Superfund Research Program

Lisa Alvarez-Cohen

University of California-Berkeley
Civil and Environmental Engineering
760 Davis Hall
Berkeley, California 94720-1710
Phone: 510-643-5969
Fax: 510-642-7483
Email: alvarez@ce.berkeley.edu

Projects

• University of California-Berkeley: Administrative Core (2000-2022)
• University of California-Berkeley: Administrative Core (2022-2027)
• University of California-Berkeley: In Situ Destruction of Halogenated Superfund Contaminants With Biological Radical Reactions (2022-2027)
• University of California-Berkeley: Meta-Omics of Microbial Communities Involved in Bioremediation (2000-2017)
• University of California-Berkeley: Metabolic Interactions Supporting Effective TCE Bioremediation under Various Biogeochemical Conditions (2014-2019)
• University of California-Berkeley: Microbial Communities that Bioremediate Chemical Mixtures (2017-2022)
• University of California-Berkeley: Research Translation Core (2006-2022)

Research Briefs

• 305 - Arsenic Complicates Groundwater Bioremediation
• 155 - Assessing Bioremediation of Chloroethenes through Stable Carbon Isotope Fractionation
• 93 - Monitoring In Situ Bioremediation of TCE

Hazardous Waste Sites

Fort Lewis (Landfill No. 5)

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

Idaho National Engineering Laboratory (USDOE)

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

Seal Beach Naval Weapons Station

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

Publications

2023

• Gushgari-Doyle S, Olivares CI, Sun M, Alvarez-Cohen L. 2023. Syntrophic interactions ameliorate arsenic inhibition of solvent-dechlorinating dehalococcoides mccartyi. Environ Sci Technol 57(38):14237-14247. doi:10.1021/acs.est.3c03807 PMID:37695749

2022

• Keren R, Meheust R, Santini JM, Thomas A, West-Roberts J, Banfield JF, Alvarez-Cohen L. 2022. Global genomic analysis of microbial biotransformation of arsenic highlights the importance of arsenic methylation in environmental and human microbiomes. CSBJ 20:559-572. doi:10.1016/j.csbj.2021.12.040
• Yi S, Harding-Marjanovic KC, Houtz EF, Antell E, Olivares CI, Nichiporuk RV, Lavarone AT, Zhuang W, Field JA, Sedlak DL, Alvarez-Cohen L. 2022. Biotransformation of 6:2 fluorotelomer thioether amido sulfonate in aqueous film-forming foams under nitrate-reducing conditions. Environ Sci Technol 56(15):10646-10655. doi:10.1021/acs.est.2c00063 PMID:35861429

2021

• Gushgari-Doyle S, Oremland RS, Keren R, Baesman SM, Banfield JF, Alvarez-Cohen L, Akob DM. 2021. Acetylene-fueled trichloroethene reductive dechlorination in a groundwater enrichment culture. MBio 12:doi:10.1128/mBio.02724-20 PMID:33531396 PMCID:PMC7858054

2020

• Gushgari-Doyle S, Alvarez-Cohen L. 2020. Effects of arsenic on trichloroethene-dechlorination activities of dehalococcoides mccartyi. Environ Sci Technol 54(2):1276-1285. doi:10.1021/acs.est.9b06527 PMID:31913608

2019

• Escalas A, Hale L, Voordeckers JW, Yang Y, Firestone MK, Alvarez-Cohen L, Zhou J. 2019. Microbial functional diversity: From concepts to applications. Ecol Evol 9:12000-12016. doi:10.1002/ece3.5670
• Mao X, Stenuit B, Tremblay J, Yu K, Tringe SG, Alvarez-Cohen L. 2019. Structural dynamics and transcriptomic analysis of dehalococcoides mccartyi within a TCE-Dechlorinating community in a completely mixed flow reactor. Water Res 158:146-156. doi:10.1016/j.watres.2019.04.038

