@article {wang_aggregating_2024,
	title = {Aggregating Synechococcus contributes to particle organic carbon export in coastal estuarine waters: Its lineage features and assembly processes},
	journal = {Science of The Total Environment},
	year = {2024},
	month = {jan},
	pages = {170368},
	issn = {00489697},
	doi = {10.1016/j.scitotenv.2024.170368},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0048969724005035},
	author = {Wang, Ting and Li, Jialin and Xu, Yandong and Zou, Tao and Qin, Song}
}
@article {dedman_alterations_2024,
	title = {Alterations in metalloprotein abundance under ocean warming in the marine green alga Micromonas pusilla using the mebipred predictive tool},
	journal = {Algal Research},
	volume = {78},
	year = {2024},
	month = {mar},
	pages = {103412},
	abstract = {Metals are essential to life, required for the functioning of a substantial fraction of proteins. Marine phytoplankton drives the oceanic carbon cycle, influencing global biogeochemistry. These organisms rely on trace metal nutrients; however how trace nutrient demand will change under ocean warming is uncertain. The currently limited annotation of metalloproteins contributes to this lack of understanding. Herein, we utilise the recently published mebipred tool to predict the metalloproteome of the globally occurring green alga, Micromonas pusilla, revealing \~{}20~\% of its reference proteome to display ion-binding properties. Using the predicted metalloproteome, and existing Gene Ontology annotation, we present a comprehensive insight towards changes in metalloprotein abundance after exposure to ocean warming conditions (+6~{\textdegree}C), using a shotgun proteomic approach. We outline that predictions must be combined with existing annotation to fully capture the metalloprotein response. Approximately 50~\% of identified metalloproteins significantly altered in abundance under warming, largely related to changes in cellular function. Notably, warming appeared to shift Fe use from photosynthesis to storage in M. pusilla, indicated by a 2.36 log2 fold-increase in ferritin and decline in abundance of photosynthetic proteins. Ocean warming will inevitably alter cellular use and demand for metal cofactors in marine phytoplankton with possible implications for biogeochemical cycling. Bioinformatics tools such as mebipred greatly expand our ability to examine such changes.},
	keywords = {Biogeochemistry, marine phytoplankton, Ocean warming, proteomics, RCC1614, Trace metals},
	issn = {2211-9264},
	doi = {10.1016/j.algal.2024.103412},
	url = {https://www.sciencedirect.com/science/article/pii/S2211926424000249},
	author = {Dedman, Craig J. and Fournier, Marjorie and Rickaby, Rosalind E. M.}
}
@mastersthesis {wink_application_2023,
	title = {Application of Flow Cytometry and Membrane Inlet Mass Spectrometry as Tools to Assess Dimethyl Sulfide Produced in Emiliania huxleyi (CHC108) Cultures},
	year = {2023},
	school = {University of Galway},
	type = {masters},
	address = {Galway},
	abstract = {Dimethyl sulphide (DMS) is a key component in the global sulphur cycle with emphasized significance in areas away from anthropogenic sources. Phytoplankton produce DMS when under stress as a defence mechanism from abiotic and biotic influences such as high wind stress and grazing. E. huxleyi was used as the phytoplankton of choice because of the cosmopolitan nature of the species along with the more robust nature of the coccolith. DMS has a high diffusion rate in the atmosphere so immediately monitoring the levels in the water column has proven difficult especially when looking at continuous input flux. In this study, membrane inlet mass spectrometry was used to monitor DMS flux over varying periods of time along with a possible variation of DMS under Mass 47 which excludes one of the methyl groups under different stressors. This continuous observation allowed for the observation in minute changes over longer periods of time rather than using the snapshot method which looks at chemical concentrations at singular points in time. This novel technique can give insights to the response times of the phytoplankton to the changing environment in real time. The added stressors to the water column did result in an increase of DMS but the lag time to the addition and the visible increase in DMS did not follow the expected trend. Of the parameters tested here, the most likely to initiate DMS production is heavy metal loading and water column acidification},
