Research Projects
Listed here are current (and past) projects in the Mattes Lab, and their funding status. This status is always subject to change. If you are interested in a particular project, please contact me.
1. Quantifying the presence and activity of vinyl chloride-degrading microorganisms in the dilute groundwater plumes by using real-time PCR.
Description of project:
Vinyl chloride (VC), a known human carcinogen with a maximum contaminant level of 2 ppb, is a significant contaminant of concern present as dilute groundwater plumes at many DoD sites. VC accumulates primarily from incomplete anaerobic biotransformation of chlorinated ethenes and ethanes, also common groundwater contaminants. Molecular biology tools (MBTs) represent an innovative approach for detecting and quantifying the presence and activity of aerobic, VC-degrading bacteria. MBTs can provide direct lines of evidence for natural attenuation of VC and will support existing anaerobic bioremediation technologies that generate VC as a metabolic intermediate. The objective of this project is to develop and validate real-time PCR techniques that can quantify both the presence and activity of aerobic VC- and/or ethene-assimilating bacteria in environmental samples from dilute groundwater plumes. Molecular biology tools such as real-time PCR (qPCR), reverse-transcription (RT)-PCR, and real-time, reverse-transcription PCR (RT-qPCR) are being used to detect and quantify the presence and activity of VC- and ethene-assimilating bacteria in pure cultures and environmental samples.
Students involved: Yang Oh Jin, postdoc, Meredith Dobson, MS Student, Stephanie Schmidt, undergraduate student
Publications associated with this project: none currently
Current Funding:
Strategic Environmental Research and Development program ($737,593) from 4/2009-3/2012.
Center for Health Effects of Environmental Contamination ($25,000) from 1/2005-1/2008.
2. Molecular microbial ecology analysis of polychlorinated-biphenyl-contaminated soils and sediments from Indiana Harbor, IN.
Description of project: Polychlorinated biphenyls (PCBs) are toxic, carcinogenic, and bioaccumulative compounds that are often found in lake and river soils and sediments. PCBs in soils and sediments represent a human health risk, especially if natural processes promote PCB volatilization and subsequent exposure to humans. Biodegradation of PCBs would reduce the risk of adverse human health effects, but this process is poorly understood in sediments. The objective of this project is to test the hypothesis that aerobic, PCB-degrading bacteria are present and active in PCB-contaminated sediments from Indiana Harbor, IN. Preliminary studies revealed aerobic PCB biodegradation potential (presence of biphenyl dioxygenase genes), but additional experiments will determine if aerobic PCB-degraders are active in these sediments. An array of experimental approaches, some of which are innovative, involving reverse-transcription (RT)-PCR, real-time RT-PCR, proteomics, and metabolite analysis are planned.
Students involved: Yi Liang, PhD student
Previous students: Laura Badke, rotating Biosciences PhD student, Laura Rogers, rotating Biosciences PhD student, Aaron Liao, undergraduate
Publications associated with this project: none currently
Current Funding: National Institutes of Environmental Health Sciences (4/01/2010-3/31/2015). Role: Co-PI on Project 5 “Phytoremediation to Degrade Airborne PCB Congeners from Soil and Groundwater Sources”
Previous Funding:
Center for Health Effects of Environmental Contamination ($30,000) from 9/2008-8/2009.
3. Evolution of a microbial biodegradation pathway in response to vinyl chloride.
Description of project: Microorganisms have the collective ability to degrade virtually all known organic compounds via catabolic pathway evolution and adaptation processes. The mechanisms controlling these processes are among those directly responsible for the vast diversity of life on Earth. In today’s world, environmental pollution by xenobiotic compounds is an increasingly prevalent concern. Microorganisms have become potentially powerful agents in efforts to remove xenobiotics from the environment, yet our understanding of xenobiotic-degrading bacteria is relatively poor. Using vinyl chloride (VC) as a model xenobiotic compound, we are investigating adaptive mechanisms that contribute to evolution of the aerobic VC biodegradation pathway in selected microbes. VC-assimilating bacteria use alkene monooxygenase to attack both VC and ethene, converting them into chlorooxirane and epoxyethane, respectively. Epoxyalkane: coenzyme M transferase (EaCoMT) catalyzes the assimilation of these toxic and reactive epoxides into central metabolism using Coenzyme M as a cofactor.
