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Global diversity and biogeography of bacterial communities in wastewater treatment plants.

Wu L, Ning D, Zhang B, Li Y, Zhang P, Shan X, Zhang Q, Brown M, Li Z, Van Nostrand JD, Ling F, Xiao N, Zhang Y, Vierheilig J, Wells GF, Yang Y, Deng Y, Tu Q, Wang A; Global Water Microbiome Consortium, Zhang T, He Z, Keller J, Nielsen PH, Alvarez PJJ, Criddle CS, Wagner M, Tiedje JM, He Q, Curtis TP, Stahl DA, Alvarez-Cohen L, Rittmann BE, Wen X, Zhou J.

Nat Microbiol. 2019 Jul;4(7):1183-1195. doi: 10.1038/s41564-019-0426-5. Epub 2019 May 13.


Structural dynamics and transcriptomic analysis of Dehalococcoides mccartyi within a TCE-Dechlorinating community in a completely mixed flow reactor.

Mao X, Stenuit B, Tremblay J, Yu K, Tringe SG, Alvarez-Cohen L.

Water Res. 2019 Jul 1;158:146-156. doi: 10.1016/j.watres.2019.04.038. Epub 2019 Apr 19.


An integrated meta-omics approach reveals substrates involved in synergistic interactions in a bisphenol A (BPA)-degrading microbial community.

Yu K, Yi S, Li B, Guo F, Peng X, Wang Z, Wu Y, Alvarez-Cohen L, Zhang T.

Microbiome. 2019 Feb 6;7(1):16. doi: 10.1186/s40168-019-0634-5.


Biotransformation of AFFF Component 6:2 Fluorotelomer Thioether Amido Sulfonate Generates 6:2 Fluorotelomer Thioether Carboxylate under Sulfate-Reducing Conditions.

Yi S, Harding-Marjanovic KC, Houtz EF, Gao Y, Lawrence JE, Nichiporuk RV, Iavarone AT, Zhuang WQ, Hansen M, Field JA, Sedlak DL, Alvarez-Cohen L.

Environ Sci Technol Lett. 2018 May 8;5(5):283-288. doi: 10.1021/acs.estlett.8b00148. Epub 2018 Apr 4.


Inhibition of anammox by sludge thermal hydrolysis and metagenomic insights.

Gu Z, Li Y, Yang Y, Xia S, Hermanowicz SW, Alvarez-Cohen L.

Bioresour Technol. 2018 Dec;270:46-54. doi: 10.1016/j.biortech.2018.08.132. Epub 2018 Sep 1.


Growth of Dehalococcoides mccartyi species in an autotrophic consortium producing limited acetate.

Ding C, Alvarez-Cohen L, He J.

Biodegradation. 2018 Oct;29(5):487-498. doi: 10.1007/s10532-018-9846-9. Epub 2018 Aug 10.


A novel Chromatiales bacterium is a potential sulfide oxidizer in multiple orders of marine sponges.

Lavy A, Keren R, Yu K, Thomas BC, Alvarez-Cohen L, Banfield JF, Ilan M.

Environ Microbiol. 2018 Feb;20(2):800-814. doi: 10.1111/1462-2920.14013. Epub 2017 Dec 15.


Metagenomic and Metatranscriptomic Analyses Reveal the Structure and Dynamics of a Dechlorinating Community Containing Dehalococcoides mccartyi and Corrinoid-Providing Microorganisms under Cobalamin-Limited Conditions.

Men Y, Yu K, Bælum J, Gao Y, Tremblay J, Prestat E, Stenuit B, Tringe SG, Jansson J, Zhang T, Alvarez-Cohen L.

Appl Environ Microbiol. 2017 Mar 31;83(8). pii: e03508-16. doi: 10.1128/AEM.03508-16. Print 2017 Apr 15.


Effects of Sulfate Reduction on Trichloroethene Dechlorination by Dehalococcoides-Containing Microbial Communities.

Mao X, Polasko A, Alvarez-Cohen L.

Appl Environ Microbiol. 2017 Mar 31;83(8). pii: e03384-16. doi: 10.1128/AEM.03384-16. Print 2017 Apr 15.


Acetylene Fuels TCE Reductive Dechlorination by Defined Dehalococcoides/Pelobacter Consortia.

Mao X, Oremland RS, Liu T, Gushgari S, Landers AA, Baesman SM, Alvarez-Cohen L.

Environ Sci Technol. 2017 Feb 21;51(4):2366-2372. doi: 10.1021/acs.est.6b05770. Epub 2017 Feb 3.


Concomitant Leaching and Electrochemical Extraction of Rare Earth Elements from Monazite.

Maes S, Zhuang WQ, Rabaey K, Alvarez-Cohen L, Hennebel T.

