {2020},
	note = {tex.mendeley-tags: RCC100,RCC4014,RCC827,RCC909},
	month = {jan},
	pages = {2020.05.19.104166},
	abstract = {Phytoplankton is a minor fraction of the global biomass playing a major role in primary production and climate. Despite improved understanding of phytoplankton diversity and genomics, we lack nanoscale subcellular imaging approaches to understand their physiology and cell biology. Here, we present a complete Focused Ion Beam - Scanning Electron Microscopy (FIB-SEM) workflow (from sample preparation to image processing) to generate nanometric 3D phytoplankton models. Tomograms of entire cells, representatives of six ecologically-successful phytoplankton unicellular eukaryotes, were used for quantitative morphometric analysis. Besides lineage-specific cellular architectures, we observed common features related to cellular energy management: i) conserved cell-volume fractions occupied by the different organelles; ii) consistent plastid-mitochondria interactions, iii) constant volumetric ratios in these energy-producing organelles. We revealed detailed subcellular features related to chromatin organization and to biomineralization. Overall, this approach opens new perspectives to study phytoplankton acclimation responses to abiotic and biotic factors at a relevant biological scale.Competing Interest StatementThe authors have declared no competing interest.},
	keywords = {RCC100, RCC4014, RCC827, RCC909},
	doi = {10.1101/2020.05.19.104166},
	url = {http://biorxiv.org/content/early/2020/05/20/2020.05.19.104166.abstract},
	author = {Uwizeye, Clarisse and Decelle, Johan and Jouneau, Pierre-Henri and Gallet, Benoit and Keck, Jean-baptiste and Schwab, Yannick and Schoehn, Guy and Zeeman, Samuel C and Falconet, Denis and Finazzi, Giovanni and Moriscot, Christine and Chevalier, Fabien and Schieber, Nicole L and Templin, Rachel and Curien, Gilles and Schwab, Yannick and Schoehn, Guy and Zeeman, Samuel C and Falconet, Denis and Finazzi, Giovanni}
}
@article {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 {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 {Meyer2020,
	title = {Sr in coccoliths of Scyphosphaera apsteinii: Partitioning behavior and role in coccolith morphogenesis},
	journal = {Geochimica et Cosmochimica Acta},
	volume = {285},
	year = {2020},
	note = {Publisher: Elsevier Ltd tex.mendeley-tags: RCC1456},
	month = {sep},
	pages = {41{\textendash}54},
	abstract = {Coccolithophores are important contributors to global calcium carbonate through their species-specific production of calcite coccoliths. Nannofossil coccolith calcite remains an important tool for paleoreconstructions through geochemical analysis of isotopic and trace element incorporation including Sr, which is a potential indicator of past surface ocean temperature and productivity. Scyphosphaera apsteinii (Zygodiscales) exhibits an unusually high Sr/Ca ratio and correspondingly high partitioning coefficient (DSr = 2.5) in their two morphologically distinct types of coccoliths: flat muroliths and barrel-like lopadoliths. Whether or not this reflects mechanistic differences in calcification compared to other coccolithophores is unknown. We therefore examined the possible role of Sr in S. apsteinii calcification by growing cells in deplete (0.33 mmol/mol Sr/Ca), ambient (9 mmol/mol Sr/Ca), and higher than ambient Sr conditions (36 and 72 mmol/mol Sr/Ca). The effects on growth, quantum efficiency of photosystem II (Fv/Fm), coccolith morphology, and calcite DSr were evaluated. No effect on S. apsteinii growth rate or Fv/Fm was observed when cells were grown in Sr/Ca between 0.33{\textendash}36 mmol/mol. However, at 72 mmol/mol Sr/Ca growth rate was significantly reduced, although Fv/Fm was unaffected. Reducing the Sr/Ca from ambient (9 mmol/mol) did not significantly alter the frequency of malformed and aberrant muroliths and lopadoliths, but at higher than ambient Sr/Ca conditions coccolith morphology was significantly disrupted. This implies that Sr is not a critical determining factor in normal coccolith calcite morphology in this dimorphic species. Using energy dispersive spectroscopy (EDS) we observed an increase in [Sr] and decrease in DSr of coccoliths as the Sr/Ca of the growth medium increased. Interestingly, muroliths had significantly lower Sr/Ca than lopadoliths at ambient and elevated [Sr], and lopadolith tips had lower Sr than bases in ambient conditions. In summary, the Sr fractionation behavior of S. apsteinii is distinct from other coccolithophores because of an unusually high DSr and inter- and intra-coccolith variability in Sr/Ca. These observations could be explained by mechanistic differences in the selectivity of the Ca2+ transport pathway or in the Sr-and Ca-binding capacity of organic components, such as polysaccharides associated with coccolithogenesis.},
	keywords = {biomineralization, Calcification, coccolith, coccolithophore, Energy dispersive spectroscopy, Fractionation, RCC1456, Sr/Ca, Strontium, Trace element},
	issn = {00167037},
	doi = {10.1016/j.gca.2020.06.023},
	author = {Meyer, Erin M. and Langer, Gerald and Brownlee, Colin and Wheeler, Glen L. and Taylor, Alison R.}
}
@article {Demory2020,
	title = {A thermal trade-off between viral production and degradation drives phytoplankton-virus population dynamics},
	journal = {bioRxiv},
	year = {2020},
	note = {Publisher: Cold Spring Harbor Laboratory tex.mendeley-tags: RCC4229,RCC4265,RCC451,RCC4523,RCC829,RCC834},
	month = {aug},
	pages = {2020.08.18.256156},
	abstract = {Marine viruses interact with their microbial hosts in dynamic environments shaped by variations in abiotic factors, including temperature. However, the impacts of temperature on viral infection of phytoplankton are not well understood. Here we coupled mathematical modeling with experimental datasets to explore the effect of temperature on three Micromonas-prasinovirus pairs. Our model shows the negative consequences of high temperatures on infection and suggests a temperature-dependent threshold between viral production and degradation. Modeling long-term dynamics in environments with different average temperatures revealed the potential for long-term host-virus coexistence, epidemic free, or habitat loss states. Hence, we generalized our model to global sea surface temperature of present and future seas and show that climate change may influence virus-host dynamics differently depending on the virus-host pair. Our study suggests that temperature-dependent changes in the infectivity of virus particles may lead to shifts in virus-host habitats in warmer oceans, analogous to projected changes in the habitats of macro-and microorganisms .},
	keywords = {RCC4229, RCC4265, RCC451, RCC4523, RCC829, RCC834},
	doi = {10.1101/2020.08.18.256156},
	url = {https://doi.org/10.1101/2020.08.18.256156},
	author = {Demory, David and Weitz, Joshua S and Baudoux, Anne-claire and Touzeau, Suzanne and Simon, Natalie and Rabouille, Sophie and Sciandra, Antoine and Bernard, Olivier}
}
@booklet {Thomas2020,
