Literature DB >> 32398798

Tara Oceans: towards global ocean ecosystems biology.

Shinichi Sunagawa1, Silvia G Acinas2, Peer Bork3,4,5, Chris Bowler6,7, Damien Eveillard7,8, Gabriel Gorsky7,9, Lionel Guidi7,9, Daniele Iudicone10, Eric Karsenti6,7,11, Fabien Lombard7,9, Hiroyuki Ogata12, Stephane Pesant13,14, Matthew B Sullivan15,16,17, Patrick Wincker7,18, Colomban de Vargas19,20.   

Abstract

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

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Year:  2020        PMID: 32398798     DOI: 10.1038/s41579-020-0364-5

Source DB:  PubMed          Journal:  Nat Rev Microbiol        ISSN: 1740-1526            Impact factor:   60.633


  124 in total

Review 1.  Molecular eco-systems biology: towards an understanding of community function.

Authors:  Jeroen Raes; Peer Bork
Journal:  Nat Rev Microbiol       Date:  2008-09       Impact factor: 60.633

2.  Primary production of the biosphere: integrating terrestrial and oceanic components

Authors: 
Journal:  Science       Date:  1998-07-10       Impact factor: 47.728

Review 3.  Microbial oceanography and the Hawaii Ocean Time-series programme.

Authors:  David M Karl; Matthew J Church
Journal:  Nat Rev Microbiol       Date:  2014-08-26       Impact factor: 60.633

4.  Marine microbial metagenomes sampled across space and time.

Authors:  Steven J Biller; Paul M Berube; Keven Dooley; Madeline Williams; Brandon M Satinsky; Thomas Hackl; Shane L Hogle; Allison Coe; Kristin Bergauer; Heather A Bouman; Thomas J Browning; Daniele De Corte; Christel Hassler; Debbie Hulston; Jeremy E Jacquot; Elizabeth W Maas; Thomas Reinthaler; Eva Sintes; Taichi Yokokawa; Sallie W Chisholm
Journal:  Sci Data       Date:  2018-09-04       Impact factor: 6.444

5.  The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families.

Authors:  Shibu Yooseph; Granger Sutton; Douglas B Rusch; Aaron L Halpern; Shannon J Williamson; Karin Remington; Jonathan A Eisen; Karla B Heidelberg; Gerard Manning; Weizhong Li; Lukasz Jaroszewski; Piotr Cieplak; Christopher S Miller; Huiying Li; Susan T Mashiyama; Marcin P Joachimiak; Christopher van Belle; John-Marc Chandonia; David A Soergel; Yufeng Zhai; Kannan Natarajan; Shaun Lee; Benjamin J Raphael; Vineet Bafna; Robert Friedman; Steven E Brenner; Adam Godzik; David Eisenberg; Jack E Dixon; Susan S Taylor; Robert L Strausberg; Marvin Frazier; J Craig Venter
Journal:  PLoS Biol       Date:  2007-03       Impact factor: 8.029

6.  Environmental genome shotgun sequencing of the Sargasso Sea.

Authors:  J Craig Venter; Karin Remington; John F Heidelberg; Aaron L Halpern; Doug Rusch; Jonathan A Eisen; Dongying Wu; Ian Paulsen; Karen E Nelson; William Nelson; Derrick E Fouts; Samuel Levy; Anthony H Knap; Michael W Lomas; Ken Nealson; Owen White; Jeremy Peterson; Jeff Hoffman; Rachel Parsons; Holly Baden-Tillson; Cynthia Pfannkoch; Yu-Hui Rogers; Hamilton O Smith
Journal:  Science       Date:  2004-03-04       Impact factor: 47.728

7.  A holistic approach to marine eco-systems biology.

Authors:  Eric Karsenti; Silvia G Acinas; Peer Bork; Chris Bowler; Colomban De Vargas; Jeroen Raes; Matthew Sullivan; Detlev Arendt; Francesca Benzoni; Jean-Michel Claverie; Mick Follows; Gaby Gorsky; Pascal Hingamp; Daniele Iudicone; Olivier Jaillon; Stefanie Kandels-Lewis; Uros Krzic; Fabrice Not; Hiroyuki Ogata; Stéphane Pesant; Emmanuel Georges Reynaud; Christian Sardet; Michael E Sieracki; Sabrina Speich; Didier Velayoudon; Jean Weissenbach; Patrick Wincker
Journal:  PLoS Biol       Date:  2011-10-18       Impact factor: 8.029

