The rocks beneath our feet are home to an astonishing array of microbial life. Extending from shallow aquifers to kilometers into the crust, the deep subsurface biosphere (DSB) contains as much organic carbon in biomass as the ocean, rivers, and lakes combined1,2. Key questions include: Who is there?, What are they doing?, and Are they dependent on the surface? To this end, we have established the Deep Mine Microbial Observatory (DeMMO), in the former Homestake Goldmine, USA. Here we continually monitor geochemistry and microbial diversity and can perform in situ experiments to query the DSB.
Modern sequencing approaches can answer “Who?”. Our work and that of others suggest that the DSB is dominated by diverse communities of very unusual, uncultivated phyla3-5. Genomic analysis is one promising avenue to answer “What?” as genomes contain the blueprints for microbial activity. Genomes obtained from subsurface organisms range from encoding diverse metabolic capability, presumably to use sparse and/or variable resources (e.g. Desulforudis and Abyssubacteria)6,7 to those with very reduced genomes indicative of syntrophic or parasitic lifestyles5.
Another approach we are taking to answer “What?” is geochemical, using thermodynamics to determine which metabolisms are profitable and isotopic analyses to track the flow of elements through microbial processes. At DeMMO a large array of sulfur, iron, manganese, and nitrogen-based metabolisms are energy yielding and microbes have shown an increased ability to tap directly into electrons for energy4,8. This abundance of chemical energy sources, independent of surficial organic carbon, opens the possibility of independent subsurface ecosystems on Earth and beyond9.
1. McMahon, S. & Parnell, J. Weighing the deep continental biosphere. FEMS Microbiol. Ecol. 87, 113–120 (2013).
2. Whitman, W. B., Coleman, D. C. & Wiebe, W. J. Prokaryotes: The unseen majority. Proceedings of the National Academy of Sciences 95, 6578–6583 (1998). 3. Lloyd, K. G., Steen, A. D., Ladau, J., Yin, J. & Crosby, L. Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes. mSystems 3, 431–12 (2018). 4. Osburn, M. R., LaRowe, D. E., Momper, L. M. & Amend, J. P. Chemolithotrophy in the continental deep subsurface: Sanford Underground Research Facility (SURF), USA. Frontiers in Microbiology 5, 1–14 (2014).
5. Probst, A. J. et al. Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO 2concentrations. Environmental Microbiology 19, 459–474 (2016).
6. Chivian, D. et al. Environmental genomics reveals a single-species ecosystem deep within Earth. Science 322, 275–278 (2008).
7. Momper, L., Jungbluth, S. P., Lee, M. D. & Amend, J. P. Energy and carbon metabolisms in a deep terrestrial subsurface fluid microbial community. ISME J 1–15 (2017). doi:10.1038/ismej.2017.94
8. Jangir, Y. et al. Isolation and Characterization of Electrochemically Active Subsurface Delftia and Azonexus Species. Frontiers in Microbiology 7, 3871–11 (2016). 9. Stamenkovic, V. et al. The next frontier for planetary and human exploration. Nature Astronomy 1–5 (2018). doi:10.1038/s41550-018-0676-9