Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities

Acinas, Silvia G.; Sánchez, Pablo; Salazar, Guillem; Cornejo-Castillo, Francisco M.; Sebastián, Marta; Logares, Ramiro; Royo-Llonch, Marta; Paoli, Lucas; Sunagawa, Shinichi; Hingamp, Pascal; Ogata, Hiroyuki; Lima-Mendez, Gipsi; Roux, Simon; González, José M.; Arrieta, Jesús M.; Alam, Intikhab S.; Kamau, Allan; Bowler, Chris; Raes, Jeroen; Pesant, Stéphane; Bork, Peer; Agustí, Susana; Gojobori, Takashi; Vaqué, Dolors; Pedrós-Alió, Carlos; Massana, Ramon; Duarte, Carlos M.; Gasol, Josep M.; Sullivan, Matthew B.

doi:10.1038/s42003-021-02112-2

Title: Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities

Journal Article · Fri May 21 00:00:00 EDT 2021 · Communications Biology

DOI:https://doi.org/10.1038/s42003-021-02112-2· OSTI ID:1826332

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Inst. of Marine Sciences (ICM), Barcelona (Spain)
Inst. of Marine Sciences (ICM), Barcelona (Spain); ETH Zurich (Switzerland)
Inst. of Marine Sciences (ICM), Barcelona (Spain); Univ. of California, Santa Cruz, CA (United States)
Inst. of Marine Sciences (ICM), Barcelona (Spain); Univ. de Las Palmas de Gran Canaria, Gran Marta (Sebastian)
ETH Zurich (Switzerland)
Univ. de Toulon, Marseille (France)
Kyoto Univ., Uji (Japan)
Univ. libre de Bruxelles (ULB), Brussels (Belgium); Interuniversity Inst. for Bioinformatics in Brussels (Belgium)
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); The Ohio State Univ., Columbus, OH (United States)
Univ. of La Laguna (Spain)
Spanish Institute of Oceanography (IEO), Santa Cruz de Tenerife (Spain)
King Abdullah Univ. of Science and Technology (KAUST), Thuwal (Saudi Arabia)
Univ. PSL, Paris (France); Research Federation for the study of Global Ocean Systems Ecology and Evolution, Paris (France)
Univ. of Leuven (Belgium); VIB Center for Microbiology, Leuven (Belgium)
European Molecular Biology Lab., European Bioinformatics Institute (EMBL-EBI), Cambridge (United Kingdom); Univ. of Bremen (Germany)
European Molecular Biology Lab., Heidelberg (Germany)
Centro Nacional de Biotecnología (CNB), Madrid (Spain)
Inst. of Marine Sciences (ICM), Barcelona (Spain); Edith Cowan Univ., Joondalup (Australia)
The Ohio State Univ., Columbus, OH (United States)

The deep sea, the largest ocean’s compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we analyze 58 metagenomes from tropical and subtropical deep oceans to generate the Malaspina Gene Database. Free-living or particle-attached lifestyles drive functional differences in bathypelagic prokaryotic communities, regardless of their biogeography. Ammonia and CO oxidation pathways are enriched in the free-living microbial communities and dissimilatory nitrate reduction to ammonium and H₂ oxidation pathways in the particle-attached, while the Calvin Benson-Bassham cycle is the most prevalent inorganic carbon fixation pathway in both size fractions. Reconstruction of the Malaspina Deep Metagenome-Assembled Genomes reveals unique non-cyanobacterial diazotrophic bacteria and chemolithoautotrophic prokaryotes. The widespread potential to grow both autotrophically and heterotrophically suggests that mixotrophy is an ecologically relevant trait in the deep ocean. These results expand our understanding of the functional microbial structure and metabolic capabilities of the largest Earth aquatic ecosystem.

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Research Organization:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1826332

Journal Information:: Communications Biology, Vol. 4, Issue 1; ISSN 2399-3642

Publisher:: Springer NatureCopyright Statement

Country of Publication:: United States

Language:: English

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