Lisa Alvarez-Cohen

Alvarez-Cohen Research Group


Jennifer Lawrence, PhD Student: 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.

jelawrence@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

blbb1111@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.

srjones@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.

pgrego100p@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.

tongliu@berkeley.edu 


Ned Antell: Ned is the lab manager and has a wide range of duties including (though not limited to): taking care of two bioreactors, lending a hand where it is needed, ordering supplies, keeping safety information up to date and most importantly, nagging his lab mates about everything.

eantell@berkeley.edu

   

Previous Group Members


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.


Sara Gushgari, Masters Student: Sara’s research focuses on understanding the mechanisms by which microbial TCE dechlorination is inhibited due to the presence of other contaminants in the subsurface (e.g. arsenic and acetylene) with a specific interest in utilizing transcriptomic and metabolomic analyses. Results are used to inform the design of engineered solutions to remediate multiple contaminants at one site.

gushgari@berkeley.edu 


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.


Shan_yi@berkeley.edu


 

Shan Yi, Postdoctoral Researcher

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.


wqzhuang@berkeley.edu
 

Wei-Qin Zhuang, Postdoctoral Researcher

Wei's 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. Wei's 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


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.