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Title

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

AuthorsAcinas, Silvia G. CSIC ORCID ; Sánchez Fernández, Pablo CSIC ORCID ; Salazar, Guillem CSIC ORCID; Cornejo-Castillo, Francisco M. CSIC ORCID; Sebastián, Marta CSIC ORCID; Logares, Ramiro CSIC ORCID ; Royo-Llonch, Marta CSIC ORCID ; Paoli, Lucas; Sunagawa, Shinichi; Hingamp, Pascal; Ogata, Hiroyuki; Lima-Mendez, Gipsi; Roux, Simon; González, José M.; Arrieta López de Uralde, Jesús M. CSIC ORCID ; Alam, Intikhab; Kamau, Allan A.; Bowler, Chris; Raes, Jeroen; Pesant, Stéphane; Bork, Peer; Agustí, Susana CSIC ORCID; Gojobori, Takashi; Vaqué, Dolors CSIC ORCID ; Sullivan, Matthew B.; Pedrós-Alió, Carlos CSIC ORCID; Massana, Ramon CSIC ORCID ; Duarte, Carlos M. CSIC ORCID; Gasol, Josep M. CSIC ORCID
Issue DateMay-2021
PublisherNature Publishing Group
CitationCommunications Biology 4: 604 (2021)
AbstractThe 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
Description15 pages, 7 figures, supplementary information https://doi.org/10.1038/s42003-021-02112-2.-- All data generated or analyzed during this study are included in this published article (and its supplementary information files). All raw sequences are publicly available at both DOE’s JGI Integrated Microbial Genomes and Microbiomes (IMG/MER) and the European Nucleotide Archive (ENA). Individual metagenome assemblies, annotation files, and alignment files can be accessed at IMG/MER. All accession numbers are listed in Supplementary Data 1. The co-assembly for the MAG dataset construction can be found through ENA at https://www.ebi.ac.uk/ena with accession number PRJEB40454, the nucleotide sequence for each MAG and their annotation files can be found through BioStudies at https://www.ebi.ac.uk/biostudies with accession S-BSST457 and also in the companion website to this manuscript at https://malaspina-public.gitlab.io/malaspina-deep-ocean-microbiome/.-- All software used in this work is publicly available distributed by their respective developers, and it is described in “Methods”, including the versions and options used. Additional custom scripts to assign taxonomy to the M-geneDB genes and to filter and format FRA results are available through BioStudies at https://www.ebi.ac.uk/biostudies with accession S-BSST457
Publisher version (URL)https://doi.org/10.1038/s42003-021-02112-2
URIhttp://hdl.handle.net/10261/241901
DOI10.1038/s42003-021-02112-2
E-ISSN2399-3642
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