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Project Publications: University of California-Berkeley: Meta-Omics of Microbial Communities Involved in Bioremediation

Superfund Research Program

Meta-Omics of Microbial Communities Involved in Bioremediation

Project Leader: Lisa Alvarez-Cohen
Grant Number: P42ES004705
Funding Period: 2000-2017
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  • Mao X, Oremland RS, Liu T, Gushgari-Doyle S, Landers AA, Baesman SM, Alvarez-Cohen L. 2017. Acetylene fuels TCE reductive dechlorination by defined Dehalococcoides/Pelobacter consortia. Environ Sci Technol 51(4):2366-2372. doi:10.1021/acs.est.6b05770 PMID:28075122


  • 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 10(8):1998-2009. doi:10.1038/ismej.2015.253 PMID:26800234 PMCID:PMC5029150
  • Brisson VL, Zhuang WQ, Alvarez-Cohen L. 2016. Bioleaching of rare earth elements from monazite sand. Biotechnol Bioeng 113(2):339-348. doi:10.1002/bit.25823 PMID:26332985
  • 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 7:1795. doi:10.3389/fmicb.2016.01795 PMID:27881975 PMCID:PMC5101538
  • Harding KC, Yi S, Weathers T, 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 50(7):3352-3361. doi:10.1021/acs.est.5b04773 PMID:26894610
  • Weathers T, Harding KC, Higgins CP, Alvarez-Cohen L, Sharp JO. 2016. Perfluoroalkyl acids inhibit reductive dechlorination of trichloroethene by repressing Dehalococcoides. Environ Sci Technol 50(1):240-248. doi:10.1021/acs.est.5b04854 PMID:26636352


  • Lee PH, Men Y, Wang S, He J, Alvarez-Cohen L. 2015. Development of a fluorescence-activated cell sorting method coupled with whole genome amplification to analyze minority and trace Dehalococcoides genomes in microbial communities. Environ Sci Technol 49(3):1585-1593. doi:10.1021/es503888y PMID:25565465
  • 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 81(6):2015-2024. doi:10.1128/AEM.03464-14 PMID:25576615 PMCID:PMC4345365
  • Men Y, Seth EC, Shan Y, Crofts TS, Allen RH, Taga ME, Alvarez-Cohen L. 2015. Identification of specific corrinoids reveals corrinoid modification in dechlorinating microbial communities. Environ Microbiol 17(12):4873-4884. doi:10.1111/1462-2920.12500 PMID:24803319 PMCID:PMC4942503
  • 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 6(1):doi:10.1128/mBio.02288-14 PMID:25626903 PMCID:PMC4324309
  • Zhuang W, Fitts JP, Ajo-Franklin CM, Maes S, Alvarez-Cohen L, Hennebel T. 2015. Recovery of critical metals using biometallurgy. Curr Opin Biotechnol 33:327-335. doi:10.1016/j.copbio.2015.03.019 PMID:25912797 PMCID:PMC4458433


  • 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 5:592. doi:10.3389/fmicb.2014.00592 PMID:25431570 PMCID:PMC4230183
  • Mason O, Scott N, Gonzalez A, Robbins-Pianka A, Bælum J, Kimbrel J, Bouskill N, Prestat E, Borglin S, Joyner D, Fortney J, Jurelevicius D, Stringfellow WT, Alvarez-Cohen L, Hazen T, Knight R, Gilbert J, Jansson J. 2014. Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. ISME J 8(7):1464-1475. doi:10.1038/ismej.2013.254 PMID:24451203 PMCID:PMC4069396
  • 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 80(7):2133-2141. doi:10.1128/aem.03477-13 PMID:24463969 PMCID:PMC3993147
  • Zhuang W, Yi S, Bill M, Brisson VL, Feng X, Men Y, Conrad ME, Tang YJ, Alvarez-Cohen L. 2014. Incomplete Wood-Ljungdahl pathway facilitates one-carbon metabolism in organohalide-respiring Dehalococcoides mccartyi. Proc Natl Acad Sci U S A 111(17):6419-6424. doi:10.1073/pnas.1321542111 PMID:24733917 PMCID:PMC4035967


  • Grostern A, Alvarez-Cohen L. 2013. RubisCO-based CO2 fixation and C1 metabolism in the actinobacterium Pseudonocardia dioxanivorans CB1190. Environ Microbiol 15(11):3040-3053. doi:10.1111/1462-2920.12144 PMID:23663433
  • Lee PH, Cheng D, West KA, Alvarez-Cohen L, He J. 2013. Isolation of two new Dehalococcoides mccartyi strains with dissimilar dechlorination functions and their characterization by comparative genomics via microarray analysis. Environ Microbiol 15(8):2293-2305. doi:10.1111/1462-2920.12099 PMID:23480482
  • Men Y, Lee PH, Harding KC, Alvarez-Cohen L. 2013. Characterization of four TCE-dechlorinating microbial enrichments grown with different cobalamin stress and methanogenic conditions. Appl Microbiol Biotechnol 97(14):6439-6450. doi:10.1007/s00253-013-4896-8 PMID:23640361
  • Sales CM, 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 79(24):7702-7708. doi:10.1128/aem.02418-13 PMID:24096414 PMCID:PMC3837796


