Publications

@article{RN304,

title = {Patterns and drivers of diatom diversity and abundance in the global ocean},

author = {J. J. Pierella Karlusich and K. Cosnier and L. Zinger and N. Henry and C. Nef and G. Bernard and E. Scalco and E. Dvorak and Coordinators Tara Oceans and F. Rocha Jimenez Vieira and E. Delage and S. Chaffron and S. Ovchinnikov and A. Zingone and C. Bowler},

url = {https://www.ncbi.nlm.nih.gov/pubmed/40216740},

doi = {10.1038/s41467-025-58027-7},

issn = {2041-1723 (Electronic) 

2041-1723 (Linking)},

year  = {2025},

date = {2025-01-01},

journal = {Nat Commun},

volume = {16},

number = {1},

pages = {3452},

abstract = {Diatoms constitute one of the most diverse and ecologically important phytoplankton groups, yet their large-scale diversity patterns and drivers of abundance are unclear due to limited observations. Here, we utilize Tara Oceans molecular and morphological data, spanning pole to pole, to describe marine diatom diversity, abundance, and environmental adaptation and acclimation strategies. The dominance of diatoms among phytoplankton in terms of relative abundance and diversity is confirmed, and the most prevalent genera are Chaetoceros, Thalassiosira, Actinocyclus and Pseudo-nitzschia. We define 25 distinct diatom communities with varying environmental preferences illustrative of different life strategies. The Arctic Ocean stands out as a diatom hotspot with 6 of the diatom communities being exclusive to it. Light harvesting and photoprotection are among the cellular functions in which natural diatom populations invest the bulk of their transcriptional efforts. This comprehensive study sheds light on marine diatom distributions, offering insights to assess impacts of global change and oceanic anthropogenic impacts.},

note = {Pierella Karlusich, Juan J 

Cosnier, Karen 

Zinger, Lucie 

Henry, Nicolas 

Nef, Charlotte 

Bernard, Guillaume 

Scalco, Eleonora 

Dvorak, Etienne 

Rocha Jimenez Vieira, Fabio 

Delage, Erwan 

Chaffron, Samuel 

Ovchinnikov, Sergey 

Zingone, Adriana 

Bowler, Chris 

eng 

735929LPI/Simons Foundation/ 

England 

2025/04/12 

Nat Commun. 2025 Apr 11;16(1):3452. doi: 10.1038/s41467-025-58027-7.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN305,

title = {A genomic approach to Porites (Anthozoa: Scleractinia) megadiversity from the Indo-Pacific},

author = {T. I. Terraneo and F. Benzoni and R. Arrigoni and M. L. Berumen and K. G. Mariappan and C. P. Antony and H. B. Harrison and C. Payri and D. Huang and A. H. Baird},

url = {https://www.ncbi.nlm.nih.gov/pubmed/39551223},

doi = {10.1016/j.ympev.2024.108238},

issn = {1095-9513 (Electronic) 

1055-7903 (Linking)},

year  = {2025},

date = {2025-01-01},

journal = {Mol Phylogenet Evol},

volume = {203},

pages = {108238},

abstract = {Porites corals are vital components of tropical reef ecosystems worldwide, serving as ecosystem engineers and hubs of biodiversity in shallow water coral reefs. Despite their ecological significance and the widespread use of Porites spp. as models for research, the richness and evolutionary relationships of species within the genus remain elusive. In this study, we analyzed genomic data from 330 colonies of Porites from 17 localities across the Indo-Pacific region based on the reduced representation genomic approach ezRAD. We retrieved 25,163 SNPs and provided a phylogenomic hypothesis for 29 nominal species and 10 unknown morphologies, recovering 15 deeply rooted molecular clades. Among these, 12 clades included samples corresponding to single distinct morphospecies. One did not match any nominal species. The remaining two clades comprised species complexes, which included various massive and encrusting morphologies commonly used in experimental biology. Within these complexes, we observed additional geographic or morphological structure, indicating complex evolutionary dynamics, possibly reflecting distinct species, isolated populations or hybridization. Additionally, a series of divergent samples underscored the importance of more sampling to define species boundaries and refine phylogenomic relationships. We also integrated our findings with previous phylogenetic datasets and their respective sampling localities, challenging traditional notions about Porites species geographic distributions. Overall, our findings indicate a need to revise past synonymies and to formally establish new species. A precise understanding of Porites species and their diversity and distributions is necessary for effective reef conservation and management.},

note = {Terraneo, Tullia I 

Benzoni, Francesca 

Arrigoni, Roberto 

Berumen, Michael L 

Mariappan, Kiruthiga G 

Antony, Chakkiath P 

Harrison, Hugo B 

Payri, Claude 

Huang, Danwei 

Baird, Andrew H 

eng 

2024/11/18 

Mol Phylogenet Evol. 2025 Feb;203:108238. doi: 10.1016/j.ympev.2024.108238. Epub 2024 Nov 16.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN302,

title = {Diatom phytochromes integrate the underwater light spectrum to sense depth},

author = {C. Duchene and J. P. Bouly and J. J. Pierella Karlusich and E. Vernay and J. Selles and B. Bailleul and C. Bowler and M. Ribera d'Alcala and A. Falciatore and M. Jaubert},

url = {https://www.ncbi.nlm.nih.gov/pubmed/39695224},

doi = {10.1038/s41586-024-08301-3},

issn = {1476-4687 (Electronic) 

0028-0836 (Linking)},

year  = {2024},

date = {2024-01-01},

journal = {Nature},

abstract = {Aquatic life is strongly structured by the distribution of light, which, besides attenuation in intensity, exhibits a continuous change in the spectrum with depth(1). The extent to which these light changes are perceived by phytoplankton through photoreceptors is still inadequately known. We addressed this issue by integrating functional studies of diatom phytochrome (DPH) photoreceptors in model species(2) with environmental surveys of their distribution and activity. Here, by developing an in vivo dose-response assay to light spectral variations mediated by DPH, we show that DPH can trigger photoreversible responses across the entire light spectrum, resulting in a change in DPH photoequilibrium with depth. By generating dph mutants in the diatom Thalassiosira pseudonana, we also demonstrate that under simulated low-blue-light conditions of ocean depth, DPH regulates photosynthesis acclimation, thus linking optical depth detection with a functional response. The latitudinal distribution of DPH-containing diatoms from permanently stratified regions to seasonally mixed regions suggests an adaptive value of DPH functions in coping with vertical displacements in the water column. By establishing DPH as a detector of optical depth, this study provides a new view of how information embedded in the underwater light field can be exploited by diatoms to modulate their physiology throughout the photic zone.},

note = {Duchene, Carole 

Bouly, Jean-Pierre 

Pierella Karlusich, Juan Jose 

Vernay, Emeline 

Selles, Julien 

Bailleul, Benjamin 

Bowler, Chris 

Ribera d'Alcala, Maurizio 

Falciatore, Angela 

Jaubert, Marianne 

eng 

England 

2024/12/19 

Nature. 2024 Dec 18. doi: 10.1038/s41586-024-08301-3.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN297,

title = {New plastids, old proteins: repeated endosymbiotic acquisitions in kareniacean dinoflagellates},

author = {A. M. Novak Vanclova and C. Nef and Z. Fussy and A. Vancl and F. Liu and C. Bowler and R. G. Dorrell},

url = {https://www.ncbi.nlm.nih.gov/pubmed/38499810},

doi = {10.1038/s44319-024-00103-y},

issn = {1469-3178 (Electronic) 

1469-221X (Linking)},

year  = {2024},

date = {2024-01-01},

journal = {EMBO Rep},

abstract = {Dinoflagellates are a diverse group of ecologically significant micro-eukaryotes that can serve as a model system for plastid symbiogenesis due to their susceptibility to plastid loss and replacement via serial endosymbiosis. Kareniaceae harbor fucoxanthin-pigmented plastids instead of the ancestral peridinin-pigmented ones and support them with a diverse range of nucleus-encoded plastid-targeted proteins originating from the haptophyte endosymbiont, dinoflagellate host, and/or lateral gene transfers (LGT). Here, we present predicted plastid proteomes from seven distantly related kareniaceans in three genera (Karenia, Karlodinium, and Takayama) and analyze their evolutionary patterns using automated tree building and sorting. We project a relatively limited ( ~ 10%) haptophyte signal pointing towards a shared origin in the family Chrysochromulinaceae. Our data establish significant variations in the functional distributions of these signals, emphasizing the importance of micro-evolutionary processes in shaping the chimeric proteomes. Analysis of plastid genome sequences recontextualizes these results by a striking finding the extant kareniacean plastids are in fact not all of the same origin, as two of the studied species (Karlodinium armiger, Takayama helix) possess plastids from different haptophyte orders than the rest.},

note = {Novak Vanclova, Anna Mg 

Nef, Charlotte 

Fussy, Zoltan 

Vancl, Adel 

Liu, Fuhai 

Bowler, Chris 

Dorrell, Richard G 

eng 

ANR-21-CE02-0014/Agence Nationale de la Recherche (ANR)/ 

ANR-20-CE13-0007/Agence Nationale de la Recherche (ANR)/ 

ANR-19-CE20-0020/Agence Nationale de la Recherche (ANR)/ 

101039760/EC | European Research Council (ERC)/ 

835067/EC | European Research Council (ERC)/ 

Momentum Fellowship 2019-2021/Centre National de la Recherche Scientifique (CNRS)/ 

835067/EC | ERC | HORIZON EUROPE European Research Council (ERC)/ 

ANR-10-LABX-54/Agence Nationale de la Recherche (ANR)/ 

ANR-1253 11-IDEX-0001-02/Universite de Recherche Paris Sciences et Lettres (PSL)/ 

90254/e-INFRA CZ/ 

England 

2024/03/19 

EMBO Rep. 2024 Mar 18. doi: 10.1038/s44319-024-00103-y.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN299,

title = {Genome-scale community modelling reveals conserved metabolic cross-feedings in epipelagic bacterioplankton communities},

author = {N. Giordano and M. Gaudin and C. Trottier and E. Delage and C. Nef and C. Bowler and S. Chaffron},

url = {https://www.ncbi.nlm.nih.gov/pubmed/38548725},

doi = {10.1038/s41467-024-46374-w},

issn = {2041-1723 (Electronic) 

2041-1723 (Linking)},

year  = {2024},

date = {2024-01-01},

journal = {Nat Commun},

volume = {15},

number = {1},

pages = {2721},

abstract = {Marine microorganisms form complex communities of interacting organisms that influence central ecosystem functions in the ocean such as primary production and nutrient cycling. Identifying the mechanisms controlling their assembly and activities is a major challenge in microbial ecology. Here, we integrated Tara Oceans meta-omics data to predict genome-scale community interactions within prokaryotic assemblages in the euphotic ocean. A global genome-resolved co-activity network revealed a significant number of inter-lineage associations across diverse phylogenetic distances. Identified co-active communities include species displaying smaller genomes but encoding a higher potential for quorum sensing, biofilm formation, and secondary metabolism. Community metabolic modelling reveals a higher potential for interaction within co-active communities and points towards conserved metabolic cross-feedings, in particular of specific amino acids and group B vitamins. Our integrated ecological and metabolic modelling approach suggests that genome streamlining and metabolic auxotrophies may act as joint mechanisms shaping bacterioplankton community assembly in the global ocean surface.},

note = {Giordano, Nils 

Gaudin, Marinna 

Trottier, Camille 

Delage, Erwan 

Nef, Charlotte 

Bowler, Chris 

Chaffron, Samuel 

eng 

862923/European Commission (EC)/ 

England 

2024/03/29 

Nat Commun. 2024 Mar 28;15(1):2721. doi: 10.1038/s41467-024-46374-w.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN296,

title = {Linking satellites to genes with machine learning to estimate phytoplankton community structure from space},

author = {R. El Hourany and J. J. Pierella Karlusich and L. Zinger and H. Loisel and M. Levy and C. Bowler},

doi = {https://doi.org/10.5194/os-20-217-2024},

year  = {2024},

date = {2024-01-01},

journal = {EGU Ocean Science},

volume = {20},

number = {1},

pages = {217-239},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN301,

title = {Complex Genomes of Early Nucleocytoviruses Revealed by Ancient Origins of Viral Aminoacyl-tRNA Synthetases},

author = {S. Kijima and H. Hikida and T. O. Delmont and M. Gaia and H. Ogata},

url = {https://www.ncbi.nlm.nih.gov/pubmed/39099254},

doi = {10.1093/molbev/msae149},

issn = {1537-1719 (Electronic) 

0737-4038 (Print)},

year  = {2024},

date = {2024-01-01},

journal = {Mol Biol Evol},

volume = {41},

number = {8},

abstract = {Aminoacyl-tRNA synthetases (aaRSs), also known as tRNA ligases, are essential enzymes in translation. Owing to their functional essentiality, these enzymes are conserved in all domains of life and used as informative markers to trace the evolutionary history of cellular organisms. Unlike cellular organisms, viruses generally lack aaRSs because of their obligate parasitic nature, but several large and giant DNA viruses in the phylum Nucleocytoviricota encode aaRSs in their genomes. The discovery of viral aaRSs led to the idea that the phylogenetic analysis of aaRSs can shed light on ancient viral evolution. However, conflicting results have been reported from previous phylogenetic studies: one posited that nucleocytoviruses recently acquired their aaRSs from their host eukaryotes, while another hypothesized that the viral aaRSs have ancient origins. Here, we investigated 4,168 nucleocytovirus genomes, including metagenome-assembled genomes (MAGs) derived from large-scale metagenomic studies. In total, we identified 780 viral aaRS sequences in 273 viral genomes. We generated and examined phylogenetic trees of these aaRSs with a large set of cellular sequences to trace evolutionary relationships between viral and cellular aaRSs. The analyses suggest that the origins of some viral aaRSs predate the last common eukaryotic ancestor. Inside viral aaRS clades, we identify intricate evolutionary trajectories of viral aaRSs with horizontal transfers, losses, and displacements. Overall, these results suggest that ancestral nucleocytoviruses already developed complex genomes with an expanded set of aaRSs in the proto-eukaryotic era.},

note = {Kijima, Soichiro 

Hikida, Hiroyuki 

Delmont, Tom O 

Gaia, Morgan 

Ogata, Hiroyuki 

eng 

22H00384/Japan Society for the Promotion of Science KAKENHI/ 

Research Unit for Development of Global Sustainability/ 

Kyoto University Research Coordination Alliance/ 

202332/WT_/Wellcome Trust/United Kingdom 

2024/08/05 

Mol Biol Evol. 2024 Aug 2;41(8):msae149. doi: 10.1093/molbev/msae149.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN300,

title = {Complementary environmental analysis and functional characterization of lower glycolysis-gluconeogenesis in the diatom plastid},

author = {R. G. Dorrell and Y. Zhang and Y. Liang and N. Gueguen and T. Nonoyama and D. Croteau and M. Penot-Raquin and S. Adiba and B. Bailleul and V. Gros and J. J. Pierella Karlusich and N. Zweig and A. R. Fernie and J. Jouhet and E. Marechal and C. Bowler},

url = {https://www.ncbi.nlm.nih.gov/pubmed/38842420},

doi = {10.1093/plcell/koae168},

issn = {1532-298X (Electronic) 

1040-4651 (Print)},

year  = {2024},

date = {2024-01-01},

journal = {Plant Cell},

volume = {36},

number = {9},

pages = {3584-3610},

abstract = {Organic carbon fixed in chloroplasts through the Calvin-Benson-Bassham Cycle can be diverted toward different metabolic fates, including cytoplasmic and mitochondrial respiration, gluconeogenesis, and synthesis of diverse plastid metabolites via the pyruvate hub. In plants, pyruvate is principally produced via cytoplasmic glycolysis, although a plastid-targeted lower glycolytic pathway is known to exist in non-photosynthetic tissue. Here, we characterized a lower plastid glycolysis-gluconeogenesis pathway enabling the direct interconversion of glyceraldehyde-3-phosphate and phospho-enol-pyruvate in diatoms, ecologically important marine algae distantly related to plants. We show that two reversible enzymes required to complete diatom plastid glycolysis-gluconeogenesis, Enolase and bis-phosphoglycerate mutase (PGAM), originated through duplications of mitochondria-targeted respiratory isoforms. Through CRISPR-Cas9 mutagenesis, integrative 'omic analyses, and measured kinetics of expressed enzymes in the diatom Phaeodactylum tricornutum, we present evidence that this pathway diverts plastid glyceraldehyde-3-phosphate into the pyruvate hub, and may also function in the gluconeogenic direction. Considering experimental data, we show that this pathway has different roles dependent in particular on day length and environmental temperature, and show that the cpEnolase and cpPGAM genes are expressed at elevated levels in high-latitude oceans where diatoms are abundant. Our data provide evolutionary, meta-genomic, and functional insights into a poorly understood yet evolutionarily recurrent plastid metabolic pathway.},

note = {Dorrell, Richard G 

Zhang, Youjun 

Liang, Yue 

Gueguen, Nolwenn 

Nonoyama, Tomomi 

Croteau, Dany 

Penot-Raquin, Mathias 

Adiba, Sandrine 

Bailleul, Benjamin 

Gros, Valerie 

Pierella Karlusich, Juan Jose 

Zweig, Nathanael 

Fernie, Alisdair R 

Jouhet, Juliette 

Marechal, Eric 

Bowler, Chris 

eng 

ANR-21-CE02-0014-01/ANR/ 

ANR-11-BTBR-0008/French Facility for Global Environment/ 

ANR-10-INBS-09-08/FRANCE GENOMIQUE/ 

ANR-10-LABX-54/MEMO LIFE/ 

ANR-11-IDEX-0001-02/PSL Research University/ 

ERC_/European Research Council/International 

835067/European Union's Horizon 2020/ 

ANR-19-CE20-0020/ANR/ 

22-PEBB-0002/PEPR AlgAdvance/ 

10-LABX-0049/European Regional Development Fund/ 

University Grenoble Alpes/ 

ANR-17-EURE-0003/Ecoles Universitaires de Recherche/ 

739582/European Union's Horizon 2020/ 

715579/European Union's Horizon 2020/ 

England 

2024/06/06 

Plant Cell. 2024 Sep 3;36(9):3584-3610. doi: 10.1093/plcell/koae168.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN298,

title = {Global Distribution and Diversity of Marine Parmales},

author = {H. Ban and H. Endo and Team EukBank and A. Kuwata and H. Ogata},

url = {https://www.ncbi.nlm.nih.gov/pubmed/38522927},

doi = {10.1264/jsme2.ME23093},

issn = {1347-4405 (Electronic) 

1342-6311 (Print)},

year  = {2024},

date = {2024-01-01},

journal = {Microbes Environ},

volume = {39},

number = {1},

abstract = {Parmales (Bolidophyceae) is a minor eukaryotic phytoplankton group, sister to diatoms, which exists as two distinct forms of unicellular organisms: silicified cells and naked flagellates. Since their discovery, many field studies on Parmales have been performed; however, their global distribution has not yet been examined in detail. We herein compiled more than 3,000 marine DNA metabarcoding datasets targeting the V4 region of the 18S rRNA gene from the EukBank database. By linking this large dataset with the latest morphological and genetic information, we provide updated estimates on the diversity and distribution of Parmales in the global ocean at a fine taxonomic resolution. Parmalean amplicon sequence variants (ASVs) were detected in nearly 90% of the samples analyzed. However, the relative abundance of parmaleans in the eukaryotic community was less than 0.2% on average, and the estimated true richness of parmalean ASVs was approximately 316 ASVs, confirming their low abundance and diversity. A phylogenetic ana-lysis divided these algae into four clades, and three known morphotypes of silicified cells were classified into three different clades. The abundance of Parmales is generally high in the poles and decreases towards the tropics, and individual clades/subclades show further distinctions in their distribution. Collectively, the present results suggest clade/subclade-specific adaptation to different ecological niches.},

note = {Ban, Hiroki 

Endo, Hisashi 

Kuwata, Akira 

Ogata, Hiroyuki 

eng 

Japan 

2024/03/25 

Microbes Environ. 2024;39(1):ME23093. doi: 10.1264/jsme2.ME23093.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN295,

title = {Genomic adaptation of giant viruses in polar oceans},

author = {L. Meng and T. O. Delmont and M. Gaia and E. Pelletier and A. Fernandez-Guerra and S. Chaffron and R. Y. Neches and J. Wu and H. Kaneko and H. Endo and H. Ogata},

url = {https://www.ncbi.nlm.nih.gov/pubmed/37828003},

doi = {10.1038/s41467-023-41910-6},

issn = {2041-1723 (Electronic) 

2041-1723 (Linking)},

year  = {2023},

date = {2023-01-01},

journal = {Nat Commun},

volume = {14},

number = {1},

pages = {6233},

abstract = {Despite being perennially frigid, polar oceans form an ecosystem hosting high and unique biodiversity. Various organisms show different adaptive strategies in this habitat, but how viruses adapt to this environment is largely unknown. Viruses of phyla Nucleocytoviricota and Mirusviricota are groups of eukaryote-infecting large and giant DNA viruses with genomes encoding a variety of functions. Here, by leveraging the Global Ocean Eukaryotic Viral database, we investigate the biogeography and functional repertoire of these viruses at a global scale. We first confirm the existence of an ecological barrier that clearly separates polar and nonpolar viral communities, and then demonstrate that temperature drives dramatic changes in the virus-host network at the polar-nonpolar boundary. Ancestral niche reconstruction suggests that adaptation of these viruses to polar conditions has occurred repeatedly over the course of evolution, with polar-adapted viruses in the modern ocean being scattered across their phylogeny. Numerous viral genes are specifically associated with polar adaptation, although most of their homologues are not identified as polar-adaptive genes in eukaryotes. These results suggest that giant viruses adapt to cold environments by changing their functional repertoire, and this viral evolutionary strategy is distinct from the polar adaptation strategy of their hosts.},

note = {Meng, Lingjie 

Delmont, Tom O 

Gaia, Morgan 

Pelletier, Eric 

Fernandez-Guerra, Antonio 

Chaffron, Samuel 

Neches, Russell Y 

Wu, Junyi 

Kaneko, Hiroto 

Endo, Hisashi 

Ogata, Hiroyuki 

eng 

Research Support, Non-U.S. Gov't 

England 

2023/10/13 

Nat Commun. 2023 Oct 12;14(1):6233. doi: 10.1038/s41467-023-41910-6.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN292,

title = {Pan-Arctic plankton community structure and its global connectivity},

author = {F. M. Ibarbalz and N. Henry and F. Mahé and M. Ardyna and A. Zingone and E. Scalco and C. Lovejoy and F. Lombard and O. Jaillon and D. Iudicone and S. Malviya and M. B. Sullivan and S. Chaffron and E. Karsenti and M. Babin and E. Boss and P. Wincker and L. Zinger and C. Vargas and C. Bowler and L. Karp-Boss and Tara Oceans Coordinators},

url = {<Go to ISI>://WOS:001173935900002},

doi = {10.1525/elementa.2022.00060},

issn = {2325-1026},

year  = {2023},

date = {2023-01-01},

journal = {Elementa-Science of the Anthropocene},

volume = {11},

number = {1},

abstract = {The Arctic Ocean (AO) is being rapidly transformed by global warming, but its biodiversity remains understudied for many planktonic organisms, in particular for unicellular eukaryotes that play pivotal roles in marine food webs and biogeochemical cycles. The aim of this study was to characterize the biogeographic ranges of species that comprise the contemporary pool of unicellular eukaryotes in the AO as a first step toward understanding mechanisms that structure these communities and identifying potential target species for monitoring. Leveraging the Tara Oceans DNA metabarcoding data, we mapped the global distributions of operational taxonomic units (OTUs) found on Arctic shelves into five biogeographic categories, identified biogeographic indicators, and inferred the degree to which AO communities of unicellular eukaryotes share members with assemblages from lower latitudes. Arctic/Polar indicator OTUs, as well as some globally ubiquitous OTUs, dominated the detection and abundance of DNA reads in the Arctic samples. OTUs detected only in Arctic samples (Arctic -exclusives) showed restricted distribution with relatively low abundances, accounting for 10-16% of the total Arctic OTU pool. OTUs with high abundances in tropical and/or temperate latitudes (non -Polar indicators) were also found in the AO but mainly at its periphery. We observed a large change in community taxonomic composition across the Atlantic -Arctic continuum, supporting the idea that advection and environmental filtering are important processes that shape plankton assemblages in the AO. Altogether, this study highlights the connectivity between the AO and other oceans, and provides a framework for monitoring and assessing future changes in this vulnerable ecosystem.},

note = {Jn8j6 

Times Cited:2 

Cited References Count:69},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN291,

title = {High Growth Rate of Diatoms Explained by Reduced Carbon Requirement and Low Energy Cost of Silica Deposition},

author = {K. Inomura and J. J. Pierella Karlusich and S. Dutkiewicz and C. Deutsch and P. J. Harrison and C. Bowler},

url = {https://www.ncbi.nlm.nih.gov/pubmed/37010412},

doi = {10.1128/spectrum.03311-22},

issn = {2165-0497 (Electronic) 

2165-0497 (Linking)},

year  = {2023},

date = {2023-01-01},

journal = {Microbiol Spectr},

volume = {11},

number = {3},

pages = {e0331122},

abstract = {The rapid growth of diatoms makes them one of the most pervasive and productive types of plankton in the world's ocean, but the physiological basis for their high growth rates remains poorly understood. Here, we evaluate the factors that elevate diatom growth rates, relative to other plankton, using a steady-state metabolic flux model that computes the photosynthetic C source from intracellular light attenuation and the carbon cost of growth from empirical cell C quotas, across a wide range of cell sizes. For both diatoms and other phytoplankton, growth rates decline with increased cell volume, consistent with observations, because the C cost of division increases with size faster than photosynthesis. However, the model predicts overall higher growth rates for diatoms due to reduced C requirements and the low energetic cost of Si deposition. The C savings from the silica frustule are supported by metatranscriptomic data from Tara Oceans, which show that the abundance of transcripts for cytoskeleton components in diatoms is lower than in other phytoplankton. Our results highlight the importance of understanding the origins of phylogenetic differences in cellular C quotas, and suggest that the evolution of silica frustules may play a critical role in the global dominance of marine diatoms. IMPORTANCE This study addresses a longstanding issue regarding diatoms, namely, their fast growth. Diatoms, which broadly are phytoplankton with silica frustules, are the world's most productive microorganisms and dominate in polar and upwelling regions. Their dominance is largely supported by their high growth rate, but the physiological reasoning behind that characteristic has been obscure. In this study, we combine a quantitative model and metatranscriptomic approaches and show that diatoms' low carbon requirements and low energy costs for silica frustule production are the key factors supporting their fast growth. Our study suggests that the effective use of energy-efficient silica as a cellular structure, instead of carbon, enables diatoms to be the most productive organisms in the global ocean.},

note = {Inomura, Keisuke 

Pierella Karlusich, Juan Jose 

Dutkiewicz, Stephanie 

Deutsch, Curtis 

Harrison, Paul J 

Bowler, Chris 

eng 

Research Support, Non-U.S. Gov't 

2023/04/04 

Microbiol Spectr. 2023 Jun 15;11(3):e0331122. doi: 10.1128/spectrum.03311-22. Epub 2023 Apr 3.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN290,

title = {Phylogenetics and taxonomy of the scleractinian coral family Euphylliidae},

author = {R. Arrigoni and J. Stolarski and T. I. Terraneo and B. W. Hoeksema and M. L. Berumen and C. Payri and S. Montano},

url = {<Go to ISI>://WOS:001010716700001},

doi = {10.1163/18759866-bja10041},

issn = {1383-4517},

year  = {2023},

date = {2023-01-01},

journal = {Contributions to Zoology},

volume = {92},

number = {2},

pages = {130-171},

abstract = {The family Euphylliidae consists of reef-building zooxanthellate scleractinian corals distributed across the Indo-Pacific. Seven extant genera comprising a total of 22 valid species are currently recognised. Recent studies have re-organised the taxonomy of the family at the genus level based on molecular and morphological data, including a comprehensiverevision of Euphyllia and the resurrection of Fimbriaphyllia. Here, three mitochondrial loci (coi, 12S rRNA, and 16S rRNA) were sequenced and morphological examinations were conducted at three scales (macro/micromorphology and microstructure of the skeleton, and polyp morphology) to study the phylogeny and taxonomy of Euphylliidae. We analysed a total of 11 valid species collected from seven Indo-Pacific localities. The monotypic genus Coeloseris, currently in Agariciidae, was also investigated since previous molecular data suggested a close relationship with the Euphylliidae. Molecular and morphological phylogenetic trees were broadly concordant in the definition of genus-level clades. All analysed genera, i.e., Ctenella, Euphyllia, Fimbriaphyllia, Galaxea, and Gyrosmilia, were reciprocally monophyletic based on molecular results. Coeloseris was nested within the family and, therefore, is formally moved into Euphylliidae. Updated morphological diagnoses are provided for each investigated genus. This study further demonstrated that a phylogenetic classification of scleractinian corals can be achieved by applying a combined morpho-molecular approach. Finally, we encourage phylogenetic and taxonomic studies of the euphylliid taxa not yet analysed molecularly, such as the monotypic genera Montigyra and Simplastrea.},

note = {J6lr6 

Times Cited:2 

Cited References Count:155},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN294,

title = {Predicting global distributions of eukaryotic plankton communities from satellite data},

author = {H. Kaneko and H. Endo and N. Henry and C. Berney and F. Mahe and J. Poulain and K. Labadie and O. Beluche and R. El Hourany and Coordinators Tara Oceans and S. Chaffron and P. Wincker and R. Nakamura and L. Karp-Boss and E. Boss and C. Bowler and C. Vargas and K. Tomii and H. Ogata},

url = {https://www.ncbi.nlm.nih.gov/pubmed/37740029},

doi = {10.1038/s43705-023-00308-7},

issn = {2730-6151 (Electronic) 

