Lisa Alvarez-Cohen

Slug
alvcohen
Type
Faculty
Headshot
Lisa Alvarez-Cohen
First Name
Lisa
Last Name
Alvarez-Cohen
Email
lisaac@berkeley.edu
Office
243 California Hall, Berkeley, CA 94720-1500
Office Phone
Office Fax
Office Hours

N/A.  Please email.

Programs
Environmental Engineering
Titles
Vice Provost for Academic Planning
Fred and Claire Sauer Professor of Environmental Engineering
Biography

Lisa Alvarez-Cohen is the Vice Provost for Academic Planning, Fred and Claire Sauer Professor, and past-Chair of the Department of Civil and Environmental Engineering and of the Faculty Senate at UC Berkeley.  She received her Bachelor’s Degree in Engineering and Applied Science from Harvard University and her M.S. and Ph.D. in Environmental Engineering and Science from Stanford University. Her research areas include biotransformation and fate of environmental water contaminants, environmental microbiology and ecology, bioremediation, biological wastewater nutrient removal, and application of molecular and isotopic techniques for studying environmental microbial communities.  She has taught both undergraduate and graduate courses in environmental microbiology, environmental engineering, and biological process engineering, and has co-authored the textbook Environmental Engineering Science.  She is a member of the National Academy of Engineering and a fellow of the American Academy of Microbiology and the Association of Environmental Engineering and Science Professors.  She has won a number of awards including the China 1,000 Talents National Award, the ASCE Simon W. Freese Environmental Engineering Award, the W. M. Keck Foundation Award for Engineering Teaching Excellence, and the National Science Foundation Young Investigator Award.

Education

PhD - Environmental Engineering and Science, Stanford University
MS - Environmental Engineering and Science, Stanford University
BA - Engineering and Applied Science, Harvard University

Research Overview

Environmental microbiology and ecology, biotransformation and fate of environmental and wastewater contaminants, and innovative molecular and isotopic techniques for studying microbial ecology of communities involved in wastewater treatment and bioremediation communities.

Research

Professor Alvarez-Cohen's research group, with exception of Chris Olivares and Emily Gonthier

Not in photo: Chris Olivares and Emily Gonthier

Professor Alvarez-Cohen's research areas include environmental microbiology and ecology, biotransformation and fate of environmental contaminants, anammox processes for nutent removal from wastewaters and innovative molecular and isotopic techniques for studying microbial ecology of complex communities. Specifically, her research focuses on the application of omics-based molecular tools and isotopic techniques to understand and optimize the bioremediation of emerging and conventional environmental contaminants by naturally occurring microorganisms and to facilitate beneficial nutrient removal from wastewater. Bioremediation and nutrient removal are processes that rely upon complex mixed microbial communities that interact to catalyze important reaction pathways. 

The Alvarez-Cohen lab takes a systems-based approach to understand communities as holistic units of interacting species, capable of performing environmentally relevant reactions.

Ongoing Research:

Trichloroethene Remediation
Trichloroethene (TCE) is a commonly detected contaminant at Superfund sites and is frequently listed on the U.S. EPA’s National Priorities List. To date, Dehalococcoides mccartyi (Dhc) strains are the only known organisms that can completely dechlorinate TCE to ethene. In situ bioremediation employing Dhc has become an important process for addressing groundwater contamination with chlorinated solvents. Although much has been learned with respect to the metabolism of Dhc-based microbial communities, the effects of geochemical perturbations on dechlorinating communities are still unknown. As other electron-accepting processes in groundwater environments might impact TCE-dechlorination, the objective of our study is to investigate how dechlorination communities respond to the changes in these conditions by constructing various Dhc-containing consortia in batch and completely mixed flow reactors (CMFRs). Ongoing experiments are analyzing the toleration for sulfate perturbation in CMFRs. Future experiments will also include the investigation about other geochemical factors’ influence, such as pH, alkalinity, on the communities. The information gained from this study will contribute to the development of engineered solutions that seek to optimize TCE dechlorination conditions.

AFFF Remediation
Poly and perfluoroalkyl substances (PFASs) are key components in aqueous film forming foams (AFFFs), complex chemical mixtures typically containing fluorinated and hydrocarbon surfactants and one or more glycol ether-based solvents, that have been widely used since the 1960s by the military and municipalities to extinguish hydrocarbon fuel fires and to prevent reignition. PFAS compounds, such as perfluorooctane sulfonate (PFOS) and perfluorooctanoate (PFOA), have recently been designated emerging contaminants due to concerns over environmental and human health effects. More specifically, PFASs are environmentally persistent, exhibit toxicity in human and animals, and can bioaccumulate. For these reasons, the use of PFOA, PFOS, and other C8 PFASs has been discontinued. 
Repeated AFFF application at training facilities where firefighting exercises were conducted in unlined pits has led to elevated levels of PFASs in groundwater at sites that are often contaminated with chlorinated solvents, such as trichloroethene (TCE) and its toxic daughter products and dioxane, a common stabilizer of chlorinated solvents. Although a number of studies have been conducted to understand the biotransformation and remediation strategies for PFASs present in AFFF, few have been evaluated the impact of biotransformation and remediation of PFASs on the remediation of common cocontaminants TCE and dioxane, or vice versa. Our research seeks to evaluate 1) the interplay of PFASs and common cocontaminants TCE and dioxane during biotransformation and remediation of these compounds, and 2) to identify effective processes or treatment trains to address AFFF, together with common cocontaminants dioxane and chlorinated solvents. Our research will provide a holistic, rather than reductionist, approach to evaluate and treat AFFF contaminated sites.

TCE/Arsenic Remediation
In situ bioremediation of chlorinated solvents is a well-researched and commonly applied strategy for subsurface remediation. However, in sites co-contaminated with arsenic, the reducing conditions promoted during chlorinated solvent bioremediation have the adverse effect of reducing immobilized As(V) to the more mobile and toxic As(III). Of the 389 chlorinated solvent contaminated sites on the National Priorities List, 228 are co-contaminated with arsenic. Therefore, there is a need to develop strategies for the dual bioremediation of chlorinated solvents and arsenic in order to provide a low-cost and low-disturbance remediation technology for these sites. 
Using a systems microbiology approach, our lab is working to create a holistic model of microbial cells and their community functions by integrating basic biological data made possible by community-scale omics technologies and new genetic manipulation technologies. These technologies allow for high-throughput investigation of the collective pool of genomes, transcripts, proteins, and metabolites present in the entire community and the ability to manipulate the flow of genetic information at multiple levels. Taken together, this data will provide a comprehensive picture of the modeled community using knowledge of its structure, its phenotypic potential, its function, and the microbial interactions within its environment. This knowledge can then be used to optimize the dual bioremediation of chlorinated solvents and arsenic.

