It is well known that only a small fraction of the marine microbial diversity, which mainly belong to the so-called rare biosphere, can be retrieved by isolation. However, this paradigm has not been fully tested at a broad scale, especially in the deep ocean and in the ocean particle microbiome. Here, we compared 16S rRNA gene sequences from a large collection (>2000) of cultured heterotrophic marine bacteria with global 16S rRNA metabarcoding (16S Tags) datasets covering surface, mesopelagic and bathypelagic ocean samples that included 16 of the 22 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, 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.

Primary Presenter: Silvia Acinas, ICM-CSIC (sacinas@icm.csic.es)

Authors:

Isabel Sanz-Sáez, Institut de Ciències del Mar, ICM-CSIC, 08003 Barcelona, Spain  (isscgg@cid.csic.es)

Pablo Sánchez, Institut de Ciències del Mar, ICM-CSIC, 08003 Barcelona, Spain  (pablosanchez@icm.csic.es)

Guillem Salazar, Institute of Microbiology, ETH Zurich,   (guillems@ethz.ch)

Shinichi Sunagawa, Institute of Microbiology, ETH Zurich  (ssunagawa@ethz.ch)

Colomban de Vargas, Sorbonne University, CNRS, Station Biologique de Roscoff.  (vargas@sb-roscoff.fr)

Chris Bowler, Institut de biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris.  (cbowler@biologie.ens.fr)

Matthew Sullivan, Departments of Microbiology and Civil, Environmental and Geodetic Engineering; The Ohio State University; Columbus, USA  (mbsulli@gmail.com)

Patrick Wincker, Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France  (pwincker@genoscope.cns.fr)

Eric Karsenti, Directors’ Research European Molecular Biology Laboratory, Heidelberg, Germany.  (karsenti@embl.de)

Carlos Pedrós-Alió, Department of Systems Biology, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain  (cpedros@cnb.csic.es)

Susana Agustí, Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.  (susana.agusti@kaust.edu.sa)

Takashi Gojobori, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia  (takashi.gojobori@kaust.edu.sa)

Carlos Duarte, Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.  (carlos.duarte@kaust.edu.sa)

Josep Gasol, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Spain  (pepgasol@icm.csic.es)

Olga Sánchez, Universitat Autonòma de Barcelona, Bellaterra, Spain  (Olga.Sanchez@uab.cat)