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

• Published in: Nature Microbiology
• 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, 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)
• Format: Article in Journal/Newspaper
• Language: English
• Published: Nature Publishing Group 2023
• Subjects: Conserve and sustainably use the oceans; seas and marine resources for sustainable development; Antarctic; New Zealand; Ross Ice Shelf; Antarc*; Antarctica; Ice Shelf
• Online Access: http://hdl.handle.net/10261/330917; https://doi.org/10.1038/s41564-023-01374-2

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) ...