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Emerging concepts on microbial processes in the bathypelagic ocean – ecology, biogeochemistry, and genomics

Nagata, Toshi and Tamburini, Christian and Arístegui, Javier and Baltar, Federico and Bochdansky, Alexander B. and Fonda-Umani, Serena and Fukuda, Hideki and Gogou, Alexandra and Hansell, Dennis A. and Hansman, Roberta L. and Herndl, Gerhard J. and Panagiotopoulos, Christos and Reinthaler, Thomas and Sohrin, Rumi and Verdugo, Pedro and Yamada, Namiha and Yamashita, Youhei and Yokokawa, Taichi and Bartlett, Douglas H. (2010) Emerging concepts on microbial processes in the bathypelagic ocean – ecology, biogeochemistry, and genomics. Deep-Sea Research. Part II, Topical Studies in Oceanography, 57 (16). pp. 1519-1536. ISSN 0967-0645.

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This paper synthesizes recent findings regarding microbial distributions and processes in the bathypelagic ocean (depth >1000 m). Abundance, production and respiration of prokaryotes reflect supplies of particulate and dissolved organic matter to the bathypelagic zone. Better resolution of carbon fluxes mediated by deep microbes requires further testing on the validity of conversion factors. Archaea, especially marine Crenarchaeota Group I, are abundant in deep waters where they can fix dissolved inorganic carbon. Viruses appear to be important in the microbial loop in deep waters, displaying remarkably high virus to prokaryote abundance ratios in some oceanic regions. Sequencing of 18S rRNA genes revealed a tremendous diversity of small-sized protists in bathypelagic waters. Abundances of heterotrophic nanoflagellates (HNF) and ciliates decrease with depth more steeply than prokaryotes; nonetheless, data indicated that HNF consumed half of prokaryote production in the bathypelagic zone. Aggregates are important habitats for deep-water microbes, which produce more extracellular enzymes (on a per-cell basis) than surface communities. The theory of marine gel formation provides a framework to unravel complex interactions between microbes and organic polymers. Recent data on the effects of hydrostatic pressure on microbial activities indicate that bathypelagic microbial activity is generally higher under in situ pressure conditions than at atmospheric pressures. High-throughput sequencing of 16S rRNA genes revealed a remarkable diversity of Bacteria in the bathypelagic ocean. Metagenomics and comparative genomics of piezophiles reveal not only the high diversity of deep sea microbes but also specific functional attributes of these piezophilic microbes, interpreted as an adaptation to the deep water environment. Taken together, the data compiled on bathypelagic microbes indicate that, despite high-pressure and low-temperature conditions, microbes in the bathypelagic ocean dynamically interact with complex mixtures of organic matter, responding to changes in the ocean’s biogeochemical state.

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Additional Information:© 2010 Elsevier Ltd. Received 2 April 2009; accepted 6 December 2009. Available online 7 March 2010. This synthesis paper is a product of the IMBER IMBIZO meeting in Florida (9-13 Nov, 2008). We thank the organizers for coordination and logistical support. T.N and H.F. were supported by a JSPS grant (KAKENHI 20310010). D.H.B. gratefully acknowledges funding from the National Science Foundation (Microbial Interactions and Processes NSF0801793 and Microbial Genome Sequencing Program NSF0827051). A.B.B. was supported by the National Science Foundation grants #NSF0550184 and #NSF0826659. D.A.H. was supported with funding from the U.S. National Science Foundation (OCE-0551332). C.T. was supported by the ANR-POTES (ANR-05-BLAN-0161-01) program supported by the Agence Nationale de la Recherche (France). G.J.H. and T.R. were supported by the Dutch Science Fund, Earth and Life Science Branch (NWO-ALW). J.A. was supported by the CAIBEX (CTM2007-66408-C02-02/MAR) project. T.Y. was supported by the Japanese Society for the Promotion of Science (JSPS) Postdoctoral Fellowship for research abroad. A.G. acknowledges funding from the Hellenic GSRT & EU (non-EU Grant No180) and SESAME project (EC Contract No GOCE-036949) funded by the European Commission's Sixth Framework Program. Chiaki Motegi provided illustrations. David L. Kirchman and Theodore T. Packard are acknowledged for helpful comments on the3H- leucine and ETS methods, respectively. We appreciate valuable comments of three anonymous reviewers.
Funding AgencyGrant Number
Japan Society for the Promotion of Science (JSPS)20310010
Agence Nationale de la Recherche (France)ANR-05-BLAN-0161-01
Earth and Life Science Branch (NWO-ALW)UNSPECIFIED
Hellenic GSRT EU180
European CommissionGOCE-036949
Subject Keywords:Bathypelagic zone; Microbial loop; Organic matter; Piezophile; Biogeochemistry; Genomics
Issue or Number:16
Record Number:CaltechAUTHORS:20100817-093626251
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:19468
Deposited By: Tony Diaz
Deposited On:17 Aug 2010 17:05
Last Modified:03 Oct 2019 01:57

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