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.

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.

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.

Ben Stenuit, Postdoctoral scholar

Ben’s research focuses on the characterization and management of microbial communities able to degrade anthropogenic compounds, such as chlorinated hydrocarbons (e.g., TCE and 1,1,1-TCA) and solvent stabilizers (e.g., 1,4-dioxane). With the advent of various high-throughput molecular biology techniques, Ben's major research objective is to improve microbial robustness for bioremediation using systems microbiology. Systems-biology approaches can provide a holistic understanding of microbial community function and a whole picture of the different interactions (synergistic or antagonistic) occurring in a complex microbial community. The multiple functional guilds that participate to the biodegradation process are investigated using data from metagenomics, targeted metagenomics (i.e., combination of stable isotope probing (SIP) and metagenomics) and high-resolution metagenomics (i.e., combination of fluorescence-activated cell sorting (FACS) and metagenomics). The primary goal of his research is to apply DNA-, rRNA- and mRNA-based stable isotope probing to study interspecies interactions (synergistic and competitive) in TCE-degrading microbial communities such as syntrophic coupling of fatty acid-oxidizing reactions and hydrogen- and acetate-scavenging reactions.

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

Shan Yi, Post-doctoral Research

Shan's major research interest is that of identifying and characterizing the crucial symbiotic interactions existing in Dehalococcoides-containing microbial communities that can efficiently dehalogenate chloroethenes into benign ethene gas. The importance of Dehalococcoides in the bioremediation of aqueous chloroethene contaminations has long been established. However, genomic analysis of Dehalococcoides spp. has revealed that this group of bacteria lack or have incomplete pathways for several of their growth-dependent nutrients and cofactors that are essential for them to achieve robust growth and effective reductive dechlorination. In order to obtain their growth-dependent nutrients and cofactors from their natural environments, Dehalococcoides spp. have to rely on the syntrophic association with their concurrent microorganisms. Shan's research, therefore, focuses on using chromatography-based analytical tools to detect and identify the community exchangeable metabolites that underpin the syntrophic association between Dehalococcoides and other community members. Quantitative gene expression methods (e.g. microarray and reverse transcription-quantitative PCR) are also used in her research to investigate the effects of the metabolites on genotypic expressions of Dehalococcoides spp. Thus, biomarkers, which are indicative of the symbiotic associations existing in dechlorinating microbial communities, can be developed from the differential genotypic expressions for evaluating bioremediation processes.

Hanah You, Master’s of Science in Civil Engineering

Hi, I am Hanah You and I am currently doing my first year of Master's degree at UC Berkeley.
I got my bachelor's degree from Yonsei University in South Korea.
I am interested in water treatments using molecular biological approaches.

Wei-Qin Zhuang, Post-doctoral Researcher

My main research interest is the study of carbon metabolism and pathways in Dehalococcoides spp., so that the potential bottleneck pathways can be identified and further optimized to maximize Dehalococcoides' dehalogenation capabilities in the bioremediation of chloroethene contaminated groundwater. Over the last decade, the dehalogenation of chlorinated compounds by Dehalococcoides has been intensively investigated, especially in regard to functional enzymes, such as reductive dehalogenases and hydrogenases. In contrast, knowledge about carbon metabolism in Dehalococcoides is still limited. Genome sequences and their annotations for several Dehalococcoides strains have provided a starting point to comprehend Dehalococcoides physiology. However, significant questions about carbon metabolism and biosynthesis pathways in this important genus remain unanswered. My research employs stable isotope (e.g. 13C, 15N) enhanced metabolite analysis which, in conjunction with genome-enabled techniques (e.g. genomics and transcriptomics), tracks the active carbon metabolic pathways in Dehalococcoides. The recognition of active metabolic pathways not only links the genotypic knowledge to the phenotypic traits of Dehalococcoides strains, but also enables the identification of the undocumented pathways and genes to fill up the knowledge gaps.

Some of Our Past Members

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