Diversity of the sub-seafloor biosphere

The sub-seafloor biosphere is immense in its extent and its heterogeneity. It spans from organic-rich nearshore sediments to deep sea nutrient-poor deposits underlying mid-oceanic gyres – the deserts of the ocean.  The environment varies in composition from gassy muds to granitic rocks, and in temperature from refrigerator-cold surface sediments to hot consolidated strata buried kilometers beneath the seafloor.

An unexplored microbial world

Only during the past two decades have we come to realize that 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 and virus 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 2.4 km below the seafloor.

Given their vast number, the microbes inhabiting the sub-seafloor biosphere are key drivers of the global carbon cycle as their combined activities control the fate of dead organic carbon - burial or mineralization to carbon dioxide. 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 the community composition, distribution and activity of the buried microorganisms.

Our agenda

At the Center for Geomicrobiology we study the diversity and distribution of sub-seafloor microbial communities in an effort to resolve the link between their identity, function and abundance. Our research includes studies of bacteria, archaea, virus and unicellular eukaryotes with the overarching goal of understanding their respective roles in the sub-seafloor ecosystem.

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 diagnostic genes are analyzed as proxies for organismal identity, metabolic function and/or abundance.

Molecular microbiology at CfG

We routinely apply different cultivation-independent approaches: We extract microbial community DNA or RNA from sub-seafloor samples for PCR-based analyses of diagnostic genes or their transcripts. We subject community DNA or RNA to metagenomic or metatranscriptomic sequencing which allows us to reconstruct the metabolic potential of the predominant microbial community members and identify lysogenic and free-living virus.

We use Fluorescence in situ hybridization (FISH, CARD-FISH) for direct visualization and identification of intact cells labeled with 16S rRNA-targeted oligonucleotide probes. This allows us to assess the abundance of defined taxonomic groups of microorganisms by direct counting.

We apply single cell genomics to study the metabolic functions of uncultivated microorganisms (http://geomicrobiology.au.dk/research/singlecelltechniques).