2730-6151 (Print)},

year  = {2023},

date = {2023-01-01},

journal = {ISME Commun},

volume = {3},

number = {1},

pages = {101},

abstract = {Satellite remote sensing is a powerful tool to monitor the global dynamics of marine plankton. Previous research has focused on developing models to predict the size or taxonomic groups of phytoplankton. Here, we present an approach to identify community types from a global plankton network that includes phytoplankton and heterotrophic protists and to predict their biogeography using global satellite observations. Six plankton community types were identified from a co-occurrence network inferred using a novel rDNA 18 S V4 planetary-scale eukaryotic metabarcoding dataset. Machine learning techniques were then applied to construct a model that predicted these community types from satellite data. The model showed an overall 67% accuracy in the prediction of the community types. The prediction using 17 satellite-derived parameters showed better performance than that using only temperature and/or the concentration of chlorophyll a. The constructed model predicted the global spatiotemporal distribution of community types over 19 years. The predicted distributions exhibited strong seasonal changes in community types in the subarctic-subtropical boundary regions, which were consistent with previous field observations. The model also identified the long-term trends in the distribution of community types, which suggested responses to ocean warming.},

note = {Kaneko, Hiroto 

Endo, Hisashi 

Henry, Nicolas 

Berney, Cedric 

Mahe, Frederic 

Poulain, Julie 

Labadie, Karine 

Beluche, Odette 

El Hourany, Roy 

Chaffron, Samuel 

Wincker, Patrick 

Nakamura, Ryosuke 

Karp-Boss, Lee 

Boss, Emmanuel 

Bowler, Chris 

de Vargas, Colomban 

Tomii, Kentaro 

Ogata, Hiroyuki 

eng 

18H02279/MEXT | Japan Society for the Promotion of Science (JSPS)/ 

19H05667/MEXT | Japan Society for the Promotion of Science (JSPS)/ 

JPMJSP2110/MEXT | Japan Science and Technology Agency (JST)/ 

ANR-10-INBS-09/Agence Nationale de la Recherche (French National Research Agency)/ 

101082021/EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ 

835067/EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ 

England 

2023/09/23 

ISME Commun. 2023 Sep 22;3(1):101. doi: 10.1038/s43705-023-00308-7.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN293,

title = {Ocean-wide comparisons of mesopelagic planktonic community structures},

author = {J. Rigonato and M. Budinich and A. A. Murillo and M. C. Brandao and J. J. Pierella Karlusich and Y. D. Soviadan and A. C. Gregory and H. Endo and F. Kokoszka and D. Vik and N. Henry and P. Fremont and K. Labadie and A. A. Zayed and C. Dimier and M. Picheral and S. Searson and J. Poulain and S. Kandels and S. Pesant and E. Karsenti and coordinators Tara Oceans and P. Bork and C. Bowler and C. Vargas and D. Eveillard and M. Gehlen and D. Iudicone and F. Lombard and H. Ogata and L. Stemmann and M. B. Sullivan and S. Sunagawa and P. Wincker and S. Chaffron and O. Jaillon},

url = {https://www.ncbi.nlm.nih.gov/pubmed/37596349},

doi = {10.1038/s43705-023-00279-9},

issn = {2730-6151 (Electronic) 

2730-6151 (Print)},

year  = {2023},

date = {2023-01-01},

journal = {ISME Commun},

volume = {3},

number = {1},

pages = {83},

abstract = {For decades, marine plankton have been investigated for their capacity to modulate biogeochemical cycles and provide fishery resources. Between the sunlit (epipelagic) layer and the deep dark waters, lies a vast and heterogeneous part of the ocean: the mesopelagic zone. How plankton composition is shaped by environment has been well-explored in the epipelagic but much less in the mesopelagic ocean. Here, we conducted comparative analyses of trans-kingdom community assemblages thriving in the mesopelagic oxygen minimum zone (OMZ), mesopelagic oxic, and their epipelagic counterparts. We identified nine distinct types of intermediate water masses that correlate with variation in mesopelagic community composition. Furthermore, oxygen, NO(3)(-) and particle flux together appeared as the main drivers governing these communities. Novel taxonomic signatures emerged from OMZ while a global co-occurrence network analysis showed that about 70% of the abundance of mesopelagic plankton groups is organized into three community modules. One module gathers prokaryotes, pico-eukaryotes and Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) from oxic regions, and the two other modules are enriched in OMZ prokaryotes and OMZ pico-eukaryotes, respectively. We hypothesize that OMZ conditions led to a diversification of ecological niches, and thus communities, due to selective pressure from limited resources. Our study further clarifies the interplay between environmental factors in the mesopelagic oxic and OMZ, and the compositional features of communities.},

note = {Rigonato, Janaina 

Budinich, Marko 

Murillo, Alejandro A 

Brandao, Manoela C 

Pierella Karlusich, Juan J 

Soviadan, Yawouvi Dodji 

Gregory, Ann C 

Endo, Hisashi 

Kokoszka, Florian 

Vik, Dean 

Henry, Nicolas 

Fremont, Paul 

Labadie, Karine 

Zayed, Ahmed A 

Dimier, Celine 

Picheral, Marc 

Searson, Sarah 

Poulain, Julie 

Kandels, Stefanie 

Pesant, Stephane 

Karsenti, Eric 

Bork, Peer 

Bowler, Chris 

de Vargas, Colomban 

Eveillard, Damien 

Gehlen, Marion 

Iudicone, Daniele 

Lombard, Fabien 

Ogata, Hiroyuki 

Stemmann, Lars 

Sullivan, Matthew B 

Sunagawa, Shinichi 

Wincker, Patrick 

Chaffron, Samuel 

Jaillon, Olivier 

eng 

England 

2023/08/19 

ISME Commun. 2023 Aug 18;3(1):83. doi: 10.1038/s43705-023-00279-9.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN289,

title = {Mirusviruses link herpesviruses to giant viruses},

author = {M. Gaia and L. Meng and E. Pelletier and P. Forterre and C. Vanni and A. Fernandez-Guerra and O. Jaillon and P. Wincker and H. Ogata and M. Krupovic and T. O. Delmont},

url = {https://www.ncbi.nlm.nih.gov/pubmed/37076623},

doi = {10.1038/s41586-023-05962-4},

issn = {1476-4687 (Electronic) 

0028-0836 (Print)},

year  = {2023},

date = {2023-01-01},

journal = {Nature},

volume = {616},

number = {7958},

pages = {783-789},

abstract = {DNA viruses have a major influence on the ecology and evolution of cellular organisms(1-4), but their overall diversity and evolutionary trajectories remain elusive(5). Here we carried out a phylogeny-guided genome-resolved metagenomic survey of the sunlit oceans and discovered plankton-infecting relatives of herpesviruses that form a putative new phylum dubbed Mirusviricota. The virion morphogenesis module of this large monophyletic clade is typical of viruses from the realm Duplodnaviria(6), with multiple components strongly indicating a common ancestry with animal-infecting Herpesvirales. Yet, a substantial fraction of mirusvirus genes, including hallmark transcription machinery genes missing in herpesviruses, are closely related homologues of giant eukaryotic DNA viruses from another viral realm, Varidnaviria. These remarkable chimaeric attributes connecting Mirusviricota to herpesviruses and giant eukaryotic viruses are supported by more than 100 environmental mirusvirus genomes, including a near-complete contiguous genome of 432 kilobases. Moreover, mirusviruses are among the most abundant and active eukaryotic viruses characterized in the sunlit oceans, encoding a diverse array of functions used during the infection of microbial eukaryotes from pole to pole. The prevalence, functional activity, diversification and atypical chimaeric attributes of mirusviruses point to a lasting role of Mirusviricota in the ecology of marine ecosystems and in the evolution of eukaryotic DNA viruses.},

note = {Gaia, Morgan 

Meng, Lingjie 

Pelletier, Eric 

Forterre, Patrick 

Vanni, Chiara 

Fernandez-Guerra, Antonio 

Jaillon, Olivier 

Wincker, Patrick 

Ogata, Hiroyuki 

Krupovic, Mart 

Delmont, Tom O 

eng 

Research Support, Non-U.S. Gov't 

England 

2023/04/20 

Nature. 2023 Apr;616(7958):783-789. doi: 10.1038/s41586-023-05962-4. Epub 2023 Apr 19.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN281,

title = {Genomic adaptation of the picoeukaryote Pelagomonas calceolata to iron-poor oceans revealed by a chromosome-scale genome sequence},

author = {N. Guerin and M. Ciccarella and E. Flamant and P. Fremont and S. Mangenot and B. Istace and B. Noel and C. Belser and L. Bertrand and K. Labadie and C. Cruaud and S. Romac and C. Bachy and M. Gachenot and E. Pelletier and A. Alberti and O. Jaillon and P. Wincker and J. M. Aury and Q. Carradec},

url = {https://www.ncbi.nlm.nih.gov/pubmed/36114260},

doi = {10.1038/s42003-022-03939-z},

issn = {2399-3642 (Electronic) 

2399-3642 (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {Commun Biol},

volume = {5},

number = {1},

pages = {983},

abstract = {The smallest phytoplankton species are key actors in oceans biogeochemical cycling and their abundance and distribution are affected with global environmental changes. Among them, algae of the Pelagophyceae class encompass coastal species causative of harmful algal blooms while others are cosmopolitan and abundant. The lack of genomic reference in this lineage is a main limitation to study its ecological importance. Here, we analysed Pelagomonas calceolata relative abundance, ecological niche and potential for the adaptation in all oceans using a complete chromosome-scale assembled genome sequence. Our results show that P. calceolata is one of the most abundant eukaryotic species in the oceans with a relative abundance favoured by high temperature, low-light and iron-poor conditions. Climate change projections based on its relative abundance suggest an extension of the P. calceolata habitat toward the poles at the end of this century. Finally, we observed a specific gene repertoire and expression level variations potentially explaining its ecological success in low-iron and low-nitrate environments. Collectively, these findings reveal the ecological importance of P. calceolata and lay the foundation for a global scale analysis of the adaptation and acclimation strategies of this small phytoplankton in a changing environment.},

note = {Guerin, Nina 

Ciccarella, Marta 

Flamant, Elisa 

Fremont, Paul 

Mangenot, Sophie 

Istace, Benjamin 

Noel, Benjamin 

Belser, Caroline 

Bertrand, Laurie 

Labadie, Karine 

Cruaud, Corinne 

Romac, Sarah 

Bachy, Charles 

Gachenot, Martin 

Pelletier, Eric 

Alberti, Adriana 

Jaillon, Olivier 

Wincker, Patrick 

Aury, Jean-Marc 

Carradec, Quentin 

eng 

ANR-10-INBS-09-08/Agence Nationale de la Recherche (French National Research Agency) 

ANR-11-BTBR-0008/Agence Nationale de la Recherche (French National Research Agency) 

England 

Commun Biol. 2022 Sep 16;5(1):983. doi: 10.1038/s42003-022-03939-z.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN287,

title = {Phytoplankton DNA metabarcoding in four sectors of the SW Atlantic in the context of the global ocean},

author = {S. V. Ayuso J. J. Karlusich Pierella F. M. Ibarbalz},

doi = {https://doi.org/10.25260/EA.22.32.3.0.1812},

year  = {2022},

date = {2022-01-01},

journal = {Ecologia Austral},

volume = {32},

pages = {835-848},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN286,

title = {Mathias Penot, Joel B. Dacks, Betsy Read and Richard G. Dorrell},

author = {M. Penot and J. B. Dacks and B. Read and R. G. Dorrell},

doi = {https://doi.org/10.1080/26388081.2022.2103732},

year  = {2022},

date = {2022-01-01},

journal = {Applied Phycology},

volume = {3},

number = {1},

pages = {340-359},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN280,

title = {Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems},

author = {D. J. Richter and R. Watteaux and T. Vannier and J. Leconte and P. Fremont and G. Reygondeau and N. Maillet and N. Henry and G. Benoit and O. Da Silva and T. O. Delmont and A. Fernandez-Guerra and S. Suweis and R. Narci and C. Berney and D. Eveillard and F. Gavory and L. Guidi and K. Labadie and E. Mahieu and J. Poulain and S. Romac and S. Roux and C. Dimier and S. Kandels and M. Picheral and S. Searson and Coordinators Tara Oceans and S. Pesant and J. M. Aury and J. R. Brum and C. Lemaitre and E. Pelletier and P. Bork and S. Sunagawa and F. Lombard and L. Karp-Boss and C. Bowler and M. B. Sullivan and E. Karsenti and M. Mariadassou and I. Probert and P. Peterlongo and P. Wincker and C. Vargas and M. Ribera d'Alcala and D. Iudicone and O. Jaillon},

url = {https://www.ncbi.nlm.nih.gov/pubmed/35920817},

doi = {10.7554/eLife.78129},

issn = {2050-084X (Electronic) 

2050-084X (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {Elife},

volume = {11},

abstract = {Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chemical, and physical context of the ocean (the 'seascape') by analyzing metagenomes of plankton communities sampled across oceans during the Tara Oceans expedition, in light of environmental data and ocean current transport. Using a consistent approach across organismal sizes that provides unprecedented resolution to measure changes in genomic composition between communities, we report a pan-ocean, size-dependent plankton biogeography overlying regional heterogeneity. We found robust evidence for a basin-scale impact of transport by ocean currents on plankton biogeography, and on a characteristic timescale of community dynamics going beyond simple seasonality or life history transitions of plankton. 

Oceans are brimming with life invisible to our eyes, a myriad of species of bacteria, viruses and other microscopic organisms essential for the health of the planet. These 'marine plankton' are unable to swim against currents and should therefore be constantly on the move, yet previous studies have suggested that distinct species of plankton may in fact inhabit different oceanic regions. However, proving this theory has been challenging; collecting plankton is logistically difficult, and it is often impossible to distinguish between species simply by examining them under a microscope. However, within the last decade, a research schooner called Tara has travelled the globe to gather thousands of plankton samples. At the same time, advances in genomics have made it possible to identify species based only on fragments of their DNA sequence. To understand the hidden geography of plankton communities in Earth's oceans, Richter et al. pored over DNA from the Tara Oceans expedition. This revealed that, despite being unable to resist the flow of water, various planktonic species which live close to the surface manage to occupy distinct, stable provinces shaped by currents. Different sizes of plankton are distributed in different sized provinces, with the smallest organisms tending to inhabit the smallest areas. Comparing DNA similarities and speeds of currents at the ocean surface revealed how these might stretch and mix plankton communities. Plankton play a critical role in the health of the ocean and the chemical cycles of planet Earth. These results could allow deeper investigation by marine modellers, ecologists, and evolutionary biologists. Meanwhile, work is already underway to investigate how climate change might impact this hidden geography. 

eng},

note = {Richter, Daniel J 

Watteaux, Romain 

Vannier, Thomas 

Leconte, Jade 

Fremont, Paul 

Reygondeau, Gabriel 

Maillet, Nicolas 

Henry, Nicolas 

Benoit, Gaetan 

Da Silva, Ophelie 

Delmont, Tom O 

Fernandez-Guerra, Antonio 

Suweis, Samir 

Narci, Romain 

Berney, Cedric 

Eveillard, Damien 

Gavory, Frederick 

Guidi, Lionel 

Labadie, Karine 

Mahieu, Eric 

Poulain, Julie 

Romac, Sarah 

Roux, Simon 

Dimier, Celine 

Kandels, Stefanie 

Picheral, Marc 

Searson, Sarah 

Pesant, Stephane 

Aury, Jean-Marc 

Brum, Jennifer R 

Lemaitre, Claire 

Pelletier, Eric 

Bork, Peer 

Sunagawa, Shinichi 

Lombard, Fabien 

Karp-Boss, Lee 

Bowler, Chris 

Sullivan, Matthew B 

Karsenti, Eric 

Mariadassou, Mahendra 

Probert, Ian 

Peterlongo, Pierre 

Wincker, Patrick 

de Vargas, Colomban 

Ribera d'Alcala, Maurizio 

Iudicone, Daniele 

Jaillon, Olivier 

eng 

Research Support, Non-U.S. Gov't 

Research Support, U.S. Gov't, Non-P.H.S. 

England 

Elife. 2022 Aug 3;11. pii: 78129. doi: 10.7554/eLife.78129.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN285,

title = {Coupling Imaging and Omics in Plankton Surveys: State-of-the-Art, Challenges, and Future Directions},

author = {J. J. Pierella Karlusich and F. Lombard and J. O. Irisson and C. Bowler and R. A. Foster},

doi = {https://doi.org/10.3389/fmars.2022.878803},

year  = {2022},

date = {2022-01-01},

journal = {Frontiers in Marine Science},

volume = {9},

pages = {878803},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN274,

title = {The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes},

author = {C. Vernette and J. Lecubin and P. Sanchez and Coordinators Tara Oceans and S. Sunagawa and T. O. Delmont and S. G. Acinas and E. Pelletier and P. Hingamp and M. Lescot},

url = {https://www.ncbi.nlm.nih.gov/pubmed/35687095},

doi = {10.1093/nar/gkac420},

issn = {1362-4962 (Electronic) 

0305-1048 (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {Nucleic Acids Res},

abstract = {Testing hypothesis about the biogeography of genes using large data resources such as Tara Oceans marine metagenomes and metatranscriptomes requires significant hardware resources and programming skills. The new release of the 'Ocean Gene Atlas' (OGA2) is a freely available intuitive online service to mine large and complex marine environmental genomic databases. OGA2 datasets available have been extended and now include, from the Tara Oceans portfolio: (i) eukaryotic Metagenome-Assembled-Genomes (MAGs) and Single-cell Assembled Genomes (SAGs) (10.2E+6 coding genes), (ii) version 2 of Ocean Microbial Reference Gene Catalogue (46.8E+6 non-redundant genes), (iii) 924 MetaGenomic Transcriptomes (7E+6 unigenes), (iv) 530 MAGs from an Arctic MAG catalogue (1E+6 genes) and (v) 1888 Bacterial and Archaeal Genomes (4.5E+6 genes), and an additional dataset from the Malaspina 2010 global circumnavigation: (vi) 317 Malaspina Deep Metagenome Assembled Genomes (0.9E+6 genes). Novel analyses enabled by OGA2 include phylogenetic tree inference to visualize user queries within their context of sequence homologues from both the marine environmental dataset and the RefSeq database. An Application Programming Interface (API) now allows users to query OGA2 using command-line tools, hence providing local workflow integration. Finally, gene abundance can be interactively filtered directly on map displays using any of the available environmental variables. Ocean Gene Atlas v2.0 is freely-available at: https://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/.},

note = {Vernette, Caroline 

Lecubin, Julien 

Sanchez, Pablo 

Sunagawa, Shinichi 

Delmont, Tom O 

Acinas, Silvia G 

Pelletier, Eric 

Hingamp, Pascal 

Lescot, Magali 

eng 

ANR-11-BTBR-0008/French Government 

ANR-10-INBS-09-08/FRANCE GENOMIQUE 

ANR-11-INBS-0013/Institut Francais de Bioinformatique 

ANR-19-CE45-0008/SeqDigger 

ANR-21-ESRE-0038/AO-EMBRC 

England 

Nucleic Acids Res. 2022 Jun 10. pii: 6605321. doi: 10.1093/nar/gkac420.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN284,

title = {Diversity and ecological footprint of Global Ocean RNA viruses},

author = {G. Dominguez-Huerta and A. A. Zayed and J. M. Wainaina and J. Guo and F. Tian and A. A. Pratama and B. Bolduc and M. Mohssen and O. Zablocki and E. Pelletier and E. Delage and A. Alberti and J. M. Aury and Q. Carradec and C. Silva and K. Labadie and J. Poulain and sign Tara Oceans Coordinators section and C. Bowler and D. Eveillard and L. Guidi and E. Karsenti and J. H. Kuhn and H. Ogata and P. Wincker and A. Culley and S. Chaffron and M. B. Sullivan},

url = {https://www.ncbi.nlm.nih.gov/pubmed/35679415},

doi = {10.1126/science.abn6358},

issn = {1095-9203 (Electronic) 

0036-8075 (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {Science},

volume = {376},

number = {6598},

pages = {1202-1208},

abstract = {DNA viruses are increasingly recognized as influencing marine microbes and microbe-mediated biogeochemical cycling. However, little is known about global marine RNA virus diversity, ecology, and ecosystem roles. In this study, we uncover patterns and predictors of marine RNA virus community- and "species"-level diversity and contextualize their ecological impacts from pole to pole. Our analyses revealed four ecological zones, latitudinal and depth diversity patterns, and environmental correlates for RNA viruses. Our findings only partially parallel those of cosampled plankton and show unexpectedly high polar ecological interactions. The influence of RNA viruses on ecosystems appears to be large, as predicted hosts are ecologically important. Moreover, the occurrence of auxiliary metabolic genes indicates that RNA viruses cause reprogramming of diverse host metabolisms, including photosynthesis and carbon cycling, and that RNA virus abundances predict ocean carbon export.},

note = {Dominguez-Huerta, Guillermo 

Zayed, Ahmed A 

Wainaina, James M 

Guo, Jiarong 

Tian, Funing 

Pratama, Akbar Adjie 

Bolduc, Benjamin 

Mohssen, Mohamed 

Zablocki, Olivier 

Pelletier, Eric 

Delage, Erwan 

Alberti, Adriana 

Aury, Jean-Marc 

Carradec, Quentin 

da Silva, Corinne 

Labadie, Karine 

Poulain, Julie 

Bowler, Chris 

Eveillard, Damien 

Guidi, Lionel 

Karsenti, Eric 

Kuhn, Jens H 

Ogata, Hiroyuki 

Wincker, Patrick 

Culley, Alexander 

Chaffron, Samuel 

Sullivan, Matthew B 

eng 

Science. 2022 Jun 10;376(6598):1202-1208. doi: 10.1126/science.abn6358. Epub 2022 Jun 9.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN275,

title = {Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean},

author = {T. O. Delmont and M. Gaia and D. D. Hinsinger and P. Fremont and C. Vanni and A. Fernandez Guerra and A. M. Eren and A. Kourlaiev and L. d'Agata and Q. Clayssen and E. Villar and K. Labadie and C. Cruaud and J. Poulain and C. Da Silva and M. Wessner and B. Noel and J. M. Aury and Tara Oceans Coordinators and C. Vargas and C. Bowler and E. Karsenti and E. Pelletier and P. Wincker and O. Jaillon},

doi = {https://doi.org/10.1016/j.xgen.2022.100123},

year  = {2022},

date = {2022-01-01},

journal = {Cell Genomics},

volume = {2},

pages = {100123},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN283,

title = {Priorities for ocean microbiome research},

author = {Foundation Tara Ocean and Oceans Tara and Laboratory European Molecular Biology and Consortium European Marine Biological Resource Centre - European Research Infrastructure},

url = {https://www.ncbi.nlm.nih.gov/pubmed/35773399},

doi = {10.1038/s41564-022-01145-5},

issn = {2058-5276 (Electronic) 

2058-5276 (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {Nat Microbiol},

volume = {7},

number = {7},

pages = {937-947},

abstract = {Microbial communities have essential roles in ocean ecology and planetary health. Microbes participate in nutrient cycles, remove huge quantities of carbon dioxide from the air and support ocean food webs. The taxonomic and functional diversity of the global ocean microbiome has been revealed by technological advances in sampling, DNA sequencing and bioinformatics. A better understanding of the ocean microbiome could underpin strategies to address environmental and societal challenges, including achievement of multiple Sustainable Development Goals way beyond SDG 14 'life below water'. We propose a set of priorities for understanding and protecting the ocean microbiome, which include delineating interactions between microbiota, sustainably applying resources from oceanic microorganisms and creating policy- and funder-friendly ocean education resources, and discuss how to achieve these ambitious goals.},

note = {(EMBL) 

(EMBRC-ERIC) 

eng 

Review 

Research Support, Non-U.S. Gov't 

England 

Nat Microbiol. 2022 Jul;7(7):937-947. doi: 10.1038/s41564-022-01145-5. Epub 2022 Jun 30.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN282,

title = {Biosynthetic potential of the global ocean microbiome},

author = {L. Paoli and H. J. Ruscheweyh and C. C. Forneris and F. Hubrich and S. Kautsar and A. Bhushan and A. Lotti and Q. Clayssen and G. Salazar and A. Milanese and C. I. Carlstrom and C. Papadopoulou and D. Gehrig and M. Karasikov and H. Mustafa and M. Larralde and L. M. Carroll and P. Sanchez and A. A. Zayed and D. R. Cronin and S. G. Acinas and P. Bork and C. Bowler and T. O. Delmont and J. M. Gasol and A. D. Gossert and A. Kahles and M. B. Sullivan and P. Wincker and G. Zeller and S. L. Robinson and J. Piel and S. Sunagawa},

url = {https://www.ncbi.nlm.nih.gov/pubmed/35732736},

doi = {10.1038/s41586-022-04862-3},

issn = {1476-4687 (Electronic) 

0028-0836 (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {Nature},

volume = {607},

number = {7917},

pages = {111-118},

abstract = {Natural microbial communities are phylogenetically and metabolically diverse. In addition to underexplored organismal groups(1), this diversity encompasses a rich discovery potential for ecologically and biotechnologically relevant enzymes and biochemical compounds(2,3). However, studying this diversity to identify genomic pathways for the synthesis of such compounds(4) and assigning them to their respective hosts remains challenging. The biosynthetic potential of microorganisms in the open ocean remains largely uncharted owing to limitations in the analysis of genome-resolved data at the global scale. Here we investigated the diversity and novelty of biosynthetic gene clusters in the ocean by integrating around 10,000 microbial genomes from cultivated and single cells with more than 25,000 newly reconstructed draft genomes from more than 1,000 seawater samples. These efforts revealed approximately 40,000 putative mostly new biosynthetic gene clusters, several of which were found in previously unsuspected phylogenetic groups. Among these groups, we identified a lineage rich in biosynthetic gene clusters ('Candidatus Eudoremicrobiaceae') that belongs to an uncultivated bacterial phylum and includes some of the most biosynthetically diverse microorganisms in this environment. From these, we characterized the phospeptin and pythonamide pathways, revealing cases of unusual bioactive compound structure and enzymology, respectively. Together, this research demonstrates how microbiomics-driven strategies can enable the investigation of previously undescribed enzymes and natural products in underexplored microbial groups and environments.},

note = {Paoli, Lucas 

Ruscheweyh, Hans-Joachim 

Forneris, Clarissa C 

Hubrich, Florian 

Kautsar, Satria 

Bhushan, Agneya 

Lotti, Alessandro 

Clayssen, Quentin 

Salazar, Guillem 

Milanese, Alessio 

Carlstrom, Charlotte I 

Papadopoulou, Chrysa 

Gehrig, Daniel 

Karasikov, Mikhail 

Mustafa, Harun 

Larralde, Martin 

Carroll, Laura M 

Sanchez, Pablo 

Zayed, Ahmed A 

Cronin, Dylan R 

Acinas, Silvia G 

Bork, Peer 

Bowler, Chris 

Delmont, Tom O 

Gasol, Josep M 

Gossert, Alvar D 

Kahles, Andre 

Sullivan, Matthew B 

Wincker, Patrick 

Zeller, Georg 

Robinson, Serina L 

Piel, Jorn 

Sunagawa, Shinichi 

eng 

835067/ERC_/European Research Council/International 

England 

Nature. 2022 Jul;607(7917):111-118. doi: 10.1038/s41586-022-04862-3. Epub 2022 Jun 22.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN272,

title = {Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome},

author = {A. A. Zayed and J. M. Wainaina and G. Dominguez-Huerta and E. Pelletier and J. Guo and M. Mohssen and F. Tian and A. A. Pratama and B. Bolduc and O. Zablocki and D. Cronin and L. Solden and E. Delage and A. Alberti and J. M. Aury and Q. Carradec and C. Silva and K. Labadie and J. Poulain and H. J. Ruscheweyh and G. Salazar and E. Shatoff and dagger Tara Oceans Coordinatorsdouble and R. Bundschuh and K. Fredrick and L. S. Kubatko and S. Chaffron and A. I. Culley and S. Sunagawa and J. H. Kuhn and P. Wincker and M. B. Sullivan and S. G. Acinas and M. Babin and P. Bork and E. Boss and C. Bowler and G. Cochrane and C. Vargas and G. Gorsky and L. Guidi and N. Grimsley and P. Hingamp and D. Iudicone and O. Jaillon and S. Kandels and L. Karp-Boss and E. Karsenti and F. Not and H. Ogata and N. Poulton and S. Pesant and C. Sardet and S. Speich and L. Stemmann and M. B. Sullivan and S. Sungawa and P. Wincker},

url = {https://www.ncbi.nlm.nih.gov/pubmed/35389782},

doi = {10.1126/science.abm5847},

issn = {1095-9203 (Electronic) 

0036-8075 (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {Science},

volume = {376},

number = {6589},

pages = {156-162},

abstract = {Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA viruses are insufficiently studied outside disease settings. In this study, we analyzed approximately 28 terabases of Global Ocean RNA sequences to expand Earth's RNA virus catalogs and their taxonomy, investigate their evolutionary origins, and assess their marine biogeography from pole to pole. Using new approaches to optimize discovery and classification, we identified RNA viruses that necessitate substantive revisions of taxonomy (doubling phyla and adding >50% new classes) and evolutionary understanding. "Species"-rank abundance determination revealed that viruses of the new phyla "Taraviricota," a missing link in early RNA virus evolution, and "Arctiviricota" are widespread and dominant in the oceans. These efforts provide foundational knowledge critical to integrating RNA viruses into ecological and epidemiological models.},

note = {Zayed, Ahmed A 

Wainaina, James M 

Dominguez-Huerta, Guillermo 

Pelletier, Eric 

Guo, Jiarong 

Mohssen, Mohamed 

Tian, Funing 

Pratama, Akbar Adjie 

Bolduc, Benjamin 

Zablocki, Olivier 

Cronin, Dylan 

Solden, Lindsey 

Delage, Erwan 

Alberti, Adriana 

Aury, Jean-Marc 

Carradec, Quentin 

da Silva, Corinne 

Labadie, Karine 

Poulain, Julie 

Ruscheweyh, Hans-Joachim 

Salazar, Guillem 

Shatoff, Elan 

Bundschuh, Ralf 

Fredrick, Kurt 

Kubatko, Laura S 

Chaffron, Samuel 

Culley, Alexander I 

Sunagawa, Shinichi 

Kuhn, Jens H 

Wincker, Patrick 

Sullivan, Matthew B 

Acinas, Silvia G 

Babin, Marcel 

Bork, Peer 

Boss, Emmanuel 

Bowler, Chris 

Cochrane, Guy 

de Vargas, Colomban 

Gorsky, Gabriel 

Guidi, Lionel 

Grimsley, Nigel 

Hingamp, Pascal 

Iudicone, Daniele 

Jaillon, Olivier 

Kandels, Stefanie 

Karp-Boss, Lee 

Karsenti, Eric 

Not, Fabrice 

Ogata, Hiroyuki 

Poulton, Nicole 

Pesant, Stephane 

Sardet, Christian 

Speich, Sabrinia 

Stemmann, Lars 

Sungawa, Shinichi 

eng 

Research Support, Non-U.S. Gov't 

Research Support, U.S. Gov't, Non-P.H.S. 