  • Brisson VL, West KA, Lee PH, Tringe SG, Brodie EL, Alvarez-Cohen L. 2012. Metagenomic analysis of a stable trichloroethene-degrading microbial community. ISME J 6:1702-1714. doi:10.1038/ismej.2012.15 PMID:22378537 PMCID:PMC3498913
  • Lee PH, Dill BD, Louie TS, Shah M, VerBerkmoes NC, Anderson GL, Zinder SH, Alvarez-Cohen L. 2012. Global transcriptomic and proteomic responses of Dehalococcoides ethenogenes strain 195 to fixed nitrogen limitation. Appl Environ Microbiol 78(5):1424-1436. doi:10.1128/AEM.06792-11 PMID:22179257 PMCID:PMC3294477
  • Lee PH, Warnecke F, Brodie EL, Macbeth TW, Conrad ME, Andersen GL, Alvarez-Cohen L. 2012. Phylogenetic microarray analysis of a microbial community performing reductive dechlorination at a TCE-contaminated site. Environ Sci Technol 46:1044-1054. doi:10.1021/es203005k PMID:22091783 PMCID:PMC3461955
  • Men Y, Feil H, VerBerkmoes NC, Shah M, Johnson DR, Lee PH, 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 6:410-421. doi:10.1038/ismej.2011.111 PMID:21881617 PMCID:PMC3260503
  • Yi S, Seth EC, Men Y, 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 78(21):7745-7752. doi:10.1128/aem.02150-12 PMID:22923412 PMCID:PMC3485714


  • Lee PH, 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 5(6):1014-1024. doi:10.1038/ismej.2010.202 PMID:21228894 PMCID:PMC3131851
  • Sales CM, Mahendra S, Grostern A, Parales RE, Goodwin LA, Woyke T, Nolan M, Lapidus A, Chertkov O, Ovchinnikova G, Sczyrba A, Alvarez-Cohen L. 2011. Genome sequence of the 1,4-dioxane-degrading Pseudonocardia dioxanivoransStrain CB1190. J Bacteriol 193(17):4549-4550. doi:10.1128/JB.00415-11 PMID:21725009 PMCID:PMC3165535
  • Zhuang WQ, Yi S, Zinder SH, Feng X, Tang YJ, Alvarez-Cohen L. 2011. Selective utilization of exogenous amino acids by Dehalococcoides ethenogenes strain 195 and its effects on growth and dechlorination activity. Appl Environ Microbiol 77:7797-7803. doi:10.1128/aem.05676-11 PMID:21890673 PMCID:PMC3209135


  • Alvarez-Cohen L, Tang YJ, Yi S, Zhuang W, Zinder SH, Keasling JD. 2009. Investigation of carbon metabolism in "Dehalococcoides ethenogenes" strain 195 by use of isotopomer and transcriptomic analyses. J Bacteriol 191(16):5224-5231. doi:10.1128/JB.00085-09 PMID:19525347 PMCID:PMC2725585
  • Johnson DR, Nemir A, Andersen GL, Zinder S, Alvarez-Cohen L. 2009. Transcriptomic microarray analysis of corrinoid responsive genes in Dehalococcoides ethenogenes strain 195. FEMS Microbiol Lett 294(2):198-206. doi:10.1111/j.1574-6968.2009.01569.x PMID:19341394
  • Lee PH, He J, Zinder S, Alvarez-Cohen L. 2009. Evidence for nitrogen fixation by "Dehalococcoides ethenogenes" strain 195. Appl Environ Microbiol 75(23):7551-7555. doi:10.1128/AEM.01886-09 PMID:19820162 PMCID:PMC2786412
  • Lee PH, VerBerkmoes NC, Andersen GL, Zinder SH, Alvarez-Cohen L. 2009. "Transcriptomic and proteomic analyses of Dehalococcoides ethenogenes Strain 195 under nitrogen limitation". In: 109th general meeting of American Society for Microbiology. Philadelphia, PA.
  • Robrock KR, Coelhan M, Sedlak DL, Alvarez-Cohen L. 2009. Aerobic biotransformation of polybrominated diphenyl ethers (PBDEs) by bacterial isolates. Environ Sci Technol 43(15):5705-11. doi:10.1021/es900411k PMID:19731666 PMCID:PMC4288821
  • Sales CM, Sharp JO, Alvarez-Cohen L. 2009. "Identification of genes involved in propane-enhanced biotransformation of N-Nltrosodimethylamine (NOMA) in two actlnomycetes". In: 109th general meeting of American Society for Microbiology. Philadelphia, PA.
  • Zhuang W, Yi S, Tang YJ, Zinder S, Keasling JD, Alvarez-Cohen L. 2009. Carbon Metabolism in "Dehalococcoides ethenogenes" strain 195. In: 109th general meeting of American Society for Microbiology. Philadelphia, PA.


