Michael Hyman
Bio
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.
Education
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
Publications
- Aerobic cometabolic biodegradation of 1,4-dioxane and its associated Co-contaminants , Current Opinion in Environmental Science & Health (2023)
- Alcohol-Dependent Cometabolic Degradation of Chlorinated Aliphatic Hydrocarbons and 1,4-Dioxane by Rhodococcus rhodochrous strain ATCC 21198 , ENVIRONMENTAL ENGINEERING SCIENCE (2023)
- Archaeal communities discovered in the phytotelmata of Nepenthes alata Blco. samples obtained from Mt. Makiling, Philippines as revealed by high-throughput molecular sequencing analysis , International Journal of Agricultural Technology (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)
Grants
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 project???s central assertion is that microbes???specifically those utilizing REY-dependent methanol dehydrogenase???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 per??? and polyfluoroalkyl substances (PFAS) precursors under conditions relevant to the aqueous film??? forming foam (AFFF)???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.
Fluorescence activated cell sorting (FACS) is a technique that involves sorting away select cells (or objects) from complex mixtures based on their intrinsic or acquired fluorescence. FACS is a transformative technology that allows the study of the unculturable microbes (which are numerically dominant in nature) and accomplish tasks that are highly laborious or impossible complete in other ways; the technology has led to significant discoveries in many microbial research fields (e.g. ecology, genetics, physiology, symbiosis/interactions, bioengineering, and bio-prospecting), and nearly single-handedly forged new fields of research, e.g. single cell genomics and transcriptomics, which involves the study of DNA and mRNA from individual cells. More than 25 North Carolina State University (NCSU) faculty, belonging to 4 colleges, have needs for FACS in their research or teaching programs; however, NCSU lacks a FACS instrument optimized for the analysis of non-mammalian microbial cells (e.g. bacteria, archaea and fungi), and to our knowledge, no ???????????????microbe optimized?????????????????? instrument is available at research universities within the Research Triangle of North Carolina (e.g. UNC-CH, Duke University). Here, funds are requested to acquire a Becton Dickinson FACSMelody flow cytometer, a versatile (3 excitation laser, 9-color detection) and ???????????????turn key?????????????????? system, which fundamentally enables microbiological research that is highly laborious or impossible to accomplish without it. The FACSMelody is powerful yet simple to use and generates easy to grasp visual (flow cytometric) data ?????????????????? making it a good potential training and educational tool for undergraduate/graduate courses and workshops. A FACSMelody system is ideal for getting FACS technology rapidly and easily into the hands of faculty in need. Overall, a FACS system for non-mammalian microbial research is needed for NCSU to be innovative, internationally competitive at attracting new faculty and highly talented students, and foster creative future proposals.
The key objective of this project is to demonstrate that a novel multiple primary substrate (MPS) cometabolic biosparging technology can meet DoD needs for reliable, flexible, and cost effective treatment of a groundwater with co-mingled 1,4-dioxane (14D) and chlorinated volatile organic compounds (CVOCs). Isobutane will be added to the aquifer to target 14D biodegradation, and methane, isobutylene, and/or propane will be added to stimulate degradation of trichloroethene (TCE) and other CVOCs present. The ability of the technology to achieve regulatory levels of 14D and CVOCs in the groundwater, and the cost of the technology will be evaluated.
Current remediation approaches for COCs including 14D, CAHs, and petroleum hydrocarbons often rely on expensive ex-situ pump-and-treat methods rather than preferable in situ treatment methods. Mixtures of COCs are also problematic, as a single in-situ process typically cannot simultaneously treat multiple COCs. In situ remediation is also often further complicated by COCs in low permeability zones that act as long-term sources of contamination.Our current SERDP-supported studies (ER2303) have shown that many bacteria grown on isobutane as a primary substrate can degrade 14D at low ppb levels via aerobic cometabolism. Our studies with a model isobutane-utilizing strain, Rhodococcus rhodochrous 21198, have shown this bacterium canalso concurrently oxidize 14D and diverse CAHs, including mixtures of 11DCE and 111TCA. While in situ biostimulation using isobutane is a potential remediation strategy for COC mixtures containing 14D, other cometabolic strategies involving isobutane-metabolizing bacteria may be more applicable for low permeability zones. For example, previous studies with other gaseous alkane-utilizing Rhodococcus strains have shown that cells grown on simple alcohols can rapidly degrade VC or mixtures of 14D and TCE. We have also shown 14D induces expression of the monooxygenase responsible for its own biodegradation in R. rhodochrous 21198 growing on alcohols. While the roles of alcohols and COCs in monooxygenase induction requires clarification, these observations suggest the broad COC-degradingactivity of gaseous alkane-utilizing bacterial strains can potentially be supported using slow release compounds (SRCs) that produce alcohols. When co-encapsulated with appropriate microorganisms, these SRCs could be useful for in situ treatment of 14D-containing COC mixtures, particularly in zones of low permeability. The overall aim of the proposed research is to develop novel aerobic cometabolic processes based on SRCs to treat COC mixtures of interest to DoD. While mixtures of 14D and CAHs will be our primary interest, the microorganisms, SRCs, and encapsulation technologies identified in these studies may be suitable for treating COC mixtures containing NDMA and other DoD-relevant contaminants.
Nitrogenous fertilizers are critical for sustaining small to large farms in the US. The Haber-Bosch process generates the majority of fixed nitrogen, but it comes at a high cost, both in terms of dollars and environmental impact. Requiring temperatures between 400-500oC and pressures of 150-250 bar, this process consumes 1-2% of global energy. Reliance on fossil fuels to power this process translates into unstable fertilizer prices and a significant release of greenhouse gases. Low-cost and carbon-neutral ammonia fertilizer production is therefore needed to improve the sustainability of our food production systems. Biological nitrogen (N2) fixation, as practiced in the farming of legumes, is attractive because of its low-energy demand, operation under ambient conditions, and point-of-use production; however, slow fixation rates and, in the case of non-legume crops, a lack of abundant N2 fixing symbiotic diazotrophs in the soil, limit the large-scale feasibility of this approach. Moreover, options to accelerate symbiotic N2 fixation rates to the industrial levels needed to compete with the Haber-Bosch process are lacking. As an alternative, we propose investigating a hybrid microbial electrochemical system to electrically enhance microbial N2 fixation rates. Bacteria in these systems consume organic matter (such as waste biomass) and generate electrical current when they respire (breathe) on anode electrodes. By exploiting their physiology, we hypothesize that we can electrically ????????????????boost??????????????? N2 fixation rates in these organisms. The overall objective of this proposal is to determine the influence of the electrical driving force on the rates, mechanisms, and pathways of microbial N2 fixation. The rationale is that with this knowledge, we can improve N2 fixation rates in these communities and optimize a scalable technological platform to produce fixed nitrogen from small-scale farms to industrial-scale applications.
Our overall aim is to develop a simple, activity-based fluorescent labeling approach for selectively quantifying metabolically active ammonia-oxidizing bacteria (AOB) and archaea (AOA) in complex soil microbial communities. These specialized microorganisms obtain all of their energy from the oxidation of ammonia (NH3) and initiate this process through the activity of ammonia monooxygenase (AMO). Collectively, these microorganisms can have large impacts on the fertilizer applications to soils and can substantially decrease fertilizer N availability to crop plants. A simple and reliable method that can predict in situ rates of AMO activity in AOA and AOB could be a useful management tool that could help decrease fertilizer waste and environmental impacts of excess fertilizer applications.