Environ Sci Technol. 2017 Feb 7;51(3):1654-1661. doi: 10.1021/acs.est.6b03675. Epub 2017 Jan 18.


Membrane Complexes of Syntrophomonas wolfei Involved in Syntrophic Butyrate Degradation and Hydrogen Formation.

Crable BR, Sieber JR, Mao X, Alvarez-Cohen L, Gunsalus R, Ogorzalek Loo RR, Nguyen H, McInerney MJ.

Front Microbiol. 2016 Nov 9;7:1795. eCollection 2016.


Effects of Aqueous Film-Forming Foams (AFFFs) on Trichloroethene (TCE) Dechlorination by a Dehalococcoides mccartyi-Containing Microbial Community.

Harding-Marjanovic KC, Yi S, Weathers TS, Sharp JO, Sedlak DL, Alvarez-Cohen L.

Environ Sci Technol. 2016 Apr 5;50(7):3352-61. doi: 10.1021/acs.est.5b04773. Epub 2016 Mar 21.


Assembly of the Caenorhabditis elegans gut microbiota from diverse soil microbial environments.

Berg M, Stenuit B, Ho J, Wang A, Parke C, Knight M, Alvarez-Cohen L, Shapira M.

ISME J. 2016 Aug;10(8):1998-2009. doi: 10.1038/ismej.2015.253. Epub 2016 Jan 22.


Perfluoroalkyl Acids Inhibit Reductive Dechlorination of Trichloroethene by Repressing Dehalococcoides.

Weathers TS, Harding-Marjanovic K, Higgins CP, Alvarez-Cohen L, Sharp JO.

Environ Sci Technol. 2016 Jan 5;50(1):240-8. doi: 10.1021/acs.est.5b04854. Epub 2015 Dec 21.


Bioleaching of rare earth elements from monazite sand.

Brisson VL, Zhuang WQ, Alvarez-Cohen L.

Biotechnol Bioeng. 2016 Feb;113(2):339-48. doi: 10.1002/bit.25823. Epub 2015 Sep 9.


Structure and distribution of inorganic components in the cake layer of a membrane bioreactor treating municipal wastewater.

Zhou L, Xia S, Alvarez-Cohen L.

Bioresour Technol. 2015 Nov;196:586-91. doi: 10.1016/j.biortech.2015.08.026. Epub 2015 Aug 14.


Aerobic Biotransformation of Fluorotelomer Thioether Amido Sulfonate (Lodyne) in AFFF-Amended Microcosms.

Harding-Marjanovic KC, Houtz EF, Yi S, Field JA, Sedlak DL, Alvarez-Cohen L.

Environ Sci Technol. 2015 Jul 7;49(13):7666-74. doi: 10.1021/acs.est.5b01219. Epub 2015 Jun 23.


Recovery of critical metals using biometallurgy.

Zhuang WQ, Fitts JP, Ajo-Franklin CM, Maes S, Alvarez-Cohen L, Hennebel T.

Curr Opin Biotechnol. 2015 Jun;33:327-35. doi: 10.1016/j.copbio.2015.03.019. Epub 2015 Apr 22. Review.


High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats.

Zhou J, He Z, Yang Y, Deng Y, Tringe SG, Alvarez-Cohen L.

MBio. 2015 Jan 27;6(1). pii: e02288-14. doi: 10.1128/mBio.02288-14. Review.


Efficient metabolic exchange and electron transfer within a syntrophic trichloroethene-degrading coculture of Dehalococcoides mccartyi 195 and Syntrophomonas wolfei.

Mao X, Stenuit B, Polasko A, Alvarez-Cohen L.

Appl Environ Microbiol. 2015 Mar;81(6):2015-24. doi: 10.1128/AEM.03464-14. Epub 2015 Jan 9.


Development of a fluorescence-activated cell sorting method coupled with whole genome amplification to analyze minority and trace Dehalococcoides genomes in microbial communities.

Lee PK, Men Y, Wang S, He J, Alvarez-Cohen L.

Environ Sci Technol. 2015 Feb 3;49(3):1585-93. doi: 10.1021/es503888y. Epub 2015 Jan 21.


A bioassay for the detection of benzimidazoles reveals their presence in a range of environmental samples.

Crofts TS, Men Y, Alvarez-Cohen L, Taga ME.

Front Microbiol. 2014 Nov 13;5:592. doi: 10.3389/fmicb.2014.00592. eCollection 2014.


Identification of specific corrinoids reveals corrinoid modification in dechlorinating microbial communities.

Men Y, Seth EC, Yi S, Crofts TS, Allen RH, Taga ME, Alvarez-Cohen L.

Environ Microbiol. 2015 Dec;17(12):4873-84. doi: 10.1111/1462-2920.12500. Epub 2014 Jun 2.


