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1. A refined picture of the native amine dehydrogenase family revealed by extensive biodiversity screening

Author: Eddy Elisée, Laurine Ducrot, Raphaël Méheust, Karine Bastard, Aurélie Fossey-Jouenne, Gideon Grogan, Eric Pelletier, Jean-Louis Petit, Mark Stam, Véronique de Berardinis, Anne Zaparucha, David Vallenet, and Carine Vergne-Vaxelaire
Subjects: Science
Abstract: Abstract Native amine dehydrogenases offer sustainable access to chiral amines, so the search for scaffolds capable of converting more diverse carbonyl compounds is required to reach the full potential of this alternative to conventional synthetic reductive aminations. Here we report a multidisciplinary strategy combining bioinformatics, chemoinformatics and biocatalysis to extensively screen billions of sequences in silico and to efficiently find native amine dehydrogenases features using computational approaches. In this way, we achieve a comprehensive overview of the initial native amine dehydrogenase family, extending it from 2,011 to 17,959 sequences, and identify native amine dehydrogenases with non-reported substrate spectra, including hindered carbonyls and ethyl ketones, and accepting methylamine and cyclopropylamine as amine donor. We also present preliminary model-based structural information to inform the design of potential (R)-selective amine dehydrogenases, as native amine dehydrogenases are mostly (S)-selective. This integrated strategy paves the way for expanding the resource of other enzyme families and in highlighting enzymes with original features.
Published: 2024
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2. Genomic adaptation of giant viruses in polar oceans

Author: Lingjie Meng, Tom O. Delmont, Morgan Gaïa, Eric Pelletier, Antonio Fernàndez-Guerra, Samuel Chaffron, Russell Y. Neches, Junyi Wu, Hiroto Kaneko, Hisashi Endo, and Hiroyuki Ogata
Subjects: Science
Abstract: 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.
Published: 2023
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3. Linking extreme seasonality and gene expression in Arctic marine protists

Author: Magdalena Wutkowska, Anna Vader, Ramiro Logares, Eric Pelletier, and Tove M. Gabrielsen
Subjects: Medicine, Science
Abstract: Abstract At high latitudes, strong seasonal differences in light availability affect marine organisms and regulate the timing of ecosystem processes. Marine protists are key players in Arctic aquatic ecosystems, yet little is known about their ecological roles over yearly cycles. This is especially true for the dark polar night period, which up until recently was assumed to be devoid of biological activity. A 12 million transcripts catalogue was built from 0.45 to 10 μm protist assemblages sampled over 13 months in a time series station in an Arctic fjord in Svalbard. Community gene expression was correlated with seasonality, with light as the main driving factor. Transcript diversity and evenness were higher during polar night compared to polar day. Light-dependent functions had higher relative expression during polar day, except phototransduction. 64% of the most expressed genes could not be functionally annotated, yet up to 78% were identified in Arctic samples from Tara Oceans, suggesting that Arctic marine assemblages are distinct from those from other oceans. Our study increases understanding of the links between extreme seasonality and biological processes in pico- and nanoplanktonic protists. Our results set the ground for future monitoring studies investigating the seasonal impact of climate change on the communities of microbial eukaryotes in the High Arctic.
Published: 2023
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4. Explainable artificial intelligence models for predicting risk of suicide using health administrative data in Quebec.

Author: Fatemeh Gholi Zadeh Kharrat, Christian Gagne, Alain Lesage, Geneviève Gariépy, Jean-François Pelletier, Camille Brousseau-Paradis, Louis Rochette, Eric Pelletier, Pascale Lévesque, Mada Mohammed, and JianLi Wang
Subjects: Medicine, Science
Abstract: Suicide is a complex, multidimensional event, and a significant challenge for prevention globally. Artificial intelligence (AI) and machine learning (ML) have emerged to harness large-scale datasets to enhance risk detection. In order to trust and act upon the predictions made with ML, more intuitive user interfaces must be validated. Thus, Interpretable AI is one of the crucial directions which could allow policy and decision makers to make reasonable and data-driven decisions that can ultimately lead to better mental health services planning and suicide prevention. This research aimed to develop sex-specific ML models for predicting the population risk of suicide and to interpret the models. Data were from the Quebec Integrated Chronic Disease Surveillance System (QICDSS), covering up to 98% of the population in the province of Quebec and containing data for over 20,000 suicides between 2002 and 2019. We employed a case-control study design. Individuals were considered cases if they were aged 15+ and had died from suicide between January 1st, 2002, and December 31st, 2019 (n = 18339). Controls were a random sample of 1% of the Quebec population aged 15+ of each year, who were alive on December 31st of each year, from 2002 to 2019 (n = 1,307,370). We included 103 features, including individual, programmatic, systemic, and community factors, measured up to five years prior to the suicide events. We trained and then validated the sex-specific predictive risk model using supervised ML algorithms, including Logistic Regression (LR), Random Forest (RF), Extreme Gradient Boosting (XGBoost) and Multilayer perceptron (MLP). We computed operating characteristics, including sensitivity, specificity, and Positive Predictive Value (PPV). We then generated receiver operating characteristic (ROC) curves to predict suicides and calibration measures. For interpretability, Shapley Additive Explanations (SHAP) was used with the global explanation to determine how much the input features contribute to the models' output and the largest absolute coefficients. The best sensitivity was 0.38 with logistic regression for males and 0.47 with MLP for females; the XGBoost Classifier with 0.25 for males and 0.19 for females had the best precision (PPV). This study demonstrated the useful potential of explainable AI models as tools for decision-making and population-level suicide prevention actions. The ML models included individual, programmatic, systemic, and community levels variables available routinely to decision makers and planners in a public managed care system. Caution shall be exercised in the interpretation of variables associated in a predictive model since they are not causal, and other designs are required to establish the value of individual treatments. The next steps are to produce an intuitive user interface for decision makers, planners and other stakeholders like clinicians or representatives of families and people with live experience of suicidal behaviors or death by suicide. For example, how variations in the quality of local area primary care programs for depression or substance use disorders or increased in regional mental health and addiction budgets would lower suicide rates.
Published: 2024
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5. Genomic adaptation of the picoeukaryote Pelagomonas calceolata to iron-poor oceans revealed by a chromosome-scale genome sequence

Author: Nina Guérin, Marta Ciccarella, Elisa Flamant, Paul Frémont, Sophie Mangenot, Benjamin Istace, Benjamin Noel, Caroline Belser, Laurie Bertrand, Karine Labadie, Corinne Cruaud, Sarah Romac, Charles Bachy, Martin Gachenot, Eric Pelletier, Adriana Alberti, Olivier Jaillon, Patrick Wincker, Jean-Marc Aury, and Quentin Carradec
Subjects: Biology (General), QH301-705.5
Abstract: Genomic inference reveals potential climate change-driven range expansion of the phytoplankton species Pelagomonas calceolata.
Published: 2022
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6. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

Author: Daniel J Richter, Romain Watteaux, Thomas Vannier, Jade Leconte, Paul Frémont, Gabriel Reygondeau, Nicolas Maillet, Nicolas Henry, Gaëtan Benoit, Ophélie Da Silva, Tom O Delmont, Antonio Fernàndez-Guerra, Samir Suweis, Romain Narci, Cédric Berney, Damien Eveillard, Frederick Gavory, Lionel Guidi, Karine Labadie, Eric Mahieu, Julie Poulain, Sarah Romac, Simon Roux, Céline Dimier, Stefanie Kandels, Marc Picheral, Sarah Searson, Tara Oceans Coordinators, Stéphane Pesant, Jean-Marc Aury, Jennifer R Brum, Claire Lemaitre, Eric Pelletier, Peer Bork, Shinichi Sunagawa, Fabien Lombard, Lee Karp-Boss, Chris Bowler, Matthew B Sullivan, Eric Karsenti, Mahendra Mariadassou, Ian Probert, Pierre Peterlongo, Patrick Wincker, Colomban de Vargas, Maurizio Ribera d'Alcalà, Daniele Iudicone, and Olivier Jaillon
Subjects: plankton biogeography, metagenomics, metabarcoding, microbial oceanography, Medicine, Science, Biology (General), QH301-705.5
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.
Published: 2022
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7. Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods

Author: Juan José Pierella Karlusich, Eric Pelletier, Fabien Lombard, Madeline Carsique, Etienne Dvorak, Sébastien Colin, Marc Picheral, Francisco M. Cornejo-Castillo, Silvia G. Acinas, Rainer Pepperkok, Eric Karsenti, Colomban de Vargas, Patrick Wincker, Chris Bowler, and Rachel A. Foster
Subjects: Science
Abstract: Nitrogen fixation by diazotrophs is critical for marine primary production. Using Tara Oceans datasets, this study combines a quantitative image analysis pipeline with metagenomic mining to provide an improved global overview of diazotroph abundance, diversity and distribution.
Published: 2021
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8. A de novo approach to disentangle partner identity and function in holobiont systems

Author: Arnaud Meng, Camille Marchet, Erwan Corre, Pierre Peterlongo, Adriana Alberti, Corinne Da Silva, Patrick Wincker, Eric Pelletier, Ian Probert, Johan Decelle, Stéphane Le Crom, Fabrice Not, and Lucie Bittner
Subjects: Holobiont, Meta-transcriptomic, De novo assembly, Marine, Plankton, k-mer based similarity, Microbial ecology, QR100-130
Abstract: Abstract Background Study of meta-transcriptomic datasets involving non-model organisms represents bioinformatic challenges. The production of chimeric sequences and our inability to distinguish the taxonomic origins of the sequences produced are inherent and recurrent difficulties in de novo assembly analyses. As the study of holobiont meta-transcriptomes is affected by challenges invoked above, we propose an innovative bioinformatic approach to tackle such difficulties and tested it on marine models as a proof of concept. Results We considered three holobiont models, of which two transcriptomes were previously published and a yet unpublished transcriptome, to analyze and sort their raw reads using Short Read Connector, a k-mer based similarity method. Before assembly, we thus defined four distinct categories for each holobiont meta-transcriptome: host reads, symbiont reads, shared reads, and unassigned reads. Afterwards, we observed that independent de novo assemblies for each category led to a diminution of the number of chimeras compared to classical assembly methods. Moreover, the separation of each partner’s transcriptome offered the independent and comparative exploration of their functional diversity in the holobiont. Finally, our strategy allowed to propose new functional annotations for two well-studied holobionts (a Cnidaria-Dinophyta, a Porifera-Bacteria) and a first meta-transcriptome from a planktonic Radiolaria-Dinophyta system forming widespread symbiotic association for which our knowledge is considerably limited. Conclusions In contrast to classical assembly approaches, our bioinformatic strategy generates less de novo assembled chimera and allows biologists to study separately host and symbiont data from a holobiont mixture. The pre-assembly separation of reads using an efficient tool as Short Read Connector is an effective way to tackle meta-transcriptomic challenges and offers bright perpectives to study holobiont systems composed of either well-studied or poorly characterized symbiotic lineages and ultimately expand our knowledge about these associations.
Published: 2018
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9. Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans

Author: Yoann Seeleuthner, Samuel Mondy, Vincent Lombard, Quentin Carradec, Eric Pelletier, Marc Wessner, Jade Leconte, Jean-François Mangot, Julie Poulain, Karine Labadie, Ramiro Logares, Shinichi Sunagawa, Véronique de Berardinis, Marcel Salanoubat, Céline Dimier, Stefanie Kandels-Lewis, Marc Picheral, Sarah Searson, Tara Oceans Coordinators, Stephane Pesant, Nicole Poulton, Ramunas Stepanauskas, Peer Bork, Chris Bowler, Pascal Hingamp, Matthew B. Sullivan, Daniele Iudicone, Ramon Massana, Jean-Marc Aury, Bernard Henrissat, Eric Karsenti, Olivier Jaillon, Mike Sieracki, Colomban de Vargas, and Patrick Wincker
Subjects: Science
Abstract: The biology of many marine protists, such as stramenopiles, remains obscure. Here, the authors exploit single-cell genomics and metagenomics to analyze the genome content and apparent oceanic distribution of seven prevalent lineages of uncultured heterotrophic stramenopiles.
Published: 2018
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10. A global ocean atlas of eukaryotic genes