	keywords = {RCC3852, ⛔ No DOI found},
	author = {Wink, Adelaide Lavenant}
}
@article {bouquet_artificial_2023,
	title = {Artificial Substrates Coupled with qPCR (AS-qPCR) Assay for the Detection of the Toxic Benthopelagic Dinoflagellate Vulcanodinium rugosum},
	journal = {Toxins},
	volume = {15},
	number = {3},
	year = {2023},
	note = {Number: 3 Publisher: Multidisciplinary Digital Publishing Institute},
	month = {mar},
	pages = {217},
	abstract = {Vulcanodinium rugosum is an emerging benthopelagic neuro-toxic dinoflagellate species responsible for seasonal Pinnatoxins and Portimines contaminations of shellfish and marine animals. This species is challenging to detect in the environment, as it is present in low abundance and difficult to be identified using light microscopy. In this work, we developed a method using artificial substrates coupled with qPCR (AS-qPCR) to detect V. rugosum in a marine environment. This sensitive, specific and easy-to-standardize alternative to current techniques does not require specialized expertise in taxonomy. After determining the limits and specificity of the qPCR, we searched for the presence of V. rugosum in four French Mediterranean lagoons using artificial substrates collected every two weeks for one year. The AS-qPCR method revealed its occurrences in summer 2021 in every studied lagoon and detected cells in more samples than light microscopy. As V. rugosum development induces shellfish contamination even at low microalga densities, the AS-qPCR method is accurate and relevant for monitoring V. rugosum in a marine environment.},
	keywords = {artificial substrate, benthopelagic, detection, PCR, RCC6328, RCC6338, RCC6344, RCC6548, RCC6550, toxins, \textitVulcanodinium rugosum},
	issn = {2072-6651},
	doi = {10.3390/toxins15030217},
	url = {https://www.mdpi.com/2072-6651/15/3/217},
	author = {Bouquet, Aur{\'e}lien and Felix, Christine and Masseret, Estelle and Reymond, Coralie and Abadie, Eric and Laabir, Mohamed and Rolland, Jean Luc}
}
@article {das_assessing_2023,
	title = {Assessing indicators of arsenic toxicity using variable fluorescence in a commercially valuable microalgae: physiological and toxicological aspects},
	journal = {Journal of Hazardous Materials},
	year = {2023},
	month = {mar},
	pages = {131215},
	abstract = {Indicators signaling Arsenic (As) stress through physiology of microalgae using non-destructive methods like variable fluorescence are rare but requisite. This study reports stress markers indicating arsenic (As) toxicity (in two concentrations 11.25{\textmu}g/L and 22.5{\textmu}g/L compared to a control) exposed to a microalga (Diacronema lutheri), using fast repetition rate fluorometry (FRRf). Growth and physiological parameters such as cell density, chl a and the maximum quantum yield Fv/Fm showed coherence and impeded after the exponential phase (day 9 - day 12) in As treatments compared to the control (p < 0.05). On contrary photo-physiological constants were elevated showing higher optical (aLHII) and functional [Sigma (σPSII)] absorption cross-section for the As treatments (p < 0.05) further implying the lack of biomass production yet an increase in light absorption. In addition, As exposure increased the energy dissipation by heat (NPQ-NSV) showing a strong relationship with the de-epoxidation ratio (DR) involving photoprotective pigments. Total As bioaccumulation by D. lutheri showed a strong affinity with Fe adsorption throughout the algal growth curve. This study suggests some prompt photo-physiological proxies signaling As contamination and endorsing its usefulness in risk assessments, given the high toxicity and ubiquitous presence of As in the ecosystem.},
	keywords = {Arsenic bioaccumulation, de-epoxidation ratio (DR), Optical absorption cross section, pigment concentrations, RCC1537},
	issn = {0304-3894},
	doi = {10.1016/j.jhazmat.2023.131215},
	url = {https://www.sciencedirect.com/science/article/pii/S0304389423004971},
	author = {Das, Shagnika and Lizon, Fabrice and Gevaert, Fran{\c c}ois and Bialais, Capucine and Duong, Gwendoline and Ouddane, Baghdad and Souissi, Sami}
}
@article {jang_assessment_2022,
	title = {Assessment of biodiversity, global distribution, and putative ecological niches of suessiacean dinoflagellates by DNA metabarcoding},
	journal = {Frontiers in Ecology and Evolution},
	volume = {10},
	year = {2022},
