Microbial oceanography of the dark ocean's pelagic realm

29 pages, 6 figures, 2 tablesThe pelagic realm of the dark ocean represents a key site for remineralization of organic matter and long-term carbon storage and burial in the biosphere. It contains the largest pool of microbes in aquatic systems, harboring nearly 75% and 50% of the prokaryotic biomass and production, respectively, of the global ocean. Genomic approaches continue to uncover the enormous and dynamic genetic variability at phylogenetic and functional levels. Deep-sea prokaryotes have comparable or even higher cell-specific extracellular enzymatic activity than do microbes in surface waters, with a high fraction of freely released exoenzymes, probably indicative of a life mode reliant on surface attachment to particles or colloids. Additionally, evidence increases that chemoautotrophy might represent a significant CO2 sink and source of primary production in the dark ocean. Recent advances challenge the paradigm of stable microbial food web structure and function and slow organic matter cycling. However, knowledge of deep-ocean food webs is still rudimentary. Dynamics of particle transformation and fate of the exported material in deep waters are still largely unknown. Discrepancies exist between estimates of carbon fluxes and remineralization rates. Recent assessments, however, suggest that integrated respiration in the dark ocean’s water column is comparable to that in the epipelagic zone, and that the dark ocean is a site of paramount importance for material cycling in the biosphere. The advent of new molecular tools and in situ sampling methodologies will improve knowledge of the dark ocean’s microbial ecosystem and resolve current discrepancies between carbon sources and metabolic requirements of deep-sea microbesThis review was stimulated by K. Timmis and benefited from the collaborative projects ‘‘Remolinos Oceánicos y Deposición Atmosférica’’ (CTM2004-06842-C03) and MALASPINA 2010, funded by the Spanish National I+D Plan, and ‘‘Transformation of dissolved organic matter (DOM) in the North Atlantic Deep Water and intermediate waters: assessing the functional and phylogenetic variability of marine bacterioplankton communities in relation to the quality of DOM’’ (TRANSAT), ‘‘Activity, rates, carbon use and high-pressure microbial ecology’’ (ARCHIMEDES), and ‘‘Influence of deep ocean viruses on prokaryotes’’ (VIPeR) funded by the Dutch Science Fund, Earth and Life Science Branch (NWO-ALW) to G.J.H. This is a contribution to the European Union Networks of Excellence EurOceans and MarBefPeer reviewe