Literature DB >> 34782724

Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean.

Marta Royo-Llonch1, Pablo Sánchez1, Clara Ruiz-González1, Guillem Salazar2, Carlos Pedrós-Alió3, Marta Sebastián1, Karine Labadie4, Lucas Paoli2, Federico M Ibarbalz5,6, Lucie Zinger5, Benjamin Churcheward7, Samuel Chaffron7,8, Damien Eveillard7,8, Eric Karsenti5,8,9, Shinichi Sunagawa2, Patrick Wincker8,10, Lee Karp-Boss11, Chris Bowler5,8, Silvia G Acinas12.   

Abstract

The role of the Arctic Ocean ecosystem in climate regulation may depend on the responses of marine microorganisms to environmental change. We applied genome-resolved metagenomics to 41 Arctic seawater samples, collected at various depths in different seasons during the Tara Oceans Polar Circle expedition, to evaluate the ecology, metabolic potential and activity of resident bacteria and archaea. We assembled 530 metagenome-assembled genomes (MAGs) to form the Arctic MAGs catalogue comprising 526 species. A total of 441 MAGs belonged to species that have not previously been reported and 299 genomes showed an exclusively polar distribution. Most Arctic MAGs have large genomes and the potential for fast generation times, both of which may enable adaptation to a copiotrophic lifestyle in nutrient-rich waters. We identified 38 habitat generalists and 111 specialists in the Arctic Ocean. We also found a general prevalence of 14 mixotrophs, while chemolithoautotrophs were mostly present in the mesopelagic layer during spring and autumn. We revealed 62 MAGs classified as key Arctic species, found only in the Arctic Ocean, showing the highest gene expression values and predicted to have habitat-specific traits. The Artic MAGs catalogue will inform our understanding of polar microorganisms that drive global biogeochemical cycles.
© 2021. The Author(s), under exclusive licence to Springer Nature Limited.

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Year:  2021        PMID: 34782724     DOI: 10.1038/s41564-021-00979-9

Source DB:  PubMed          Journal:  Nat Microbiol        ISSN: 2058-5276            Impact factor:   17.745


  69 in total

1.  Seasonal patterns in Arctic prasinophytes and inferred ecology of Bathycoccus unveiled in an Arctic winter metagenome.

Authors:  Nathalie Joli; Adam Monier; Ramiro Logares; Connie Lovejoy
Journal:  ISME J       Date:  2017-03-07       Impact factor: 10.302

2.  High bicarbonate assimilation in the dark by Arctic bacteria.

Authors:  Laura Alonso-Sáez; Pierre E Galand; Emilio O Casamayor; Carlos Pedrós-Alió; Stefan Bertilsson
Journal:  ISME J       Date:  2010-06-17       Impact factor: 10.302

Review 3.  Microbial ecology of the cryosphere: sea ice and glacial habitats.

Authors:  Antje Boetius; Alexandre M Anesio; Jody W Deming; Jill A Mikucki; Josephine Z Rapp
Journal:  Nat Rev Microbiol       Date:  2015-09-07       Impact factor: 60.633

4.  Unique archaeal assemblages in the Arctic Ocean unveiled by massively parallel tag sequencing.

Authors:  Pierre E Galand; Emilio O Casamayor; David L Kirchman; Marianne Potvin; Connie Lovejoy
Journal:  ISME J       Date:  2009-03-26       Impact factor: 10.302

5.  Winter-to-summer changes in the composition and single-cell activity of near-surface Arctic prokaryotes.

Authors:  Laura Alonso-Sáez; Olga Sánchez; Josep M Gasol; Vanessa Balagué; Carlos Pedrós-Alio
Journal:  Environ Microbiol       Date:  2008-06-28       Impact factor: 5.491

6.  The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes.

Authors:  David L Kirchman; Matthew T Cottrell; Connie Lovejoy
Journal:  Environ Microbiol       Date:  2010-02-03       Impact factor: 5.491

Review 7.  Marine Bacterioplankton Seasonal Succession Dynamics.

Authors:  Carina Bunse; Jarone Pinhassi
Journal:  Trends Microbiol       Date:  2017-01-17       Impact factor: 17.079

8.  Role for urea in nitrification by polar marine Archaea.

Authors:  Laura Alonso-Sáez; Alison S Waller; Daniel R Mende; Kevin Bakker; Hanna Farnelid; Patricia L Yager; Connie Lovejoy; Jean-Éric Tremblay; Marianne Potvin; Friederike Heinrich; Marta Estrada; Lasse Riemann; Peer Bork; Carlos Pedrós-Alió; Stefan Bertilsson
Journal:  Proc Natl Acad Sci U S A       Date:  2012-10-01       Impact factor: 11.205

9.  Abundance, diversity, and activity of ammonia-oxidizing prokaryotes in the coastal Arctic ocean in summer and winter.

Authors:  Glenn D Christman; Matthew T Cottrell; Brian N Popp; Elizabeth Gier; David L Kirchman
Journal:  Appl Environ Microbiol       Date:  2011-01-14       Impact factor: 4.792

Review 10.  Scientists' warning to humanity: microorganisms and climate change.

Authors:  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; Scott C Weaver; Eric A Webb; Nicole S Webster
Journal:  Nat Rev Microbiol       Date:  2019-06-18       Impact factor: 60.633

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  7 in total

1.  A genome and gene catalog of glacier microbiomes.

Authors:  Yongqin Liu; Mukan Ji; Tao Yu; Julian Zaugg; Alexandre M Anesio; Zhihao Zhang; Songnian Hu; Philip Hugenholtz; Keshao Liu; Pengfei Liu; Yuying Chen; Yingfeng Luo; Tandong Yao
Journal:  Nat Biotechnol       Date:  2022-06-27       Impact factor: 68.164

2.  The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes.

Authors:  Caroline Vernette; Julien Lecubin; Pablo Sánchez; Shinichi Sunagawa; Tom O Delmont; Silvia G Acinas; Eric Pelletier; Pascal Hingamp; Magali Lescot
Journal:  Nucleic Acids Res       Date:  2022-06-10       Impact factor: 19.160

3.  Active lithoautotrophic and methane-oxidizing microbial community in an anoxic, sub-zero, and hypersaline High Arctic spring.

Authors:  Elisse Magnuson; Ianina Altshuler; Miguel Á Fernández-Martínez; Ya-Jou Chen; Catherine Maggiori; Jacqueline Goordial; Lyle G Whyte
Journal:  ISME J       Date:  2022-04-08       Impact factor: 11.217

Review 4.  Microbial oxidation of atmospheric trace gases.

Authors:  Chris Greening; Rhys Grinter
Journal:  Nat Rev Microbiol       Date:  2022-04-12       Impact factor: 78.297

Review 5.  Considerations for constructing a protein sequence database for metaproteomics.

Authors:  J Alfredo Blakeley-Ruiz; Manuel Kleiner
Journal:  Comput Struct Biotechnol J       Date:  2022-01-21       Impact factor: 7.271

Review 6.  Diatoms and Their Microbiomes in Complex and Changing Polar Oceans.

Authors:  Reuben Gilbertson; Emma Langan; Thomas Mock
Journal:  Front Microbiol       Date:  2022-03-25       Impact factor: 5.640

7.  Diverse Genomic Traits Differentiate Sinking-Particle-Associated versus Free-Living Microbes throughout the Oligotrophic Open Ocean Water Column.

Authors:  Andy O Leu; John M Eppley; Andrew Burger; Edward F DeLong
Journal:  mBio       Date:  2022-07-12       Impact factor: 7.786

  7 in total

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