	abstract = {Dinoflagellates in the family Suessiaceae, so-called suessiacean dinoflagellates, play diverse roles in aquatic ecosystems, being distributed from tropical to polar waters and from marine to freshwater habitats and encompassing free-living forms, symbionts, and parasites. Despite their importance due to the variety of ecological roles and biodiversity, very few studies have characterized small suessiacean species. Recent advances in molecular techniques could provide insights into the yet unexplored ecological roles they play in aquatic environments. Using a global DNA metabarcoding dataset, this study elucidated the hidden biodiversity, global distribution, and ecological characteristics of suessiacean dinoflagellates. The results of this study indicated that the family Suessiaceae was the sixth highest in terms of read count and the ninth highest in terms of amplicon sequence variant (ASV) richness from a total of 42 categorized dinoflagellate families, suggesting that their global abundance has been greatly underestimated. Furthermore, metabarcodes of suessiacean dinoflagellates were found to be cosmopolitan in distribution, although the ecological niche of each taxon was distinctly different within the group based on their latitudinal and vertical distribution patterns. Moreover, phylogenetic analysis discovered at least five new phylogenetic groups and three new individual species within the family. Collectively, the findings of this study highlight the significance of suessiacean dinoflagellates in global aquatic ecosystems and reveal the importance of big data obtained from environmental DNA in exploring the ecological functions of understudied species.},
	keywords = {RCC2013},
	issn = {2296-701X},
	doi = {10.3389/fevo.2022.1010854},
	url = {https://www.frontiersin.org/articles/10.3389/fevo.2022.1010854},
	author = {Jang, Se Hyeon}
}
@article {stewart_altitudinal_2021,
	title = {Altitudinal Zonation of Green Algae Biodiversity in the French Alps},
	journal = {Frontiers in Plant Science},
	volume = {12},
	year = {2021},
	pages = {1066},
	abstract = {Mountain environments are marked by an altitudinal zonation of habitat types. They are home to a multitude of terrestrial green algae, who have to cope with abiotic conditions specific to high elevation, e.g., high UV irradiance, alternating desiccation, rain and snow precipitations, extreme diurnal variations in temperature and chronic scarceness of nutrients. Even though photosynthetic green algae are primary producers colonizing open areas and potential markers of climate change, their overall biodiversity in the Alps has been poorly studied so far, in particular in soil, where algae have been shown to be key components of microbial communities. Here, we investigated whether the spatial distribution of green algae followed the altitudinal zonation of the Alps, based on the assumption that algae settle in their preferred habitats under the pressure of parameters correlated with elevation. We did so by focusing on selected representative elevational gradients at distant locations in the French Alps, where soil samples were collected at different depths. Soil was considered as either a potential natural habitat or temporary reservoir of algae. We showed that algal DNA represented a relatively low proportion of the overall eukaryotic diversity as measured by a universal Eukaryote marker. We designed two novel green algae metabarcoding markers to amplify the Chlorophyta phylum and its Chlorophyceae class, respectively. Using our newly developed markers, we showed that elevation was a strong correlate of species and genus level distribution. Altitudinal zonation was thus determined for about fifty species, with proposed accessions in reference databases. In particular, Planophila laetevirens and Bracteococcus ruber related species as well as the snow alga Sanguina genus were only found in soil starting at 2,000 m above sea level. Analysis of environmental and bioclimatic factors highlighted the importance of pH and nitrogen/carbon ratios in the vertical distribution in soil. Capacity to grow heterotrophically may determine the Trebouxiophyceae over Chlorophyceae ratio. The intensity of freezing events (freezing degree days), proved also determinant in Chlorophyceae distribution. Guidelines are discussed for future, more robust and precise analyses of environmental algal DNA in mountain ecosystems and address green algae species distribution and dynamics in response to environmental changes.},
