Skip Navigation

Search Results for Most Frequently Published Journals (Superfund Research Program)

Superfund Research Program

Search Results

Applied and Environmental Microbiology (137 articles)



  • Mutter TY, Zylstra GJ. 2021. Differential roles of three different upper pathway meta ring cleavage product hydrolases in the degradation of dibenzo-p-dioxin and dibenzofuran by Sphingomonas wittichii strain RW1. Appl Environ Microbiol 87:doi:10.1128/AEM.01067-21 PMID:34469199 PMCID:PMC8552877
  • Mutter TY, Zylstra GJ. 2021. Separate upper pathway ring cleavage dioxygenases are required for growth of Sphingomonas wittichii strain RW1 on dibenzofuran and dibenzo-p-dioxin. Appl Environ Microbiol 87:doi:10.1128/AEM.02464-20 PMID:33741618


  • Kushwaha P, Neilson JW, Barberan A, Chen Y, Fontana CG, Butterfield BJ, Maier RM. 2020. Arid ecosystem vegetation canopy-gap dichotomy: Influence on soil microbial composition and nutrient cycling functional potential. Appl Environ Microbiol 87(5):doi:10.1128/AEM.02780-20 PMID:33310716 (ahead of print)


  • 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
  • Vogtmann E, Chen J, Kibriya MG, Chen Y, Islam T, Eunes M, Ahmed A, Naher J, Rahman A, Amir A, Shi J, Abnet CC, Nelson H, Knight R, Chia N, Ahsan H, Sinha R. 2017. Comparison of fecal collection methods for microbiota studies in Bangladesh. Appl Environ Microbiol 83(10):e00361-17. doi:10.1128/aem.00361-17 PMID:28258145 PMCID:PMC5411505


  • 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
  • Rodgers-Vieira EA, Zhang Z, Adrion AC, Gold A, Aitken MD. 2015. Identification of anthraquinone-degrading bacteria in soil contaminated with polycyclic aromatic hydrocarbons. Appl Environ Microbiol 81(11):3775-3781. doi:10.1128/AEM.00033-15 PMID:25819957 PMCID:PMC4421061


  • Cologgi DL, Speers AM, Bullard BA, Kelly SD, Reguera G. 2014. Enhanced uranium immobilization and reduction by Geobacter sulfurreducens biofilms. Appl Environ Microbiol 80(21):6638-6646. doi:10.1128/AEM.02289-14 PMID:25128347 PMCID:PMC4249037
  • Gutierrez T, Rhodes G, Mishamandani S, Berry D, Whitman WB, Nichols PD, Semple KT, Aitken MD. 2014. Polycyclic aromatic hydrocarbon degradation of phytoplankton-associated Arenibacter spp and description of Arenibacter algicola sp nov, an aromatic hydrocarbon-degrading bacterium. Appl Environ Microbiol 80(2):618-628. doi:10.1128/AEM.03104-13 PMID:24212584 PMCID:PMC3911095
  • 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


  • Geszvain K, McCarthy JK, Tebo BM. 2013. Elimination of manganese (II, III) oxidation in Pseudomonas putida GB-1 by a double knockout of two putative multicopper oxidase genes. Appl Environ Microbiol 79(1):357-366. doi:10.1128/aem.01850-12 PMID:23124227 PMCID:PMC3536112
  • Gutierrez T, Green DH, Nichols PD, Whitman WB, Semple KT, Aitken MD. 2013. Polycyclovorans algicola gen nov, sp nov, an aromatic-hydrocarbon-degrading marine bacterium found associated with laboratory cultures of marine phytoplankton. Appl Environ Microbiol 79(1):205-214. doi:10.1128/AEM.02833-12 PMID:23087039 PMCID:PMC3536080
  • Rhodes AN, Fulthorpe RR, Tiedje JM. 2013. Probing the functional diversity of global pristine soil communities with 3-chlorobenzoate reveals that communities of generalists dominate catabolic transformation. Appl Environ Microbiol 79(22):6932-6940. doi:10.1128/AEM.01905-13 PMID:23995940 PMCID:PMC3811530
  • 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