Nitrogen Removal from Wastewater by Anammox
The Haber-Bosch process has drastically influenced the earth’s nitrogen cycle by doubling the global rate of nitrogen gas transformation to reactive nitrogen. In aquatic ecosystems, reactive nitrogen is often a limiting nutrient that, when released, can promote proliferation of primary producers, leading to eutrophication, reduction of biodiversity, and production of toxins.  Anaerobic ammonium oxidation (anammox) is the basis for an innovative biological treatment process for the removal of reactive nitrogen from wastewater effluent. Anammox bioreactors are 60% more energy efficient than the more traditional process of sequential nitrification-denitrification, and can be operated at approximately 10% of the cost. Today, over 100 full-scale anammox bioreactors have been installed worldwide and are in operation for the remediation of ammonium-rich, in-plant municipal wastewater streams. However, these processes are plagued by long start-up times and unstable operation. Further, the bacteria responsible for anammox have very low growth rates, are inhibited by a variety of factors, and have not yet been isolated. Few studies have examined anammox bacterial response to perturbations on a cellular level, or the role of other bacteria within anammox enrichments under fluctuating reactor conditions. The Alvarez-Cohen lab seeks to fill this gap by identifying the molecular mechanisms for anammox responses to perturbations and the metabolic roles played by other community members within anammox enrichments. Recent advancements in meta-omics based systems biology technologies provide powerful tools for analyzing the metabolism and interactions pertinent to anammox performance at the community level. Coupled with novel applications of stable isotope tracers, the Alvarez-Cohen lab seeks to generate a fundamental, community-based understanding of anammox enrichments enabling more comprehensive control and widespread adoption of this promising technology.

Previous Alvarez-Cohen Research Group
 

LAC Group 2011

 

 

Previous research projects include:

Metabolic degradation of 1,4-dioxane by Pseudonocardia dioxanivorans strain CB1190: genomic and post-genomic studies

1,4-dioxane (dioxane) is an emerging groundwater contaminant that is a probable human carcinogen and a confirmed animal carcinogen. Since it has historically been used as a chlorinated solvent stabilizer, dioxane is frequently found co-mingled with chlorinated solvents, such as 1,1,1-trichloroethane. Unlike chlorinated solvents, however, dioxane is not easily removed from the environment by volatilization or sorption processes, so alternative decontamination processes are required. Fortunately, several strains of aerobic bacteria with the capacity to degrade dioxane have been identified, so the bioremediation of dioxane-contaminated groundwater with such bacteria is a potential technology.

Our lab has been studying one of the few bacterial strains that can fully metabolize dioxane, using dioxane as both a carbon and energy source for growth. This bacterium, Pseudonocardia dioxanivorans strain CB1190, was originally isolated from industrial sludge from a dioxane-contaminated site in South Carolina. While the kinetics of dioxane-degradation by strain CB1190 have been extensively studied, our knowledge of the enzyme systems and gene-regulation mechanisms involved in growth on dioxane is currently very limited. For this reason, in conjunction with the Joint Genome Institute, we are having the genome of strain CB1190 determined by high throughput sequencing technologies. An insight into strain CB1190's genetic complement will permit genome-enabled studies to better understand the bacterium's dioxane-degrading capability. These studies include:

  • 1. Identification of the enzymes (e.g. monooxygenases) involved in the activation of the dioxane ring and investigation of their expression and regulation in the presence of competing carbon sources such as formate or the related cyclic ether tetrahydrofuran.
  • 2. In collaboration with Dr. Yinjie Tang at Washington University, using isotopomer technology to determine the biochemical pathway for dioxane incorporation into central metabolism, thus exploring strain CB1190's ability to grow (rather than co-metabolize) on dioxane.
  • 3. Using full genome expression microarrays to investigate the genes involved in nitrogen metabolism, particularly strain CB1190's ability to fix dinitrogen (N2), which is potentially important for environments limited in fixed-nitrogen.
  • 4. In collaboration with Dr. Rebecca Parales at UC Davis, developing a genetic system for strain CB1190 to permit gene knockouts for confirming the involvement of candidate genes in dioxane metabolism.

The results of this study will provide a mechanistic understanding of the degradation of 1,4-dioxane and the growth of Pseudonocardia dioxanivorans strain CB1190, further providing a foundation for developing tools to monitor and enhance the bioremediation of dioxane in natural and engineered systems.

Funded by the Strategic Environmental Research and Development Program and in collaboration with Shaily Mahendra at UCLA.

Oxygenase-Catalyzed Biodegradation of Emerging Water Contaminants: 1,4-Dioxane and N-Nitrosodimethylamine

This research examines the biodegradation of the emerging water contaminants 1,4-dioxane and N-nitrosodimethylamine (NDMA). Both 1,4-dioxane and NDMA are probable human carcinogens and confirmed animal carcinogens. Neither is significantly attenuated in the environment by volatilization or sorption processes. Due to its widespread use as a solvent stabilizer, 1,4-dioxane is frequently found comingled with chlorinated solvents at DoD and DoE sites; while NDMA is found as a degradation byproduct in proximity to aerospace facilities that used hydrazine-based rocket fuel.

Although the carcinogenic threats of 1,4-dioxane and NDMA have been understood for many years, they have not historically been considered important water quality issues, mostly due to lack of awareness about their potential occurrence in drinking water supplies. However, with recent advances in analytical methods and growing public awareness of their occurrence in drinking water supplies, 1,4-dioxane and NDMA are emerging as important water contaminants. Consequently, a better understanding of the effects of bacterial degradation on the fate and persistence of 1,4-dioxane and NDMA in the environment is needed.

This study will identify organisms, and more importantly a class of enzymes, capable of aerobically biodegrading 1,4-dioxane and NDMA. Furthermore, this study will elucidate the biochemical pathways responsible for 1,4-dioxane and NDMA degradation, quantify reaction kinetics, and develop models to predict those kinetics. It will also explore the effects of co-contaminants (e.g. 1,1,1-TCA, DCE, toluene, and chloroform) and inducing substrates (e.g., methane, propane, butane) on the contaminant degradation rates.

The results of this study will provide a mechanistic understanding of degradation of 1,4-dioxane and NDMA by aerobic microorganisms and as such it will provide a foundation for the bioremediation of these contaminants in natural and engineered systems.

Funded by the Strategic Environmental Research and Development Program.



Mass spectrometry for dioxane biodegradation pathway

Quantifying Gene Expression to Predict and Optimize Reductive Dechlorination by Dehalococcoides spp.