8.  The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific.

Authors:  Douglas B Rusch; Aaron L Halpern; Granger Sutton; Karla B Heidelberg; Shannon Williamson; Shibu Yooseph; Dongying Wu; Jonathan A Eisen; Jeff M Hoffman; Karin Remington; Karen Beeson; Bao Tran; Hamilton Smith; Holly Baden-Tillson; Clare Stewart; Joyce Thorpe; Jason Freeman; Cynthia Andrews-Pfannkoch; Joseph E Venter; Kelvin Li; Saul Kravitz; John F Heidelberg; Terry Utterback; Yu-Hui Rogers; Luisa I Falcón; Valeria Souza; Germán Bonilla-Rosso; Luis E Eguiarte; David M Karl; Shubha Sathyendranath; Trevor Platt; Eldredge Bermingham; Victor Gallardo; Giselle Tamayo-Castillo; Michael R Ferrari; Robert L Strausberg; Kenneth Nealson; Robert Friedman; Marvin Frazier; J Craig Venter
Journal:  PLoS Biol       Date:  2007-03       Impact factor: 8.029

9.  Open science resources for the discovery and analysis of Tara Oceans data.

Authors:  Stéphane Pesant; Fabrice Not; Marc Picheral; Stefanie Kandels-Lewis; Noan Le Bescot; Gabriel Gorsky; Daniele Iudicone; Eric Karsenti; Sabrina Speich; Romain Troublé; Céline Dimier; Sarah Searson
Journal:  Sci Data       Date:  2015-05-26       Impact factor: 6.444

10.  The ocean sampling day consortium.

Authors:  Anna Kopf; Mesude Bicak; Renzo Kottmann; Julia Schnetzer; Ivaylo Kostadinov; Katja Lehmann; Antonio Fernandez-Guerra; Christian Jeanthon; Eyal Rahav; Matthias Ullrich; Antje Wichels; Gunnar Gerdts; Paraskevi Polymenakou; Giorgos Kotoulas; Rania Siam; Rehab Z Abdallah; Eva C Sonnenschein; Thierry Cariou; Fergal O'Gara; Stephen Jackson; Sandi Orlic; Michael Steinke; Julia Busch; Bernardo Duarte; Isabel Caçador; João Canning-Clode; Oleksandra Bobrova; Viggo Marteinsson; Eyjolfur Reynisson; Clara Magalhães Loureiro; Gian Marco Luna; Grazia Marina Quero; Carolin R Löscher; Anke Kremp; Marie E DeLorenzo; Lise Øvreås; Jennifer Tolman; Julie LaRoche; Antonella Penna; Marc Frischer; Timothy Davis; Barker Katherine; Christopher P Meyer; Sandra Ramos; Catarina Magalhães; Florence Jude-Lemeilleur; Ma Leopoldina Aguirre-Macedo; Shiao Wang; Nicole Poulton; Scott Jones; Rachel Collin; Jed A Fuhrman; Pascal Conan; Cecilia Alonso; Noga Stambler; Kelly Goodwin; Michael M Yakimov; Federico Baltar; Levente Bodrossy; Jodie Van De Kamp; Dion Mf Frampton; Martin Ostrowski; Paul Van Ruth; Paul Malthouse; Simon Claus; Klaas Deneudt; Jonas Mortelmans; Sophie Pitois; David Wallom; Ian Salter; Rodrigo Costa; Declan C Schroeder; Mahrous M Kandil; Valentina Amaral; Florencia Biancalana; Rafael Santana; Maria Luiza Pedrotti; Takashi Yoshida; Hiroyuki Ogata; Tim Ingleton; Kate Munnik; Naiara Rodriguez-Ezpeleta; Veronique Berteaux-Lecellier; Patricia Wecker; Ibon Cancio; Daniel Vaulot; Christina Bienhold; Hassan Ghazal; Bouchra Chaouni; Soumya Essayeh; Sara Ettamimi; El Houcine Zaid; Noureddine Boukhatem; Abderrahim Bouali; Rajaa Chahboune; Said Barrijal; Mohammed Timinouni; Fatima El Otmani; Mohamed Bennani; Marianna Mea; Nadezhda Todorova; Ventzislav Karamfilov; Petra Ten Hoopen; Guy Cochrane; Stephane L'Haridon; Kemal Can Bizsel; Alessandro Vezzi; Federico M Lauro; Patrick Martin; Rachelle M Jensen; Jamie Hinks; Susan Gebbels; Riccardo Rosselli; Fabio De Pascale; Riccardo Schiavon; Antonina Dos Santos; Emilie Villar; Stéphane Pesant; Bruno Cataletto; Francesca Malfatti; Ranjith Edirisinghe; Jorge A Herrera Silveira; Michele Barbier; Valentina Turk; Tinkara Tinta; Wayne J Fuller; Ilkay Salihoglu; Nedime Serakinci; Mahmut Cerkez Ergoren; Eileen Bresnan; Juan Iriberri; Paul Anders Fronth Nyhus; Edvardsen Bente; Hans Erik Karlsen; Peter N Golyshin; Josep M Gasol; Snejana Moncheva; Nina Dzhembekova; Zackary Johnson; Christopher David Sinigalliano; Maribeth Louise Gidley; Adriana Zingone; Roberto Danovaro; George Tsiamis; Melody S Clark; Ana Cristina Costa; Monia El Bour; Ana M Martins; R Eric Collins; Anne-Lise Ducluzeau; Jonathan Martinez; Mark J Costello; Linda A Amaral-Zettler; Jack A Gilbert; Neil Davies; Dawn Field; Frank Oliver Glöckner
Journal:  Gigascience       Date:  2015-06-19       Impact factor: 6.524