	keywords = {rcc, RCC1055, RCC130, RCC1563, RCC2501, RCC2960, RCC3402, RCC443, RCC4743, RCC537, RCC581, RCC6, RCC7, RCC891},
	issn = {1664-462X},
	doi = {10.3389/fpls.2021.679428},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2021.679428},
	author = {Stewart, Adeline and Rioux, Delphine and Boyer, Fr{\'e}deric and Gielly, Ludovic and Pompanon, Fran{\c c}ois and Saillard, Am{\'e}lie and Thuiller, Wilfried and Valay, Jean-Gabriel and Mar{\'e}chal, {\'E}ric and Coissac, Eric}
}
@article {Trefaut2020,
	title = {Annual phytoplankton dynamics in coastal waters from fildes bay, western antarctic peninsula},
	journal = {Scientific Reports},
	volume = {11},
	number = {1},
	year = {2021},
	note = {tex.mendeley-tags: RCC2265,RCC2289,RCC4582,RCC4586,RCC5152},
	month = {dec},
	pages = {1368},
	abstract = {Year-round reports of phytoplankton dynamics in the West Antarctic Peninsula are rare and mainly limited to microscopy and/or pigment-based studies. We analyzed the phytoplankton community from coastal waters of Fildes Bay in the West Antarctic Peninsula between January 2014 and 2015 using metabarcoding of the nuclear and plastidial 18/16S rRNA gene from both size-fractionated and flow cytometry sorted samples. Overall 14 classes of photosynthetic eukaryotes were present in our samples with the following dominating: Bacillariophyta (diatoms), Pelagophyceae and Dictyochophyceae for division Ochrophyta, Mamiellophyceae and Pyramimonadophyceae for division Chlorophyta, Haptophyta and Cryptophyta. Each metabarcoding approach yielded a different image of the phytoplankton community with for example Prymnesiophyceae more prevalent in plastidial metabarcodes and Mamiellophyceae in nuclear ones. Diatoms were dominant in the larger size fractions and during summer, while Prymnesiophyceae and Cryptophyceae were dominant in colder seasons. Pelagophyceae were particularly abundant towards the end of autumn (May). In addition of Micromonas polaris and Micromonas sp. clade B3, both previously reported in Arctic waters, we detected a new Micromonas 18S rRNA sequence signature, close to, but clearly distinct from M. polaris , which potentially represents a new clade specific of the Antarctic. These results highlight the need for complementary strategies as well as the importance of year-round monitoring for a comprehensive description of phytoplankton communities in Antarctic coastal waters.},
	keywords = {RCC2265, RCC2289, RCC4582, RCC4586, RCC5152},
	issn = {2045-2322},
	doi = {10.1038/s41598-020-80568-8},
	url = {http://biorxiv.org/content/early/2020/10/27/2020.10.27.356600.abstract http://www.nature.com/articles/s41598-020-80568-8},
	author = {Trefault, Nicole and de la Iglesia, Rodrigo and Moreno-Pino, Mario and Lopes dos Santos, Adriana and G{\'e}rikas Ribeiro, Catherine and Parada-Pozo, G{\'e}nesis and Cristi, Antonia and Marie, Dominique and Vaulot, Daniel}
}
@article {Bestion2020,
	title = {Abrupt declines in marine phytoplankton production driven by warming and biodiversity loss in a microcosm experiment},
	journal = {Ecology Letters},
	volume = {23},
	number = {3},
	year = {2020},
	note = {tex.mendeley-tags: RCC1303,RCC1512,RCC4221,RCC623,RCC626,RCC652,RCC80,RCC834},
	month = {mar},
	pages = {457{\textendash}466},
	abstract = {Rising sea surface temperatures are expected to lead to the loss of phytoplankton biodiversity. However, we currently understand very little about the interactions between warming, loss of phytoplankton diversity and its impact on the oceans{\textquoteright} primary production. We experimentally manipulated the species richness of marine phytoplankton communities under a range of warming scenarios, and found that ecosystem production declined more abruptly with species loss in communities exposed to higher temperatures. Species contributing positively to ecosystem production in the warmed treatments were those that had the highest optimal temperatures for photosynthesis, implying that the synergistic impacts of warming and biodiversity loss on ecosystem functioning were mediated by thermal trait variability. As species were lost from the communities, the probability of taxa remaining that could tolerate warming diminished, resulting in abrupt declines in ecosystem production. Our results highlight the potential for synergistic effects of warming and biodiversity loss on marine primary production.},