Recently, we found that several pure, ethene-assimilating Mycobacterium strains, initially unable to grow on VC, gradually adapted to growth on VC after extended incubations. These results suggest that we are observing microbial evolutionary processes in “real-time”. Because the mechanisms responsible for and the genetic basis of these physiological changes are unknown, a timely opportunity exists to delineate the mechanisms responsible for the adaptation. We are focusing our efforts on uncovering the genetic basis for increased EaCoMT activity in VC-adapted strain JS623 by directly comparing unadapted and VC-adapted “versions” of strain JS623. Our working hypothesis is that increased EaCoMT activity in VC-adapted strain JS623 results from increases in total numbers of EaCoMT and/or Coenzyme M biosynthesis genes in the genome. Physiological, biochemical, and molecular biology techniques are being employed in this study, which include whole cell assays, enzyme assays, real-time, reverse transcription PCR, genomic library construction and DNA sequencing. Our rationale for this work is to operate at the interface of the life sciences and engineering so that a better understanding of the evolutionary forces shaping the diversity of microbial life is gained while providing the opportunity to develop new technologies to benefit society and the environment.
Students involved: Yang Oh Jin, postdoc.
Publications associated with this project:
Jin, Y.O., Cheung, S., Coleman, N.V. and Mattes, T.E., 2010. Missense mutations in epoxyalkane coenzyme M transferase are associated with adaptation to vinyl chloride in Mycobacterium sp. strain JS623. Applied and Environmental Microbiology (76:3413-3419)
Jin, Y.O. and Mattes, T.E., 2008. Adaptation of aerobic, ethene-assimilating Mycobacterium strains to vinyl chloride as a growth substrate. Environmental Science and Technology. (42: 4784-4789).
Current Funding: none
Previous Funding:
The Biological Sciences Funding Program, Office of Vice President for Research ($29,500) from 6/2008-6/2009.
4. Development of proteomic techniques for detecting functional VC/ethene-oxidizing microbes in environmental samples
Description of project:
As the genomic age matures, environmental engineers and scientists have begun to appreciate the power of genomics and proteomics techniques for the study and solution of environmental problems. Early in the genomic age, funding for the majority of the genome sequencing projects was driven by human health concerns. More recently, the DOE’s Joint Genome Institute and The Institute for Genomic Research have sequenced the genomes of a diverse array of microbes with environmental relevance. Once such recently sequenced microorganism is the aerobic vinyl chloride (VC)-assimilating Nocardioides sp. strain JS614. This exciting development provides new opportunities to conduct proteomics studies with JS614 as a model system to achieve a significant scientific advance in the fields of environmental microbiology and biotechnology.
In this project, we are developing and applying proteomics techniques to detect and quantify a specific protein from soil. The alpha subunit (EtnC) of the alkene monooxygenase (AkMO), from strain JS614 is being targeted in this study. AkMO is a soluble di-iron monooxygenase that catalyzes the first step in aerobic VC biodegradation. The EtnC gene is a possible biomarker that signals the presence and activity of VC-assimilating bacteria. We are optimizing a protein extraction technique suitable for recovery of EtnC from environmental samples, digesting the protein sample containing EtnC with an appropriate protease(s) so that peptides unique to EtnC from JS614 are produced, and subjecting the peptide fragments to liquid chromatography tandem mass spectrometry (LC-MS/MS) to effect EtnC detection. Absolute quantification of peptides unique to EtnC will be achieved using iTRAQ isobaric stable isotope tags. The main goals are to determine the detection limit of EtnC in soil and to ultimately search for EtnC at contaminated site that appears to be undergoing aerobic natural attenuation of VC.Students involved: none currently
Previous students: Adina Chuang, PhD student, Stephanie Fleckenstein, undergraduate student
Publications associated with this project:
Chuang, A.S, and Mattes, T.E., 2007. Identification of polypeptides expressed in response to vinyl chloride, ethene, and epoxyethane in Nocardioides sp. strain JS614 using peptide mass fingerprinting. Applied and Environmental Microbiology (73:4368-4372).