This study will apply gene expression analysis techniques to evaluate, predict, and optimize Dehalococcoides spp. reductive dechlorination activity in complex laboratory and field-site microbial communities.  Based on the observation that Dehalococcoides spp. grow and dechlorinate less robustly in pure culture than in mixed communities, molecular techniques will be used to compare increasingly complex communities, ranging from pure and enrichment cultures to soil microcosms and field samples, in order to identify expression-based markers that correlate with robustness of dechlorination activity. First, the per-cell dechlorination rate will be compared across a suite of communities to determine the predictive value of several fundamental metrics such as the cell density of Dehalococcoides spp., the identity and quantity of reductase genes present, and the expression level of each reductase gene. Second, whole-genome microarrays of D. ethenogenes 195 will be used to compare the suite of communities and identify novel genes whose expression is closely correlated with per-cell dechlorination rates.  Genes identified by microarrays to be potentially good expression markers will be further analyzed by real time quantitative PCR (qPCR). Third, identified predictive markers will be tested on field-site samples from the Idaho National Environmental Engineering Laboratory, where lactate injection to promote in situ bioremediation of trichloroethene (TCE) is ongoing, to seek correlations of degradation activity gradients with gene expression across space and time. Finally, predictive kinetic models for reductive dechlorination will be developed that incorporate the presence, copy number, and expression level of specific genes and the expression of validated and field-tested correlative genes.

Funded by the National Science Foundation, BES-01-0504244.



Hierarchical clustering of genes differentially expressed as Dehalococcoidesethenogenes transitions from the early-exponential (EE) to the late-stationary (LS) growth phases. The color gradient from blue to yellow represents increasing gene expression.

Application of Microarrays to Identify Biomarkers of Reductive Dehalogenating-Microbial Communities

(In collaboration with Gary Andersen and Eoin Brodie at Lawrence Berkeley National Laboratory and Stephen Zinder at Cornell University)

Background. Tetrachloroethene (PCE) and trichloroethene (TCE) have been widely used as industrial solvents and, as a result of poor storage and disposal practices, are now common contaminants of groundwater resources. Fortunately, PCE and TCE can be effectively biodegraded in anaerobic environments by reductive dechlorination processes. Recent progress has been made towards exploiting these processes for bioremediation applications. There remains a need, however, for appropriate and cost-effective biomarkers for assessing, monitoring, and optimizing the performance of these processes. Biomarker development has primarily focused on identifying nucleic acid sequences, peptides, proteins, or lipids of organisms that catalyze biodegradation reactions of interest. Although promising, such approaches are limited in that they do not address the roles of organisms that support and/or enhance the activity of dechlorinating organisms. Novel biomarkers that quantify the presence, abundance, and activity of supporting organisms are therefore needed to more effectively assess and optimize dechlorination processes.

Objective. In this research, we will identify 16S-rRNA-based phylogenetic and mRNA-based functional biomarkers diagnostic of microbial communities that support the robust growth and activity of chlorinated ethene-degrading organisms, with particular emphasis on Dehalococcoides species. Members of the Dehalococcoides genus can degrade chlorinated ethenes completely to ethene and also degrade a wide range of other chlorinated aromatic and aliphatic pollutants.

Summary of Process/Technology. We will apply state-of-the-art microarray-based tools to identify relevant biomarkers. A 16S-rRNA microarray that targets 9000 unique microbial phylogenies will be applied to identify key Archaea and Bacteria that are present and active in a range of Dehalococcoides-containing microbial communities, including enrichment cultures, soil microcosms, and groundwater samples. We will then construct defined co- and tri-cultures that contain Dehalococcoides and one or more of the key supportive organisms. Constructed cultures that exhibit enhanced and sustained rates of dechlorination and/or novel metabolic capabilities, such as the ability to use organic acids as electron donors, will be identified and the 16S-rRNA genes of the supporting organisms will be selected as phylogenetic biomarkers. In addition, a genomic expression microarray that targets the Dehalococcoides genus will be applied to the constructed cultures, to robust enrichment cultures, and to environmental samples to identify functional biomarkers indicative of the activity and/or functional role of supporting organisms. Finally, quantitative PCR will be used to derive correlations between the quantitative detection of these biomarkers, chlorinated ethene degrading activity, and the metabolic requirements of the microbial communities. These models will provide novel tools for assessing the structure and total biodegradative potential of Dehalococcoides in uncharacterized microbial communities.

Benefits. The broadest significance of the proposed work is that it will lead to improved strategies for optimizing in situ bioremediation technologies. The biomarkers developed here could shorten the bioremediation process feedback cycle by replacing traditional diagnostics, such as microcosm responses that are monitored over weeks, with appropriate 16S-rRNA- and gene expression-based diagnostics that can be monitored within hours. Furthermore, the insights gained about important ecological interactions within reductive dechlorinating microbial communities will improve our ability to design, construct, and optimize bioaugmentation and biostimulation systems.

Funded by Strategic Environmental Research and Development Program (SERDP).



Shown in the figures above are preliminary data of bacterial and archaeal populations that exhibit the greatest changes over the course of treatment at Ft. Lewis, Seattle, a TCE-contaminated site that has undergone in-situ bioremediation.

Using Molecular and Isotopic Tools to Characterize the Biodegradation of Chlorinated Ethenes and Ethanes

This project focuses on the comprehensive understanding of the fate and transport of chlorinated solvents in the subsurface, specifically those transformation pathways resulting from biodegradation processes. Emphasis is placed on the use of various molecular and isotopic tools to measure the biological transformation of chlorinated ethenes and ethanes, as well as the expanded characterization of the microorganisms responsible for their degradation. Tools and techniques that are used to characterize the biodegradation include: carbon isotope fractionation analyses, microarrays, and (RT) – qPCR. These analyses aid in the understanding of the activity and distribution of dehalogenating microorganisms in both laboratory and field environments.

The collection and analysis of environmental samples from various contaminated field sites allows for the in situ examination of complex microbial communities. These studies seek to assess the impacts of an active remediation system on the biological degradation of chlorinated ethenes, as well as examine the in situ physiology and metabolism of Dehalococcoides spp. The various aforementioned molecular and isotopic tools are used on the samples to investigate certain physical and biological processes. This includes monitoring the presence and expression of applicable taxonomic and functional genes at various time points before, during, and after remediation activities. These field studies are also complemented with fundamental laboratory experiments that are designed to determine the variability and specificity of the information provided by these tools. For example, the variation in stable isotope fractionation patterns of chlorinated solvents in laboratory cultures has been examined to determine whether the physiological state of the microorganism impacts the observed fractionation pattern. Achievable growth conditions were systematically varied in order to determine whether there are potential variations in the subsequent isotopic fractionation. This is ultimately important for understanding field-derived fractionation data.