2018

• Lavy A, Keren R, Yu K, Thomas BC, Alvarez-Cohen L, Banfield JF, Ilan M. 2018. A novel Chromatiales bacterium is a potential sulfide oxidizer in multiple orders of marine sponges. Environ Microbiol 20:800-814. doi:10.1111/1462-2920.14013 PMID:29194919 PMCID:PMC5812793
• Yi S, Harding-Marjanovic KC, Houtz EF, Gao Y, Lawrence JE, Nichiporuk RV, Iavarone A, Zhuang W, Field JA, Sedlak DL, Alvarez-Cohen L. 2018. Biotransformation of AFFF component 6:2 fluorotelomer thioether amido sulfonate generates 6:2 fluorotelomer thioether carboxylate under sulfate-reducing conditions. Environ Sci Technol Lett 5:283-288. doi:10.1021/acs.estlett.8b00148 PMID:30705920 PMCID:PMC6350918

2017

• 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
• Mao X, Polasko A, Alvarez-Cohen L. 2017. Effects of sulfate reduction on trichloroethene dechlorination by Dehalococcoides-containing microbial communities. Appl Environ Microbiol 83(8):e03384-16. doi:10.1128/AEM.03384-16 PMID:28159790 PMCID:PMC5377507
• Men Y, Yu K, Baelum J, Gao Y, Tremblay J, Prestat E, Stenuit B, Tringe SG, Jansson J, Zhang T, Alvarez-Cohen L. 2017. Metagenomic and metatranscriptomic analyses reveal the structure and dynamics of a dechlorinating community containing Dehalococcoides mccartyi and corrinoid-providing microorganisms under cobalamin-limited conditions. Appl Environ Microbiol 83(8):e03508-16. doi:10.1128/aem.03508-16 PMID:28188205 PMCID:PMC5377501

2016

• 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

2015

• 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

2014

• 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

2013

• 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
• Mahendra S, Grostern A, Alvarez-Cohen L. 2013. The impact of chlorinated solvent co-contaminants on the biodegradation kinetics of 1,4 dioxane. Chemosphere 91(1):88-92. doi:10.1016/j.chemosphere.2012.10.104 PMID:23237300
• 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
• West KA, Lee PH, Johnson DR, Zinder SH, Alvarez-Cohen L. 2013. Global gene expression of dehalococcoides within a robust dynamic TCE-dechlorinating community under conditions of periodic substrate supply. Biotechnol Bioeng 110(5):1333-41. doi:10.1002/bit.24819 PMID:23280440

2012

• 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
• 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 78(9):3298-3308. doi:10.1128/AEM.00067-12 PMID:22327578 PMCID:PMC3346452
• 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

2011

• 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

2009

• 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.
• Men Y, Harding KC, Feil H, Andersen GL, Zinder SH, Alvarez-Cohen L. 2009. Application of molecular and analytical tools to track enrichment of reductive dechlorination cultures from a TCE-contaminated groundwater site. In: ASM 109th General Meeting. Philadelphia,
• 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.

2008

• Feil H, Men Y, Zinder SH, Andersen GL, Alvarez-Cohen L. 2008. Differential expression by Dehalococcoides ethenogenes 195 growing syntrophically with Desulfovibrio vulgaris Hildenborough or In tri-culture with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense. In: Annual Meeting, December 7-9. Pacific Grove, CA.
• 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, Brodie EL, Macbeth TW, Deeb RA, Sorenson KS, Andersen GL, Alvarez-Cohen L. 2008. From Individuals to community: molecular tools shed lights into the environmentally relevant organisms. In: Selected oral presentation at Remediation of Chlorinated and Recalcitrant Compounds Sixth International Conference. Monterey, CA.
• 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
• Zeng XY, Simonich SL, Robrock KR, Korytar P, Alvarez-Cohen L, Barofsky DF. 2008. Development and validation of a congener specific photodegradation model for PBDEs. Environ Toxicol Chem 27(12):2427-2435. PMID:18613751

2007

• 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
• 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 73(21):6930-6938. doi:10.1128/AEM.01697-07 PMID:17873074 PMCID:PMC2074979

2006

• He J, Holmes VF, Lee PH, Alvarez-Cohen L. 2006. Optimizing growth of dehalococcoides ethenogenes strain 195 in defined medium. In: Proceedings of the 106^th General Meeting of the American Society for Microbiology, May 21 - May 25. Orlando, FL.
• He J, Robrock KR, Alvarez-Cohen L. 2006. Microbial reductive debromination of polybrominated diphenyl ethers (PBDEs). Environ Sci Technol 40(14):4429-4434. PMID:16903281
• 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 106^th 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 106^th 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 106^th 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 106^th 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 106^th 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.

