Graduation Year


Document Type




Degree Name

Doctor of Philosophy (Ph.D.)


Microbiology, Molecular Biology and Biochemistry

Degree Granting Department

Cell Biology, Microbiology, and Molecular Biology

Major Professor

James R. Garey, Ph.D.

Committee Member

Kathleen M. Scott, Ph.D.

Committee Member

Jonathan G. Wynn, Ph.D.

Committee Member

James T. Riordan, Ph.D.


anchialine, aquifer, geochemistry, hydrology, microbial


The overall goal of this dissertation is to define the hydrological, geochemical, and biological characteristics of a Karst Estuary. These types of estuaries represent a unique ecosystem created by freshwater inputs from direct flow through karst conduits and/or diffuse flow through a karst matrix. In order to determine the characteristics of a Karst Estuary we monitored short-term tidal fluctuations, long-term rainfall patterns, aquifer levels, spring discharge, multiple geochemical parameters, microbial communities in the water column and sediment, and macrofaunal communities in the sediment along a transect from a submarine spring through the Gulf of Mexico. Four sites were selected along a spring/marine transect and one nearby freshwater spring was used as a reference site. Datasondes were deployed in the nearshore brackish submarine spring to measure discharge volume, tidal fluctuations, and physical water parameters for two years. Water column and sediment samples were collected quarterly from both springs and the surrounding surface sites over the same time period. An isotopic/trace element mass balance method was used to determine the hydrogeological conditions of the spring discharge with three possible sources: 1) freshwater from the upper portion of the Upper Floridan aquifer, 2) freshwater from the lower portion of the Upper Floridan aquifer, and 3) saltwater from the Gulf of Mexico. Archaea, Bacteria, and microbial eukaryote communities were analyzed using molecular techniques, and macrofauna communities were determined using light microscopy. Correlation analyses were conducted to compare all studied biological communities to the hydrological and geochemical data in order to determine the influence of aquifer discharge. Within the water column of the submarine spring conduit, there were no significant differences of the sampled parameters over short sampling distances (m) and periods (hr). Spring discharge was found to be negatively correlated with tidal level and directly correlated with aquifer level. The brackish nature of the spring discharge is primarily due to simple mixing between the Gulf of Mexico saltwater and freshwater from the lower portion of the Upper Floridan aquifer originating from the mixing zone beneath the estuary. The composition of the spring discharge varied seasonally, showing increased marine influence at the beginning of the wet season. Tropical Storm Debby, June 2012, resulted in measurable freshwater inputs to spring discharge from the upper portion of the Upper Floridan aquifer. The number of spring reversals (salt water intrusion events) increased as the dry season progressed, stopped reversing immediately after Tropical Storm Debby, and then gradually increased into the next dry season. Statistically significant geochemical differences were found along the spring/marine transect on each collection date and seasonally at the individual sites. The major finding was that the primary driver of change in all of the studied biological communities of this Karst Estuary is the volume of aquifer discharge and the gradients formed by aquifer discharge and not the geochemical fluctuations within the system. Events that result in shifting the mixing zone inland have dramatic impacts on the biological communities of these environments. Karst Estuaries are a newly discovered type of ecosystem that are different from surface estuaries in that they are formed by aquifer discharge which is more stable in terms of geochemistry than water discharged to the sea via surface rivers.