Master of Science (MS)


Environmental Sciences

Document Type



Traditional methods for assessing in situ microbial communities often provide limited information on substrate utilization in bioremediation processes. The goal of this research was to assess new methods for describing the microbial communities found in the groundwater and affected contaminated soils documenting changes in community structure, population dynamics, substrate utilization and biodegradation of constituents of concern (CoC) during a site remediation. Two in situ bioremediation pilot studies using biological plugs are being conducted, one in the California San Francisco Bay Area (Sunnyvale) and one in the East Texas Piney Woods (Longhorn). The hypothesis is that changes in community structure, population dynamics, substrate utilization and biodegradation of CoC will be successfully described by EcoPlate™ and MicroPlate™ (Biolog, LLC) assays, population counts, and MicroTox® acute toxicity tests. Chlorinated aliphatic hydrocarbon and heterotroph plate counts were used to find the number of colony-forming units. The biological plugs successfully introduced chlorinated aliphatic degrading microorganisms to affected areas. At the Sunnyvale site, the average colony forming unit (CFU)/ml tracked reductions in CoC from August 2012 through January 2014. Reductions in CoC, in particular, trichloroethylene (TCE), were seen over a defined time frame of months to years for Sunnyvale. There was a correlation among increased microbial species diversity and abundance and decreased CoC. The average well color development (AWCD) maximum value increased almost 10 fold, the functional diversity and Shannon-Weaver index values showed notable improvement, and the carbon substrate utilization did not show major changes across all monitoring wells on site. At the Longhorn site, the average CFU/ml varied in population totals providing no clear indication of CoC reduction. Plate counts decreased initially but then started to rise again. The number of samples with a high functional diversity and AWCD also increased. Unfortunately, more samples showed a zero for the Shannon-Weaver index. Carbon substrate utilization showed modest improvement. Since the Longhorn site has been in operation for only 1.5 years compared to Sunnyvale’s 5 years, a clearer picture of Sunnyvale’s improvement may be seen. Assays provided correlated assessment of community viability and functionality for both sites.



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Committee Chair

Portier, Ralph