Lisa Alvarez-Cohen

Vice Provost for Academic Planning
Fred and Claire Sauer Professor of Environmental Engineering
Research Interests
Environmental microbiology and ecology, Biotransformation, Wastewater contaminants, Molecular & isotopic techniques, Microbial communities

243 California Hall

Office Hours
Alvarez-Cohen headshot

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. Cohen’s research focuses on biotransformation and the fate of environmental water contaminants, environmental microbiology and ecology, bioremediation, biological wastewater nutrient removal, and the application of molecular and isotopic techniques for studying environmental microbial communities. She has won many 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 Young Investigator Award. She is also a member of several professional organizations, including the National Academy of Engineering, the American Academy of Microbiology, and the Association of Environmental Engineering and Science Professors.


Ph.D., Environmental Engineering and Science, Stanford University

M.S., Environmental Engineering and Science, Stanford University

B.A., Engineering, and Applied Science, Harvard University

Cohen's research focuses on environmental microbiology and ecology, biotransformation and fate of environmental contaminants, anammox processes for nutrient removal from wastewaters and innovative molecular and isotopic techniques for studying the microbial ecology of complex communities. Her research group looks at the application of omics-based molecular tools and isotopic techniques to understand and optimize the bioremediation of emerging and conventional environmental contaminants to facilitate beneficial nutrient removal from wastewater. Bioremediation and nutrient removal rely upon complex mixed microbial communities that interact to catalyze important reaction pathways. Here are a few of the research projects the Alvarez-Cohen lab is currently working on below:

  • 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 evaluated the impact of biotransformation and remediation of PFASs on the remediation of common co-contaminants TCE and dioxane, or vice versa. Our research seeks to evaluate 1) the interplay of PFASs and common co-contaminants 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 co-contaminants dioxane and chlorinated solvents. Our research will provide a holistic, rather than reductionist, approach to evaluating and treating 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 the 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 research projects include:


No mentions in News


No mentions in Spotlights

Student Updates

No mentions in Student Updates