Funded by the Chevron Energy Technology Company

Characterizing the fate and biotransformation of fluorochemicals in aqueous film forming forms (AFFF)

AFFF are complex mixtures of fluorocarbon surfactants, hydrocarbon surfactants, and solvents that were designed to spontaneously spread over hydrocarbon-fuel fires to extinguish flames and to prevent re-ignition. Repeated applications of AFFF at military fire-training sites have resulted in hundreds of fluorochemical-contaminated groundwater, sediment, and soil sites. The fate and transport of perfluorinated compounds (PFCs) in the environment is not well understood and the biodegradation potential for many of these pollutants has not been established. Additionally, because halogenated solvents, such as trichloroethene (TCE) were routinely ignited for fire-training activities, many of the sites may have significant co-contamination of chlorinated ethenes.

The goals of our research are to determine the biodegradability of fluorinated contaminants and other priority pollutants under redox conditions representative of groundwater at fire training sites. We are studying these processes using microcosms derived from both pristine and AFFF-contaminated soils as well as TCE-degrading enrichment cultures. Various molecular tools are being employed to characterize AFFF-utilizing microbial communities and identify active microorganisms, as well as to determine changes in microbial community structure upon exposure to AFFF. By developing a better understanding of the biotransformation of AFFF fluorochemical contaminants and their effects on the biodegradation of co-contaminants (e.g. TCE) in the subsurface, our study will contribute to remediation approaches that greatly decrease the time and cost required to monitor and treat contaminated soil and groundwater systems.

Corrinoid coenzyme requirement for effective TCE bioremediation using Dehalococcoides

Microorganisms of the Dehalococcoides (Dhc) genus play a crucial role in remediating groundwater contaminated by chlorinated solvents. Their unique metabolic ability to convert chlorinated solvents such as per- and tri-chloroethene to innocuous end product ethene is attributed to corrinoid-dependent reductive dehalogenases. Corrinoids, the required coenzymes for reductive dehalogenase activity, are a group of cobalt-containing molecules (including vitamin B12) that have wide structural variability in the lower axial ligand. The currently known Dhcstrains cannot synthesize corrinoids de novo and thus have to obtain them from the environment. It has been reported that corrinoid limitation, which can impact the robustness and efficiency of dechlorination, can be avoided either by adding exogenous vitamin B12 or by growing Dhcin microbial consortia containing microorganisms capable of corrinoid synthesis.

Currently, little is known about the actual corrinoid species that Dhcobtains from their environment and needs to support their physiological functions.  The goal of this study is to investigate both the corrinoid forms present in effective TCE-dechlorinating microbial communities and the structural specificity of the corrinoid coenzymes required by Dhc.  The corrinoid forms and concentrations are being determined in the effective TCE-dechlorinating microbial communities that have been enriched with no external B12 amendment.  The Dhc physiological responses to these corrinoid forms are being characterized.  This study contributes both to our understanding of the corrinoid syntrophic interactions in effective TCE-dechlorinating microbial communities and to the structure-function relationship of corrinoid coenzymes on the metabolic fitness of Dhc.

Meta-omics of Microbial Communities Involved in Bioremediation

This research seeks to advance our fundamental understanding of microbial communities that are capable of bioremediating environmental contaminants. We will apply systems biology approaches to study biodegradation abilities and interactions within microbial communities that remediate two water contaminants, trichloroethene (TCE) and 1,4-dioxane (dioxane), both of which are common problems at Superfund sites.

Despite broadly dissimilar biodegradation mechanisms, the bioremediation processes for TCE and dioxane both rely upon the activities of mixed microbial communities for achieving effective remediation goals. Consequently, there is a need for comprehensive and effective approaches to assess, predict, and optimize the performance of these complex microbial communities. Key functional degraders involved in these bioremediation processes, such as Dehalococcoides spp. for TCE dechlorination and Pseudonocardia spp. for dioxane degradation, have been studied in pure cultures, and mechanistic understanding of the degradation pathways have been elucidated. Although useful, such a reductionist understanding of key degrading microorganisms is not directly applicable to microbially diverse environmental samples. The lack of a comprehensive understanding of the effects of microbial community structure and its physiological characteristics on the capabilities of key degrading microorganisms is a barrier to progress in the field. In addition, there is a need to develop quantitative predictive tools for bioremediation assessment and process control.

Therefore, this project will focus on a holistic understanding of the population dynamics, metabolisms and functional interactions that shape the bioremediation of Superfund contaminants. This research will pioneer meta-omics approaches to elucidate microbial community structure-function relationships within complex systems, leading to improved abilities to design and optimize bioremediation processes, which, in turn, will decrease the cost and time required for remediation and reduce the exposure associated with groundwater contamination.

In this research, we will examine communities using a variety of high-throughput molecular biology tools, such as metagenomic analysis of isotopically enriched DNA (combination of stable isotope probing and next generation sequencing technology) or application of microarray hybridization using custom-designed microarrays.

Funded by National Institute of Environmental Health Sciences (NIEHS - Superfund Research Program)

Biodegradation of the Flame Retardants Polybrominated Diphenyl Ethers

Polybrominated Diphenyl Ethers (PBDEs) are flame retardants that have been used for over thirty years in a wide range of consumer textile and plastic products, such as TVs, sofas and automobiles. Some PBDEs, in particular ones with five bromines, are endocrine disruptors and have thus been banned in certain states and countries. The fate of these compounds in the environment is unknown.

Our research studies the fate of PBDEs in anaerobic and aerobic environments though biotransformation by bacteria. We have found that PBDE can be reductively debrominated by anaerobic bacteria, whereby the bromines are progressively removed and replaced with hydrogen. The more highly brominated PBDEs are however less toxic and can become more toxic if this transformation occurs.
 
We are currently studying the pathways and kinetics of this process using two-dimensional chromatography in order to separate and identify all possible degradation products. Our goal is to understand whether toxic byproducts can potentially accumulate in the environment due to biotransformation by bacteria.

Funded by UC Center for Water Resources.


Two-dimensional GC chromatogram of a PBDE standard.