Author: Quentin Carradec, Eric Pelletier, Corinne Da Silva, Adriana Alberti, Yoann Seeleuthner, Romain Blanc-Mathieu, Gipsi Lima-Mendez, Fabio Rocha, Leila Tirichine, Karine Labadie, Amos Kirilovsky, Alexis Bertrand, Stefan Engelen, Mohammed-Amin Madoui, Raphaël Méheust, Julie Poulain, Sarah Romac, Daniel J. Richter, Genki Yoshikawa, Céline Dimier, Stefanie Kandels-Lewis, Marc Picheral, Sarah Searson, Tara Oceans Coordinators, Olivier Jaillon, Jean-Marc Aury, Eric Karsenti, Matthew B. Sullivan, Shinichi Sunagawa, Peer Bork, Fabrice Not, Pascal Hingamp, Jeroen Raes, Lionel Guidi, Hiroyuki Ogata, Colomban de Vargas, Daniele Iudicone, Chris Bowler, and Patrick Wincker
Subjects: Science
Abstract: Marine microbial eukaryotes and zooplankton display enormous diversity and largely unexplored physiologies. Here, the authors use metatranscriptomics to analyze four organismal size fractions from open-ocean stations, providing the largest reference collection of eukaryotic transcripts from any single biome.
Published: 2018
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11. Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels

Author: Lizbeth Sayavedra, Manuel Kleiner, Ruby Ponnudurai, Silke Wetzel, Eric Pelletier, Valerie Barbe, Nori Satoh, Eiichi Shoguchi, Dennis Fink, Corinna Breusing, Thorsten BH Reusch, Philip Rosenstiel, Markus B Schilhabel, Dörte Becher, Thomas Schweder, Stephanie Markert, Nicole Dubilier, and Jillian M Petersen
Subjects: symbiosis, sulfur oxidizer, toxins, Bathymodiolus, Medicine, Science, Biology (General), QH301-705.5
Abstract: Bathymodiolus mussels live in symbiosis with intracellular sulfur-oxidizing (SOX) bacteria that provide them with nutrition. We sequenced the SOX symbiont genomes from two Bathymodiolus species. Comparison of these symbiont genomes with those of their closest relatives revealed that the symbionts have undergone genome rearrangements, and up to 35% of their genes may have been acquired by horizontal gene transfer. Many of the genes specific to the symbionts were homologs of virulence genes. We discovered an abundant and diverse array of genes similar to insecticidal toxins of nematode and aphid symbionts, and toxins of pathogens such as Yersinia and Vibrio. Transcriptomics and proteomics revealed that the SOX symbionts express the toxin-related genes (TRGs) in their hosts. We hypothesize that the symbionts use these TRGs in beneficial interactions with their host, including protection against parasites. This would explain why a mutualistic symbiont would contain such a remarkable ‘arsenal’ of TRGs.
Published: 2015
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12. Enrichment and genome sequence of the group I.1a ammonia-oxidizing Archaeon 'Ca. Nitrosotenuis uzonensis' representing a clade globally distributed in thermal habitats.

Author: Elena V Lebedeva, Roland Hatzenpichler, Eric Pelletier, Nathalie Schuster, Sandra Hauzmayer, Aleksandr Bulaev, Nadezhda V Grigor'eva, Alexander Galushko, Markus Schmid, Marton Palatinszky, Denis Le Paslier, Holger Daims, and Michael Wagner
Subjects: Medicine, Science
Abstract: The discovery of ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota and the high abundance of archaeal ammonia monooxygenase subunit A encoding gene sequences in many environments have extended our perception of nitrifying microbial communities. Moreover, AOA are the only aerobic ammonia oxidizers known to be active in geothermal environments. Molecular data indicate that in many globally distributed terrestrial high-temperature habits a thaumarchaeotal lineage within the Nitrosopumilus cluster (also called "marine" group I.1a) thrives, but these microbes have neither been isolated from these systems nor functionally characterized in situ yet. In this study, we report on the enrichment and genomic characterization of a representative of this lineage from a thermal spring in Kamchatka. This thaumarchaeote, provisionally classified as "Candidatus Nitrosotenuis uzonensis", is a moderately thermophilic, non-halophilic, chemolithoautotrophic ammonia oxidizer. The nearly complete genome sequence (assembled into a single scaffold) of this AOA confirmed the presence of the typical thaumarchaeotal pathways for ammonia oxidation and carbon fixation, and indicated its ability to produce coenzyme F420 and to chemotactically react to its environment. Interestingly, like members of the genus Nitrosoarchaeum, "Candidatus N. uzonensis" also possesses a putative artubulin-encoding gene. Genome comparisons to related AOA with available genome sequences confirmed that the newly cultured AOA has an average nucleotide identity far below the species threshold and revealed a substantial degree of genomic plasticity with unique genomic regions in "Ca. N. uzonensis", which potentially include genetic determinants of ecological niche differentiation.
Published: 2013
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13. Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA.

Author: Téo Lemane, Nolan Lezzoche, Julien Lecubin, Eric Pelletier, Magali Lescot, Rayan Chikhi, and Pierre Peterlongo
Published: 2024
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14. Establishing the ELIXIR Microbiome Community [version 1; peer review: awaiting peer review]

Author: Robert D. Finn, Bachir Balech, Josephine Burgin, Physilia Chua, Erwan Corre, Cymon J. Cox, Claudio Donati, Vitor Martins dos Santos, Bruno Fosso, John Hancock, Katharina F. Heil, Naveed Ishaque, Varsha Kale, Benoit J. Kunath, Claudine Médigue, Evangelos Pafilis, Graziano Pesole, Lorna Richardson, Monica Santamaria, Tim Van Den Bossche, Juan Antonio Vizcaíno, Haris Zafeiropoulos, Nils P. Willassen, Eric Pelletier, and Bérénice Batut
Subjects: Opinion Article, Articles, Microbiome, ELIXIR Community, White Paper
Abstract: Microbiome research has grown substantially over the past decade in terms of the range of biomes sampled, identified taxa, and the volume of data derived from the samples. In particular, experimental approaches such as metagenomics, metabarcoding, metatranscriptomics and metaproteomics have provided profound insights into the vast, hitherto unknown, microbial biodiversity. The ELIXIR Marine Metagenomics Community, initiated amongst researchers focusing on marine microbiomes, has concentrated on promoting standards around microbiome-derived sequence analysis, as well as understanding the gaps in methods and reference databases, and solutions to computational overheads of performing such analyses. Nevertheless, the methods used and the challenges faced are not confined to marine studies, but are broadly applicable to all other biomes. Thus, expanding this Community to a more inclusive ELIXIR Microbiome Community will enable it to encompass a broad range of biomes and link expertise across ‘omics technologies. Furthermore, engaging with a large number of researchers will improve the efficiency and sustainability of bioinformatics infrastructure and resources for microbiome research (standards, data, tools, workflows, training), which will enable a deeper understanding of the function and taxonomic composition of the different microbial communities.
Published: 2024
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15. The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes.

Author: Caroline Vernette, Julien Lecubin, Pablo Sánchez, Silvia G. Acinas, Marcel Babin, Peer Bork, Emmanuel Boss, Chris Bowler, Guy Cochrane, Colomban de Vargas, Gabriel Gorsky, Lionel Guidi, Nigel Grimsley, Pascal Hingamp, Daniele Iudicone, Olivier Jaillon, Stefanie Kandels-Lewis, Lee Karp-Boss, Eric Karsenti, Fabrice Not, Hiroyuki Ogata, Nicole Poulton, Stephane Pesant, Christian Sardet, Sabrina Speich, Lars Stemmann, Matthew B. Sullivan, Shinichi Sunagawa, Patrick Wincker, Tom O. Delmont, Eric Pelletier, and Magali Lescot
Published: 2022
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16. Mirusviruses link herpesviruses to giant viruses

Author: Morgan Gaïa, Lingjie Meng, Eric Pelletier, Patrick Forterre, Chiara Vanni, Antonio Fernandez-Guerra, Olivier Jaillon, Patrick Wincker, Hiroyuki Ogata, Mart Krupovic, Tom O. Delmont, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Global Oceans Systems Ecology & Evolution - Tara Oceans (GOSEE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Aix Marseille Université (AMU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Université de Toulon (UTLN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche pour le Développement (IRD [France-Nord])-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-European Molecular Biology Laboratory (EMBL)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Université australe du Chili, Kyoto University, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Département de Microbiologie - Department of Microbiology, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Universität Bremen, University of Copenhagen = Københavns Universitet (UCPH), Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), This study was supported in part by FRANCE GENOMIQUE (ANR-10-INBS-09), the Japan Society for the Promotion of Science KAKENHI (18H02279 and 22H00384), the Research Unit for Development of Global Sustainability, Kyoto University Research Coordination Alliance, and the International Collaborative Research Program of the Institute for Chemical Research, Kyoto University (2022-26, 2021-29 and 2020-28). M.K. was supported by grants from the l’Agence Nationale de la Recherche (ANR-20-CE20-0009-02 and ANR-21-CE11-0001-01), M.G. was supported by ANR ALGALVIRUS ANR-17-CE02-0012, and T.O.D. was supported by ANR HYDROGEN ANR-14-CE23-0001., ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-20-CE20-0009,VIROMET,Devoiler le virome des archées methanogenes(2020), ANR-21-CE11-0001,ArcFus,Protéines de classe II de fusion membranaire chez les archées(2021), ANR-17-CE02-0012,ALGALVIRUS,Adaptations Génomique des Algues Marines aux Virus(2017), and ANR-14-CE23-0001,HydroGen,Metagenomique comparative comme instrument de mesure pour la biodiversité. Application à l'étude de la vie dans les océans(2014)
Subjects: Marine biology, Phylogenetics, Multidisciplinary, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Metagenomics, Evolutionary genetics, Viral genetics
Abstract: DNA viruses have a major influence on the ecology and evolution of cellular organisms, but their overall diversity and evolutionary trajectories remain elusive. 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, 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., 新規ウイルス門の発見 --ヘルペスウイルスの起源の解明に寄与--. 京都大学プレスリリース. 2023-04-20.
Published: 2023
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17. The Ocean Gene Atlas: exploring the biogeography of plankton genes online.