	title = {USE OF AN AMPHIDINOL FOR ITS FUNGICIDAL AND/OR BACTERICIDAL ACTIVITY ON FUNGI, OOMYCETES AND/OR PATHOGENIC BACTERIA OF PLANTS AND CROP SEEDS},
	number = {20200100499},
	year = {2020},
	note = {tex.mendeley-tags: RCC1436},
	keywords = {? No DOI found, RCC1436},
	url = {http://www.freepatentsonline.com/y2020/0100499.html},
	author = {Thomas, Yann and Thiebeauld, Odon}
}
@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 {Decelle2019,
	title = {Algal remodeling in a ubiquitous planktonic photosymbiosis},
	journal = {Current Biology},
	volume = {29},
	number = {6},
	year = {2019},
	note = {Publisher: Cell Press tex.mendeley-tags: RCC1719},
	month = {mar},
	pages = {968{\textendash}978.e4},
	abstract = {Photosymbiosis between single-celled hosts and microalgae is common in oceanic plankton, especially in oligotrophic surface waters. However, the functioning of this ecologically important cell-cell interaction and the subcellular mechanisms allowing the host to accommodate and benefit from its microalgae remain enigmatic. Here, using a combination of quantitative single-cell structural and chemical imaging techniques (FIB-SEM, nanoSIMS, Synchrotron X-ray fluorescence), we show that the structural organization, physiology, and trophic status of the algal symbionts (the haptophyte Phaeocystis) significantly change within their acantharian hosts compared to their free-living phase in culture. In symbiosis, algal cell division is blocked, photosynthesis is enhanced, and cell volume is increased by up to 10-fold with a higher number of plastids (from 2 to up to 30) and thylakoid membranes. The multiplication of plastids can lead to a 38-fold increase of the total plastid volume in a cell. Subcellular mapping of nutrients (nitrogen and phosphorous) and their stoichiometric ratios shows that symbiotic algae are impoverished in phosphorous and suggests a higher investment in energy-acquisition machinery rather than in growth. Nanoscale imaging also showed that the host supplies a substantial amount of trace metals (e.g., iron and cobalt), which are stored in algal vacuoles at high concentrations (up to 660 ppm). Sulfur mapping reveals a high concentration in algal vacuoles that may be a source of antioxidant molecules. Overall, this study unveils an unprecedented morphological and metabolic transformation of microalgae following their integration into a host, and it suggests that this widespread symbiosis is a farming strategy wherein the host engulfs and exploits microalgae.},
	keywords = {RCC1719},
	issn = {0960-9822},
	doi = {10.1016/J.CUB.2019.01.073},
	url = {https://www.sciencedirect.com/science/article/abs/pii/S0960982219301320$\#$undfig1},
	author = {Decelle, Johan and Stryhanyuk, Hryhoriy and Gallet, Benoit and Veronesi, Giulia and Schmidt, Matthias and Balzano, Sergio and Marro, Sophie and Uwizeye, Clarisse and Jouneau, Pierre-Henri and Lupette, Josselin and Jouhet, Juliette and Mar{\'e}chal, {\'E}ric and Schwab, Yannick and Schieber, Nicole L. and Tucoulou, R{\'e}mi and Richnow, Hans and Finazzi, Giovanni and Musat, Niculina}
}
@article {Helliwell2019,
	title = {Alternative mechanisms for fast na + /ca 2+ signaling in eukaryotes via a novel class of single-domain voltage-gated channels},
	journal = {Current Biology},
	volume = {29},
	number = {9},
	year = {2019},
	note = {tex.mendeley-tags: RCC299},
	pages = {1503{\textendash}1511.e6},
	abstract = {Rapid Na + /Ca 2+ -based action potentials govern essential cellular functions in eukaryotes, from the motile responses of unicellular protists, such as Paramecium [1, 2], to complex animal neuromuscular activity [3]. A key innovation underpinning this fundamental signaling process has been the evolution of four-domain voltage-gated Na + /Ca 2+ channels (4D-Ca v s/Na v s). These channels are widely distributed across eukaryote diversity [4], albeit several eukaryotes, including land plants and fungi, have lost voltage-sensitive 4D-Ca v /Na v s [5{\textendash}7]. Because these lineages appear to lack rapid Na + /Ca 2+ -based action potentials, 4D-Ca v /Na v s are generally considered necessary for fast Na + /Ca 2+ -based signaling [7]. However, the cellular mechanisms underpinning the membrane physiology of many eukaryotes remain unexamined. Eukaryotic phytoplankton critically influence our climate as major primary producers. Several taxa, including the globally abundant diatoms, exhibit membrane excitability [8{\textendash}10]. We previously demonstrated that certain diatom genomes encode 4D-Ca v /Na v s [4] but also proteins of unknown function, resembling prokaryote single-domain, voltage-gated Na + channels (BacNa v s) [4]. Here, we show that single-domain channels are actually broadly distributed across major eukaryote phytoplankton lineages and represent three novel classes of single-domain channels, which we refer collectively to as EukCats. Functional characterization of diatom EukCatAs indicates that they are voltage-gated Na + - and Ca 2+ -permeable channels, with rapid kinetics resembling metazoan 4D-Ca v s/Na v s. In Phaeodactylum tricornutum, which lacks 4D-Ca v /Na v s, EukCatAs underpin voltage-activated Ca 2+ signaling important for membrane excitability, and mutants exhibit impaired motility. EukCatAs therefore provide alternative mechanisms for rapid Na + /Ca 2+ signaling in eukaryotes and may functionally replace 4D-Ca v s/Na v s in pennate diatoms. Marine phytoplankton thus possess unique signaling mechanisms that may be key to environmental sensing in the oceans. Diatoms exhibit fast animal-like action potentials, but many species lack 4D-Ca v /Na v channels that underpin membrane excitability in animals. Diatoms do encode novel 1D voltage-gated channels (EukCatAs). Helliwell, Chrachri et al. show that EukCatAs are fast Na + and Ca 2+ channels that provide alternative mechanisms for rapid signaling in eukaryotes.},
	keywords = {action potentials, BacNa v, calcium channel, diatoms, EukCats, gliding motility, ion selectivity, RCC299, signaling, single-domain channel, voltage-gated channel},
	issn = {09609822},
	doi = {10.1016/j.cub.2019.03.041},
	author = {Helliwell, Katherine E. and Chrachri, Abdul and Koester, Julie A. and Wharam, Susan and Verret, Frederic and Taylor, Alison R. and Wheeler, Glen L. and Brownlee, Colin}
}
@article {Lim2019,
	title = {In vitro enzymatic activity assays implicate the existence of the chlorophyll cycle in chlorophyll b-Containing cyanobacteria},
	journal = {Plant and Cell Physiology},
	number = {August},
	year = {2019},
	note = {tex.mendeley-tags: RCC1774},
	month = {aug},
	pages = {1{\textendash}12},
