Plankton networks driving carbon export in the oligotrophic ocean.
Lionel Guidi,Samuel Chaffron,Lucie Bittner,Damien Eveillard,Abdelhalim Larhlimi,Simon Roux,Youssef Darzi,Stéphane Audic,Léo Berline,Jennifer R. Brum,Luis Pedro Coelho,Julio Cesar Ignacio Espinoza,Shruti Malviya,Shinichi Sunagawa,Céline Dimier,Stefanie Kandels-Lewis,Marc Picheral,Julie Poulain,Sarah Searson,Lars Stemmann,Fabrice Not,Pascal Hingamp,Sabrina Speich,Mick Follows,Lee Karp-Boss,Emmanuel Boss,Hiroyuki Ogata,Stephane Pesant,Jean Weissenbach,Patrick Wincker,Silvia G. Acinas,Peer Bork,Daniele Iudicone,Matthew B. Sullivan,Jeroen Raes,Eric Karsenti,Chris Bowler,Gabriel Gorsky +37 more
TLDR
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.read more
Citations
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mixOmics: An R package for 'omics feature selection and multiple data integration
TL;DR: MixOmics is introduced, an R package dedicated to the multivariate analysis of biological data sets with a specific focus on data exploration, dimension reduction and visualisation and extends Projection to Latent Structure models for discriminant analysis.
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Scientists' Warning to Humanity: Microorganisms and Climate Change
Ricardo Cavicchioli,William J. Ripple,Kenneth N. Timmis,Farooq Azam,Lars R. Bakken,Matthew Baylis,Michael J. Behrenfeld,Antje Boetius,Philip W. Boyd,Aimée T. Classen,Thomas W. Crowther,Roberto Danovaro,Christine M. Foreman,Jef Huisman,David A. Hutchins,Janet K. Jansson,David M. Karl,Britt Koskella,David B. Mark Welch,Jennifer B. H. Martiny,Mary Ann Moran,Victoria J. Orphan,David S. Reay,Justin V. Remais,Virginia I. Rich,Brajesh K. Singh,Lisa Y. Stein,Frank J. Stewart,Matthew B. Sullivan,Madeleine J. H. van Oppen,Madeleine J. H. van Oppen,Scott C. Weaver,Eric A. Webb,Nicole S. Webster,Nicole S. Webster +34 more
TL;DR: This Consensus Statement documents the central role and global importance of microorganisms in climate change biology and puts humanity on notice that the impact of climate change will depend heavily on responses of micro organisms, which are essential for achieving an environmentally sustainable future.
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Otso Ovaskainen,Otso Ovaskainen,Gleb Tikhonov,Anna Norberg,F. Guillaume Blanchet,F. Guillaume Blanchet,Leo L. Duan,David B. Dunson,Tomas Roslin,Nerea Abrego,Nerea Abrego +10 more
TL;DR: HMSC is operationalise the HMSC framework as a hierarchical Bayesian joint species distribution model, and is implemented as R- and Matlab-packages which enable computationally efficient analyses of large data sets.
Journal ArticleDOI
Marine DNA Viral Macro- and Microdiversity from Pole to Pole.
Ann C. Gregory,Ahmed A. Zayed,Nádia Conceição-Neto,Ben Temperton,Ben Bolduc,Adriana Alberti,Mathieu Ardyna,Ksenia Arkhipova,Margaux Carmichael,Corinne Cruaud,Céline Dimier,Céline Dimier,Guillermo Dominguez-Huerta,Joannie Ferland,Stefanie Kandels,Yunxiao Liu,Claudie Marec,Stephane Pesant,Marc Picheral,Sergey Pisarev,Julie Poulain,Jean-Éric Tremblay,Dean R. Vik,Silvia G. Acinas,Marcel Babin,Peer Bork,Emmanuel Boss,Chris Bowler,Guy Cochrane,Colomban de Vargas,Michael J. Follows,Gabriel Gorsky,Nigel Grimsley,Lionel Guidi,Pascal Hingamp,Daniele Iudicone,Olivier Jaillon,Stefanie Kandels-Lewis,Lee Karp-Boss,Eric Karsenti,Fabrice Not,Hiroyuki Ogata,Nicole J. Poulton,Jeroen Raes,Christian Sardet,Sabrina Speich,Lars Stemmann,Matthew B. Sullivan,Shinichi Sunagawa,Patrick Wincker,Alexander I. Culley,Bas E. Dutilh,Bas E. Dutilh,Simon Roux +53 more
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Phage Puppet Masters of the Marine Microbial Realm
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References
More filters
Journal ArticleDOI
Fast gapped-read alignment with Bowtie 2
TL;DR: Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
Journal ArticleDOI
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Christian Quast,Elmar Pruesse,Pelin Yilmaz,Jan Gerken,Timmy Schweer,Pablo Yarza,Jörg Peplies,Frank Oliver Glöckner +7 more
TL;DR: The extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
Journal ArticleDOI
Search and clustering orders of magnitude faster than BLAST
TL;DR: UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters and offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.
Journal ArticleDOI
WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder,Steve Horvath +1 more
TL;DR: The WGCNA R software package is a comprehensive collection of R functions for performing various aspects of weighted correlation network analysis that includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software.
Journal ArticleDOI
Primary Production of the Biosphere: Integrating Terrestrial and Oceanic Components
TL;DR: Integrating conceptually similar models of the growth of marine and terrestrial primary producers yielded an estimated global net primary production of 104.9 petagrams of carbon per year, with roughly equal contributions from land and oceans.
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