Science. 2022 Apr 8;376(6589):156-162. doi: 10.1126/science.abm5847. Epub 2022 Apr 7.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN264,

title = {Restructuring of plankton genomic biogeography in the surface ocean under climate change},

author = {P. Fremont and M. Gehlen and M. Vrac and J. Leconte and T. O. Delmont and P. Wincker and D. Iudicone and O. Jaillon},

url = {<Go to ISI>://WOS:000778096800004},

doi = {10.1038/s41558-022-01314-8},

issn = {1758-678x},

year  = {2022},

date = {2022-01-01},

journal = {Nature Climate Change},

volume = {12},

number = {4},

pages = {393-+},

abstract = {The impact of climate change on diversity, functioning and biogeography of marine plankton remains a major unresolved issue. Here environmental niches are evidenced for plankton communities at the genomic scale for six size fractions from viruses to meso-zooplankton. The spatial extrapolation of these niches portrays ocean partitionings south of 60 degrees N into climato-genomic provinces characterized by signature genomes. By 2090, under the RCP8.5 future climate scenario, provinces are reorganized over half of the ocean area considered, and almost all provinces are displaced poleward. Particularly, tropical provinces expand at the expense of temperate ones. Sea surface temperature is identified as the main driver of changes (50%), followed by phosphate (11%) and salinity (10%). Compositional shifts among key planktonic groups suggest impacts on the nitrogen and carbon cycles. Provinces are linked to estimates of carbon export fluxes which are projected to decrease, on average, by 4% in response to biogeographical restructuring. 

The authors define the global environmental niches of plankton from nano- (viruses) to meso-zooplankton (small metazoans) using metagenomic data. They assess reorganizations under climate change and the environmental drivers of change, with focus on the impacts on nitrogen and carbon fluxes.},

note = {0l4fc 

Times Cited:0 

Cited References Count:77},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN263,

title = {A robust approach to estimate relative phytoplankton cell abundances from metagenomes},

author = {J. J. Pierella Karlusich and E. Pelletier and L. Zinger and F. Lombard and A. Zingone and S. Colin and J. M. Gasol and R. G. Dorrell and N. Henry and E. Scalco and S. G. Acinas and P. Wincker and C. Vargas and C. Bowler},

url = {https://www.ncbi.nlm.nih.gov/pubmed/35108459},

doi = {10.1111/1755-0998.13592},

issn = {1755-0998 (Electronic) 

1755-098X (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {Mol Ecol Resour},

abstract = {Phytoplankton account for >45% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages containing chloroplasts. Genetic surveys of phytoplankton communities generally consist of PCR amplification of bacterial (16S), nuclear (18S) and/or chloroplastic (16S) rRNA marker genes from DNA extracted from environmental samples. However, our appreciation of phytoplankton abundance or biomass is limited by PCR-amplification biases, rRNA gene copy number variations across taxa, and the fact that rRNA genes do not provide insights into metabolic traits such as photosynthesis. Here, we targeted the photosynthetic gene psbO from metagenomes to circumvent these limitations: the method is PCR-free, and the gene is universally and exclusively present in photosynthetic prokaryotes and eukaryotes, mainly in one copy per genome. We applied and validated this new strategy with the size-fractionated marine samples collected by Tara Oceans, and showed improved correlations with flow cytometry and microscopy than when based on rRNA genes. Furthermore, we revealed unexpected features of the ecology of these ecosystems, such as the high abundance of picocyanobacterial aggregates and symbionts in the ocean, and the decrease in relative abundance of phototrophs towards the larger size classes of marine dinoflagellates. To facilitate the incorporation of psbO in molecular-based surveys, we compiled a curated database of >18,000 unique sequences. Overall, psbO appears to be a promising new gene marker for molecular-based evaluations of entire phytoplankton communities.},

note = {Pierella Karlusich, Juan Jose 

Pelletier, Eric 

Zinger, Lucie 

Lombard, Fabien 

Zingone, Adriana 

Colin, Sebastien 

Gasol, Josep M 

Dorrell, Richard G 

Henry, Nicolas 

Scalco, Eleonora 

Acinas, Silvia G 

Wincker, Patrick 

de Vargas, Colomban 

Bowler, Chris 

eng 

FFEM - French Facility for Global Environment (Fonds Francais pour l'Environnement Mondial) 

ANR-1253 11-IDEX-0001-02/Universite de Recherche Paris Sciences et Lettres (PSL) 

835067/European Research Council (ERC) European Research Council (ERC) under the European Union's Horizon 2020 

CNRS Momentum Fellowship 2019-2021 

ANR-10-LABX-54/French Government "Investissements d'Avenir" Programmes MEMO LIFE 

ANR-11-BTBR-0008/OCEANOMICS 

ANR-10-INBS-09/France Genomique 

England 

Mol Ecol Resour. 2022 Feb 2. doi: 10.1111/1755-0998.13592.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN262,

title = {Giant Viruses Encode Actin-Related Proteins},

author = {V. Da Cunha and M. Gaia and H. Ogata and O. Jaillon and T. O. Delmont and P. Forterre},

url = {https://www.ncbi.nlm.nih.gov/pubmed/35150280},

doi = {10.1093/molbev/msac022},

issn = {1537-1719 (Electronic) 

0737-4038 (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {Mol Biol Evol},

volume = {39},

number = {2},

abstract = {The emergence of the eukaryotic cytoskeleton is a critical yet puzzling step of eukaryogenesis. Actin and actin-related proteins (ARPs) are ubiquitous components of this cytoskeleton. The gene repertoire of the Last Eukaryotic Common Ancestor (LECA) would have therefore harbored both actin and various ARPs. Here, we report the presence and expression of actin-related genes in viral genomes (viractins) of some Imitervirales, a viral order encompassing the giant Mimiviridae. Phylogenetic analyses suggest an early recruitment of an actin-related gene by viruses from ancient protoeukaryotic hosts before the emergence of modern eukaryotes, possibly followed by a back transfer that gave rise to eukaryotic actins. This supports a coevolutionary scenario between pre-LECA lineages and their viruses, which could have contributed to the emergence of the modern eukaryotic cytoskeleton.},

note = {Da Cunha, Violette 

Gaia, Morgan 

Ogata, Hiroyuki 

Jaillon, Olivier 

Delmont, Tom O 

Forterre, Patrick 

eng 

Research Support, Non-U.S. Gov't 

Mol Biol Evol. 2022 Feb 3;39(2). pii: 6527639. doi: 10.1093/molbev/msac022.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN261,

title = {Patterns of eukaryotic diversity from the surface to the deep-ocean sediment},

author = {T. Cordier and I. B. Angeles and N. Henry and F. Lejzerowicz and C. Berney and R. Morard and A. Brandt and M. A. Cambon-Bonavita and L. Guidi and F. Lombard and P. M. Arbizu and R. Massana and C. Orejas and J. Poulain and C. R. Smith and P. Wincker and S. Arnaud-Haond and A. J. Gooday and C. Vargas and J. Pawlowski},

url = {https://www.ncbi.nlm.nih.gov/pubmed/35119936},

doi = {10.1126/sciadv.abj9309},

issn = {2375-2548 (Electronic) 

2375-2548 (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {Sci Adv},

volume = {8},

number = {5},

pages = {eabj9309},

abstract = {Remote deep-ocean sediment (DOS) ecosystems are among the least explored biomes on Earth. Genomic assessments of their biodiversity have failed to separate indigenous benthic organisms from sinking plankton. Here, we compare global-scale eukaryotic DNA metabarcoding datasets (18S-V9) from abyssal and lower bathyal surficial sediments and euphotic and aphotic ocean pelagic layers to distinguish plankton from benthic diversity in sediment material. Based on 1685 samples collected throughout the world ocean, we show that DOS diversity is at least threefold that in pelagic realms, with nearly two-thirds represented by abundant yet unknown eukaryotes. These benthic communities are spatially structured by ocean basins and particulate organic carbon (POC) flux from the upper ocean. Plankton DNA reaching the DOS originates from abundant species, with maximal deposition at high latitudes. Its seafloor DNA signature predicts variations in POC export from the surface and reveals previously overlooked taxa that may drive the biological carbon pump.},

note = {Cordier, Tristan 

Angeles, Ines Barrenechea 

Henry, Nicolas 

Lejzerowicz, Franck 

Berney, Cedric 

Morard, Raphael 

Brandt, Angelika 

Cambon-Bonavita, Marie-Anne 

Guidi, Lionel 

Lombard, Fabien 

Arbizu, Pedro Martinez 

Massana, Ramon 

Orejas, Covadonga 

Poulain, Julie 

Smith, Craig R 

Wincker, Patrick 

Arnaud-Haond, Sophie 

Gooday, Andrew J 

de Vargas, Colomban 

Pawlowski, Jan 

eng 

Sci Adv. 2022 Feb 4;8(5):eabj9309. doi: 10.1126/sciadv.abj9309. Epub 2022 Feb 4.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN259,

title = {Patterns of mesozooplankton community composition and vertical fluxes in the global ocean},

author = {Yawouvi Dodji Soviadan and Fabio Benedetti and Manoela C. Brandao and Sakina-Dorothee Ayata and Jean-Olivier Irisson and Jean Louis Jamet and Rainer Kiko and Fabien Lombard and Kissao Gnandi and Lars Stemmann},

url = {https://www.sciencedirect.com/science/article/pii/S0079661121002007},

doi = {https://doi.org/10.1016/j.pocean.2021.102717},

issn = {0079-6611},

year  = {2022},

date = {2022-01-01},

journal = {Progress in Oceanography},

volume = {200},

pages = {102717},

abstract = {Vertical variations in physical and chemical conditions drive changes in marine zooplankton community composition. In turn, zooplankton communities play a critical role in regulating the transfer of organic matter produced in the surface ocean to deeper layers. Yet, the links between zooplankton community composition and the strength of vertical fluxes of particles remain elusive, especially on a global scale. Here, we provide a comprehensive analysis of variations in zooplankton community composition and vertical particle flux in the upper kilometer of the global ocean. Zooplankton samples were collected across five depth layers and vertical particle fluxes were assessed using continuous profiles of the Underwater Vision Profiler (UVP5) at 57 stations covering seven ocean basins. Zooplankton samples were analysed using a Zooscan and individual organisms were classified into 19 groups for the quantitative analyses. Zooplankton abundance, biomass and vertical particle flux decreased from the surface to 1000 m depth at all latitudes. The zooplankton abundance decrease rate was stronger at sites characterised by oxygen minima (<5µmol O2.kg−1) where most zooplankton groups showed a marked decline in abundance, except the jellyfishes, molluscs, annelids, large protists and a few copepod families. The attenuation rate of vertical particle fluxes was weaker at such oxygen-depleted sites. Canonical redundancy analyses showed that the epipelagic zooplankton community composition depended on the temperature, on the phytoplankton size distribution and the surface large particulate organic matter while oxygen was an additional important factor for structuring zooplankton in the mesopelagic. Our results further suggest that future changes in surface phytoplankton size and taxa composition and mesopelagic oxygen loss might lead to profound shift in zooplankton abundance and community structure in both the euphotic and mesopelagic ocean. These changes may affect the vertical export and hereby the strength of the biological carbon pump.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN288,

title = {Whole-genome scanning reveals environmental selection mechanisms that shape diversity in populations of the epipelagic diatom Chaetoceros},

author = {C. Nef and M. A. Madoui and E. Pelletier and C. Bowler},

url = {https://www.ncbi.nlm.nih.gov/pubmed/36441816},

doi = {10.1371/journal.pbio.3001893},

issn = {1545-7885 (Electronic) 

1544-9173 (Print)},

year  = {2022},

date = {2022-01-01},

journal = {PLoS Biol},

volume = {20},

number = {11},

pages = {e3001893},

abstract = {Diatoms form a diverse and abundant group of photosynthetic protists that are essential players in marine ecosystems. However, the microevolutionary structure of their populations remains poorly understood, particularly in polar regions. Exploring how closely related diatoms adapt to different environments is essential given their short generation times, which may allow rapid adaptations, and their prevalence in marine regions dramatically impacted by climate change, such as the Arctic and Southern Oceans. Here, we address genetic diversity patterns in Chaetoceros, the most abundant diatom genus and one of the most diverse, using 11 metagenome-assembled genomes (MAGs) reconstructed from Tara Oceans metagenomes. Genome-resolved metagenomics on these MAGs confirmed a prevalent distribution of Chaetoceros in the Arctic Ocean with lower dispersal in the Pacific and Southern Oceans as well as in the Mediterranean Sea. Single-nucleotide variants identified within the different MAG populations allowed us to draw a landscape of Chaetoceros genetic diversity and revealed an elevated genetic structure in some Arctic Ocean populations. Gene flow patterns of closely related Chaetoceros populations seemed to correlate with distinct abiotic factors rather than with geographic distance. We found clear positive selection of genes involved in nutrient availability responses, in particular for iron (e.g., ISIP2a, flavodoxin), silicate, and phosphate (e.g., polyamine synthase), that were further supported by analysis of Chaetoceros transcriptomes. Altogether, these results highlight the importance of environmental selection in shaping diatom diversity patterns and provide new insights into their metapopulation genomics through the integration of metagenomic and environmental data.},

note = {Nef, Charlotte 

Madoui, Mohammed-Amin 

Pelletier, Eric 

Bowler, Chris 

eng 

Research Support, Non-U.S. Gov't 

2022/11/29 

PLoS Biol. 2022 Nov 28;20(11):e3001893. doi: 10.1371/journal.pbio.3001893. eCollection 2022 Nov.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN260,

title = {Global drivers of eukaryotic plankton biogeography in the sunlit ocean},

author = {G. Sommeria-Klein and R. Watteaux and F. M. Ibarbalz and J. J. Pierella Karlusich and D. Iudicone and C. Bowler and H. Morlon},

url = {https://www.ncbi.nlm.nih.gov/pubmed/34709919},

doi = {10.1126/science.abb3717},

issn = {1095-9203 (Electronic) 

0036-8075 (Linking)},

year  = {2021},

date = {2021-01-01},

journal = {Science},

volume = {374},

number = {6567},

pages = {594-599},

abstract = {Eukaryotic plankton are a core component of marine ecosystems with exceptional taxonomic and ecological diversity, yet how their ecology interacts with the environment to drive global distribution patterns is poorly understood. In this work, we use Tara Oceans metabarcoding data, which cover all major ocean basins, combined with a probabilistic model of taxon co-occurrence to compare the biogeography of 70 major groups of eukaryotic plankton. We uncover two main axes of biogeographic variation. First, more-diverse groups display clearer biogeographic patterns. Second, large-bodied consumers are structured by oceanic basins, mostly through the main current systems, whereas small-bodied phototrophs are structured by latitude and follow local environmental conditions. Our study highlights notable differences in biogeographies across plankton groups and investigates their determinants at the global scale.},

note = {Sommeria-Klein, Guilhem 

Watteaux, Romain 

Ibarbalz, Federico M 

Pierella Karlusich, Juan Jose 

Iudicone, Daniele 

Bowler, Chris 

Morlon, Helene 

eng 

Research Support, Non-U.S. Gov't 

Science. 2021 Oct 29;374(6567):594-599. doi: 10.1126/science.abb3717. Epub 2021 Oct 28.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN258,

title = {Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean},

author = {M. Royo-Llonch and P. Sanchez and C. Ruiz-Gonzalez and G. Salazar and C. Pedros-Alio and M. Sebastian and K. Labadie and L. Paoli and M. Ibarbalz F and L. Zinger and B. Churcheward and Coordinators Tara Oceans and S. Chaffron and D. Eveillard and E. Karsenti and S. Sunagawa and P. Wincker and L. Karp-Boss and C. Bowler and S. G. Acinas},

url = {https://www.ncbi.nlm.nih.gov/pubmed/34782724},

doi = {10.1038/s41564-021-00979-9},

issn = {2058-5276 (Electronic) 

2058-5276 (Linking)},

year  = {2021},

date = {2021-01-01},

journal = {Nat Microbiol},

volume = {6},

number = {12},

pages = {1561-1574},

abstract = {The role of the Arctic Ocean ecosystem in climate regulation may depend on the responses of marine microorganisms to environmental change. We applied genome-resolved metagenomics to 41 Arctic seawater samples, collected at various depths in different seasons during the Tara Oceans Polar Circle expedition, to evaluate the ecology, metabolic potential and activity of resident bacteria and archaea. We assembled 530 metagenome-assembled genomes (MAGs) to form the Arctic MAGs catalogue comprising 526 species. A total of 441 MAGs belonged to species that have not previously been reported and 299 genomes showed an exclusively polar distribution. Most Arctic MAGs have large genomes and the potential for fast generation times, both of which may enable adaptation to a copiotrophic lifestyle in nutrient-rich waters. We identified 38 habitat generalists and 111 specialists in the Arctic Ocean. We also found a general prevalence of 14 mixotrophs, while chemolithoautotrophs were mostly present in the mesopelagic layer during spring and autumn. We revealed 62 MAGs classified as key Arctic species, found only in the Arctic Ocean, showing the highest gene expression values and predicted to have habitat-specific traits. The Artic MAGs catalogue will inform our understanding of polar microorganisms that drive global biogeochemical cycles.},

note = {Royo-Llonch, Marta 

Sanchez, Pablo 

Ruiz-Gonzalez, Clara 

Salazar, Guillem 

Pedros-Alio, Carlos 

Sebastian, Marta 

Labadie, Karine 

Paoli, Lucas 

M Ibarbalz, Federico 

Zinger, Lucie 

Churcheward, Benjamin 

Chaffron, Samuel 

Eveillard, Damien 

Karsenti, Eric 

Sunagawa, Shinichi 

Wincker, Patrick 

Karp-Boss, Lee 

Bowler, Chris 

Acinas, Silvia G 

eng 

Research Support, Non-U.S. Gov't 

England 

Nat Microbiol. 2021 Dec;6(12):1561-1574. doi: 10.1038/s41564-021-00979-9. Epub 2021 Nov 15.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN257,

title = {Macroscale patterns of oceanic zooplankton composition and size structure},

author = {M. C. Brandao and F. Benedetti and S. Martini and Y. D. Soviadan and J. O. Irisson and J. B. Romagnan and A. Elineau and C. Desnos and L. Jalabert and A. S. Freire and M. Picheral and L. Guidi and G. Gorsky and C. Bowler and L. Karp-Boss and N. Henry and C. Vargas and M. B. Sullivan and Coordinators Tara Oceans Consortium and L. Stemmann and F. Lombard},

url = {https://www.ncbi.nlm.nih.gov/pubmed/34344925},

doi = {10.1038/s41598-021-94615-5},

issn = {2045-2322 (Electronic) 

2045-2322 (Linking)},

year  = {2021},

date = {2021-01-01},

journal = {Sci Rep},

volume = {11},

number = {1},

pages = {15714},

abstract = {Ocean plankton comprise organisms from viruses to fish larvae that are fundamental to ecosystem functioning and the provision of marine services such as fisheries and CO2 sequestration. The latter services are partly governed by variations in plankton community composition and the expression of traits such as body size at community-level. While community assembly has been thoroughly studied for the smaller end of the plankton size spectrum, the larger end comprises ectotherms that are often studied at the species, or group-level, rather than as communities. The body size of marine ectotherms decreases with temperature, but controls on community-level traits remain elusive, hindering the predictability of marine services provision. Here, we leverage Tara Oceans datasets to determine how zooplankton community composition and size structure varies with latitude, temperature and productivity-related covariates in the global surface ocean. Zooplankton abundance and median size decreased towards warmer and less productive environments, as a result of changes in copepod composition. However, some clades displayed the opposite relationships, which may be ascribed to alternative feeding strategies. Given that climate models predict increasingly warmed and stratified oceans, our findings suggest that zooplankton communities will shift towards smaller organisms which might weaken their contribution to the biological carbon pump.},

note = {Brandao, Manoela C 

Benedetti, Fabio 

Martini, Severine 

Soviadan, Yawouvi Dodji 

Irisson, Jean-Olivier 

Romagnan, Jean-Baptiste 

Elineau, Amanda 

Desnos, Corinne 

Jalabert, Laetitia 

Freire, Andrea S 

Picheral, Marc 

Guidi, Lionel 

Gorsky, Gabriel 

Bowler, Chris 

Karp-Boss, Lee 

Henry, Nicolas 

de Vargas, Colomban 

Sullivan, Matthew B 

Stemmann, Lars 

Lombard, Fabien 

eng 

Research Support, Non-U.S. Gov't 

England 

Sci Rep. 2021 Aug 3;11(1):15714. doi: 10.1038/s41598-021-94615-5.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN256,

title = {Environmental vulnerability of the global ocean epipelagic plankton community interactome},

author = {S. Chaffron and E. Delage and M. Budinich and D. Vintache and N. Henry and C. Nef and M. Ardyna and A. A. Zayed and P. C. Junger and P. E. Galand and C. Lovejoy and A. E. Murray and H. Sarmento and coordinators Tara Oceans and S. G. Acinas and M. Babin and D. Iudicone and O. Jaillon and E. Karsenti and P. Wincker and L. Karp-Boss and M. B. Sullivan and C. Bowler and C. Vargas and D. Eveillard},

url = {https://www.ncbi.nlm.nih.gov/pubmed/34452910},

doi = {10.1126/sciadv.abg1921},

issn = {2375-2548 (Electronic) 

2375-2548 (Linking)},

year  = {2021},

date = {2021-01-01},

journal = {Sci Adv},

volume = {7},

number = {35},

abstract = {Marine plankton form complex communities of interacting organisms at the base of the food web, which sustain oceanic biogeochemical cycles and help regulate climate. Although global surveys are starting to reveal ecological drivers underlying planktonic community structure and predicted climate change responses, it is unclear how community-scale species interactions will be affected by climate change. Here, we leveraged Tara Oceans sampling to infer a global ocean cross-domain plankton co-occurrence network-the community interactome-and used niche modeling to assess its vulnerabilities to environmental change. Globally, this revealed a plankton interactome self-organized latitudinally into marine biomes (Trades, Westerlies, Polar) and more connected poleward. Integrated niche modeling revealed biome-specific community interactome responses to environmental change and forecasted the most affected lineages for each community. These results provide baseline approaches to assess community structure and organismal interactions under climate scenarios while identifying plausible plankton bioindicators for ocean monitoring of climate change.},

note = {Chaffron, Samuel 

Delage, Erwan 

Budinich, Marko 

Vintache, Damien 

Henry, Nicolas 

Nef, Charlotte 

Ardyna, Mathieu 

Zayed, Ahmed A 

Junger, Pedro C 

Galand, Pierre E 

Lovejoy, Connie 

Murray, Alison E 

Sarmento, Hugo 

Acinas, Silvia G 

Babin, Marcel 

Iudicone, Daniele 

Jaillon, Olivier 

Karsenti, Eric 

Wincker, Patrick 

Karp-Boss, Lee 

Sullivan, Matthew B 

Bowler, Chris 

de Vargas, Colomban 

Eveillard, Damien 

eng 

Sci Adv. 2021 Aug 27;7(35). pii: 7/35/eabg1921. doi: 10.1126/sciadv.abg1921. Print 2021 Aug.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN255,

title = {efam: an expanded, metaproteome-supported HMM profile database of viral protein families},

author = {A. A. Zayed and D. Lucking and M. Mohssen and D. Cronin and B. Bolduc and A. C. Gregory and K. R. Hargreaves and P. D. Piehowski and R. A. White and E. L. Huang and J. N. Adkins and S. Roux and C. Moraru and M. B. Sullivan},

url = {https://www.ncbi.nlm.nih.gov/pubmed/34132786},

doi = {10.1093/bioinformatics/btab451},

issn = {1367-4811 (Electronic) 

1367-4803 (Linking)},

year  = {2021},

date = {2021-01-01},

journal = {Bioinformatics},

abstract = {MOTIVATION: Viruses infect, reprogram, and kill microbes, leading to profound ecosystem consequences, from elemental cycling in oceans and soils to microbiome-modulated diseases in plants and animals. Although metagenomic datasets are increasingly available, identifying viruses in them is challenging due to poor representation and annotation of viral sequences in databases. RESULTS: Here we establish efam, an expanded collection of Hidden Markov Model (HMM) profiles that represent viral protein families conservatively identified from the Global Ocean Virome 2.0 dataset. This resulted in 240,311 HMM profiles, each with at least 2 protein sequences, making efam >7-fold larger than the next largest, pan-ecosystem viral HMM profile database. Adjusting the criteria for viral contig confidence from "conservative" to "eXtremely Conservative" resulted in 37,841 HMM profiles in our efam-XC database. To assess the value of this resource, we integrated efam-XC into VirSorter viral discovery software to discover viruses from less-studied, ecologically distinct oxygen minimum zone (OMZ) marine habitats. This expanded database led to an increase in viruses recovered from every tested OMZ virome by approximately 24% on average (up to approximately 42%) and especially improved the recovery of often-missed shorter contigs (<5 kb). Additionally, to help elucidate lesser-known viral protein functions, we annotated the profiles using multiple databases from the DRAM pipeline and virion-associated metaproteomic data, which doubled the number of annotations obtainable by standard, single-database annotation approaches. Together, these marine resources (efam and efam-XC) are provided as searchable, compressed HMM databases that will be updated bi-annually to help maximize viral sequence discovery and study from any ecosystem. AVAILABILITY: The resources are available on the iVirus platform at (doi.org/10.25739/9vze-4143). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},

note = {Zayed, Ahmed A 

Lucking, Dominik 

Mohssen, Mohamed 

Cronin, Dylan 

Bolduc, Ben 

Gregory, Ann C 

Hargreaves, Katherine R 

Piehowski, Paul D 

White, Richard A 

Huang, Eric L 

Adkins, Joshua N 

Roux, Simon 

Moraru, Cristina 

Sullivan, Matthew B 

eng 

England 

Bioinformatics. 2021 Jun 16. pii: 6300514. doi: 10.1093/bioinformatics/btab451.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN254,

title = {Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods},

author = {J. J. Pierella Karlusich and E. Pelletier and F. Lombard and M. Carsique and E. Dvorak and S. Colin and M. Picheral and F. M. Cornejo-Castillo and S. G. Acinas and R. Pepperkok and E. Karsenti and C. Vargas and P. Wincker and C. Bowler and R. A. Foster},

url = {https://www.ncbi.nlm.nih.gov/pubmed/34230473},

doi = {10.1038/s41467-021-24299-y},

issn = {2041-1723 (Electronic) 

2041-1723 (Linking)},

year  = {2021},

date = {2021-01-01},

journal = {Nat Commun},

volume = {12},

number = {1},

pages = {4160},

abstract = {Nitrogen fixation has a critical role in marine primary production, yet our understanding of marine nitrogen-fixers (diazotrophs) is hindered by limited observations. Here, we report a quantitative image analysis pipeline combined with mapping of molecular markers for mining >2,000,000 images and >1300 metagenomes from surface, deep chlorophyll maximum and mesopelagic seawater samples across 6 size fractions (<0.2-2000 mum). We use this approach to characterise the diversity, abundance, biovolume and distribution of symbiotic, colony-forming and particle-associated diazotrophs at a global scale. We show that imaging and PCR-free molecular data are congruent. Sequence reads indicate diazotrophs are detected from the ultrasmall bacterioplankton (<0.2 mum) to mesoplankton (180-2000 mum) communities, while images predict numerous symbiotic and colony-forming diazotrophs (>20 microm). Using imaging and molecular data, we estimate that polyploidy can substantially affect gene abundances of symbiotic versus colony-forming diazotrophs. Our results support the canonical view that larger diazotrophs (>10 mum) dominate the tropical belts, while unicellular cyanobacterial and non-cyanobacterial diazotrophs are globally distributed in surface and mesopelagic layers. We describe co-occurring diazotrophic lineages of different lifestyles and identify high-density regions of diazotrophs in the global ocean. Overall, we provide an update of marine diazotroph biogeographical diversity and present a new bioimaging-bioinformatic workflow.},

note = {Pierella Karlusich, Juan Jose 

Pelletier, Eric 

Lombard, Fabien 

Carsique, Madeline 

Dvorak, Etienne 

Colin, Sebastien 

Picheral, Marc 

Cornejo-Castillo, Francisco M 

Acinas, Silvia G 

Pepperkok, Rainer 

Karsenti, Eric 

de Vargas, Colomban 

Wincker, Patrick 

Bowler, Chris 

Foster, Rachel A 

eng 

Research Support, Non-U.S. Gov't 

England 

Nat Commun. 2021 Jul 6;12(1):4160. doi: 10.1038/s41467-021-24299-y.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN253,

title = {Discovery of Viral Myosin Genes With Complex Evolutionary History Within Plankton},

author = {S. Kijima and T. O. Delmont and U. Miyazaki and M. Gaia and H. Endo and H. Ogata},

url = {https://www.ncbi.nlm.nih.gov/pubmed/34163457},

doi = {10.3389/fmicb.2021.683294},

issn = {1664-302X (Print) 