Characterizing and Evolving the Propane Monooxygenase for N-Nitrosodimethylamine Biodegradation and Green Chemistry

(in collaboration with William Mohn and Lindsey Eltis of University of British Columbia, Vancouver, and Thomas Wood at Texas A&M)

Recent advancements in analytical detection methods have led to a growing awareness of the presence of N-nitrosodimethylamine (NDMA) in many drinking water sources. NDMA is a member of extremely-potent carcinogens, nitrosamines, whose occurrence in the environment has been linked to decomposition of hydrazine-based rocket fuels and chlorination of water and wastewater.

Bacterial strains expressing specific types of monooxygenases have demonstrated the ability to degrade NDMA, with induction of the propane monooxygenase in Rhodococcus sp. RR1 leading to the fastest rates of degradation. In addition to NDMA, other environmental contaminants such as trichloroethene (TCE), methyl tert-butyl ether (MTBE), and chloroform can be degraded by bacterial strains induced on propane. Despite its apparent versatility as a bacterial enzyme system, very little is known about bacterial propane monooxygenases.

The goal of this project is to characterize and evolve the propane monooxygenase enzyme, to better understand the nature of this enzyme to degrade NDMA and other xenobiotics, and to enhance the transformation rates of those compounds.

Our approach is to first use the fully annotated genome of Rhodococcus sp. RHA1, a strain similar to RR1, to identify and heterologously express the gene cluster coding for propane monooxygenase in a recombinant clones.

The second goal is to purify the components of the propane monooxygenase from the recombinant clones to investigate enzyme activity reconstituted in vitro and for crystallization. Both the recombinant clones and the purified propane monooxygenase will identify the enzymes xenobiotic transformation abilities.

The final goal is to use random and site-specific mutagenesis for directed evolution of the propane monooxygenase in order to improve transformation of xenobiotics. This will be the first instance that protein engineering will be applied to increase the degradation abilities of a propane monooxygenase. Evolved enzymes will be evaluated for green chemistry applications, such as for producing dyes or pharmaceuticals.

Funded by National Institute of Health.

 

Transcriptomic evidence for the role of propane monooxygenase in NDMA degradation. Growth of Rhodococcus sp. RHA1 on propane greatly enhances the rate of NDMA degradation. A DNA microarray was used to determine which enzyme is responsible for NDMA degradation under propane growth conditions. The microarray plot (above) shows a 125-fold increase in expression levels of a propane monooxygenase gene (prmA) when RHA1 transcripts from growth on propane are compared to that on pyruvate. These results suggests that a propane monooxygenase is responsible for NDMA degradation. Additional molecular biology strategies, such as qRT-PCR, knockout phenotypes and recombinant clones, will be used to verify these microarray findings.

CV File
Awards

•     Elected Fellow of the Association of Environmental Engineering and Science Professors   2019

•     SERDP Project of the Year Award, Environmental Restoration     2017

•     China 1,000 Talents National Award, Foreign National Expert     2016

•     ASCE Simon W. Freese Environmental Engineering Award     2014

•     Honorary Professor, Tongji University, Shanghai, P.R. of China     2013

•     Elected to the National Academy of Engineering     2010

•     Named one of “6 Scientists on the Cutting Edge of Energy and Environmental     2009
Research” by USNews and World Report                                                                  

•     Advisor to winner of CH2M Hill/AEESP Outstanding Doctoral Dissertation Award     2008

•     Environmental Science and Technology Excellence in Review Award     2006

•     Association of Environmental Engineering and Science Professors Distinguished Service Award     2003

•     Elected Fellow of the American Academy of Microbiology     2002

•     Awarded the Fred and Claire Sauer Chair in Environmental Engineering     2001

•     National Science Foundation Young Investigator Award     1994-1999

•     W. M. Keck Foundation Award for Engineering Teaching Excellence     1994

     Advisor to one undergraduate and three graduate student winners of     1994, 1998
Water Environment Federation Student Paper Competition and graduate
winner of the American Society of Civil Engineers Student Essay Competition

     Voted “Most Entertaining Lecturer” and “Most Enthusiastic Professor” by     1993, 1996
Berkeley Undergraduate Chapter of the American Society of Civil Engineers

     Department of Energy Environmental Restoration and Waste Management     1992-1994
Junior Faculty Award

•     Association of Environmental Engineering Professors Doctoral Thesis Award     1992

     University of California President's Post-Doctoral Fellowship     1991

     Switzer Foundation Graduate Scholarship     1989-1991

     AWWA Larson Aquatic Research Support Scholarship     1989

     American Chemical Society Graduate Student Award in Environmental Chemistry    1989                                                                              

     National Science Foundation Predoctoral Fellowship     1985-1988

Teaching

Professor Alvarez-Cohen teaches graduate and undergraduate courses in environmental microbiology, environmental engineering, biological process engineering. She is the co-author of the undergraduate textbook, Environmental Engineering Science.

Students

Alvarez-Cohen Research Group Current Members

eantell@berkeley.edu

eantell@berkeley.edu

Ned Antell, PhD Student

Ned is a PhD student interested in biological, chemical, and physical solutions to water and wastewater treatment. Prior to graduate school, Ned was lab manager in the Alvarez-Cohen lab for three years where he studied the anammox process for nitrogen-rich waste streams in addition to fulfilling other managerial duties.

Grace Campbell

gracecampbell@berkeley.edu

Grace Campbell, Undergraduate Student Researcher

Grace is in her senior year studying Environmental Engineering Science and her second year assisting in the Alvarez-Cohen lab as an undergraduate researcher.  She is currently a ReNUWit Research Scholar focused on studying the downstream effects of the transformation of poly- and perfluoroalkyl substances (PFASs) on bioremediation of 1,4-Dioxane.  Grace is interested in chemical transformation of pollutants in groundwater and pollutant transport and fate.

Emily Cook

emilycook@berkeley.edu

Emily Cook, PhD Student

Emily's research is chemistry-focused, looking at the transformation of per- and polyfluoroalkyl substances (PFASs) by heat-activated persulfate oxidation. She works to make chemical oxidation a feasible in situ remediation strategy for PFAS-contaminated sites around the country. Her current question is if PFSAs (with a sulfonic acid head group) can somehow be manipulated to be transformed via persulfate. 

gonthiea@berkeley.edu

gonthiea@berkeley.edu

Emily Gonthier, PhD Student

Emily is fascinated by the ability of microorganisms to both shape and adapt to the environment around them. Her research focuses on elucidating the microbial metabolisms and community interactions that drive the nutrient cycling and pollutant transformation necessary to improve water quality in engineered natural treatment systems.

ray_keren@berkeley.edu

ray_keren@berkeley.edu

Ray Keren, Post Doc

Ray's research interests is in microbial metabolism. He is part of the Superfund group working on developing an integrated bioremediation system for both arsenic and TCE in sediment and groundwater. Another project he is partaking in is the study of microbial communities in an anammox bioreactor, with an emphasis on the community dynamics and metabolic interdependencies. Ray studies these metabolic processes by using bioinformatic analysis of metagenomic and genomic data. Ray completed his PhD in microbiology at Tel Aviv university with Prof. Micha Ilan.