Author: Emilie Villar, Thomas Vannier, Caroline Vernette, Magali Lescot, Miguelangel Cuenca, Aurélien Alexandre, Paul Bachelerie, Thomas Rosnet, Eric Pelletier, Shinichi Sunagawa, and Pascal Hingamp
Published: 2018
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18. PhotoEukStein: Towards an omics-based definition of unicellular eukaryote phototrophs functional traits via metabolic modelling

Author: Marie Burel, Antoine Régimbeau, Samuel Chaffron, Damien Eveillard, and Eric Pelletier
Abstract: Defining biological functional traits for unicellular organisms relies on comprehending the set and combination of the biochemical reactions their genomes encode for. This network of biochemical reactions defines the metabolic strategy organisms and communities used to grow in a given environment. While prokaryotes have been the ideal target for reconstructing and analysing these metabolic networks, eukaryotes lagged behind due to the complexity of their genomes and the paucity of knowledge on their metabolism.Here, we developed PhotoEukstein, a meta-metabolic model for unicellular phototroph eukaryotes allowing a fast and automated top-down derivation of Genome-Scale Metabolic models directly from genomes. We applied it to a diverse collection of 559 environmental genomes and transcriptomes of marine eukaryote unicellular plankton.We show these models allow to predict functional traits that cannot be purely deducted from taxonomic information or listing of metabolic reactions encoded by the genome. They provide the opportunity to build connections with Earth System Models to pinpoint environmental parameters needed to parametrise specific functional traits.
Published: 2023
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19. Genomic adaptation of the picoeukaryote $Pelagomonas\ calceolata$ to iron-poor oceans revealed by a chromosome-scale genome sequence

Author: Nina Guérin, Marta Ciccarella, Elisa Flamant, Paul Frémont, Sophie Mangenot, Benjamin Istace, Benjamin Noel, Caroline Belser, Laurie Bertrand, Karine Labadie, Corinne Cruaud, Sarah Romac, Charles Bachy, Martin Gachenot, Eric Pelletier, Adriana Alberti, Olivier Jaillon, Patrick Wincker, Jean-Marc Aury, Quentin Carradec, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Global Oceans Systems Ecology & Evolution - Tara Oceans (GOSEE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Aix Marseille Université (AMU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Université de Toulon (UTLN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche pour le Développement (IRD [France-Nord])-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-European Molecular Biology Laboratory (EMBL)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Université australe du Chili, Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Thank the Tara Expedition Foundation and their partners for the organization of marine scientific expeditions (http://oceans.taraexpeditions.org), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), and ANR-11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011)
Subjects: Nitrates, Acclimatization, Iron, Oceans and Seas, Medicine (miscellaneous), Genomics, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Chromosomes, General Biochemistry, Genetics and Molecular Biology, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Phytoplankton, General Agricultural and Biological Sciences, Stramenopiles
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.
Published: 2022
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20. Genomic differentiation of three pico‐phytoplankton species in the Mediterranean Sea

Author: Ophélie Da Silva, Sakina‐Dorothée Ayata, Enrico Ser‐Giacomi, Jade Leconte, Eric Pelletier, Cécile Fauvelot, Mohammed‐Amin Madoui, Lionel Guidi, Fabien Lombard, Lucie Bittner, Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Sorbonne Université (SU), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)
Subjects: [SDV.EE]Life Sciences [q-bio]/Ecology, environment, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BID]Life Sciences [q-bio]/Biodiversity, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Microbiology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, Ecology, Evolution, Behavior and Systematics, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; For more than a decade, high-throughput sequencing has transformed the study of marine planktonic communities and has highlighted the extent of protist diversity in these ecosystems. Nevertheless, little is known relative to their genomic diversity at the species-scale as well as their major speciation mechanisms. An increasing number of data obtained from global scale sampling campaigns is becoming publicly available, and we postulate that metagenomic data could contribute to deciphering the processes shaping protist genomic differentiation in the marine realm. As a proof of concept, we developed a findable, accessible, interoperable and reusable (FAIR) pipeline and focused on the Mediterranean Sea to study three a priori abundant protist species: Bathycoccus prasinos, Pelagomonas calceolata and Phaeocystis cordata. We compared the genomic differentiation of each species in light of geographic, environmental and oceanographic distances. We highlighted that isolation-byenvironment shapes the genomic differentiation of B. prasinos, whereas P. cordata is impacted by geographic distance (i.e. isolation-by-distance). At present time, the use of metagenomics to accurately estimate the genomic differentiation of protists remains challenging since coverages are lower compared to traditional population surveys. However, our approach sheds light on ecological and evolutionary processes occurring within natural marine populations and paves the way for future protist population metagenomic studies.
Published: 2022
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21. Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae

Author: Richard G Dorrell, Alan Kuo, Zoltan Füssy, Elisabeth H Richardson, Asaf Salamov, Nikola Zarevski, Nastasia J Freyria, Federico M Ibarbalz, Jerry Jenkins, Juan Jose Pierella Karlusich, Andrei Stecca Steindorff, Robyn E Edgar, Lori Handley, Kathleen Lail, Anna Lipzen, Vincent Lombard, John McFarlane, Charlotte Nef, Anna MG Novák Vanclová, Yi Peng, Chris Plott, Marianne Potvin, Fabio Rocha Jimenez Vieira, Kerrie Barry, Colomban de Vargas, Bernard Henrissat, Eric Pelletier, Jeremy Schmutz, Patrick Wincker, Joel B Dacks, Chris Bowler, Igor V Grigoriev, Connie Lovejoy, Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Charles University [Prague] (CU), University of Alberta, Université Laval [Québec] (ULaval), HudsonAlpha Genome Sequencing Center, University of Alabama in Huntsville (UAH), Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), King Abdulaziz University, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), ANR-21-CE02-0014,PanArctica,Caractérisation phylogénétique, écologique et physiologique de le pan-génome des algues Arctiques(2021), and ANR-22-ERCS-0018,ChloroMosaic,Caractérisation moléculaire du réussite environnemental de la chloroplaste secondaire rouge(2022)
Subjects: Ecology, Bacteria, Arctic Regions, Health, Toxicology and Mutagenesis, Oceans and Seas, Gene Transfer, Plant Science, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biochemistry, Genetics and Molecular Biology (miscellaneous), Horizontal, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Microalgae, Ice Cover, Life Below Water
Abstract: Microbial communities in the world ocean are affected strongly by oceanic circulation, creating characteristic marine biomes. The high connectivity of most of the ocean makes it difficult to disentangle selective retention of colonizing genotypes (with traits suited to biome specific conditions) from evolutionary selection, which would act on founder genotypes over time. The Arctic Ocean is exceptional with limited exchange with other oceans and ice covered since the last ice age. To test whether Arctic microalgal lineages evolved apart from algae in the global ocean, we sequenced four lineages of microalgae isolated from Arctic waters and sea ice. Here we show convergent evolution and highlight geographically limited HGT as an ecological adaptive force in the form of PFAM complements and horizontal acquisition of key adaptive genes. Notably, ice-binding proteins were acquired and horizontally transferred among Arctic strains. A comparison withTaraOceans metagenomes and metatranscriptomes confirmed mostly Arctic distributions of these IBPs. The phylogeny of Arctic-specific genes indicated that these events were independent of bacterial-sourced HGTs in Antarctic Southern Ocean microalgae.
Published: 2022
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22. Changes in functional composition and gene expression in eukaryotic plankton at the Atlantic-Arctic Polar front

Author: Paul Frémont, Corinne Da Silva, Lucia Campese, Émilie Villar, Achal Rastogi, Jean-Marc Aury, Chris Bowler, Lee Karp Boss, Patrick Wincker, Eric Pelletier, Marion Gehlen, Daniele Iudicone, and Olivier Jaillon
Abstract: Planktonic communities are shaped by ocean currents and participate in multiple global biogeochemical cycles. Unraveling how the functions of communities respond to strong environmental gradients will improve our understanding of the interactions between climate change and marine ecosystems. Here, we investigate changes in functions and gene expression of eukaryotic plankton transiting between the North Atlantic Ocean (NAO) in winter and the Arctic Ocean (AO) in spring/summer using metatranscriptomes and metagenomes fromTaraOceans. In Arctic communities, functions involved in maintaining the protein pool and translation machinery appear to be more active. Four major phylogenetically distant algal groups are abundant in both basins and show similar strategies at transcriptional level, including increased expression of some functions related to cold acclimation. These results shade lights on gene expression strategies shared by cosmopolitan phototrophs of widely separated lineages.
Published: 2022
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23. Author Reply to Peer Reviews of Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae

Author: Richard G Dorrell, Alan Kuo, Zoltan Fussy, Elisabeth H Richardson, Asaf Salamov, Nikola Zarevski, Nastasia J Freyria, Federico M Ibarbalz, Jerry Jenkins, Juan J Pierella Karlusich, Andrei Stecca Steindorff, Robyn E Edgar, Lori Howell Handley, Kathleen Lail, Anna Lipzen, Vincent Lombard, John McFarlane, Charlotte Nef, Anna MG Novak Vanclova, Yi Peng, Chris Plott, Marianne Potvin, FABIO RJ Vieira, Kerrie Barry, Colomban de Vargas, Bernard Henrissat, Eric Pelletier, Jeremy Schmutz, Patrick Wincker, Joel B. Dacks, Chris Bowler, Igor Vasilij Grigoriev, and Connie Lovejoy
Published: 2022
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24. Late Pennsylvanian–Early Permian Tectonically Driven Stratigraphic Sequences and Carbonate Sedimentation Along Northern Margin of Sverdrup Basin (Otto Fiord Depression, Arctic Canada)

Author: Benoit Beauchamp, Daniel Calvo González, Charles M. Henderson, Daria V. Baranova, Hanyue Wang, and Eric Pelletier
Abstract: A thick succession of upper Paleozoic carbonate rocks and minor chert crops out north of the head of Otto Fiord (northwest [NW] Ellesmere Island, Nunavut) in the Canadian Arctic Archipelago. These rocks accumulated in a tectonic subbasin—the Otto Fiord Depression (OFD)—of the Sverdrup Basin that likely originated through rifting during late Early Carboniferous (Serpukhovian). Following a long interval of passive subsidence that allowed a thick succession of Moscovian–Kasimovian carbonate rocks to fill the OFD, tectonic activity resumed during the Gzhelian (Late Pennsylvanian). This resulted in rapid collapse of the depression along its axis and simultaneous uplifts of its margins, a style of tectonism in accord with the inferred basin-wide shift to a transpressional–transtensional stress regime at that time. Late Pennsylvanian–Early Permian sedimentation in the OFD led to the development of four long-term (second-order) transgressive–regressive sequences of early Gzhelian–middle Asselian (
Published: 2022
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25. Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean

Author: Tom O. Delmont, Morgan Gaia, Damien D. Hinsinger, Paul Frémont, Chiara Vanni, Antonio Fernandez-Guerra, A. Murat Eren, Artem Kourlaiev, Leo d'Agata, Quentin Clayssen, Emilie Villar, Karine Labadie, Corinne Cruaud, Julie Poulain, Corinne Da Silva, Marc Wessner, Benjamin Noel, Jean-Marc Aury, Colomban de Vargas, Chris Bowler, Eric Karsenti, Eric Pelletier, Patrick Wincker, Olivier Jaillon, Shinichi Sunagawa, Silvia G. Acinas, Peer Bork, Christian Sardet, Lars Stemmann, Magali Lescot, Marcel Babin, Gabriel Gorsky, Nigel Grimsley, Lionel Guidi, Pascal Hingamp, Stefanie Kandels, Daniele Iudicone, Hiroyuki Ogata, Stéphane Pesant, Matthew B. Sullivan, Fabrice Not, Karp-Boss Lee, Emmanuel Boss, Guy Cochrane, Michael Follows, Nicole Poulton, Jeroen Raes, Mike Sieracki, Sabrina Speich, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Tara Oceans-GOSEE (FR2022), Centre for GeoGenetics, Natural History Museum of Denmark, Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), The University of Chicago Medicine [Chicago], Life & Soft [Fontenay-aux-Roses], Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie physico-chimique (IBPC (FR_550)), BABIN, Marcel, Global Oceans Systems Ecology & Evolution - Tara Oceans (GOSEE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Aix Marseille Université (AMU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Université de Toulon (UTLN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche pour le Développement (IRD [France-Nord])-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-European Molecular Biology Laboratory (EMBL)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Université australe du Chili, ANR-17-CE02-0012,ALGALVIRUS,Adaptations Génomique des Algues Marines aux Virus(2017), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, University of Copenhagen = Københavns Universitet (UCPH), Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Carl Von Ossietzky Universität Oldenburg = Carl von Ossietzky University of Oldenburg (OFFIS), Tara Oceans Coordinators, Agencia Estatal de Investigación (España), Carl Von Ossietzky Universität Oldenburg, and Not, Fabrice
Subjects: [SDE] Environmental Sciences, functions, metagenomics, Tara Oceans, Planktonic eukaryotes, Genomics metagenomics, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, anvi'o, evolution, [SDE]Environmental Sciences, genomics, anvi’o, ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Conserve and sustainably use the oceans, seas and marine resources for sustainable development
Abstract: 18 pages, 4 figures, supplemental information https://doi.org/10.1016/j.xgen.2022.100123.-- Data and code availability: • All data our study generated are publicly available at http://www.genoscope.cns.fr/tara/. The link provides access to the 11 raw metagenomic co-assemblies, the FASTA files for 713 MAGs and SAGs, the ∼10 million protein-coding sequences (nucleotides, amino acids and gff format), and the curated DNA-dependent RNA polymerase genes (MAGs and SAGs and METdb transcriptomes). This link also provides access to the supplemental figures and the Supplemental material. Finally, code development within anvi’o for the BUSCO single copy core genes is available at https://github.com/merenlab/anvio. • Original code has been deposited at Zenodo and is publicly available. The accession number is listed in the key resources table. • Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request, Marine planktonic eukaryotes play critical roles in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billion Tara Oceans metagenomic reads from polar, temperate, and tropical sunlit oceans to reconstruct and manually curate more than 700 abundant and widespread eukaryotic environmental genomes ranging from 10 Mbp to 1.3 Gbp. This genomic resource covers a wide range of poorly characterized eukaryotic lineages that complement long-standing contributions from culture collections while better representing plankton in the upper layer of the oceans. We performed the first, to our knowledge, comprehensive genome-wide functional classification of abundant unicellular eukaryotic plankton, revealing four major groups connecting distantly related lineages. Neither trophic modes of plankton nor its vertical evolutionary history could completely explain the functional repertoire convergence of major eukaryotic lineages that coexisted within oceanic currents for millions of years, Tara Oceans (which includes the Tara Oceans and Tara Oceans Polar Circle expeditions) would not exist without the leadership of the Tara Ocean Foundation and the continuous support of 23 institutes (https://oceans.taraexpeditions.org/). We thank the commitment of the following people and sponsors who made this singular expedition possible: CNRS (in particular Groupement de Recherche GDR3280 and the Research Federation for the Study of Global Ocean Systems Ecology and Evolution FR2022/Tara GOSEE), the European Molecular Biology Laboratory (EMBL), Genoscope/CEA, the French Ministry of Research and the French Governement ‘Investissement d’Avenir’ programs Oceanomics (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09), ATIGE Genopole postdoctoral fellowship, HYDROGEN/ANR-14-CE23-0001, MEMO LIFE (ANR-10-LABX-54), PSL Research University (ANR-11-IDEX-0001-02) and EMBRC-France (ANR-10-INBS-02), Fund for Scientific Research—Flanders, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR (projects ALGALVIRUS ANR-17-CE02- 0012, PHYTBACK/ANR-2010-1709-01, POSEIDON/ANR-09-BLAN-0348, PROMETHEUS/ANR-09-PCS-GENM-217, TARA-GIRUS/ANR-09-PCS-GENM-218), EU FP7 (MicroB3/No. 287589, IHMS/HEALTH-F4-2010-261376), Genopole, CEA DRF Impulsion program, OCEANOMICS (project no. ANR-11-BTBR-0008), ERC Advanced Award Diatomic (grant agreement No 835067) to CB. The authors also thank Agnès B. and E. Bourgois, the Prince Albert II de Monaco Foundation, the Veolia Foundation, the EDF Foundation, Region Bretagne, Lorient Agglomeration, Worldcourier, Illumina, Serge Ferrari, and the Fonds Francais pour l'Environnement Mondial for support and commitment. [...] Part of the computations were performed using the platine, titane, and curie HPC machine provided through GENCI grants (t2011076389, t2012076389, t2013036389, t2014036389, t2015036389, and t2016036389, With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)
Published: 2022
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26. Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome

Author: Ahmed A, Zayed, James M, Wainaina, Guillermo, Dominguez-Huerta, Eric, Pelletier, Jiarong, Guo, Mohamed, Mohssen, Funing, Tian, Akbar Adjie, Pratama, Benjamin, Bolduc, Olivier, Zablocki, Dylan, Cronin, Lindsey, Solden, Erwan, Delage, Adriana, Alberti, Jean-Marc, Aury, Quentin, Carradec, Corinne, da Silva, Karine, Labadie, Julie, Poulain, Hans-Joachim, Ruscheweyh, Guillem, Salazar, Elan, Shatoff, Ralf, Bundschuh, Kurt, Fredrick, Laura S, Kubatko, Samuel, Chaffron, Alexander I, Culley, Shinichi, Sunagawa, Jens H, Kuhn, Patrick, Wincker, Matthew B, Sullivan, Silvia G, Acinas, Marcel, Babin, Peer, Bork, Emmanuel, Boss, Chris, Bowler, Guy, Cochrane, Colomban, de Vargas, Gabriel, Gorsky, Lionel, Guidi, Nigel, Grimsley, Pascal, Hingamp, Daniele, Iudicone, Olivier, Jaillon, Stefanie, Kandels, Lee, Karp-Boss, Eric, Karsenti, Fabrice, Not, Hiroyuki, Ogata, Nicole, Poulton, Stéphane, Pesant, Christian, Sardet, Sabrinia, Speich, Lars, Stemmann, Shinichi, Sungawa, Department of Microbiology [Columbus], Ohio State University [Columbus] (OSU), Global Oceans Systems Ecology & Evolution - Tara Oceans (GOSEE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Aix Marseille Université (AMU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Université de Toulon (UTLN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche pour le Développement (IRD [France-Nord])-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-European Molecular Biology Laboratory (EMBL)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Université australe du Chili, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Combinatoire et Bioinformatique (LS2N - équipe COMBI), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Department of Physics, The Ohio State University, Department of Statistics, the Ohio State University Columbus, Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Université Laval [Québec] (ULaval), Institute of Microbiology, Department of Biology, ETH Zurich, Institute of Microbiology, Department of Microbiology, The Ohio state university, Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes université - UFR des Sciences et des Techniques (Nantes univ - UFR ST), Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Sciences et technologie, and Nantes Université (Nantes Univ)
Subjects: Multidisciplinary, Virome, Oceans and Seas, [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], Genome, Viral, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Biological Evolution, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDE]Environmental Sciences, Viruses, RNA, RNA Viruses, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecosystem, Phylogeny, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
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 ≈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.
Published: 2022
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27. A case–control study on predicting population risk of suicide using health administrative data: a research protocol

Author: JianLi Wang, Fatemeh Gholi Zadeh Kharrat, Jean-François Pelletier, Louis Rochette, Eric Pelletier, Pascale Lévesque, Victoria Massamba, Camille Brousseau-Paradis, Mada Mohammed, Geneviève Gariépy, Christian Gagné, and Alain Lesage
Subjects: General Medicine
Abstract: IntroductionSuicide has a complex aetiology and is a result of the interaction among the risk and protective factors at the individual, healthcare system and population levels. Therefore, policy and decision makers and mental health service planners can play an important role in suicide prevention. Although a number of suicide risk predictive tools have been developed, these tools were designed to be used by clinicians for assessing individual risk of suicide. There have been no risk predictive models to be used by policy and decision makers for predicting population risk of suicide at the national, provincial and regional levels. This paper aimed to describe the rationale and methodology for developing risk predictive models for population risk of suicide.Methods and analysisA case–control study design will be used to develop sex-specific risk predictive models for population risk of suicide, using statistical regression and machine learning techniques. Routinely collected health administrative data in Quebec, Canada, and community-level social deprivation and marginalisation data will be used. The developed models will be transformed into the models that can be readily used by policy and decision makers. Two rounds of qualitative interviews with end-users and other stakeholders were proposed to understand their views about the developed models and potential systematic, social and ethical issues for implementation; the first round of qualitative interviews has been completed. We included 9440 suicide cases (7234 males and 2206 females) and 661 780 controls for model development. Three hundred and forty-seven variables at individual, healthcare system and community levels have been identified and will be included in least absolute shrinkage and selection operator regression for feature selection.Ethics and disseminationThis study is approved by the Health Research Ethnics Committee of Dalhousie University, Canada. This study takes an integrated knowledge translation approach, involving knowledge users from the beginning of the process.
Published: 2023
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28. Plankton-infecting relatives of herpesviruses clarify the evolutionary trajectory of giant viruses

Author: Morgan Gaïa, Lingjie Meng, Eric Pelletier, Patrick Forterre, Chiara Vanni, Antonio Fernandez-Guerra, Olivier Jaillon, Patrick Wincker, Hiroyuki Ogata, Mart Krupovic, and Tom O. Delmont
Abstract: DNA viruses have a major influence on the ecology and evolution of cellular organisms, but their overall diversity and evolutionary trajectories remain elusive. Here, we performed 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 realmDuplodnaviria, with the major capsid protein fold being a likely structural intermediate between the capsid proteins ofCaudoviricetes(tailed phages) andHerpesvirales(animal-infecting viruses). Yet, a substantial fraction of ‘Mirusviricota’genes, including hallmark transcription machinery genes missing in herpesviruses, are closely related homologs of large and giant eukaryotic DNA viruses from another viral realm. The remarkable chimeric attributes of ‘Mirusviricota’ provide missing links in the evolution of both herpesviruses and giant viruses. Furthermore, mirusviruses are widespread and transcriptionally active from pole to pole, encoding complex functional traits used during the infection of microbial eukaryotes. The ‘Mirusviricota’ prevalence, functional activity, diversification, and atypical evolutionary traits point to a lasting role of mirusviruses in the ecology of marine ecosystems that might have not only predated but also contributed to the emergence of herpesviruses and giant viruses.
Published: 2021
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29. Functional repertoire convergence of distantly related eukaryotic plankton lineages revealed by genome-resolved metagenomics