Chuang, A.S., Jin, Y.O., Schmidt, L.S., Li, Y., Fogel, S., Smoler, D. and Mattes,T.E., 2010 . Proteomic analysis of ethene-enriched groundwater microcosms from a vinyl chloride-contaminated site. Environmental Science and Technology (44:1594-1601).
Current Funding: Josh is currently supported by IIHR and the graduate school via bridging funds.
Previous Funding:
SGER: Can specific proteins be detected and quantified in soil using proteomics techniques? National Science Foundation Small Grant for Exploratory Research ($73,656) from 11/1007 - 4/2009.
ICRU Scholar Assistant (supports Stephanie Fleckenstein) ($2,500) from 8/2008-5/2009.
5. Analysis of microbial community structure in an RDX-contaminated aquifer undergoing biostimulation with acetate.
Description of project:
Biological treatment (biotreatment) is the selected remedy for remediation of RDX from groundwater in offsite locations at the IAAP. Biological Treatment involves the addition of designed amounts of sodium acetate into wells that are installed in transects perpendicular to groundwater flow. Eventually, several transects may be installed to treat the entire plume. At this time, a single injection transect comprising 19 injection wells has been installed at the uppermost - and likely the most contaminated location - of the RDX plume. Several monitoring wells have been installed in the vicinity to collect groundwater for chemical, biochemical, and microbial analyses to evaluate the effectiveness of the acetate injections. This phase of treatment is expected to last for one year during which four quarters of well monitoring data will be collected and analyzed. The results will be used for treatment at other locations of the plume.
The prime purpose of injecting acetate into the groundwater is to encourage anaerobic conditions that are required for microbially-induced degradation of RDX. Acetate injection is expected to consume the native dissolved oxygen and reduce the oxidation-reduction potential (ORP) significantly, thereby attaining and sustaining conditions that are optimal for RDX reduction. Therefore, the redox conditions in groundwater following acetate injection are expected to evolve from oxic to iron-reducing, sulfur-reducing, and possibly methane-reducing levels during the course of treatment.
The initial goal of this project (funded by TetraTech) was monitor the effect of acetate injections on the subsurface groundwater microbial community. We tracked changes in community composition by amplifying community 16S rRNA genes and separating the mixture with either Denaturing Gradient Gel Electrophoresis (DGGE) or Terminal Restriction Fragment Length Polymorphism (T-RFLP) ananlysis. Ribosomal RNA genes sequences were determined by cloning and sequenced.
Recently, the project has taken a new turn. We are also investigating the effect that acetate injections are having on the eukaryotic microbial community in the aquifer. This portion of the project is funded by a NSF EAGER grant.
Students involved: Josh Livermore, PhD student
Publications associated with this project: none currently
Current Funding: none
Previous Funding:
EAGER: Perturbation of eukaryotic dynamics in a biostimulated groundwater aquifer. ($125,235) from 3/2010 - 5/2011.
Molecular biology analyses of RDX-contaminated offsite groundwater at the Iowa Army Ammunition Plant (IAAP). TetraTech, Inc. ($148,000) from 1/2008-12/2009.
6. Development of alkene monooxygenase (AkMO) systems for biocatalytic applications.
In this project we have investigated and partially optimized enzymatic production of enantiopure epoxyalkanes (e.g. propylene oxide) using alkene monooxygenase (AkMO) from Nocardioides sp. strain JS614
AkMOs are targets for development into environmentally beneficial industrial scale biocatalysis applications. Molecular oxygen is utilized by AkMOs, which is far less toxic than most chemical oxidants currently employed in certain catalysis applications. Bacterial cultures are renewable resources that are easily grown in large quantities in relatively nontoxic reaction media and can be frozen in an induced state for extended periods. Strain JS614 was chosen for study because it catalyzes epoxidations, which are reactions of interest to the chemical, agrochemical or pharmaceutical industries.