	keywords = {biodiversity, biodiversity loss, climate change, ecosystem functioning, phytoplankton, RCC1303, rcc1512, RCC4221, RCC623, RCC626, RCC652, RCC80, RCC834, thermal per-},
	issn = {1461-023X},
	doi = {10.1111/ele.13444},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ele.13444},
	author = {Bestion, Elvire and Barton, Samuel and Garc{\'\i}a, Francisca C. and Warfield, Ruth and Yvon-Durocher, Gabriel},
	editor = {Hillebrand, Helmut}
}
@article {Nissimov2020,
	title = {Aquatic virus culture collection: an absent (but necessary) safety net for environmental microbiologists},
	journal = {Applied Phycology},
	volume = {00},
	number = {00},
	year = {2020},
	note = {Publisher: Taylor \& Francis},
	pages = {1{\textendash}15},
	keywords = {algae, Aquatic viruses, bacteria, biological preservation, community resource, culture collection, genetic and metabolic diversity},
	issn = {2638-8081},
	doi = {10.1080/26388081.2020.1770123},
	url = {https://doi.org/10.1080/26388081.2020.1770123 https://www.tandfonline.com/doi/full/10.1080/26388081.2020.1770123},
	author = {Nissimov, Jozef I and Campbell, Christine N and Probert, Ian and Wilson, William H}
}
@article {Pan2020,
	title = {Assessments of first feeding protocols on the larviculture of California grunion Leuresthes tenuis (Osteichthyes: Atherinopsidae)},
	journal = {Aquaculture Research},
	volume = {51},
	number = {7},
	year = {2020},
	note = {Publisher: Blackwell Publishing Ltd tex.mendeley-tags: RCC350},
	month = {jul},
	pages = {3054{\textendash}3058},
	keywords = {California grunion, Copepod, larval rearing, live feed, quiescent egg, RCC350},
	issn = {13652109},
	doi = {10.1111/are.14637},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/are.14637},
	author = {Pan, Yen Ju and D{\'e}pos{\'e}, Emilien and Souissi, Anissa and H{\'e}nard, St{\'e}phane and Schaadt, Mike and Mastro, Ed and Souissi, Sami}
}
@article {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 {Meng2018,
	title = {Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network},
	journal = {Molecular Ecology},
	year = {2018},
	note = {tex.mendeley-tags: RCC1491,RCC1516,RCC3387,RCC3468,RCC3507},
	pages = {0{\textendash}2},
	abstract = {Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and used a sequence similarity network (SSN) to compare the underlying genomic basis of functional features within the group. This approach constitutes the most comprehensive picture to date of the genomic potential of dinoflagellates. A core predicted proteome composed of 252 connected components (CCs) of putative conserved protein domains (pCDs) was identified. Of these, 206 were novel and 16 lacked any functional annotation in public databases. Integration of functional information in our network analyses allowed investigation of pCDs specifically associated to functional traits. With respect to toxicity, sequences homologous to those of proteins found in species with toxicity potential (e.g. sxtA4 and sxtG) were not specific to known toxin-producing species. Although not fully specific to symbiosis, the most represented functions associated with proteins involved in the symbiotic trait were related to membrane processes and ion transport. Overall, our SSN approach led to identification of 45,207 and 90,794 specific and constitutive pCDs of respectively the toxic and symbiotic species represented in our analyses. Of these, 56\% and 57\% respectively (i.e. 25,393 and 52,193 pCDs) completely lacked annotation in public databases. This stresses the extent of our lack of knowledge, while emphasizing the potential of SSNs to identify candidate pCDs for further functional genomic characterization. This article is protected by copyright. All rights reserved.},
	keywords = {Genomics/Proteomics, Microbial Biology, Molecular Evolution, Protists, rcc1491, RCC1516, RCC3387, rcc3468, rcc3507, transcriptomics},
	issn = {09621083},
	doi = {10.1111/mec.14579},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/29624751\%0Ahttp://doi.wiley.com/10.1111/mec.14579},
	author = {Meng, Arnaud and Corre, Erwan and Probert, Ian and Gutierrez-Rodriguez, Andres and Siano, Raffaele and Annamale, Anita and Alberti, Adriana and Da Silva, Corinne and Wincker, Patrick and Le Crom, St{\'e}phane and Not, Fabrice and Bittner, Lucie}
}
@article {Mahmoud2017,
	title = {Adaptation to blue light in marine synechococcus requires MpeU, an enzyme with similarity to phycoerythrobilin lyase isomerases},