2005

• 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

2004

• 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.

2003

• 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 103^rd 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 103^rd General Meeting of the American Society for Microbiology, May 18-22. Washington, DC.

2002

• 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

2001

• Deeb RA, Hu H, Hanson JR, Scow KM, Alvarez-Cohen L. 2001. Substrate interactions in BTEX and MTBE mixtures by an MTBE-degrading isolate. Environ Sci Technol 35(2):312-317. PMID:11347603

2000

• Chu K, Alvarez-Cohen L. 2000. Treatment of chlorinated solvents by nitrogen-fixing and nitrate-supplied methane oxidizers in columns packed with unsaturated porous media. Environ Sci Technol 34(9):1784-1793.
• Chu K, Song DL, Conrad ME, Alvarez-Cohen L. 2000. Fractionation of stable carbon isotopes during the biodegradation of chlorinated solvents. In: Proceedings of the Second International Conference: Remediation of Chlorinated and Other Recalcitrant Compounds. Monterey, CA.
• Deeb RA, Alvarez-Cohen L. 2000. Aerobic biotransformation of gasoline aromatics in mult-component mixtures. Bioremediat J 4(20:171-176.
• Deeb RA, Hanson JR, Scow KM, Alvarez-Cohen L. 2000. Substrate interactions during the biodegradation of MTBE and BTEX mixtures. In: Proceedings of the Second International Conference: Remediation of Chlorinated and Other Recalcitrant Compounds. Monterey, CA.
• Deeb RA, Nishino SF, Spain JC, Hu H, Scow KM, Alvarez-Cohen L. 2000. MTBE and benzene biodegradation by a bacterial isolate via two independent monooxygenase-initiated pathways. In: Preprints of Extended Abstracts: American Chemical Society Annual Meeting. San Francisco, CA. pp.280-282.
• Deeb RA, Scow KM, Alvarez-Cohen L. 2000. Aerobic MTBE biodegradation: an examination of past studies, current challenges and future research directions. Biodegradation 11(2-3):171-186. PMID:11440243

1999

• Bhupathiraju VK, Hernandez M, Krauter P, Alvarez-Cohen L. 1999. A new direct microscopy based method for evaluating in-situ bioremediation. J Hazard Mater 67(3):299-312. PMID:10370182
• Bhupathiraju VK, Hernandez M, Landfear D, Alvarez-Cohen L. 1999. Application of a tetrazolium dye as an indicator of viability in anaerobic bacteria. J Microbiol Methods 37(3):231-243. PMID:10480267
• Chu K, Alvarez-Cohen L. 1999. Evaluation of toxic effects of aeration and trichloroethylene oxidation on methanotrophic bacteria grown with different nitrogen sources. Appl Environ Microbiol 65(2):766-772. PMID:9925614
• Chu K, Vernalia J, Alvarez-Cohen L. 1999. Evaluation Of Nitrogen Sources For Bioremediation Of Trichloroethylene In Unsaturated Porous Media. In: Proceedings of the International In Situ and On-site Bioreclamation Symposium. San Diego, CA.
• Conrad ME, Templeton AS, Daley PF, Alvarez-Cohen L. 1999. Isotopic evidence for biological controls on migration of petroleum hydrocarbons. Organic Geochemistry 30(8A):843-859.
• Conrad ME, Templeton AS, Daley PF, Alvarez-Cohen L. 1999. Seasonally-induced fluctuations in microbial production and consumption of methane during the bioremediation of aged subsurface refinery contamination. Environ Sci Technol 33(22):4061-4068.
• Deeb RA, Alvarez-Cohen L. 1999. Temperature effects and substrate interactions during the aerobic biotransformation of BTEX mixtures by toluene-enriched consortia and Rhodococcus rhodochrous. Biotechnol Bioeng 62(5):526-536. PMID:10099561
• Deeb RA, Spain JC, Alvarez-Cohen L. 1999. Aerobic metabolism of gasoline aromatics by two Rhodococcus ruber strains. In: Proceedings of the Annual Meeting of the Society for Industrial Microbiology. San Diego, CA.
• Deeb RA, Spain JC, Alvarez-Cohen L. 1999. Mineralization of benzene, toluene, ethylbenzene, m-xylene, and p-xylene by two Rhodococcus species. In: Proceedings of the Annual Meeting of the American Society for Microbiology. Chicago, IL.
• Deeb RA, Spain JC, Alvarez-Cohen L. 1999. Mineralization of BTEX compounds and MTBE in pollutant mixtures by enriched and pure microbial cultures. In: Proceedings of the Fifth International Battelle Symposium on In-situ and On-site Bioremediation. San Diego, CO.
• Richardson RE, Bhupathiraju VK, Song DL, Goulet TA, Alvarez-Cohen L. 1999. Molecular characterization of a TCE-dechlorinating anaerobic mixed culture. In: Proceedings of the Annual Meeting of the American Society for Microbiology. Anaheim, CA.
• Richardson RE, James CA, Alvarez-Cohen L. 1999. Bacterial Rebound in Soils Following Steam Injection: Stimulating PAH Degraders. In: Proceedings of the International In Situ and On-site Bioreclamation Symposium. San Diego, CA.
• Richardson RE, James CA, Alvarez-Cohen L. 1999. Bacterial rebound in soils following steam injection: stimulating PAH degraders. In: Proceedings of the Fifth International Battelle Symposium on In-situ and On-site Bioremediation. San Diego, CO.
• Song DL, Alvarez-Cohen L, Conrad ME, Sorenson KS. 1999. Monitoring of enhanced in-situ bioremediation of trichloroethylene using stable carbon isotopes. In: Proceedings of the American Society for Microbiology Specialty Meeting on Subsurface Microbiology. Vail, CO.