	abstract = {In plants, chlorophyll (Chl) a and b are interconvertible by the action of three enzymes{\textemdash}chlorophyllide a oxygenase, Chl b reductase (CBR) and 7-hydroxymethyl chlorophyll a reductase (HCAR). These reactions are collectively referred to as the Chl cycle. In plants, this cyclic pathway ubiquitously exists and plays essential roles in acclimation to different light conditions at various developmental stages. By contrast, only a limited number of cyanobacteria species produce Chl b, and these include Prochlorococcus, Prochloron, Prochlorothrix and Acaryochloris. In this study, we investigated a possible existence of the Chl cycle in Chl b synthesizing cyanobacteria by testing in vitro enzymatic activities of CBR and HCAR homologs from Prochlorothrix hollandica and Acaryochloris RCC1774. All of these proteins show respective CBR and HCAR activity in vitro, indicating that both cyanobacteria possess the potential to complete the Chl cycle. It is also found that CBR and HCAR orthologs are distributed only in the Chl b-containing cyanobacteria that habitat shallow seas or freshwater, where light conditions change dynamically, whereas they are not found in Prochlorococcus species that usually habitat environments with fixed lighting. Taken together, our results implicate a possibility that the Chl cycle functions for light acclimation in Chl b-containing cyanobacteria.},
	keywords = {chlorophyll cyanobacterium, evolution promiscuous activity, RCC1774},
	issn = {0032-0781},
	doi = {10.1093/pcp/pcz157},
	url = {https://academic.oup.com/pcp/advance-article/doi/10.1093/pcp/pcz157/5544940},
	author = {Lim, Hyunseok and Tanaka, Ayumi and Tanaka, Ryouichi and Ito, Hisashi}
}
@article {Tsuboi2019,
	title = {Short-term changes in marine prokaryotic and eukaryotic microalgal communities exposed to the leachate of a seafloor hydrothermal sulfide},
	journal = {Water, Air, \& Soil Pollution},
	volume = {230},
	year = {2019},
	note = {tex.mendeley-tags: RCC,RCC1089,RCC262},
	pages = {175},
	abstract = {The effects of increased mining of seafloor massive sulfide deposits on marine ecosystems have not been characterized. In this study, the impact of leaching metals from a hydrothermal sulfide on photosynthetic protist and cyanobacterial communities in marine environments was investigated by amplicon analyses of small subunit rDNA (SSU rDNA) and rRNA (SSU rRNA). Seawater samples collected from the Iheya North region and Suruga Bay, Japan, were incubated with or without a leachate containing zinc, copper, cadmium, and manganese, of the actual seafloor hydrothermal sulfide from the Hakurei site in the Izena Hole region. The relative abundances of prasinophytes, diatom protists, and the cyanobacteria Synechococcus decreased substantially during incubation with leachate, indicating the vulnerability of these lineages to the leachate. Phylogenetic analysis based on the cyanobacterial phycocyanin cpcBA/rpcBA operon obtained from samples incubated with or without leachate indicated that the individual lineages of Synechococcus can determine sensitivity to heavy metals in different marine regions as well as particular clades and ecotypes.},
	keywords = {rcc, RCC1089, RCC262},
	doi = {10.1007/s11270-019-4224-8},
	author = {Tsuboi, Shun and Yamaguchi, Haruyo and Fuchida, Shigeshi and Koshikawa, Hiroshi and Kawachi, Masanobu}
}
@article {Kashiyama2019,
	title = {Taming chlorophylls by early eukaryotes underpinned algal interactions and the diversification of the eukaryotes on the oxygenated Earth},
	journal = {The ISME Journal},
	year = {2019},
	note = {Publisher: Springer US tex.mendeley-tags: RCC164,RCC22,RCC24,RCC375,RCC916},
	month = {feb},
	pages = {1},
	abstract = {Extant eukaryote ecology is primarily sustained by oxygenic photosynthesis, in which chlorophylls play essential roles. The exceptional photosensitivity of chlorophylls allows them to harvest solar energy for photosynthesis, but on the other hand, they also generate cytotoxic reactive oxygen species. A risk of such phototoxicity of the chlorophyll must become particularly prominent upon dynamic cellular interactions that potentially disrupt the mechanisms that are designed to quench photoexcited chlorophylls in the phototrophic cells. Extensive examination of a wide variety of phagotrophic, parasitic, and phototrophic microeukaryotes demonstrates that a catabolic process that converts chlorophylls into nonphotosensitive 132,173-cyclopheophorbide enols (CPEs) is phylogenetically ubiquitous among extant eukaryotes. The accumulation of CPEs is identified in phagotrophic algivores belonging to virtually all major eukaryotic assemblages with the exception of Archaeplastida, in which no algivorous species have been reported. In addition, accumulation of CPEs is revealed to be common among phototrophic microeukaryotes (i.e., microalgae) along with dismantling of their secondary chloroplasts. Thus, we infer that CPE-accumulating chlorophyll catabolism (CACC) primarily evolved among algivorous microeukaryotes to detoxify chlorophylls in an early stage of their evolution. Subsequently, it also underpinned photosynthetic endosymbiosis by securing close interactions with photosynthetic machinery containing abundant chlorophylls, which led to the acquisition of secondary chloroplasts. Our results strongly suggest that CACC, which allowed the consumption of oxygenic primary producers, ultimately permitted the successful radiation of the eukaryotes throughout and after the late Proterozoic global oxygenation.},
	keywords = {Biochemistry, Biogeochemistry, Cellular microbiology, microbial ecology, RCC164, RCC22, RCC24, RCC375, RCC916},
	issn = {1751-7362},
	doi = {10.1038/s41396-019-0377-0},
	url = {http://www.nature.com/articles/s41396-019-0377-0},
	author = {Kashiyama, Yuichiro and Yokoyama, Akiko and Shiratori, Takashi and Hess, Sebastian and Not, Fabrice and Bachy, Charles and Gutierrez-Rodriguez, Andres and Kawahara, Jun and Suzaki, Toshinobu and Nakazawa, Masami and Ishikawa, Takahiro and Maruyama, Moe and Wang, Mengyun and Chen, Man and Gong, Yingchun and Seto, Kensuke and Kagami, Maiko and Hamamoto, Yoko and Honda, Daiske and Umetani, Takahiro and Shihongi, Akira and Kayama, Motoki and Matsuda, Toshiki and Taira, Junya and Yabuki, Akinori and Tsuchiya, Masashi and Hirakawa, Yoshihisa and Kawaguchi, Akane and Nomura, Mami and Nakamura, Atsushi and Namba, Noriaki and Matsumoto, Mitsufumi and Tanaka, Tsuyoshi and Yoshino, Tomoko and Higuchi, Rina and Yamamoto, Akihiro and Maruyama, Tadanobu and Yamaguchi, Aika and Uzuka, Akihiro and Miyagishima, Shinya and Tanifuji, Goro and Kawachi, Masanobu and Kinoshita, Yusuke and Tamiaki, Hitoshi}
}
@article {Turmel2019,
	title = {Tracing the evolution of the plastome and mitogenome in the chloropicophyceae uncovered convergent tRNA gene losses and a variant plastid genetic code},
	journal = {Genome Biology and Evolution},
	volume = {in press},
	year = {2019},
	note = {tex.mendeley-tags: RCC15,RCC1871,RCC2335,RCC2339,RCC287,RCC3374,RCC3402,RCC4434,RCC4572,RCC4656,RCC696,RCC856,RCC998,RCC999},
	month = {apr},
	keywords = {RCC15, RCC1871, RCC2335, RCC2339, RCC287, RCC3374, RCC3402, RCC4434, RCC4572, RCC4656, RCC696, RCC856, RCC998, RCC999},
	issn = {1759-6653},
	doi = {10.1093/gbe/evz074},
	url = {https://www.biorxiv.org/content/10.1101/530998v1 https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evz074/5425330},
	author = {Turmel, Monique and dos Santos, Adriana Lopes and Otis, Christian and Sergerie, Roxanne and Lemieux, Claude},
	editor = {Archibald, John}
}
@article {Kuwata2018,
	title = {Bolidophyceae, a sister picoplanktonic group of diatoms {\textendash} a review},
