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.
KAUST Repository Item: Exported on 2023-09-05
Acknowledged KAUST grant number(s): OSR#3362
Acknowledgements: We thank our fellow scientists and the crew and chief scientists of cruises ATP, MIFASOL and Malaspina and all scientist involved in the monthly sampling at the BBMO. We thank the people and sponsors who participated in the Tara Oceans Expedition 2009–2013 (http://oceans.taraexpeditions.org) for sampling collection. The project Malaspina 2010 Expedition (ref. CSD2008–00077) was funded by the Spanish Ministry of Economy and Competitiveness, Science and Innovation through the Consolider-Ingenio program. Other funding support were from Projects Arctic Tipping Points (ATP, contract #226248), in the FP7 program of the European Union, and DOREMI (CTM2012–34294) from the Spanish Ministry of Economy and Competitiveness, which allowed the collection of samples from the Arctic and NW Mediterranean Sea, respectively. Research, including laboratory experiments and analyses, was mainly funded by grant MAGGY, Plan Nacional I+D+I 2017 (CTM2017–87736-R), Polar EcoGen, Plan Nacional I+D+I 2020 (PID2020-116489RB-I00), and the Swiss National Science Foundation (SNSF) through project grant 205321_184955. Further funding was obtained from the King Abdullah University of Science and Technology (KAUST) under subaward agreement OSR#3362 and project MIAU-S3 (ref. RTI2018–101025-B-I00) from the Spanish Ministry of Economy and Competitiveness. This work benefited from the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S).