1998

• Alvarez-Cohen L, Conrad ME, Templeton AS, Udell KS, Daley PF, Bhupathiraju VK. 1998. Stable and Radioisotopes for Monitoring Intrinsic Bioremediation of Chlorinated Solvents. In: Proceedings from the First International Conference on Remediation of Chlorinated and Recalcitrant Compounds: Physical, Chemical, and Thermal Technologies. Monterey, CA.
• Bhupathiraju VK, Alvarez-Cohen L. 1998. Developing A Tool For Evaluating In Situ Bioremediation Under Anaerobic Conditions. In: Proceedings of the Annual Meeting of American Society for Microbiology, Atlanta, GA. Atlanta, GA.
• Chu K, Alvarez-Cohen L. 1998. Effect of nitrogen source on growth and trichloroethylene degradation by methane-oxidizing bacteria. Appl Environ Microbiol 64(9):3451-3457. PMID:9726896 PMCID:PMC106746

1997

• Bhupathiraju VK, Alvarez-Cohen L, Conrad ME, Templeton AS, Daley PF, Hernandez M, Holman HN, Hunt JR, Krauter P. 1997. Innovative Techniques for Assessment of Intrinsic Bioremediation at Alameda Naval Air Station. In: Proceedings of the 4^th International In Situ and On-Site Bioremediation Symposium. New Orleans, LA.
• Chang H, Alvarez-Cohen L. 1997. Two-stage methanotrophic bioreactor for the treatment of chlorinated organic wastewater. Water Res 31(8):2026-2036.
• Deeb RA, Alvarez-Cohen L. 1997. The Mineralization of BTEX Mixtures by Environmental Cultures. In: Proceedings of the 4^th International In Situ and On-Site Bioremediation Symposium. New Orleans, LA.

1996

• Chang H, Alvarez-Cohen L. 1996. Biodegradation of individual and multiple chlorinated aliphatic hydrocarbons by methane-oxidizing cultures. Appl Environ Microbiol 62(9):3371-3377. PMID:8795228
• Conrad ME, Templeton AS, Daley PF, Alvarez-Cohen L. 1996. Coupled Methanogenesis And Methane Oxidation Of Petroleum Hydrocarbons. In: Proceedings of the Geological Society of America National Meeting. Denver, CO.

1995

• Chang H, Alvarez-Cohen L. 1995. A model for the cometabolic degradation of chlorinated organics. Environ Sci Technol 29(9):2357-2367. PMID:22280279
• Chang H, Alvarez-Cohen L. 1995. Transformation capacities of chlorinated organics by mixed cultures enriched on methane, propane, toluene or phenol. Biotechnol Bioeng 45:440-449. PMID:18623237