A ubiquitous gammaproteobacterial clade dominates expression of sulfur oxidation genes across the mesopelagic ocean

A ubiquitous gammaproteobacterial clade dominates expression of sulfur oxidation genes across the mesopelagic ocean

21 pages, 6 figures, supplementary information https://doi.org/10.1038/s41564-023-01374-2.-- Data availability: The sequence data generated in this study have been deposited in the EMBL Nucleotide Sequence Database (ENA) database under Bioproject PRJEB35712 (metagenomic and metatranscriptomic raw reads, metagenomic and metatranscriptomic assemblies, metagenomic assembled genomes and single-cell amplified genomes) and in the NCBI Sequence Read Archive (SRA) under Bioproject PRJNA593264 (16S rRNA amplicon reads).-- Code availability: Scripts available at Zenodo (https://doi.org/10.5281/zenodo.7721930.2023)

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Main Authors: Baltar, Federico, Martínez-Pérez, Clara, Amano, Chie, Vial, Marion, Robaina-Estévez, Semidán, Reinthaler, Thomas, Herndl, Gerhard J., Zhao, Zihao, Logares, Ramiro, Morales, Sergio E., González, José M.
Other Authors: New Zealand Antarctic Research Institute
Format: artículo biblioteca
Language:English
Published: Nature Publishing Group 2023-04
Subjects:Conserve and sustainably use the oceans, seas and marine resources for sustainable development,
Online Access:http://hdl.handle.net/10261/330917
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institution ICM ES
collection DSpace
country España
countrycode ES
component Bibliográfico
access En linea
databasecode dig-icm-es
tag biblioteca
region Europa del Sur
libraryname Biblioteca del ICM España
language English
topic Conserve and sustainably use the oceans, seas and marine resources for sustainable development
Conserve and sustainably use the oceans, seas and marine resources for sustainable development
spellingShingle Conserve and sustainably use the oceans, seas and marine resources for sustainable development
Conserve and sustainably use the oceans, seas and marine resources for sustainable development
Baltar, Federico
Martínez-Pérez, Clara
Amano, Chie
Vial, Marion
Robaina-Estévez, Semidán
Reinthaler, Thomas
Herndl, Gerhard J.
Zhao, Zihao
Logares, Ramiro
Morales, Sergio E.
González, José M.
A ubiquitous gammaproteobacterial clade dominates expression of sulfur oxidation genes across the mesopelagic ocean
description 21 pages, 6 figures, supplementary information https://doi.org/10.1038/s41564-023-01374-2.-- Data availability: The sequence data generated in this study have been deposited in the EMBL Nucleotide Sequence Database (ENA) database under Bioproject PRJEB35712 (metagenomic and metatranscriptomic raw reads, metagenomic and metatranscriptomic assemblies, metagenomic assembled genomes and single-cell amplified genomes) and in the NCBI Sequence Read Archive (SRA) under Bioproject PRJNA593264 (16S rRNA amplicon reads).-- Code availability: Scripts available at Zenodo (https://doi.org/10.5281/zenodo.7721930.2023)
author2 New Zealand Antarctic Research Institute
author_facet New Zealand Antarctic Research Institute
Baltar, Federico
Martínez-Pérez, Clara
Amano, Chie
Vial, Marion
Robaina-Estévez, Semidán
Reinthaler, Thomas
Herndl, Gerhard J.
Zhao, Zihao
Logares, Ramiro
Morales, Sergio E.
González, José M.
format artículo
topic_facet Conserve and sustainably use the oceans, seas and marine resources for sustainable development
author Baltar, Federico
Martínez-Pérez, Clara
Amano, Chie
Vial, Marion
Robaina-Estévez, Semidán
Reinthaler, Thomas
Herndl, Gerhard J.
Zhao, Zihao
Logares, Ramiro
Morales, Sergio E.
González, José M.
author_sort Baltar, Federico
title A ubiquitous gammaproteobacterial clade dominates expression of sulfur oxidation genes across the mesopelagic ocean
title_short A ubiquitous gammaproteobacterial clade dominates expression of sulfur oxidation genes across the mesopelagic ocean
title_full A ubiquitous gammaproteobacterial clade dominates expression of sulfur oxidation genes across the mesopelagic ocean
title_fullStr A ubiquitous gammaproteobacterial clade dominates expression of sulfur oxidation genes across the mesopelagic ocean
title_full_unstemmed A ubiquitous gammaproteobacterial clade dominates expression of sulfur oxidation genes across the mesopelagic ocean