1664-302X (Linking)},

year  = {2021},

date = {2021-01-01},

journal = {Front Microbiol},

volume = {12},

pages = {683294},

abstract = {Nucleocytoplasmic large DNA viruses (NCLDVs) infect diverse eukaryotes and form a group of viruses with capsids encapsulating large genomes. Recent studies are increasingly revealing a spectacular array of functions encoded in their genomes, including genes for energy metabolisms, nutrient uptake, as well as cytoskeleton. Here, we report the discovery of genes homologous to myosins, the major eukaryotic motor proteins previously unrecognized in the virosphere, in environmental genomes of NCLDVs from the surface of the oceans. Phylogenetic analyses indicate that most viral myosins (named "virmyosins") belong to the Imitervirales order, except for one belonging to the Phycodnaviridae family. On the one hand, the phylogenetic positions of virmyosin-encoding Imitervirales are scattered within the Imitervirales. On the other hand, Imitervirales virmyosin genes form a monophyletic group in the phylogeny of diverse myosin sequences. Furthermore, phylogenetic trends for the virmyosin genes and viruses containing them were incongruent. Based on these results, we argue that multiple transfers of myosin homologs have occurred not only from eukaryotes to viruses but also between viruses, supposedly during co-infections of the same host. Like other viruses that use host motor proteins for their intracellular transport or motility, these viruses may use the virally encoded myosins for the intracellular trafficking of giant viral particles.},

note = {Kijima, Soichiro 

Delmont, Tom O 

Miyazaki, Urara 

Gaia, Morgan 

Endo, Hisashi 

Ogata, Hiroyuki 

eng 

Switzerland 

Front Microbiol. 2021 Jun 7;12:683294. doi: 10.3389/fmicb.2021.683294. eCollection 2021.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN251,

title = {Phylogenomics of Porites from the Arabian Peninsula},

author = {T. I. Terraneo and F. Benzoni and R. Arrigoni and A. H. Baird and K. G. Mariappan and Z. H. Forsman and M. K. Wooster and J. Bouwmeester and A. Marshell and M. L. Berumen},

url = {https://www.ncbi.nlm.nih.gov/pubmed/33813021},

doi = {10.1016/j.ympev.2021.107173},

issn = {1095-9513 (Electronic) 

1055-7903 (Linking)},

year  = {2021},

date = {2021-01-01},

journal = {Mol Phylogenet Evol},

volume = {161},

pages = {107173},

abstract = {The advent of high throughput sequencing technologies provides an opportunity to resolve phylogenetic relationships among closely related species. By incorporating hundreds to thousands of unlinked loci and single nucleotide polymorphisms (SNPs), phylogenomic analyses have a far greater potential to resolve species boundaries than approaches that rely on only a few markers. Scleractinian taxa have proved challenging to identify using traditional morphological approaches and many groups lack an adequate set of molecular markers to investigate their phylogenies. Here, we examine the potential of Restriction-site Associated DNA sequencing (RADseq) to investigate phylogenetic relationships and species limits within the scleractinian coral genus Porites. A total of 126 colonies were collected from 16 localities in the seas surrounding the Arabian Peninsula and ascribed to 12 nominal and two unknown species based on their morphology. Reference mapping was used to retrieve and compare nearly complete mitochondrial genomes, ribosomal DNA, and histone loci. De novo assembly and reference mapping to the P. lobata coral transcriptome were compared and used to obtain thousands of genome-wide loci and SNPs. A suite of species discovery methods (phylogenetic, ordination, and clustering analyses) and species delimitation approaches (coalescent-based, species tree, and Bayesian Factor delimitation) suggested the presence of eight molecular lineages, one of which included six morphospecies. Our phylogenomic approach provided a fully supported phylogeny of Porites from the Arabian Peninsula, suggesting the power of RADseq data to solve the species delineation problem in this speciose coral genus.},

note = {Terraneo, Tullia I 

Benzoni, Francesca 

Arrigoni, Roberto 

Baird, Andrew H 

Mariappan, Kiruthiga G 

Forsman, Zac H 

Wooster, Michael K 

Bouwmeester, Jessica 

Marshell, Alyssa 

Berumen, Michael L 

eng 

Mol Phylogenet Evol. 2021 Apr 2;161:107173. doi: 10.1016/j.ympev.2021.107173.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN252,

title = {Carbon Dioxide Concentration Mechanisms in Natural Populations of Marine Diatoms: Insights From Tara Oceans},

author = {Juan José Pierella Karlusich and Chris Bowler and Haimanti Biswas},

url = {https://www.frontiersin.org/article/10.3389/fpls.2021.657821},

doi = {10.3389/fpls.2021.657821},

issn = {1664-462X},

year  = {2021},

date = {2021-01-01},

journal = {Frontiers in Plant Science},

volume = {12},

number = {659},

abstract = {Marine diatoms, the most successful photoautotrophs in the ocean, efficiently sequester a significant part of atmospheric CO_{2} to the ocean interior through their participation in the biological carbon pump. However, it is poorly understood how marine diatoms fix such a considerable amount of CO_{2}, which is vital information toward modeling their response to future CO_{2} levels. The Tara Oceans expeditions generated molecular data coupled with in situ biogeochemical measurements across the main ocean regions, and thus provides a framework to compare diatom genetic and transcriptional flexibility under natural CO_{2} variability. The current study investigates the interlink between the environmental variability of CO_{2} and other physicochemical parameters with the gene and transcript copy numbers of five key enzymes of diatom CO_{2} concentration mechanisms (CCMs): Rubisco activase and carbonic anhydrase (CA) as part of the physical pathway, together with phosphoenolpyruvate carboxylase, phosphoenolpyruvate carboxykinase, and malic enzyme as part of the potential C4 biochemical pathway. Toward this aim, we mined >200 metagenomes and >220 metatranscriptomes generated from samples of the surface layer of 66 globally distributed sampling sites and corresponding to the four main size fractions in which diatoms can be found: 0.8–5 μm, 5–20 μm, 20–180 μm, and 180–2,000 μm. Our analyses revealed that the transcripts for the enzymes of the putative C4 biochemical CCM did not in general display co-occurring profiles. The transcripts for CAs were the most abundant, with an order of magnitude higher values than the other enzymes, thus implying the importance of physical CCMs in diatom natural communities. Among the different classes of this enzyme, the most prevalent was the recently characterized iota class. Consequently, very little information is available from natural diatom assemblages about the distribution of this class. Biogeographic distributions for all the enzymes show different abundance hotspots according to the size fraction, pointing to the influence of cell size and aggregation in CCMs. Environmental correlations showed a complex pattern of responses to CO_{2} levels, total phytoplankton biomass, temperature, and nutrient concentrations. In conclusion, we propose that biophysical CCMs are prevalent in natural diatom communities.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN250,

title = {Quantitative Assessment of Nucleocytoplasmic Large DNA Virus and Host Interactions Predicted by Co-occurrence Analyses},

author = {L. Meng and H. Endo and R. Blanc-Mathieu and S. Chaffron and R. Hernandez-Velazquez and H. Kaneko and H. Ogata},

url = {https://www.ncbi.nlm.nih.gov/pubmed/33883262},

doi = {10.1128/mSphere.01298-20},

issn = {2379-5042 (Electronic) 

2379-5042 (Linking)},

year  = {2021},

date = {2021-01-01},

journal = {mSphere},

volume = {6},

number = {2},

abstract = {Nucleocytoplasmic large DNA viruses (NCLDVs) are highly diverse and abundant in marine environments. However, the knowledge of their hosts is limited because only a few NCLDVs have been isolated so far. Taking advantage of the recent large-scale marine metagenomics census, in silico host prediction approaches are expected to fill the gap and further expand our knowledge of virus-host relationships for unknown NCLDVs. In this study, we built co-occurrence networks of NCLDVs and eukaryotic taxa to predict virus-host interactions using Tara Oceans sequencing data. Using the positive likelihood ratio to assess the performance of host prediction for NCLDVs, we benchmarked several co-occurrence approaches and demonstrated an increase in the odds ratio of predicting true positive relationships 4-fold compared to random host predictions. To further refine host predictions from high-dimensional co-occurrence networks, we developed a phylogeny-informed filtering method, Taxon Interaction Mapper, and showed it further improved the prediction performance by 12-fold. Finally, we inferred virophage-NCLDV networks to corroborate that co-occurrence approaches are effective for predicting interacting partners of NCLDVs in marine environments.IMPORTANCE NCLDVs can infect a wide range of eukaryotes, although their life cycle is less dependent on hosts compared to other viruses. However, our understanding of NCLDV-host systems is highly limited because few of these viruses have been isolated so far. Co-occurrence information has been assumed to be useful to predict virus-host interactions. In this study, we quantitatively show the effectiveness of co-occurrence inference for NCLDV host prediction. We also improve the prediction performance with a phylogeny-guided method, which leads to a concise list of candidate host lineages for three NCLDV families. Our results underpin the usage of co-occurrence approaches for the metagenomic exploration of the ecology of this diverse group of viruses.},

note = {Meng, Lingjie 

Endo, Hisashi 

Blanc-Mathieu, Romain 

Chaffron, Samuel 

Hernandez-Velazquez, Rodrigo 

Kaneko, Hiroto 

Ogata, Hiroyuki 

eng 

mSphere. 2021 Apr 21;6(2). pii: 6/2/e01298-20. doi: 10.1128/mSphere.01298-20.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN246,

title = {Integrative systematics of the scleractinian coral genera Caulastraea, Erythrastrea and Oulophyllia},

author = {Roberto Arrigoni and Danwei Huang and Michael L. Berumen and Ann F. Budd and Simone Montano and Zoe T. Richards and Tullia I. Terraneo and Francesca Benzoni},

url = {https://doi.org/10.1111/zsc.12481},

doi = {10.1111/zsc.12481},

issn = {0300-3256},

year  = {2021},

date = {2021-01-01},

journal = {Zoologica Scripta},

abstract = {Abstract Modern systematics integrating molecular and morphological data has greatly improved our understanding of coral evolutionary relationships during the last two decades and led to a deeply revised taxonomy of the order Scleractinia. The family Merulinidae (Cnidaria: Scleractinia) was recently subjected to a series of revisions following this integrated approach but the phylogenetic affinities of several genera ascribed to it remain unknown. Here, we partially fill this gap through the study of 89 specimens belonging to all 10 valid species from four genera (Caulastraea, Erythrastrea, Oulophyllia and Dipsastraea) collected from 14 localities across the Indo-Pacific realm. Four molecular loci (histone H3, COI, ITS and IGR) were sequenced, and a total of 44 skeletal morphological characters (macromorphology, micromorphology and microstructure) were analysed. Molecular phylogenetic analyses revealed that the phaceloid Caulastraea species are split into two distinct lineages. A species previously ascribed to the genus Dipsastraea, Dipsastraea maxima, is also recovered in one on these lineages. Furthermore, Erythrastrea is nested within Oulophyllia. The molecular reconstructions of evolutionary relationships are further corroborated by multiscale morphological evidence. To resolve the taxonomy of these genera, Astraeosmilia is resurrected to accommodate Astraeosmilia connata, Astraeosmilia curvata, Astraeosmilia tumida and Astraeosmilia maxima, with Caulastraea retaining Caulastraea furcata and Caulastraea echinulata. Based on the examination of type material, Erythrastrea flabellata is considered an objective synonym of Lobophyllia wellsi, which is transferred to Oulophyllia following the obtained morpho-molecular results. This work further confirms that an integrated morpho-molecular approach based on a rigorous phylogenetic framework is fundamental for an objective classification that reflects the evolutionary history of scleractinian corals.},

note = {https://doi.org/10.1111/zsc.12481},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN215,

title = {Complex Response of the Chlorarachniophyte Bigelowiella natans to Iron Availability},

author = {E. Kotabova and R. Malych and J. J. Pierella Karlusich and E. Kazamia and M. Eichner and J. Mach and E. Lesuisse and C. Bowler and O. Prasil and R. Sutak},

url = {https://www.ncbi.nlm.nih.gov/pubmed/33563784},

doi = {10.1128/mSystems.00738-20},

issn = {2379-5077 (Print) 

2379-5077 (Linking)},

year  = {2021},

date = {2021-01-01},

journal = {mSystems},

volume = {6},

number = {1},

abstract = {The productivity of the ocean is largely dependent on iron availability, and marine phytoplankton have evolved sophisticated mechanisms to cope with chronically low iron levels in vast regions of the open ocean. By analyzing the metabarcoding data generated from the Tara Oceans expedition, we determined how the global distribution of the model marine chlorarachniophyte Bigelowiella natans varies across regions with different iron concentrations. We performed a comprehensive proteomics analysis of the molecular mechanisms underpinning the adaptation of B. natans to iron scarcity and report on the temporal response of cells to iron enrichment. Our results highlight the role of phytotransferrin in iron homeostasis and indicate the involvement of CREG1 protein in the response to iron availability. Analysis of the Tara Oceans metagenomes and metatranscriptomes also points to a similar role for CREG1, which is found to be widely distributed among marine plankton but to show a strong bias in gene and transcript abundance toward iron-deficient regions. Our analyses allowed us to define a new subfamily of the CobW domain-containing COG0523 putative metal chaperones which are involved in iron metabolism and are restricted to only a few phytoplankton lineages in addition to B. natans At the physiological level, we elucidated the mechanisms allowing a fast recovery of PSII photochemistry after resupply of iron. Collectively, our study demonstrates that B. natans is well adapted to dynamically respond to a changing iron environment and suggests that CREG1 and COG0523 are important components of iron homeostasis in B. natans and other phytoplankton.IMPORTANCE Despite low iron availability in the ocean, marine phytoplankton require considerable amounts of iron for their growth and proliferation. While there is a constantly growing knowledge of iron uptake and its role in the cellular processes of the most abundant marine photosynthetic groups, there are still largely overlooked branches of the eukaryotic tree of life, such as the chlorarachniophytes. In the present work, we focused on the model chlorarachniophyte Bigelowiella natans, integrating physiological and proteomic analyses in culture conditions with the mining of omics data generated by the Tara Oceans expedition. We provide unique insight into the complex responses of B. natans to iron availability, including novel links to iron metabolism conserved in other phytoplankton lineages.},

note = {Kotabova, Eva 

Malych, Ronald 

Pierella Karlusich, Juan Jose 

Kazamia, Elena 

Eichner, Meri 

Mach, Jan 

Lesuisse, Emmanuel 

Bowler, Chris 

Prasil, Ondrej 

Sutak, Robert 

eng 

mSystems. 2021 Feb 9;6(1). pii: 6/1/e00738-20. doi: 10.1128/mSystems.00738-20.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN218,

title = {The Ocean barcode atlas: A web service to explore the biodiversity and biogeography of marine organisms},

author = {C. Vernette and N. Henry and J. Lecubin and C. Vargas and P. Hingamp and M. Lescot},

url = {https://www.ncbi.nlm.nih.gov/pubmed/33434383},

doi = {10.1111/1755-0998.13322},

issn = {1755-0998 (Electronic) 

1755-098X (Linking)},

year  = {2021},

date = {2021-01-01},

journal = {Mol Ecol Resour},

abstract = {The Ocean Barcode Atlas (OBA) is a user friendly web service designed for biologists who wish to explore the biodiversity and biogeography of marine organisms locked in otherwise difficult to mine planetary scale DNA metabarcode data sets. Using just a web browser, a comprehensive picture of the diversity of a taxon or a barcode sequence is visualized graphically on world maps and interactive charts. Interactive results panels allow dynamic threshold adjustments and the display of diversity results in their environmental context measured at the time of sampling (temperature, oxygen, latitude, etc). Ecological analyses such as alpha and beta-diversity plots are produced via publication quality vector graphics representations. Currently, the Ocean Barcode Altas is deployed online with the (i) Tara Oceans eukaryotic 18S-V9 rDNA metabarcodes; (ii) Tara Oceans 16S/18S rRNA mi Tags; and (iii) 16S-V4 V5 metabarcodes collected during the Malaspina-2010 expedition. Additional prokaryotic or eukaryotic plankton barcode data sets will be added upon availability, given they provide the required complement of barcodes (including raw reads to compute barcode abundance) associated with their contextual environmental variables. Ocean Barcode Atlas is a freely-available web service at: http://oba.mio.osupytheas.fr/ocean-atlas/.},

note = {Vernette, Caroline 

Henry, Nicolas 

Lecubin, Julien 

de Vargas, Colomban 

Hingamp, Pascal 

Lescot, Magali 

eng 

ANR-11-BTBR-0008/French Government 'Investissements d'Avenir' programmes OCEANOMICS 

ANR-10-INBS-09-08/FRANCE GENOMIQUE 

ANR-11-INBS-0013/Institut Francais de Bioinformatique (IFB) 

ANR-10-LABX-54/MEMO LIFE 

ANR-11-IDEX-0001-02/PSL* Research University 

ANR-19-CE45-0008/ANR SeqDigger 

England 

Mol Ecol Resour. 2021 Jan 12. doi: 10.1111/1755-0998.13322.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN216,

title = {Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean},

author = {H. Kaneko and R. Blanc-Mathieu and H. Endo and S. Chaffron and T. O. Delmont and M. Gaia and N. Henry and R. Hernandez-Velazquez and C. H. Nguyen and H. Mamitsuka and P. Forterre and O. Jaillon and C. Vargas and M. B. Sullivan and C. A. Suttle and L. Guidi and H. Ogata},

url = {https://www.ncbi.nlm.nih.gov/pubmed/33490910},

doi = {10.1016/j.isci.2020.102002},

issn = {2589-0042 (Electronic) 

2589-0042 (Linking)},

year  = {2021},

date = {2021-01-01},

journal = {iScience},

volume = {24},

number = {1},

pages = {102002},

abstract = {The biological carbon pump, in which carbon fixed by photosynthesis is exported to the deep ocean through sinking, is a major process in Earth's carbon cycle. The proportion of primary production that is exported is termed the carbon export efficiency (CEE). Based on in-lab or regional scale observations, viruses were previously suggested to affect the CEE (i.e., viral "shunt" and "shuttle"). In this study, we tested associations between viral community composition and CEE measured at a global scale. A regression model based on relative abundance of viral marker genes explained 67% of the variation in CEE. Viruses with high importance in the model were predicted to infect ecologically important hosts. These results are consistent with the view that the viral shunt and shuttle functions at a large scale and further imply that viruses likely act in this process in a way dependent on their hosts and ecosystem dynamics.},

note = {Kaneko, Hiroto 

Blanc-Mathieu, Romain 

Endo, Hisashi 

Chaffron, Samuel 

Delmont, Tom O 

Gaia, Morgan 

Henry, Nicolas 

Hernandez-Velazquez, Rodrigo 

Nguyen, Canh Hao 

Mamitsuka, Hiroshi 

Forterre, Patrick 

Jaillon, Olivier 

de Vargas, Colomban 

Sullivan, Matthew B 

Suttle, Curtis A 

Guidi, Lionel 

Ogata, Hiroyuki 

eng 

iScience. 2020 Dec 29;24(1):102002. doi: 10.1016/j.isci.2020.102002. eCollection 2021 Jan 22.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN249,

title = {Exploration of marine phytoplankton: From their historical appreciation to the omics era},

author = {Juan José Pierella Karlusich and Federico Ibarbalz and Chris Bowler},

doi = {10.1093/plankt/fbaa049},

year  = {2020},

date = {2020-01-01},

journal = {Journal of Plankton Research},

volume = {42},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN181,

title = {Biogeography of marine giant viruses reveals their interplay with eukaryotes and ecological functions},

author = {H. Endo and R. Blanc-Mathieu and Y. Li and G. Salazar and N. Henry and K. Labadie and C. Vargas and M. B. Sullivan and C. Bowler and P. Wincker and L. Karp-Boss and S. Sunagawa and H. Ogata},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32895519},

doi = {10.1038/s41559-020-01288-w},

issn = {2397-334X (Electronic) 

2397-334X (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Nat Ecol Evol},

volume = {4},

number = {12},

pages = {1639-1649},

abstract = {Nucleocytoplasmic large DNA viruses (NCLDVs) are ubiquitous in marine environments and infect diverse eukaryotes. However, little is known about their biogeography and ecology in the ocean. By leveraging the Tara Oceans pole-to-pole metagenomic data set, we investigated the distribution of NCLDVs across size fractions, depths and biomes, as well as their associations with eukaryotic communities. Our analyses reveal a heterogeneous distribution of NCLDVs across oceans, and a higher proportion of unique NCLDVs in the polar biomes. The community structures of NCLDV families correlate with specific eukaryotic lineages, including many photosynthetic groups. NCLDV communities are generally distinct between surface and mesopelagic zones, but at some locations they exhibit a high similarity between the two depths. This vertical similarity correlates to surface phytoplankton biomass but not to physical mixing processes, which suggests a potential role of vertical transport in structuring mesopelagic NCLDV communities. These results underscore the importance of the interactions between NCLDVs and eukaryotes in biogeochemical processes in the ocean.},

note = {Endo, Hisashi 

Blanc-Mathieu, Romain 

Li, Yanze 

Salazar, Guillem 

Henry, Nicolas 

Labadie, Karine 

de Vargas, Colomban 

Sullivan, Matthew B 

Bowler, Chris 

Wincker, Patrick 

Karp-Boss, Lee 

Sunagawa, Shinichi 

Ogata, Hiroyuki 

eng 

Research Support, Non-U.S. Gov't 

England 

Nat Ecol Evol. 2020 Dec;4(12):1639-1649. doi: 10.1038/s41559-020-01288-w. Epub 2020 Sep 7.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN209,

title = {Diversity and distribution of marine heterotrophic bacteria from a large culture collection},

author = {I. Sanz-Saez and G. Salazar and P. Sanchez and E. Lara and M. Royo-Llonch and E. L. Sa and T. Lucena and M. J. Pujalte and D. Vaque and C. M. Duarte and J. M. Gasol and C. Pedros-Alio and O. Sanchez and S. G. Acinas},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32660423},

doi = {10.1186/s12866-020-01884-7},

issn = {1471-2180 (Electronic) 

1471-2180 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {BMC Microbiol},

volume = {20},

number = {1},

pages = {207},

abstract = {BACKGROUND: Isolation of marine microorganisms is fundamental to gather information about their physiology, ecology and genomic content. To date, most of the bacterial isolation efforts have focused on the photic ocean leaving the deep ocean less explored. We have created a marine culture collection of heterotrophic bacteria (MARINHET) using a standard marine medium comprising a total of 1561 bacterial strains, and covering a variety of oceanographic regions from different seasons and years, from 2009 to 2015. Specifically, our marine collection contains isolates from both photic (817) and aphotic layers (744), including the mesopelagic (362) and the bathypelagic (382), from the North Western Mediterranean Sea, the North and South Atlantic Ocean, the Indian, the Pacific, and the Arctic Oceans. We described the taxonomy, the phylogenetic diversity and the biogeography of a fraction of the marine culturable microorganisms to enhance our knowledge about which heterotrophic marine isolates are recurrently retrieved across oceans and along different depths. RESULTS: The partial sequencing of the 16S rRNA gene of all isolates revealed that they mainly affiliate with the classes Alphaproteobacteria (35.9%), Gammaproteobacteria (38.6%), and phylum Bacteroidetes (16.5%). In addition, Alteromonas and Erythrobacter genera were found the most common heterotrophic bacteria in the ocean growing in solid agar medium. When comparing all photic, mesopelagic, and bathypelagic isolates sequences retrieved from different stations, 37% of them were 100% identical. This percentage increased up to 59% when mesopelagic and bathypelagic strains were grouped as the aphotic dataset and compared to the photic dataset of isolates, indicating the ubiquity of some bacterial isolates along different ocean depths. Finally, we isolated three strains that represent a new species, and the genome comparison and phenotypic characterization of two of these strains (ISS653 and ISS1889) concluded that they belong to a new species within the genus Mesonia. CONCLUSIONS: Overall, this study highlights the relevance of culture-dependent studies, with focus on marine isolated bacteria from different oceanographic regions and depths, to provide a more comprehensive view of the culturable marine bacteria as part of the total marine microbial diversity.},

note = {Sanz-Saez, Isabel 

Salazar, Guillem 

Sanchez, Pablo 

Lara, Elena 

Royo-Llonch, Marta 

Sa, Elisabet L 

Lucena, Teresa 

Pujalte, Maria J 

Vaque, Dolors 

Duarte, Carlos M 

Gasol, Josep M 

Pedros-Alio, Carlos 

Sanchez, Olga 

Acinas, Silvia G 

eng 

CSD2008-00077/Ministerio de Ciencia, Innovacion y Universidades/International 

CTM2017-87736-R/Ministerio de Ciencia, Innovacion y Universidades/International 

BIOSENSOMICS/Fundacion BBVA/International 

OSR-2014-CC-1973-02/King Abdullah University of Science and Technology/International 

CTM2015-70340-R/Ministerio de Economia y Competitividad/International 

#226248/FP7 Ideas: European Research Council/International 

CTM2012-34294/Ministerio de Economia, Industria y Competitividad, Gobierno de Espana/International 

RTI2018-101025-B-I00/Ministerio de Economia, Industria y Competitividad, Gobierno de Espana/International 

Research Support, Non-U.S. Gov't 

England 

BMC Microbiol. 2020 Jul 13;20(1):207. doi: 10.1186/s12866-020-01884-7.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN182,

title = {Investigating population-scale allelic differential expression in wild populations of Oithona similis (Cyclopoida, Claus, 1866)},

author = {R. Laso-Jadart and K. Sugier and E. Petit and K. Labadie and P. Peterlongo and C. Ambroise and P. Wincker and J. L. Jamet and M. A. Madoui},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32884665},

doi = {10.1002/ece3.6588},

issn = {2045-7758 (Print) 

2045-7758 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Ecol Evol},

volume = {10},

number = {16},

pages = {8894-8905},

abstract = {Acclimation allowed by variation in gene or allele expression in natural populations is increasingly understood as a decisive mechanism, as much as adaptation, for species evolution. However, for small eukaryotic organisms, as species from zooplankton, classical methods face numerous challenges. Here, we propose the concept of allelic differential expression at the population-scale (psADE) to investigate the variation in allele expression in natural populations. We developed a novel approach to detect psADE based on metagenomic and metatranscriptomic data from environmental samples. This approach was applied on the widespread marine copepod, Oithona similis, by combining samples collected during the Tara Oceans expedition (2009-2013) and de novo transcriptome assemblies. Among a total of 25,768 single nucleotide variants (SNVs) of O. similis, 572 (2.2%) were affected by psADE in at least one population (FDR < 0.05). The distribution of SNVs under psADE in different populations is significantly shaped by population genomic differentiation (Pearson r = 0.87},

note = {Laso-Jadart, Romuald 

Sugier, Kevin 

Petit, Emmanuelle 

Labadie, Karine 

Peterlongo, Pierre 

Ambroise, Christophe 

Wincker, Patrick 

Jamet, Jean-Louis 

Madoui, Mohammed-Amin 

eng 

England 

Ecol Evol. 2020 Aug 4;10(16):8894-8905. doi: 10.1002/ece3.6588. eCollection 2020 Aug.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN186,

title = {Mesonia oceanica sp. nov., isolated from oceans during the Tara oceans expedition, with a preference for mesopelagic waters},

author = {T. Lucena and I. Sanz-Saez and D. R. Arahal and S. G. Acinas and O. Sanchez and C. Pedros-Alio and R. Aznar and M. J. Pujalte},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32589567},

doi = {10.1099/ijsem.0.004296},

issn = {1466-5034 (Electronic) 

1466-5026 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Int J Syst Evol Microbiol},

volume = {70},

number = {7},

pages = {4329-4338},

abstract = {Strain ISS653(T), isolated from Atlantic seawater, is a yellow pigmented, non-motile, Gram-reaction-negative rod-shaped bacterium, strictly aerobic and chemoorganotrophic, slightly halophilic (1-15 % NaCl) and mesophilic (4-37 degrees C), oxidase- and catalase-positive and proteolytic. Its major cellular fatty acids are iso-C15 : 0, iso-C15 : 0 2-OH, and iso-C17 : 0 3-OH; the major identified phospholipid is phosphatidylethanolamine and the major respiratory quinone is MK6. Genome size is 4.28 Mbp and DNA G+C content is 34.9 mol%. 16S rRNA gene sequence similarity places the strain among members of the family Flavobacteriaceae, with the type strains of Mesonia phycicola (93.2 %), Salegentibacter mishustinae (93.1 %) and Mesonia mobilis (92.9 %) as closest relatives. Average amino acid identity (AAI) and average nucleotide identity (ANI) indices show highest values with M. mobilis (81 % AAI; 78.9 % ANI), M. phycicola (76 % AAI; 76.3 % ANI), Mesonia maritima (72 % AAI, 74.9 % ANI), Mesonia hippocampi (64 % AAI, 70.8 % ANI) and Mesonia algae (68 % AAI; 72.2 % ANI). Phylogenomic analysis using the Up-to-date-Bacterial Core Gene set (UBCG) merges strain ISS653(T) in a clade with species of the genus Mesonia. We conclude that strain ISS653(T) represents a novel species of the genus Mesonia for which we propose the name Mesonia oceanica sp. nov., and strain ISS653(T) (=CECT 9532(T)=LMG 31236(T)) as the type strain. A second strain of the species, ISS1889 (=CECT 30008) was isolated from Pacific Ocean seawater. Data obtained throughout the Tara oceans expedition indicate that the species is more abundant in the mesopelagic dark ocean than in the photic layer and it is more frequent in the South Pacific, Indian and North Atlantic oceans.},

note = {Lucena, Teresa 

Sanz-Saez, Isabel 

Arahal, David R 

Acinas, Silvia G 

Sanchez, Olga 

Pedros-Alio, Carlos 

Aznar, Rosa 

Pujalte, Maria J 

eng 

England 

Int J Syst Evol Microbiol. 2020 Jul;70(7):4329-4338. doi: 10.1099/ijsem.0.004296.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN195,

title = {Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics},

author = {A. Vorobev and M. Dupouy and Q. Carradec and T. O. Delmont and A. Annamale and P. Wincker and E. Pelletier},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32205368},

doi = {10.1101/gr.253070.119},

issn = {1549-5469 (Electronic) 