  • 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
  • Gutierrez T, Aitken MD, Nichols PD, Whitman WB. 2012. Porticoccus hydrocarbonoclasticus sp nov, an aromatic hydrocarbon-degrading bacterium identified in laboratory cultures of marine phytoplankton. Appl Environ Microbiol 78(3):628-637. doi:10.1128/AEM.06398-11 PMID:22139001 PMCID:PMC3264135
  • Hartmann EM, Badalamenti JP, Krajmalnik-Brown R, Halden RU. 2012. Quantitative PCR for tracking the megaplasmid-borne biodegredation potential of a model sphingomonad. Appl Environ Microbiol 78:4493-4496. doi:10.1128/aem.00715-12 PMID:22492441 PMCID:PMC3370553
  • 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
  • Singleton D, Hu J, Aitken MD. 2012. Heterologous expression of polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase genes from a novel pyrene-degrading betaproteobacterium. Appl Environ Microbiol 78(10):3552-3559. doi:10.1128/AEM.00173-12 PMID:22427500 PMCID:PMC3346350
  • 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


  • Belchik SM, Kennedy DW, Dohnalkova AC, Wang Y, Sevinc PC, Wu H, Lin Y, Lu HP, Fredrickson JK, Shi L. 2011. Extracellular reduction of hexavalent chromium by cytochromes MtrC and OmcA of Shewanella oneidensis MR-1. Appl Environ Microbiol 77:4035-4041. doi:10.1128/AEM.02463-10 PMID:21498755 PMCID:PMC3131624
  • Gutierrez T, Singleton D, Aitken MD, Semple KT. 2011. Stable isotope probing of an algal bloom to identify uncultivated members of the Rhodobacteraceae associated with low-molecular-weight polycyclic aromatic hydrocarbon degradation. Appl Environ Microbiol 77(21):7856-7860. doi:10.1128/AEM.06200-11 PMID:21926219 PMCID:PMC3209190
  • Iwai S, Johnson TA, Chai B, Hashsham SA, Tiedje JM. 2011. Comparison of the specificities and efficacies of primers for aromatic dioxygenase gene analysis of environmental samples. Appl Environ Microbiol 77:3551-3557. doi:10.1128/aem.00331-11 PMID:21498766 PMCID:PMC3127589
  • Jones MD, Singleton D, Sun W, Aitken MD. 2011. Multiple DNA extractions coupled with stable-isotope probing of anthracene-degrading bacteria in contaminated soil. Appl Environ Microbiol 77(9):2984-2991. doi:10.1128/AEM.01942-10 PMID:21398486 PMCID:PMC3126383
  • Kim D, Yoo M, Choi KY, Kang BS, Kim TK, Hong SG, Zylstra GJ, Kim E. 2011. Differential degradation of bicyclics with aromatic and alicyclic rings by Rhodococcus sp strain DK17. Appl Environ Microbiol 77:8280-8287. doi:10.1128/AEM.06359-11 PMID:21965391 PMCID:PMC3233041
  • Lee TK, Lee J, Sul WJ, Iwai S, Chai B, Tiedje JM, Park J. 2011. Novel biphenyl-oxidizing bacteria and dioxygenase genes from a Korean tidal mudflat. Appl Environ Microbiol 77:3888-3891. doi:10.1128/aem.00023-11 PMID:21498748 PMCID:PMC3127585
  • 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



  • Anderson CR, Johnson HA, Caputo N, Davis RE, Torpey JW, Tebo BM. 2009. Mn(II) oxidation is catalyzed by heme peroxidases in "Aurantimonas manganoxydans" strain SI85-9A1 and Erythrobacter sp strain SD-21. Appl Environ Microbiol 75(12):4130-4138. doi:10.1128/AEM.02890-08 PMID:19411418 PMCID:PMC2698374
  • Iverson SL, Maier RM. 2009. Effects of compost on colonization of roots of plants grown in metalliferous mine tailings, as examined by fluorescence in situ hybridization. Appl Environ Microbiol 75(3):842-847. doi:10.1128/AEM.01434-08 PMID:19047384 PMCID:PMC2632157
  • Lamendella R, Santo Domingo JW, Yannarell AC, Ghosh S, DiGiovanni G, Mackie RI, Oerther DB. 2009. Evaluation of swine-specific PCR assays used for fecal source tracking and analysis of molecular diversity of swine-specific "bacteroidales" populations. Appl Environ Microbiol 75(18):5787-5796. doi:10.1128/AEM.00448-09 PMID:19633126 PMCID:PMC2747877
  • 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
  • Lu T, Stroot PG, Oerther DB. 2009. Reverse transcription of 16S rRNA to monitor ribosome-synthesizing bacterial populations in the environment. Appl Environ Microbiol 75(13):4589-4598. doi:10.1128/AEM.02970-08 PMID:19395563 PMCID:PMC2704851
  • Mailloux BJ, Alexandrova E, Keimowitz AR, Wovkulich K, Freyer GA, Herron M, Stolz JF, Kenna TC, Pichler T, Polizzotto ML, Dong H, Bishop ME, Knappett PS. 2009. Microbial mineral weathering for nutrient acquisition releases arsenic. Appl Environ Microbiol 75(8):2558-2565. doi:10.1128/AEM.02440-07 PMID:19251899 PMCID:PMC2675215
  • Singleton D, Guzman Ramirez L, Aitken MD. 2009. Characterization of a polycyclic aromatic hydrocarbon degradation gene cluster in a phenanthrene-degrading Acidovorax strain. Appl Environ Microbiol 75(9):2613-2620. doi:10.1128/AEM.01955-08 PMID:19270134 PMCID:PMC2681696
  • Sul WJ, Park J, Quensen JF, Rodrigues JM, Seliger L, Tsoi TV, Zylstra GJ, Tiedje JM. 2009. DNA-stable isotope probing integrated with metagenomics for retrieval of biphenyl dioxygenase genes from polychlorinated biphenyl-contaminated river sediment. Appl Environ Microbiol 75(17):5501-5506. doi:10.1128/AEM.00121-09 PMID:19648381 PMCID:PMC2737913


