Omics of deep biosphere

SNIC 2018/13-4


Swestore Medium

Principal Investigator:

Mark Dopson



Start Date:


End Date:


Primary Classification:

10606: Microbiology (medical to be 30109 and agricultural to be 40302)

Secondary Classification:

10610: Bioinformatics and Systems Biology (methods development to be 10203)



The deep terrestrial subsurface environment is distinct from the shallow subsurface due to significantly longer groundwater residence times and represents regional rather than local precipitation-responsive hydrology. The presence of a large, deep subsurface biomass has fundamental scientific implications as well as practical impact on large-scale engineering projects, e.g. storage of nuclear waste and basic ecosystem services such as the clean-up of surface water through microbial transformation. The latest estimate of the "deep biosphere" is that it contains 2 - 19% of the Earth’s total biomass. Despite its importance in nutrient cycling and processes such as bioremediation of contaminated aquifers, deposition of nuclear waste, and storage of carbon dioxide, the deep biosphere is one of the least understood ecosystems on earth. This is because most studies have been carried out in the photosynthesis driven surface milieu or in the laboratory where "feast and famine" culturing is significantly different to the stable, extremely oligotrophic environment in the sub-surface. Several critical question for the deep biosphere remain unanswered and include: are the microorganisms are active or dormant?; do deep biosphere microorganisms use special adaptations to maintain their viability under low energy flux conditions?; and how deep biosphere microorganisms respond to a changing environment? These questions are being addressed by investigating the metabolic activity of microorganisms found in various groundwater types that are representative of deep sub-surface environments at the terrestrial and marine interface. To address these issues, extensive sequencing of community DNA and RNA are being carried out. The research group of the PI has a well established record of publications in the deep biosphere field, and at the moment is expanding the available datasets through a Community Science Program with JGI-DOE, aimed at the massive production and analysis of metagenomics data. The resultant data will answer fundamental questions related to the earth's energy and nutrient cycles.