  • 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 74(9):2864-2872. doi:10.1128/AEM.02208-07 PMID:18310438 PMCID:PMC2394897
  • Lee PH, Macbeth TW, Sorenson KS, 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 74(9):2728-2739. doi:10.1128/AEM.02199-07 PMID:18326677 PMCID:PMC2394903
  • Robrock KR, Korytar P, Alvarez-Cohen L. 2008. Pathways for the anaerobic microbial debromination of polybrominated diphenyl ethers. Environ Sci Technol 42(8):2845-52. doi:10.1021/es0720917 PMID:18497133
  • West K, Johnson DR, Hu P, DeSantis TZ, Brodie EL, Lee PH, Feil H, Andersen GL, Zinder S, Alvarez-Cohen L. 2008. Comparative genomics of "Dehalococcoides ethenogenes" 195 and an enrichment culture containing unsequenced "Dehalococcoides" strains. Appl Environ Microbiol 74(11):3533-3540. doi:10.1128/AEM.01835-07 PMID:18359838 PMCID:PMC2423027


  • He J, Holmes VF, Lee PH, Alvarez-Cohen L. 2007. Influence of vitamin B-12 and cocultures on the growth of Dehalococcoides isolates in defined medium. Appl Environ Microbiol 73(9):2847-2853. PMID:17337553
  • Lee PH, Conrad ME, Alvarez-Cohen L. 2007. Stable carbon isotope fractionation of chloroethenes by dehalorespiring isolates. Environ Sci Technol 41(12):4277-85. PMID:17626425


  • He J, Holmes VF, Lee PH, Alvarez-Cohen L. 2006. Optimizing growth of dehalococcoides ethenogenes strain 195 in defined medium. In: Proceedings of the 106th General Meeting of the American Society for Microbiology, May 21 - May 25. Orlando, FL.
  • Holmes VF, He J, Lee PH, Alvarez-Cohen L. 2006. Discrimination of multiple dehalococcoides strains in a TCE enrichment by quantification of their reductive dehalogenase genes. Appl Environ Microbiol 72(9):5877-5883. PMID:16957207
  • Johnson DR, He J, Hu P, Andersen GL, Zinder SH, Alvarez-Cohen L. 2006. Whole-genome transcription analysis of dehalococcoides ethenogenis strain 195 reveals a cobalamin ( vitamin B12) regulon. In: Proceedings of the 106th General Meeting of the American Society for Microbiology, May 21 - May 25. Orlando, FL.
  • Johnson DR, He J, Lee PH, Brodie EL, Hu P, Andersen GL, Zinder SH, Alvarez-Cohen L. 2006. Effect of exposure to cell-free spent media from different reductive dechlorinating mixed cultures on whole-genome transcription in dehalococcoides ethenogenes strain 195. In: Proceedings of the 106th General Meeting of the American Society for Microbiology, May 21 - May 25. Orlando, FL.
  • Johnson DR, He J, Lee PH, DeSantis TZ, Hu P, Andersen GL, Zinder SH, Alvarez-Cohen L. 2006. Comparative Transcriptomics of Dehalococcoides ethenognenes Strain 195 and Dehalococcoides sp. Strain BAV1. In: Proceedings of the 106th General Meeting of the American Society for Microbiology, May 21 - May 25. Orlando, FL.
  • Lee PH, Conrad ME, Alvarez-Cohen L. 2006. Stable carbon isotope fracionation of chloroethenes by dehalogenating isolates. In: Proceedings of the 106th General Meeting of the American Society for Microbiology, May 21 - May 25. Orlando, FL.
  • Lee PH, 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 72(9):6161-6168. doi:10.1128/AEM.01070-06 PMID:16957242 PMCID:PMC1563655
  • Mahendra S, Alvarez-Cohen L. 2006. Kinetics of 1,4-dioxane biodegradation by monooxygenase-expressing bacteria. Environ Sci Technol 40(17):5435-42. PMID:16999122
  • Rahm BG, chauhan S, Holmes VF, Macbeth TW, Sorenson KS, Alvarez-Cohen L. 2006. Molecular characterization of microbial populations at two sites with differing reductive dechlorination abilities. Biodegradation 17(6):523-534. doi:10.1007/s10532-005-9023-9 PMID:16477354
  • Robrock KR, He J, Korytar P, de Boer J, Alvarez-Cohen L. 2006. Degradation of polybrominated diphenyl ethers by dehalococcoides species. In: Proceedings of the 106th General Meeting of the American Society for Microbiology, May 21 - May 25. Orlando, FL.
  • Templeton AS, Chu K, Alvarez-Cohen L, Conrad ME. 2006. Variable carbon isotope fractionation expressed by aerobic methane-oxidizing bacteria. Geochim Cosmochim Acta 70(7):1739-1752.