	journal = {Frontiers in Marine Science},
	volume = {5},
	year = {2018},
	note = {tex.mendeley-tags: RCC1657,RCC201,RCC205,RCC206,RCC212,RCC239},
	month = {oct},
	pages = {370},
	keywords = {RCC1657, RCC201, RCC205, RCC206, rcc212, RCC239},
	issn = {2296-7745},
	doi = {10.3389/fmars.2018.00370},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2018.00370/full},
	author = {Kuwata, Akira and Yamada, Kazumasa and Ichinomiya, Mutsuo and Yoshikawa, Shinya and Tragin, Margot and Vaulot, Daniel and Lopes dos Santos, Adriana}
}
@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 {Trainic,
	title = {Infection dynamics of a bloom-forming alga and its virus determine airborne coccolith emission from seawater},
	journal = {iScience},
	year = {2018},
	note = {tex.mendeley-tags: RCC1216},
	month = {aug},
	abstract = {Summary Sea spray aerosols (SSA), have a profound effect on the climate; however, the contribution of oceanic microbial activity to SSA is not fully established. We assessed aerosolization of the calcite units (coccoliths) that compose the exoskeleton of the cosmopolitan bloom-forming coccolithophore, Emiliania huxleyi. Airborne coccolith emission occurs in steady-state conditions and increases by an order of magnitude during E. huxleyi infection by E. huxleyi virus (EhV). Airborne to seawater coccolith ratio is 1:108, providing estimation of airborne concentrations from seawater concentrations. The coccoliths{\textquoteright} unique aerodynamic structure yields a characteristic settling velocity of \~0.01 cm s-1, \~25 times slower than average sea salt particles, resulting in coccolith fraction enrichment in the air. The calculated enrichment was established experimentally, indicating that coccoliths may be key contributors to coarse mode SSA surface area, comparable with sea salt aerosols. This study suggests a coupling between key oceanic microbial interactions and fundamental atmospheric processes like SSA formation.},
	keywords = {Atmospheric Science, Biogeoscience, Earth Sciences, Marine Organism, RCC1216},
	issn = {25890042},
	doi = {10.1016/j.isci.2018.07.017},
	url = {https://www.cell.com/iscience/fulltext/S2589-0042(18)30105-6 https://linkinghub.elsevier.com/retrieve/pii/S2589004218301056},
	author = {Trainic, Miri and Koren, Ilan and Sharoni, Shlomit and Frada, Miguel and Segev, Lior and Rudich, Yinon and Vardi, Assaf}
}
@article {Rastogi2017,
	title = {Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms},
	journal = {Scientific Reports},
	volume = {8},
	number = {1},
	year = {2018},
	note = {ISBN: 4159801823106 Publisher: Springer US tex.mendeley-tags: RCC2967},
	month = {dec},
	pages = {4834},
	abstract = {2 3 Diatoms are one of the most successful and ecologically important groups of eukaryotic 4 phytoplankton in the modern ocean. Deciphering their genomes is a key step towards better 5 understanding of their biological innovations, evolutionary origins, and ecological 6 underpinnings. Here, we have used 90 RNA-Seq datasets from different growth conditions 7 combined with published expressed sequence tags and protein sequences from multiple taxa 8 to explore the genome of the model diatom Phaeodactylum tricornutum, and introduce 1,489 9 novel genes. The new annotation additionally permitted the discovery for the first time of 10 extensive alternative splicing (AS) in diatoms, including intron retention and exon skipping 11 which increases the diversity of transcripts to regulate gene expression in response to nutrient 12 limitations. In addition, we have used up-to-date reference sequence libraries to dissect the 13 taxonomic origins of diatom genomes. We show that the P. tricornutum genome is replete in 14 lineage-specific genes, with up to 47\% of the gene models present only possessing 15 orthologues in other stramenopile groups. Finally, we have performed a comprehensive de 16 novo annotation of repetitive elements showing novel classes of TEs such as SINE, MITE, LINE 17 and TRIM/LARD. This work provides a solid foundation for future studies of diatom gene 18 function, evolution and ecology.},
	keywords = {RCC2967},
	issn = {2045-2322},
	doi = {10.1038/s41598-018-23106-x},
	url = {https://www.biorxiv.org/content/early/2017/08/14/176024\%0Ahttp://dx.doi.org/10.1101/176024 http://www.nature.com/articles/s41598-018-23106-x},
	author = {Rastogi, Achal and Maheswari, Uma and Dorrell, Richard G. and Vieira, Fabio Rocha Jimenez and Maumus, Florian and Kustka, Adam and McCarthy, James and Allen, Andy E. and Kersey, Paul and Bowler, Chris and Tirichine, Leila}
}
@article {Henriquez-Castillo2018,
	title = {Ostreococcus tauri luminescent reporter lines as biosensors for detecting pollution from copper-mine tailing effluents in coastal environments},
	journal = {Frontiers in Environmental Science},
	volume = {6},
	number = {May},
	year = {2018},
	note = {tex.mendeley-tags: RCC745},
	month = {may},
	pages = {1{\textendash}11},
	keywords = {biosensors, CDKA, copper pollution, ferritin, frontiers in environmental science, frontiersin, luciferase reporter, mine tailings, org, Ostreococcus, RCC745, www},
	issn = {2296-665X},
	doi = {10.3389/fenvs.2018.00022},
	url = {https://www.frontiersin.org/article/10.3389/fenvs.2018.00022/full},
	author = {Henr{\'\i}quez-Castillo, Carlos and Botebol, Hugo and Mouton, Adelaide and Ram{\'\i}rez-Flandes, Salvador and Lozano, Jean-Claude and Lelandais, Gaelle and Andrade, Santiago and Trefault, Nicole and de la Iglesia, Rodrigo and Bouget, Fran{\c c}ois-Yves}
}
@article {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 {LopesdosSantos2016,
	title = {Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters},
	journal = {The ISME Journal},
	volume = {11},
	number = {2},
	year = {2017},
	note = {tex.mendeley-tags: 2016,RCC1019,RCC1021,RCC1032,RCC1043,RCC1124,RCC138,RCC15,RCC1871,RCC19,RCC227,RCC2335,RCC2337,RCC2339,RCC287,RCC297,RCC3368,RCC3373,RCC3374,RCC3375,RCC3376,RCC3402,RCC4429,RCC4430,RCC4434,RCC4656,RCC696,RCC700,RCC701,RCC712,RCC713,RCC717,RCC719,RCC722,RCC726,RCC856,RCC857,RCC917,RCC996,RCC997,RCC998,RCC999,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo},
	month = {feb},
	pages = {512{\textendash}528},
	keywords = {2016, MACUMBA, MicroB3, RCC1019, RCC1021, RCC1032, RCC1043, RCC1124, RCC138, RCC15, RCC1871, RCC19, RCC227, RCC2335, RCC2337, RCC2339, RCC287, RCC297, RCC3368, RCC3373, RCC3374, RCC3375, RCC3376, RCC3402, RCC4429, RCC4430, RCC4434, RCC4656, RCC696, RCC700, RCC701, RCC712, RCC713, RCC717, RCC719, RCC722, RCC726, RCC856, RCC857, RCC917, RCC996, RCC997, RCC998, RCC999, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo},
	issn = {1751-7362},
	doi = {10.1038/ismej.2016.120},
	url = {http://www.nature.com/doifinder/10.1038/ismej.2016.120},
	author = {Lopes dos Santos, Adriana and Gourvil, Priscillia and Tragin, Margot and No{\"e}l, Mary-H{\'e}l{\`e}ne and Decelle, Johan and Romac, Sarah and Vaulot, Daniel}
}
@article {Walter2017,
	title = {Ecogenomics and taxonomy of cyanobacteria phylum},
	journal = {Frontiers in Microbiology},
	volume = {8},
	number = {November},
