UC Berkeley

Engineered bioprocesses rely on the complex, intricate interactions and exchanges among members of microbial communities. Development of robust engineered solutions requires deep understanding of the impacts of perturbations on key metabolisms and interactions within these communities. Trichloroethene (TCE) – a toxic, chlorinated chemical – has been commonly used as an industrial solvent for decades. Due to poor storage and handling practices, it has also become a highly prevalent groundwater contaminant. However, it is rare that TCE is the only contaminant of concern in groundwaters. A plethora of other toxic compounds are often found with TCE, including organic, inorganic, geogenic, and anthropogenic compounds and their transformation products. The main goal of this research was to observe the impacts of two common TCE co-contaminants, arsenic and acetylene, on the metabolisms and functions of TCE-dechlorinating communities and investigate remediation solutions for multi-contaminant groundwaters.

Acetylene can be produced at TCE-contaminated sites from abiotic degradation of TCE by zero-valent iron or in-situ reactions with minerals, e.g. iron sulfides. Acetylene is known in microbiology as an inhibitor of microbial metabolisms such as methanogenesis and nitrate reduction. However, little is known about the impacts of acetylene on TCE dechlorination. In this research, I found that acetylene inhibits TCE dechlorination by Dehalococcoides mccartyi and D. mccartyi-containing communities. However, this inhibition is reversible upon bioaugmentation with anaerobic acetylenotrophs such as Pelobacter SFB93. Fermentation of acetylene was able to support TCE dechlorination as the sole electron donor and organic carbon source. I enriched a microbial community from contaminated groundwater that coupled acetylene fermentation with TCE dechlorination. In this enrichment, I discovered the first anaerobic acetylenotroph in the phylum Actinobacteria and studied the putative acetylene hydratase enzymes present using metagenome analysis in combination with Hidden Markov Models. I found that inhibition by acetylene contamination in TCE-containing groundwaters can be reversed via bioaugmentation and utilized as an electron donor and carbon source for TCE dechlorination by D. mccartyi.

Arsenic is among the most frequent co-contaminants with TCE and is derived from both anthropogenic and geogenic sources. Arsenic is a particularly interesting co-contaminant, as TCE-dechlorinating conditions also cause reduction of arsenate (As(V)) to arsenite (As(III)) and subsequent solubilization, increasing the toxicity of arsenic present in the system. In this research, I characterized the effects of both As(V) and As(III) on TCE dechlorination by D. mccartyi in axenic culture and defined consortia of syntrophic partners using physiological, transcriptomic, and metabolomic analyses. I utilized changes in genetic expression and extracellular metabolite profiles in response to amendment of arsenic to determine the responses of the organisms to the presence of arsenic as well as potential changes in nutrient exchange among consortium members. I identified amino acids and TCA cycle intermediates as nutrients that may be exchanged among organisms in TCE-dechlorinating communities and utilized these results to investigate the most effective solutions for biostimulation of TCE dechlorination in arsenic-containing environments. I also investigated bioaugmentation of TCE/arsenic-containing microcosms with arsenosulfide-mineral-biostimulating organism Desulfosporosinus auripigmenti, but robust TCE dechlorination relied on highly specific environmental conditions. The results of this research will inform future bioremediation strategies for mixed-contaminant sites.