Date of Award

Spring 1-1-2011

Document Type


Degree Name

Doctor of Philosophy (PhD)


Geological Sciences

First Advisor

Alexis S. Templeton

Second Advisor

Stephen J. Mojzsis

Third Advisor

G. Lang Farmer


Microbial life unambiguously inhabits the deep, terrestrial subsurface. Although the nutrient and energy sources supporting deep life are largely unconstrained, they are likely to be geochemically–derived. Novel organisms and energy sources are consistently discovered in the subsurface, and expand the range of microbial diversity and biogeochemical processes encountered on Earth. This dissertation connects metabolisms predicted to support subsurface life inhabiting the fluids circulating through granite fractures and pore spaces in Henderson Mine, Colorado at a depth of 3000 feet to the specific microbes that are detected by culture-dependent and independent methods. The thermodynamics of potential inorganic redox reactions in Henderson fluids reveal that oxidation of metals (Fe, Mn), and reduced sulfur and nitrogen compounds with O2 can support microbes energetically, as can metabolisms utilizing nitrate, nitrite or metal-oxides as electron acceptors. Sulfate reduction is not favorable in Henderson fluids, in contrast to other deep mines where it is a dominant metabolism. Targeted culturing of chemolithoautotrophic microbes from Henderson resulted in the isolation of Ralstonia HM08–01 that grows by oxidizing Fe(II) with OO2 at circumneutral pH. This organism was abundant in 16S rRNA clone libraries of Henderson fluids, signifying that Fe–oxidation may support a significant proportion of biomass. The Fe–oxides produced in experiments were colloidal (50–100 nm diameter), persistent phases that would influence metal and nutrient transport if they form at Henderson. Aside from iron, ammonium (>100 μM in borehole fluids) is an important energy source at Henderson. Nitrification is possibly mediated by Crenarchaea living in the Henderson fluids that possess the amoA gene for ammonia oxidation, and Nitrospira bacteria that possess the nxrB gene for nitrite oxidation. Although NH4+ substituted into K+–bearing minerals could theoretically supply subsurface microbes with geological ammonium, no ammonium was detected in Henderson minerals. Phylogenetic analysis of nifH genes for nitrogen fixation present at Henderson suggest the novel phylum of Henderson candidate division bacteria may be nitrogen fixers, and that ammonium is sourced biologically. These findings inform the reactions that are known to support subsurface life, the source of nutrients and energy sources for subsurface life, and the diversity of life that inhabits the subsurface.