Show simple item record

dc.contributor.authorAcinas, Silvia G.
dc.contributor.authorSánchez, Pablo
dc.contributor.authorSalazar, Guillem
dc.contributor.authorCornejo-Castillo, Francisco M.
dc.contributor.authorSebastián, Marta
dc.contributor.authorLogares, Ramiro
dc.contributor.authorRoyo-Llonch, Marta
dc.contributor.authorPaoli, Lucas
dc.contributor.authorSunagawa, Shinichi
dc.contributor.authorHingamp, Pascal
dc.contributor.authorOgata, Hiroyuki
dc.contributor.authorLima-Mendez, Gipsi
dc.contributor.authorRoux, Simon
dc.contributor.authorGonzález, José M.
dc.contributor.authorArrieta, Jesús M.
dc.contributor.authorAlam, Intikhab
dc.contributor.authorKamau, Allan
dc.contributor.authorBowler, Chris
dc.contributor.authorRaes, Jeroen
dc.contributor.authorPesant, Stéphane
dc.contributor.authorBork, Peer
dc.contributor.authorAgusti, Susana
dc.contributor.authorGojobori, Takashi
dc.contributor.authorVaqué, Dolors
dc.contributor.authorSullivan, Matthew B.
dc.contributor.authorPedrós-Alió, Carlos
dc.contributor.authorMassana, Ramon
dc.contributor.authorDuarte, Carlos M.
dc.contributor.authorGasol, Josep M.
dc.date.accessioned2021-05-24T13:01:40Z
dc.date.available2021-05-24T13:01:40Z
dc.date.issued2021-05-21
dc.date.submitted2020-09-25
dc.identifier.citationAcinas, S. G., Sánchez, P., Salazar, G., Cornejo-Castillo, F. M., Sebastián, M., Logares, R., … Gasol, J. M. (2021). Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. Communications Biology, 4(1). doi:10.1038/s42003-021-02112-2
dc.identifier.issn2399-3642
dc.identifier.pmid34021239
dc.identifier.doi10.1038/s42003-021-02112-2
dc.identifier.urihttp://hdl.handle.net/10754/669234
dc.description.abstractAbstractThe 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.
dc.description.sponsorshipWe thank the R/V Hespérides captain and crew, the chief scientists in Malaspina expedition legs, and all project participants for their help in making this project possible. This work was funded by the Spanish Ministry of Economy and Competitiveness (MINECO) through the Consolider-Ingenio program (Malaspina 2010 Expedition, ref. CSD2008-00077). The sequencing of 58 bathypelagic metagenomes was done by the U.S. Department of Energy Joint Genome Institute, supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02 05CH11231 to SGA (CSP 612 “Microbial metagenomics and transcriptomics from a global deep-ocean expedition”). Additional funding was provided by the project MAGGY (CTM2017-87736-R) to S.G.A. from the Spanish Ministry of Economy and Competitiveness, Grup de Recerca 2017SGR/1568 from Generalitat de Catalunya, and King Abdullah University of Science and Technology (KAUST) under contract OSR #3362 and by funding of the EMFF Program of the European Union (MERCLUB project, Grant Agreement 863584). The ICM researchers have had the institutional support of the “Severo Ochoa Centre of Excellence” accreditation (CEX2019-000928-S). High-Performance computing analyses were run at the Marine Bioinformatics Service (MARBITS, https://marbits.icm.csic.es) of the Institut de Ciències del Mar (ICM-CSIC), Barcelona, Supercomputing Center (Grant BCV-2013-2-0001) and KAUST’s Ibex HPC. We thank Shook Studio for assistance with figure design and implementation and the anonymous reviewers for their comments to improve this manuscript. This paper is dedicated to the memory of Professor Vladimir B. Bajic, 2019.
dc.publisherSpringer Science and Business Media LLC
dc.relation.urlhttp://www.nature.com/articles/s42003-021-02112-2
dc.rightsThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.
dc.rights.urihttps://creativecommons.org/licenses/by/4.0
dc.titleDeep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities
dc.typeArticle
dc.contributor.departmentKing Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia.
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentMarine Science Program
dc.contributor.departmentRed Sea Research Center (RSRC)
dc.contributor.departmentBioscience Program
dc.identifier.journalCommunications Biology
dc.eprint.versionPublisher's Version/PDF
dc.identifier.volume4
dc.identifier.issue1
kaust.personAlam, Intikhab S.
kaust.personKamau, Allan
kaust.personAgusti, Susana
kaust.personGojobori, Takashi
kaust.personDuarte, Carlos M.
kaust.grant.numberOSR #3362
dc.date.accepted2021-04-16
refterms.dateFOA2021-05-24T13:04:25Z
kaust.acknowledged.supportUnitIbex
kaust.acknowledged.supportUnitOSR


Files in this item

Thumbnail
Name:
deep ocean.pdf
Size:
2.272Mb
Format:
PDF
Description:
Published version

This item appears in the following Collection(s)

Show simple item record

This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.
Except where otherwise noted, this item's license is described as This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.