ARTICLE IN PRESS Deep Sea Research II 57 2010 1519 1536 Contents lists available at ScienceDirect Deep Sea Research II journal homepage www elsevier com locate dsr2 Emerging concepts on microbial processes in the bathypelagic ocean ecology biogeochemistry and genomics Toshi Nagata a n Christian Tamburini b Javier Ar stegui c Federico Baltar c Alexander B Bochdansky d Serena Fonda Umani e Hideki Fukuda f Alexandra Gogou g Dennis A Hansell h Roberta L Hansman i Gerhard J Herndl j Christos Panagiotopoulos b Thomas Reinthaler j Rumi Sohrin k Pedro Verdugo l Namiha Yamada m Youhei Yamashita n 1 Taichi Yokokawa o Douglas H Bartlett p a Marine Biogeochemistry Group Ocean Research Institute The University of Tokyo 1 15 1 Minami dai Nakano Tokyo 164 8639 Japan Universite de la Me diterrane e Centre d Oce anologie de Marseille LMGEM UMR 6117 CNRS INSU 163 Avenue de Luminy 13288 Marseille Cedex 09 France Facultad de Ciencias del Mar Universidad de Las Palmas de Gran Canaria 35017 Las Palmas de Gran Canaria Islas Canarias Spain d Department of Ocean Earth and Atmospheric Sciences Old Dominion University 4600 Elkhorn Ave Norfolk 23529 VA USA e Department of Life Sciences University of Trieste v Valerio 28 1 Trieste 34127 TS Italy f International Coastal Research Center Ocean Research Institute The University of Tokyo 2 106 1 Akahama Otsuchi town Kamihei county Iwate 028 1102 Japan g Hellenic Centre for Marine Research Institute of Oceanography 46 7 km Athens Sounion Av 19013 Anavyssos Greece h Division of Marine and Atmospheric Chemistry Rosenstiel School of Marine and Atmospheric Science University of Miami 4600 Rickenbacker Causeway Miami FL 33149 USA i Division of Geological and Planetary Sciences California Institute of Technology MC 100 23 1200 E California Blvd Pasadena CA 91125 USA j Department of Biological Oceanography Royal Netherlands Institute for Sea Research NIOZ PO box 59 1790AB Den Burg the Netherlands University of Vienna Department of Marine Biology Althanstrasse 14 1090 Vienna Austria k Institute of Geosciences Shizuoka University 836 Oya Suruga ku Shizuoka 422 8529 Japan l Department of Bioengineering University of Washington Friday Harbor Laboratories 620 University Rd Friday Harbor 98250 WA USA m National Institute of Advanced Industrial Science and Technology AIST Tsukuba AIST West 16 1 Onogawa Tsukuba 305 8569 Japan n Southeast Environmental Research Center Florida International University OE 148 University Park Miami FL 33199 USA o Biological Oceanography Royal Netherlands Institute for Sea Research NIOZ PO box 59 1790AB Den Burg the Netherlands p Marine Biology Research Division Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography University of California San Diego La Jolla CA 92093 0202 USA b c a r t i c l e in fo abstract Article history Received 2 April 2009 Accepted 6 December 2009 Available online 7 March 2010 This paper synthesizes recent ndings regarding microbial distributions and processes in the bathypelagic ocean depth 4 1000 m Abundance production and respiration of prokaryotes re ect supplies of particulate and dissolved organic matter to the bathypelagic zone Better resolution of carbon uxes 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 x 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 nano agellates 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 Keywords Bathypelagic zone Microbial loop Organic matter Piezophile Biogeochemistry Genomics n Corresponding author Present address Marine Biogeochemistry Group Atmosphere and Ocean Research Institute The University of Tokyo 5 1 5 Kashiwanoha Kashiwa Chiba 277 8564 Japan Tel fax 81 4 7136 6090 E mail addresses nagata aori u tokyo ac jp T Nagata christian tamburini univmed fr C Tamburini jAristegui dbio ulpgc es J Ar stegui federico baltar102 doctorandos ulpgc es F Baltar abochdan odu edu A Bochdansky s fonda units it S Fonda Umani hfukuda ori u tokyo ac jp H Fukuda agogou ath hcmr gr A Gogou dhansell rsmas miami edu D A Hansell rhansman caltech edu R L Hansman gerhard herndl univie ac at G J Herndl christos panagiotopoulos univmed fr C Panagiotopoulos thomas reinthaler univie ac at T Reinthaler srshori ipc shizuoka ac jp R Sohrin verdugo u washington edu P Verdugo namiha yamada aist go jp N Yamada yamashiy u edu yamashi ees hokudai ac jp Y Yamashita taichi yokokawa nioz nl T Yokokawa dbartlett ucsd edu D H Bartlett 1 Present address Faculty of Environmental Earth Science Hokkaido University N10 W5 Kita ku Sapporo Hokkaido 060 0810 Japan 0967 0645 see front matter 2010 Elsevier Ltd All rights reserved doi 10 1016 j dsr2 2010 02 019 ARTICLE IN PRESS 1520 T Nagata et al Deep Sea Research II 57 2010 1519 1536 high diversity of deep sea microbes but also speci c 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 2010 Elsevier Ltd All rights reserved 1 Introduction The bathypelagic zone at ocean depths 41000 m is the largest but least understood aquatic habitat on our planet accounting