The deep-sea is the largest biome of the biosphere, and contains more than half of the whole ocean's microbes. Uncovering their general patterns of diversity and community structure at a global scale remains a great challenge, as only fragmentary information of deep-sea microbial diversity exists based on regional-scale studies. Here we report the first globally comprehensive survey of the prokaryotic communities inhabiting the bathypelagic ocean using high-throughput sequencing of the 16S rRNA gene. This work identifies the dominant prokaryotes in the pelagic deep ocean and reveals that 50% of the operational taxonomic units (OTUs) belong to previously unknown prokaryotic taxa, most of which are rare and appear in just a few samples. We show that whereas the local richness of communities is comparable to that observed in previous regional studies, the global pool of prokaryotic taxa detected is modest (∼3600 OTUs), as a high proportion of OTUs are shared among samples. The water masses appear to act as clear drivers of the geographical distribution of both particle-attached and free-living prokaryotes. In addition, we show that the deep-oceanic basins in which the bathypelagic realm is divided contain different particle-attached (but not free-living) microbial communities. The combination of the aging of the water masses and a lack of complete dispersal are identified as the main drivers for this biogeographical pattern. All together, we identify the potential of the deep ocean as a reservoir of still unknown biological diversity with a higher degree of spatial complexity than hitherto considered.
Bibliographical noteKAUST Repository Item: Exported on 2020-10-01
Acknowledgements: This work was supported by the Spanish Ministry of Science and Innovation through project Consolider-Ingenio Malaspina 2010 (CSD2008-00077). We thank our fellow scientists and the crew and ship scientists of the different cruise legs for smooth operation. We particularly thank E Borrull, C Diez, E Lara and D Vaque for help in DNA sampling and the rest of the microbiologists for sharing data. We would also like to thank the Physical Oceanography Malaspina team B2 for the acquisition, processing and calibration of the CTD data and TS Catala for the help on delineating water masses. Sequencing at the Joint Genome Intitute was supported by US Department of Energy Joint Genome Intitute 2011 Microbes Program grant CSP 602 grant to SGA. The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231. We also thank R Logares and the Barcelona Supercomputer Center for providing access to the MareNostrum Supercomputer (grants BCV-2011-2-0003/3-0005, 2012-1-0006/2-0002 to R Logares). Additional funding was provided by Spanish Ministry of Science and Innovation grant CGL2011-26848/BOS MicroOcean PANGENOMICS and the Spanish Ministry of Economy and Competitivity grant MALASPI-NOMICS (CTM2011-15461-E). GS and FMCC held PhD JAE-Predoc (CSIC) and FPI (MICINN) fellowships respectively and SGA was supported by FP7-OCEAN-2011 project 'Micro B3'.