Mason King

masonking@berkeley.edu

Mason King, Lab Manager

Mason provides purchasing, inventory, and lab safety assistance to the LAC group. He operates and maintains various bioreactors including anammox and TCE dechlorinating consortia. Mason is interested in the intersection of sustainable water technologies and policy. He currently works on Life Cycle Assessment (LCA) applied to biological nutrient removal processes in wastewater treatment. 

zhihao_niu@berkeley.edu

zhihao_niu@berkeley.edu

Zhihao Niu, visiting PhD, Tongji University

Zhihao focuses on biological processes for wastewater treatment. Currently, he is investigating the start-up of anammox biofilm membrane reactor and nanoparticles’ effect on anammox biomass. He aims to figure out the mechanism of anammox’s response to external shock and accelerate the start-up of anammox bioreactors.

olivarec@berkeley.edu

olivarec@berkeley.edu

Chris Olivares, Post Doc

As part of the AFFF group, Chris Olivares researches chemical and biological transformations of poly- and per-fluoroalkyl substances (PFASs) present in sites polluted with aqueous fire-fighting foam formulations (AFFF) and co-contaminants. In particular, he is interested in 1) employing targeted and non-targeted mass spectrometry tools to identify transformation pathways of PFASs and microbial metabolites, and 2) studying the interactions between PFAS and co-contaminant biodegrading/biotransforming microbial communities. When not in the lab, he enjoys swimming with Cal's Fuego swim team. Chris received his PhD in Environmental Engineering from the University of Arizona, where he worked on biotransformation and toxicity of insensitive munitions components.

Sophia Steffens

sdsteffens@berkeley.edu

Sophia Steffens, PhD Student

Sophia is studying the solution behavior of groundwater contaminants with the goal of devising new strategies for their treatment and removal. She is passionate about sustainable agriculture and hopes to gear her work towards improving agricultural water management.

msun@berkeley.edu

msun@berkeley.edu

Mohan Sun, PhD Student

Mohan’s research mainly focuses on utilizing engineering methods to enhance in situ bioremediation of trichloroethene (TCE) using Dehalococcoides mccartyi (Dhc)-containing consortia. Mohan works with classic batch reactors and completely mixed flow reactors to simulate and investigate various naturally-occurring geochemical conditions’ effects on TCE dechlorination consortia.

Mohan also utilizes transcriptomics (RNA-Seq) and metabolomics to understand the differential gene expression and metabolites exchange among the different members of the consortia.

Finally, Mohan participates in using CRISPR Cas9 to knock out genes of interest in the genome of Desulfovibrio vulgaris Hildenborough (DvH), thus investigating the syntrophic relationship between DvH and Dhc.

eric_troyer@berkeley.edu

eric_troyer@berkeley.edu

Eric Troyer, PhD Student

Hi. I’m Eric. I’m working on the pfas-cinating subject of PFAS groundwater remediation and analysis. Since the elements composing PFASs are held together by stronger bonds than those shared between Voldemort and his horcruxes, they provide a unique challenge to remediate. Yet, the fun in science comes from its difficulties (and the free seminar cookies), and our lab has excellent people and equipment to work on the PFAS remediation problem. The pfas-ter we figure it out the better!

ktsou95@berkeley.edu

ktsou95@berkeley.edu

Katerina Tsou, PhD student

Katerina is interested in the bioremediation of organic contaminants. She is currently in the Aqueous Film Forming Foam (AFFF) group focused on developing microbial technology and is looking forward to discovering more about its role in making the environment safer.

caw87@berkeley.edu

caw87@berkeley.edu

Christian White, PhD Student

Christian is interested in the development of microbial techniques to improve sustainable wastewater treatment. In research, he is interested in using omic techniques to study anammox, anaerobic ammonium oxidative, bacteria, their metabolic pathways, and different inhibitors to their conversion of ammonium to nitrogen gas.

Previous Members

Sara Gushgari-Doyle

sarakgdoyle@gmail.com 

Sara Gushgari-Doyle, PhD

Sara's doctoral research focused on understanding signal and nutrient exchanges among members of microbial communities in a variety of environments and metabolisms using laboratory and "-omics" analyses. Specifically, she worked on remediation of contaminant mixture sites (e.g. chlorinated solvents and metalloids). After obtaining her PhD, she went on to a postdoctoral scholar position at Lawrence Berkeley National Laboratory in the Chakraborty group.

Shan Yi

shan.yi@auckland.ac.nz

Shan Yi, PhD

Shan Yi is a Lecturer in the Department of Chemical and Materials Engineering at the University of Auckland, New Zealand. Before taking this position, Shan was an Assistant Project Scientist in the Department of Civil and Environmental Engineering at the University of California, Berkeley. Broadly speaking, her research addresses microbial metabolism and syntrophic interactions and their impact on the performance of engineering bioprocesses. More recently, Shan has focused on investigating the biotransformation and remediation of per- and polyfluoroalkyl substances (PFAS) to tackle pressing PFAS contamination problems worldwide. Shan obtained her Ph.D. in Environmental Engineering from Nanyang Technological University in Singapore and her baccalaureate in Biochemical Engineering from Tianjin University in China.

Webpage link: https://unidirectory.auckland.ac.nz/profile/shan-yi

Twitter link: https://twitter.com/shanmyi

Wei-Qin Zhuang

wq.zhuang@auckland.ac.nz

Wei-Qin Zhuang, PhD

Dr. Wei-Qin Zhuang has a bachelor's degree in Bio-Chemical Engineering from Tianjin University in China. Both his master’s and Ph.D. degrees in Environmental Engineering were obtained from Nanyang Technological University in Singapore. His dissertation was focused on developing an innovative aerobic granulation system to treat industrial wastewater. After his Ph.D. defense, he joined the University of California at Berkeley as a postdoctoral fellow in the Department of Civil and Environmental Engineering where he investigated central metabolisms in important bioremediation anaerobic bacteria by using genetic engineering, genomics and metagenomics, and metabolomics techniques. Prior to joining the University of Auckland, he worked as an Assistant Scientist at the Center for Re-Inventing the Nation’s Urban Water Infrastructure (ReNUWIt) at UC Berkeley to develop an energy and cost-effective nitrogen removal process built upon anaerobic ammonium oxidation (anammox) bacteria.

