Ariel Grostern, Post-doctoral researcher

1,4-dioxane is a groundwater contaminant that is also a possible human carcinogen. Particular strains of aerobic bacteria and fungi have been shown to use dioxane as a carbon and energy source, which may allow for the possibility of using bioremediation as a means to clean up contaminated sites. I am studying one of these bacteria, Pseudonocardia dioxanivorans strain CB1190, for the purpose of improving our understanding of dioxane metabolism. The genome of strain CB1190 is currently being sequenced and annotated; this sequence will allow us to discover which enzyme systems are involved in dioxane metabolism, how the genes encoding these enzymes are regulated, and how dioxane is incorporated into the cell to serve as a carbon and energy source.

Katie Harding, PhD student

The goals of Katie’s research are to understand the fate and transport of chlorinated solvents in the subsurface, specifically those transformation pathways resulting from biodegradation processes. The use of molecular and biochemical tools that can be used to monitor and assess degradation in situ are studied, including stable carbon isotope fractionation and various molecular techniques such as qPCR, with the ultimate goal of improving bioremediation strategies. These research objectives include 1) understanding the variation in stable isotope fractionation patterns of chlorinated solvents in lab cultures and subsequently merging those observations with field and enrichment-derived fractionations to illuminate processes contributing to the variation, and 2) the continued characterization of key organisms responsible for chlorinated solvent degradation, Dehalococcoides spp. and other supporting microorganisms, including their distribution and activity in field environments.

Patrick K. H. Lee, PhD., Post-Doctoral Researcher

With the isolation of novel species that possess tremendous metabolic capability and the annotation of their genomes, bioremediation is a promising solution to overcome the problem of TCE contamination in groundwater aquifers. The goals of my research are to optimize the activity of Dehalococcoides spp. in reductive dechlorination and develop molecular biomarkers to monitor the physiology of the organisms in a heterogeneous environment. Available genomic information is used to guide the development of biomarkers that focus on DNA and the more labile RNA. Laboratory experiments as well as field studies are being carried out to test any hypothesis. Tools such as PCR, qPCR, RT-qPCR, microarray, and sequencing are used to achieve the research objectives.

Tiffany Louie, Lab Technician/Manager

Tiffany has several responsibilities, which include but are not limited to:

Tiffany is currently involved in research to verify the presence of a compound produced by Dehalococcoides ethenogenes during restricted growth conditions that negatively affects its own growth. This involves cloning of the gene responsible for production of this compound, attempting different methods of assaying for the compound, and gene product purification.

Yujie Men, PhD Student

Yujie’s research focuses on the identification of novel biomarkers indicative of active TCE dechlorination from Dehalococcoides-containing microbial communities, which are originally enriched from anaerobic environments such as groundwater and sediments. Firstly, microbial communities with TCE dechlorination activities were enriched using different conditions, such as type of electron donor, amount of TCE, presence of corrinoid, etc. Secondly, analytical and molecular tools were applied to these enrichment cultures in order to compare characteristics of TCE degradation, cell growth, as well as the presence and expression of dechlorination related genes, thus certain biomarkers could be nominated and verified finally. Molecular tools that have been and going to be used include quantitative PCR (qPCR), reverse transcription quantitative PCR (RT-qPCR), clone library techniques, microarray targeting at the whole-genome of Dehalococcoides ethenogenes strain 195, quad-genome microarray targeting at genomes of 4 well-known Dehalococcoides strains, etc. Analytical methods involve gas chromatography (GC) for chlorinated solvents detecting and high performance liquid chromatography (HPLC) for the detection of organic acids, as well as different types of corrinoids. For example, cyanocoblamin (vitamin B12) is an essential element required by Dehalococcoides. Currently, a non-vitamin B12 feeding microbial community was obtained, which still possesses the same dechlorination activities as the one with vitamin B12 feeding. Yujie is now trying to identify which bacteria within this community is responsible for providing corrinoids to Dehalococcoides, and in which way it is fulfilling the supportive job.

Peerapong Pornwongthong, M.Eng in Environmental Engineering

Peerapong Pornwongthong’s research focuses on the optimization of activity of Dehaloccocoides spp in reductive chlorination. He has chosen two biological factors, bacteriophages and bacteria to study. The emphasis is on the roles of both factors, which may affect the growth of bacteria and the ability of reductive chlorination. The main tools that has been used to detect the significance of these factors in terms of the functions of the bacterial culture and co-culture are molecular and analytical methods such as PCR, quantitative PCR (qPCR), reverse transcription quantitative PCR (RT-PCR), sequencing, nanodrop, high performance liquid chromatography (HPLC), and gas chromatography (GC).

Christopher M. Sales, PhD candidate in Environmental Engineering

My research focuses on developing an understanding of the biological systems involved in the aerobic biodegradation of the emerging water contaminant 1,4-dioxane.

Although many internet blogs focus on 1,4-dioxane as a contaminate in cosmetics and personal care products due to its accidental production during the ethoxylation process in cosmetic manufacturing, 1,4-dioxane has emerged as a groundwater contaminant because of its use as a stabilizer in widely used chlorinated solvents such as trichloroethylene (TCE), perchloroethylene (PCE), and 1,1,1-trichloroethane (1,1,1-TCA).

To further our understanding of the biological mechanisms involved in 1,4-dioxane biodegradation, we are currently working with the DOE Joint Genome Institute (JGI) on sequencing the genome of Pseudonocardia dioxanivorans CB1190. This genomic sequencing data will build the foundation to employ transcriptomic, proteomic, fluxomic, and metabolomic technologies to gain insight into the biomolecular systems in P. dioxanivorans that confer its unique ability to biodegrade and gain metabolic energy and carbon from 1,4-dioxane.

Kimberlee West, PhD candidate in Environmental Engineering

Kimberlee is working on ways to make the biodegradation of chlorinated solvents a more effective and efficient remediation strategy. She is studying the Dehalococcoides, the only bacteria known to completely detoxify PCE to the innocuous compound ethene. Because Dehalococcoides grows more robustly in mixed microbial communities, research focuses on gene expression of complete consortia in which Dehalococcoides plays a major role. Her interests lie in using molecular techniques like microarrays and pyrosequncing to investigate the genetics of active microbial dechlorination to increase the likelihood of successful bioremediation.

Kimberlee’s Other Interests

Some of Our Past Members

Professor Lisa Alvarez-Cohen
Dept of Civil and Environmental Engineering
University of Calfornia, Berkeley