Project 4: Meta-Omics of Microbial Communities Involved in Bioremediation (Archived)


Trichloroethene (TCE), a common chlorinated solvent, and 1,4-dioxane (dioxane), a solvent stabilizer, both are frequent groundwater contaminants at Superfund sites. Although microbial degradation reactions can effectively transform these contaminants, lack of a holistic and ecologically relevant understanding of the interspecies complexity of subsurface microbial communities impedes the application of robust and effective in situ bioremediation of these compounds. The overall goal of this research is to identify and examine the community-level metabolic interactions that shape the biodegradation capabilities of bioremediating communities.  The fundamental understanding of microbial communities from a systems microbiology point of view will be developed by utilizing community-scale tools on two dissimilar model communities that function within different redox environments, i.e. anaerobic and aerobic, to remediate TCE and dioxane, respectively. We hypothesize that important interspecies interactions and keystone functions that regulate multiple community behaviors will be identified by applying an integrated meta-omics based approach, which in turn will provide insights to facilitate engineering efficient bioremediation processes.  DNA-based stable isotope probing will be used to distinguish and identify functional organisms and the important interdependent relationships within communities capable of biodegrading TCE or dioxane. Targeted metagenomic analyses will then be employed to reveal the metabolic and functional diversity of interdependent biodegrading organisms and their supporting or inhibiting partners in the communities.  Comprehensive metatranscriptomic analyses based on mRNA-targeted microarrays will be employed to investigate the global gene expression in the communities under different environmental perturbations in order to reveal microbial behaviors in response to the changes. In order to design diagnostic tools that can be applied to query environmental samples at TCE and dioxane-contaminated sites, we will identify and validate quantitative biomarkers for key metabolic as well as interacting genes using quantitative expression analyses in conjunction with community metabolite-analyses.  Finally, we will apply the diagnostic tools developed throughout the research to examine environmental samples to assess microbial behaviors and interactions in these samples in order to guide and optimize in situ bioremediation strategies.

This is relevant because TCE and dioxane, suspected human carcinogens, are common groundwater contaminants at Superfund sites. This research focuses on gaining a holistic understanding and developing novel biomarkers of the community-level metabolism and interactions that shape the bioremediation capabilities of subsurface microbial communities.  Results from this research will meet SRP research goals by facilitating the assessment, design and optimization of in situ bioremediation of TCE and dioxane-contaminated sites.

Project Leadership

Lisa Alvarez-Cohen, PhD

Fred and Claire Sauer Professor of Environmental Engineering

Department of Civil and Environmental Engineering, College of Engineering
University of California, Berkeley

Project Update


We developed a methodology to understand the interactions between bacteriophages and bacteria during TCE bioremediation. We identified the conditions that drive the native bacterial community to remove the dissolved forms of arsenic by precipitiation in order to enable D. mccartyi to remediate TCE. We are currently testing the stability of the precipitates under alternating anaerobic and aerobic conditions.


Project 4 of the UC Berkeley Superfund Research Program during the period of 2016-2017, led by Prof. Lisa Alvarez-Cohen (CEE Dept.) and Jillian Banfield (EPS Dept.) focuses on advancing our fundamental understanding of microbial communities involved in bioremediation. To pursue this goal, we have been analyzing a variety of bioremediation communities using systems biology approaches to study metabolite exchanges that support bioremediation. This past year, we mainly focused on two objectives of our project In the first objective, we used a set of novel bioinformatics tools developed by the Banfield group to reanalyze existing metagenomic data from three TCE-detoxifying bioreactors. Our analysis focused on bacteriophages (viruses affecting bacteria) and their roles affecting bioreactor efficiency. Bacteriophages (phages) are usually overlooked in engineered environments albeit their important influence on bacterial communities. We began by identifying the phage DNA in the metagenomes and assembling it into full phage genomes. Next, we aimed to identify the bacterial host (or hosts) of the phages using the bacterial CRISPR-Cas gene groups.  These genes are a type of bacterial immunity system containing small phage DNA sequences that were archived by the bacterium after surviving phage attacks. Matching these small phase DNA sequences in bacteria to the phage genomes, we can better understand the interactions between phages and bacteria during TCE bioremediation.