1088-9051 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Genome Res},

volume = {30},

number = {4},

pages = {647-659},

abstract = {Large-scale metagenomic and metatranscriptomic data analyses are often restricted by their gene-centric approach, limiting the ability to understand organismal and community biology. De novo assembly of large and mosaic eukaryotic genomes from complex meta-omics data remains a challenging task, especially in comparison with more straightforward bacterial and archaeal systems. Here, we use a transcriptome reconstruction method based on clustering co-abundant genes across a series of metagenomic samples. We investigated the co-abundance patterns of approximately 37 million eukaryotic unigenes across 365 metagenomic samples collected during the Tara Oceans expeditions to assess the diversity and functional profiles of marine plankton. We identified approximately 12,000 co-abundant gene groups (CAGs), encompassing approximately 7 million unigenes, including 924 metagenomics-based transcriptomes (MGTs, CAGs larger than 500 unigenes). We demonstrated the biological validity of the MGT collection by comparing individual MGTs with available references. We identified several key eukaryotic organisms involved in dimethylsulfoniopropionate (DMSP) biosynthesis and catabolism in different oceanic provinces, thus demonstrating the potential of the MGT collection to provide functional insights on eukaryotic plankton. We established the ability of the MGT approach to capture interspecies associations through the analysis of a nitrogen-fixing haptophyte-cyanobacterial symbiotic association. This MGT collection provides a valuable resource for analyses of eukaryotic plankton in the open ocean by giving access to the genomic content and functional potential of many ecologically relevant eukaryotic species.},

note = {Vorobev, Alexey 

Dupouy, Marion 

Carradec, Quentin 

Delmont, Tom O 

Annamale, Anita 

Wincker, Patrick 

Pelletier, Eric 

eng 

Research Support, Non-U.S. Gov't 

Genome Res. 2020 Apr;30(4):647-659. doi: 10.1101/gr.253070.119. Epub 2020 Mar 23.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN248,

title = {Towards a rigorous species delimitation framework for scleractinian corals based on RAD sequencing: the case study of Leptastrea from the Indo-Pacific},

author = {Roberto Arrigoni and Michael Berumen and Kiruthiga Mariappan and Pieter Beck and Ann Hulver and Simone Montano and Michel Pichon and Giovanni Strona and Tullia Isotta Terraneo and Francesca Benzoni},

doi = {10.1007/s00338-020-01924-8},

year  = {2020},

date = {2020-01-01},

journal = {Coral Reefs},

volume = {39},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN198,

title = {Diatoms Are Selective Segregators in Global Ocean Planktonic Communities},

author = {F. Vincent and C. Bowler},

url = {https://www.ncbi.nlm.nih.gov/pubmed/31964765},

doi = {10.1128/mSystems.00444-19},

issn = {2379-5077 (Print) 

2379-5077 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {mSystems},

volume = {5},

number = {1},

abstract = {Diatoms are a major component of phytoplankton, believed to be responsible for around 20% of the annual primary production on Earth. As abundant and ubiquitous organisms, they are known to establish biotic interactions with many other members of plankton. Through analyses of cooccurrence networks derived from the Tara Oceans expedition that take into account both biotic and abiotic factors in shaping the spatial distributions of species, we show that only 13% of diatom pairwise associations are driven by environmental conditions; the vast majority are independent of abiotic factors. In contrast to most other plankton groups, on a global scale, diatoms display a much higher proportion of negative correlations with other organisms, particularly toward potential predators and parasites, suggesting that their biogeography is constrained by top-down pressure. Genus-level analyses indicate that abundant diatoms are not necessarily the most connected and that species-specific abundance distribution patterns lead to negative associations with other organisms. In order to move forward in the biological interpretation of cooccurrence networks, an open-access extensive literature survey of diatom biotic interactions was compiled, of which 18.5% were recovered in the computed network. This result reveals the extent of what likely remains to be discovered in the field of planktonic biotic interactions, even for one of the best-known organismal groups.IMPORTANCE Diatoms are key phytoplankton in the modern ocean that are involved in numerous biotic interactions, ranging from symbiosis to predation and viral infection, which have considerable effects on global biogeochemical cycles. However, despite recent large-scale studies of plankton, we are still lacking a comprehensive picture of the diversity of diatom biotic interactions in the marine microbial community. Through the ecological interpretation of both inferred microbial association networks and available knowledge on diatom interactions compiled in an open-access database, we propose an ecosystems approach for exploring diatom interactions in the ocean.},

note = {Vincent, Flora 

Bowler, Chris 

eng 

mSystems. 2020 Jan 21;5(1). pii: 5/1/e00444-19. doi: 10.1128/mSystems.00444-19.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN208,

title = {Diversity and evolution of bacterial bioluminescence genes in the global ocean},

author = {T. Vannier and P. Hingamp and F. Turrel and L. Tanet and M. Lescot and Y. Timsit},

url = {https://www.ncbi.nlm.nih.gov/pubmed/33575578},

doi = {10.1093/nargab/lqaa018},

issn = {2631-9268 (Electronic) 

2631-9268 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {NAR Genom Bioinform},

volume = {2},

number = {2},

pages = {lqaa018},

abstract = {Although bioluminescent bacteria are the most abundant and widely distributed of all light-emitting organisms, the biological role and evolutionary history of bacterial luminescence are still shrouded in mystery. Bioluminescence has so far been observed in the genomes of three families of Gammaproteobacteria in the form of canonical lux operons that adopt the CDAB(F)E(G) gene order. LuxA and luxB encode the two subunits of bacterial luciferase responsible for light-emission. Our deep exploration of public marine environmental databases considerably expands this view by providing a catalog of new lux homolog sequences, including 401 previously unknown luciferase-related genes. It also reveals a broader diversity of the lux operon organization, which we observed in previously undescribed configurations such as CEDA, CAED and AxxCE. This expanded operon diversity provides clues for deciphering lux operon evolution and propagation within the bacterial domain. Leveraging quantitative tracking of marine bacterial genes afforded by planetary scale metagenomic sampling, our study also reveals that the novel lux genes and operons described herein are more abundant in the global ocean than the canonical CDAB(F)E(G) operon.},

note = {Vannier, Thomas 

Hingamp, Pascal 

Turrel, Floriane 

Tanet, Lisa 

Lescot, Magali 

Timsit, Youri 

eng 

England 

NAR Genom Bioinform. 2020 Mar 14;2(2):lqaa018. doi: 10.1093/nargab/lqaa018. eCollection 2020 Jun.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN190,

title = {Tara Oceans: towards global ocean ecosystems biology},

author = {S. Sunagawa and S. G. Acinas and P. Bork and C. Bowler and Coordinators Tara Oceans and D. Eveillard and G. Gorsky and L. Guidi and D. Iudicone and E. Karsenti and F. Lombard and H. Ogata and S. Pesant and M. B. Sullivan and P. Wincker and C. Vargas},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32398798},

doi = {10.1038/s41579-020-0364-5},

issn = {1740-1534 (Electronic) 

1740-1526 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Nat Rev Microbiol},

volume = {18},

number = {8},

pages = {428-445},

abstract = {A planetary-scale understanding of the ocean ecosystem, particularly in light of climate change, is crucial. Here, we review the work of Tara Oceans, an international, multidisciplinary project to assess the complexity of ocean life across comprehensive taxonomic and spatial scales. Using a modified sailing boat, the team sampled plankton at 210 globally distributed sites at depths down to 1,000 m. We describe publicly available resources of molecular, morphological and environmental data, and discuss how an ecosystems biology approach has expanded our understanding of plankton diversity and ecology in the ocean as a planetary, interconnected ecosystem. These efforts illustrate how global-scale concepts and data can help to integrate biological complexity into models and serve as a baseline for assessing ecosystem changes and the future habitability of our planet in the Anthropocene epoch.},

note = {Sunagawa, Shinichi 

Acinas, Silvia G 

Bork, Peer 

Bowler, Chris 

Eveillard, Damien 

Gorsky, Gabriel 

Guidi, Lionel 

Iudicone, Daniele 

Karsenti, Eric 

Lombard, Fabien 

Ogata, Hiroyuki 

Pesant, Stephane 

Sullivan, Matthew B 

Wincker, Patrick 

de Vargas, Colomban 

eng 

Research Support, Non-U.S. Gov't 

Research Support, U.S. Gov't, Non-P.H.S. 

Review 

England 

Nat Rev Microbiol. 2020 Aug;18(8):428-445. doi: 10.1038/s41579-020-0364-5. Epub 2020 May 12.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN173,

title = {Genome Resolved Biogeography of Mamiellales},

author = {J. Leconte and L. F. Benites and T. Vannier and P. Wincker and G. Piganeau and O. Jaillon},

url = {https://www.ncbi.nlm.nih.gov/pubmed/31936086},

doi = {10.3390/genes11010066},

issn = {2073-4425 (Electronic) 

2073-4425 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Genes (Basel)},

volume = {11},

number = {1},

abstract = {Among marine phytoplankton, Mamiellales encompass several species from the genera Micromonas, Ostreococcus and Bathycoccus, which are important contributors to primary production. Previous studies based on single gene markers described their wide geographical distribution but led to discussion because of the uneven taxonomic resolution of the method. Here, we leverage genome sequences for six Mamiellales species, two from each genus Micromonas, Ostreococcus and Bathycoccus, to investigate their distribution across 133 stations sampled during the Tara Oceans expedition. Our study confirms the cosmopolitan distribution of Mamiellales and further suggests non-random distribution of species, with two triplets of co-occurring genomes associated with different temperatures: Ostreococcus lucimarinus, Bathycoccus prasinos and Micromonas pusilla were found in colder waters, whereas Ostreococcus spp. RCC809, Bathycoccus spp. TOSAG39-1 and Micromonas commoda were more abundant in warmer conditions. We also report the distribution of the two candidate mating-types of Ostreococcus for which the frequency of sexual reproduction was previously assumed to be very low. Indeed, both mating types were systematically detected together in agreement with either frequent sexual reproduction or the high prevalence of a diploid stage. Altogether, these analyses provide novel insights into Mamiellales' biogeography and raise novel testable hypotheses about their life cycle and ecology.},

note = {Leconte, Jade 

Benites, L Felipe 

Vannier, Thomas 

Wincker, Patrick 

Piganeau, Gwenael 

Jaillon, Olivier 

eng 

Research Support, Non-U.S. Gov't 

Switzerland 

Genes (Basel). 2020 Jan 7;11(1). pii: genes11010066. doi: 10.3390/genes11010066.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN204,

title = {Into the bloom: Molecular response of pelagic tunicates to fluctuating food availability},

author = {P. Sordino and S. D'Aniello and E. Pelletier and P. Wincker and V. Nittoli and L. Stemmann and M. G. Mazzocchi and F. Lombard and D. Iudicone and L. Caputi},

url = {https://www.ncbi.nlm.nih.gov/pubmed/31793138},

doi = {10.1111/mec.15321},

issn = {1365-294X (Electronic) 

0962-1083 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Mol Ecol},

volume = {29},

number = {2},

pages = {292-307},

abstract = {The planktonic tunicates appendicularians and thaliaceans are highly efficient filter feeders on a wide range of prey size including bacteria and have shorter generation times than any other marine grazers. These traits allow some tunicate species to reach high population densities and ensure their success in a favourable environment. However, there are still few studies focusing on which genes and gene pathways are associated with responses of pelagic tunicates to environmental variability. Herein, we present the effect of food availability increase on tunicate community and gene expression at the Marquesas Islands (South-East Pacific Ocean). By using data from the Tara Oceans expedition, we show that changes in phytoplankton density and composition trigger the success of a dominant larvacean species (an undescribed appendicularian). Transcriptional signature to the autotroph bloom suggests key functions in specific physiological processes, i.e., energy metabolism, muscle contraction, membrane trafficking, and proteostasis. The relative abundance of reverse transcription-related Pfams was lower at bloom conditions, suggesting a link with adaptive genetic diversity in tunicates in natural ecosystems. Downstream of the bloom, pelagic tunicates were outcompeted by copepods. Our work represents the first metaomics study of the biological effects of phytoplankton bloom on a key zooplankton taxon.},

note = {Sordino, Paolo 

D'Aniello, Salvatore 

Pelletier, Eric 

Wincker, Patrick 

Nittoli, Valeria 

Stemmann, Lars 

Mazzocchi, Maria Grazia 

Lombard, Fabien 

Iudicone, Daniele 

Caputi, Luigi 

eng 

England 

Mol Ecol. 2020 Jan;29(2):292-307. doi: 10.1111/mec.15321. Epub 2019 Dec 18.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN203,

title = {Ecological and functional capabilities of an uncultured Kordia sp},

author = {M. Royo-Llonch and P. Sanchez and J. M. Gonzalez and C. Pedros-Alio and S. G. Acinas},

url = {https://www.ncbi.nlm.nih.gov/pubmed/31831198},

doi = {10.1016/j.syapm.2019.126045},

issn = {1618-0984 (Electronic) 

0723-2020 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Syst Appl Microbiol},

volume = {43},

number = {1},

pages = {126045},

abstract = {Cultivable bacteria represent only a fraction of the diversity in microbial communities. However, the official procedures for classification and characterization of a novel prokaryotic species still rely on isolates. Nevertheless, due to single cell genomics, it is possible to retrieve genomes from environmental samples by sequencing them individually, and to assign specific genes to a specific taxon, regardless of their ability to grow in culture. In this study, a complete description was performed for uncultured Kordia sp. TARA_039_SRF, a proposed novel species within the genus Kordia, using culture-independent techniques. The type material was a high-quality draft genome (94.97% complete, 4.65% gene redundancy) co-assembled using ten nearly identical single amplified genomes (SAGs) from surface seawater in the North Indian Ocean during the Tara Oceans Expedition. The assembly process was optimized to obtain the best possible assembly metrics and a less fragmented genome. The closest relative of the species was Kordia periserrulae, which shared 97.56% similarity of the 16S rRNA gene, 75% orthologs and 89.13% average nucleotide identity. The functional potential of the proposed novel species included proteorhodopsin, the ability to incorporate nitrate, cytochrome oxidases with high affinity for oxygen, and CAZymes that were unique features within the genus. Its abundance at different depths and size fractions was also evaluated together with its functional annotation, revealing that its putative ecological niche could be particles of phytoplanktonic origin. It could putatively attach to these particles and consume them while sinking to the deeper and oxygen depleted layers of the North Indian Ocean.},

note = {Royo-Llonch, M 

Sanchez, P 

Gonzalez, J M 

Pedros-Alio, C 

Acinas, S G 

eng 

Germany 

Syst Appl Microbiol. 2020 Jan;43(1):126045. doi: 10.1016/j.syapm.2019.126045. Epub 2019 Nov 22.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN243,

title = {Phytoplankton in the Tara Ocean},

author = {Juan José Pierella Karlusich and Federico Ibarbalz and Chris Bowler},

doi = {10.1146/annurev-marine-010419-010706},

year  = {2020},

date = {2020-01-01},

journal = {Annual Review of Marine Science},

volume = {12},

pages = {233-265},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN244,

title = {Observational Needs Supporting Marine Ecosystems Modeling and Forecasting: From the Global Ocean to Regional and Coastal Systems},

author = {Antonietta Capotondi and Michael Jacox and Chris Bowler and Maria Kavanaugh and Patrick Lehodey and Daniel Barrie and Stephanie Brodie and Samuel Chaffron and Wei Cheng and Daniela F. Dias and Damien Eveillard and Lionel Guidi and Daniele Iudicone and Nicole S. Lovenduski and Janet A. Nye and Ivonne Ortiz and Douglas Pirhalla and Mercedes Pozo Buil and Vincent Saba and Scott Sheridan and Samantha Siedlecki and Aneesh Subramanian and Colomban Vargas and Emanuele Di Lorenzo and Scott C. Doney and Albert J. Hermann and Terrence Joyce and Mark Merrifield and Arthur J. Miller and Fabrice Not and Stephane Pesant},

url = {https://www.frontiersin.org/article/10.3389/fmars.2019.00623},

doi = {10.3389/fmars.2019.00623},

issn = {2296-7745},

year  = {2019},

date = {2019-01-01},

journal = {Frontiers in Marine Science},

volume = {6},

number = {623},

abstract = {Many coastal areas host rich marine ecosystems and are also centers of economic activities, including fishing, shipping and recreation. Due to the socioeconomic and ecological importance of these areas, predicting relevant indicators of the ecosystem state on sub-seasonal to interannual timescales is gaining increasing attention. Depending on the application, forecasts may be sought for variables and indicators spanning physics (e.g., sea level, temperature, currents), chemistry (e.g., nutrients, oxygen, pH), and biology (from viruses to top predators). Many components of the marine ecosystem are known to be influenced by leading modes of climate variability, which provide a physical basis for predictability. However, prediction capabilities remain limited by the lack of a clear understanding of the physical and biological processes involved, as well as by insufficient observations for forecast initialization and verification. The situation is further complicated by the influence of climate change on ocean conditions along coastal areas, including sea level rise, increased stratification, and shoaling of oxygen minimum zones. Observations are thus vital to all aspects of marine forecasting: statistical and/or dynamical model development, forecast initialization, and forecast validation, each of which has different observational requirements, which may be also specific to the study region. Here, we use examples from United States (U.S.) coastal applications to identify and describe the key requirements for an observational network that is needed to facilitate improved process understanding, as well as for sustaining operational ecosystem forecasting. We also describe new holistic observational approaches, e.g., approaches based on acoustics, inspired by Tara Oceans or by landscape ecology, which have the potential to support and expand ecosystem modeling and forecasting activities by bridging global and local observations.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN130,

title = {Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome},

author = {G. Salazar and L. Paoli and A. Alberti and J. Huerta-Cepas and H. J. Ruscheweyh and M. Cuenca and C. M. Field and L. P. Coelho and C. Cruaud and S. Engelen and A. C. Gregory and K. Labadie and C. Marec and E. Pelletier and M. Royo-Llonch and S. Roux and P. Sanchez and H. Uehara and A. A. Zayed and G. Zeller and M. Carmichael and C. Dimier and J. Ferland and S. Kandels and M. Picheral and S. Pisarev and J. Poulain and Coordinators Tara Oceans and S. G. Acinas and M. Babin and P. Bork and C. Bowler and C. Vargas and L. Guidi and P. Hingamp and D. Iudicone and L. Karp-Boss and E. Karsenti and H. Ogata and S. Pesant and S. Speich and M. B. Sullivan and P. Wincker and S. Sunagawa},

url = {https://www.ncbi.nlm.nih.gov/pubmed/31730850},

doi = {10.1016/j.cell.2019.10.014},

issn = {1097-4172 (Electronic) 

0092-8674 (Linking)},

year  = {2019},

date = {2019-01-01},

journal = {Cell},

volume = {179},

number = {5},

pages = {1068-1083 e21},

abstract = {Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms. VIDEO ABSTRACT.},

note = {Salazar, Guillem 

Paoli, Lucas 

Alberti, Adriana 

Huerta-Cepas, Jaime 

Ruscheweyh, Hans-Joachim 

Cuenca, Miguelangel 

Field, Christopher M 

Coelho, Luis Pedro 

Cruaud, Corinne 

Engelen, Stefan 

Gregory, Ann C 

Labadie, Karine 

Marec, Claudie 

Pelletier, Eric 

Royo-Llonch, Marta 

Roux, Simon 

Sanchez, Pablo 

Uehara, Hideya 

Zayed, Ahmed A 

Zeller, Georg 

Carmichael, Margaux 

Dimier, Celine 

Ferland, Joannie 

Kandels, Stefanie 

Picheral, Marc 

Pisarev, Sergey 

Poulain, Julie 

Acinas, Silvia G 

Babin, Marcel 

Bork, Peer 

Bowler, Chris 

de Vargas, Colomban 

Guidi, Lionel 

Hingamp, Pascal 

Iudicone, Daniele 

Karp-Boss, Lee 

Karsenti, Eric 

Ogata, Hiroyuki 

Pesant, Stephane 

Speich, Sabrina 

Sullivan, Matthew B 

Wincker, Patrick 

Sunagawa, Shinichi 

eng 

Cell. 2019 Nov 14;179(5):1068-1083.e21. doi: 10.1016/j.cell.2019.10.014.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN129,

title = {Global Trends in Marine Plankton Diversity across Kingdoms of Life},

author = {F. M. Ibarbalz and N. Henry and M. C. Brandao and S. Martini and G. Busseni and H. Byrne and L. P. Coelho and H. Endo and J. M. Gasol and A. C. Gregory and F. Mahe and J. Rigonato and M. Royo-Llonch and G. Salazar and I. Sanz-Saez and E. Scalco and D. Soviadan and A. A. Zayed and A. Zingone and K. Labadie and J. Ferland and C. Marec and S. Kandels and M. Picheral and C. Dimier and J. Poulain and S. Pisarev and M. Carmichael and S. Pesant and Coordinators Tara Oceans and M. Babin and E. Boss and D. Iudicone and O. Jaillon and S. G. Acinas and H. Ogata and E. Pelletier and L. Stemmann and M. B. Sullivan and S. Sunagawa and L. Bopp and C. Vargas and L. Karp-Boss and P. Wincker and F. Lombard and C. Bowler and L. Zinger},

url = {https://www.ncbi.nlm.nih.gov/pubmed/31730851},

doi = {10.1016/j.cell.2019.10.008},

issn = {1097-4172 (Electronic) 

0092-8674 (Linking)},

year  = {2019},

date = {2019-01-01},

journal = {Cell},

volume = {179},

number = {5},

pages = {1084-1097 e21},

abstract = {The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus clades using both molecular and imaging data from Tara Oceans. We show a decline of diversity for most planktonic groups toward the poles, mainly driven by decreasing ocean temperatures. Projections into the future suggest that severe warming of the surface ocean by the end of the 21(st) century could lead to tropicalization of the diversity of most planktonic groups in temperate and polar regions. These changes may have multiple consequences for marine ecosystem functioning and services and are expected to be particularly significant in key areas for carbon sequestration, fisheries, and marine conservation. VIDEO ABSTRACT.},

note = {Ibarbalz, Federico M 

Henry, Nicolas 

Brandao, Manoela C 

Martini, Severine 

Busseni, Greta 

Byrne, Hannah 

Coelho, Luis Pedro 

Endo, Hisashi 

Gasol, Josep M 

Gregory, Ann C 

Mahe, Frederic 

Rigonato, Janaina 

Royo-Llonch, Marta 

Salazar, Guillem 

Sanz-Saez, Isabel 

Scalco, Eleonora 

Soviadan, Dodji 

Zayed, Ahmed A 

Zingone, Adriana 

Labadie, Karine 

Ferland, Joannie 

Marec, Claudie 

Kandels, Stefanie 

Picheral, Marc 

Dimier, Celine 

Poulain, Julie 

Pisarev, Sergey 

Carmichael, Margaux 

Pesant, Stephane 

Babin, Marcel 

Boss, Emmanuel 

Iudicone, Daniele 

Jaillon, Olivier 

Acinas, Silvia G 

Ogata, Hiroyuki 

Pelletier, Eric 

Stemmann, Lars 

Sullivan, Matthew B 

Sunagawa, Shinichi 

Bopp, Laurent 

de Vargas, Colomban 

Karp-Boss, Lee 

Wincker, Patrick 

Lombard, Fabien 

Bowler, Chris 

Zinger, Lucie 

eng 

Cell. 2019 Nov 14;179(5):1084-1097.e21. doi: 10.1016/j.cell.2019.10.008.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN140,

title = {Assessing the viral content of uncultured picoeukaryotes in the global-ocean by single cell genomics},

author = {Y. M. Castillo and J. F. Mangot and L. F. Benites and R. Logares and M. Kuronishi and H. Ogata and O. Jaillon and R. Massana and M. Sebastian and D. Vaque},

url = {https://www.ncbi.nlm.nih.gov/pubmed/31448836},

doi = {10.1111/mec.15210},

issn = {1365-294X (Electronic) 

0962-1083 (Linking)},

year  = {2019},

date = {2019-01-01},

journal = {Mol Ecol},

volume = {28},

number = {18},

pages = {4272-4289},

abstract = {Viruses are the most abundant biological entities on Earth and have fundamental ecological roles in controlling microbial communities. Yet, although their diversity is being increasingly explored, little is known about the extent of viral interactions with their protist hosts as most studies are limited to a few cultivated species. Here, we exploit the potential of single-cell genomics to unveil viral associations in 65 individual cells of 11 essentially uncultured stramenopiles lineages sampled during the Tara Oceans expedition. We identified viral signals in 57% of the cells, covering nearly every lineage and with narrow host specificity signal. Only seven out of the 64 detected viruses displayed homologies to known viral sequences. A search for our viral sequences in global ocean metagenomes showed that they were preferentially found at the DCM and within the 0.2-3 microm size fraction. Some of the viral signals were widely distributed, while others geographically constrained. Among the viral signals we detected an endogenous mavirus virophage potentially integrated within the nuclear genome of two distant uncultured stramenopiles. Virophages have been previously reported as a cell's defence mechanism against other viruses, and may therefore play an important ecological role in regulating protist populations. Our results point to single-cell genomics as a powerful tool to investigate viral associations in uncultured protists, suggesting a wide distribution of these relationships, and providing new insights into the global viral diversity.},

note = {Castillo, Yaiza M 

Mangot, Jean-Francois 

Benites, Luiz Felipe 

Logares, Ramiro 

Kuronishi, Megumi 

Ogata, Hiroyuki 

Jaillon, Olivier 

Massana, Ramon 

Sebastian, Marta 

Vaque, Dolors 

eng 

Research Support, Non-U.S. Gov't 

England 

Mol Ecol. 2019 Sep;28(18):4272-4289. doi: 10.1111/mec.15210. Epub 2019 Sep 24.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN136,

title = {Single cell ecogenomics reveals mating types of individual cells and ssDNA viral infections in the smallest photosynthetic eukaryotes},

author = {L. F. Benites and N. Poulton and K. Labadie and M. E. Sieracki and N. Grimsley and G. Piganeau},

url = {https://www.ncbi.nlm.nih.gov/pubmed/31587637},

doi = {10.1098/rstb.2019.0089},

issn = {1471-2970 (Electronic) 

0962-8436 (Linking)},

year  = {2019},

date = {2019-01-01},

journal = {Philos Trans R Soc Lond B Biol Sci},

volume = {374},

number = {1786},

pages = {20190089},

abstract = {Planktonic photosynthetic organisms of the class Mamiellophyceae include the smallest eukaryotes (less than 2 microm), are globally distributed and form the basis of coastal marine ecosystems. Eight complete fully annotated 13-22 Mb genomes from three genera, Ostreococcus, Bathycoccus and Micromonas, are available from previously isolated clonal cultured strains and provide an ideal resource to explore the scope and challenges of analysing single cell amplified genomes (SAGs) isolated from a natural environment. We assembled data from 12 SAGs sampled during the Tara Oceans expedition to gain biological insights about their in situ ecology, which might be lost by isolation and strain culture. Although the assembled nuclear genomes were incomplete, they were large enough to infer the mating types of four Ostreococcus SAGs. The systematic occurrence of sequences from the mitochondria and chloroplast, representing less than 3% of the total cell's DNA, intimates that SAGs provide suitable substrates for detection of non-target sequences, such as those of virions. Analysis of the non-Mamiellophyceae assemblies, following filtering out cross-contaminations during the sequencing process, revealed two novel 1.6 and 1.8 kb circular DNA viruses, and the presence of specific Bacterial and Oomycete sequences suggests that these organisms might co-occur with the Mamiellales. This article is part of a discussion meeting issue 'Single cell ecology'.},

note = {Benites, L Felipe 

Poulton, Nicole 

Labadie, Karine 

Sieracki, Michael E 

Grimsley, Nigel 

Piganeau, Gwenael 

eng 

Research Support, Non-U.S. Gov't 

Research Support, U.S. Gov't, Non-P.H.S. 

England 

Philos Trans R Soc Lond B Biol Sci. 2019 Nov 25;374(1786):20190089. doi: 10.1098/rstb.2019.0089. Epub 2019 Oct 7.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN145,

title = {Meta-omics reveals genetic flexibility of diatom nitrogen transporters in response to environmental changes},

author = {G. Busseni and F. R. J. Vieira and A. Amato and E. Pelletier and J. J. Pierella Karlusich and M. I. Ferrante and P. Wincker and A. Rogato and C. Bowler and R. Sanges and L. Maiorano and M. Chiurazzi and M. R. d'Alcala and L. Caputi and D. Iudicone},

url = {https://www.ncbi.nlm.nih.gov/pubmed/31259367},

doi = {10.1093/molbev/msz157},

issn = {1537-1719 (Electronic) 

0737-4038 (Linking)},

year  = {2019},

date = {2019-01-01},

journal = {Mol Biol Evol},

abstract = {Diatoms (Bacillariophyta), one of the most abundant and diverse groups of marine phytoplankton, respond rapidly to the supply of new nutrients, often out-competing other phytoplankton. Herein, we integrated analyses of the evolution, distribution and expression modulation of two gene families involved in diatom nitrogen uptake (DiAMT1 and DiNRT2), in order to infer the main drivers of divergence in a key functional trait of phytoplankton. Our results suggest that major steps in the evolution of the two gene families reflected key events triggering diatom radiation and diversification. Their expression is modulated in the contemporary ocean by seawater temperature, nitrate and iron concentrations. Moreover, the differences in diversity and expression of these gene families throughout the water column hint at a possible link with bacterial activity. This study represents a proof-of-concept of how a holistic approach may shed light on the functional biology of organisms in their natural environment.},

note = {Busseni, Greta 

Vieira, Fabio Rocha Jimenez 

Amato, Alberto 

Pelletier, Eric 

Pierella Karlusich, Juan J 

Ferrante, Maria I 

Wincker, Patrick 

Rogato, Alessandra 

Bowler, Chris 

Sanges, Remo 

Maiorano, Luigi 

Chiurazzi, Maurizio 

d'Alcala, Maurizio Ribera 

Caputi, Luigi 

Iudicone, Daniele 

eng 

Mol Biol Evol. 2019 Jul 1. pii: 5525704. doi: 10.1093/molbev/msz157.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN143,

title = {The Earth Is Small for "Leviathans": Long Distance Dispersal of Giant Viruses across Aquatic Environments},

author = {Y. Li and H. Endo and Y. Gotoh and H. Watai and N. Ogawa and R. Blanc-Mathieu and T. Yoshida and H. Ogata},

url = {https://www.ncbi.nlm.nih.gov/pubmed/31378760},

doi = {10.1264/jsme2.ME19037},

issn = {1347-4405 (Electronic) 

1342-6311 (Linking)},

year  = {2019},

date = {2019-01-01},

journal = {Microbes Environ},

volume = {34},

number = {3},

pages = {334-339},

abstract = {Giant viruses of 'Megaviridae' have the ability to widely disperse around the globe. We herein examined 'Megaviridae' communities in four distinct aquatic environments (coastal and offshore seawater, brackish water, and hot spring freshwater), which are distantly located from each other (between 74 and 1,765 km), using a meta-barcoding method. We identified between 593 and 3,627 OTUs in each sample. Some OTUs were detected in all five samples tested as well as in many of the Tara Oceans metagenomes, suggesting the existence of viruses of this family in a wide range of habitats and the ability to circulate on the planet.},

note = {Li, Yanze 

Endo, Hisashi 

Gotoh, Yasuhiro 

Watai, Hiroyasu 

Ogawa, Nana 

Blanc-Mathieu, Romain 

Yoshida, Takashi 

Ogata, Hiroyuki 

eng 

Japan 

Microbes Environ. 2019 Sep 25;34(3):334-339. doi: 10.1264/jsme2.ME19037. Epub 2019 Aug 3.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN153,

title = {Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems},

author = {M. E. Sieracki and N. J. Poulton and O. Jaillon and P. Wincker and C. Vargas and L. Rubinat-Ripoll and R. Stepanauskas and R. Logares and R. Massana},

url = {https://www.ncbi.nlm.nih.gov/pubmed/30988337},

doi = {10.1038/s41598-019-42487-1},

issn = {2045-2322 (Electronic) 

2045-2322 (Linking)},

year  = {2019},

date = {2019-01-01},

journal = {Sci Rep},

volume = {9},

number = {1},

pages = {6025},

abstract = {Marine planktonic protists are critical components of ocean ecosystems and are highly diverse. Molecular sequencing methods are being used to describe this diversity and reveal new associations and metabolisms that are important to how these ecosystems function. We describe here the use of the single cell genomics approach to sample and interrogate the diversity of the smaller (pico- and nano-sized) protists from a range of oceanic samples. We created over 900 single amplified genomes (SAGs) from 8 Tara Ocean samples across the Indian Ocean and the Mediterranean Sea. We show that flow cytometric sorting of single cells effectively distinguishes plastidic and aplastidic cell types that agree with our understanding of protist phylogeny. Yields of genomic DNA with PCR-identifiable 18S rRNA gene sequence from single cells was low (15% of aplastidic cell sorts, and 7% of plastidic sorts) and tests with alternate primers and comparisons to metabarcoding did not reveal phylogenetic bias in the major protist groups. There was little evidence of significant bias against or in favor of any phylogenetic group expected or known to be present. The four open ocean stations in the Indian Ocean had similar communities, despite ranging from 14 degrees N to 20 degrees S latitude, and they differed from the Mediterranean station. Single cell genomics of protists suggests that the taxonomic diversity of the dominant taxa found in only several hundreds of microliters of surface seawater is similar to that found in molecular surveys where liters of sample are filtered.},

note = {Sieracki, M E 

Poulton, N J 

Jaillon, O 

Wincker, P 

de Vargas, C 

Rubinat-Ripoll, L 

Stepanauskas, R 

Logares, R 

Massana, R 

eng 

Research Support, Non-U.S. Gov't 

Research Support, U.S. Gov't, Non-P.H.S. 