  • Dick GJ, Podell S, Johnson HA, Rivera-Espinoza Y, Bernier-Latmani R, McCarthy JK, Torpey JW, Clement BG, Gaasterland T, Tebo BM. 2008. Genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp strain SI85-9A1. Appl Environ Microbiol 74(9):2646-2658. doi:10.1128/AEM.01656-07 PMID:18344346 PMCID:PMC2394881
  • Dick GJ, Torpey JW, Beveridge TJ, Tebo BM. 2008. Direct identification of a bacterial manganese(II) oxidase, the multicopper oxidase MnxG, from spores of several different marine Bacillus species. Appl Environ Microbiol 74(5):1527-1534. PMID:18165363
  • 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
  • Mendez MO, Neilson JW, Maier RM. 2008. Characterization of a bacterial community in an abandoned semiarid lead-zinc mine tailing site. Appl Environ Microbiol 74(12):3899-3907. doi:10.1128/AEM.02883-07 PMID:18424534 PMCID:PMC2446573
  • Mendez MO, Neilson JW, Maier RM. 2008. Microbiological and geochemical characterization of fluvially deposited sulfidic mine tailings. Appl Environ Microbiol 74:3899-3907. PMID:10103249
  • Nozawa-Inoue M, Jien M, Hamilton NS, Stewart V, Scow KM, Hristova KR. 2008. Quantitative detection of perchlorate-reducing bacteria by real-time PCR targeting the perchlorate reductase gene. Appl Environ Microbiol 74(6):1941-1944. doi:10.1128/AEM.01658-07 PMID:18245250 PMCID:PMC2268300
  • Schuler L, Ni Chadhain SM, Jouanneau Y, Meyer C, Zylstra GJ, Hols P, Agathos SN. 2008. Characterization of a novel angular dioxygenase from fluorene-degrading Sphingomonas sp strain LB126. Appl Environ Microbiol 74(4):1050-1057. doi:10.1128/AEM.01627-07 PMID:18156320 PMCID:PMC2258591
  • 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
  • Hristova KR, Schmidt R, Chakicherla AY, Legler TC, Wu J, Chain PS, Scow KM, Kane SR. 2007. Comparative transcriptome analysis of Methylibium petroleiphilum PM1 exposed to the fuel oxygenates methyl tert-butyl ether and ethanol. Appl Environ Microbiol 73(22):7347-7357. doi:10.1128/AEM.01604-07 PMID:17890343 PMCID:PMC2168209
  • 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