The second objective dealt with remediation of soil and ground water co-contaminated with arsenic and TCE. Our previous results showed that the TCE-detoxifying bacterium, Dehalococcoides mccartyi is sensitive to water-dissolved forms of arsenic (arsenate and arsenite). The main focus of this current research is identifying the conditions that drive the native bacterial community to remove the dissolved forms of arsenic by precipitation in order to enable D. mccartyi to remediate TCE. Our results show that arsenic is precipitated with sulfur by dual reduction of arsenate and sulfate using lactate as the electron donor. We are currently testing the stability of the precipitates under alternating anaerobic and aerobic conditions.

In the portion of the project dealt with remediation of soil and ground water co-contaminated with arsenic and TCE, we found that TCE degradation is inhibited under high arsenic concentrations, since Dehalococcoides mccartyi is sensitive to water-dissolved forms of arsenic (arsenate and arsenite), but once the arsenic is sufficiently removed, D. mccartyi can degrade TCE. While microbial communities are expected to vary from site to site, we hypothesize that the functions related to arsenic precipitation are redundant and found in all microbial communities. Our results show that arsenic is precipitated with sulfur under anaerobic conditions, with lactate as the carbon source. The mineral (orpiment) is formed by dual reduction of arsenate and sulfate. Further, we were able to show that the orpiment is formed under various concentrations of arsenate and sulfate. This is important since previous reports in the literature claimed the mineral is not stable at increasing sulfide concentrations (formed by the reduction of sulfate). We are currently testing the stability of the mineral under aerobic conditions.

Project Update Archive

Project News

Project 4 Leader Lisa Alvarez-Cohen continues as a Member of the Board of Scientific Councilors, National Center for Environmental Health/Agency for Toxic Substances and Disease Registry, US Centers for Disease Control and Prevention and as the Division 4 Liaison to NRC committees, National Academy of Engineering.

Selected Presentations:
  • Sun, M., S. Gushgari, X. Mao, A. Polasko, T. Liu, J. H. Bae, and Alvarez-Cohen L. 2016. “Effects of Geochemical Perturbations on Dehalococcoides mccartyi-containing Dechlorinating Consortia”, Superfund 30th Anniversary Annual meeting, Durham, NC.
  • Keren R., Brisson V., Xinwei, M., Yujie, M., Yu K., Banfield J., and Alvarez-Cohen L. 2016. “Metagenomic analysis of mobile elements and phage in trichloroethene (TCE) dechlorinating communities”, ACS Annual meeting, San Francisco, CA.
  • Keren R., Brisson V., Xinwei, M., Yujie, M., Yu K., Banfield J., and Alvarez-Cohen L. 2016. “Metagenomic analysis of mobile elements and phage in trichloroethene (TCE) dechlorinating communities”, Superfund 30th Anniversary Annual meeting, Durham, NC.
  • Yi, S., E.F. Houtz, K.C. Harding, J.A. Field, D.L. Sedlak, L. Alvarez-Cohen. Identification of anaerobic biotransformation products of 6:2 fluorotelomer thioamidosulfonate in aqueous film-forming. 252th ACS National Meeting and Exposition, Philadelphia, PA, August 21-25, 2016. (Oral presentation)
  • Cook, E., Troyer, E., Keren, R., Liu, T., and Alvarez-Cohen, L. 2016 “Investigating the biogeochemical interactions involved in simultaneous TCE and Arsenic in situ bioremediation”, 2016 AGU Fall Meeting, San Francisco, CA.
News Archive

Selected Publications


Mao X, Oremland R, Liu T, Gushgari S, Landers A, Baesman S, Alvarez-Cohen L (2017) Acetylene fuels TCE reductive dechlorination by defined Dehalococcoides/Pelobacter consortia. Environ Sci Technol. Feb 21;51(4):2366-72. DOI: 10.1021/acs.est.6b05770. PMID:28075122. [PDF]