	journal = {Frontiers in Microbiology},
	volume = {8},
	number = {February},
	year = {2017},
	note = {tex.mendeley-tags: 2017,rcc555,sbr?hyto?app},
	month = {feb},
	pages = {243},
	abstract = {Marine Synechococcus cyanobacteria have successfully adapted to environments with different light colors, which likely contributes to this genus being the second most abundant photosynthetic microorganism worldwide. Populations of Synechococcus that grow in deep, blue ocean waters contain large amounts of the blue-light absorbing chromophore phycourobilin (PUB) in their light harvesting complexes (phycobilisomes). Here we show that all Synechococcus strains adapted to blue light possess a gene called mpeU. MpeU is structurally similar to phycobilin lyases, enzymes that ligate chromophores to phycobiliproteins. Interruption of mpeU caused a reduction in PUB content, produced impaired phycobilisomes and reduced growth rate more strongly in blue than green light. When mpeU was reintroduced in the mpeU mutant background, the mpeU-less phenotype was complemented in terms of PUB content and phycobilisome content. Fluorescence spectra of mpeU mutant cells and purified phycobilisomes revealed red-shifted phycoerythrin emission peaks, likely indicating a defect in chromophore ligation to phycoerythrin-I (PE-I) or phycoerythrin-II (PE-II). Our results suggest that MpeU is a lyase-isomerase that attaches a phycoerythrobilin to a PEI or PEII subunit and isomerizes it to PUB. MpeU is therefore an important determinant in adaptation of Synechococcus spp. to capture photons in blue light environments throughout the world{\textquoteright}s oceans.},
	keywords = {2017, Blue light, light harvesting complex, Lyase isomerase, marine cyanobacteria, Marine Synechococcus, phycobilin, Phycobilisome, Phycoerythrin, Phycourobilin, rcc555, sbr?hyto?app},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2017.00243},
	url = {http://journal.frontiersin.org/article/10.3389/fmicb.2017.00243/full},
	author = {Mahmoud, Rania M. and Sanfilippo, Joseph E. and Nguyen, Adam A. and Strnat, Johann A. and Partensky, Fr{\'e}d{\'e}ric and Garczarek, Laurence and Abo El Kassem, Nabil and Kehoe, David M. and Schluchter, Wendy M.}
}
@article {Pittera2016,
	title = {Adaptive thermostability of light-harvesting complexes in marine picocyanobacteria},
	journal = {The ISME Journal},
	volume = {11},
	number = {1},
	year = {2017},
	note = {tex.mendeley-tags: 2016,rcc1594,rcc1682,rcc2380,rcc2382,rcc752,rcc791},
	pages = {112{\textendash}124},
	keywords = {2016, rcc1594, rcc1682, rcc2380, rcc2382, rcc752, rcc791},
	issn = {1751-7362},
	doi = {10.1038/ismej.2016.102},
	url = {http://www.nature.com/doifinder/10.1038/ismej.2016.102},
	author = {Pittera, Justine and Partensky, Fr{\'e}d{\'e}ric and Six, Christophe}
}
@article {Gu2017,
	title = {Adenoides sinensis , a new sand-dwelling dinoflagellate species from China and reexamination of A. eludens from an Atlantic strain},
	journal = {Phycologia},
	volume = {57},
	number = {October},
	year = {2017},
	note = {tex.mendeley-tags: 2017,RCC1982,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {1{\textendash}13},
	abstract = {The sand-dwelling?1dinoflagellate generaAdenoidesandPseudadenoidesare morphologically very close butdistinct in their molecular phylogeny. We established three cultures by isolating single cells from sand samples collected inintertidal zones of Qingdao (Yellow Sea), Dongshan (South China Sea) and Brittany (English Channel, North Atlantic,France). Strain morphology was examined with light and scanning electron microscopy, and both large subunitribosomal DNA (LSU rDNA) and small subunit ribosomal DNA (SSU rDNA) sequences were amplified. Molecularphylogeny, corroborated by morphological examination showing the existence of a ventral pore, confirmed theidentification of the French strain (RCC1982) asAdenoides eludens. The Chinese strains differed fromAdenoides eludensin two additional posterior intercalary plates and differed fromPseudadenoidesin one additional apical plate having theplate formula of Po, Cp, X, 50,600, 4S, 5000, 5p, 10000or alternatively Po, Cp, X, 50,600, 5S, 5000, 3p, 20000. Maximumlikelihood and Bayesian inference carried out with concatenated LSU and SSU sequences demonstrated that the Chinesestrains were closely related but different fromA. eludensand, in corroboration with morphological evidence, supportedtheir classification as a distinct species,Adenoides sinensis sp. nov. Morphological and molecular results confirmed theclose relationship between the two generaAdenoidesandPseudadenoides.},