England 

Sci Rep. 2019 Apr 15;9(1):6025. doi: 10.1038/s41598-019-42487-1.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN150,

title = {Marine DNA Viral Macro- and Microdiversity from Pole to Pole},

author = {A. C. Gregory and A. A. Zayed and N. Conceicao-Neto and B. Temperton and B. Bolduc and A. Alberti and M. Ardyna and K. Arkhipova and M. Carmichael and C. Cruaud and C. Dimier and G. Dominguez-Huerta and J. Ferland and S. Kandels and Y. Liu and C. Marec and S. Pesant and M. Picheral and S. Pisarev and J. Poulain and J. E. Tremblay and D. Vik and Coordinators Tara Oceans and M. Babin and C. Bowler and A. I. Culley and C. Vargas and B. E. Dutilh and D. Iudicone and L. Karp-Boss and S. Roux and S. Sunagawa and P. Wincker and M. B. Sullivan},

url = {https://www.ncbi.nlm.nih.gov/pubmed/31031001},

doi = {10.1016/j.cell.2019.03.040},

issn = {1097-4172 (Electronic) 

0092-8674 (Linking)},

year  = {2019},

date = {2019-01-01},

journal = {Cell},

volume = {177},

number = {5},

pages = {1109-1123 e14},

abstract = {Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow, and metabolic outputs. However, ecosystem-level impacts of viral community diversity remain difficult to assess due to classification issues and few reference genomes. Here, we establish an approximately 12-fold expanded global ocean DNA virome dataset of 195,728 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models.},

note = {Gregory, Ann C 

Zayed, Ahmed A 

Conceicao-Neto, Nadia 

Temperton, Ben 

Bolduc, Ben 

Alberti, Adriana 

Ardyna, Mathieu 

Arkhipova, Ksenia 

Carmichael, Margaux 

Cruaud, Corinne 

Dimier, Celine 

Dominguez-Huerta, Guillermo 

Ferland, Joannie 

Kandels, Stefanie 

Liu, Yunxiao 

Marec, Claudie 

Pesant, Stephane 

Picheral, Marc 

Pisarev, Sergey 

Poulain, Julie 

Tremblay, Jean-Eric 

Vik, Dean 

Babin, Marcel 

Bowler, Chris 

Culley, Alexander I 

de Vargas, Colomban 

Dutilh, Bas E 

Iudicone, Daniele 

Karp-Boss, Lee 

Roux, Simon 

Sunagawa, Shinichi 

Wincker, Patrick 

Sullivan, Matthew B 

eng 

T32 AI112542/AI/NIAID NIH HHS/ 

Research Support, N.I.H., Extramural 

Research Support, Non-U.S. Gov't 

Research Support, U.S. Gov't, Non-P.H.S. 

Cell. 2019 May 16;177(5):1109-1123.e14. doi: 10.1016/j.cell.2019.03.040. Epub 2019 Apr 25.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN242,

title = {Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems},

author = {Luigi Caputi and Quentin Carradec and Damien Eveillard and Amos Kirilovsky and Eric Pelletier and Juan José Pierella Karlusich and Fabio Vieira and Emilie Villar and Samuel Chaffron and Shruti Malviya and Eleonora Scalco and Silvia Acinas and Adriana Alberti and Jean-Marc Aury and Anne-Sophie Benoiston and Alexis Bertrand and Tristan Biard and Lucie Bittner and Martine Boccara and Jean Weissenbach},

doi = {10.1029/2018GB006022},

year  = {2019},

date = {2019-01-01},

journal = {Global Biogeochemical Cycles},

volume = {33},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN125,

title = {Mixotrophic protists display contrasted biogeographies in the global ocean},

author = {E. Faure and F. Not and A. S. Benoiston and K. Labadie and L. Bittner and S. D. Ayata},

url = {https://www.ncbi.nlm.nih.gov/pubmed/30643201},

doi = {10.1038/s41396-018-0340-5},

issn = {1751-7370 (Electronic) 

1751-7362 (Linking)},

year  = {2019},

date = {2019-01-01},

journal = {ISME J},

volume = {13},

number = {4},

pages = {1072-1083},

abstract = {Mixotrophy, or the ability to acquire carbon from both auto- and heterotrophy, is a widespread ecological trait in marine protists. Using a metabarcoding dataset of marine plankton from the global ocean, 318,054 mixotrophic metabarcodes represented by 89,951,866 sequences and belonging to 133 taxonomic lineages were identified and classified into four mixotrophic functional types: constitutive mixotrophs (CM), generalist non-constitutive mixotrophs (GNCM), endo-symbiotic specialist non-constitutive mixotrophs (eSNCM), and plastidic specialist non-constitutive mixotrophs (pSNCM). Mixotrophy appeared ubiquitous, and the distributions of the four mixotypes were analyzed to identify the abiotic factors shaping their biogeographies. Kleptoplastidic mixotrophs (GNCM and pSNCM) were detected in new zones compared to previous morphological studies. Constitutive and non-constitutive mixotrophs had similar ranges of distributions. Most lineages were evenly found in the samples, yet some of them displayed strongly contrasted distributions, both across and within mixotypes. Particularly divergent biogeographies were found within endo-symbiotic mixotrophs, depending on the ability to form colonies or the mode of symbiosis. We showed how metabarcoding can be used in a complementary way with previous morphological observations to study the biogeography of mixotrophic protists and to identify key drivers of their biogeography.},

note = {Faure, Emile 

Not, Fabrice 

Benoiston, Anne-Sophie 

Labadie, Karine 

Bittner, Lucie 

Ayata, Sakina-Dorothee 

eng 

Research Support, Non-U.S. Gov't 

England 

ISME J. 2019 Apr;13(4):1072-1083. doi: 10.1038/s41396-018-0340-5. Epub 2019 Jan 14.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN160,

title = {Discovering millions of plankton genomic markers from the Atlantic Ocean and the Mediterranean Sea},

author = {M. Arif and J. Gauthier and K. Sugier and D. Iudicone and O. Jaillon and P. Wincker and P. Peterlongo and M. A. Madoui},

url = {https://www.ncbi.nlm.nih.gov/pubmed/30575285},

doi = {10.1111/1755-0998.12985},

issn = {1755-0998 (Electronic) 

1755-098X (Linking)},

year  = {2019},

date = {2019-01-01},

journal = {Mol Ecol Resour},

volume = {19},

number = {2},

pages = {526-535},

abstract = {Comparison of the molecular diversity in all plankton populations present in geographically distant water columns may allow for a holistic view of the connectivity, isolation and adaptation of organisms in the marine environment. In this context, a large-scale detection and analysis of genomic variants directly in metagenomic data appeared as a powerful strategy for the identification of genetic structures and genes under natural selection in plankton. Here, we used discosnp++, a reference-free variant caller, to produce genetic variants from large-scale metagenomic data and assessed its accuracy on the copepod Oithona nana in terms of variant calling, allele frequency estimation and population genomic statistics by comparing it to the state-of-the-art method. discosnp ++ produces variants leading to similar conclusions regarding the genetic structure and identification of loci under natural selection. discosnp++ was then applied to 120 metagenomic samples from four size fractions, including prokaryotes, protists and zooplankton sampled from 39 tara Oceans sampling stations located in the Atlantic Ocean and the Mediterranean Sea to produce a new set of marine genomic markers containing more than 19 million of variants. This new genomic resource can be used by the community to relocate these markers on their plankton genomes or transcriptomes of interest. This resource will be updated with new marine expeditions and the increase of metagenomic data (availability: http://bioinformatique.rennes.inria.fr/taravariants/).},

note = {Arif, Majda 

Gauthier, Jeremy 

Sugier, Kevin 

Iudicone, Daniele 

Jaillon, Olivier 

Wincker, Patrick 

Peterlongo, Pierre 

Madoui, Mohammed-Amin 

eng 

ANR-10-INBS-09-08/Agence Nationale de la Recherche 

ANR-11- BTBR-0008/Agence Nationale de la Recherche 

ANR-14-CE23-0001/Agence Nationale de la Recherche 

England 

Mol Ecol Resour. 2019 Mar;19(2):526-535. doi: 10.1111/1755-0998.12985.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN163,

title = {UCYN-A3, a newly characterized open ocean sublineage of the symbiotic N2 -fixing cyanobacterium Candidatus Atelocyanobacterium thalassa},

author = {F. M. Cornejo-Castillo and M. D. C. Munoz-Marin and K. A. Turk-Kubo and M. Royo-Llonch and H. Farnelid and S. G. Acinas and J. P. Zehr},

url = {https://www.ncbi.nlm.nih.gov/pubmed/30255541},

doi = {10.1111/1462-2920.14429},

issn = {1462-2920 (Electronic) 

1462-2912 (Linking)},

year  = {2019},

date = {2019-01-01},

journal = {Environ Microbiol},

volume = {21},

number = {1},

pages = {111-124},

abstract = {The symbiotic unicellular cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A) is one of the most abundant and widespread nitrogen (N2 )-fixing cyanobacteria in the ocean. Although it remains uncultivated, multiple sublineages have been detected based on partial nitrogenase (nifH) gene sequences, including the four most commonly detected sublineages UCYN-A1, UCYN-A2, UCYN-A3 and UCYN-A4. However, very little is known about UCYN-A3 beyond the nifH sequences from nifH gene diversity surveys. In this study, single cell sorting, DNA sequencing, qPCR and CARD-FISH assays revealed discrepancies involving the identification of sublineages, which led to new information on the diversity of the UCYN-A symbiosis. 16S rRNA and nifH gene sequencing on single sorted cells allowed us to identify the 16S rRNA gene of the uncharacterized UCYN-A3 sublineage. We designed new CARD-FISH probes that allowed us to distinguish and observe UCYN-A2 in a coastal location (SIO Pier; San Diego) and UCYN-A3 in an open ocean location (Station ALOHA; Hawaii). Moreover, we reconstructed about 13% of the UCYN-A3 genome from Tara Oceans metagenomic data. Finally, our findings unveil the UCYN-A3 symbiosis in open ocean waters suggesting that the different UCYN-A sublineages are distributed along different size fractions of the plankton defined by the cell-size ranges of their prymnesiophyte hosts.},

note = {Cornejo-Castillo, Francisco M 

Munoz-Marin, Maria Del Carmen 

Turk-Kubo, Kendra A 

Royo-Llonch, Marta 

Farnelid, Hanna 

Acinas, Silvia G 

Zehr, Jonathan P 

eng 

Biosensomics to SGA (Convocatoria 2015 de ayudas Fundacion BBVA a investigadores y creadores culturales)/International 

FPI (BES-2014-068285)/Consejo Superior de Investigaciones Cientificas/International 

493.01/Gordon and Betty Moore Foundation/International 

Marie Curie International Outgoing Fellowship/International 

329108/Simons Collaboration on Ocean Processes and Ecology (SCOPE)/International 

545171/Simons Foundation/International 

Spanish Ministry of Economy, Industry and Competitiveness/International 

VR 637-2013-7502/Svenska Forskningsradet Formas/International 

Research Support, Non-U.S. Gov't 

England 

Environ Microbiol. 2019 Jan;21(1):111-124. doi: 10.1111/1462-2920.14429. Epub 2018 Nov 8.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN241,

title = {Degenerate PCR Primers to Reveal the Diversity of Giant Viruses in Coastal Waters},

author = {Yanze Li and Pascal Hingamp and Hiroyasu Watai and Hisashi Endo and Takashi Yoshida and Hiroyuki Ogata},

doi = {10.3390/v10090496},

year  = {2018},

date = {2018-01-01},

journal = {Viruses},

volume = {10},

pages = {496},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN101,

title = {Clade-specific diversification dynamics of marine diatoms since the Jurassic},

author = {E. Lewitus and L. Bittner and S. Malviya and C. Bowler and H. Morlon},

url = {https://www.ncbi.nlm.nih.gov/pubmed/30349092},

doi = {10.1038/s41559-018-0691-3},

issn = {2397-334X (Electronic) 

2397-334X (Linking)},

year  = {2018},

date = {2018-01-01},

journal = {Nat Ecol Evol},

volume = {2},

number = {11},

pages = {1715-1723},

abstract = {Diatoms are one of the most abundant and diverse groups of phytoplankton and play a major role in marine ecosystems and the Earth's biogeochemical cycles. Here we combine DNA metabarcoding data from the Tara Oceans expedition with palaeoenvironmental data and phylogenetic models of diversification to analyse the diversity dynamics of marine diatoms. We reveal a primary effect of variation in carbon dioxide partial pressure (pCO2) on early diatom diversification, followed by a major burst of diversification in the late Eocene epoch, after which diversification is chiefly affected by sea level, an influx of silica availability and competition with other planktonic groups. Our results demonstrate a remarkable heterogeneity of diversification dynamics across diatoms and suggest that a changing climate will favour some clades at the expense of others.},

note = {Lewitus, Eric 

Bittner, Lucie 

Malviya, Shruti 

Bowler, Chris 

Morlon, Helene 

eng 

294823/European Research Council/International 

616419/European Research Council/International 

Research Support, Non-U.S. Gov't 

England 

Nat Ecol Evol. 2018 Nov;2(11):1715-1723. doi: 10.1038/s41559-018-0691-3. Epub 2018 Oct 22.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN240,

title = {Morphological and genetic divergence between Mediterranean and Caribbean populations of Madracis pharensis (Heller 1868) (Scleractinia, Pocilloporidae): Too much for one species?},

author = {Francesca Benzoni and Roberto Arrigoni and Michael Berumen and Marco Taviani and Pim Bongaerts and Pedro Frade},

doi = {10.11646/zootaxa.4471.3.3},

year  = {2018},

date = {2018-01-01},

journal = {Zootaxa},

volume = {4471},

pages = {473–492},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN99,

title = {Worldwide Occurrence and Activity of the Reef-Building Coral Symbiont Symbiodinium in the Open Ocean},

author = {J. Decelle and Q. Carradec and X. Pochon and N. Henry and S. Romac and F. Mahe and M. Dunthorn and A. Kourlaiev and C. R. Voolstra and P. Wincker and C. Vargas},

url = {https://www.ncbi.nlm.nih.gov/pubmed/30416058},

doi = {10.1016/j.cub.2018.09.024},

issn = {1879-0445 (Electronic) 

0960-9822 (Linking)},

year  = {2018},

date = {2018-01-01},

journal = {Curr Biol},

volume = {28},

number = {22},

pages = {3625-3633 e3},

abstract = {The dinoflagellate microalga Symbiodinium sustains coral reefs, one of the most diverse ecosystems of the biosphere, through mutualistic endosymbioses with a wide diversity of benthic hosts [1]. Despite its ecological and economic importance, the presence of Symbiodinium in open oceanic waters remains unknown, which represents a significant knowledge gap to fully understand the eco-evolutionary trajectory and resilience of endangered Symbiodinium-based symbioses. Here, we document the existence of Symbiodinium (i.e., now the family Symbiodiniaceae [2]) in tropical- and temperate-surface oceans using DNA and RNA metabarcoding of size-fractionated plankton samples collected at 109 stations across the globe. Symbiodinium from clades A and C were, by far, the most prevalent and widely distributed lineages (representing 0.1% of phytoplankton reads), while other lineages (clades B, D, E, F, and G) were present but rare. Concurrent metatranscriptomics analyses using the Tara Oceans gene catalog [3] revealed that Symbiodinium clades A and C were transcriptionally active in the open ocean and expressed core metabolic pathways (e.g., photosynthesis, carbon fixation, glycolysis, and ammonium uptake). Metabarcodes and expressed genes of clades A and C were detected in small and large plankton size fractions, suggesting the existence of a free-living population and a symbiotic lifestyle within planktonic hosts, respectively. However, high-resolution genetic markers and microscopy are required to confirm the life history of oceanic Symbiodinium. Overall, the previously unknown, metabolically active presence of Symbiodinium in oceanic waters opens up new avenues for investigating the potential of this oceanic reservoir to repopulate coral reefs following stress-induced bleaching.},

note = {Decelle, Johan 

Carradec, Quentin 

Pochon, Xavier 

Henry, Nicolas 

Romac, Sarah 

Mahe, Frederic 

Dunthorn, Micah 

Kourlaiev, Artem 

Voolstra, Christian R 

Wincker, Patrick 

de Vargas, Colomban 

eng 

Research Support, Non-U.S. Gov't 

England 

Curr Biol. 2018 Nov 19;28(22):3625-3633.e3. doi: 10.1016/j.cub.2018.09.024. Epub 2018 Nov 8.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN123,

title = {Coral responses to a repeat bleaching event in Mayotte in 2010},

author = {D. O. Obura and L. Bigot and F. Benzoni},

url = {https://www.ncbi.nlm.nih.gov/pubmed/30083452},

doi = {10.7717/peerj.5305},

issn = {2167-8359 (Print) 

2167-8359 (Linking)},

year  = {2018},

date = {2018-01-01},

journal = {PeerJ},

volume = {6},

pages = {e5305},

abstract = {Background: High sea surface temperatures resulted in widespread coral bleaching and mortality in Mayotte Island (northern Mozambique channel, Indian Ocean: 12.1 degrees S, 45.1 degrees E) in April-June 2010. Methods: Twenty three representative coral genera were sampled quantitatively for size class distributions during the peak of the bleaching event to measure its impact. Results: Fifty two percent of coral area was impacted, comprising 19.3% pale, 10.7% bleached, 4.8% partially dead and 17.5% recently dead. Acropora, the dominant genus, was the second most susceptible to bleaching (22%, pale and bleached) and mortality (32%, partially dead and dead), only exceeded by Pocillopora (32% and 47%, respectively). The majority of genera showed intermediate responses, and the least response was shown by Acanthastrea and Leptastrea (6% pale and bleached). A linear increase in bleaching susceptibility was found from small colonies (<2.5 cm, 83% unaffected) to large ones (>80 cm, 33% unaffected), across all genera surveyed. Maximum mortality in 2010 was estimated at 32% of coral area or biomass, compared to half that (16%), by colony abundance. Discussion: Mayotte reefs have displayed a high level of resilience to bleaching events in 1983, 1998 and the 2010 event reported here, and experienced a further bleaching event in 2016. However, prospects for continued resilience are uncertain as multiple threats are increasing: the rate of warming experienced (0.1 degrees C per decade) is some two to three times less than projected warming in coming decades, the interval between severe bleaching events has declined from 16 to 6 years, and evidence of chronic mortality from local human impacts is increasing. The study produced four recommendations for reducing bias when monitoring and assessing coral bleaching: coral colony size should be measured, unaffected colonies should be included in counts, quadrats or belt transects should be used and weighting coefficients in the calculation of indices should be used with caution.},

note = {Obura, David O 

Bigot, Lionel 

Benzoni, Francesca 

eng 

PeerJ. 2018 Aug 2;6:e5305. doi: 10.7717/peerj.5305. eCollection 2018.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN105,

title = {Ubiquitous abundance distribution of non-dominant plankton across the global ocean},

author = {E. Ser-Giacomi and L. Zinger and S. Malviya and C. De Vargas and E. Karsenti and C. Bowler and S. De Monte},

url = {https://www.ncbi.nlm.nih.gov/pubmed/29915345},

doi = {10.1038/s41559-018-0587-2},

issn = {2397-334X (Electronic) 

2397-334X (Linking)},

year  = {2018},

date = {2018-01-01},

journal = {Nat Ecol Evol},

volume = {2},

number = {8},

pages = {1243-1249},

abstract = {Marine plankton populate 70% of Earth's surface, providing the energy that fuels ocean food webs and contributing to global biogeochemical cycles. Plankton communities are extremely diverse and geographically variable, and are overwhelmingly composed of low-abundance species. The role of this rare biosphere and its ecological underpinnings are however still unclear. Here, we analyse the extensive dataset generated by the Tara Oceans expedition for marine microbial eukaryotes (protists) and use an adaptive algorithm to explore how metabarcoding-based abundance distributions vary across plankton communities in the global ocean. We show that the decay in abundance of non-dominant operational taxonomic units, which comprise over 99% of local richness, is commonly governed by a power-law. Despite the high spatial turnover in species composition, the power-law exponent varies by less than 10% across locations and shows no biogeographical signature, but is weakly modulated by cell size. Such striking regularity suggests that the assembly of plankton communities in the dynamic and highly variable ocean environment is governed by large-scale ubiquitous processes. Understanding their origin and impact on plankton ecology will be important for evaluating the resilience of marine biodiversity in a changing ocean.},

note = {Ser-Giacomi, Enrico 

Zinger, Lucie 

Malviya, Shruti 

De Vargas, Colomban 

Karsenti, Eric 

Bowler, Chris 

De Monte, Silvia 

eng 

R25GM067110 /NH/NIH HHS/ 

Research Support, N.I.H., Extramural 

Research Support, Non-U.S. Gov't 

England 

Nat Ecol Evol. 2018 Aug;2(8):1243-1249. doi: 10.1038/s41559-018-0587-2. Epub 2018 Jun 18.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN107,

title = {The Ocean Gene Atlas: exploring the biogeography of plankton genes online},

author = {E. Villar and T. Vannier and C. Vernette and M. Lescot and M. Cuenca and A. Alexandre and P. Bachelerie and T. Rosnet and E. Pelletier and S. Sunagawa and P. Hingamp},

url = {https://www.ncbi.nlm.nih.gov/pubmed/29788376},

doi = {10.1093/nar/gky376},

issn = {1362-4962 (Electronic) 

0305-1048 (Linking)},

year  = {2018},

date = {2018-01-01},

journal = {Nucleic Acids Res},

volume = {46},

number = {W1},

pages = {W289-W295},

abstract = {The Ocean Gene Atlas is a web service to explore the biogeography of genes from marine planktonic organisms. It allows users to query protein or nucleotide sequences against global ocean reference gene catalogs. With just one click, the abundance and location of target sequences are visualized on world maps as well as their taxonomic distribution. Interactive results panels allow for adjusting cutoffs for alignment quality and displaying the abundances of genes in the context of environmental features (temperature, nutrients, etc.) measured at the time of sampling. The ease of use enables non-bioinformaticians to explore quantitative and contextualized information on genes of interest in the global ocean ecosystem. Currently the Ocean Gene Atlas is deployed with (i) the Ocean Microbial Reference Gene Catalog (OM-RGC) comprising 40 million non-redundant mostly prokaryotic gene sequences associated with both Tara Oceans and Global Ocean Sampling (GOS) gene abundances and (ii) the Marine Atlas of Tara Ocean Unigenes (MATOU) composed of >116 million eukaryote unigenes. Additional datasets will be added upon availability of further marine environmental datasets that provide the required complement of sequence assemblies, raw reads and contextual environmental parameters. Ocean Gene Atlas is a freely-available web service at: http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/.},

note = {Villar, Emilie 

Vannier, Thomas 

Vernette, Caroline 

Lescot, Magali 

Cuenca, Miguelangel 

Alexandre, Aurelien 

Bachelerie, Paul 

Rosnet, Thomas 

Pelletier, Eric 

Sunagawa, Shinichi 

Hingamp, Pascal 

eng 

Research Support, Non-U.S. Gov't 

England 

Nucleic Acids Res. 2018 Jul 2;46(W1):W289-W295. doi: 10.1093/nar/gky376.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN108,

title = {Endocytosis-mediated siderophore uptake as a strategy for Fe acquisition in diatoms},

author = {E. Kazamia and R. Sutak and J. Paz-Yepes and R. G. Dorrell and F. R. J. Vieira and J. Mach and J. Morrissey and S. Leon and F. Lam and E. Pelletier and J. M. Camadro and C. Bowler and E. Lesuisse},

url = {https://www.ncbi.nlm.nih.gov/pubmed/29774236},

doi = {10.1126/sciadv.aar4536},

issn = {2375-2548 (Electronic) 

2375-2548 (Linking)},

year  = {2018},

date = {2018-01-01},

journal = {Sci Adv},

volume = {4},

number = {5},

pages = {eaar4536},

abstract = {Phytoplankton growth is limited in vast oceanic regions by the low bioavailability of iron. Iron fertilization often results in diatom blooms, yet the physiological underpinnings for how diatoms survive in chronically iron-limited waters and outcompete other phytoplankton when iron becomes available are unresolved. We show that some diatoms can use siderophore-bound iron, and exhibit a species-specific recognition for siderophore types. In Phaeodactylum tricornutum, hydroxamate siderophores are taken up without previous reduction by a high-affinity mechanism that involves binding to the cell surface followed by endocytosis-mediated uptake and delivery to the chloroplast. The affinity recorded is the highest ever described for an iron transport system in any eukaryotic cell. Collectively, our observations suggest that there are likely a variety of iron uptake mechanisms in diatoms besides the well-established reductive mechanism. We show that iron starvation-induced protein 1 (ISIP1) plays an important role in the uptake of siderophores, and through bioinformatics analyses we deduce that this protein is largely diatom-specific. We quantify expression of ISIP1 in the global ocean by querying the Tara Oceans atlas of eukaryotic genes and show a link between the abundance and distribution of diatom-associated ISIP1 with ocean provinces defined by chronic iron starvation.},

note = {Kazamia, Elena 

Sutak, Robert 

Paz-Yepes, Javier 

Dorrell, Richard G 

Vieira, Fabio Rocha Jimenez 

Mach, Jan 

Morrissey, Joe 

Leon, Sebastien 

Lam, France 

Pelletier, Eric 

Camadro, Jean-Michel 

Bowler, Chris 

Lesuisse, Emmanuel 

eng 

Research Support, Non-U.S. Gov't 

Sci Adv. 2018 May 16;4(5):eaar4536. doi: 10.1126/sciadv.aar4536. eCollection 2018 May.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN239,

title = {Uncovering hidden coral diversity: a new cryptic lobophylliid scleractinian from the Indian Ocean},

author = {Roberto Arrigoni and Michael Berumen and Jarosław Stolarski and Tullia Isotta Terraneo and Francesca Benzoni},

doi = {10.1111/cla.12346},

year  = {2018},

date = {2018-01-01},

journal = {Cladistics},

volume = {35},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN122,

title = {Taxon Richness of "Megaviridae" Exceeds those of Bacteria and Archaea in the Ocean},

author = {T. Mihara and H. Koyano and P. Hingamp and N. Grimsley and S. Goto and H. Ogata},

url = {https://www.ncbi.nlm.nih.gov/pubmed/29806626},

doi = {10.1264/jsme2.ME17203},

issn = {1347-4405 (Electronic) 

1342-6311 (Linking)},

year  = {2018},

date = {2018-01-01},

journal = {Microbes Environ},

volume = {33},

number = {2},

pages = {162-171},

abstract = {Since the discovery of the giant mimivirus, evolutionarily related viruses have been isolated or identified from various environments. Phylogenetic analyses of this group of viruses, tentatively referred to as the family "Megaviridae", suggest that it has an ancient origin that may predate the emergence of major eukaryotic lineages. Environmental genomics has since revealed that Megaviridae represents one of the most abundant and diverse groups of viruses in the ocean. In the present study, we compared the taxon richness and phylogenetic diversity of Megaviridae, Bacteria, and Archaea using DNA-dependent RNA polymerase as a common marker gene. By leveraging existing microbial metagenomic data, we found higher richness and phylogenetic diversity in this single viral family than in the two prokaryotic domains. We also obtained results showing that the evolutionary rate alone cannot account for the observed high diversity of Megaviridae lineages. These results suggest that the Megaviridae family has a deep co-evolutionary history with diverse marine protists since the early "Big-Bang" radiation of the eukaryotic tree of life.},

note = {Mihara, Tomoko 

Koyano, Hitoshi 

Hingamp, Pascal 

Grimsley, Nigel 

Goto, Susumu 

Ogata, Hiroyuki 

eng 

Comparative Study 

Japan 

Microbes Environ. 2018 Jul 4;33(2):162-171. doi: 10.1264/jsme2.ME17203. Epub 2018 May 25.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN111,

title = {Nanoplanktonic diatoms are globally overlooked but play a role in spring blooms and carbon export},

author = {K. Leblanc and B. Queguiner and F. Diaz and V. Cornet and M. Michel-Rodriguez and X. Durrieu de Madron and C. Bowler and S. Malviya and M. Thyssen and G. Gregori and M. Rembauville and O. Grosso and J. Poulain and C. Vargas and M. Pujo-Pay and P. Conan},

url = {https://www.ncbi.nlm.nih.gov/pubmed/29507291},

doi = {10.1038/s41467-018-03376-9},

issn = {2041-1723 (Electronic) 