	year = {2017},
	note = {tex.mendeley-tags: RCC307},
	month = {nov},
	keywords = {charting biodiversity, ecological niches, genome-based microbial taxonomy, high-throughput sequencing technology, metagenome, microbial ecology, RCC307},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2017.02132},
	url = {http://journal.frontiersin.org/article/10.3389/fmicb.2017.02132/full},
	author = {Walter, Juline M. and Coutinho, Felipe H. and Dutilh, Bas E. and Swings, Jean and Thompson, Fabiano L. and Thompson, Cristiane C.}
}
@article {Moutier2017,
	title = {Evolution of the scattering properties of phytoplankton cells from flow cytometry measurements},
	journal = {PLoS ONE},
	volume = {12},
	number = {7},
	year = {2017},
	note = {ISBN: 1111111111 tex.mendeley-tags: RCC1,RCC950},
	abstract = {Combining a modern, data-analytic perspective with a focus on applications in the social sciences, the Second Edition of Applied Regression Analysis and Generalized Linear Models provides in-depth coverage of regression analysis, generalized linear models, and closely related methods. Although the text is largely accessible to readers with a modest background in statistics and mathematics, author John Fox also presents more advanced material throughout the book. Key Updates to the Second Edition:Provides greatly enhanced coverage of generalized linear models, with an emphasis on models for categorical and count data Offers new chapters on missing data in regression models and on methods of model selection Includes expanded treatment of robust regression, time-series regression, nonlinear regression, and nonparametric regression Incorporates new examples using larger data sets Includes an extensive Web site at http://www.sagepub.com/fox that presents appendixes, data sets used in the book and for data-analytic exercises, and the data-analytic exercises themselves Intended Audience: This core text will be a valuable resource for graduate students and researchers in the social sciences (particularly sociology, political science, and psychology) and other disciplines that employ linear and related models for data analysis. High Praise for the First Edition: Even though the book is written with social scientists as the target audience, the depth of material and how it is conveyed give it far broader appeal. Indeed, I recommend it as a useful learning text and resource for researchers and students in any field that applies regression or linear models (that is, most everyone), including courses for undergraduate statistics majors.... The author is to be commended for giving us this book, which I trust will find a wide and enduring readership.-JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION [T]his wonderfully comprehensive book focuses on regression analysis and linear models.... We enthusiastically recommend this book {\textemdash} having used it in class, we know that it is thorough and well liked by students. -CHANCE},
	keywords = {RCC1, RCC950},
	issn = {19326203},
	doi = {10.1371/journal.pone.0181180},
	author = {Moutier, William and Dufor{\^e}t-Gaurier, Lucile and Thyssen, M{\'e}lilotus and Loisel, Hubert and M{\'e}riaux, Xavier and Courcot, Lucie and Dessailly, David and R{\^e}ve, Anne H{\'e}l{\`e}ne and Gr{\'e}gori, Gerald and Alvain, S{\'e}verine and Barani, Aude and Brutier, Laurent and Dugenne, Mathilde}
}
@article {Monier2017,
	title = {Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton},
	journal = {Proceedings of the National Academy of Sciences},
	year = {2017},
	note = {tex.mendeley-tags: RCC1107,RCC1621,RCC2573,RCC2593,RCC745,RCC809},
	pages = {201708097},
	keywords = {rcc1107, RCC1621, RCC2573, RCC2593, RCC745, RCC809},
	issn = {0027-8424},
	doi = {10.1073/pnas.1708097114},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1708097114},
	author = {Monier, Adam and Chambouvet, Aurelie and Milner, David S. and Attah, Victoria and Terrado, Ram{\'o}n and Lovejoy, Connie and Moreau, Herv{\'e} and Santoro, Alyson E. and Derelle, Evelyne and Richards, Thomas A.}
}
@article {Soitamo2017,
	title = {Photoinhibition in marine picocyanobacteria},
	journal = {Physiologia Plantarum},
	volume = {161},
	number = {1},
	year = {2017},
	note = {Publisher: John Wiley \& Sons, Ltd (10.1111) tex.mendeley-tags: RCC156,RCC2366,RCC296,RCC407},
	month = {sep},
	pages = {97{\textendash}108},
	abstract = {Marine Synechococcus and Prochlorococcus cyanobacteria have different antenna compositions although they are genetically near to each other, and different strains thrive in very different illumination conditions. We measured growth and photoinhibition of PSII in two low-light and one high-light Prochlorococcus strains and in one Synechococcus strain. All strains were found to be able to shortly utilize moderate or even high light, but the low-light strains bleached rapidly in moderate light. Measurements of photoinhibition in the presence of the antibiotic lincomycin showed that a low-light Prochlorococcus strain was more sensitive than a high-light strain and both were more sensitive than the marine Synechococcus. The action spectrum of photoinhibition showed an increase from blue to ultraviolet wavelengths in all strains, suggesting contribution of manganese absorption to photoinhibition, but blue light caused less photoinhibition in marine cyanobacteria than expected on the basis of earlier results from plants and cyanobacteria. The visible-light part of the action spectrum resembled the absorption spectrum of the organism, suggesting that photosynthetic antenna pigments, especially divinyl chlorophylls, have a more important role as photoreceptors of visible-light photoinhibition in marine cyanobacteria than in other photoautotrophs.},
	keywords = {RCC156, RCC2366, rcc296, RCC407},
	issn = {0031-9317},
	doi = {10.1111/ppl.12571},
	url = {https://doi.org/10.1111/ppl.12571},
	author = {Soitamo, Arto and Havurinne, Vesa and Tyystj{\"a}rvi, Esa}
}
@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 {Simon2017,
	title = {Revision of the genus micromonas manton et parke (chlorophyta, mamiellophyceae), of the type species m. pusilla (butcher) manton \& parke and of the species m. commoda van baren, bachy and worden and description of two new species based on the genetic},
	journal = {Protist},
	volume = {168},
	number = {5},
	year = {2017},
	note = {tex.mendeley-tags: 2017,RCC1109,RCC114,RCC2306,RCC2308,RCC299,RCC372,RCC373,RCC418,RCC434,RCC447,RCC448,RCC449,RCC450,RCC451,RCC461,RCC465,RCC472,RCC497,RCC498,RCC570,RCC629,RCC647,RCC658,RCC676,RCC692,RCC746,RCC803,RCC804,RCC805,RCC806,RCC807,RCC808,RCC828,RCC829,RCC830,RCC831,RCC833,RCC834,RCC835,RCC836,sbr?hyto$_\textrmd$ipo},
	month = {nov},
	pages = {612{\textendash}635},
	keywords = {2017, ASSEMBLE, rcc, RCC1109, RCC114, RCC2306, RCC2308, RCC299, RCC372, RCC373, RCC418, RCC434, RCC447, RCC448, RCC449, RCC450, RCC451, RCC461, RCC465, RCC472, RCC497, RCC498, RCC570, RCC629, RCC647, RCC658, RCC676, RCC692, RCC746, RCC803, RCC804, RCC805, RCC806, RCC807, RCC808, RCC828, RCC829, RCC830, RCC831, RCC833, RCC834, RCC835, RCC836, SBR$_\textrmP$hyto$_\textrmD$IPO, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto$_\textrmd$ipo},
