Top abundant deep ocean heterotrophic bacteria can be retrieved by cultivation
Sanz-Sáez, Isabel (Institut de Ciències del Mar. Departament de Biologia Marina i Oceanografia)
Sánchez, Pablo (Institut de Ciències del Mar. Departament de Biologia Marina i Oceanografia)
Salazar, Guillem (Institute of Microbiology. Department of Biology)
Sunagawa, Shinichi (Institute of Microbiology. Department of Biology)
de Vargas, Colomban (Sorbonne University)
Bowler, Chris (Université Paris)
Sullivan, Matthew B. (The Ohio State University. Departments of Microbiology and Civil)
Wincker, Patrick (Université Evry)
Karsenti, Eric (Research Federation for the Study of Global Ocean Systems Ecology and Evolution)
Pedrós-Alió, Carlos (Centro Nacional de Biotecnología)
Agustí, Susana (King Abdullah University of Science and Technology)
Gojobori, Takashi (King Abdullah University of Science and Technology)
Duarte, Carlos M. (King Abdullah University of Science and Technology)
Gasol, Josep M. (Institut de Ciències del Mar. Departament de Biologia Marina i Oceanografia)
Sánchez Martínez, M. Olga (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)
Acinas, Silvia G. (Institut de Ciències del Mar. Departament de Biologia Marina i Oceanografia)

Data:	2023
Resum:	Traditional culture techniques usually retrieve a small fraction of the marine microbial diversity, which mainly belong to the so-called rare biosphere. However, this paradigm has not been fully tested at a broad scale, especially in the deep ocean. Here, we examined the fraction of heterotrophic bacterial communities in photic and deep ocean layers that could be recovered by culture-dependent techniques at a large scale. We compared 16S rRNA gene sequences from a collection of 2003 cultured heterotrophic marine bacteria with global 16S rRNA metabarcoding datasets (16S TAGs) covering surface, mesopelagic and bathypelagic ocean samples that included 16 of the 23 samples used for isolation. These global datasets represent 60 322 unique 16S amplicon sequence variants (ASVs). Our results reveal a significantly higher proportion of isolates identical to ASVs in deeper ocean layers reaching up to 28% of the 16S TAGs of the bathypelagic microbial communities, which included the isolation of 3 of the top 10 most abundant 16S ASVs in the global bathypelagic ocean, related to the genera Sulfitobacter, Halomonas and Erythrobacter. These isolates contributed differently to the prokaryotic communities across different plankton size fractions, recruiting between 38% in the free-living fraction (0. 2-0. 8 µm) and up to 45% in the largest particles (20-200 µm) in the bathypelagic ocean. Our findings support the hypothesis that sinking particles in the bathypelagic act as resource-rich habitats, suitable for the growth of heterotrophic bacteria with a copiotroph lifestyle that can be cultured, and that these cultivable bacteria can also thrive as free-living bacteria.
Ajuts:	European Commission 226248 Agencia Estatal de Investigación CTM2017-87736-R Agencia Estatal de Investigación PID2020-116489RB-I00 Agencia Estatal de Investigación RTI2018-101025-B-I00 Ministerio de Ciencia e Innovación CSD2008-00077 Ministerio de Economía y Competitividad CTM2012-34294 Ministerio de Ciencia e Innovación CEX2019-000928-S
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Matèria:	Microbial ecology ; Environmental microbiology
Publicat a:	ISME Communications, Vol. 3, Issue 1 (December 2023) , art.92, ISSN 2730-6151

DOI: 10.1038/s43705-023-00290-0
PMID: 37660234

13 p, 2.4 MB

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