2041-1723 (Linking)},

year  = {2018},

date = {2018-01-01},

journal = {Nat Commun},

volume = {9},

number = {1},

pages = {953},

abstract = {Diatoms are one of the major primary producers in the ocean, responsible annually for ~20% of photosynthetically fixed CO2 on Earth. In oceanic models, they are typically represented as large (>20 microm) microphytoplankton. However, many diatoms belong to the nanophytoplankton (2-20 microm) and a few species even overlap with the picoplanktonic size-class (<2 microm). Due to their minute size and difficulty of detection they are poorly characterized. Here we describe a massive spring bloom of the smallest known diatom (Minidiscus) in the northwestern Mediterranean Sea. Analysis of Tara Oceans data, together with literature review, reveal a general oversight of the significance of these small diatoms at the global scale. We further evidence that they can reach the seafloor at high sinking rates, implying the need to revise our classical binary vision of pico- and nanoplanktonic cells fueling the microbial loop, while only microphytoplankton sustain secondary trophic levels and carbon export.},

note = {Leblanc, Karine 

Queguiner, Bernard 

Diaz, Frederic 

Cornet, Veronique 

Michel-Rodriguez, Monica 

Durrieu de Madron, Xavier 

Bowler, Chris 

Malviya, Shruti 

Thyssen, Melilotus 

Gregori, Gerald 

Rembauville, Mathieu 

Grosso, Olivier 

Poulain, Julie 

de Vargas, Colomban 

Pujo-Pay, Mireille 

Conan, Pascal 

eng 

287589/European Research Council/International 

Research Support, Non-U.S. Gov't 

England 

Nat Commun. 2018 Mar 5;9(1):953. doi: 10.1038/s41467-018-03376-9.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN238,

title = {Competition between Silicifiers and Non-silicifiers in the Past and Present Ocean and Its Evolutionary Impacts},

author = {Katharine R. Hendry and Alan O. Marron and Flora Vincent and Daniel J. Conley and Marion Gehlen and Federico M. Ibarbalz and Bernard Quéguiner and Chris Bowler},

url = {https://www.frontiersin.org/article/10.3389/fmars.2018.00022},

doi = {10.3389/fmars.2018.00022},

issn = {2296-7745},

year  = {2018},

date = {2018-01-01},

journal = {Frontiers in Marine Science},

volume = {5},

number = {22},

abstract = {Competition is a central part of the evolutionary process, and silicification is no exception: between biomineralized and non-biomineralized organisms, between siliceous and non-siliceous biomineralizing organisms, and between different silicifying groups. Here we discuss evolutionary competition at various scales, and how this has affected biogeochemical cycles of silicon, carbon, and other nutrients. Across geological time we examine how fossils, sediments, and isotopic geochemistry can provide evidence for the emergence and expansion of silica biomineralization in the ocean, and competition between silicifying organisms for silicic acid. Metagenomic data from marine environments can be used to illustrate evolutionary competition between groups of silicifying and non-silicifying marine organisms. Modern ecosystems also provide examples of arms races between silicifiers as predators and prey, and how silicification can be used to provide a competitive advantage for obtaining resources. Through studying the molecular biology of silicifying and non-silicifying species we can relate how they have responded to the competitive interactions that are observed, and how solutions have evolved through convergent evolutionary dynamics.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN112,

title = {Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria},

author = {T. Grebert and H. Dore and F. Partensky and G. K. Farrant and E. S. Boss and M. Picheral and L. Guidi and S. Pesant and D. J. Scanlan and P. Wincker and S. G. Acinas and D. M. Kehoe and L. Garczarek},

url = {https://www.ncbi.nlm.nih.gov/pubmed/29440402},

doi = {10.1073/pnas.1717069115},

issn = {1091-6490 (Electronic) 

0027-8424 (Linking)},

year  = {2018},

date = {2018-01-01},

journal = {Proc Natl Acad Sci U S A},

volume = {115},

number = {9},

pages = {E2010-E2019},

abstract = {Marine Synechococcus cyanobacteria are major contributors to global oceanic primary production and exhibit a unique diversity of photosynthetic pigments, allowing them to exploit a wide range of light niches. However, the relationship between pigment content and niche partitioning has remained largely undetermined due to the lack of a single-genetic marker resolving all pigment types (PTs). Here, we developed and employed a robust method based on three distinct marker genes (cpcBA, mpeBA, and mpeW) to estimate the relative abundance of all known Synechococcus PTs from metagenomes. Analysis of the Tara Oceans dataset allowed us to reveal the global distribution of Synechococcus PTs and to define their environmental niches. Green-light specialists (PT 3a) dominated in warm, green equatorial waters, whereas blue-light specialists (PT 3c) were particularly abundant in oligotrophic areas. Type IV chromatic acclimaters (CA4-A/B), which are able to dynamically modify their light absorption properties to maximally absorb green or blue light, were unexpectedly the most abundant PT in our dataset and predominated at depth and high latitudes. We also identified populations in which CA4 might be nonfunctional due to the lack of specific CA4 genes, notably in warm high-nutrient low-chlorophyll areas. Major ecotypes within clades I-IV and CRD1 were preferentially associated with a particular PT, while others exhibited a wide range of PTs. Altogether, this study provides important insights into the ecology of Synechococcus and highlights the complex interactions between vertical phylogeny, pigmentation, and environmental parameters that shape Synechococcus community structure and evolution.},

note = {Grebert, Theophile 

Dore, Hugo 

Partensky, Frederic 

Farrant, Gregory K 

Boss, Emmanuel S 

Picheral, Marc 

Guidi, Lionel 

Pesant, Stephane 

Scanlan, David J 

Wincker, Patrick 

Acinas, Silvia G 

Kehoe, David M 

Garczarek, Laurence 

eng 

Research Support, Non-U.S. Gov't 

Proc Natl Acad Sci U S A. 2018 Feb 27;115(9):E2010-E2019. doi: 10.1073/pnas.1717069115. Epub 2018 Feb 12.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN120,

title = {Neobodonids are dominant kinetoplastids in the global ocean},

author = {O. Flegontova and P. Flegontov and S. Malviya and J. Poulain and C. Vargas and C. Bowler and J. Lukes and A. Horak},

url = {https://www.ncbi.nlm.nih.gov/pubmed/29266706},

doi = {10.1111/1462-2920.14034},

issn = {1462-2920 (Electronic) 

1462-2912 (Linking)},

year  = {2018},

date = {2018-01-01},

journal = {Environ Microbiol},

volume = {20},

number = {2},

pages = {878-889},

abstract = {Kinetoplastid flagellates comprise basal mostly free-living bodonids and derived obligatory parasitic trypanosomatids, which belong to the best-studied protists. Due to their omnipresence in aquatic environments and soil, the bodonids are of ecological significance. Here, we present the first global survey of marine kinetoplastids and compare it with the strikingly different patterns of abundance and diversity in their sister clade, the diplonemids. Based on analysis of 18S rDNA V9 ribotypes obtained from 124 sites sampled during the Tara Oceans expedition, our results show generally low to moderate abundance and diversity of planktonic kinetoplastids. Although we have identified all major kinetoplastid lineages, 98% of kinetoplastid reads are represented by neobodonids, namely specimens of the Neobodo and Rhynchomonas genera, which make up 59% and 18% of all reads, respectively. Most kinetoplastids have small cell size (0.8-5 microm) and tend to be more abundant in the mesopelagic as compared to the euphotic zone. Some of the most abundant operational taxonomic units have distinct geographical distributions, and three novel putatively parasitic neobodonids were identified, along with their potential hosts.},

note = {Flegontova, Olga 

Flegontov, Pavel 

Malviya, Shruti 

Poulain, Julie 

de Vargas, Colomban 

Bowler, Chris 

Lukes, Julius 

Horak, Ales 

eng 

Research Support, Non-U.S. Gov't 

England 

Environ Microbiol. 2018 Feb;20(2):878-889. doi: 10.1111/1462-2920.14034.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN118,

title = {The epibiotic life of the cosmopolitan diatom Fragilariopsis doliolus on heterotrophic ciliates in the open ocean},

author = {F. J. Vincent and S. Colin and S. Romac and E. Scalco and L. Bittner and Y. Garcia and R. M. Lopes and J. R. Dolan and A. Zingone and C. Vargas and C. Bowler},

url = {https://www.ncbi.nlm.nih.gov/pubmed/29348580},

doi = {10.1038/s41396-017-0029-1},

issn = {1751-7370 (Electronic) 

1751-7362 (Linking)},

year  = {2018},

date = {2018-01-01},

journal = {ISME J},

volume = {12},

number = {4},

pages = {1094-1108},

abstract = {Diatoms are a diverse and ecologically important group of phytoplankton. Although most species are considered free living, several are known to interact with other organisms within the plankton. Detailed imaging and molecular characterization of any such partnership is, however, limited, and an appraisal of the large-scale distribution and ecology of such consortia was never attempted. Here, observation of Tara Oceans samples from the Benguela Current led to the detection of an epibiotic association between a pennate diatom and a tintinnid ciliate. We identified the diatom as Fragilariopsis doliolus that possesses a unique feature to form barrel-shaped chains, associated with seven different genera of tintinnids including five previously undescribed associations. The organisms were commonly found together in the Atlantic and Pacific Ocean basins, and live observations of the interaction have been recorded for the first time. By combining confocal and scanning electron microscopy of individual consortia with the sequencing of high-resolution molecular markers, we analyzed their distribution in the global ocean, revealing morpho-genetically distinct tintinnid haplotypes and biogeographically structured diatom haplotypes. The diatom was among the most abundant in the global ocean. We show that the consortia were particularly prevalent in nutrient-replete conditions, rich in potential predators. These observations support the hypothesis of a mutualistic symbiosis, wherein diatoms acquire increased motility and tintinnids benefit from silicification through increased protection, and highlight that such associations may be more prevalent than currently appreciated.},

note = {Vincent, Flora J 

Colin, Sebastien 

Romac, Sarah 

Scalco, Eleonora 

Bittner, Lucie 

Garcia, Yonara 

Lopes, Rubens M 

Dolan, John R 

Zingone, Adriana 

de Vargas, Colomban 

Bowler, Chris 

eng 

294823/European Research Council/International 

Research Support, Non-U.S. Gov't 

England 

ISME J. 2018 Apr;12(4):1094-1108. doi: 10.1038/s41396-017-0029-1. Epub 2018 Jan 18.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN94,

title = {Locality and diel cycling of viral production revealed by a 24 h time course cross-omics analysis in a coastal region of Japan},

author = {T. Yoshida and Y. Nishimura and H. Watai and N. Haruki and D. Morimoto and H. Kaneko and T. Honda and K. Yamamoto and P. Hingamp and Y. Sako and S. Goto and H. Ogata},

url = {https://www.ncbi.nlm.nih.gov/pubmed/29382948},

doi = {10.1038/s41396-018-0052-x},

issn = {1751-7370 (Electronic) 

1751-7362 (Linking)},

year  = {2018},

date = {2018-01-01},

journal = {ISME J},

volume = {12},

number = {5},

pages = {1287-1295},

abstract = {Viruses infecting microorganisms are ubiquitous and abundant in the ocean. However, it is unclear when and where the numerous viral particles we observe in the sea are produced and whether they are active. To address these questions, we performed time-series analyses of viral metagenomes and microbial metatranscriptomes collected over a period of 24 h at a Japanese coastal site. Through mapping the metatranscriptomic reads on three sets of viral genomes ((i) 878 contigs of Osaka Bay viromes (OBV), (ii) 1766 environmental viral genomes from marine viromes, and (iii) 2429 reference viral genomes), we revealed that all the local OBV contigs were transcribed in the host fraction. This indicates that the majority of viral populations detected in viromes are active, and suggests that virions are rapidly diluted as a result of diffusion, currents, and mixing. Our data further revealed a peak of cyanophage gene expression in the afternoon/dusk followed by an increase of genomes from their virions at night and less-coherent infectious patterns for viruses putatively infecting various groups of heterotrophs. This suggests that cyanophages drive the diel release of cyanobacteria-derived organic matter into the environment and viruses of heterotrophic bacteria might have adapted to the population-specific life cycles of hosts.},

note = {Yoshida, Takashi 

Nishimura, Yosuke 

Watai, Hiroyasu 

Haruki, Nana 

Morimoto, Daichi 

Kaneko, Hiroto 

Honda, Takashi 

Yamamoto, Keigo 

Hingamp, Pascal 

Sako, Yoshihiko 

Goto, Susumu 

Ogata, Hiroyuki 

eng 

Research Support, Non-U.S. Gov't 

England 

ISME J. 2018 May;12(5):1287-1295. doi: 10.1038/s41396-018-0052-x. Epub 2018 Jan 30.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN237,

title = {Influence of diatom diversity on the ocean biological carbon pump},

author = {Paul Tréguer and Chris Bowler and Brivaela Moriceau and Stephanie Dutkiewicz and Marion Gehlen and Olivier Aumont and Lucie Bittner and Richard Dugdale and Zoe Finkel and Daniele Iudicone and Oliver Jahn and Lionel Guidi and Marine Lasbleiz and Karine Leblanc and Marina Levy and Philippe Pondaven},

url = {https://doi.org/10.1038/s41561-017-0028-x},

doi = {10.1038/s41561-017-0028-x},

issn = {1752-0908},

year  = {2018},

date = {2018-01-01},

journal = {Nature Geoscience},

volume = {11},

number = {1},

pages = {27-37},

abstract = {Diatoms sustain the marine food web and contribute to the export of carbon from the surface ocean to depth. They account for about 40% of marine primary productivity and particulate carbon exported to depth as part of the biological pump. Diatoms have long been known to be abundant in turbulent, nutrient-rich waters, but observations and simulations indicate that they are dominant also in meso- and submesoscale structures such as fronts and filaments, and in the deep chlorophyll maximum. Diatoms vary widely in size, morphology and elemental composition, all of which control the quality, quantity and sinking speed of biogenic matter to depth. In particular, their silica shells provide ballast to marine snow and faecal pellets, and can help transport carbon to both the mesopelagic layer and deep ocean. Herein we show that the extent to which diatoms contribute to the export of carbon varies by diatom type, with carbon transfer modulated by the Si/C ratio of diatom cells, the thickness of the shells and their life strategies; for instance, the tendency to form aggregates or resting spores. Model simulations project a decline in the contribution of diatoms to primary production everywhere outside of the Southern Ocean. We argue that we need to understand changes in diatom diversity, life cycle and plankton interactions in a warmer and more acidic ocean in much more detail to fully assess any changes in their contribution to the biological pump.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN92,

title = {Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans},

author = {Y. Seeleuthner and S. Mondy and V. Lombard and Q. Carradec and E. Pelletier and M. Wessner and J. Leconte and J. F. Mangot and J. Poulain and K. Labadie and R. Logares and S. Sunagawa and V. Berardinis and M. Salanoubat and C. Dimier and S. Kandels-Lewis and M. Picheral and S. Searson and Coordinators Tara Oceans and S. Pesant and N. Poulton and R. Stepanauskas and P. Bork and C. Bowler and P. Hingamp and M. B. Sullivan and D. Iudicone and R. Massana and J. M. Aury and B. Henrissat and E. Karsenti and O. Jaillon and M. Sieracki and C. Vargas and P. Wincker},

url = {https://www.ncbi.nlm.nih.gov/pubmed/29358710},

doi = {10.1038/s41467-017-02235-3},

issn = {2041-1723 (Electronic) 

2041-1723 (Linking)},

year  = {2018},

date = {2018-01-01},

journal = {Nat Commun},

volume = {9},

number = {1},

pages = {310},

abstract = {Single-celled eukaryotes (protists) are critical players in global biogeochemical cycling of nutrients and energy in the oceans. While their roles as primary producers and grazers are well appreciated, other aspects of their life histories remain obscure due to challenges in culturing and sequencing their natural diversity. Here, we exploit single-cell genomics and metagenomics data from the circumglobal Tara Oceans expedition to analyze the genome content and apparent oceanic distribution of seven prevalent lineages of uncultured heterotrophic stramenopiles. Based on the available data, each sequenced genome or genotype appears to have a specific oceanic distribution, principally correlated with water temperature and depth. The genome content provides hypotheses for specialization in terms of cell motility, food spectra, and trophic stages, including the potential impact on their lifestyles of horizontal gene transfer from prokaryotes. Our results support the idea that prominent heterotrophic marine protists perform diverse functions in ocean ecology.},

note = {Seeleuthner, Yoann 

Mondy, Samuel 

Lombard, Vincent 

Carradec, Quentin 

Pelletier, Eric 

Wessner, Marc 

Leconte, Jade 

Mangot, Jean-Francois 

Poulain, Julie 

Labadie, Karine 

Logares, Ramiro 

Sunagawa, Shinichi 

de Berardinis, Veronique 

Salanoubat, Marcel 

Dimier, Celine 

Kandels-Lewis, Stefanie 

Picheral, Marc 

Searson, Sarah 

Pesant, Stephane 

Poulton, Nicole 

Stepanauskas, Ramunas 

Bork, Peer 

Bowler, Chris 

Hingamp, Pascal 

Sullivan, Matthew B 

Iudicone, Daniele 

Massana, Ramon 

Aury, Jean-Marc 

Henrissat, Bernard 

Karsenti, Eric 

Jaillon, Olivier 

Sieracki, Mike 

de Vargas, Colomban 

Wincker, Patrick 

eng 

294823/European Research Council/International 

Research Support, Non-U.S. Gov't 

England 

Nat Commun. 2018 Jan 22;9(1):310. doi: 10.1038/s41467-017-02235-3.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN116,

title = {A global ocean atlas of eukaryotic genes},

author = {Q. Carradec and E. Pelletier and C. Da Silva and A. Alberti and Y. Seeleuthner and R. Blanc-Mathieu and G. Lima-Mendez and F. Rocha and L. Tirichine and K. Labadie and A. Kirilovsky and A. Bertrand and S. Engelen and M. A. Madoui and R. Meheust and J. Poulain and S. Romac and D. J. Richter and G. Yoshikawa and C. Dimier and S. Kandels-Lewis and M. Picheral and S. Searson and Coordinators Tara Oceans and O. Jaillon and J. M. Aury and E. Karsenti and M. B. Sullivan and S. Sunagawa and P. Bork and F. Not and P. Hingamp and J. Raes and L. Guidi and H. Ogata and C. Vargas and D. Iudicone and C. Bowler and P. Wincker},

url = {https://www.ncbi.nlm.nih.gov/pubmed/29371626},

doi = {10.1038/s41467-017-02342-1},

issn = {2041-1723 (Electronic) 

2041-1723 (Linking)},

year  = {2018},

date = {2018-01-01},

journal = {Nat Commun},

volume = {9},

number = {1},

pages = {373},

abstract = {While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry.},

note = {Carradec, Quentin 

Pelletier, Eric 

Da Silva, Corinne 

Alberti, Adriana 

Seeleuthner, Yoann 

Blanc-Mathieu, Romain 

Lima-Mendez, Gipsi 

Rocha, Fabio 

Tirichine, Leila 

Labadie, Karine 

Kirilovsky, Amos 

Bertrand, Alexis 

Engelen, Stefan 

Madoui, Mohammed-Amin 

Meheust, Raphael 

Poulain, Julie 

Romac, Sarah 

Richter, Daniel J 

Yoshikawa, Genki 

Dimier, Celine 

Kandels-Lewis, Stefanie 

Picheral, Marc 

Searson, Sarah 

Jaillon, Olivier 

Aury, Jean-Marc 

Karsenti, Eric 

Sullivan, Matthew B 

Sunagawa, Shinichi 

Bork, Peer 

Not, Fabrice 

Hingamp, Pascal 

Raes, Jeroen 

Guidi, Lionel 

Ogata, Hiroyuki 

de Vargas, Colomban 

Iudicone, Daniele 

Bowler, Chris 

Wincker, Patrick 

eng 

294823/European Research Council/International 

Research Support, Non-U.S. Gov't 

England 

Nat Commun. 2018 Jan 25;9(1):373. doi: 10.1038/s41467-017-02342-1.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN90,

title = {Surface ocean metabarcoding confirms limited diversity in planktonic foraminifera but reveals unknown hyper-abundant lineages},

author = {R. Morard and M. J. Garet-Delmas and F. Mahe and S. Romac and J. Poulain and M. Kucera and C. Vargas},

url = {https://www.ncbi.nlm.nih.gov/pubmed/29416071},

doi = {10.1038/s41598-018-20833-z},

issn = {2045-2322 (Electronic) 

2045-2322 (Linking)},

year  = {2018},

date = {2018-01-01},

journal = {Sci Rep},

volume = {8},

number = {1},

pages = {2539},

abstract = {Since the advent of DNA metabarcoding surveys, the planktonic realm is considered a treasure trove of diversity, inhabited by a small number of abundant taxa, and a hugely diverse and taxonomically uncharacterized consortium of rare species. Here we assess if the apparent underestimation of plankton diversity applies universally. We target planktonic foraminifera, a group of protists whose known morphological diversity is limited, taxonomically resolved and linked to ribosomal DNA barcodes. We generated a pyrosequencing dataset of ~100,000 partial 18S rRNA foraminiferal sequences from 32 size fractioned photic-zone plankton samples collected at 8 stations in the Indian and Atlantic Oceans during the Tara Oceans expedition (2009-2012). We identified 69 genetic types belonging to 41 morphotaxa in our metabarcoding dataset. The diversity saturated at local and regional scale as well as in the three size fractions and the two depths sampled indicating that the diversity of foraminifera is modest and finite. The large majority of the newly discovered lineages occur in the small size fraction, neglected by classical taxonomy. These unknown lineages dominate the bulk [>0.8 microm] size fraction, implying that a considerable part of the planktonic foraminifera community biomass has its origin in unknown lineages.},

note = {Morard, Raphael 

Garet-Delmas, Marie-Jose 

Mahe, Frederic 

Romac, Sarah 

Poulain, Julie 

Kucera, Michal 

de Vargas, Colomban 

eng 

Research Support, Non-U.S. Gov't 

England 

Sci Rep. 2018 Feb 7;8(1):2539. doi: 10.1038/s41598-018-20833-z.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN236,

title = {Pan-Arctic optical characteristics of colored dissolved organic matter: Tracing dissolved organic carbon in changing Arctic waters using satellite ocean color data},

author = {Atsushi Matsuoka and Emmanuel Boss and Marcel Babin and Lee Karp-Boss and Mark Hafez and Alex Chekalyuk and Christopher W. Proctor and P. Jeremy Werdell and Annick Bricaud},

url = {https://www.sciencedirect.com/science/article/pii/S0034425717303632},

doi = {https://doi.org/10.1016/j.rse.2017.08.009},

issn = {0034-4257},

year  = {2017},

date = {2017-01-01},

journal = {Remote Sensing of Environment},

volume = {200},

pages = {89-101},

abstract = {Light absorption of the colored fraction of dissolved organic matter (CDOM) is a dominant optical component of the Arctic Ocean (AO). Here we show Pan-Arctic characteristics of CDOM light absorption for various Arctic regions covering both coastal and oceanic waters during the Tara Oceans Polar Circle expedition. The Siberian (or eastern) side of the AO is characterized by higher CDOM absorption values compared to the North American (or western) side. This is due to the difference in watersheds between the eastern and western sides of the AO and is consistent with an Arctic absorption database recently built by Matsuoka et al. (2014). A direct comparison between in situ and satellite data demonstrates that CDOM absorption is derived Arctic-wide from satellite ocean color data with an average uncertainty of 12% (root mean square error of 0.3m−1) using our previously published algorithm. For river-influenced coastal waters, we found a single and highly significant relationship between concentrations of dissolved organic carbon (DOC) and CDOM absorption (r2>0.94) covering major Arctic river mouths. By applying this in situ relationship to satellite-derived CDOM absorption, DOC concentrations in the surface waters are estimated for river-influenced coastal waters with an average uncertainty of 28%. Implications for the monitoring of DOC concentrations in Arctic coastal waters are discussed.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN74,

title = {Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes},

author = {S. Colin and L. P. Coelho and S. Sunagawa and C. Bowler and E. Karsenti and P. Bork and R. Pepperkok and C. Vargas},

url = {https://www.ncbi.nlm.nih.gov/pubmed/29087936},

doi = {10.7554/eLife.26066},

issn = {2050-084X (Electronic) 

2050-084X (Linking)},

year  = {2017},

date = {2017-01-01},

journal = {Elife},

volume = {6},

abstract = {We present a 3D-fluorescence imaging and classification tool for high throughput analysis of microbial eukaryotes in environmental samples. It entails high-content feature extraction that permits accurate automated taxonomic classification and quantitative data about organism ultrastructures and interactions. Using plankton samples from the Tara Oceans expeditions, we validate its applicability to taxonomic profiling and ecosystem analyses, and discuss its potential for future integration of eukaryotic cell biology into evolutionary and ecological studies.},

note = {Colin, Sebastien 

Coelho, Luis Pedro 

Sunagawa, Shinichi 

Bowler, Chris 

Karsenti, Eric 

Bork, Peer 

Pepperkok, Rainer 

de Vargas, Colomban 

eng 

Validation Study 

England 

Elife. 2017 Oct 31;6. doi: 10.7554/eLife.26066.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN235,

title = {Biological and physical influences on marine snowfall at the equator},

author = {R. Kiko and A. Biastoch and P. Brandt and S. Cravatte and H. Hauss and R. Hummels and I. Kriest and F. Marin and A. M P McDonnell and A. Oschlies and M. Picheral and F. U. Schwarzkopf and A. M. Thurnherr and L. Stemmann},

url = {https://doi.org/10.1038/ngeo3042},

doi = {10.1038/ngeo3042},

issn = {1752-0908},

year  = {2017},

date = {2017-01-01},

journal = {Nature Geoscience},

volume = {10},

number = {11},

pages = {852-858},

abstract = {High primary productivity in the equatorial Atlantic and Pacific oceans is one of the key features of tropical ocean biogeochemistry and fuels a substantial flux of particulate matter towards the abyssal ocean. How biological processes and equatorial current dynamics shape the particle size distribution and flux, however, is poorly understood. Here we use high-resolution size-resolved particle imaging and Acoustic Doppler Current Profiler data to assess these influences in equatorial oceans. We find an increase in particle abundance and flux at depths of 300 to 600 m at the Atlantic and Pacific equator, a depth range to which zooplankton and nekton migrate vertically in a daily cycle. We attribute this particle maximum to faecal pellet production by these organisms. At depths of 1,000 to 4,000 m, we find that the particulate organic carbon flux is up to three times greater in the equatorial belt (1° S–1° N) than in off-equatorial regions. At 3,000 m, the flux is dominated by small particles less than 0.53 mm in diameter. The dominance of small particles seems to be caused by enhanced active and passive particle export in this region, as well as by the focusing of particles by deep eastward jets found at 2° N and 2° S. We thus suggest that zooplankton movements and ocean currents modulate the transfer of particulate carbon from the surface to the deep ocean.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN89,

title = {Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis},

author = {D. Lopez-Escardo and X. Grau-Bove and A. Guillaumet-Adkins and M. Gut and M. E. Sieracki and I. Ruiz-Trillo},

url = {https://www.ncbi.nlm.nih.gov/pubmed/28887541},

doi = {10.1038/s41598-017-11466-9},

issn = {2045-2322 (Electronic) 

2045-2322 (Linking)},

year  = {2017},

date = {2017-01-01},

journal = {Sci Rep},

volume = {7},

number = {1},

pages = {11025},

abstract = {Single-cell genomics (SCG) appeared as a powerful technique to get genomic information from uncultured organisms. However, SCG techniques suffer from biases at the whole genome amplification step that can lead to extremely variable numbers of genome recovery (5-100%). Thus, it is unclear how useful can SCG be to address evolutionary questions on uncultured microbial eukaryotes. To provide some insights into this, we here analysed 3 single-cell amplified genomes (SAGs) of the choanoflagellate Monosiga brevicollis, whose genome is known. Our results show that each SAG has a different, independent bias, yielding different levels of genome recovery for each cell (6-36%). Genes often appear fragmented and are split into more genes during annotation. Thus, analyses of gene gain and losses, gene architectures, synteny and other genomic features can not be addressed with a single SAG. However, the recovery of phylogenetically-informative protein domains can be up to 55%. This means SAG data can be used to perform accurate phylogenomic analyses. Finally, we also confirm that the co-assembly of several SAGs improves the general genomic recovery. Overall, our data show that, besides important current limitations, SAGs can still provide interesting and novel insights from poorly-known, uncultured organisms.},

note = {Lopez-Escardo, David 

Grau-Bove, Xavier 

Guillaumet-Adkins, Amy 

Gut, Marta 

Sieracki, Michael E 

Ruiz-Trillo, Inaki 

eng 

Evaluation Study 

Research Support, Non-U.S. Gov't 

England 

Sci Rep. 2017 Sep 8;7(1):11025. doi: 10.1038/s41598-017-11466-9.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN88,

title = {Exploring Microdiversity in Novel Kordia sp. (Bacteroidetes) with Proteorhodopsin from the Tropical Indian Ocean via Single Amplified Genomes},

author = {M. Royo-Llonch and I. Ferrera and F. M. Cornejo-Castillo and P. Sanchez and G. Salazar and R. Stepanauskas and J. M. Gonzalez and M. E. Sieracki and S. Speich and L. Stemmann and C. Pedros-Alio and S. G. Acinas},

url = {https://www.ncbi.nlm.nih.gov/pubmed/28790980},

doi = {10.3389/fmicb.2017.01317},

issn = {1664-302X (Print) 

