Marine deep sediment microbial communities

Abstract

A new biosphere of bacteria, archaea, and eukaryotes in deep marine subsurface sediments, characterized by unexpected evolutionary depth and metabolic diversity, is currently being explored by gene sequencing surveys, cell counts, molecular quantification studies, and cultivations. Although cultivable bacteria have been detected and quantified in deep marine sediments decades ago (Morita and Zobell 1955), the pioneering work by John R. Parkes and colleagues provided comprehensive proof of the deep microbial biosphere in subsurface marine sediments, by integrating microbial cell counts, Most-Probable-Number counts, characterizations of subsurface bacterial isolates, geochemical porewater profiles, and measurements of microbial process rates (Parkes et al. 1994). Total cell numbers and biomass of this subsurface biosphere account for a major portion of all living biomass (Whitman et al. 1998; Parkes et al. 2000). Specific phylum-level lineages of bacteria and archaea occur consistently in marine subsurface sediments, often in distinctly structured communities that reflect specific subsurface habitats and geochemical settings, and that are distinct from the surface biosphere. Investigating the activity, metabolism, biogeochemical role, and energy and carbon sources of subsurface bacteria, archaea, and eukaryotes remains an ongoing challenge of deep subsurface microbiology. Most deep sediment samples for deep subsurface microbial research were recovered through the Ocean Drilling Program (ODP) and its successor, the Integrated Ocean Drilling Program (IODP). Deep sediment sampling expeditions have to a very large extent provided the sediment samples, subsurface habitat characterizations, and biogeochemical process studies that have nurtured, and continue to develop, the field of deep subsurface microbiology (D'Hondt et al. 2007).