title_sort ubiquitous gammaproteobacterial clade dominates expression of sulfur oxidation genes across the mesopelagic ocean
publisher Nature Publishing Group
publishDate 2023-04
url http://hdl.handle.net/10261/330917
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spelling dig-icm-es-10261-3309172023-07-12T10:50:22Z A ubiquitous gammaproteobacterial clade dominates expression of sulfur oxidation genes across the mesopelagic ocean Baltar, Federico Martínez-Pérez, Clara Amano, Chie Vial, Marion Robaina-Estévez, Semidán Reinthaler, Thomas Herndl, Gerhard J. Zhao, Zihao Logares, Ramiro Morales, Sergio E. González, José M. New Zealand Antarctic Research Institute Austrian Science Fund European Research Council European Commission Ministerio de Economía y Competitividad (España) Ministerio de Ciencia, Innovación y Universidades (España) Agencia Estatal de Investigación (España) Conserve and sustainably use the oceans, seas and marine resources for sustainable development 21 pages, 6 figures, supplementary information https://doi.org/10.1038/s41564-023-01374-2.-- Data availability: The sequence data generated in this study have been deposited in the EMBL Nucleotide Sequence Database (ENA) database under Bioproject PRJEB35712 (metagenomic and metatranscriptomic raw reads, metagenomic and metatranscriptomic assemblies, metagenomic assembled genomes and single-cell amplified genomes) and in the NCBI Sequence Read Archive (SRA) under Bioproject PRJNA593264 (16S rRNA amplicon reads).-- Code availability: Scripts available at Zenodo (https://doi.org/10.5281/zenodo.7721930.2023) The deep ocean (>200 m depth) is the largest habitat on Earth. Recent evidence suggests sulfur oxidation could be a major energy source for deep ocean microbes. However, the global relevance and the identity of the major players in sulfur oxidation in the oxygenated deep-water column remain elusive. Here we combined single-cell genomics, community metagenomics, metatranscriptomics and single-cell activity measurements on samples collected beneath the Ross Ice Shelf in Antarctica to characterize a ubiquitous mixotrophic bacterial group (UBA868) that dominates expression of RuBisCO genes and of key sulfur oxidation genes. Further analyses of the gene libraries from the ‘Tara Oceans’ and ‘Malaspina’ expeditions confirmed the ubiquitous distribution and global relevance of this enigmatic group in the expression of sulfur oxidation and dissolved inorganic carbon fixation genes across the global mesopelagic ocean. Our study also underscores the unrecognized importance of mixotrophic microbes in the biogeochemical cycles of the deep ocean This research was facilitated by the New Zealand Antarctic Research Institute (NZARI)-funded Aotearoa New Zealand Ross Ice Shelf Program. Samples for MICRO-CARD-FISH were collected on several research cruises led by M. Simon (Sonne 248 cruise), B. Quéguiner and I. Obernosterer (MobyDick) and L. J. A. Gerringa (Geotraces-1). F.B. was supported by the Austrian Science Fund (FWF) projects OCEANIDES (P34304-B), ENIGMA (TAI534), EXEBIO (P35248) and OCEANBIOPLAST (P35619-B). G.J.H. was supported by the FWF project ARTEMIS (P28781-B21) and I486-B09 and by the ERC under the European Community’s 7th Framework Programme (FP7/2007-2013)/ERC grant agreement no. 268595 (MEDEA project). R.L. was supported by INTERACTOMICS, CTM2015-69936-P, and J.M.G. by project PID2019-110011RB-C32 (Spanish Ministry of Science and Innovation, Spanish State Research Agency, doi: 10.13039/501100011033) With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S) Peer reviewed 2023-07-12T10:49:53Z 2023-07-12T10:49:53Z 2023-04 artículo Nature Microbiology 8: 1137-1148 (2023) CEX2019-000928-S http://hdl.handle.net/10261/330917 10.1038/s41564-023-01374-2 2058-5276 en #PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# info:eu-repo/grantAgreement/EC/FP7/268595 info:eu-repo/grantAgreement/MINECO//CTM2015-69936-P/ES/DESVELANDO INTERACCIONES ECOLOGICAS ESENCIALES EN COMUNIDADES MICROBIANAS MARINAS MEDIANTE EL USO DE METODOS OMICOS/ info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2019-110011RB-C32/ES/UN ENFOQUE DE ESTUDIO DE LA ECOLOGIA MICROBIANA BASADO EN RASGOS Y GREMIOS/ https://doi.org/10.1038/s41564-023-01374-2 Sí none Nature Publishing Group

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