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4.  Discovery of nondiazotrophic Trichodesmium species abundant and widespread in the open ocean.

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5.  Biosynthetic potential of the global ocean microbiome.

Authors:  Hans-Joachim Ruscheweyh; Clarissa C Forneris; Florian Hubrich; Lucas Paoli; Satria Kautsar; Agneya Bhushan; Alessandro Lotti; Quentin Clayssen; Guillem Salazar; Alessio Milanese; Charlotte I Carlström; Chrysa Papadopoulou; Daniel Gehrig; Mikhail Karasikov; Harun Mustafa; Martin Larralde; Laura M Carroll; Pablo Sánchez; Ahmed A Zayed; Dylan R Cronin; Silvia G Acinas; Peer Bork; Chris Bowler; Tom O Delmont; Josep M Gasol; Alvar D Gossert; André Kahles; Matthew B Sullivan; Patrick Wincker; Georg Zeller; Serina L Robinson; Jörn Piel; Shinichi Sunagawa
Journal:  Nature       Date:  2022-06-22       Impact factor: 69.504

Review 6.  Priorities for ocean microbiome research.

Authors: 
Journal:  Nat Microbiol       Date:  2022-06-30       Impact factor: 30.964

7.  Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR.

Authors:  Robert M Waterhouse; Anne-Françoise Adam-Blondon; Donat Agosti; Petr Baldrian; Bachir Balech; Erwan Corre; Robert P Davey; Henrik Lantz; Graziano Pesole; Christian Quast; Frank Oliver Glöckner; Niels Raes; Anna Sandionigi; Monica Santamaria; Wouter Addink; Jiri Vohradsky; Amandine Nunes-Jorge; Nils Peder Willassen; Jerry Lanfear
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Review 8.  Nanochitin: Chemistry, Structure, Assembly, and Applications.

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9.  Tree-aggregated predictive modeling of microbiome data.

Authors:  Jacob Bien; Xiaohan Yan; Léo Simpson; Christian L Müller
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10.  Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model.

Authors:  Shion Hosoda; Tsukasa Fukunaga; Michiaki Hamada
Journal:  Bioinformatics       Date:  2021-07-12       Impact factor: 6.937

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