Connecting Dominant Bacterial Dechlorination Pathways To Environmental Drivers

Abstract

Bacterial dechlorination of chlorinated contaminants has been well studied as a method for bioremediation of common chlorinated contaminants yet efforts can still be made to improve bioremediation and help it become a more robust technique. The work presented in this dissertation analyzes microbial communities in uncontaminated environments to better understand what promotes dechlorination in uncontaminated environments and which dechlorination processes are dominant in various environments. An understanding of the capabilities of these bacteria in uncontaminated sites can be used to improve bioremediation techniques. Organohalide respiring bacteria are slow growing and can be difficult to enrich and isolate for further study. A method was developed to rapidly select for putative organohalide respiring bacteria. Organohalide respiring bacteria were found to be at higher ratios than other bacteria at the interface between aqueous media and a hydrophobic liquid. Trichloroethene and hexadecane were both tested, and the fraction of Dehalococcoides-like bacteria was found to increase up 20 times at the interface in just 20 minutes. This shows that the selection was a result of physical interactions and not growth. After the selection process, the bacteria were still viable and capable of dechlorinating TCE. This method was verified with a PCB enrichment culture, uncontaminated sediment, and anaerobic digester sludge. The metagenomes of urban lakes with no known chlorinated contaminants and of bacteria enriched with chlorinated natural organic matter (Cl-NOM) were analyzed for genes of enzymes capable of dechlorination. The lake sediments had varying degrees of urban impact. Both reductive dehalogenase (rdh) genes and non-respiratory dehalogenase (dh) genes were found in the metagenomes with the dh genes typically at higher frequencies. The one exception was the uncontaminated lake sediment enriched with chlorinated natural organic matter. This showed an increase in the rdh genes compared to the bacteria enriched with only natural organic matter. These findings show that rdh genes can be enriched for with high concentrations of chlorinated natural organic matter; but in uncontaminated lake sediments with lower concentrations of organochlorines, dh’s are the dominant dechlorination mechanism. qPCR primers were developed to target specific rdh and dh genes to track them through the enrichment period with Cl-NOM and in more lakes with varying degrees of urban impact. Some of the dh and rdh genes were found in multiple lakes while others were specific to one or two, indicating that some enzymes capable of dechlorination are more widely distributed in the environment than others. The presence and concentrations of specific genes was not an indication of the ability of the lake sediment to dechlorinate trichloroethene, a common environmental contaminant. The types of Cl-NOM that are preferentially dechlorinated and how enrichment with different types of Cl-NOM affect the ability to dechlorinate contaminants was investigated with PCB contaminated soil. The Cl-NOM was fractionated into three broad groups based on hydrophobicity. The least hydrophobic fraction was found to be dechlorinated more readily followed by the moderate hydrophobicity; however, it was the moderate hydrophobic fraction that promoted the dechlorination of trichloroethene and tetrachlorobenzene. During the enrichment period, known organohalide respiring bacteria were enriched as well as several other bacteria that have unknown dehalogenation potential. Additionally, dh genes and not rdh genes were shown to increase in concentration demonstrating that bacteria utilizing other dechlorination mechanisms could be important for bioremediation and chlorine cycling as well. The dechlorination potential of bacteria in the Soudan Mine, a carbon limited system with higher concentrations of iron and chloride, was analyzed. The dh and rdh genes in metagenomes from groundwater in three boreholes were analyzed. Dh genes were found at higher frequencies than rdh genes. Bacteria capable of dechlorination may have a metabolic advantage in this carbon limited system because it allows them to utilize Cl-NOM.