Abstract

Throughout the world’s oceans, the sediments that cover the seafloor, and the cracks and fissures of the basaltic ocean crust, are permeated by microbial life (1, 2). As these bacteria and archaea are mostly not available in laboratory culture and thus elude direct physiological characterization, Jørgensen et al. correlate geochemical regimes in subseafloor sediments with in situ abundance of specific groups of uncultured bacteria and archaea to infer their habitat preferences, to develop specific hypotheses about their metabolism, and to design promising cultivation strategies (3).

The abundance of microbial cells in subseafloor sediments correlates with sedimentation rate and distance from land; cell densities in seafloor sediment generally increase toward continental margins and shelves, and decline toward the open ocean (1). This pattern is consistent with the observation that bacteria and archaea in the subsurface assimilate buried organic carbon as heterotrophic anaerobes (4). In principle, more specific information about carbon and energy sources of the subsurface biosphere could be obtained by culturing representative species and genera of subsurface bacteria and archaea, followed by study of defined enrichments and pure cultures in the laboratory. However, selectively enriching and isolating subsurface microorganisms in the absence of specific hypotheses that could guide such an effort remains an ongoing challenge. Although some progress has been made, the major evolutionary lineages of subsurface bacteria and archaea have so far remained uncultured or contain very few cultured representatives; therefore, the specific metabolic activities and biogeochemical roles of most subsurface microorganisms are obscure (5, 6). Given these limitations, a systematic study of the in situ geochemical conditions of a microbial subsurface environment should reveal much about the physiological preferences and …