Author: Emilie Villar, Corinne Cruaud, de Vargas C, Patrick Wincker, Chiara Vanni, Da Silva C, Chris Bowler, Karine Labadie, Julie Poulain, Clayssen Q, Eric Karsenti, Leo d’Agata, Guerra Af, Eric Pelletier, Olivier Jaillon, Eren Am, Kourlaiev A, Paul Frémont, Jean-Marc Aury, Morgan Gaia, Damien Daniel Hinsinger, Tom O. Delmont, Bernard Noël, Wessner M, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), The Globe Institute, The University of Chicago Medicine [Chicago], Station biologique de Roscoff, Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), European Molecular Biology Laboratory (EMBL), ANR-11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-09-GENM-0032,TARA-GIRUS,Inventaire et ressources génétiques de virus géants à ADN dans les milieux marins sur Tara-Oceans(2009), ANR-14-CE23-0001,HydroGen,Metagenomique comparative comme instrument de mesure pour la biodiversité. Application à l'étude de la vie dans les océans(2014), ANR-10-LABX-0054,MEMOLIFE,Memory in living systems: an integrated approach(2010), ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), ANR-10-INBS-0002,EMBRC-France,CENTRE NATIONAL DE RESSOURCES BIOLOGIQUES MARINES(2010), ANR-17-CE02-0012,ALGALVIRUS,Adaptations Génomique des Algues Marines aux Virus(2017), ANR-10-BLAN-1709,PHYTBACK,Rétroactions écologie-climat dues à l'évolution de la taille et de la forme du phytoplancton(2010), ANR-09-BLAN-0348,POSEIDON(2009), ANR-09-GENM-0031,PROMETHEUS,Approches génomiques pour l?analyse de la biodiversité fonctionnelle des protistes océaniques de l?expédition Tara-Oceans.(2009), European Project: 287589,EC:FP7:KBBE,FP7-OCEAN-2011,MICRO B3(2012), European Project: 261376,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,IHMS(2011), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS)
Subjects: Marine eukaryotes, Tara Oceans, single-cellgenomics, Marine life, Genomics, Biology, phylogeny, Genome, 03 medical and health sciences, 0302 clinical medicine, Phylogenetics, evolution, genomics, 14. Life underwater, 030304 developmental biology, open ocean, functions, 0303 health sciences, metagenomics, Phylogenetic tree, fungi, plankton, 15. Life on land, Plankton, Multicellular organism, Metagenomics, Evolutionary biology, [SDE]Environmental Sciences, anvi’o, ecology, 030217 neurology & neurosurgery
Abstract: Marine planktonic eukaryotes play a critical role in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billion metagenomic reads from 143 Tara Oceans stations to reconstruct and manually curate more than 700 abundant and widespread eukaryotic metagenome-assembled genomes ranging from 10 Mbp to up to 1.3 Gbp. The resulting non-redundant genomic resource of 25 billion nucleotides that describe 10 million genes covers a wide range of poorly characterized unicellular and multicellular eukaryotic lineages that complement the long-standing contributions of culture efforts to survey the tree of marine life while better representing plankton from the open ocean. Phylogeny of the DNA-dependent RNA polymerase placed this genomic resource in a comprehensive evolutionary framework that provided insights into the relationships of eukaryotic supergroups. From there, classification of unicellular eukaryotic plankton based on functions encoded in their genes revealed four major groups connecting distantly related lineages such as the diatoms and green algae. There has been a recurrent problem in understanding the interplay between eukaryotes’ vertical evolution and their phenotype. By disentangling phylogenetic signals from functional trends with genomics, we found that neither the classical trophic mode of plankton nor its vertical evolutionary history could fully explain the genomic functional landscape of marine eukaryotes that coexisted for millions of years. Cover Navigating on the map of plankton genomics with Tara Oceans and anvi’o: a comprehensive genome-resolved metagenomic survey dedicated to eukaryotic plankton.
Published: 2021

30. Genomic adaptation of the picoeukaryote Pelagomonas calceolata to iron-poor oceans revealed by a chromosome-scale genome sequence

Author: Nina Guérin, Marta Ciccarella, Elisa Flamant, Paul Frémont, Sophie Mangenot, Benjamin Istace, Benjamin Noel, Sarah Romac, Charles Bachy, Martin Gachenot, Eric Pelletier, Adriana Alberti, Olivier Jaillon, Corinne Cruaud, Patrick Wincker, Jean-Marc Aury, and Quentin Carradec
Subjects: Picoeukaryote, biology, Ecology, Phytoplankton, Ecosystem, Marine ecosystem, Adaptation, biology.organism_classification, Algal bloom, Relative species abundance, Trophic level
Abstract: SummaryThe smallest phytoplankton species are key actors in oceans biogeochemical cycling and their abundance and distribution are affected with global environmental changes. Picoalgae (cells Pelagomonas calceolata. We identified unusual large low-GC and gene-rich regions potentially representing centromeres. These particular genomic structures could be explained by the absence of genes from a recombination pathway involving double Holiday Junctions. We identified a large repertoire of genes involved in inorganic nitrogen sensing and uptake and several genes replacing iron-requiring proteins potentially explaining P. calceolata ecological success in oligotrophic waters. Finally, based on this high-quality assembly, we evaluated P. calceolata relative abundance in all oceans using environmental Tara Oceans datasets. Our results suggest that P. calceolata is one of the most abundant eukaryotic species in the oceans with a relative abundance favoured by high temperature 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. 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 picoalgae in a changing environment.
Published: 2021
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31. Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean

Author: Eric Pelletier, A. Murat Eren, Patrick Wincker, Rachel A. Foster, Tom O. Delmont, Juan José Pierella Karlusich, Jessika Fuessel, Iva Veseli, Chris Bowler, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), The University of Chicago Medicine [Chicago], Stockholm University, ANR-11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-10-LABX-0054,MEMOLIFE,Memory in living systems: an integrated approach(2010), ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), ANR-16-CE01-0008,PHYTOMET,Étude métallomique du phytoplancton: effet de l'acidification des océans sur la séquestration du fer(2016), European Project: 835067,DIATOMIC, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), delmont, tom, Biotech - Bioressources - Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques - - OCEANOMICS2011 - ANR-11-BTBR-0008 - BTBR - VALID, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, Memory in living systems: an integrated approach - - MEMOLIFE2010 - ANR-10-LABX-0054 - LABX - VALID, INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE - - Amidex2011 - ANR-11-IDEX-0001 - IDEX - VALID, Étude métallomique du phytoplancton: effet de l'acidification des océans sur la séquestration du fer - - PHYTOMET2016 - ANR-16-CE01-0008 - AAPG2016 - VALID, and Untangling eco-evolutionary impacts on diatom genomes over timescales relevant to current climate change - DIATOMIC - 835067 - INCOMING
Subjects: [SDE] Environmental Sciences, Nitrogen balance, Nitrogen, Oceans and Seas, Population, Biodiversity, Heterotroph, Cyanobacteria, Microbiology, Article, 03 medical and health sciences, Microbial ecology, Nitrogen Fixation, Seawater, 14. Life underwater, education, Phylogeny, Ecology, Evolution, Behavior and Systematics, Primary productivity, 030304 developmental biology, 0303 health sciences, education.field_of_study, biology, 030306 microbiology, Ecology, Correction, Pelagic zone, Plankton, biology.organism_classification, Trichodesmium, Metagenomics, [SDE]Environmental Sciences, Nitrogen fixation, Metagenome, Diazotroph
Abstract: Biological nitrogen fixation is a major factor contributing to microbial primary productivity in the open ocean. The current view depicts a few cyanobacterial diazotrophs as the most relevant marine nitrogen fixers, whereas heterotrophic diazotrophs are more diverse and considered to have lower impacts on the nitrogen balance. Here, we used 891 Tara Oceans metagenomes to create a manually curated, non-redundant genomic database corresponding to free-living, as well as filamentous, colony-forming, particle-attached and symbiotic bacterial and archaeal populations occurring in the surface of five oceans and two seas. Notably, the database provided the genomic content of eight cyanobacterial diazotrophs including Trichodesmium populations and a newly discovered population similar to Richelia, as well as 40 heterotrophic bacterial diazotrophs organized into three main functional groups that considerably expand the known diversity of abundant marine nitrogen fixers compared to previous genomic surveys. Critically, these 48 populations may account for more than 90% of cells containing known nifH genes and occurring in the sunlit ocean, suggesting that the genomic characterization of the most abundant marine diazotrophs may be nearing completion. The newly identified heterotrophic bacterial diazotrophs are widespread, express their nifH genes in situ, and co-occur under nitrate-depleted conditions in large size fractions where they might form aggregates providing the low-oxygen microenvironments required for nitrogen fixation. Most significantly, we found heterotrophic bacterial diazotrophs to be more abundant than cyanobacterial diazotrophs in most metagenomes from the open oceans and seas. This large-scale environmental genomic survey emphasizes the considerable potential of heterotrophs in the marine nitrogen balance.
Published: 2021
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32. A robust approach to estimate relative phytoplankton cell abundance from metagenomes

Author: Patrick Wincker, Sébastien Colin, Chris Bowler, Pierella Karlusich Jj, Richard G. Dorrell, de Vargas C, Josep M. Gasol, Adriana Zingone, Eleonora Scalco, Fabien Lombard, Lucie Zinger, Eric Pelletier, and Silvia G. Acinas
Subjects: 0303 health sciences, Biomass (ecology), Phototroph, 030306 microbiology, fungi, 15. Life on land, Ribosomal RNA, Biology, Genome, 03 medical and health sciences, 13. Climate action, Evolutionary biology, Abundance (ecology), Metagenomics, Phytoplankton, 14. Life underwater, Relative species abundance, 030304 developmental biology
Abstract: Phytoplankton account for >45% of primary production on Earth, and hence have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found across many of the major clades of the tree of life, including prokaryotes (cyanobacteria) and multiple eukaryotic lineages. Phytoplankton communities are generally studied by PCR amplification of rRNA marker genes from the DNA extracted from environmental samples and high-throughput sequencing of the amplicons. 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 do not provide insights into metabolic traits such as photosynthesis (i.e., it is sometimes difficult to distinguish an rRNA sequence of a phytoplanktonic species from a phylogenetically close non-photosynthetic species). In addition, rRNA marker genes fail to capture both cyanobacteria and photosynthetic eukaryotes simultaneously, thus hampering assessment of the entire phytoplankton community. Here, we propose to use the core single-copy photosynthetic gene psbO extracted from metagenomes to circumvent these limitations: the method is PCR-free, and the gene is present in both prokaryotes and eukaryotes, mainly in one copy per genome. We applied and validated this new strategy with the Tara Oceans datasets, and showed in most cases improved correlations with flow cytometry and microscopy than when based on rRNA genes. Furthermore, we revealed unexpected features of the ecology of these organisms, 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 communities of dinoflagellates. To facilitate the incorporation of psbO in future molecular-based surveys, we released a curated database including >20,000 unique sequences. Overall, psbO appears to be a promising new gene marker for improving molecular-based evaluations of phytoplankton communities.
Published: 2021
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33. Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes

Author: Ouardia Ait-Mohamed, Giselle McCallum, Erwann Corre, Benoît Perez-Lamarque, Chris Bowler, Kyle R. Frischkorn, Hélène Morlon, Andrew K Watson, Guillemette Audren de Kerdrel, Juan José Pierella Karlusich, Richard G. Dorrell, Guillaume Blanc, Adrien Villain, Adriana Alberti, Eric Pelletier, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Biology [Concordia], Concordia University [Montreal], Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Fédération de recherche de Roscoff (FR2424), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Chloroplasts, Gene Transfer, Horizontal, Lineage (evolution), In silico, Computational biology, Biology, Cyanobacteria, 010603 evolutionary biology, 01 natural sciences, Genome, [SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, 03 medical and health sciences, Phylogenomics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Symbiosis, Gene, Phylogeny, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Diatoms, 0303 health sciences, Multidisciplinary, Endosymbiosis, Phylogenetic tree, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Biological Sciences, DNA Fingerprinting, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Horizontal gene transfer, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology
Abstract: Horizontal gene transfer (HGT) is an important source of novelty in eukaryotic genomes. This is particularly true for the ochrophytes, a diverse and important group of algae. Previous studies have shown that ochrophytes possess a mosaic of genes derived from bacteria and eukaryotic algae, acquired through chloroplast endosymbiosis and from HGTs, although understanding of the time points and mechanisms underpinning these transfers has been restricted by the depth of taxonomic sampling possible. We harness an expanded set of ochrophyte sequence libraries, alongside automated and manual phylogenetic annotation, in silico modeling, and experimental techniques, to assess the frequency and functions of HGT across this lineage. Through manual annotation of thousands of single-gene trees, we identify continuous bacterial HGT as the predominant source of recently arrived genes in the model diatom Phaeodactylum tricornutum. Using a large-scale automated dataset, a multigene ochrophyte reference tree, and mathematical reconciliation of gene trees, we note a probable elevation of bacterial HGTs at foundational points in diatom evolution, following their divergence from other ochrophytes. Finally, we demonstrate that throughout ochrophyte evolutionary history, bacterial HGTs have been enriched in genes encoding secreted proteins. Our study provides insights into the sources and frequency of HGTs, and functional contributions that HGT has made to algal evolution.
Published: 2021
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34. Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods

Author: Colomban de Vargas, Madeline Carsique, Patrick Wincker, Marc Picheral, Fabien Lombard, Rainer Pepperkok, Etienne Dvorak, Silvia G. Acinas, Francisco M. Cornejo-Castillo, Sébastien Colin, Chris Bowler, Eric Karsenti, Juan José Pierella Karlusich, Rachel A. Foster, Eric Pelletier, Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Tara Oceans-GOSEE (FR2022), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), European Molecular Biology Laboratory [Heidelberg] (EMBL), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), ECOlogy of MArine Plankton (ECOMAP), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Stockholm University, Fonds Français pour l'Environnement Mondial, Knut and Alice Wallenberg Foundation, European Research Council, European Commission, Agence Nationale de la Recherche (France), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), HAL-SU, Gestionnaire, Global Oceans Systems Ecology & Evolution - Tara Oceans (GOSEE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Aix Marseille Université (AMU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Université de Toulon (UTLN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche pour le Développement (IRD [France-Nord])-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-European Molecular Biology Laboratory (EMBL)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Université australe du Chili, ANR-16-CE01-0008,PHYTOMET,Étude métallomique du phytoplancton: effet de l'acidification des océans sur la séquestration du fer(2016), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Aquatic Organisms, Nitrogen, Mesopelagic zone, Oceans and Seas, Science, General Physics and Astronomy, Cyanobacteria, [SDU.STU.OC] Sciences of the Universe [physics]/Earth Sciences/Oceanography, Article, General Biochemistry, Genetics and Molecular Biology, Molecular Imprinting, 03 medical and health sciences, Microbial ecology, Nitrogen Fixation, Element cycles, Seawater, 14. Life underwater, Symbiosis, Nitrogen cycle, Phylogeny, Microbial biooceanography, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 030304 developmental biology, Ecological niche, Marine biology, 0303 health sciences, Deep chlorophyll maximum, Multidisciplinary, Bacteria, Environmental microbiology, 030306 microbiology, Ecology, [SDE.IE]Environmental Sciences/Environmental Engineering, Bacterioplankton, General Chemistry, New production, Plankton, 3. Good health, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, Global distribution, 13. Climate action, Metagenomics, Nitrogen fixation, Environmental science, [SDE.IE] Environmental Sciences/Environmental Engineering, Diazotroph, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: This article is contribution number 118 of Tara Oceans.-- 18 pages, 10 figures, supplementary information https://doi.org/10.1038/s41467-021-24299-y.-- Data availability: The authors declare that all the data supporting the findings of this study are publicly available in the following repositories and in the supplementary information files of this paper. The contextual data are available in Pangaea (www.pangaea.de)21 with the identifier https://doi.org/10.1594/PANGAEA.875582. Flow cytometry data23,108 are available in Mendeley Data (https://data.mendeley.com) with the identifier https://doi.org/10.17632/p9r9wttjkm.2. The confocal microscopy30 and UVP533 images annotated as diazotrophs in the current work and their corresponding metadata were submitted to the EMBL-EBI repository BioStudies (www.ebi.ac.uk/biostudies) under accession S-BSST529; while the whole image databases and their metadata are available at Ecotaxa (confocal microscopy of 5–20 µm sized-fractionated samples: https://ecotaxa.obs-vlfr.fr/prj/3365; confocal microscopy of 20–180 μm sized-fractionated samples: https://ecotaxa.obs-vlfr.fr/prj/2274; UVP5: https://ecotaxa.obs-vlfr.fr/prj/579). Tara Oceans metagenomes22,24,25 are archived at ENA under the accession numbers: PRJEB1787, PRJEB1788, PRJEB4352, PRJEB4419, PRJEB9691, PRJEB9740, and PRJEB9742. The nifH and recA catalogs were compiled from Integrated Microbial Genomes (IMG, https://img.jgi.doe.gov/); Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP; https://github.com/dib-lab/dib-MMETSP); OM-Reference Gene Catalog version 2 (OM-RGC-v2, https://www.ocean-microbiome.org/); Tara Oceans assemblies (Supplementary Table 8 from ref. 16); and the nifH database (version April 2014) curated and hosted at Zehr Lab, University of California, Santa Cruz, CA, USA (https://www.jzehrlab.com/nifh). The 10 nifH sequences generated in the clone libraries of the current work were submitted to ENA under the accession numbers: MW590317–MW590326. Source data are provided with this paper, 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 (20 µm). 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 μm) 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, This work has been supported by the FFEM - French Facility for Global Environment, French Government ‘Investissements d’Avenir’ programs OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08), MEMO LIFE (ANR-10-LABX-54), and PSL Research University (ANR-11-IDEX-0001-02). R.A.F. acknowledges funding from Knut and Alice Wallenberg foundation. C.B. acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Diatomic; grant agreement No. 835067) and Agence Nationale de la Recherche “Phytomet” (ANR-16-CE01-0008) projects. F.M.C.-C. acknowledges funding from the European Union’s Horizon 2020 research program under the Marie Sklodowska-Curie grant agreement No. 749380 (UCYN2PLAST). S.G.A. acknowledges funding from the project “MAGGY” (CTM2017-87736-R) from the Spanish Ministry of Economy and Competitiveness and the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S). J.J.P.K. acknowledges postdoctoral funding from the Fonds Français pour l’Environnement Mondial
Published: 2021
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35. L'adaptació de nínxol va promoure la diversificació evolutiva del depredadors petits del oceà

Author: Ina M. Deutschmann, Aurélie Labarre, Ramiro Logares, Michael E. Sieracki, Eric Pelletier, Aleix Obiol, Ramon Massana, Francisco Latorre, Anders K. Krabberød, Olivier Jaillon, Corinne Cruaud, Ministerio de Ciencia e Innovación (España), Ministerio de Economía y Empresa (España), Ministerio de Economía y Competitividad (España), Research Council of Norway, Agencia Estatal de Investigación (España), European Commission, CSIC - Unidad de Recursos de Información Científica para la Investigación (URICI), and Universitat Politècnica de Catalunya. Doctorat en Ciències del Mar
Subjects: Internationality, Enginyeria agroalimentària::Ciències de la terra i de la vida::Biologia [Àrees temàtiques de la UPC], Glycoside Hydrolases, Oceans and Seas, Niche, Biology, Predation, Evolution (Biology), Eukaryotic cells, 03 medical and health sciences, MAST-4, Species Specificity, Phagocytosis, Animals, Marine ecosystem, 14. Life underwater, Selection, Genetic, Functional group (ecology), Ecosystem, Phylogeny, 030304 developmental biology, Trophic level, 0303 health sciences, Multidisciplinary, Geography, Ecology, Phylogenetic tree, 030306 microbiology, Cèl·lules eucariotes, Protists, Biological Sciences, Adaptation, Physiological, Biological Evolution, Biogeography, 13. Climate action, Evolutionary biology, Predatory Behavior, Adaptation, Niche adaptation, Stramenopiles, Ecoevolution, Evolució (Biologia)
Abstract: 10 pages, 5 figures, supporting information https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2020955118/-/DCSupplemental.-- Data Availability: DNA sequences and metadata from the Malaspina expedition are publicly available at the European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena; accession numbers PRJEB23913 (66) [18S rRNA genes] and PRJEB25224 (68) [16S rRNA genes]). DNA sequences from Tara Oceans are also stored at ENA with the accession numbers PRJEB6603 (76) for the SAGs, PRJEB6609 (101) for the metatranscriptomes, and PRJEB4352 (100) for the metagenomes (reference Datasets S1 and S4). Genome coassemblies, coding sequence predictions, and amino acid predictions have been deposited in FigShare (DOI: 10.6084/m9.figshare.13072322) (89). All other study data are included in the article and/or supporting information, Unicellular eukaryotic predators play a crucial role in the functioning of the ocean ecosystem by recycling nutrients and energy that are channeled to upper trophic levels. Traditionally, these evolutionarily diverse organisms have been combined into a single functional group (heterotrophic flagellates), overlooking their organismal differences. Here, we investigated four evolutionarily related species belonging to one cosmopolitan group of uncultured marine picoeukaryotic predators: marine stramenopiles (MAST)-4 (species A, B, C, and E). Co-occurrence and distribution analyses in the global surface ocean indicated contrasting patterns in MAST-4A and C, suggesting adaptation to different temperatures. We then investigated whether these spatial distribution patterns were mirrored by MAST-4 genomic content using single-cell genomics. Analyses of 69 single cells recovered 66 to 83% of the MAST-4A/B/C/E genomes, which displayed substantial interspecies divergence. MAST-4 genomes were similar in terms of broad gene functional categories, but they differed in enzymes of ecological relevance, such as glycoside hydrolases (GHs), which are part of the food degradation machinery in MAST-4. Interestingly, MAST-4 species featuring a similar GH composition (A and C) coexcluded each other in the surface global ocean, while species with a different set of GHs (B and C) appeared to be able to coexist, suggesting further niche diversification associated with prey digestion. We propose that differential niche adaptation to temperature and prey type has promoted adaptive evolutionary diversification in MAST-4. We show that minute ocean predators from the same phylogenetic group may have different biogeography and genomic content, which needs to be accounted for to better comprehend marine food webs, F.L. was supported by the Spanish National Program Formación de Personal Investigador 2016 (BES-2016-076317, Ministerio de Ciencia e Innovación, Spain). R.L. was supported by a Ramón y Cajal fellowship (RYC-2013-12554, Ministerio de Economía y Empresa, Spain). This work was supported by the projects INTERACTOMICS (Unveiling Core Ecological Interactions in Marine Microbial Communities Using Omics Approaches) (CTM2015-69936-P, MINECO, Spain, to R.L.), MicroEcoSystems (240904, Research Council of Norway, to R.L.), and MINIME (Microbial Evolution and Population Genomics in a Changing Ocean) (PID2019-105775RB-I00, Agencia Estatal de Investigación Spain, to R.L.). I.M.D. and A.L. were supported by the European Union’s Horizon 2020 research and innovation program under Marie Skłodowska-Curie Grant Agreement No. 675752 (SINGEK [Promoting Single Cell Genomics to Explore the Ecology and Evolution of Hidden Microeukaryotes]: http://www.singek.eu). We thank the Consejo Superior de Investigaciones Científicas (CSIC) Open Access Publication Support Initiative through the Unit of Information Resources for Research for helping to cover publication fees, With funding from the Spanish government through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)
Published: 2021

36. Metagenomic Mining for Amine Dehydrogenase Discovery

Author: Véronique de Berardinis, Eric Pelletier, Anne Zaparucha, Carine Vergne-Vaxelaire, Andreas S. Bommarius, Jean Louis Petit, Aurélie Jouenne, Adam A. Caparco, Bettina Bommarius, Julie A. Champion, School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA (ChBE), Global Oceans Systems Ecology & Evolution - Tara Oceans (GOSEE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Aix Marseille Université (AMU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Université de Toulon (UTLN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche pour le Développement (IRD [France-Nord])-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-European Molecular Biology Laboratory (EMBL)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Université australe du Chili, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Green chemistry, biology, Biochemistry, Metagenomics, Biocatalysis, Chemistry, [SDV]Life Sciences [q-bio], [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Amine dehydrogenase, biology.protein, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, General Chemistry, Enzyme catalysis
Published: 2020
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37. Correction to: Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean

Author: Tom O. Delmont, Juan José Pierella Karlusich, Iva Veseli, Jessika Fuessel, A. Murat Eren, Rachel A. Foster, Chris Bowler, Patrick Wincker, and Eric Pelletier
Subjects: Microbiology, Ecology, Evolution, Behavior and Systematics
Published: 2022
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38. Towards standards for human fecal sample processing in metagenomic studies