Incomplete Wood-Ljungdahl pathway facilitates one-carbon metabolism in organohalide-respiring Dehalococcoides mccartyi.

Zhuang WQ, Yi S, Bill M, Brisson VL, Feng X, Men Y, Conrad ME, Tang YJ, Alvarez-Cohen L.

Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6419-24. doi: 10.1073/pnas.1321542111. Epub 2014 Apr 14.


Sustainable growth of Dehalococcoides mccartyi 195 by corrinoid salvaging and remodeling in defined lactate-fermenting consortia.

Men Y, Seth EC, Yi S, Allen RH, Taga ME, Alvarez-Cohen L.

Appl Environ Microbiol. 2014 Apr;80(7):2133-41. doi: 10.1128/AEM.03477-13. Epub 2014 Jan 24.


Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill.

Mason OU, Scott NM, Gonzalez A, Robbins-Pianka A, Bælum J, Kimbrel J, Bouskill NJ, Prestat E, Borglin S, Joyner DC, Fortney JL, Jurelevicius D, Stringfellow WT, Alvarez-Cohen L, Hazen TC, Knight R, Gilbert JA, Jansson JK.

ISME J. 2014 Jul;8(7):1464-75. doi: 10.1038/ismej.2013.254. Epub 2014 Jan 23.


Oxidation of the cyclic ethers 1,4-dioxane and tetrahydrofuran by a monooxygenase in two Pseudonocardia species.

Sales CM, Grostern A, Parales JV, Parales RE, Alvarez-Cohen L.

Appl Environ Microbiol. 2013 Dec;79(24):7702-8. doi: 10.1128/AEM.02418-13. Epub 2013 Oct 4.


Effects of varying growth conditions on stable carbon isotope fractionation of trichloroethene (TCE) by tceA-containing Dehalococcoides mccartyi strains.

Harding KC, Lee PK, Bill M, Buscheck TE, Conrad ME, Alvarez-Cohen L.

Environ Sci Technol. 2013;47(21):12342-50. doi: 10.1021/es402617q. Epub 2013 Oct 15.


RubisCO-based CO2 fixation and C1 metabolism in the actinobacterium Pseudonocardia dioxanivorans CB1190.

Grostern A, Alvarez-Cohen L.

Environ Microbiol. 2013 Nov;15(11):3040-53. doi: 10.1111/1462-2920.12144. Epub 2013 May 13.


Characterization of four TCE-dechlorinating microbial enrichments grown with different cobalamin stress and methanogenic conditions.

Men Y, Lee PK, Harding KC, Alvarez-Cohen L.

Appl Microbiol Biotechnol. 2013 Jul;97(14):6439-50. doi: 10.1007/s00253-013-4896-8. Epub 2013 May 3.


Isolation of two new Dehalococcoides mccartyi strains with dissimilar dechlorination functions and their characterization by comparative genomics via microarray analysis.

Lee PK, Cheng D, West KA, Alvarez-Cohen L, He J.

Environ Microbiol. 2013 Aug;15(8):2293-305. doi: 10.1111/1462-2920.12099. Epub 2013 Mar 11.


Global gene expression of Dehalococcoides within a robust dynamic TCE-dechlorinating community under conditions of periodic substrate supply.

West KA, Lee PK, Johnson DR, Zinder SH, Alvarez-Cohen L.

Biotechnol Bioeng. 2013 May;110(5):1333-41. doi: 10.1002/bit.24819. Epub 2013 Feb 9.


The impact of chlorinated solvent co-contaminants on the biodegradation kinetics of 1,4-dioxane.

Mahendra S, Grostern A, Alvarez-Cohen L.

Chemosphere. 2013 Mar;91(1):88-92. doi: 10.1016/j.chemosphere.2012.10.104. Epub 2012 Dec 10.


Versatility in corrinoid salvaging and remodeling pathways supports corrinoid-dependent metabolism in Dehalococcoides mccartyi.

Yi S, Seth EC, Men YJ, Stabler SP, Allen RH, Alvarez-Cohen L, Taga ME.

Appl Environ Microbiol. 2012 Nov;78(21):7745-52. doi: 10.1128/AEM.02150-12. Epub 2012 Aug 24.


Metagenomic analysis of a stable trichloroethene-degrading microbial community.

Brisson VL, West KA, Lee PK, Tringe SG, Brodie EL, Alvarez-Cohen L.

ISME J. 2012 Sep;6(9):1702-14. doi: 10.1038/ismej.2012.15. Epub 2012 Mar 1.


Glyoxylate metabolism is a key feature of the metabolic degradation of 1,4-dioxane by Pseudonocardia dioxanivorans strain CB1190.

Grostern A, Sales CM, Zhuang WQ, Erbilgin O, Alvarez-Cohen L.