  • Colquhoun DR, Schwab KJ, Cole RN, Halden RU. 2006. Detection of norovirus capsid protein in authentic standards and in stool extracts by matrix-assisted laser desorption ionization and nanospray mass spectrometry. Appl Environ Microbiol 72(4):2749-2755.
  • Cordova-Kreylos AL, Cao Y, Green PG, Hwang H, Kuivila KM, LaMontagne MG, Van De Werfhorst L, Holden PA, Scow KM. 2006. Diversity, composition, and geographical distribution of microbial communities in California salt marsh sediments. Appl Environ Microbiol 72(5):3357-3366. PMID:16672478
  • Denef VJ, Klappenbach JA, Patrauchan MA, Florizone C, Rodrigues JM, Tsoi TV, Verstraete W, Tiedje JM, Eltis LD. 2006. Genetic and genomic insights into the role of benzoate-catabolic pathway redundancy in Burkholderia xenovorans LB400. Appl Environ Microbiol 72(1):585-595. doi:10.1128/AEM.72.1.585-595.2006 PMID:16391095 PMCID:PMC1352278
  • Dick GJ, Lee YE, Tebo BM. 2006. Manganese(II)-oxidizing Bacillus spores in Guaymas Basin hydrothermal sediments and plumes. Appl Environ Microbiol 72(5):3184-3190. doi:10.1128/AEM.72.5.3184-3190.2006 PMID:16672456 PMCID:PMC1472353
  • Drees KP, Neilson JW, Betancourt JL, Quade J, Henderson DA, Pryor BM, Maier RM. 2006. Bacterial community structure in the hyperarid core of the Atacama Desert, Chile. Appl Environ Microbiol 72(12):7902-7908. doi:10.1128/AEM.01305-06 PMID:17028238 PMCID:PMC1694221
  • 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
  • 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
  • Ni Chadhain SM, Norman RS, Pesce KV, Kukor JJ, Zylstra GJ. 2006. Microbial dioxygenase gene population shifts during polycyclic aromatic hydrocarbon biodegradation. Appl Environ Microbiol 72(6):4078-4087. doi:10.1128/AEM.02969-05 PMID:16751518 PMCID:PMC1489606
  • Parnell JJ, Park J, Denef VJ, Tsoi TV, Hashsham SA, Quensen JF, Tiedje JM. 2006. Coping with polychlorinated biphenyl (PCB) toxicity: physiological and genome-wide responses of Burkholderia xenovorans LB400 to PCB-mediated stress. Appl Environ Microbiol 72(10):6607-14. PMID:17021212


  • Bencheikh-Latmani R, Williams SM, Haucke L, Criddle CS, Wu L, Zhou J, Tebo BM. 2005. Global transcriptional profiling of Shewanella oneidensis MR-1 during Cr(VI) and U(VI) reduction. Appl Environ Microbiol 71(11):7453-7460. doi:10.1128/AEM.71.11.7453-7460.2005 PMID:16269787 PMCID:PMC1287662
  • 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
  • Nozawa-Inoue M, Scow KM, Rolston DE. 2005. Reduction of perchlorate and nitrate by microbial communities in vadose soil. Appl Environ Microbiol 71(7):3928-3934. doi:10.1128/AEM.71.7.3928-3934.2005 PMID:16000806 PMCID:PMC1169015
  • Singleton D, Powell SN, Sangaiah R, Gold A, Ball LM, Aitken MD. 2005. Stable-isotope probing of bacteria capable of degrading salicylate, naphthalene, or phenanthrene in a bioreactor treating contaminated soil. Appl Environ Microbiol 71(3):1202-1209. doi:10.1128/AEM.71.3.1202-1209.2005 PMID:15746319 PMCID:PMC1065189


  • Bodour AA, Guerrero-Barajas C, Jiorle BV, Malcomson ME, Paull AK, Somogyi A, Trinh LN, Bates RB, Maier RM. 2004. Structure and characterization of flavolipids, a novel group of biosurfactants produced by Flavobacterium sp. Strain MTN11. Appl Environ Microbiol 70(1):114-120. PMID:14711632
  • Denef VJ, Park J, Tsoi TV, Rouillard JM, Zhang H, Wibbenmeyer JA, Verstraete W, Gulari E, Hashsham SA, Tiedje JM. 2004. Biphenyl and benzoate metabolism in a genomic context: outlining genome-wide metabolic networks in Burkholderia xenovorans LB400. Appl Environ Microbiol 70(8):4961-4970. PMID:15294836
  • Norman RS, Moeller P, McDonald TJ, Morris PJ. 2004. Effect of pyocyanin on a crude-oil-degrading microbial community. Appl Environ Microbiol 70(7):4004-4011. doi:10.1128/AEM.70.7.4004-4011.2004 PMID:15240276 PMCID:PMC444818
  • Okano Y, Hristova KR, Leutenegger CM, Jackson LE, Denison RF, Gebreyesus B, Lebauer D, Scow KM. 2004. Application of real-time PCR to study effects of ammonium on population size of ammonia-oxidizing bacteria in soil. Appl Environ Microbiol 70(2):1008-1016. PMID:14766583
  • Sierra-Alvarez R, Cortinas I, Yenal U, Field JA. 2004. Methanogenic inhibition by arsenic compounds. Appl Environ Microbiol 70(9):5488-5691. PMID:15345461