Webpage linkhttps://unidirectory.auckland.ac.nz/profile/wq-zhuang

Twitter linkhttps://twitter.com/WeiQinZhuang1


jelawrence@berkeley.edu 

Jennifer Lawrence, PhD

Jennifer is interested in the development of microbial technologies for sustainable wastewater treatment.  Currently, she is studying the interactions between anaerobic ammonium oxidizing bacteria and zeolite particles for the enhanced removal of nitrogen from wastewater effluent.  Jennifer is interested in this technology's applications in both developed and developing countries.

Yilu Sun
yl_sun@berkeley.edu

Yilu Sun, visiting PhD, Institute of Technology (HIT)

Yilu is interested in bioremediation and microbial technologies for persistent pollutions treatment. Recently, he is focusing on the in situ remediation of aqueous film forming foams (AFFF) with chlorinated compounds and 1,4-dioxane as potential co-contaminants using the dual approach of heat-activated persulfate oxidation and bioremediation.

Xuening Zhang
xnzhang@berkeley.edu

Xuening Zhang, visiting PhD, Harbin Institute of Technology (HIT)

Xuening is interested in evaluating the role of soluble microbial products (SMPs) in biological wastewater treatment system. Currently, she is investigating the effect of SMPs and extracellular polymeric substance (EPSs) on the interaction among denitrifiers, dissimilatory nitrate reduction to ammonium (DNRA) bacteria and anammox communities in anammox bioreactors.

Siang Chen Wu
wusc@berkeley.edu

Siang Chen Wu, Post Doc

Siang Chen is interested in many environmental microorganisms and especially in their environmentally friendly applications in bioremediation and bioenergy aspects. He completed his Ph.D. in Environmental Engineering at National Chung Hsing University with Prof. Chi-Mei Lee. Currently, he gets involved in the anammox group and continuously focuses on our ongoing goals: (i) comprehensively understanding the metabolism of the anammox bacteria by integrated omics analyses; (ii) trying to isolate the slow-growing anammox bacteria; and (iii) proposing useful strategies to build up a robust anammox community and to accelerate the start-up speed for anammox bioreactors.


blbb1111@berkeley.edu

Jae Ho Bae, Junior Specialist

Jae Ho's research interest is in chemical kinetics in open and closed environmental systems. He is part of the chlorinated solvents group, which works to keep our water sources, such as aquifers, free of contamination. His research is focused on developing innovative bioremediation techniques that are both economical and reliable.  Jae Ho received his B.S. in Chemical Engineering from UC Berkeley in 2015


srjones@berkeley.edu

Stephanie Jones, Post Doc

Stephanie is studying microbial mechanisms of bioremediation. She completed her Ph. D. in Chemistry at UC Berkeley with Prof. Michelle Chang in collaboration with Prof. Arash Komeili.


pgrego100p@berkeley.edu

Patrick Gregoire, Post Doc

Patrick has a Ph.D. in Microbiology specialized in extremophilic anaerobic bacteria. He’s interested in discovering more bacteria and their role in the environment. Patrick is part of the anammox group and is facing two challenges 1) trying to isolate the bacterium 2) in the absence of pure culture, understand the metabolism of those bacteria using an anaerobic continuous flow membrane reactor.


tongliu@berkeley.edu

Tong Liu, Post Doc

I am most interested in bioremediation and microbial ecology. At the moment my work is mostly oriented towards investigating geochemical impacts on TCE-dechlorinating consortia by “-omics” analysis.


kharding@berkeley.edu
 

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.


xmao1@berkeley.edu

Xinwei Mao, PhD Student

Xinwei's PhD research focuses on understanding the electron flows in TCE-dechlorinating microbial communities using modeling and molecular biology tools, with a specific interest in the physiology and modeling the anaerobic TCE-dechlorinating syntrophic microbial consortia.


menyj@berkeley.edu

 

Yujie Men, Postdoctoral Researcher

Yujie received her PhD degree in the Alvarez-Cohen research group and is now continuing as a Postdoctoral Researcher. Her research mainly focuses on: 1) investigating the microbial ecological interactions between the TCE-dechlorinating anaerobic microorganism Dehalococcoides mccartyi and its supportive microorganisms within microbial communities. Chlorinated ethenes have long been known as common groundwater contaminants in the United States. D. mccartyi is, so far, the only microorganism capable of reductively dechlorinating chloroethenes to ethene. Corrinoids such as cobalamin are essential cofactors of reductive dehalogenases, but cannot be synthesized by D. mccartyi strains. Recent studies have shown that D. mccartyi can grow in communities without cobalamin amendment. Yujie is currently trying to identify potential corrinoid- providing microorganisms within these communities and understand the essential nutrient exchange between D. mccartyi and those supportive microorganisms; 2) developing energy sustainable domestic wastewater treatment techniques using direct anaerobic digestion in membrane bioreactors. Conventional domestic wastewater treatment has large footprint, uses a vast amount of energy for aeration with little energy recovered from the sewage, and generates excess activated sludge which costs more space and money to deal with. Direct anaerobic digestion of wastewater converts the organic matters in the influent into methane, which by careful collection can be used as energy source, thus may turn the municipal wastewater treatment plant from energy-negative to energy-neutral or even energy-positive. Yujie is conducting studies on making the direct anaerobic digestion more stable and robust, as well as improving the treatment process to meet the more and more stringent regulation standards on organics and nutrients in the effluent. A variety of lab approaches are applied in her research, including molecular tools such as PCR, quantitative real-time PCR (qPCR), cloning techniques, microarray and next generation sequencing technologies; analytical tools such as gas chromatography (GC), high performance liquid chromatography (HPLC), as well as liquid chromatography tandem mass spectrometry (LC/MS/MS).


renatonm@berkeley.edu
 

Renato Montagnolli, Visiting Scholar

Renato is a visiting student currently conducting his research at University of California, Berkeley on perfluorinated compounds biotransformation along with petroleum hidrocarbon co-contaminants. He is a doctoral student in Applied Microbiology at Sao Paulo State University, Brazil. He has a master's degree in Life Sciences and Microbiology. As an environmental microbiologist, he has been conducting his research on petroleum biodegradation kinetics as well as biosurfactant production by Bacillus subtilies for the last 5 years. He had his research sponsored by Petrobras during his bachelor of science degree in Biology from Sao Paulo State University, Institute of Life Sciencies, Brazil.

Ben Stenuit
benstenuit@gmail.com
 

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.


