scispace - formally typeset
Search or ask a question
Author

Céline Dimier

Bio: Céline Dimier is an academic researcher from University of Paris. The author has contributed to research in topics: Plankton & Oceanography. The author has an hindex of 17, co-authored 24 publications receiving 5646 citations. Previous affiliations of Céline Dimier include Pierre-and-Marie-Curie University & École Normale Supérieure.

Papers
More filters
Journal ArticleDOI
22 May 2015-Science
TL;DR: This work identifies ocean microbial core functionality and reveals that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.
Abstract: Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture of functional diversity, microbial community structure, and their ecological determinants remains a grand challenge. We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans samples from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with >40 million nonredundant, mostly novel sequences from viruses, prokaryotes, and picoeukaryotes. Using 139 prokaryote-enriched samples, containing >35,000 species, we show vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.

1,934 citations

Journal ArticleDOI
Colomban de Vargas1, Colomban de Vargas2, Stéphane Audic1, Stéphane Audic2, Nicolas Henry1, Nicolas Henry2, Johan Decelle2, Johan Decelle1, Frédéric Mahé1, Frédéric Mahé3, Frédéric Mahé2, Ramiro Logares4, Enrique Lara, Cédric Berney1, Cédric Berney2, Noan Le Bescot1, Noan Le Bescot2, Ian Probert2, Ian Probert1, Margaux Carmichael5, Margaux Carmichael1, Margaux Carmichael2, Julie Poulain6, Sarah Romac2, Sarah Romac1, Sébastien Colin1, Sébastien Colin5, Sébastien Colin2, Jean-Marc Aury6, Lucie Bittner, Samuel Chaffron7, Samuel Chaffron8, Micah Dunthorn3, Stefan Engelen6, Olga Flegontova9, Olga Flegontova10, Lionel Guidi1, Lionel Guidi2, Aleš Horák9, Aleš Horák10, Olivier Jaillon11, Olivier Jaillon2, Olivier Jaillon6, Gipsi Lima-Mendez7, Gipsi Lima-Mendez8, Julius Lukeš10, Julius Lukeš9, Julius Lukeš12, Shruti Malviya5, Raphael Morard13, Raphael Morard1, Raphael Morard2, Matthieu Mulot, Eleonora Scalco14, Raffaele Siano15, Flora Vincent5, Flora Vincent8, Adriana Zingone14, Céline Dimier1, Céline Dimier2, Céline Dimier5, Marc Picheral1, Marc Picheral2, Sarah Searson1, Sarah Searson2, Stefanie Kandels-Lewis16, Tara Oceans Coordinators17, Silvia G. Acinas4, Peer Bork18, Peer Bork16, Chris Bowler5, Gabriel Gorsky2, Gabriel Gorsky1, Nigel Grimsley2, Nigel Grimsley19, Pascal Hingamp20, Daniele Iudicone14, Fabrice Not1, Fabrice Not2, Hiroyuki Ogata17, Stephane Pesant13, Jeroen Raes8, Jeroen Raes7, Michael E. Sieracki21, Michael E. Sieracki22, Sabrina Speich5, Sabrina Speich23, Lars Stemmann1, Lars Stemmann2, Shinichi Sunagawa16, Jean Weissenbach6, Jean Weissenbach2, Jean Weissenbach11, Patrick Wincker2, Patrick Wincker11, Patrick Wincker6, Eric Karsenti5, Eric Karsenti16 
22 May 2015-Science
TL;DR: Diversity emerged at all taxonomic levels, both within the groups comprising the ~11,200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies.
Abstract: Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during the circumglobal Tara Oceans expedition. We analyzed 18S ribosomal DNA sequences across the intermediate plankton-size spectrum from the smallest unicellular eukaryotes (protists, >0.8 micrometers) to small animals of a few millimeters. Eukaryotic ribosomal diversity saturated at ~150,000 operational taxonomic units, about one-third of which could not be assigned to known eukaryotic groups. Diversity emerged at all taxonomic levels, both within the groups comprising the ~11,200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies. Most eukaryotic plankton biodiversity belonged to heterotrophic protistan groups, particularly those known to be parasites or symbiotic hosts.

1,378 citations

Journal ArticleDOI
22 May 2015-Science
TL;DR: It is found that environmental factors are incomplete predictors of community structure and associations across plankton functional types and phylogenetic groups to be nonrandomly distributed on the network and driven by both local and global patterns.
Abstract: Species interaction networks are shaped by abiotic and biotic factors. Here, as part of the Tara Oceans project, we studied the photic zone interactome using environmental factors and organismal abundance profiles and found that environmental factors are incomplete predictors of community structure. We found associations across plankton functional types and phylogenetic groups to be nonrandomly distributed on the network and driven by both local and global patterns. We identified interactions among grazers, primary producers, viruses, and (mainly parasitic) symbionts and validated network-generated hypotheses using microscopy to confirm symbiotic relationships. We have thus provided a resource to support further research on ocean food webs and integrating biological components into ocean models.