1664-302X (Linking)},

year  = {2017},

date = {2017-01-01},

journal = {Front Microbiol},

volume = {8},

pages = {1317},

abstract = {Marine Bacteroidetes constitute a very abundant bacterioplankton group in the oceans that plays a key role in recycling particulate organic matter and includes several photoheterotrophic members containing proteorhodopsin. Relatively few marine Bacteroidetes species have been described and, moreover, they correspond to cultured isolates, which in most cases do not represent the actual abundant or ecologically relevant microorganisms in the natural environment. In this study, we explored the microdiversity of 98 Single Amplified Genomes (SAGs) retrieved from the surface waters of the underexplored North Indian Ocean, whose most closely related isolate is Kordia algicida OT-1. Using Multi Locus Sequencing Analysis (MLSA) we found no microdiversity in the tested conserved phylogenetic markers (16S rRNA and 23S rRNA genes), the fast-evolving Internal Transcribed Spacer and the functional markers proteorhodopsin and the beta-subunit of RNA polymerase. Furthermore, we carried out a Fragment Recruitment Analysis (FRA) with marine metagenomes to learn about the distribution and dynamics of this microorganism in different locations, depths and size fractions. This analysis indicated that this taxon belongs to the rare biosphere, showing its highest abundance after upwelling-induced phytoplankton blooms and sinking to the deep ocean with large organic matter particles. This uncultured Kordia lineage likely represents a novel Kordia species (Kordia sp. CFSAG39SUR) that contains the proteorhodopsin gene and has a widespread spatial and vertical distribution. The combination of SAGs and MLSA makes a valuable approach to infer putative ecological roles of uncultured abundant microorganisms.},

note = {Royo-Llonch, Marta 

Ferrera, Isabel 

Cornejo-Castillo, Francisco M 

Sanchez, Pablo 

Salazar, Guillem 

Stepanauskas, Ramunas 

Gonzalez, Jose M 

Sieracki, Michael E 

Speich, Sabrina 

Stemmann, Lars 

Pedros-Alio, Carlos 

Acinas, Silvia G 

eng 

Switzerland 

Front Microbiol. 2017 Jul 25;8:1317. doi: 10.3389/fmicb.2017.01317. eCollection 2017.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN79,

title = {New insights into global biogeography, population structure and natural selection from the genome of the epipelagic copepod Oithona},

author = {M. A. Madoui and J. Poulain and K. Sugier and M. Wessner and B. Noel and L. Berline and K. Labadie and A. Cornils and L. Blanco-Bercial and L. Stemmann and J. L. Jamet and P. Wincker},

url = {https://www.ncbi.nlm.nih.gov/pubmed/28636804},

doi = {10.1111/mec.14214},

issn = {1365-294X (Electronic) 

0962-1083 (Linking)},

year  = {2017},

date = {2017-01-01},

journal = {Mol Ecol},

volume = {26},

number = {17},

pages = {4467-4482},

abstract = {In the epipelagic ocean, the genus Oithona is considered as one of the most abundant and widespread copepods and plays an important role in the trophic food web. Despite its ecological importance, little is known about Oithona and cyclopoid copepods genomics. Therefore, we sequenced, assembled and annotated the genome of Oithona nana. The comparative genomic analysis integrating available copepod genomes highlighted the expansions of genes related to stress response, cell differentiation and development, including genes coding Lin12-Notch-repeat (LNR) domain proteins. The Oithona biogeography based on 28S sequences and metagenomic reads from the Tara Oceans expedition showed the presence of O. nana mostly in the Mediterranean Sea (MS) and confirmed the amphitropical distribution of Oithona similis. The population genomics analyses of O. nana in the Northern MS, integrating the Tara Oceans metagenomic data and the O. nana genome, led to the identification of genetic structure between populations from the MS basins. Furthermore, 20 loci were found to be under positive selection including four missense and eight synonymous variants, harbouring soft or hard selective sweep patterns. One of the missense variants was localized in the LNR domain of the coding region of a male-specific gene. The variation in the B-allele frequency with respect to the MS circulation pattern showed the presence of genomic clines between O. nana and another undefined Oithona species possibly imported through Atlantic waters. This study provides new approaches and results in zooplankton population genomics through the integration of metagenomic and oceanographic data.},

note = {Madoui, Mohammed-Amin 

Poulain, Julie 

Sugier, Kevin 

Wessner, Marc 

Noel, Benjamin 

Berline, Leo 

Labadie, Karine 

Cornils, Astrid 

Blanco-Bercial, Leocadio 

Stemmann, Lars 

Jamet, Jean-Louis 

Wincker, Patrick 

eng 

England 

Mol Ecol. 2017 Sep;26(17):4467-4482. doi: 10.1111/mec.14214. Epub 2017 Jul 25.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN87,

title = {The evolution of diatoms and their biogeochemical functions},

author = {A. S. Benoiston and F. M. Ibarbalz and L. Bittner and L. Guidi and O. Jahn and S. Dutkiewicz and C. Bowler},

url = {https://www.ncbi.nlm.nih.gov/pubmed/28717023},

doi = {10.1098/rstb.2016.0397},

issn = {1471-2970 (Electronic) 

0962-8436 (Linking)},

year  = {2017},

date = {2017-01-01},

journal = {Philos Trans R Soc Lond B Biol Sci},

volume = {372},

number = {1728},

abstract = {In contemporary oceans diatoms are an important group of eukaryotic phytoplankton that typically dominate in upwelling regions and at high latitudes. They also make significant contributions to sporadic blooms that often occur in springtime. Recent surveys have revealed global information about their abundance and diversity, as well as their contributions to biogeochemical cycles, both as primary producers of organic material and as conduits facilitating the export of carbon and silicon to the ocean interior. Sequencing of diatom genomes is revealing the evolutionary underpinnings of their ecological success by examination of their gene repertoires and the mechanisms they use to adapt to environmental changes. The rise of the diatoms over the last hundred million years is similarly being explored through analysis of microfossils and biomarkers that can be traced through geological time, as well as their contributions to seafloor sediments and fossil fuel reserves. The current review aims to synthesize current information about the evolution and biogeochemical functions of diatoms as they rose to prominence in the global ocean.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'.},

note = {Benoiston, Anne-Sophie 

Ibarbalz, Federico M 

Bittner, Lucie 

Guidi, Lionel 

Jahn, Oliver 

Dutkiewicz, Stephanie 

Bowler, Chris 

eng 

Review 

England 

Philos Trans R Soc Lond B Biol Sci. 2017 Sep 5;372(1728). pii: rstb.2016.0397. doi: 10.1098/rstb.2016.0397.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN76,

title = {A myovirus encoding both photosystem I and II proteins enhances cyclic electron flow in infected Prochlorococcus cells},

author = {S. Fridman and J. Flores-Uribe and S. Larom and O. Alalouf and O. Liran and I. Yacoby and F. Salama and B. Bailleul and F. Rappaport and T. Ziv and I. Sharon and F. M. Cornejo-Castillo and A. Philosof and C. L. Dupont and P. Sanchez and S. G. Acinas and F. L. Rohwer and D. Lindell and O. Beja},

url = {https://www.ncbi.nlm.nih.gov/pubmed/28785078},

doi = {10.1038/s41564-017-0002-9},

issn = {2058-5276 (Electronic) 

2058-5276 (Linking)},

year  = {2017},

date = {2017-01-01},

journal = {Nat Microbiol},

volume = {2},

number = {10},

pages = {1350-1357},

abstract = {Cyanobacteria are important contributors to primary production in the open oceans. Over the past decade, various photosynthesis-related genes have been found in viruses that infect cyanobacteria (cyanophages). Although photosystem II (PSII) genes are common in both cultured cyanophages and environmental samples (1-4) , viral photosystem I (vPSI) genes have so far only been detected in environmental samples (5,6) . Here, we have used a targeted strategy to isolate a cyanophage from the tropical Pacific Ocean that carries a PSI gene cassette with seven distinct PSI genes (psaJF, C, A, B, K, E, D) as well as two PSII genes (psbA, D). This cyanophage, P-TIM68, belongs to the T4-like myoviruses, has a prolate capsid, a long contractile tail and infects Prochlorococcus sp. strain MIT9515. Phage photosynthesis genes from both photosystems are expressed during infection, and the resultant proteins are incorporated into membranes of the infected host. Moreover, photosynthetic capacity in the cell is maintained throughout the infection cycle with enhancement of cyclic electron flow around PSI. Analysis of metagenomic data from the Tara Oceans expedition (7) shows that phages carrying PSI gene cassettes are abundant in the tropical Pacific Ocean, composing up to 28% of T4-like cyanomyophages. They are also present in the tropical Indian and Atlantic Oceans. P-TIM68 populations, specifically, compose on average 22% of the PSI-gene-cassette carrying phages. Our results suggest that cyanophages carrying PSI and PSII genes are likely to maintain and even manipulate photosynthesis during infection of their Prochlorococcus hosts in the tropical oceans.},

note = {Fridman, Svetlana 

Flores-Uribe, Jose 

Larom, Shirley 

Alalouf, Onit 

Liran, Oded 

Yacoby, Iftach 

Salama, Faris 

Bailleul, Benjamin 

Rappaport, Fabrice 

Ziv, Tamar 

Sharon, Itai 

Cornejo-Castillo, Francisco M 

Philosof, Alon 

Dupont, Christopher L 

Sanchez, Pablo 

Acinas, Silvia G 

Rohwer, Forest L 

Lindell, Debbie 

Beja, Oded 

eng 

England 

Nat Microbiol. 2017 Oct;2(10):1350-1357. doi: 10.1038/s41564-017-0002-9. Epub 2017 Aug 7.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN77,

title = {Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition},

author = {A. Alberti and J. Poulain and S. Engelen and K. Labadie and S. Romac and I. Ferrera and G. Albini and J. M. Aury and C. Belser and A. Bertrand and C. Cruaud and C. Da Silva and C. Dossat and F. Gavory and S. Gas and J. Guy and M. Haquelle and E. Jacoby and O. Jaillon and A. Lemainque and E. Pelletier and G. Samson and M. Wessner and Team Genoscope Technical and S. G. Acinas and M. Royo-Llonch and F. M. Cornejo-Castillo and R. Logares and B. Fernandez-Gomez and C. Bowler and G. Cochrane and C. Amid and P. T. Hoopen and C. De Vargas and N. Grimsley and E. Desgranges and S. Kandels-Lewis and H. Ogata and N. Poulton and M. E. Sieracki and R. Stepanauskas and M. B. Sullivan and J. R. Brum and M. B. Duhaime and B. T. Poulos and B. L. Hurwitz and Coordinators Tara Oceans Consortium and S. Pesant and E. Karsenti and P. Wincker},

url = {https://www.ncbi.nlm.nih.gov/pubmed/28763055},

doi = {10.1038/sdata.2017.93},

issn = {2052-4463 (Electronic) 

2052-4463 (Linking)},

year  = {2017},

date = {2017-01-01},

journal = {Sci Data},

volume = {4},

pages = {170093},

abstract = {A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems.},

note = {Alberti, Adriana 

Poulain, Julie 

Engelen, Stefan 

Labadie, Karine 

Romac, Sarah 

Ferrera, Isabel 

Albini, Guillaume 

Aury, Jean-Marc 

Belser, Caroline 

Bertrand, Alexis 

Cruaud, Corinne 

Da Silva, Corinne 

Dossat, Carole 

Gavory, Frederick 

Gas, Shahinaz 

Guy, Julie 

Haquelle, Maud 

Jacoby, E'krame 

Jaillon, Olivier 

Lemainque, Arnaud 

Pelletier, Eric 

Samson, Gaelle 

Wessner, Mark 

Acinas, Silvia G 

Royo-Llonch, Marta 

Cornejo-Castillo, Francisco M 

Logares, Ramiro 

Fernandez-Gomez, Beatriz 

Bowler, Chris 

Cochrane, Guy 

Amid, Clara 

Hoopen, Petra Ten 

De Vargas, Colomban 

Grimsley, Nigel 

Desgranges, Elodie 

Kandels-Lewis, Stefanie 

Ogata, Hiroyuki 

Poulton, Nicole 

Sieracki, Michael E 

Stepanauskas, Ramunas 

Sullivan, Matthew B 

Brum, Jennifer R 

Duhaime, Melissa B 

Poulos, Bonnie T 

Hurwitz, Bonnie L 

Pesant, Stephane 

Karsenti, Eric 

Wincker, Patrick 

eng 

Dataset 

Research Support, Non-U.S. Gov't 

England 

Sci Data. 2017 Aug 1;4:170093. doi: 10.1038/sdata.2017.93.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN234,

title = {The Arctic Ocean as a dead end for floating plastics in the North Atlantic branch of the Thermohaline Circulation},

author = {Andrés Cózar and Elisa Marti and Carlos Duarte and Juan Lomas and Erik Sebille and Thomas Ballatore and Víctor Eguíluz and Juan González-Gordillo and Maria Luiza Pedrotti and Fidel Echevarría and Romain Troublè and Xabier Irigoien},

doi = {10.1126/sciadv.1600582},

year  = {2017},

date = {2017-01-01},

journal = {Science Advances},

volume = {3},

pages = {e1600582},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN86,

title = {Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean},

author = {Y. Nishimura and H. Watai and T. Honda and T. Mihara and K. Omae and S. Roux and R. Blanc-Mathieu and K. Yamamoto and P. Hingamp and Y. Sako and M. B. Sullivan and S. Goto and H. Ogata and T. Yoshida},

url = {https://www.ncbi.nlm.nih.gov/pubmed/28261669},

doi = {10.1128/mSphere.00359-16},

issn = {2379-5042 (Print) 

2379-5042 (Linking)},

year  = {2017},

date = {2017-01-01},

journal = {mSphere},

volume = {2},

number = {2},

abstract = {Metagenomics has revealed the existence of numerous uncharacterized viral lineages, which are referred to as viral "dark matter." However, our knowledge regarding viral genomes is biased toward culturable viruses. In this study, we analyzed 1,600 (1,352 nonredundant) complete double-stranded DNA viral genomes (10 to 211 kb) assembled from 52 marine viromes. Together with 244 previously reported uncultured viral genomes, a genome-wide comparison delineated 617 genus-level operational taxonomic units (OTUs) for these environmental viral genomes (EVGs). Of these, 600 OTUs contained no representatives from known viruses, thus putatively corresponding to novel viral genera. Predicted hosts of the EVGs included major groups of marine prokaryotes, such as marine group II Euryarchaeota and SAR86, from which no viruses have been isolated to date, as well as Flavobacteriaceae and SAR116. Our analysis indicates that marine cyanophages are already well represented in genome databases and that one of the EVGs likely represents a new cyanophage lineage. Several EVGs encode many enzymes that appear to function for an efficient utilization of iron-sulfur clusters or to enhance host survival. This suggests that there is a selection pressure on these marine viruses to accumulate genes for specific viral propagation strategies. Finally, we revealed that EVGs contribute to a 4-fold increase in the recruitment of photic-zone viromes compared with the use of current reference viral genomes. IMPORTANCE Viruses are diverse and play significant ecological roles in marine ecosystems. However, our knowledge of genome-level diversity in viruses is biased toward those isolated from few culturable hosts. Here, we determined 1,352 nonredundant complete viral genomes from marine environments. Lifting the uncertainty that clouds short incomplete sequences, whole-genome-wide analysis suggests that these environmental genomes represent hundreds of putative novel viral genera. Predicted hosts include dominant groups of marine bacteria and archaea with no isolated viruses to date. Some of the viral genomes encode many functionally related enzymes, suggesting a strong selection pressure on these marine viruses to control cellular metabolisms by accumulating genes.},

note = {Nishimura, Yosuke 

Watai, Hiroyasu 

Honda, Takashi 

Mihara, Tomoko 

Omae, Kimiho 

Roux, Simon 

Blanc-Mathieu, Romain 

Yamamoto, Keigo 

Hingamp, Pascal 

Sako, Yoshihiko 

Sullivan, Matthew B 

Goto, Susumu 

Ogata, Hiroyuki 

Yoshida, Takashi 

eng 

mSphere. 2017 Mar 1;2(2). pii: mSphere00359-16. doi: 10.1128/mSphere.00359-16. eCollection 2017 Mar-Apr.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN81,

title = {Biogeography and diversity of Collodaria (Radiolaria) in the global ocean},

author = {T. Biard and E. Bigeard and S. Audic and J. Poulain and A. Gutierrez-Rodriguez and S. Pesant and L. Stemmann and F. Not},

url = {https://www.ncbi.nlm.nih.gov/pubmed/28338675},

doi = {10.1038/ismej.2017.12},

issn = {1751-7370 (Electronic) 

1751-7362 (Linking)},

year  = {2017},

date = {2017-01-01},

journal = {ISME J},

volume = {11},

number = {6},

pages = {1331-1344},

abstract = {Collodaria are heterotrophic marine protists that exist either as large colonies composed of hundreds of cells or as large solitary cells. All described species so far harbour intracellular microalgae as photosymbionts. Although recent environmental diversity surveys based on molecular methods demonstrated their consistently high contribution to planktonic communities and their worldwide occurrence, our understanding of their diversity and biogeography is still very limited. Here we estimated the 18S ribosomal DNA (rDNA) gene copies per collodarian cell for solitary (5770+/-1960 small subunit (SSU) rDNA copies) and colonial specimens (37 474+/-17 799 SSU rDNA copies, for each individual cell within a colony) using single-specimen quantitative PCR. We then investigated the environmental diversity of Collodaria within the photic zone through the metabarcoding survey from the Tara Oceans expedition and found that the two collodarian families Collosphaeridae and Sphaerozoidae contributed the most to the collodarian diversity and encompassed mostly cosmopolitan taxa. Although the biogeographical patterns were homogeneous within each biogeochemical biome considered, we observed that coastal biomes were consistently less diverse than oceanic biomes and were dominated by the Sphaerozoidae while the Collosphaeridae were dominant in the open oceans. The significant relationships with six environmental variables suggest that collodarian diversity is influenced by the trophic status of oceanic provinces and increased towards more oligotrophic regions.},

note = {Biard, Tristan 

Bigeard, Estelle 

Audic, Stephane 

Poulain, Julie 

Gutierrez-Rodriguez, Andres 

Pesant, Stephane 

Stemmann, Lars 

Not, Fabrice 

eng 

England 

ISME J. 2017 Jun;11(6):1331-1344. doi: 10.1038/ismej.2017.12. Epub 2017 Mar 24.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN69,

title = {A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications},

author = {R. Arrigoni and B. Vacherie and F. Benzoni and F. Stefani and E. Karsenti and O. Jaillon and F. Not and F. Nunes and C. Payri and P. Wincker and V. Barbe},

url = {https://www.ncbi.nlm.nih.gov/pubmed/27889948},

doi = {10.1111/1755-0998.12640},

issn = {1755-0998 (Electronic) 

1755-098X (Linking)},

year  = {2017},

date = {2017-01-01},

journal = {Mol Ecol Resour},

volume = {17},

number = {5},

pages = {1054-1071},

abstract = {Scleractinian corals (i.e. hard corals) play a fundamental role in building and maintaining coral reefs, one of the most diverse ecosystems on Earth. Nevertheless, their phylogenies remain largely unresolved and little is known about dispersal and survival of their planktonic larval phase. The small subunit ribosomal RNA (SSU rRNA) is a commonly used gene for DNA barcoding in several metazoans, and small variable regions of SSU rRNA are widely adopted as barcode marker to investigate marine plankton community structure worldwide. Here, we provide a large sequence data set of the complete SSU rRNA gene from 298 specimens, representing all known extant reef coral families and a total of 106 genera. The secondary structure was extremely conserved within the order with few exceptions due to insertions or deletions occurring in the variable regions. Remarkable differences in SSU rRNA length and base composition were detected between and within acroporids (Acropora, Montipora, Isopora and Alveopora) compared to other corals. The V4 and V9 regions seem to be promising barcode loci because variation at commonly used barcode primer binding sites was extremely low, while their levels of divergence allowed families and genera to be distinguished. A time-calibrated phylogeny of Scleractinia is provided, and mutation rate heterogeneity is demonstrated across main lineages. The use of this data set as a valuable reference for investigating aspects of ecology, biology, molecular taxonomy and evolution of scleractinian corals is discussed.},

note = {Arrigoni, Roberto 

Vacherie, Benoit 

Benzoni, Francesca 

Stefani, Fabrizio 

Karsenti, Eric 

Jaillon, Olivier 

Not, Fabrice 

Nunes, Flavia 

Payri, Claude 

Wincker, Patrick 

Barbe, Valerie 

eng 

England 

Mol Ecol Resour. 2017 Sep;17(5):1054-1071. doi: 10.1111/1755-0998.12640. Epub 2017 Jan 23.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN43,

title = {Survey of the green picoalga Bathycoccus genomes in the global ocean},

author = {T. Vannier and J. Leconte and Y. Seeleuthner and S. Mondy and E. Pelletier and J. M. Aury and C. Vargas and M. Sieracki and D. Iudicone and D. Vaulot and P. Wincker and O. Jaillon},

url = {https://www.ncbi.nlm.nih.gov/pubmed/27901108},

doi = {10.1038/srep37900},

issn = {2045-2322 (Electronic) 

2045-2322 (Linking)},

year  = {2016},

date = {2016-01-01},

journal = {Sci Rep},

volume = {6},

pages = {37900},

abstract = {Bathycoccus is a cosmopolitan green micro-alga belonging to the Mamiellophyceae, a class of picophytoplankton that contains important contributors to oceanic primary production. A single species of Bathycoccus has been described while the existence of two ecotypes has been proposed based on metagenomic data. A genome is available for one strain corresponding to the described phenotype. We report a second genome assembly obtained by a single cell genomics approach corresponding to the second ecotype. The two Bathycoccus genomes are divergent enough to be unambiguously distinguishable in whole DNA metagenomic data although they possess identical sequence of the 18S rRNA gene including in the V9 region. Analysis of 122 global ocean whole DNA metagenome samples from the Tara-Oceans expedition reveals that populations of Bathycoccus that were previously identified by 18S rRNA V9 metabarcodes are only composed of these two genomes. Bathycoccus is relatively abundant and widely distributed in nutrient rich waters. The two genomes rarely co-occur and occupy distinct oceanic niches in particular with respect to depth. Metatranscriptomic data provide evidence for gain or loss of highly expressed genes in some samples, suggesting that the gene repertoire is modulated by environmental conditions.},

note = {Vannier, Thomas 

Leconte, Jade 

Seeleuthner, Yoann 

Mondy, Samuel 

Pelletier, Eric 

Aury, Jean-Marc 

de Vargas, Colomban 

Sieracki, Michael 

Iudicone, Daniele 

Vaulot, Daniel 

Wincker, Patrick 

Jaillon, Olivier 

eng 

Research Support, Non-U.S. Gov't 

Research Support, U.S. Gov't, Non-P.H.S. 

England 

Sci Rep. 2016 Nov 30;6:37900. doi: 10.1038/srep37900.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN44,

title = {Extreme Diversity of Diplonemid Eukaryotes in the Ocean},

author = {O. Flegontova and P. Flegontov and S. Malviya and S. Audic and P. Wincker and C. Vargas and C. Bowler and J. Lukes and A. Horak},

url = {https://www.ncbi.nlm.nih.gov/pubmed/27875689},

doi = {10.1016/j.cub.2016.09.031},

issn = {1879-0445 (Electronic) 

0960-9822 (Linking)},

year  = {2016},

date = {2016-01-01},

journal = {Curr Biol},

volume = {26},

number = {22},

pages = {3060-3065},

abstract = {The world's oceans represent by far the largest biome, with great importance for the global ecosystem [1-4]. The vast majority of ocean biomass and biodiversity is composed of microscopic plankton. Recent results from the Tara Oceans metabarcoding study revealed that a significant part of the plankton in the upper sunlit layer of the ocean is represented by an understudied group of heterotrophic excavate flagellates called diplonemids [5, 6]. We have analyzed the diversity and distribution patterns of diplonemid populations on the extended set of Tara Oceans V9 18S rDNA metabarcodes amplified from 850 size- fractionated plankton communities sampled across 123 globally distributed locations, for the first time also including samples from the mesopelagic zone, which spans the depth from about 200 to 1,000 meters. Diplonemids separate into four major clades, with the vast majority falling into the deep-sea pelagic diplonemid clade. Remarkably, diversity of this clade inferred from metabarcoding data surpasses even that of dinoflagellates, metazoans, and rhizarians, qualifying diplonemids as possibly the most diverse group of marine planktonic eukaryotes. Diplonemids display strong vertical separation between the photic and mesopelagic layers, with the majority of their relative abundance and diversity occurring in deeper waters. Globally, diplonemids display no apparent biogeographic structuring, with a few hyperabundant cosmopolitan operational taxonomic units (OTUs) dominating their communities. Our results suggest that the planktonic diplonemids are among the key heterotrophic players in the largest ecosystem of our biosphere, yet their roles in this ecosystem remain unknown.},

note = {Flegontova, Olga 

Flegontov, Pavel 

Malviya, Shruti 

Audic, Stephane 

Wincker, Patrick 

de Vargas, Colomban 

Bowler, Chris 

Lukes, Julius 

Horak, Ales 

eng 

Research Support, Non-U.S. Gov't 

England 

Curr Biol. 2016 Nov 21;26(22):3060-3065. doi: 10.1016/j.cub.2016.09.031.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN46,

title = {Full-field interferometry for counting and differentiating aquatic biotic nanoparticles: from laboratory to Tara Oceans},

author = {M. Boccara and Y. Fedala and C. V. Bryan and M. Bailly-Bechet and C. Bowler and A. C. Boccara},

url = {https://www.ncbi.nlm.nih.gov/pubmed/27699134},

doi = {10.1364/BOE.7.003736},

issn = {2156-7085 (Print) 

2156-7085 (Linking)},

year  = {2016},

date = {2016-01-01},

journal = {Biomed Opt Express},

volume = {7},

number = {9},

pages = {3736-3746},

abstract = {There is a huge abundance of viruses and membrane vesicles in seawater. We describe a new full-field, incoherently illuminated, shot-noise limited, common-path interferometric detection method that we couple with the analysis of Brownian motion to detect, quantify, and differentiate biotic nanoparticles. We validated the method with calibrated nanoparticles and homogeneous DNA or RNA viruses. The smallest virus size that we characterized with a suitable signal-to-noise ratio was around 30 nm in diameter. Analysis of Brownian motions revealed anisotropic trajectories for myoviruses.We further applied the method for vesicles detection and for analysis of coastal and oligotrophic samples from Tara Oceans circumnavigation.},

note = {Boccara, Martine 

Fedala, Yasmina 

Bryan, Catherine Venien 

Bailly-Bechet, Marc 

Bowler, Chris 

Boccara, Albert Claude 

eng 

Biomed Opt Express. 2016 Aug 29;7(9):3736-3746. doi: 10.1364/BOE.7.003736. eCollection 2016 Sep 1.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN68,

title = {Species delimitation in the reef coral genera Echinophyllia and Oxypora (Scleractinia, Lobophylliidae) with a description of two new species},

author = {R. Arrigoni and M. L. Berumen and C. A. Chen and T. I. Terraneo and A. H. Baird and C. Payri and F. Benzoni},

url = {https://www.ncbi.nlm.nih.gov/pubmed/27593164},

doi = {10.1016/j.ympev.2016.08.023},

issn = {1095-9513 (Electronic) 

1055-7903 (Linking)},

year  = {2016},

date = {2016-01-01},

journal = {Mol Phylogenet Evol},

volume = {105},

pages = {146-159},

abstract = {Scleractinian corals are affected by environment-induced phenotypic plasticity and intraspecific morphological variation caused by genotype. In an effort to identify new strategies for resolving this taxonomic issue, we applied a molecular approach for species evaluation to two closely related genera, Echinophyllia and Oxypora, for which few molecular data are available. A robust multi-locus phylogeny using DNA sequence data across four loci of both mitochondrial (COI, ATP6-NAD4) and nuclear (histone H3, ITS region) origin from 109 coral colonies was coupled with three independent putative species delimitation methods based on barcoding threshold (ABGD) and coalescence theory (PTP, GMYC). Observed overall congruence across multiple genetic analyses distinguished two traditional species (E. echinoporoides and O. convoluta), a species complex composed of E. aspera, E. orpheensis, E. tarae, and O. glabra, whereas O. lacera and E. echinata were indistinguishable with the sequenced loci. The combination of molecular species delimitation approaches and skeletal character observations allowed the description of two new reef coral species, E. bulbosa sp. n. from the Red Sea and E. gallii sp. n. from the Maldives and Mayotte. This work demonstrated the efficiency of multi-locus phylogenetic analyses and recently developed molecular species delimitation approaches as valuable tools to disentangle taxonomic issues caused by morphological ambiguities and to re-assess the diversity of scleractinian corals.},

note = {Arrigoni, Roberto 

Berumen, Michael L 

Chen, Chaolun Allen 

Terraneo, Tullia I 

Baird, Andrew H 

Payri, Claude 

Benzoni, Francesca 

eng 

Mol Phylogenet Evol. 2016 Dec;105:146-159. doi: 10.1016/j.ympev.2016.08.023. Epub 2016 Sep 1.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN232,

title = {When forms meet genes: Revision of the scleractinian genera Micromussa and Homophyllia (Lobophylliidae) with a description of two new species and one new genus},

author = {Roberto Arrigoni and Francesca Benzoni and Danwei Huang and Hironobu Fukami and Chaolun Chen and Michael Berumen and Mia Hoogenboom and Damian Thomson and Bert Hoeksema and Ann Budd and Yuna Zayasu and Tullia Isotta Terraneo and Yuko Kitano and Andrew Baird},

doi = {10.1163/18759866-08504002},

year  = {2016},

date = {2016-01-01},

journal = {Contributions to zoology Bijdragen tot de dierkunde},

volume = {85},

pages = {387-422},

keywords = {},

pubstate = {published},

tppubtype = {article}

}