Mao X, Polasko A, Alvarez-Cohen L (2017) The Effects of sulfate reduction on TCE dechlorination by Dehalococcoides-containing microbial communities. Appl Environ Microbiol. Feb 3. DOI: 10.1128/AEM.03384-16. [Epub ahead of print]. PMID: 28159790. [PDF]


Crable BR, Sieber JR, Mao X, Alvarez-Cohen L, Gunsalus R, Ogorzalek Loo RR, Nguyen H, McInerney MJ (2016) Membrane complexes of Syntrophomonas wolfei involved in syntrophic butyrate degradation and hydrogen formation. Front Microbiol. Nov 9;7:1795. PMCID: PMC5101538. [PDF]

Harding-Marjanovic KC, Yi S, Weathers TS, Sharp JO, Sedlak DL, Alvarez-Cohen L (2016) Effects of Aqueous Film-Forming Foams (AFFFs) on Trichloroethene (TCE) Dechlorination by a Dehalococcoides mccartyi-Containing Microbial Community. Environ Sci Technol. Apr 5;50(7):3352-61. PMID: 26894610. DOI: 10.1021/acs.est.5b04773. [PDF]

Berg M, Stenuit B, Ho J, Wang A, Parke C, Knight M, Alvarez-Cohen L, Shapira M (2016) Assembly of the Caenorhabditis elegans gut microbiota from diverse soil microbial environments. ISME J. Aug;10(8):1998-2009. PMID: 26800234 DOI: 10.1038/ismej.2015.253. [PDF]

Weathers TS, Harding-Marjanovic K, Higgins CP, Alvarez-Cohen L, Sharp JO (2016) Perfluoroalkyl Acids Inhibit Reductive Dechlorination of Trichloroethene by Repressing Dehalococcoides. Environ Sci Technol. Jan 5;50(1):240-8. PMID: 26636352. DOI: 10.1021/acs.est.5b04854. [PDF]

Brisson VL, Zhuang WQ, Alvarez-Cohen L (2016) Bioleaching of rare earth elements from monazite sand. Biotechnol Bioeng. Feb;113(2):339-48. PMID: 26332985. DOI: 10.1002/bit.25823. [PDF]


Zhou L, Xia S, Alvarez-Cohen L (2015) Structure and distribution of inorganic components in the cake layer of a membrane bioreactor treating municipal wastewater. Bioresour Technol. Nov;196:586-91. PMID: 26298402. DOI: 10.1016/j.biortech.2015.08.026. [PDF]

Harding-Marjanovic KC, Houtz EF, Yi S, Field JA, Sedlak DL, Alvarez-Cohen L (2015) Aerobic Biotransformation of Fluorotelomer Thioether Amido Sulfonate (Lodyne) in AFFF-Amended Microcosms. Environ Sci Technol. Jul 7;49(13):7666-74. PMID: 2604823. DOI: 10.1021/acs.est.5b01219. [PDF]

Zhuang WQ, Fitts JP, Ajo-Franklin CM, Maes S, Alvarez-Cohen L, Hennebel T (2015) Recovery of critical metals using biometallurgy. Curr Opin Biotechnol. Jun;33:327-35. PMCID: 26042823. [PDF]

Zhou J, He Z, Yang Y, Deng Y, Tringe SG, Alvarez-Cohen L (2015) High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats. MBio. Jan 27;6(1). PMCID: PMC4324309. [PDF]

Mao X, Stenuit B, Polasko A, Alvarez-Cohen L (2015) Efficient metabolic exchange and electron transfer within a syntrophic trichloroethene-degrading coculture of Dehalococcoides mccartyi 195 and Syntrophomonas wolfei. Appl Environ Microbiol. Mar;81(6):2015-24. PMCID PMC4345365. [PDF]

Lee PK, Men Y, Wang S, He J, Alvarez-Cohen L (2015) Development of a fluorescence-activated cell sorting method coupled with whole genome amplification and microarray method to analyze minority and trace Dehalococcoides genomes without isolation. Environ. Sci. Technol. Feb 3;49(3):1585-1593. PMID: 25565465. DOI: 10.1021/es503888y. [PDF]


Crofts TS, Men Y, Alvarez-Cohen L, Taga ME (2014) A bioassay for the detection of benzimidazoles reveals their presence in a range of environmental samples. Front. Microbiol. Nov 13;5:592. PMCID: PMC4230183. [PDF]

Men Y, Seth EC, Yi S, Crofts TS, Allen RH, Taga ME, Alvarez-Cohen L (2014) Identification of specific corrinoids reveals corrinoid modification in dechlorinating microbial communities under different enrichment conditions. Environ. Microbiol. 17(12):4873–4884.