717 citations

Journal ArticleDOI
22 May 2015-Science
TL;DR: These investigations establish a global ocean dsDNA viromic data set with analyses supporting the seed-bank hypothesis to explain how oceanic viral communities maintain high local diversity.
Abstract: Viruses influence ecosystems by modulating microbial population size, diversity, metabolic outputs, and gene flow. Here, we use quantitative double-stranded DNA (dsDNA) viral-fraction metagenomes (viromes) and whole viral community morphological data sets from 43 Tara Oceans expedition samples to assess viral community patterns and structure in the upper ocean. Protein cluster cataloging defined pelagic upper-ocean viral community pan and core gene sets and suggested that this sequence space is well-sampled. Analyses of viral protein clusters, populations, and morphology revealed biogeographic patterns whereby viral communities were passively transported on oceanic currents and locally structured by environmental conditions that affect host community structure. Together, these investigations establish a global ocean dsDNA viromic data set with analyses supporting the seed-bank hypothesis to explain how oceanic viral communities maintain high local diversity.

588 citations

Journal ArticleDOI
29 Sep 2016-Nature
TL;DR: A global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts is presented to present a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks.
Abstract: Ocean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting 'global ocean virome' dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups). This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks.

557 citations


Cited by
More filters
01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

10,124 citations

Journal ArticleDOI
TL;DR: The K EGG pathway maps are now integrated with network variation maps in the NETWORK database, as well as with conserved functional units of KEGG modules and reaction modules in the MODULE database, and the KO database for functional orthologs continues to be improved.
Abstract: KEGG (https://www.kegg.jp/) is a manually curated resource integrating eighteen databases categorized into systems, genomic, chemical and health information. It also provides KEGG mapping tools, which enable understanding of cellular and organism-level functions from genome sequences and other molecular datasets. KEGG mapping is a predictive method of reconstructing molecular network systems from molecular building blocks based on the concept of functional orthologs. Since the introduction of the KEGG NETWORK database, various diseases have been associated with network variants, which are perturbed molecular networks caused by human gene variants, viruses, other pathogens and environmental factors. The network variation maps are created as aligned sets of related networks showing, for example, how different viruses inhibit or activate specific cellular signaling pathways. The KEGG pathway maps are now integrated with network variation maps in the NETWORK database, as well as with conserved functional units of KEGG modules and reaction modules in the MODULE database. The KO database for functional orthologs continues to be improved and virus KOs are being expanded for better understanding of virus-cell interactions and for enabling prediction of viral perturbations.

2,087 citations

Journal ArticleDOI
TL;DR: It is argued that the improvements in reusability, reproducibility and comprehensiveness are sufficiently great that ASVs should replace OTUs as the standard unit of marker-gene analysis and reporting.
Abstract: Recent advances have made it possible to analyze high-throughput marker-gene sequencing data without resorting to the customary construction of molecular operational taxonomic units (OTUs): clusters of sequencing reads that differ by less than a fixed dissimilarity threshold. New methods control errors sufficiently such that amplicon sequence variants (ASVs) can be resolved exactly, down to the level of single-nucleotide differences over the sequenced gene region. The benefits of finer resolution are immediately apparent, and arguments for ASV methods have focused on their improved resolution. Less obvious, but we believe more important, are the broad benefits that derive from the status of ASVs as consistent labels with intrinsic biological meaning identified independently from a reference database. Here we discuss how these features grant ASVs the combined advantages of closed-reference OTUs—including computational costs that scale linearly with study size, simple merging between independently processed data sets, and forward prediction—and of de novo OTUs—including accurate measurement of diversity and applicability to communities lacking deep coverage in reference databases. We argue that the improvements in reusability, reproducibility and comprehensiveness are sufficiently great that ASVs should replace OTUs as the standard unit of marker-gene analysis and reporting.

1,977 citations

Journal ArticleDOI
22 May 2015-Science
TL;DR: This work identifies ocean microbial core functionality and reveals that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.
Abstract: Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture of functional diversity, microbial community structure, and their ecological determinants remains a grand challenge. We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans samples from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with >40 million nonredundant, mostly novel sequences from viruses, prokaryotes, and picoeukaryotes. Using 139 prokaryote-enriched samples, containing >35,000 species, we show vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.

1,934 citations