• Biology of methanogenic archaea
• Anaerobic conversion of organic wastes to biomethane
• Microbial reductive dehalogenation of organochlorines, in situtreatment of persistent organic pollutants in sediment and soil

Biology of methanogenic Archaea

This research program is divided into three projects: 1) regulation of gene transcription; 2) mechanisms of desiccation resistance in the context of exobiology; 3) conversion of aquaculture waste into biomethane. The controlled expression of gene products involved in methanogenesis is essential for complete biomass conversion and bioremediation in anaerobic sediments, however, the mechanisms of catabolic gene regulation in the third lineage, the Archaea, is not yet known. The goal of the first project is use genetic approaches combined with genomics and proteomics to determine whether gene expression in the Archaea functions by mechanisms that are analogous to the other two lineages, Bacteria and Eucarya, or by mechanisms that are unique to this phylogenetic line. Regardless of which mechanism(s) is revealed by this investigation, the results will provide further insight into the global molecular strategies of gene regulation. In the second project we are studying the mechanisms of adaptation by M. barkeri to extreme conditions using biochemical, genomic and genetic approaches. By defining the adaptive strategies of M. barkeri the project will seek to redefine the range of physiological parameters for survival and identify on a molecular level the unique mechanisms that enable this species to maintain viability after extended periods of desiccation. The third area of research is the development of effective biological waste treatment for closed marine recirculating aquaculture systems. Such systems conserve water, allow treatment of polluted water within a closed loop and offer improved control of effluent discharge, thereby reducing the environmental impact of the system. The goals of this study are to reduce solid output from highly saline recirculated aquaculture systems by anaerobic digestion to biomethane and to test the feasibility of harvesting the resulting biomethane as energy source for the system.

Microbial Reductive Dehalogenation of Organochlorines

This research program is divided into three projects: 1) biology of PCB dehalogenating microbes; 2) kinetics of microbial dehalogenation; 3) in situ bioremediation of PCB contaminated sediments. Coastal anaerobic sediments are the ultimate global sinks for accumulation of chlorinated hydrocarbons such as polychlorinated biphenyls (PCBs) where reductive dehalogenation may have a significant role in their biotransformation. Understanding this microbial process is critical for making management decisions concerning both remediation and risk assessment of PCB-impacted coastal regions. Our lab and collaborators have for the first time identified two PCB dechlorinating microbes and based on this discovery we developed molecular ribosomal probe assays for detection of PCB dechlorinating biocatalysts in PCB impacted sediments. We are also studying the physiology and kinetics of the microbes that catalyze PCB dehalogention. Results of these studies will provide fundamental information on the biocatalytic processes required to develop bioremediation strategies and promote intrinsic PCB transformation in impacted marine harbor sediments and dredge deposition sites. In addition to developing approaches for in situ bioremediation of PCBs, our research will expand our understanding of the organismal and metabolic biocomplexity that is potentially available for dehalogenation processes in coastal sediments.