	keywords = {2017, rcc, RCC1982, sbr?hyto$_\textrmd$ipo},
	doi = {10.2216/17-76.1},
	author = {Gu, Haifeng and Li, Xintian and Chom{\'e}rat, Nicolas and Luo, Zhaohe and Sarno, Diana and Gourvil, Priscillia and Balzano, Sergio and Siano, Raffaele}
}
@article {Ni2016,
	title = {Arctic Micromonas uses protein pools and non-photochemical quenching to cope with temperature restrictions on Photosystem II protein turnover},
	journal = {Photosynthesis Research},
	volume = {131},
	number = {2},
	year = {2017},
	note = {ISBN: 1112001603 Publisher: Springer Netherlands tex.mendeley-tags: 2016,RCC806},
	month = {feb},
	pages = {203{\textendash}220},
	keywords = {2016, {\'a}, Photoinactivation, photoinactivation {\'a} xanthophyll cycle, Photosystem II, Prasinophyte, prasinophyte {\'a} photosystem ii, RCC806, Xanthophyll cycle},
	issn = {0166-8595},
	doi = {10.1007/s11120-016-0310-6},
	url = {http://link.springer.com/10.1007/s11120-016-0310-6},
	author = {Ni, Guangyan and Zimbalatti, Gabrielle and Murphy, Cole D. and Barnett, Audrey B. and Arsenault, Christopher M. and Li, Gang and Cockshutt, Amanda M. and Campbell, Douglas A.}
}
@article {Simmons2016,
	title = {Abundance and biogeography of picoprasinophyte ecotypes and other phytoplankton in the eastern north pacific ocean},
	journal = {Applied and Environmental Microbiology},
	volume = {82},
	number = {6},
	year = {2016},
	note = {tex.mendeley-tags: 2016,rcc},
	month = {mar},
	pages = {1693{\textendash}1705},
	abstract = {Eukaryotic algae within the picoplankton size class (<=2 ??m in diameter) are important marine primary producers, but their spatial and ecological distributions are not well characterized. Here, we studied three picoeukaryotic prasinophyte genera and their cyanobacterial counterparts, Prochlorococcus and Synechococcus , during two cruises along a North Pacific transect characterized by different ecological regimes. Picoeukaryotes and Synechococcus reached maximum abundances of 1.44 {\texttimes} 10 5 and 3.37 {\texttimes} 10 5 cells ? ml -1 , respectively, in mesotrophic waters, while Prochlorococcus reached 1.95 {\texttimes} 10 5 cells ? ml -1 in the oligotrophic ocean. Of the picoeukaryotes, Bathycoccus was present at all stations in both cruises, reaching 21,368 {\textpm} 327 18S rRNA gene copies ? ml -1 . Micromonas and Ostreococcus clade OI were detected only in mesotrophic and coastal waters and Ostreococcus clade OII only in the oligotrophic ocean. To resolve proposed Bathycoccus ecotypes, we established genetic distances for 1,104 marker genes using targeted metagenomes and the Bathycoccus prasinos genome. The analysis was anchored in comparative genome analysis of three Ostreococcus species for which physiological and environmental data are available to facilitate data interpretation. We established that two Bathycoccus ecotypes exist, named here BI (represented by coastal isolate Bathycoccus prasinos ) and BII. These share 82\% {\textpm} 6\% nucleotide identity across homologs, while the Ostreococcus spp. share 75\% {\textpm} 8\%. We developed and applied an analysis of ecomarkers to metatranscriptomes sequenced here and published -omics data from the same region. The results indicated that the Bathycoccus ecotypes cooccur more often than Ostreococcus clades OI and OII do. Exploratory analyses of relative transcript abundances suggest that Bathycoccus NRT2.1 and AMT2.2 are high-affinity NO 3 - and low-affinity NH 4 + transporters, respectively, with close homologs in multiple picoprasinophytes. Additionally, in the open ocean, where dissolved iron concentrations were low (0.08 nM), there appeared to be a shift to the use of nickel superoxide dismutases (SODs) from Mn/Fe/Cu SODs closer inshore. Our study documents the distribution of picophytoplankton along a North Pacific ecological gradient and offers new concepts and techniques for investigating their biogeography.},
	keywords = {2016, rcc},
	issn = {0099-2240},
	doi = {10.1128/AEM.02730-15},
	url = {http://aem.asm.org/lookup/doi/10.1128/AEM.02730-15},
	author = {Simmons, Melinda P. and Sudek, Sebastian and Monier, Adam and Limardo, Alexander J. and Jimenez, Valeria and Perle, Christopher R. and Elrod, Virginia A. and Pennington, J. Timothy and Worden, Alexandra Z.},
	editor = {Schloss, P. D.}
}