	issn = {14344610},
	doi = {10.1016/j.protis.2017.09.002},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S1434461017300780},
	author = {Simon, Nathalie and Foulon, Elodie and Grulois, Daphne and Six, Christophe and Desdevises, Yves and Latimier, Marie and Le Gall, Florence and Tragin, Margot and Houdan, Aude and Derelle, Evelyne and Jouenne, Fabien and Marie, Dominique and Le Panse, Sophie and Vaulot, Daniel and Marin, Birger}
}
@article {Leliaert2016,
	title = {Chloroplast phylogenomic analyses reveal the deepest-branching lineage of the Chlorophyta, Palmophyllophyceae class. nov.},
	journal = {Scientific Reports},
	volume = {6},
	year = {2016},
	note = {tex.mendeley-tags: 2016,RCC15,RCC299},
	month = {may},
	pages = {25367},
	keywords = {2016, RCC15, RCC299},
	issn = {2045-2322},
	doi = {10.1038/srep25367},
	url = {http://www.nature.com/articles/srep25367},
	author = {Leliaert, Frederik and Tronholm, Ana and Lemieux, Claude and Turmel, Monique and DePriest, Michael S. and Bhattacharya, Debashish and Karol, Kenneth G. and Fredericq, Suzanne and Zechman, Frederick W. and Lopez-Bautista, Juan M.}
}
@article {Engesmo2016,
	title = {New insights into the morphology and phylogeny of Heterosigma akashiwo (Raphidophyceae), with the description of Heterosigma minor sp. nov .},
	journal = {Phycologia},
	volume = {55},
	number = {3},
	year = {2016},
	note = {tex.mendeley-tags: 2016,rcc1501,rcc1502},
	month = {may},
	pages = {279{\textendash}294},
	keywords = {2016, rcc1501, rcc1502},
	issn = {0031-8884},
	doi = {10.2216/15-115.1},
	url = {http://www.phycologia.org/doi/10.2216/15-115.1},
	author = {Engesmo, Anette and Eikrem, Wenche and Seoane, Sergio and Smith, Kirsty and Edvardsen, Bente and Hofgaard, Antje and Tomas, Carmelo R.}
}
@article {Tragin2016,
	title = {Phylogenetic diversity and ecology of green micro algae in marine systems},
	journal = {Perspectives in Phycology},
	volume = {in press},
	year = {2016},
	note = {tex.mendeley-tags: 2016,rcc,sbr?hyto$_\textrmd$ipo},
	keywords = {2016, ? No DOI found, rcc, sbr?hyto$_\textrmd$ipo},
	author = {Tragin, M and Lopes dos Santos, Adriana and Christen, R. and Vaulot, D.}
}
@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 {Coutinho2015,
	title = {Comparative genomics of Synechococcus and proposal of the new genus Parasynechococcus},
	journal = {PeerJ},
	year = {2015},
	note = {tex.mendeley-tags: rcc},
	pages = {e{\textendash}1522},
	keywords = {rcc},
	issn = {2167-8359},
	doi = {10.7717/peerj.1522},
	author = {Coutinho, Felipe and Tschoeke, Diogo Antonio and Thompson, Fabiano and Thomson, Cristiane}
}
@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 {Kamikawa2015,
	title = {Multiple losses of photosynthesis in Nitzschia (Bacillariophyceae)},
	journal = {Phycological Research},
	volume = {63},
	year = {2015},
	note = {tex.mendeley-tags: rcc},
	pages = {19{\textendash}28},
	abstract = {In order to obtain insights into the evolution of colorless (apochlorotic) diatoms, we investigated newly established apochlorotic strains of Nitzschia spp. using light and electron microscopy and molecular phylogenetic analyses. Fluores- cence microscopic observations demonstrated that the apochlorotic diatoms lack chlorophylls. Transmission electron microscopy of two apochlorotic strains also demonstrated that their plastids lacked thylakoids; instead, having four- membrane-bound organelles without thylakoids, similar to nonphotosynthetic plastid remnants. From the apochlorotic strains, we also found plastid small subunit rRNA genes that were unusually long branched in phylogenetic analyses, as observed in other nonphotosynthetic plastids. Molecular phylogenetic analysis of the nucleus-encoded large subunit rRNA genes showed eight distinct lineages for apochlo- rotic diatoms. The eight apochlorotic lineages were not monophyletic, suggesting that the loss of photosynthesis took place multiple times independently within Nitzschia. Several diatoms, including Nitzschia spp., are mixotrophic, which is an expected mode of nutrition that would help explain the evolutionary switch from a photosynthetic lifestyle to a heterotrophic lifestyle. Key},
	keywords = {apochlorotic diatoms, genetic diversity, large subunit rrna, molecular phylogenetic analysis, nonphotosynthetic plastids, plastid 16s rrna, rcc},
	issn = {13220829},
	doi = {10.1111/pre.12072},
	url = {http://doi.wiley.com/10.1111/pre.12072},
	author = {Kamikawa, Ryoma and Yubuki, Naoji and Yoshida, Masaki and Taira, Misaka and Nakamura, Noriaki and Ishida, Ken-ichiro and Leander, Brian S. and Miyashita, Hideaki and Hashimoto, Tetsuo and Mayama, Shigeki and Inagaki, Yuji}
}
@article {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 {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 {Kashtan2014,
	title = {Single-cell genomics reveals hundreds of coexisting subpopulations in wild prochlorococcus},
	journal = {Science},
	volume = {344},
	number = {6182},
	year = {2014},
	note = {tex.mendeley-tags: RCC278},
	pages = {416{\textendash}420},
	abstract = {Extensive genomic diversity within coexisting members of a microbial species has been revealed through selected cultured isolates and metagenomic assemblies. Yet, the cell-by-cell genomic composition of wild uncultured populations of co-occurring cells is largely unknown. In this work, we applied large-scale single-cell genomics to study populations of the globally abundant marine cyanobacterium Prochlorococcus. We show that they are composed of hundreds of subpopulations with distinct {\textquotedblleft}genomic backbones,{\textquotedblright} each backbone consisting of a different set of core gene alleles linked to a small distinctive set of flexible genes. These subpopulations are estimated to have diverged at least a few million years ago, suggesting ancient, stable niche partitioning. Such a large set of coexisting subpopulations may be a general feature of free-living bacterial species with huge populations in highly mixed habitats.},
	keywords = {RCC278},
	doi = {10.1126/science.1248575},
	url = {http://www.sciencemag.org/content/344/6182/416.abstract},
	author = {Kashtan, Nadav and Roggensack, Sara E and Rodrigue, S{\'e}bastien and Thompson, Jessie W and Biller, Steven J and Coe, Allison and Ding, Huiming and Marttinen, Pekka and Malmstrom, Rex R and Stocker, Roman and Follows, Michael J and Stepanauskas, Ramunas and Chisholm, Sallie W}
}
@article {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 {Drescher2012,
	title = {Coccolithogenesis in scyphosphaera apsteinii (prymnesiophyceae)},
	journal = {Journal of Phycology},
	volume = {48},
	number = {6},
	year = {2012},
	note = {tex.mendeley-tags: RCC1456},
	pages = {1343{\textendash}1361},