Zhuang WQ, Yi S, Bill M, Brisson V, Feng X, Men Y, Conrad ME, Tang YJ, Alvarez-Cohen L (2014) The incomplete Wood-Ljungdahl pathway enables an unconventional one carbon metabolism in Dehalococcoides mccartyi. Proc. Natl. Acad. Sci. U. S. A. Apr 29;111(17): 6419-6424. PMCID: PMC4035967. [PDF]

Men Y, Seth EC, Yi S, Allen RH, Taga ME, Alvarez-Cohen L (2014) Sustainable growth of Dehalococcoides mccartyi 195 by corrinoid salvaging and remodeling in defined lactate-fermenting consortia. Appl. Environ. Microbiol. Apr;80(7):2133-2141. PMCID: PMC3993147. [PDF]

Zhou J, He Z, Yang Y, Deng Y, Tringe SG, Alvarez-Cohen L (2014) High-throughput metagenomic technologies for complex microbial community analysis. mBio. Jan 27;6(1):e02288-14. PMCID: PMC4324309. [PDF]


Sales C M, Grostern A, Parales JV, Parales RE, Alvarez-Cohen L (2013) Oxidation of the cyclic ethers 1,4-dioxane and tetrahydrofuran by a monooxygenase in two Pseudonocardia species. Appl. Environ. Microbiol. Dec;79(24):7702-7708. PMCID: PMC3837796. [PDF]

Mahendra SA, Grostern A, Alvarez-Cohen L (2013) The impact of chlorinated solvent co-contaminants on the biodegradation kinetics of 1,4-dioxane. Chemosphere. Mar;91:88-92. PMID: 23237300. DOI: 10.1016/j.chemosphere.2012.10.104. [PDF]


Mahendra S, Grostern A, Alvarez-Cohen L (2012) The impact of chlorinated solvent co-contaminants on the biodegradation kinetics of 1,4-dioxane. Chemosphere. Dec 10; PMID: 23237300 (PMC Journal- In Progress). [PDF]

West KA, Lee PK, Johnson DR, Zinder SH, Alvarez-Cohen L (2012) Global gene expression of Dehalococcoides within a robust dynamic TCE-dechlorinating community under conditions of periodic substrate supply. Biotechnol Bioeng. Dec 27;doi: 10.1002/bit.24819. PMID: 23280440 (PMC Journal – In Process). [PDF]

Yi S, Seth EC, Men YJ, Stabler SP, Allen RH, Alvarez-Cohen L, Taga ME (2012) Versatility in corrinoid salvaging and remodeling pathways supports corrinoid-dependent metabolism in Dehalococcoides mccartyi. Appl Environ Microbiol. Nov;78(21):7745-7752. PMCID: PMC3485714. [PDF]

Grostern A, Sales CM, Zhuang WQ, Erbilgin O, Alvarez-Cohen L (2012) Glyoxylate metabolism is a key feature of the metabolic degradation of 1,4-dioxane by Pseudonocardia dioxanivorans strain CB1190. Appl. Environ. Microbiol. May;78(9):3298-3308. PMCID: PMC3346452. [PDF]

Lee PK, Dill BD, Louie TS, Shah M, VerBerkmoes NC, Andersen GL, Zinder SH, Alvarez-Cohen L (2012) Global transcriptomic and proteomic responses of Dehalococcoides ethenogenes strain 195 to fixed nitrogen limitation. Appl. Environ. Microbiol. Mar;78(5):1424-36. PMCID: PMC3294477. [PDF]