Appl Environ Microbiol. 2012 May;78(9):3298-308. doi: 10.1128/AEM.00067-12. Epub 2012 Feb 10.


Global transcriptomic and proteomic responses of Dehalococcoides ethenogenes strain 195 to fixed nitrogen limitation.

Lee PK, Dill BD, Louie TS, Shah M, Verberkmoes NC, Andersen GL, Zinder SH, Alvarez-Cohen L.

Appl Environ Microbiol. 2012 Mar;78(5):1424-36. doi: 10.1128/AEM.06792-11. Epub 2011 Dec 16.


Phylogenetic microarray analysis of a microbial community performing reductive dechlorination at a TCE-contaminated site.

Lee PK, Warnecke F, Brodie EL, Macbeth TW, Conrad ME, Andersen GL, Alvarez-Cohen L.

Environ Sci Technol. 2012 Jan 17;46(2):1044-54. doi: 10.1021/es203005k. Epub 2011 Dec 27.


Selective utilization of exogenous amino acids by Dehalococcoides ethenogenes strain 195 and its effects on growth and dechlorination activity.

Zhuang WQ, Yi S, Feng X, Zinder SH, Tang YJ, Alvarez-Cohen L.

Appl Environ Microbiol. 2011 Nov;77(21):7797-803. doi: 10.1128/AEM.05676-11. Epub 2011 Sep 2.


Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: global transcriptomic and proteomic analyses.

Men Y, Feil H, Verberkmoes NC, Shah MB, Johnson DR, Lee PK, West KA, Zinder SH, Andersen GL, Alvarez-Cohen L.

ISME J. 2012 Feb;6(2):410-21. doi: 10.1038/ismej.2011.111. Epub 2011 Sep 1.


Genome sequence of the 1,4-dioxane-degrading Pseudonocardia dioxanivorans strain CB1190.

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.

J Bacteriol. 2011 Sep;193(17):4549-50. doi: 10.1128/JB.00415-11. Epub 2011 Jul 1.


Comparative genomics of two newly isolated Dehalococcoides strains and an enrichment using a genus microarray.

Lee PK, Cheng D, Hu P, West KA, Dick GJ, Brodie EL, Andersen GL, Zinder SH, He J, Alvarez-Cohen L.

ISME J. 2011 Jun;5(6):1014-24. doi: 10.1038/ismej.2010.202. Epub 2011 Jan 13.


Biphenyl and ethylbenzene dioxygenases of Rhodococcus jostii RHA1 transform PBDEs.

Robrock KR, Mohn WW, Eltis LD, Alvarez-Cohen L.

Biotechnol Bioeng. 2011 Feb;108(2):313-21. doi: 10.1002/bit.22952.


Application of a congener-specific debromination model to study photodebromination, anaerobic microbial debromination, and FE0 reduction of polybrominated diphenyl ethers.

Zeng X, Massey Simonich SL, Robrock KR, Korytár P, Alvarez-Cohen L, Barofsky DF.

Environ Toxicol Chem. 2010 Apr;29(4):770-8. doi: 10.1002/etc.119.


Bacterial community structure in geographically distributed biological wastewater treatment reactors.

Xia S, Duan L, Song Y, Li J, Piceno YM, Andersen GL, Alvarez-Cohen L, Moreno-Andrade I, Huang CL, Hermanowicz SW.

Environ Sci Technol. 2010 Oct 1;44(19):7391-6. doi: 10.1021/es101554m.


Carbon flow of heliobacteria is related more to clostridia than to the green sulfur bacteria.

Tang KH, Feng X, Zhuang WQ, Alvarez-Cohen L, Blankenship RE, Tang YJ.

J Biol Chem. 2010 Nov 5;285(45):35104-12. doi: 10.1074/jbc.M110.163303. Epub 2010 Aug 31.


Functional characterization of propane-enhanced N-nitrosodimethylamine degradation by two actinomycetales.

Sharp JO, Sales CM, Alvarez-Cohen L.

Biotechnol Bioeng. 2010 Dec 15;107(6):924-32. doi: 10.1002/bit.22899.


Evidence for nitrogen fixation by "Dehalococcoides ethenogenes" strain 195.

Lee PK, He J, Zinder SH, Alvarez-Cohen L.

Appl Environ Microbiol. 2009 Dec;75(23):7551-5. doi: 10.1128/AEM.01886-09. Epub 2009 Oct 9. Review.


Influence of trace erythromycin and eryhthromycin-H2O on carbon and nutrients removal and on resistance selection in sequencing batch reactors (SBRs).

Fan C, Lee PK, Ng WJ, Alvarez-Cohen L, Brodie EL, Andersen GL, He J.

Appl Microbiol Biotechnol. 2009 Nov;85(1):185-95. doi: 10.1007/s00253-009-2201-7.

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