  • Johnson DR, Lee PH, 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 71(7):3866-3871. doi:10.1128/AEM.71.7.3866-3871.2005 PMID:16000799 PMCID:PMC1169012
  • Johnson DR, Lee PH, Holmes VF, Fortin AC, Alvarez-Cohen L. 2005. Transcriptional expression of the tceA gene in a dehalococcoides-containing microbial enrichment. Appl Environ Microbiol 71(11):7145-7151. PMID:16269753
  • Mahendra S, Alvarez-Cohen L. 2005. Pseudonocardia dioxanivorans sp nov, a novel actinomycete that grows on 1,4-dioxane. Int J Syst Evol Microbiol 55(Pt2):593-598. doi:10.1099/ijs.0.63085-0 PMID:15774630
  • Sharp JO, Wood TK, Alvarez-Cohen L. 2005. Aerobic biodegradation of N-nitrosodimethylamine (NDMA) by axenic bacterial strains. Biotechnol Bioeng 89(5):608-618. PMID:15672376


  • Chu K, Mahendra S, Song DL, Conrad ME, Alvarez-Cohen L. 2004. Stable carbon isotope fractionation during aerobic biodegradation of chlorinated ethenes. Environ Sci Technol 38(11):3126-3130. PMID:15224745
  • French JE, Rossi A, Kirk T, Blackwelder D, Sorenson KS, Rahm BG, Alvarez-Cohen L, Le S, Pound M, Tamashiro P. 2004. Phased in situ Biostimulation/Bioaugmentation Pilot Testing in a Coastal Aquifer. In: Seventh International Symposium on in situ and on-site Bioremediation, 2004, Vol.7. Orlando, FL.


  • Alvarez-Cohen L, Conrad ME. 2003. The Application of Molecular and Isotopic Techniques to Track Reductively Dechlorinating Microbial Communities. In: US-Vietnam Scientific Workshop on Dioxin Screening, Remediation Methodologies and Site Characterization. Hanoi, Viet Nam.
  • Mahendra S, Alvarez-Cohen L. 2003. Aerobic Biodegradation of 1,4-Dioxane. In: Proceedings of the 103rd General Meeting of the American Society for Microbiology, May 18-22. Washington, DC.
  • Mitch WA, Sharp JO, Rhodes Trussell R, Valentine RL, Alvarez-Cohen L, Sedlak DL. 2003. N-nitrosodimethylamine (NDMA) as a drinking water contaminant: a review. Environ Eng Sci 20(5):389-404.
  • Rahm BG, Fortin AC, Holmes VF, Wu C, Richardson RE, Alvarez-Cohen L. 2003. Application of Real-Time PCR to Quantify Reductive Dechlorination of TCE. In: Proceedings of the 103rd General Meeting of the American Society for Microbiology, May 18-22. Washington, DC.


  • Bhupathiraju VK, Krauter P, Holman HN, Conrad ME, Daley PF, Templeton AS, Hunt JR, Hernandez M, Alvarez-Cohen L. 2002. Assessment of in-situ bioremediation at a refinery waste-contaminated site and an aviation gasoline contaminated site. Biodegradation 13(2):79-90. PMID:12449311
  • Richardson RE, Bhupathiraju VK, Song DL, Goulet TA, Alvarez-Cohen L. 2002. Phylogenetic characterization of microbial communities that reductively dechlorinate TCE based upon a combination of molecular techniques. Environ Sci Technol 36(12):2652-2662. PMID:12099461
  • Richardson RE, James CA, Bhupathiraju VK, Alvarez-Cohen L. 2002. Microbial activity in soils following steam treatment. Biodegradation 13(4):285-295. PMID:12521292
  • Song DL, Conrad ME, Sorenson KS, Alvarez-Cohen L. 2002. Stable carbon isotope fractionation during enhanced in situ bioremediation of trichloroethene. Environ Sci Technol 36(10):2262-2268. PMID:12038839
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