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Comparative genomics of surface and deep subsurface prokaryotes

Chesapeake Bay Impact Structure Drilling Project
Macalady et al. 2005

The earth's subsurface is a vast repository of poorly-characterized microorganisms. In contrast to surface environments where light and fixed organic carbon power a rapidly-evolving, productive microbial biosphere, electron donors and acceptors for energy generation in the deep subsurface are limited to inorganic solutes in aquifers and pore fluids, rock-forming minerals, and/or compounds resulting from water-rock interactions. Further constraints on microbial growth rates in the subsurface are imposed by the scarcity of nutrients such as nitrogen and phosphorous. For these reasons, it is expected that growth rates and turnover times of microbial populations living in the deep subsurface will be orders of magnitude slower compared with populations at the surface. Microorganisms sequestered in the deep subsurface thus represent slowly-evolving populations that can be compared with surface microbial life to yield information about evolutionary rates.

Assigning absolute timescales for microbial evolution and transport are two of the outstanding current problems in geomicrobiology. Impact craters such as the Chesapeake Bay structure present a unique opportunity for studying microbial transport and evolution. Because the rocks were sterilized at a known time, microorganisms currently found in the impact rocks must have originated from organisms alive at the surface no earlier than the time of the impact. (Although horizontal transport of older organisms from surrounding rocks is possible, the large size of the crater makes this unlikely for rocks at the center of the impact.)   Two scenarios can be described representing the extremes of microbial transport rates. If transport rates are very slow, no microorganisms will have reached the crater basement since the Eocene. If transport rates are very fast, microbial species deep within the impact crater will be closely related to populations at or nearer to the surface. The high density and great depth of fracturing at the impact site suggest that rates of microbial transport at this site will be near the maximum rates for continental crustal basement rocks. Three approaches for comparing the evolutionary relationships between surface and subsurface microorganisms are proposed, including pyrosequencing/environmental genomics. Although the technical challenges inherent in applying these techniques to low-biomass subsurface samples are expected to be significant, the scientific goals of the proposed work can be achieved if only one or two depth intervals within the basement rocks yield DNA or culturable microorganisms for genetic analysis.