  • Bodour AA, Drees KP, Maier RM. 2003. Distribution of biosurfactant-producing bacteria in undisturbed and contaminated arid southwestern soils. Appl Environ Microbiol 69(6):3280-3287. PMID:12788727
  • Hristova KR, Gebreyesus B, Mackay DM. 2003. Naturally occurring bacteria similar to the methyl tert-butyl ether (MTBE)-degrading strain PM1 are present in MTBE-contaminated groundwater. Appl Environ Microbiol 69(5):2616-2623. PMID:12732529
  • Law AM, Aitken MD. 2003. Bacterial chemotaxis to naphthalene desorbing from a nonaqueous liquid. Appl Environ Microbiol 69(10):5968-5973. PMID:14532051
  • Meek IB, Peplow AW, Ake CL, Phillips TD, Beremand MN. 2003. Tri1 encodes the cytochrome P450 monooxygenase for C-8 hydroxylation during trichothecene biosynthesis in Fusarium sporotrichioides and resides upstream of another new Tri gene. Appl Environ Microbiol 69(3):1607-1613. PMID:12620849
  • Morrison A, Coughlin K, Shine JP, Coull BA, Rex A. 2003. Receiver operating characteristic curve analysis of beach water quality indicator variables. Appl Environ Microbiol 69(11):6405-6411. PMID:14602593
  • Peplow AW, Meek IB, Wiles MC, Phillips TD, Beremand MN. 2003. Tri16 is required for esterification of position C-8 during trichothecene mycotoxin production by Fusarium sporotrichioides. Appl Environ Microbiol 69(10):5935-5940. PMID:14532047


  • Cervantes FJ, Dijksma W, Duong-Dac T, Ivanova AE, Lettinga G, Field JA. 2002. Anaerobic mineralization of toluene by enriched sediments with quinones and humus as terminal electron acceptors. Appl Environ Microbiol 67(10):4471-4478. PMID:11571145
  • Francis CM, Tebo BM. 2002. Enzymatic manganese(II) oxidation by metabolically dormant spores of diverse Bacillus species. Appl Environ Microbiol 68(2):874-880. PMID:11823231 PMCID:PMC126666
  • Park J, Kukor JJ, Abriola LM. 2002. Characterization of the adaptive response to trichloroethylene-mediated stresses in Ralstonia pickettii PKO1. Appl Environ Microbiol 68(11):5231-5240. PMID:12406709 PMCID:PMC129943


  • Cheung P, Kinkle BK. 2001. Mycobacterium diversity and pyrene mineralization in petroleum-contaminated soils. Appl Environ Microbiol 67(5):2222-2229. doi:10.1128/AEM.67.5.2222-2229.2001 PMID:11319104 PMCID:PMC92859
  • Cheung P, Kinkle BK. 2001. Pyrene degradation and mycobacterial diversity in petroleum-contaminated soils. Appl Environ Microbiol 67(5):2222-2229.
  • Chiavelli DA, Marsh JW, Taylor RK. 2001. The mannose-sensitive hemagglutinin of Vibrio cholerae promotes adherence to zooplankton. Appl Environ Microbiol 67(7):3220-3225. PMID:11425745
  • Francis CM, Co E, Tebo BM. 2001. Enzymatic manganese(II) oxidation by a marine alpha-proteobacterium. Appl Environ Microbiol 67(9):4024-4029. PMID:11526000 PMCID:PMC93124
  • Hristova KR, Lutenegger CM, Scow KM. 2001. Detection and quantification of methyl tert-butyl ether-degrading strain PM1 by real-time TaqMan PCR. Appl Environ Microbiol 67(11):5154-5160. PMID:11679339
  • Kahng H, Malinverni J, Majko MM, Kukor JJ. 2001. Genetic and functional analysis of the tbc operons for catabolism of alkyl- and chloroaromatic compounds in Burkholderia sp strain JS150. Appl Environ Microbiol 67(10):4805-4816. PMID:11571188 PMCID:PMC93235
  • Roane TM, Josephson KL, Pepper IL. 2001. Dual-bioaugmentation strategy to enhance remediation of cocontaminated soil. Appl Environ Microbiol 67(7):3208-3215. PMID:11425743