	abstract = {Coccolithophores are the most significant producers of marine biogenic calcite, although the intracellular calcification process is poorly understood. In the case of Scyphosphaera apsteinii Lohmann 1902, flat ovoid muroliths and bulky, vase-shaped lopadoliths with a range of intermediate morphologies may be produced by a single cell. This polymorphic species is within the Zygodiscales, a group that remains understudied with respect to ultrastructure and coccolith ontogeny. We therefore undertook an analysis of cell ultrastructure, morphology, and coccolithogenesis. The cell ultrastructure showed many typical haptophyte features, with calcification following a similar pattern to that described for other heterococcolith bearing species including Emiliania huxleyi. Of particular significance was the reticular body role in governing fine-scale morphology, specifically the central pore formation of the coccolith. Our observations also highlighted the essential role of the inter- and intracrystalline organic matrix in growth and arrangement of the coccolith calcite. S. apsteinii secreted mature coccoliths that attached to the plasma membrane via fibrillar material. Time-lapse light microscopy demonstrated secretion of lopadoliths occurred base first before being actively repositioned at the cell surface. Significantly, growth irradiance influenced the coccosphere composition with fewer lopadoliths being formed relative to muroliths at higher light intensities. Overall, our observations support dynamic metabolic (i.e., in response to growth irradiance), sensory and cytoskeletal control over the morphology and secretion of polymorphic heterococcoliths. With a basic understanding of calcification established, S. apsteinii could be a valuable model to further study coccolithophore calcification and cell physiological responses to ocean acidification.},
	keywords = {Calcification, coccolithogenesis, coccolithophore, organic matrix, rcc, RCC1456, reticular body, secretion, ultrastructure, Zygodiscales},
	doi = {10.1111/j.1529-8817.2012.01227.x},
	url = {http://dx.doi.org/10.1111/j.1529-8817.2012.01227.x},
	author = {Drescher, Brandon and Dillaman, Richard M and Taylor, Alison R}
}
@article {Treusch2012,
	title = {Phytoplankton distribution patterns in the northwestern Sargasso Sea revealed by small subunit rRNA genes from plastids},
	journal = {The ISME journal},
	volume = {6},
	year = {2012},
	note = {Publisher: International Society for Microbial Ecology tex.mendeley-tags: Micromonas,RCC,rcc},
	pages = {481{\textendash}492},
	keywords = {Bathycoccus, CHRYSOPHYCEAE, key?aper, Micromonas, Ostreococcus, pelagophyceae, Prasinophyceae, Prymnesiophyceae, QPCR, rcc, TRFLP},
	doi = {10.1038/ismej.2011.117},
	url = {http://dx.doi.org/10.1038/ismej.2011.117 http://www.nature.com/ismej/journal/vaop/ncurrent/suppinfo/ismej2011117s1.html},
	author = {Treusch, Alexander H and Demir-Hilton, Elif and Vergin, Kevin L and Worden, Alexandra Z and Carlson, Craig A and Donatz, Michael G and Burton, Robert M and Giovannoni, Stephen J}
}
@article {Baines2012,
	title = {Significant silicon accumulation by marine picocyanobacteria},
	journal = {Nature Geoscience},
	volume = {5},
	number = {12},
	year = {2012},
	note = {arXiv: 9605103 [cs] ISBN: 1752-08941?752-0908 Publisher: Nature Publishing Group tex.arxivid: cs/9605103 tex.mendeley-tags: rcc1084,rcc1086,rcc752},
	pages = {886{\textendash}891},
	abstract = {The marine silicon cycle is thought to be intimately tied to the carbon cycle through its effect on the growth of diatoms. These unicellular algae form substantial blooms in cold, nutrient-rich waters. Their dense, siliceous cell walls promote the sinking of particulate matter, and all the carbon and nutrients contained therein1. As such, diatoms are thought to be the primary organisms responsible for the low levels of dissolved silicon observed in the surface ocean and the export of mineral silica to depth. Here, we use synchrotron X-ray fluorescence microscopy to determine the elemental composition of individual diatoms and cyanobacterial cells from the eastern equatorial Pacific and the Sargasso Sea.We show that cells of Synechococcus, a small unicellular marine cyanobacterium that dominates in nutrient-depleted waters2, can exhibit cellular ratios of silicon to sulphur, and silicon to phosphorus, approaching those detected in diatoms in the same location. Silicon accumulation was also observed in cultured Synechococcus strains. We estimate that the water column inventory of silicon in Synechococcus can exceed that of diatomsinsomecases.We suggest that picocyanobacteriamay exert a previously unrecognized influence on the oceanic silicon cycle, especially in nutrient-poorwaters.},
	keywords = {rcc1084, RCC1086, rcc752},
	issn = {1752-0894},
	doi = {10.1038/ngeo1641},
	url = {http://www.nature.com/doifinder/10.1038/ngeo1641},
	author = {Baines, Stephen B. and Twining, Benjamin S. and Brzezinski, Mark a. and Krause, Jeffrey W. and Vogt, Stefan and Assael, Dylan and McDaniel, Hannah}
}
@article {Thompson2012,
	title = {Unicellular cyanobacterium symbiotic with a single-celled eukaryotic alga},
	journal = {Science},
	volume = {337},
	number = {6101},
	year = {2012},
	note = {tex.mendeley-tags: 2012,microb3,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {1546{\textendash}1550},
	abstract = {Symbioses between nitrogen (N)2{\textendash}fixing prokaryotes and photosynthetic eukaryotes are important for nitrogen acquisition in N-limited environments. Recently, a widely distributed planktonic uncultured nitrogen-fixing cyanobacterium (UCYN-A) was found to have unprecedented genome reduction, including the lack of oxygen-evolving photosystem II and the tricarboxylic acid cycle, which suggested partnership in a symbiosis. We showed that UCYN-A has a symbiotic association with a unicellular prymnesiophyte, closely related to calcifying taxa present in the fossil record. The partnership is mutualistic, because the prymnesiophyte receives fixed N in exchange for transferring fixed carbon to UCYN-A. This unusual partnership between a cyanobacterium and a unicellular alga is a model for symbiosis and is analogous to plastid and organismal evolution, and if calcifying, may have important implications for past and present oceanic N2 fixation.},
	keywords = {2012, MicroB3, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	doi = {10.1126/science.1222700},
	url = {http://www.sciencemag.org/content/337/6101/1546.abstract},
	author = {Thompson, Anne W and Foster, Rachel A and Krupke, Andreas and Carter, Brandon J and Musat, Niculina and Vaulot, Daniel and Kuypers, Marcel M M and Zehr, Jonathan P}
}
@article {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 {Luo2011,
	title = {Individual genome assembly from complex community short-read metagenomic datasets},
	journal = {The ISME journal},
	volume = {6},
	year = {2011},
	note = {Publisher: International Society for Microbial Ecology tex.mendeley-tags: RCC307},
	pages = {898{\textendash}901},
	keywords = {RCC307},
	doi = {10.1038/ismej.2011.147},
	url = {http://dx.doi.org/10.1038/ismej.2011.147 http://www.nature.com/ismej/journal/vaop/ncurrent/suppinfo/ismej2011147s1.html},
	author = {Luo, Chengwei and Tsementzi, Despina and Kyrpides, Nikos C and Konstantinidis, Konstantinos T}
}
@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 {Rokitta2011,