Author: Rajna Hercog, Paul W. O'Toole, Melanie Tramontano, Thomas Carton, Michael Blaut, Muriel Derrien, John Penders, Ruth Ann Luna, Karen P. Scott, Milena Popova, Jillian R.M. Brown, Volker Mai, Francisco Guarner, Adriana Alberti, Nicolas Pons, Anne Druesne, Kiran Raosaheb Patil, Bhagirath Singh, Delphine M. Saulnier, Kathleen Slezak, Georg Zeller, Joël Doré, Clémentine Mery, Jennifer C. Martin, Jana Junick, Masahira Hattori, Harry J. Flint, Eric Pelletier, Florence Levenez, Liping Zhao, James Versalovic, Ingeborg Klymiuk, Jens Roat Kultima, Matthew R. Hayward, Shinichi Sunagawa, Søren Persson, Hans G.H.J. Heilig, Ferris Elias Jung, S. Dusko Ehrlich, Patrick Veiga, Anne Salonen, Stéphanie Cools-Portier, Chaysavanh Manichanh, Laurie Bertrand, Willem M. de Vos, Luis Pedro Coelho, B. Brett Finlay, Michelle C. Daigneault, Paul I. Costea, Céline Orvain, Philippe Langella, Johan E. T. van Hylckama Vlieg, Marja Driessen, Erwin G. Zoetendal, Emma Allen-Vercoe, Peer Bork, Hidetoshi Morita, Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), MetaGenoPolis, Institut National de la Recherche Agronomique (INRA), European Community's Seventh Framework Programme via International Human Microbiome Standards [HEALTH-F4-2010-261376], Scottish Government Rural and Environmental Science and Analytical Services, EMBL, European Project: 261376,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,IHMS(2011), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), MetaGénoPolis, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Med Microbiol, Infect Dis & Infect Prev, RS: CAPHRI - R4 - Health Inequities and Societal Participation, RS: NUTRIM - R2 - Liver and digestive health, and RS: NUTRIM - R2 - Gut-liver homeostasis
Subjects: Quality Control, 0301 basic medicine, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV]Life Sciences [q-bio], Sample (material), 030106 microbiology, Sample processing, Biomedical Engineering, bacterial-dna, Bioengineering, Chemical Fractionation, Biology, Microbiology, Applied Microbiology and Biotechnology, diversity, dna-extraction methods, Feces, 03 medical and health sciences, Human gut, Species Specificity, Microbiologie, human gut microbiota, Biological variation, Humans, Life Science, Microbiome, VLAG, disease, Bacteria, business.industry, Computational Biology, DNA, DNA extraction, Biotechnology, 030104 developmental biology, Cardiovascular and Metabolic Diseases, Metagenomics, Molecular Medicine, business
Abstract: International audience; Technical variation in metagenomic analysis must be minimized to confidently assess the contributions of microbiota to human health. Here we tested 21 representative DNA extraction protocols on the same fecal samples and quantified differences in observed microbial community composition. We compared them with differences due to library preparation and sample storage, which we contrasted with observed biological variation within the same specimen or within an individual over time. We found that DNA extraction had the largest effect on the outcome of metagenomic analysis. To rank DNA extraction protocols, we considered resulting DNA quantity and quality, and we ascertained biases in estimates of community diversity and the ratio between Gram-positive and Gram-negative bacteria. We recommend a standardized DNA extraction method for human fecal samples, for which transferability across labs was established and which was further benchmarked using a mock community of known composition. Its adoption will improve comparability of human gut microbiome studies and facilitate meta-analyses.
Published: 2017
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39. Evolutionary diversification of tiny ocean predators

Author: Francisco Latorre, Ina M. Deutschmann, Aurelie Labarre, Aleix Obiol, Anders Krabberød, Eric Pelletier, Michael E. Sieracki, Corinne Cruaud, Olivier Jaillon, Ramon Massana, Ramiro Logares, and Ministerio de Ciencia e Innovación (España)
Abstract: FPI 2016 - BES-2016-076317
Published: 2020

40. Into the bloom: Molecular response of pelagic tunicates to fluctuating food availability

Author: Daniele Iudicone, Maria Grazia Mazzocchi, Valeria Nittoli, Salvatore D'Aniello, Lars Stemmann, Paolo Sordino, Fabien Lombard, Luigi Caputi, Patrick Wincker, Eric Pelletier, Stazione Zoologica Anton Dohrn (SZN), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, 010603 evolutionary biology, 01 natural sciences, Algal bloom, Zooplankton, 03 medical and health sciences, Phytoplankton, Genetics, Animals, DNA Barcoding, Taxonomic, 14. Life underwater, Urochordata, Ecology, Evolution, Behavior and Systematics, Ecosystem, Community, biology, Ecology, fungi, Pelagic zone, Plankton, biology.organism_classification, Tunicate, 030104 developmental biology, [SDE]Environmental Sciences, Bloom, Transcriptome
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.
Published: 2019
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41. Addendum: Enterotypes of the human gut microbiome.

Author: Manimozhiyan Arumugam, Jeroen Raes, Eric Pelletier, Denis Le Paslier, Takuji Yamada, Daniel R. Mende, Gabriel R. Fernandes, Julien Tap, Thomas Brüls, Jean-Michel Batto, Marcelo Bertalan, Natalia Borruel, Francesc Casellas, Leyden Fernández, Laurent Gautier, Torben Hansen, Masahira Hattori, Tetsuya Hayashi, Michiel Kleerebezem, Ken Kurokawa, Marion Leclerc, Florence Levenez, Chaysavanh Manichanh, Henrik Bjørn Nielsen, Trine Nielsen, Nicolas Pons, Julie Poulain, Junjie Qin, Thomas Sicheritz-Pontén, Sebastian Tims, David Torrents, Edgardo Ugarte, Erwin G. Zoetendal, Jun Wang 0004, Francisco Guarner, Oluf Pedersen, Willem M. de Vos, Søren Brunak, Joël Dore, MetaHIT consortium, Jean Weissenbach, S. Dusko Ehrlich, and Peer Bork
Published: 2014
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42. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

Author: Guillem Salazar, Lucas Paoli, Adriana Alberti, Jaime Huerta-Cepas, Hans-Joachim Ruscheweyh, Miguelangel Cuenca, Christopher M. Field, Luis Pedro Coelho, Corinne Cruaud, Stefan Engelen, Ann C. Gregory, Karine Labadie, Claudie Marec, Eric Pelletier, Marta Royo-Llonch, Simon Roux, Pablo Sánchez, Hideya Uehara, Ahmed A. Zayed, Georg Zeller, Margaux Carmichael, Céline Dimier, Joannie Ferland, Stefanie Kandels, Marc Picheral, Sergey Pisarev, Julie Poulain, Silvia G. Acinas, Marcel Babin, Peer Bork, Chris Bowler, Colomban de Vargas, Lionel Guidi, Pascal Hingamp, Daniele Iudicone, Lee Karp-Boss, Eric Karsenti, Hiroyuki Ogata, Stephane Pesant, Sabrina Speich, Matthew B. Sullivan, Patrick Wincker, Shinichi Sunagawa, Emmanuel Boss, Guy Cochrane, Michael Follows, Gabriel Gorsky, Nigel Grimsley, Olivier Jaillon, Stefanie Kandels-Lewis, Fabrice Not, Nicole Poulton, Jeroen Raes, Christian Sardet, Lars Stemmann, European Commission, Ministerio de Economía y Competitividad (España), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Takuvik Joint International Laboratory ULAVAL-CNRS, Université Laval [Québec] (ULaval)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Instituto de Fisica [Mexico] (UASLP), Universidad Autonoma de San Luis Potosi [México] (UASLP), Institute of Microbiology and Swiss Institute of Bioinformatics, CNS, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Center for Genomic Regulation (CRG-UPF), CIBER de Epidemiología y Salud Pública (CIBERESP), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), European Molecular Biology Laboratory [Heidelberg] (EMBL), Bayer Cropscience, Immunobiologie Cellulaire et Moléculaire des Infections Parasitaires, Université Pierre et Marie Curie - Paris 6 (UPMC)-IFR113-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire d'Océanographie Physique et Spatiale (LOPS), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Ohio State University [Columbus] (OSU), Institut de Chimie de Clermont-Ferrand - Clermont Auvergne (ICCF), Sigma CLERMONT (Sigma CLERMONT)-Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), European Molecular Biology Laboratory [Grenoble] (EMBL), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Takuvik Joint ULaval/CNRS Laboratory, Centre National de la Recherche Scientifique (CNRS)-Laval University [Québec], Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Génomique d'Evry (IG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Spain] (CSIC), University of Maine, European Molecular Biology Laboratory European Bioinformatics Institute, Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Department of Earth, Atmospheric and Planetary Sciences [MIT, Cambridge] (EAPS), Massachusetts Institute of Technology (MIT), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Biologie intégrative des organismes marins (BIOM), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Sezione Ecologia Marina Integrata, Stazione Zoologica Anton Dohrn (SZN), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Bigelow Laboratory for Ocean Sciences, Department of Bioscience Engineering, Vrije Universiteit Brussel (VUB), Laboratoire de Biologie du Développement de Villefranche sur mer (LBDV), Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Laboratoire de physique des océans (LPO), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Université Paris-Saclay, Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Centro de Investigaciones Biológicas (CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Kyoto University, Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Kyoto University [Kyoto], Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), and Centre National de la Recherche Scientifique (CNRS)-Université Laval [Québec] (ULaval)
Subjects: ASSEMBLY PROCESSES, Effects of global warming on oceans, DIVERSITY, microbial ecology, global ocean microbiome, CARBON, 0302 clinical medicine, biogeochemistry, Gene expression, ComputingMilieux_MISCELLANEOUS, 0303 health sciences, CLIMATE-CHANGE, Geography, Microbiota, Temperature, CYANOBACTERIA, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], GENOME, BACTERIA, community turnover, Life Sciences & Biomedicine, Biochemistry & Molecular Biology, SURFACE, Oceans and Seas, Tara Oceans, Biology, Article, metagenome, General Biochemistry, Genetics and Molecular Biology, ocean warming, 03 medical and health sciences, eco-systems biology, Microbial ecology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], metatranscriptome, Seawater, RNA, Messenger, 14. Life underwater, Gene, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 030304 developmental biology, Science & Technology, Biogeochemistry, Molecular Sequence Annotation, Cell Biology, Environmental variation, Gene Expression Regulation, Cardiovascular and Metabolic Diseases, 13. Climate action, Metagenomics, Evolutionary biology, BIODIVERSITY, sense organs, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Transcriptome, 030217 neurology & neurosurgery, gene expression change, BIOGEOGRAPHY
Abstract: This article is contribution number 94 of Tara Oceans.-- 37 pages, 20 figures, 1 table, supplementary information https://doi.org/10.1016/j.cell.2019.10.014.-- All raw reads are available through ENA at https://www.ebi.ac.uk/ena using the identifiers listed in https://doi.org/10.5281/zenodo.3473199. Processed data are accessible at https://www.ebi.ac.uk/biostudies/studies/S-BSST297, and additional information is provided in https://doi.org/10.5281/zenodo.3473199 and at the companion website: https://www.ocean-microbiome.org. Scripts used in this manuscript are available through a Github repository at https://github.com/SushiLab/omrgc_v2_scripts, 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, Tara Oceans (that includes both the Tara Oceans and Tara Oceans Polar Circle expeditions) would not exist without the leadership of the Tara Expeditions Foundation and the continuous support of 23 institutes (https://oceans.taraexpeditions.org). We further thank the commitment of the following sponsors: CNRS (in particular Groupement de Recherche GDR3280 and the Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE); European Molecular Biology Laboratory (EMBL); Genoscope/CEA; the French Ministry of Research; the French Government “Investissements d’Avenir” programmes OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08), MEMO LIFE (ANR-10-LABX-54), and PSL∗ Research University (ANR-11-IDEX-0001-02); Gordon and Betty Moore Foundation (award 3790); the US National Science Foundation (OCE#1536989 and OCE#1829831 to M.B.S.); the European Union’s Horizon 2020 research and innovation programme (grant agreement 686070); and the Ohio Supercomputer and the EMBL and ETH Zürich HPC facilities for computational support. Funding for the collection and processing of the TARA data set was provided by NASA Ocean Biology and Biogeochemistry program under grants NNX11AQ14G, NNX09AU43G, NNX13AE58G, and NNX15AC08G to the University of Maine and Canada Excellence Research Chair on Remote sensing of Canada’s new Arctic frontier Canada Foundation for Innovation. C.B. acknowledges funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement 835067). S.G.A. thanks the Spanish Ministry of Economy and Competitiveness (CTM2017-87736-R). S. Sunagawa. is supported by the ETH and the Helmut Horten Foundation and by funding from the Swiss National Foundation (205321_184955)
Published: 2019
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43. Exposure to Ambient Air Pollutants and the Onset of Dementia: An Administrative Cohort Study in Québec