KimberleeW@gmail.com


 

Kimberlee West, PhD Student

A few years ago, the EPA finalized its 25 year health assessment of trichloroethene (TCE), escalating TCE to "carcinogenic to humans" status. They estimated typical daily intakes by the general US population at 13 μg/day by inhalation and 0.2 μg/day from water ingestion. Kim hopes to minimize this risk by improving understanding of TCE biodegradation in the environment. Specifically, Kim is examining genetic systems within a TCE-degrading microbial community to learn how and why Dehalococcoides bacteria are able to  dechlorinate TCE at relatively high rates and grow robustly and stably in consortia. Kim is comparing metagenomic, transcriptomic, and proteomic data from an enrichment culture, looking for information on Dehalococcoides and supporting or competing organisms that can be applied to TCE bioremediation strategies.


bhfeil@nature.berkeley.edu

Helene Feil, PhD, Associate Specialist

The major goal of Helene's research is to optimize the microbial reduction of pollutants such as trichloroethene (TCE). TCE can be converted to harmless byproducts by a variety of microbial processes. She is looking at the genomic and transcriptomic levels to understand how these microbial communities work together to effectively reduce these toxic chlorinated solvents. She is interested in the interaction of Dehalococcoides strains with anaerobic bacterial and archeal species to identify key metabolic and other important genes used in TCE reduction. Her research will also examine the effects of various chemicals on the TCE reduction capabilities of Dehalococcoides spp. A combination of various molecular biology tools such as microarrays, quantitative and RT-PCR , as well as chemical analysis such as gas chromatography will be used to examine the transcriptome of these organisms during the various experiments. The study of stable microcosms for optimal TCE reduction can prove useful for effective bioremediation of polluted sites.


ggggggg@berkeley.edu

Georgia Green, Undergraduate student

Georgia Green, an undergraduate in her senior year, is currently working with enriched cultures of Dehalococcoides ethenogenes 195 to determine whether naturally occurring soil constituents, such as humics and quinones, can be used as electron acceptors. A positive result would help explain the wide distribution of Dehalococcoides spp. on the planet, prior to soil and groundwater contamination by chlorinated solvents.

Georgia plans to work with the Lydia Sohn Mechanical Engineering Laboratory to further develop the Electronic Cell Typing technique. Thus far, the technique has been used to quantify DNA in single eukaryotic cells. Georgia hopes to modify the process such that RNA can be quantified in prokaryotic cells. She is working with E. coli as a model species.


ariel.grostern@berkeley.edu

Ariel Grostern, Postdoctoral 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. Ariel is 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.


daverj@ce.berkeley.edu

David R. Johnson, PhD Student

David's current research focuses on identifying RNA-based phylogenetic and functional biomarkers indicative of microbial communities that completely degrade PCE to ethene. To identify RNA-based biomarkers, he is applying two types of high-density microarrays to analyze the PCE-to-ethene dechlorinating bacterium Dehalococcoides ethenogenes. He is applying a 16S-rRNA phylogenetic array to identify and quantify key organisms that are present and active in Dehalococcoides-containing microbial communities. He is also applying whole-genome arrays to characterize global transcription changes when this organism is subjected to stress conditions, such as cobalamin (vitamin B12) limitations, and as this organism transitions from the exponential to stationary growth phases. Finally, his  previous work focused on applying RT-qPCR to characterize the expression of the tceA reductive dehalogenase gene under differing environmental conditions and to identify correlations between tceA expression levels and reductive dehalogenation activity.

Patrick Lee
leep@berkeley.edu

Patrick K. H. Lee, Postdoctoral 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
tslouie@berkeley.edu

Tiffany Louie, Lab Technician/Manager

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

  • Maintaining "The Bomb" (A biological reactor that is over ten years old, contains TCE-degrading microorganisms sampled from the Alameda Naval Air Station, and looks like a bomb).
  • Laboratory safety
  • Laboratory repairs
  • Purchasing and receiving
  • Research support for other group members

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.


icytyl@berkeley.edu

Peerapong Pornwongthong, MEng

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).


robrock@berkeley.edu
Kristin Robrock, PhD

Kristin is studying the biodegradation of Polybrominated Diphenyl Ethers (PBDEs) which are flame retardants that have been used for thirty years in manufactured products such as computers, TVs, furniture and automobiles. Recently, toxicology studies have shown that penta-brominated PBDEs are endocrine disruptors at low concentrations. They have been banned and removed from the market although more highly brominated PBDEs continue to be used. Anaerobic bacteria, however, are capable of removing bromines from highly brominted PBDEs creating the toxic penta-brominated PBDEs in the process. Kristin is studying which species can degrade PBDEs, the degradation pathway and the timescales involved. She hopes that her data will help regulators ban PBDEs entirely.

Christopher.Sales@berkeley.edu
Christopher M. Sales, PhD

Christopher's 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, Christopher et al. 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.

zhangyinghr@yahoo.com

Zhang Ying, Visiting Scholar
School of Resources & Environment, Northeast Agricultural University (NEAU), China

Zhang's goal is to identify 16S-rRNA-based phylogenetic and mRNA-based functional biomarkers diagnostic of microbial communities that support the robust growth and activity of chlorinated ethene-degrading organisms. In particular, she will focus on biomarkers indicative of organisms species. Members of this genus can degrade chlorinated ethenes completely to ethene and also degrade a wide range of other chlorinated aromatic and aliphatic pollutants.

The broadest significance of the proposed work is that it will lead to improved strategies for optimizing in situ bioremediation technologies. The biomarkers developed here could shorten the bioremediation process feedback cycle by replacing traditional diagnostics, such as microcosm responses that are monitored over weeks, with appropriate 16S-rRNA- and gene expression-based diagnostics that can be monitored within hours. Furthermore, the insights gained about important ecological interactions within reductive dechlorinating microbial communities will improve the ability to design, construct, and optimize bioaugmentation and biostimulation systems.


yuyinphoebe@berkeley.edu

Yin Yu, Visiting PhD Student from Tsinghua University

Yin's study focuses on the capabilities of monooxygenase-expressing bacteria to cometabolically degrading carbamazepine (CBZ), one of the most concerned emerging micropollutants in water systems. CBZ is widely used as antiepileptic or anticonvulsant drug. It is metabolized in human liver by monooxygenases, such as cytochrome P-450 enzymes, which suggests that it is possible for bacterial monooxygenases to catalyze CBZ biotrasformation. In this study, monooxygenase-expressing bacteria were induced with individual substrates to express monooxygenase enzymes, which are similar in structures and functions to the one catalyzing carbamazepine degradation reactions in human liver. She will try to evaluate the capabilities of these strains to cometabolize CBZ, measure the degradation kinetics, and analyze the transformation pathways.

Publications

Selected Recent Publications