Men Y, Feil H, VerBerkmoes NC, Shah MB, Johnson DR, Lee PK, West KA, Zinder SH, Andersen GL, Alvarez-Cohen L (2012) Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: global transcriptomic and proteomic analyses. ISME J. Feb 6;6(2):410-421. PMCID: PMC3260503. [PDF]

Lee PK, Warnecke F, Brodie E, Macbeth T, Conrad ME, Andersen G, Alvarez-Cohen L (2012) Phylogenetic microarray analysis of a microbial community performing reductive dechlorination at a TCE-contaminated site. Environ. Sci. Technol. Jan 17;46(2):1044-1054. PMCID: PMC3461955. [PDF]


Lee PK, Cheng D, Hu P, West KA, Dick GJ, Brodie EL, Andersen GL, Zinder SH, He J, Alvarez-Cohen L (2011) Comparative genomics of two newly isolated Dehalococcoides strains and an enrichment using a genus microarray. ISME J. Jun;5(6):1014-24. PMCID: PMC3131851. [PDF]


Robrock KR, Mohn WW, Eltis LD, Alvarez-Cohen L (2010) Biphenyl and ethylbenzene dioxygenases of Rhodococcus jostii RHA1 transform PBDEs. Biotechnol Bioeng. Feb;108(2):313-21. PMID 20872819. [PDF]


Lee PK, He J, Zinder SH, Alvarez-Cohen L (2009) Evidence for nitrogen fixation by “Dehalococcoides ethenogenes” strain 195. Appl Environ Microbiol. Dec; 75(23):7551-5. PMID: 19820162. PMCID: PMC2786412. [PDF]

Tang YJ, Yi S, Zhuang WQ, Zinder SH, Keasling JD, Alvarez-Cohen L (2009) Investigation of carbon metabolism in “Dehalococcoides ethenogenes” strain 195 by use of isotopomer and transcriptomic analyses. J Bacteriol. Aug; 191(16):5224-31. PMID: 19525347. PMCID: PMC2725585. [PDF]

Robrock KR, Coelhan M, Sedlak DL, Alvarez-Cohent L (2009) Aerobic biotransformation of polybrominated diphenyl ethers (PBDEs) by bacterial isolates. Environ Sci Technol. Aug 1; 43(15):5705-11. PMID: 19731666. [PDF]

Johnson DR, Nemir A, Andersen GL, Zinder SH, Alvarez-Cohen L (2009) Transcriptomic microarray analysis of corrinoid responsive genes in Dehalococcoides ethenogenes strain 195. FEMS Microbiol Lett. May; 294(2):198-206. PMID: 19341394. [PDF]


West KA, Johnson DR, Hu P, DeSantis TZ, Brodie EL, Lee PK, Feil H, Andersen GL, Zinder SH, Alvarez-Cohen L (2008) Comparative genomics of “Dehalococcoides ethenogenes” 195 and an enrichment culture containing unsequenced “Dehalococcoides” strains. Appl Environ Microbiol. Jun; 74(11):3533-40. PMID: 18359838. PMCID: PMC2423027. [PDF]

Johnson DR, Brodie EL, Hubbard AE, Andersen GL, Zinder SH, Alvarez-Cohen L (2008) Temporal transcriptomic microarray analysis of “Dehalococcoides ethenogenes” strain 195 during the transition into stationary phase. Appl Environ Microbiol. May; 74(9):2864-72. PMID: 18310438. PMCID: PMC2394897. [PDF]

Lee PK, Macbeth TW, Sorenson KS, Jr., Deeb RA, Alvarez-Cohen L (2008) Quantifying genes and transcripts to assess the in situ physiology of “Dehalococcoides” spp. in a trichloroethene-contaminated groundwater site. Appl Environ Microbiol. May; 74(9):2728-39. PMID: 18326677. PMCID: PMC2394903. [PDF]

Robrock KR, Korytar P, Alvarez-Cohen L (2008) Pathways for the anaerobic microbial debromination of polybrominated diphenyl ethers. Environ Sci Technol. Apr 15; 42(8):2845-52. PMID: 18497133. [PDF]


