Quantifying Subsurface Nitrate Transport and Remediation Using Gene Expression and Finite Element Models

Open Access
Bachmann, Matthew
Graduate Program:
Doctor of Philosophy
Document Type:
Date of Defense:
May 02, 2007
Committee Members:
  • Lee Kump, Committee Chair
  • John Michael Regan, Committee Chair
  • Susan Louise Brantley, Committee Member
  • Christopher Howard House, Committee Member
  • florida keys
  • wastewater
  • denitrification
  • nirS
  • q-rt-pcr
  • tidal pumping
Nitrate, typically derived from agricultural runoff and wastewater disposal, is the most widespread groundwater contaminant in the United States. A series of two- and three-dimensional finite-element groundwater models are presented here to simulate groundwater nitrate transport and remediation in the Florida Keys, where wastewater injection is suspected of contributing to the deterioration of the offshore coral reef. These models include quantification of the hydrogeology of reversing groundwater flow due to tidal pumping and nitrate removal rates based on a new application of a molecular technique for measuring microbial respiration rates. Physical constraints on tidal pumping, including comparisons of net to total submarine groundwater discharge rates and the variable-density mixing of recirculated seawater, were derived from observed tidal properties and published aquifer characteristics, with model calibration to previously conducted tracer experiments. The model demonstrates that even moderate tidal fluctuations are capable of driving reversing groundwater flow patterns, with net groundwater velocities and tracer distributions that closely match field measurements. Tidally pumped contaminant plumes were shown to be more dispersed than plumes in comparable static flow fields. Microbial denitrification rates were correlated with the relative abundance of the expressed nitrite-reductase gene nirS as measured by Quantitative Reverse Transcriptase Polymerase Reaction (Q-RT-PCR), to determine if gene expression is proportional to the rate of the metabolic process facilitated by the gene product. Measured denitrification rates by cultures of Paracoccus denitrificans varied from 1.67 to 50.5 mg/l/hour, and relative gene transcript abundances varied from 16 to 303 copies/ml. The relationship between nirS gene expression and denitrification was linear (R2 = 0.98) at denitrification rates above 4 mg/l/hour, suggesting that Q-RT-PCR may be an effective tool for assessing the rate of denitrification by Paracoccus denitrificans. A variety of different kinetic models for nutrient removal were applied to the variable-density groundwater flow model of the Florida Keys to assess total nutrient loading rates to the coastal environment. Model results suggest that wastewater-derived nutrients in the Keys are discharged within several meters of shore, and that the eutrophication of the offshore coral reef ecosystem is thus not attributable to long range subsurface nutrient transport.