Graduation Year


Document Type




Degree Name

Doctor of Philosophy (Ph.D.)

Degree Granting Department

Biology (Cell Biology, Microbiology, Molecular Biology)

Major Professor

James Garey, Ph.D.

Committee Member

Sarina Ergas, Ph.D.

Committee Member

Prahathees Eswara, Ph.D.

Committee Member

Jason Gulley, Ph.D.


aquifer, biogeochemistry, eDNA, karst, microbial ecology


The subsurface hosts diverse microbial community assemblages and functions. These communities play an important role in biogeochemical cycling and groundwater purification. Many physicochemical factors affect microbial communities and can cause short-term or long-term perturbations. Subsurface microbes are susceptible to anthropogenic changes in the environment, which can be caused by nutrient inputs or municipal groundwater extraction. Despite the importance of the subsurface microbiome, these microbial communities are poorly characterized. This dissertation describes the characterization of spatiotemporal drivers of subsurface microbial communities through a variety of techniques that include eDNA analyses, bioinformatics, hydrochemical analyses, stable isotope geochemistry, and multivariate statistics. Three coastal sinkholes and three coastal wells were used to characterize the spatiotemporal variation in microbial communities and hydrochemistry in the subsurface. Hydrochemistry appears to play an important role in determining the types of microbes that inhabit the different groundwater zones of a stratified sinkhole called Hospital Hole. Different

groundwater zones in Hospital Hole hosted unique microbial community assemblages and estimated metabolic functions, but taxa implicated in sulfur and nitrogen cycling were identified in all zones. Seasonal patterns of microbial community assemblages and potential metabolic functions were not identified. A single physicochemical parameter was not implicated in microbial community change for the different zones. Hurricane Irma did not appear cause a large perturbation in the microbial communities in Hospital Hole, suggesting that local hydrogeology is important to subsurface microbial community changes. Similarities between the hydrochemistry and microbial communities of three coastal sinkholes and three coastal wells suggest that microbial communities from sinkholes could be used as a model for aquifer microbial community interactions. These findings also suggest that wells may become highly sulfidic like the sinkholes if sulfate and organic material are available. Differences in the microbial communities between and within sediment, biofilm, and water column samples in three different sinkholes demonstrated subsurface heterogeneity. These communities varied in

community composition and the abundance of their estimated metabolic functions. Surface runoff into the Monte Conca cave system in Sicily, Italy caused large perturbations in the microbial communities in a sulfidic spring pool. During the dry season, the microbial community in this sulfidic spring pool was comprised primarily of sulfur oxidizing bacteria. These sulfur oxidizers could utilize sulfide present in the spring pool and the oxygenated air of the cave. Heavy rains in the wet season caused surface runoff into the cave. Escherichia, a fecal microbe, and Lysinibacillus, a soil-derived microbe, displaced the sulfur-oxidizing communities in the wet season. These taxa were likely derived when surface runoff carried these organisms from soils in the surrounding agricultural areas into the cave system. One sampling date appeared to show a transition between the wet and dry seasons when microbes from both seasons were present in the spring pool. This dissertation identified several potential causes of spatiotemporal changes in subsurface microbial communities. These changes include the following: differences in groundwater hydrochemistry, differences in seasonal physicochemical parameters, hurricanes and tropical storms, and connectivity to the surface. Subsurface ecosystems appear to be vulnerable to

anthropogenic inputs, which may contain Escherichia and other biological contaminants. This dissertation demonstrates the complexity of microbial communities within the subsurface and emphasizes the spatiotemporal causes of subsurface heterogeneity.