Author: Eric Pelletier, Rick Burnett, Céline Plante, Larisa Ines Yankoty, Philippe Gamache, Ling Liu, Michel Fournier, Audrey Smargiassi, and Sophie Goudreau
Subjects: Pollutant, business.industry, Air pollution, medicine.disease, medicine.disease_cause, Ambient air, Air pollutants, Environmental health, mental disorders, General Earth and Planetary Sciences, Medicine, Dementia, business, General Environmental Science, Cohort study
Abstract: Effects of air pollutants are related to oxidative stress which is also linked to the pathogenesis of dementia including Alzheimer’s and associated diseases. We assessed associations between ...
Published: 2018
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44. DNA and RNA backups v1

Author: Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame Jacoby, Olivier Jaillon, Arnaud Lemainque, Eric Pelletier, Gaëlle Samson, Marc Wessner, Genoscope Technical Team, Silvia G. Acinas, Marta Royo-Llonch, Francisco M. Cornejo-Castillo, Ramiro Logares, Beatriz Fernández-Gómez, Chris Bowler, Guy Cochrane, Clara Amid, Petra Ten Hoopen, Colomban De Vargas, Nigel Grimsley, Elodie Desgranges, Stefanie Kandels-Lewis, Hiroyuki Ogata, Nicole Poulton, Michael E. Sieracki, Ramunas Stepanauskas, Matthew B. Sullivan, Jennifer R. Brum, Melissa B. Duhaime, Bonnie T. Poulos, Bonnie L. Hurwitz, Stéphane Pesant, Eric Karsenti, and Patrick Wincker
Subjects: chemistry.chemical_compound, Biochemistry, chemistry, RNA, DNA
Abstract: This protocol is part of Nucleic acids preparationsforViral to metazoan marine plankton nucleotide sequences from theTaraOceans expedition.
Published: 2018
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45. Sequencing and data quality control v1

Author: Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame Jacoby, Olivier Jaillon, Arnaud Lemainque, Eric Pelletier, Gaëlle Samson, Marc Wessner, Genoscope Technical Team, Silvia G. Acinas, Marta Royo-Llonch, Francisco M. Cornejo-Castillo, Ramiro Logares, Beatriz Fernández-Gómez, Chris Bowler, Guy Cochrane, Clara Amid, Petra Ten Hoopen, Colomban De Vargas, Nigel Grimsley, Elodie Desgranges, Stefanie Kandels-Lewis, Hiroyuki Ogata, Nicole Poulton, Michael E. Sieracki, Ramunas Stepanauskas, Matthew B. Sullivan, Jennifer R. Brum, Melissa B. Duhaime, Bonnie T. Poulos, Bonnie L. Hurwitz, Stéphane Pesant, Eric Karsenti, and Patrick Wincker
Subjects: Computer science, Data quality, Control (management), Data mining, computer.software_genre, computer
Abstract: This protocol describes the sequencing and data quality control for theTaraOceans expedition and is part ofViral to metazoan marine plankton nucleotide sequences from theTaraOceans expedition. Figure 3:Overview of experimental pipeline from nucleic acids to sequences. (Red crosses highlight QC steps where experiments can be stopped.)
Published: 2018
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46. Sequencing library preparation v1

Author: Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame Jacoby, Olivier Jaillon, Arnaud Lemainque, Eric Pelletier, Gaëlle Samson, Marc Wessner, Genoscope Technical Team, Silvia G. Acinas, Marta Royo-Llonch, Francisco M. Cornejo-Castillo, Ramiro Logares, Beatriz Fernández-Gómez, Chris Bowler, Guy Cochrane, Clara Amid, Petra Ten Hoopen, Colomban De Vargas, Nigel Grimsley, Elodie Desgranges, Stefanie Kandels-Lewis, Hiroyuki Ogata, Nicole Poulton, Michael E. Sieracki, Ramunas Stepanauskas, Matthew B. Sullivan, Jennifer R. Brum, Melissa B. Duhaime, Bonnie T. Poulos, Bonnie L. Hurwitz, Stéphane Pesant, Eric Karsenti, and Patrick Wincker
Subjects: Computer science, Library preparation, Operating system, computer.software_genre, computer, Protocol (object-oriented programming)
Abstract: This protocol describes the sequencing library preparation for theTaraOceans expedition and is part ofViral to metazoan marine plankton nucleotide sequences from theTaraOceans expedition. Figure 1: Overview of -omics analysis strategy applied on Tara Oceans samples.
Published: 2018
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47. Handling of genomics samples v1

Author: Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame Jacoby, Olivier Jaillon, Arnaud Lemainque, Eric Pelletier, Gaëlle Samson, Marc Wessner, Genoscope Technical Team, Silvia G. Acinas, Marta Royo-Llonch, Francisco M. Cornejo-Castillo, Ramiro Logares, Beatriz Fernández-Gómez, Chris Bowler, Guy Cochrane, Clara Amid, Petra Ten Hoopen, Colomban De Vargas, Nigel Grimsley, Elodie Desgranges, Stefanie Kandels-Lewis, Hiroyuki Ogata, Nicole Poulton, Michael E. Sieracki, Ramunas Stepanauskas, Matthew B. Sullivan, Jennifer R. Brum, Melissa B. Duhaime, Bonnie T. Poulos, Bonnie L. Hurwitz, Stéphane Pesant, Eric Karsenti, and Patrick Wincker
Subjects: Genomics, Computational biology, Biology
Abstract: This protocol describes the handling of genomics samples for the Tara Oceans expedition and is part ofViral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition. Figure 1: Overview of -omics analysis strategy applied on Tara Oceans samples.
Published: 2018
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48. Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition v1

Author: Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame Jacoby, Olivier Jaillon, Arnaud Lemainque, Eric Pelletier, Gaëlle Samson, Marc Wessner, Genoscope Technical Team, Silvia G. Acinas, Marta Royo-Llonch, Francisco M. Cornejo-Castillo, Ramiro Logares, Beatriz Fernández-Gómez, Chris Bowler, Guy Cochrane, Clara Amid, Petra Ten Hoopen, Colomban De Vargas, Nigel Grimsley, Elodie Desgranges, Stefanie Kandels-Lewis, Hiroyuki Ogata, Nicole Poulton, Michael E. Sieracki, Ramunas Stepanauskas, Matthew B. Sullivan, Jennifer R. Brum, Melissa B. Duhaime, Bonnie T. Poulos, Bonnie L. Hurwitz, Stéphane Pesant, Eric Karsenti, and Patrick Wincker
Abstract: The protocols in this collection are from the Alberti A., et al manuscript (Alberti A. 2017, Scientific Data). These protocols 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). This collection complements other efforts to provide a full description of experiments and open science resources generated from theTaraOceans project, further extending their value for the study of the world’s planktonic ecosystems.' From the Methods section: 'The generation of information-rich data from marine plankton samples presents unique challenges that are inherent to the particular sampling conditions at sea and the wide spectrum of organisms included in that environment. All processing steps, including biomass collection, sample preservation, nucleic acids extractions and sequencing library preparation, are critical and require specific protocols and robust methods in order to ensure comparability of results and limit potential biases. Our methods were either developed specifically forTaraOceans samples or carefully selected among existing ones in order to meet the requirements of our sequencing strategy and to produce optimized datasets for downstream bioinformatics analyses, as for example the production of overlapping reads from metagenomics libraries to facilitate assembly. They are presented in five sub-sections, starting with a brief description of how samples were handled between the research vessel and the processing laboratories (protocol 1). Protocol 2reports on DNA and RNA extractions procedures for -omics analyses, including the generation of amplified genomic DNA from uncultured isolated unicellular eukaryotes. The generation of 18S and 16S rRNA amplicons from DNA of specific size-fractions is described in protocol 3 and Illumina libraries preparation in protocol 4. Sequencing procedures and post-sequencing data processing are described in protocol 5. For details on the onboard sampling protocols, see Pesantet al.'
Published: 2018
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49. Nucleic acids preparations v1

Author: Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame Jacoby, Olivier Jaillon, Arnaud Lemainque, Eric Pelletier, Gaëlle Samson, Marc Wessner, Genoscope Technical Team, Silvia G. Acinas, Marta Royo-Llonch, Francisco M. Cornejo-Castillo, Ramiro Logares, Beatriz Fernández-Gómez, Chris Bowler, Guy Cochrane, Clara Amid, Petra Ten Hoopen, Colomban De Vargas, Nigel Grimsley, Elodie Desgranges, Stefanie Kandels-Lewis, Hiroyuki Ogata, Nicole Poulton, Michael E. Sieracki, Ramunas Stepanauskas, Matthew B. Sullivan, Jennifer R. Brum, Melissa B. Duhaime, Bonnie T. Poulos, Bonnie L. Hurwitz, Stéphane Pesant, Eric Karsenti, and Patrick Wincker
Subjects: Biochemistry, Nucleic acid
Abstract: This protocol describes thenucleic acids preparations for theTaraOceans expedition and is part ofViral to metazoan marine plankton nucleotide sequences from theTaraOceans expedition. Figure 1: Overview of -omics analysis strategy applied on Tara Oceans samples.
Published: 2018
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50. 18S and 16S rRNA genes amplicon generation for eukaryotic and prokaryotic metabarcoding v1

Author: Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame Jacoby, Olivier Jaillon, Arnaud Lemainque, Eric Pelletier, Gaëlle Samson, Marc Wessner, Genoscope Technical Team, Silvia G. Acinas, Marta Royo-Llonch, Francisco M. Cornejo-Castillo, Ramiro Logares, Beatriz Fernández-Gómez, Chris Bowler, Guy Cochrane, Clara Amid, Petra Ten Hoopen, Colomban De Vargas, Nigel Grimsley, Elodie Desgranges, Stefanie Kandels-Lewis, Hiroyuki Ogata, Nicole Poulton, Michael E. Sieracki, Ramunas Stepanauskas, Matthew B. Sullivan, Jennifer R. Brum, Melissa B. Duhaime, Bonnie T. Poulos, Bonnie L. Hurwitz, Stéphane Pesant, Eric Karsenti, and Patrick Wincker
Subjects: Genetics, Amplicon, Biology, 16S ribosomal RNA, Gene
Abstract: This protocol describes the 18S and 16S rRNA genes amplicon generation for eukaryotic and prokaryotic metabarcoding for theTaraOceans expedition and is part ofViral to metazoan marine plankton nucleotide sequences from theTaraOceans expedition. Figure 1: Overview of -omics analysis strategy applied on Tara Oceans samples.
Published: 2018
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