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Lars Stemmann

Bio: Lars Stemmann is an academic researcher from University of Paris. The author has contributed to research in topics: Zooplankton & Plankton. The author has an hindex of 40, co-authored 100 publications receiving 8050 citations. Previous affiliations of Lars Stemmann include Texas A&M University & Pierre-and-Marie-Curie University.


Papers
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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 Mahé2, Frédéric Mahé3, Ramiro Logares4, Enrique Lara, Cédric Berney1, Cédric Berney2, Noan Le Bescot2, Noan Le Bescot1, Ian Probert2, Ian Probert1, Margaux Carmichael5, Margaux Carmichael2, Margaux Carmichael1, Julie Poulain6, Sarah Romac2, Sarah Romac1, Sébastien Colin5, Sébastien Colin2, Sébastien Colin1, 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 Jaillon6, Olivier Jaillon1, Gipsi Lima-Mendez7, Gipsi Lima-Mendez8, Julius Lukeš10, Julius Lukeš9, Julius Lukeš12, Shruti Malviya5, Raphael Morard2, Raphael Morard1, Raphael Morard13, Matthieu Mulot, Eleonora Scalco14, Raffaele Siano15, Flora Vincent5, Flora Vincent8, Adriana Zingone14, Céline Dimier5, Céline Dimier1, Céline Dimier2, Marc Picheral2, Marc Picheral1, Sarah Searson2, Sarah Searson1, Stefanie Kandels-Lewis16, Tara Oceans Coordinators17, Silvia G. Acinas4, Peer Bork16, Peer Bork18, Chris Bowler5, Gabriel Gorsky2, Gabriel Gorsky1, Nigel Grimsley1, Nigel Grimsley19, Pascal Hingamp20, Daniele Iudicone14, Fabrice Not2, Fabrice Not1, Hiroyuki Ogata17, Stephane Pesant13, Jeroen Raes8, Jeroen Raes7, Michael E. Sieracki21, Michael E. Sieracki22, Sabrina Speich23, Sabrina Speich5, Lars Stemmann2, Lars Stemmann1, Shinichi Sunagawa16, Jean Weissenbach1, Jean Weissenbach11, Jean Weissenbach6, Patrick Wincker6, Patrick Wincker11, Patrick Wincker1, 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
28 Apr 2016-Nature
TL;DR: It is shown that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and that the relative abundance of a few bacterial and viral genes can predict a significant fraction of the variability in carbon export in these regions.
Abstract: The biological carbon pump is the process by which CO2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure driving the process remains largely uncharacterized. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve our understanding of carbon export in the oligotrophic ocean. We show that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and highlight unexpected taxa such as Radiolaria and alveolate parasites, as well as Synechococcus and their phages, as lineages most strongly associated with carbon export in the subtropical, nutrient-depleted, oligotrophic ocean. Additionally, we show that the relative abundance of a few bacterial and viral genes can predict a significant fraction of the variability in carbon export in these regions.

556 citations

Journal ArticleDOI
16 May 2019-Cell
TL;DR: An ∼12-fold expanded global ocean DNA virome dataset is established of 195,728 viral populations, now including the Arctic Ocean, and it is validated that these populations form discrete genotypic clusters.

441 citations


Cited by
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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: In marine ecosystems, rising atmospheric CO2 and climate change are associated with concurrent shifts in temperature, circulation, stratification, nutrient input, oxygen content, and ocean acidification, with potentially wide-ranging biological effects.
Abstract: In marine ecosystems, rising atmospheric CO2 and climate change are associated with concurrent shifts in temperature, circulation, stratification, nutrient input, oxygen content, and ocean acidification, with potentially wideranging biological effects. Population-level shifts are occurring because of physiological intolerance to new environments, altered dispersal patterns, and changes in species interactions. Together with local climate-driven invasion and extinction, these processes result in altered community structure and diversity, including possible emergence of novel ecosystems. Impacts are particularly striking for the poles and the tropics, because of the sensitivity of polar ecosystems to sea-ice retreat and poleward species migrations as well as the sensitivity of coral-algal symbiosis to minor increases in temperature. Midlatitude upwelling systems, like the California Current, exhibit strong linkages between climate and species distributions, phenology, and demography. Aggregated effects may modify energy and material flows as well as biogeochemical cycles, eventually impacting the overall ecosystem functioning and services upon which people and societies depend.

2,136 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