  • Al-Tahhan RA, Sandrin TR, Bodour AA, Maier RM. 2000. Rhamnolipid-induced removal of lipopolysaccharide from Pseudomonas aeruginosa: effect on cell surface properties and interaction with hydrophobic substrates. Appl Environ Microbiol 66(8):3262-3268. PMID:10919779
  • Hohnstock AM, Stuart-Keil KG, Kull EE, Madsen EL. 2000. Naphthalene and donor cell density influence field conjugation of naphthalene catabolism plasmids. Appl Environ Microbiol 66(7):3088-3092. PMID:10877811
  • Kazunga C, Aitken MD. 2000. Products from the incomplete metabolism of pyrene by polycyclic aromatic hydrocarbon-degrading bacteria. Appl Environ Microbiol 66:1917-1922. PMID:10788360
  • Macalady JL, Mack EE, Nelson DC, Scow KM. 2000. Sediment microbial community structure and mercury methylation in mercury-polluted Clear Lake, California. Appl Environ Microbiol 66(4):1479-1488. PMID:10742230
  • Newby DT, Gentry TJ, Pepper IL. 2000. Comparison of 2,4-dichlorophenoxyacetic acid degradation and plasmid transfer in soil resulting from bioaugmentation with two different pJP4 donors. Appl Environ Microbiol 66(8):3399-3407. PMID:10919798
  • Newby DT, Josephson KL, Pepper IL. 2000. Detection and characterization of plasmid pJP4 transfer to indigenous soil bacteria. Appl Environ Microbiol 66(1):290-296. PMID:10618238


  • 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
  • Hanson JR, Ackerman CE, Scow KM. 1999. Biodegradation of methyl tert-butyl ether by a bacterial pure culture. Appl Environ Microbiol 65(11):4788-4792. PMID:10543787 PMCID:PMC91645
  • Hanson JR, Macalady JL, Harris D, Scow KM. 1999. Linking toluene degradation with specific microbial populations in soil. Appl Environ Microbiol 65(12):5403-5408. PMID:10583996 PMCID:PMC91736
  • Hrywna Y, Tsoi TV, Maltseva OV, Quensen JF, Tiedje JM. 1999. Construction and characterization of two recombinant bacteria that grow on ortho- and para-substituted chlorobiphenyls. Appl Environ Microbiol 65(5):2163-2169. PMID:10224015
  • Marx RB, Aitken MD. 1999. Quantification of chemotaxis to naphthalene by Pseudomonas putida G7. Appl Environ Microbiol 65:2847-2852. PMID:10388674
  • Miller DN, Bryant JE, Madsen EL, Ghiorse WC. 1999. Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl Environ Microbiol 65(11):4715-4724. PMID:10543776
  • Morisseau C, Ward BL, Gilchrist DG, Hammock BD. 1999. Multiple epoxide hydrolases in Alternaria alternata f. sp. lycopersici and their relationship to medium composition and host-specific toxin production. Appl Environ Microbiol 65(6):2388-2395. PMID:10347018
  • Nelson YM, Lion LW, Ghiorse WC, Shuler ML. 1999. Production of biogenic Mn oxides by Leptothrix discophora SS-1 in a chemically defined growth medium and evaluation of their Pb absorption characteristics. Appl Environ Microbiol 65:175-180. PMID:9872777
  • Tsoi TV, Plotnikova EG, Cole JR, Guerin WF, Bagdasarian M, Tiedje JM. 1999. Cloning, expression, and nucleotide sequence of the Pseudomonas aeruginosa 142 ohb genes coding for oxygenolytic ortho dehalogenation of halobenzoates. Appl Environ Microbiol 65(5):2151-2162. PMID:10224014 PMCID:PMC91311
  • Ye D, Quensen JF, Tiedje JM, Boyd SA. 1999. 2-Bromoethanesulfonate, sulfate, molybdate, and ethanesulfonate inhibit anaerobic dechlorination of polychlorobiphenyls by pasteurized microorganisms. Appl Environ Microbiol 65:327-329. PMID:9872802


