Mineralogical controls on microbial community structure and biogeochemical processes in subsurface environments

Nearly every ecological habitat in the microbiological world is predominately occupied by complex assemblages of multicellular, multifunctional communities attached to surfaces as biofilms. The motivating factors for this stationary community lifestyle appear to be as diverse as the organisms that occupy these habitats. However, there are also many commonalities primarily relating to nutritional requirements and environmental tolerances. Broadly, this dissertation focuses primarily on linking these motivating factors to specific microorganisms within diverse biofilm communities attached to mineral surfaces. To do this I used continuous-flow laboratory biofilm reactors (inoculated with a diverse subsurface biofilm community) to assess the roles of surface type, media pH, and carbon and phosphate availability on biofilm accumulation, community structure, function, and phylogenetic variability. I demonstrate that in nutrient-limited systems, taxonomy and growth of biofilm communities is highly dependent on surface chemistry to support their nutritional requirements and environmental tolerances. Moreover I present rigorous statistical evidence that, for a variety of environments, microbial communities attached to similar natural surfaces types (carbonates vs. silicates vs. aluminosilicates) are more phylogenetically similar. I find that surface type controls up to 90% of the variance in phylogenetic diversity of a system regardless of environmental pressures. This is strong evidence that mineral selection is genetically ingrained. We provide validated methodology for the use of continuous flow-bioreactors to expose the fundamentally dynamic nature of microbial structure within biofilms. I demonstrate that these shifts in community structure can occur rapidly, impacting geochemistry and carbonate mineral solubility. Specifically, carbonate dissolution is highly accelerated under autotrophic conditions dominated by sulfur-oxidizers. Immediately after adding acetate the community shifts to heterotrophic sulfur-reducers resulting in carbonate precipitation. Additionally, these functional shifts can be inferred by monitoring geochemical indicators (δ13CCO2, [CO2], Ca2+, and pH). I provide evidence that the responsiveness of carbonate system reactions to the metabolic products of sulfuric acid cave ecosystems are ideal model ecosystems for studying the effects of microbial community structure on stable carbon isotope fractionation. I submit that biogeochemical interactions with mineral surfaces have influenced development, evolution, and diversification of microbial life. Throughout geologic time, microorganisms have enhanced survival by colonizing mineral surfaces and developing complex biofilm communities genetically primed for specific mineral habitats.