The research in this laboratory focuses on the enzymology, pathways and physiology of microorganisms that degrade environmental contaminants. The organisms we study are primarily hydrocarbon-oxidizing strains that degrade compounds such as trichloroethylene (TCE), methyl tertiary butyl ether (MTBE) and 1,4-dioxane (14D). The approaches used in this laboratory range from the isolation and characterization of novel strains through to genomic and proteomic analyses of individual strains and microbial communities. Many of these approaches make use of stable isotopes. Our goal is to understand the mechanisms utilized by naturally occurring microorganisms to degrade contaminants and to use this information to help develop appropriate treatment strategies that maximize the activities of these microorganisms in contaminated environments.
MBA Oregan State University 2001
Ph.D. Biochemistry University of Bristol, UK 1985
B.S. Botany University College, University of London, UK 1980
Area(s) of Expertise
Bioremediation, Microbial Physiology, Enzymology, Environmental Microbiology
- Alcohol-Dependent Cometabolic Degradation of Chlorinated Aliphatic Hydrocarbons and 1,4-Dioxane by Rhodococcus rhodochrous strain ATCC 21198 , ENVIRONMENTAL ENGINEERING SCIENCE (2023)
- Diyne inactivators and activity-based fluorescent labeling of phenol hydroxylase in Pseudomonas sp. CF600 , FEMS MICROBIOLOGY LETTERS (2023)
- Identifying the enzyme responsible for initiating aerobic acetylene metabolism in Rhodococcus rhodochrous ATCC 33258 , JOURNAL OF BIOLOGICAL CHEMISTRY (2023)
- Pilot-scale biofiltration of 1,4-dioxane at drinking water-relevant concentrations , WATER RESEARCH (2023)
- Single-well push-pull tests evaluating isobutane as a primary substrate for promoting in situ cometabolic biotransformation reactions , BIODEGRADATION (2022)
- Draft Genome Sequences of Four Aerobic Isobutane-Metabolizing Bacteria , MICROBIOLOGY RESOURCE ANNOUNCEMENTS (2021)
- Long-term cometabolic transformation of 1,1,1-trichloroethane and 1,4-dioxane by Rhodococcus rhodochrous ATCC 21198 grown on alcohols slowly produced by orthosilicates , JOURNAL OF CONTAMINANT HYDROLOGY (2021)
- Co-encapsulation of slow release compounds and Rhodococcus rhodochrous ATCC 21198 in gellan gum beads to promote the long-term aerobic cometabolic transformation of 1,1,1-trichloroethane, cis-1,2-dichloroethene and 1,4-dioxane , Environmental Science: Processes & Impacts (2020)
- 1,4-Dioxane in drinking water: Emerging for forty years and still unregulated , Current Opinion in Environmental Science & Health (2019)
- Aerobic cometabolism of 1,4-dioxane by isobutane-utilizing microorganisms including Rhodococcus rhodochrous strain 21198 in aquifer microcosms: Experimental and modeling study , SCIENCE OF THE TOTAL ENVIRONMENT (2019)
Many critical processes depend on metalloenzymes, and scarcity of the trace metals required for these enzymes may limit their activity, thus causing potential bottlenecks biogeochemical cycles. A recent revision to the microbial tree of life has revealed widespread and abundant soil bacteria that produce lanthanum-dependent methanol dehydrogenase, an enzyme potentially important in their metabolism and the cycling of carbon in soil. This exciting discovery further expands the periodic table of life and raises many questions about the biogeochemistry of lanthanum and other rare earth elements (REYs). Our research projectâ€™s central assertion is that microbesâ€”specifically those utilizing REY-dependent methanol dehydrogenaseâ€”will require a specific REY uptake strategy, akin to other biologically necessary trace metals. We propose to utilize cutting-edge coordination, soil, and analytical chemistry approaches to identify and characterize ligands that promote solubilization and binding of REYs from soils. The successful completion of the project will result in a transformative new paradigm for the transport of REYs in biological systems, and may provide significant advance in other related fields.
This project has two aims: First, we propose to develop a molecular biological tool (MBT) using activity based labeling (ABL) that can associate biomarkers such as monooxygenases with the biotransformation rate of key perâ€ and polyfluoroalkyl substances (PFAS) precursors under conditions relevant to the aqueous filmâ€ forming foam (AFFF)â€impacted sites. Second, we propose to assess the extent of sequestration of end products from precursors biotransformation into biomass and better understand the environmental fate of PFAS precursors.
The overall aim of this project is to evaluate the use of aerobic alkane-oxidizing bacteria for the in situ cometabolic degradation of 1,4-dioxane (14D). The project will involve testing field samples for the stimulation of either indigenous gaseous alkane and alkyne-metabolizing bacteria, testing the potential for bioaugmentation of field samples and detecting the presence of active alkane-oxidizing bacteria in field samples using activity-based labeling of catalytically active monooxygenases.
The alkane-oxidizing bacterium Rhodococcus rhodochrous ATCC 21198 can degrade 1,4-dioxane (14D) at high rates for over 300 days when it is co-encapsulated in gellan gum with orthosilicate slow release compounds (SRCs) that hydrolyze to produce alcohols. The overall goal of this project is to further develop this co-encapsulation technology for passive and sustainable aerobic cometabolic systems for the treatment of emerging contaminants such as N-nitrosodimethylamine (NDMA), 1,2,3-trichloropropane (TCP), as well as important contaminant mixtures such as 14D and its common co-contaminants, 1,1,1 trichloroethane and cis-dichloroethene.The contaminant-degrading activity of ATCC 21198 is due to non-specific, alkane-inducible monooxygenases that normally function to initiate alkane catabolism. In the absence of alkanes, the factors that control expression of these monooxygenases and enable sustained contaminant degradation are unknown but are key to further developing the co-encapsulation technology. Activity measurements, activity-based monooxygenase labeling and whole cell proteome analyses will be used to separately characterize the effects of alcohols, SRCs, starvation, encapsulation, and non-growth supporting contaminants on expression of monooxygenases and other enzymes in strain ATCC 21198. The physiological and enzymatic changes that occur the 300-day life cycle of this strain when co-encapsulated with model SRCs will also be determined. Similar genome-enabled approaches will also be used to identify other pure cultures with alternative monooxygenase complements that can sustainably degrade chlorinated ethenes (trichloroethene, vinyl chloride and 1,1-dichloroethene), and emerging contaminants (NDMA, and TCP) when co-encapsulated with SRCs. The activities of the co-encapsulated strains will be tested in batch reactors containing beads with single cultures and SRC as well as bead mixtures with different cultures and SRCs.
The project objective is to use apply a recently-developed activity-based labeling (ABL) technique to detect, and identify contaminant-degrading monooxygenase enzymes expressed by native or augmented microorganisms. The 2-step technique involves an initial inactivation of target enzymes using diyne probes with subsequent use of copper-catalyzed alkyne/Azide cycloaddition (CuAAC) reaction which generates a fluorescent protein adduct. This adduct can be detected and quantified by a number of different analytical approaches such as SDS-PAGE, microscopy, and flow cytometry. The technical objective of the proposed work will be to use ABL approaches to support a concurrent but separately funded study that aims to demonstrate that in situ aerobic cometabolic treatment of dilute plumes of chlorinated volatile organic compounds (CVOC)s can be achieved using bacteria grown on substrates including 2-butanol and benzyl alcohol. The ABL technique is expected to provide data that will enable the accompanying project to confirm the role of specific monooxygenases in in situ contaminant biodegradation and to determine the abundance of bacteria expressing these specific monooxygenases.