The sub-seafloor biosphere is immense in its extent and its heterogeneity. It spans from eutrophicated nearshore sediments to pressurized nutrient-poor deserts underlying deep oceanic waters; it varies in composition from gassy muds to granitic rocks, and in temperature from refrigerator-cold surface sediments to boiling-hot parts buried kilometers underneath the seafloor.

An unexplored microbial world

Only during the past two decades have we come to realize that together these buried environments sustain a living biomass matching that of the land and sea in terms of both organismal diversity and numbers. The sub-seafloor biosphere is, however, a microbial world as only microbes survive permanent burial. Although the microbial biomass and activity are highest near the sediment surface, microbial cells pervade into the deepest sediments so far studied 1.6 km below the seafloor.

Given their vast number, the microbes inhabiting the sub-seafloor biosphere must be key drivers of the global carbon cycle as their activities control the fate of dead organic carbon - burial or mineralization to CO2. Yet even so the identity and function of these permanently buried microorganisms remain unknown by large. As a consequence it is unclear which types of metabolism are of key importance for sustaining the enormous sub-seafloor biomass and which mechanisms control their distribution and activity.

Our agenda

Center for Geomicrobiology studies the diversity of sub-seafloor microbial communities in an effort to resolve the link between identity, function and abundance of their members. Because most microbes resist growing under controlled laboratory conditions, the diversity of microbial communities can only be comprehensively explored via cultivation-independent molecular methods where signature genes are analyzed as proxies for organismal identity, metabolic function and/or abundance.

Molecular microbiology at CfG

We routinely apply two different methodological cultivation-independent approaches. One is based on extraction and purification of community DNA or RNA from sub-seafloor samples followed by PCR-based analyses of the diversity and/or abundance of signature genes or their transcripts. We interrogate 16S rRNA genes as a general taxonomic marker as well as a range of functional genes as markers for different metabolic guilds such as for example sulfur cycling microbes (apsA and dsrAB), methanogens and methanotrophs (mcrA) and acetogens (acs). The other approach, fluorescence in situ hybridization (FISH, CARD-FISH) is based on microscopical visualization of intact cells labeled with 16S rRNA-targeted oligonucleotide probes. This technique allows us to assess the abundance of defined taxonomic groups of microorganisms by direct counting and to label and identify single cells of particular interest as targets for subsequent single cell analyses (http://geomicrobiology.au.dk/research/singlecelltechniques).

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