2014 Grant Recipients

Ashley M. Bandy ($3000)
Ph.D. Candidate
Department of Earth and Environmental Sciences
University of Kentucky

Mobility of Stable Isotope-Labeled Escherichia coli Karst Terrains

Abstract - Currently, bacterial transport in karst aquifers is not well understood. Bacterial contamination of karst aquifers is a large concern across the globe. Groundwater tracers typically used in karst systems include fluorescent dyes and latex microspheres. These tracers do not exhibit surface properties and transport behaviors mimicking those of bacteria and pathogens, and therefore are not good proxies for risk assessment involving microorganisms. The proposed project will expand upon a proof-of-concept study tagging nonpathogenic Escherichia coli (E. coli) with stable isotopes (15N and 13C) to use as a tracer in a karst basin. A trace will be conducted using labeled E. coli in conjunction with fluorescent dyes and latex microspheres in the Cane Run karst aquifer in central Kentucky and through epikarst above Cave Spring Caverns near Bowling Green, Kentucky. It is hypothesized that dyes, microspheres, and bacteria tracers will show differential transport times in the Cane Run/Royal Spring basin under normal flow conditions, with microorganisms arriving at the spring prior to microspheres or conservative dyes. For the epikarst trace above Cave Spring Caverns, the E. coli isolate that exhibits higher attachment efficiency in saturated granular columns is expected to have higher attenuation and emerge from the epikarst after the isolate that exhibits lower attachment efficiency. These two types of E. coli will have different transport times than microspheres or dyes and may take many storm events before they are flushed through the epikarst. Isotope analysis will be used in conjunction with genetic markers to monitor breakthrough of tracer bacteria.


David Brankovits ($3000)
Ph.D. Candidate
Marine Biology Interdisciplinary Program
Texas A&M University at Galveston

A Biogeochemical Investigation of a Methane-Dependent Anchialine Cave Ecosystem

Abstract- Energy limited flooded coastal cave systems are likely to utilize similar processes as those occurring in chemosynthesis-based oceanic ecosystems. Preliminary data from my dissertation research suggests methane may be the primary source of carbon and energy for a unique subsurface ecosystem in the tropics. I propose advanced molecular biological, lipid biomarker, and stable isotope techniques to test this premise. I will examine the following hypotheses in a coastal cave system in the Yucatan Peninsula in Mexico: (1) methane is seeping into the aquifer from overlying soils and is being consumed by methanotrophic ('methane-eating') microbes in the water column of a subterranean estuary; (2) methanotrophic bacteria inhabiting the groundwater are being consumed by the unique cave-adapted invertebrate community; (3) methanotrophic bacteria contribute significant chemosynthetically-produced organic matter to higher levels of the food web (i.e., cave-adapted shrimps).

The proposed study will provide a comprehensive biogeochemical description of carbon cycling and the fate of methane in the water column of a coastal cave system in the Yucatan Peninsula. Characterizingthe microbial community, biogeochemical pathways, and carbon flow will expand our understanding on the ecology of anchialine caves. This study will significantly increase the knowledge on chemosynthetically-based ecosystems and the importance of methane for certain subterranean food webs. Moreover, demonstrating that an underground ecosystem is fueled by methane (powerful greenhouse gas) will have potential implications in studying globally relevant biogeochemical processes (e.g., methane sinks) for environmental purposes.


Brian M. Carlson ($3000)
Ph.D. Candidate
Department of Biological Sciences
University of Cincinnati

Creating High-Density GBS-Based Linkage Mapping Resources for Use in Astyanax mexicanus, the Blind Mexican Cavefish

Abstract - The ability to conduct genome-level studies aimed at illuminating the genetic underpinnings of traits of interest has led to significant advances in our understanding of a wide variety of interesting and ecologically relevant traits. In the past, however, the cost of sequencing-intensive methodologies has made such studies difficult or impossible for those working in non-model and emerging model systems. In such cases, alternate approaches such as the construction and use of linkage maps have proven both necessary and valuable. The blind Mexican cavefish, Astyanax-mexicanus, is an emerging model fish system consisting of a derived cave morphotype and an extant surface morphotype. Here, I propose the use of cost-efficient next-generation sequencing technologies to generate the data necessary to create high-density linkage maps for use in this species, which has become the model of choice for many researchers interested in the evolutionary consequences of cave colonization. Additionally, I propose strategies that will allow researchers to leverage genomic resources for a related model fish species, as well as early drafts of genomic resources for Astyanax mexicanus itself, to determine the genes and genomic intervals associated with the anonymous markers from which these linkage maps are constructed.


John Wall ($1000)
Ph.D. Student
Department of Marine, Earth & Atmospheric Sciences
North Carolina State University

High-Resolution Morphometric Analysis of Sinkholes and Depressions within Karst Geology

Abstract -The proliferation of Light Detection and Ranging (LiDAR) surveys conducted at the county and state levels over the past decade provides increasingly high-resolution topographic data that can be used to quantify the geomorphology of karst terrains. Current methods to map sinkholes and depressions within karst geology typically employ coarse resolution topographic data. From this coarse data closed-contours are manually digitized which is time intensive. We will show that sinkholes and depressions can be delineated accurately using semi-automated methods operating on high-resolution Digital Elevation Models (DEM). This will be done by using standard Geospatial Information System (GIS) hydrologic tools to fill depressions within the DEM. The initial DEM will then be subtracted from the filled DEM resulting in detected depressions or sinkholes. These results will then be compared to the state inventories. Results will be used to test proposed scaling relationships for the size and distribution of sinkholes and depressions. The resulting catalog of sinkholes and depressions can then be used for hazard and risk assessment, cultural resource management and ecological habitat identification.