  • 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
  • DuTeau NM, Bull Rogers JD, Bartholomay CT, Reardon KF. 1998. Species-specific oligonucleotides for enumeration of Pseudomonas putida F1, Burkholderia sp strain JS150, and Bacillus subtilis ATCC 7003 in biodegradation experiments. Appl Environ Microbiol 64(12):4994-4999. PMID:9835594 PMCID:PMC90954
  • Tay ST, Hemond HF, Polz MF, Cavanaugh CM, DeJesus I, Krumholz LR. 1998. Two new Mycobacterium strains and their role in toluene degradation in a contaminated stream. Appl Environ Microbiol 64(5):1715-1720. PMID:9572941 PMCID:PMC106220
  • Tellez CM, Gaus KP, Graham DW, Arnold RG, Guzman R. 1998. Isolation of copper biochelates from Methylosinus trichosporium OB3b and soluble methane monooxygenase mutants. Appl Environ Microbiol 64(3):1115-1122. PMID:9501450


  • Fuller ME, Scow KM. 1997. Impact of trichloroethylene and toluene on nitrogen cycling in soil. Appl Environ Microbiol 63(10):4015-4019. PMID:9327567
  • Herman DC, Zhang Y, Maier RM. 1997. Rhamnolipid (biosurfactant) effects on cell aggregation and biodegradation of residual hexadecane under saturated flow conditions. Appl Environ Microbiol 63(9):3622-3627. PMID:9293014
  • Johnson GR, Olsen RH. 1997. Multiple pathways for toluene degradation in Burkholderia sp. strain JS150. Appl Environ Microbiol 63(10):4047-4052. PMID:9327568
  • Kim J, Rhee G. 1997. Population dynamics of polychlorinated biphenyl-dechlorinating microorganisms in contaminated sediments. Appl Environ Microbiol 63(5):1771-1776. PMID:16535594
  • Leahy JG, Olsen RH, Johnson GR. 1997. Cross-regulation of toluene monooxygenases by the transcriptional activators TbmR and TbuT. Appl Environ Microbiol 63(9):3736-3739. PMID:9293027
  • Massol-Deya A, Weller R, Rios-Hernandez L, Zhou J, Hickey RF, Tiedje JM. 1997. Succession and convergence of biofilm communities in fixed-film reactors treating aromatic hydrocarbons in groundwater. Appl Environ Microbiol 63(1):270-276. PMID:8979355
  • Siering PL, Ghiorse WC. 1997. Development and application of 16S ribosomal RNA-targeted probes for detection of iron- and manganese-oxidizing sheathed bacteria in environmental samples. Appl Environ Microbiol 63:644-651. PMID:9023942
  • Zhou J, Palumbo AV, Tiedje JM. 1997. Sensitive detection of a novel class of toluene-degrading denitrifiers, Azoarcus tolulyticus, with small-subunit rRNA primers and probes. Appl Environ Microbiol 63(6):2384-2390. PMID:9172359 PMCID:PMC168532


  • 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
  • Chee-Sanford JC, Frost JW, Fries MR, Zhou J, Tiedje JM. 1996. Evidence for acetyl coenzyme A and cinnamoyl coenzyme A in the anaerobic toluene mineralization pathway in Azoarcus tolulyticus Tol-4. Appl Environ Microbiol 62(3):964-973. PMID:8975623
  • DiGiovanni GD, Neilson JW, Pepper IL, Sinclair NA. 1996. Gene transfer of Alcaligenes eutrophus JMP134 plasmid pJP4 to indigenous soil recipients. Appl Environ Microbiol 62(7):2521-2526. PMID:8779592
  • Gray JP, Herwig RP. 1996. Phylogenetic analysis of the bacterial communities in marine sediments. Appl Environ Microbiol 62(11):4049-4059. PMID:8899989 PMCID:PMC168226
  • Grimberg SJ, Stringfellow WT, Aitken MD. 1996. Quantifying the biodegradation of phenanthrene by Pseudomonas stutzeri P16 in the presence of a nonionic surfactant. Appl Environ Microbiol 62(7):2387-2392. PMID:8779577
  • Kukor JJ, Olsen RH. 1996. Catechol 2,3-dioxygenases functional in oxygen-limited (hypoxic) environments. Appl Environ Microbiol 62(5):1728-1740. PMID:8633871 PMCID:PMC167947
  • Leahy JG, Byrne AM, Olsen RH. 1996. Comparison of factors influencing trichloroethylene degradation by toluene-oxidizing bacteria. Appl Environ Microbiol 62(3):825-833. PMID:8975612
  • Migaud ME, Chee-Sanford JC, Tiedje JM, Frost JW. 1996. Benzylfumaric, benzylmaleic, Z- and E-phenylitaconic acids: synthesis, characterization and correlation with a metabolite generated by Azoarcus tolulyticus strain Tol-4 during anaerobic toluene degradation. Appl Environ Microbiol 62(3):974-978. PMID:8975624
  • Schneider JR, Grosser RJ, Jayasimhulu K, Xue W, Warshawsky D. 1996. Degradation of pyrene, benz(a)anthracene and benzo(a)pyrene by Mycobacterium sp. strain RJGII.135, Isolated from a former coal gasification site. Appl Environ Microbiol 62(1):13-19. PMID:8572690
  • Sutton SD, Pfaller SL, Shann JR, Warshawsky D, Kinkle BK, Vestal JR. 1996. Aerobic biodegradation of 4-methylquinoline by a soil bacterium. Appl Environ Microbiol 62(8):2910-2914. PMID:8702284
  • Zhou J, Bruns MA, Tiedje JM. 1996. DNA recovery from soils of diverse composition. Appl Environ Microbiol 62:316-322. PMID:8593035