@article {Countway2006,
	title = {Abundance and distribution of Ostreococcus sp in the San Pedro Channel, California, as revealed by quantitative PCR},
	journal = {Applied and Environmental Microbiology},
	volume = {72},
	number = {4},
	year = {2006},
	note = {tex.mendeley-tags: Micromonas,RCC,rcc},
	pages = {2496{\textendash}2506},
	abstract = {Ostreococcus is a genus of widely distributed marine phytoplankton which are picoplanktonic in size ({\textexclamdown} 2 mu m) and capable of rapid growth. Although Ostreococcus has been detected around the world, little quantitative information exists on its contribution to planktonic communities. We designed and implemented a genus-specific TaqMan-based quantitative PCR (qPCR) assay to investigate the dynamics and ecology of Ostreococcus at the USC Microbial Observatory (eastern North Pacific). Samples were collected from 5 m and the deep chlorophyll maximum (DCM) between September 2000 and August 2002. Ostreococcus abundance at 5 m was generally {\textexclamdown} 5.0 X 10(3) cells ml(-1), with a maximum of 8.2 X 10(4) cells ml(-1). Ostreococcus abundance was typically higher at the DCM, with a maximum of 3.2 X 10(5) cells ml(-1). The vertical distribution of Ostreococcus was examined in March 2005 and compared to the distribution of phototrophic picoeukaryotes (PPE) measured by flow cytometry. The largest contribution to PPE abundance by Ostreococcus was similar to 70\% and occurred at 30 m, near the DCM. Despite its relatively low abundance, the depth-integrated standing stock of Ostreococcus in March 2005 was similar to 30 mg C m(-2). Our work provides a new technique for quantifying the abundance of Ostreococcus and demonstrates the seasonal dynamics of this genus and its contribution to picoeukaryote biomass at our coastal sampling station.},
	keywords = {16s-ribosomal-rna, Biology-, english-channel, eukaryotic-picoplankton, in-situ-hybridization, marine-ecosystems, microbial-populations, microbiology-, Micromonas, pfiesteria-piscicida, rcc, Real-time-pcr, sp-nov, tauri-chlorophyta},
	doi = {10.1128/AEM.72.4.2496-2506.2006},
	author = {Countway, P D and Caron, D A}
}
@article {Fuller2006,
	title = {Analysis of photosynthetic picoeukaryote diversity at open ocean sites in the Arabian Sea using a PCR biased towards marine algal plastids},
	journal = {Aquatic Microbial Ecology},
	volume = {43},
	year = {2006},
	note = {tex.mendeley-tags: 2006,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {79{\textendash}93},
	keywords = {2006, PICOCEAN, PICODIV, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	doi = {10.3354/ame043079},
	author = {Fuller, Nicholas J and Campbell, Colin and Allen, David J and Pitt, Frances D and Le Gall, F and Vaulot, Daniel and Scanlan, David J}
}
@article {Not2002,
	title = {Application of fluorescent in situ hybridization coupled with tyramide signal amplification (FISH-TSA) to assess eukaryotic picoplankton composition},
	volume = {28},
	year = {2002},
	note = {Publication Title: Aquatic microbial ecology tex.mendeley-tags: RCC,rcc},
	pages = {157{\textendash}166},
	abstract = {Photosynthetic picoeukaryotes (phytoplankton cells with a diameter smaller than 2 to 3 ??m) contribute significantly to both biomass and primary production in the oligotrophic open ocean and coastal waters, at certain times of the year. The identification of these organisms is difficult because of their small size and simple morphology, therefore hindering detailed ecological studies of their distribution and role. In this paper, we demonstrate the use of oligonucleotide probes specific to algal classes or to lower order taxa in combination with fluorescent in situ hybridization and tyramide signal amplification (FISH-TSA) to determine eukaryotic picophytoplankton diversity. Target cells were detected and enumerated using epifluorescence microscopy. The sensitivity of the technique and the specificity of the probes were tested on pure and mixed picoplanktonic strains, as well as on natural samples from the English Channel. In these samples, the community was dominated by cells belonging to the division Chlorophyta. Haptophyta, Bolidophyceae and Pelagophyceae were also detected at low abundance. The FISH-TSA method is readily applicable to the study of picoplankton diversity in natural communities.},
	keywords = {rcc},
	issn = {0948-3055},
	doi = {10.3354/ame028157},
	author = {Not, F and Simon, N and Biegala, IC and Vaulot, D}
}