	title = {Transcriptome analyses reveal differential gene expression patterns between the life-cycle stages of Emiliania huxleyi (Haptophyta) and reflect specialization to different ecological niches},
	journal = {Journal of Phycology},
	volume = {47},
	number = {4},
	year = {2011},
	note = {Publisher: Blackwell Publishing Ltd tex.mendeley-tags: 2011,rcc,sbr?hyto?ppo},
	pages = {829{\textendash}838},
	abstract = {Coccolithophores, especially the abundant, cosmopolitan species Emiliania huxleyi (Lohmann) W. W. Hay et H. P. Mohler, are one of the main driving forces of the oceanic carbonate pump and contribute significantly to global carbon cycling, due to their ability to calcify. A recent study indicates that termination of diploid blooms by viral infection induces life-cycle transition, and speculation has arisen about the role of the haploid, noncalcifying stage in coccolithophore ecology. To explore gene expression patterns in both life-cycle stages, haploid and diploid cells of E. huxleyi (RCC 1217 and RCC 1216) were acclimated to limiting and saturating photon flux densities. Transcriptome analyses were performed to assess differential genomic expression related to different ploidy levels and acclimation light intensities. Analyses indicated that life-cycle stages exhibit different properties of regulating genome expression (e.g., pronounced gene activation and gene silencing in the diploid stage), proteome maintenance (e.g., increased turnover of proteins in the haploid stage), as well as metabolic processing (e.g., pronounced primary metabolism and motility in the haploid stage and calcification in the diploid stage). Furthermore, higher abundances of transcripts related to endocytotic and digestive machinery were observed in the diploid stage. A qualitative feeding experiment indicated that both life-cycle stages are capable of particle uptake (0.5 ??m diameter) in late-stationary growth phase. Results showed that the two life-cycle stages represent functionally distinct entities that are evolutionarily shaped to thrive in the environment they typically inhabit.},
	keywords = {2011, endocytosis, Life-cycle stages, microarray, quantitative RT-PCR, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo, transcriptome profiling},
	doi = {10.1111/j.1529-8817.2011.01014.x},
	url = {http://dx.doi.org/10.1111/j.1529-8817.2011.01014.x},
	author = {Rokitta, Sebastian D and de Nooijer, Lennart J and Trimborn, Scarlett and de Vargas, Colomban and Rost, Bj{\"o}rn and John, Uwe}
}
@article {Turmel2010,
	title = {A deviant genetic code in the reduced mitochondrial genome of the picoplanktonic green alga pycnococcus provasolii},
	journal = {Journal of Molecular Evolution},
	volume = {70},
	number = {2},
	year = {2010},
	note = {ISBN: 0022-2844 tex.mendeley-tags: RCC299},
	pages = {203{\textendash}214},
	abstract = {Reduction in size of flagellated chlorophytes occurred multiple times during evolution, providing the opportunity to study the consequences of cell reduction on genome architecture. Recent investigations on the chloroplast genomes of the tiny prasinophyceans Ostreococcus tauri (Mamiellales), Micromonas sp. RCC299 (Mamiellales), and Pycnococcus provasolii (Pseudocourfieldiales) highlighted their extreme compaction and reduced gene repertoires. Genome compaction is also exemplified by the Ostreococcus and Micromonas mitochondrial DNAs (mtDNAs) although they have retained almost all of the about 65 genes presumably present in the mitochondria of ancestral prasinophyceans. In this study, the mitochondrial genome of Pycnococcus was sequenced and compared to those of previously examined chlorophytes. Our results document the first case where cellular reduction of a free-living alga was accompanied by marked reduction in gene content of both the mitochondrial and chloroplast genomes. At 24,321 bp, the intronless Pycnococcus mitochondrial genome falls within the lower size range displayed by green algal mtDNAs. The 36 conserved genes, specifying two rRNAs with conventional structures, 16 tRNAs and 18 proteins, are all encoded on the same DNA strand and represent 88\% of the genome. Besides a pronounced codon bias, the protein-coding genes feature a variant genetic code characterized by the use of TGA (normally a stop codon) to code for tryptophan, and the unprecedented use of TTA and TTG (normally leucine codons) as stop codons. We conclude that substantial reduction of the mitochondrial genome occurred in at least three independent chlorophyte lineages and that this process entailed a number of convergent changes in these lineages.},
	keywords = {RCC299},
	doi = {10.1007/s00239-010-9322-6},
	author = {Turmel, Monique and Otis, Christian and Lemieux, Claude}
}
@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 {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 {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 {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 {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 {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 {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 {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 {OKelly2003,
	title = {A transient bloom of {\textexclamdown}i{\textquestiondown}Ostreococcus{\textexclamdown}/i{\textquestiondown} (chlorophyta, prasinophyceae) in west neck bay, long island, new york},
	journal = {Journal of Phycology},
	volume = {39},
	number = {5},
	year = {2003},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {850{\textendash}854},
	abstract = {The smallest known eukaryote, Ostreococcus tauri Courties et Chretiennot-Dinet, was first reported as the dominant picoplankter in a French lagoon known for its diverse phytoplankton community and high oyster productivity. Long-term seasonal blooms of this picoeukaryote were observed in association with stable plankton communities. On 5 June 2001, a distinctive monotypic picoplankton bloom was detected by flow cytometry as part of an ongoing study of "brown tide" (Aureococcus anophagefferens) bloom initiation in Long Island bays. The bloom reached a concentration of 5 x 10(5) cells.mL(-1) in West Neck Bay and lasted less than 2 weeks. Epifluorescence microscopy and TEM indicated that the bloom organism was an Ostreococcus-like picoalga, the first ever observed in a Long Island bay. Many cells of this alga contained numerous virus-like particles. The Ostreococcus-like picoalga, which resembles O. tauri, was rare in samples collected the following week. Instead, a substantial increase in the Synechococcus population was observed. Such rapid population changes have not previously been reported for Ostreococcus. Viral lysis and grazing by heterotrophic nanoflagellates may have contributed to the rapid decline of the Ostreococcus-like cells in West Neck Bay.},
	keywords = {Aureococcus Anophagefferens Pelagophyceae, bloom dynamics, Gen, Microalga, Ostreococcus, picoalgae, picoplankton, rcc},
	doi = {10.1046/j.1529-8817.2003.02201.x},
	author = {O{\textquoteright}Kelly, C J and Sieracki, M E and Thier, E C and Hobson, I C}
}
@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}
}
