Date of Award


Degree Type


Degree Name

Doctor of Philosophy



Major Professor

Annette S. Engel

Committee Members

Larry D. McKay, Terry C. Hazen, Steve W. Wilhelm, Susan M. Pfiffner


Development of regional groundwater carbon budgets hinges on the ability to quantify and monitor biogeochemical processes controlled by microbial recycling of natural dissolved organic matter (DOM) in carbon-limited (oligotrophic) areas. DOM is the major reservoir of organic carbon in aquatic ecosystems. However, isolation and characterization of DOM in oligotrophic freshwater systems has been limited by operational protocols and instrumentation. The goals of this research were to investigate the seasonal dynamics of microbially-driven organic matter degradation in a karst groundwater system influenced by surface water, and to identify analytical tools and biomarkers to measure long-term hydro-ecological trends in the Appalachian region. To this end, a novel, inexpensive solid phase extraction technique was adapted to isolate and concentrate macromolecular functional groups in DOM rapidly from small (< 5 L) volumes of surface and cave stream waters in the field. Isolates of macromolecular functional groups indicated that DOM quality varied both diurnally and seasonally in surface water recharge due to photo-degradation, as well as hydrological and climatological factors. Seasonal DOM quality in the cave stream was constant, despite water residence times (during spring and summer) that ranged from less than 24 hours to more than 7 days. The structure of microbial communities responsible for surface-derived DOM transformations varied significantly between surface recharge and cave stream at low flow conditions. Seasonal DOM transformations also significantly varied with microbial physiological responses to stressors along the flow path, due to transport, temperature fluctuations, and nutrient limitation. This research links environmental and microbial processes in a karst groundwater-surface water system and provides evidence that quantification of carbon cycling in oligotrophic systems based on the macromolecular DOM transformations can be estimated and utilized in regional to global carbon cycle budgets.

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