Sharp JO, Sales CM, LeBlanc JC, Liu J, Wood TK, Eltis LD, Mohn WW, Alvarez-Cohen L (2007) An inducible propane monooxygenase is responsible for N-nitrosodimethylamine degradation by Rhodococcus sp. strain RHA1. Appl Environ Microbiol. Nov; 73(21):6930-8. PMID: 17873074. PMCID: PMC2074979. [PDF]

Lee PK, Conrad ME, Alvarez-Cohen L (2007) Stable carbon isotope fractionation of chloroethenes by dehalorespiring isolates. Environ Sci Technol. Jun 15; 41(12):4277-85. PMID: 17626425. [PDF]

He J, Holmes VF, Lee PK, Alvarez-Cohen L (2007) Influence of vitamin B12 and cocultures on the growth of Dehalococcoides isolates in defined medium. Appl Environ Microbiol. May; 73(9):2847-53. PMID: 17337553. PMC1892872. [PDF]


Rahm BG, Chauhan S, Holmes VF, Macbeth TW, Sorenson KS, Jr., Alvarez-Cohen L (2006) Molecular characterization of microbial populations at two sites with differing reductive dechlorination abilities. Biodegradation. Dec; 17(6):523-34. PMID: 16477354. [PDF]

Holmes VF, He J, Lee PK, Alvarez-Cohen L (2006) Discrimination of multiple Dehalococcoides strains in a trichloroethene enrichment by quantification of their reductive dehalogenase genes. Appl Environ Microbiol. Sep; 72(9):5877-83. PMID: 16957207. PMC1563660. [PDF]

Lee PK, Johnson DR, Holmes VF, He J, Alvarez-Cohen L (2006) Reductive dehalogenase gene expression as a biomarker for physiological activity of Dehalococcoides spp. Appl Environ Microbiol. Sep; 72(9):6161-8. PMID: 16957242. PMCID: PMC1563655. [PDF]

Mahendra S, Alvarez-Cohen L (2006) Kinetics of 1,4-dioxane biodegradation by monooxygenase-expressing bacteria. Environ Sci Technol. Sep 1; 40(17):5435-42. PMID: 16999122. [PDF]

He J, Robrock KR, Alvarez-Cohen L (2006) Microbial reductive debromination of polybrominated diphenyl ethers (PBDEs). Environ Sci Technol. Jul 15; 40(14):4429-34. PMID: 16903281. [PDF]


Johnson DR, Lee PK, Holmes VF, Fortin AC, Alvarez-Cohen L (2005) Transcriptional expression of the tceA gene in a Dehalococcoides-containing microbial enrichment. Appl Environ Microbiol. Nov; 71(11):7145-51. PMID: 16269753. PMCID: PMC1287711. [PDF]

Freeborn RA, West KA, Bhupathiraju VK, Chauhan S, Rahm BG, Richardson RE, Alvarez-Cohen L (2005) Phylogenetic analysis of TCE-dechlorinating consortia enriched on a variety of electron donors. Environ Sci Technol. Nov 1; 39(21):8358-68. PMID: 16294874. [PDF]


Johnson DR, Lee PK, Holmes VF, Alvarez-Cohen L (2005) An internal reference technique for accurately quantifying specific mRNAs by real-time PCR with application to the tceA reductive dehalogenase gene. Appl Environ Microbiol. Jul; 71(7):3866-71. PMID: 16000799. PMC1169012. [PDF]

Mahendra S, Alvarez-Cohen L (2005) Pseudonocardia dioxanivorans sp. nov., a novel actinomycete that grows on 1,4-dioxane. Int J Syst Evol Microbiol. Mar; 55(Pt 2):593-8. PMID: 15774630. [PDF]

Sharp JO, Wood TK, Alvarez-Cohen L (2005) Aerobic biodegradation of N-nitrosodimethylamine (NDMA) by axenic bacterial strains. Biotechnol Bioeng. Mar 5; 89(5):608-18. PMID: PMC15672376. [PDF]