Students involved: none currently
Previous students: Carmen Owens, MS student. Julie Karceski, undergraduate student; Adina Chuang, PhD student.
Publications associated with this project: Owens, C.R., Karceski, J.K., and Mattes, T.E., 2009. Gaseous alkene biotransformation and enantioselective epoxyalkane formation by Nocardioides sp. strain JS614. Applied Microbiology and Biotechnology, (84:685-692).
Current Funding: none
Previous Funding:
Development of alkene monooxygenase (AkMO) systems for biocatalytic applications. Center for Environmentally Beneficial Catalysis ($120,000) from 1/2005-8/2008.
7. Discovery of agricultural and industrial byproduct biocatalysts by bacterial genome mining.
Description of project:
With the development of high-throughput genome sequencing technology and the completion of the human genome in 2003, the resulting infrastructure and technology improvement has facilitated sequencing of bacterial genomes at an increasing rate. The resulting bacterial gene pool contains a plethora of novel biocatalysts waiting to be discovered and developed for conversion of agricultural and industrial byproducts into more useful compounds. Recently, the genome of the chlorinated solvent-degrading Polaromonas sp. strain JS666 was completely sequenced. Analysis of the JS666 genome sequence suggested that strain JS666 possessed many potential biocatalysts, including a gene cluster that putatively converts ferulic acid, a component of corn cobs and kernel hulls, into vanillic acid and possibly vanillin, a valuable flavoring compound and fragrance. The main objective of this project is to develop procedures for validating genome analysis data by confirming that strain JS666 can degrade ferulic acid, identifying the genes that participate in this reaction, and identifying metabolic intermediates. A parallel objective is to evaluate the biocatalytic potential of strain JS666 for production of value-added products from agricultural wastes. This set of procedures can subsequently be used to uncover additional biocatalysts in the JS666 genome, in other organisms that have had their genomes sequenced.
Students involved: Anne Alexander, PhD student
Former students: Stephanie Fleckenstein, undergraduate student.
Publications associated with this project:
Mattes, T.E., Alexander, A.K., Richardson, P.M., Han, C.S, Munk, A.C., Stothard, P. and Coleman, N.V. 2008. The genome of Polaromonas sp. strain JS666: Insights into the evolution of a hydrocarbon- and xenobiotic-degrading bacteria, and features of relevance to biotechnology. Applied and Environmental Microbiology, (74: 6405-6416).
Current Funding: none
Previous Funding:
Biotechnology Byproducts Consortium ($35,950) from 1/2007-8/2008.
8. Regulatory mechanisms controlling induction of alkene monooxygenase in Nocardioides sp. strain JS614.
Description of project:
Nocardioides sp. strain JS614 utilizes vinyl chloride (VC) and ethene as carbon and energy sources. The bacterial metabolism of these alkenes is of particular interest because of its possible applications for bioremediation and biocatalytic applications. The first enzyme in the VC/ethene biochemical pathway is an alkene monooxygenase (AkMO) which catalyzes the addition of an oxygen atom to the alkene to form the corresponding epoxide. Variable extended lag periods of 3-7 days for growth on alkenes (i.e. VC and ethene) were observed after 24-h carbon starvation of alkene-grown JS614 cultures or after growth on carbon sources such as acetate, glucose, glycerol, succinate, and pyruvate. Initial studies suggest that the extended lag period is a result of AkMO induction difficulties under these particular physiological conditions. It is the goal of this study to better understand induction of AkMO in strain JS614 by examining in more detail its response to different growth and physiological conditions.
Students involved: None currently.
Previous students: Adina Chuang, PhD. student, Andrea Rogers, undergraduate student
Publications associated with this project:
Mattes, T.E, Coleman, N.V, Chuang, A.S, Rogers, A.J, Spain, J.C, and Gossett, J.M., 2007. Mechanism controlling the extended lag period associated with vinyl chloride starvation in Nocardioides sp. strain JS614. Archives of Microbiology. (187:217-226)
Current Funding: None
Previous Funding:
Iowa Reseach Experiences for Undergraduates ($3,000) from 1/2006-6/2007.