  • Dybas MJ, Tatara G, Criddle CS. 1995. Localization and characterization of the carbon tetrachloride transformation activity of Pseudomonas sp. strain KC. Appl Environ Microbiol 61(2):758-762. PMID:16534941
  • Govindaswami M, Feldhake DJ, Kinkle BK, Mindell DP, Loper JC. 1995. Phylogenetic comparison of two polycyclic aromatic hydrocarbon-degrading mycobacteria. Appl Environ Microbiol 61(9):3221-3226. PMID:7574631 PMCID:PMC167601
  • Gross MJ, Logan BE. 1995. The influence of different chemical treatments on transport of Alcaligenes paradoxus in porous media. Appl Environ Microbiol 61(5):1750-1756. PMID:7646012
  • Johnson GR, Olsen RH. 1995. Nucleotide sequence analysis of genes encoding a toluene/benzene-2-monooxygenase from Pseudomonas sp strain JS150. Appl Environ Microbiol 61(9):3336-3346. PMID:7574644 PMCID:PMC167614
  • Picardal F, Arnold RG, Huey BB. 1995. Effects of electron donor and accepter condition on the reductive dehalogenation of teracholoromethane by Shewanella putrefaciens 200. Appl Environ Microbiol 61:8-12. PMID:7887629
  • Stringfellow WT, Aitken MD. 1995. Competitive metabolism of naphthalene, methylnaphthalenes and fluorene by phenanthrene-degrading pseudomonads. Appl Environ Microbiol 61:357-362. PMID:7887615


  • Neilson JW, Josephson KL, Pepper IL, Arnold RG, DiGiovanni GD, Sinclair NA. 1994. Frequency of horizontal gene transfer of a large catabolic plasmid (pJP4) in soil. Appl Environ Microbiol 60:4053-4058. PMID:7993092
  • Ortega-Calvo JJ, Alexander M. 1994. Roles of bacterial attachment and spontaneous partitioning in the biodegradation of naphthalene initially present in nonaqueous-phase liquids. Appl Environ Microbiol 60(7):2643-2646. PMID:8074534


  • Tatara G, Dybas MJ, Criddle CS. 1993. Effects of medium and trace metals on the kinetics of carbon tetrachloride transformation by Pseudomonas sp. strain KC. Appl Environ Microbiol 59(7):2126-2131. PMID:8357248


  • Neilson JW, Josephson KL, Pillai SD, Pepper IL. 1992. Polymerase chain reaction and gene probe detection of the 2,4-dichlorophenoxyacetic acid degradation plasmid pJP4. Appl Environ Microbiol 58:1271-1275. PMID:1599246
  • Smith GB, Tiedje JM. 1992. Isolation and characterization of a nitrite reductase gene and its use as a probe for denitrifying bacteria. Appl Environ Microbiol 58(1):376-384. PMID:1539983 PMCID:PMC195218


  • Grosser RJ, Warshawsky D, Vestal JR. 1991. Indigenous and enhanced mineralization of pyrene, benzo(a)-pyrene and carbazole in soils. Appl Environ Microbiol 57:3462-3469. PMID:1785924


  • Criddle CS, DeWitt JT, Grbic-Galic D, McCarty PL. 1990. Transformation of carbon tetrachloride by Pseudomonas sp. strain KC under denitrification conditions. Appl Environ Microbiol 56(11):3240-3246. PMID:2268146
to Top