Superfund Research Program

Molecular Insight into Polyaromatic Toxicant Degradation by Microbial Communities

Project Leader: James M. Tiedje
Grant Number: P42ES004911
Funding Period: 2000 - 2013

Project-Specific Links

Publications

2014

• Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown C, Porras-Alfaro A, Kuske CR, Tiedje JM. 2014. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 42(Databaseissue):D633-D642. doi:10.1093/nar/gkt1244 PMID:24288368 PMCID:PMC3965039

2013

• Fish JA, Chai B, Wang Q, Sun Y, Brown C, Tiedje JM, Cole JR. 2013. FunGene: The functional gene pipeline and repository. Front Microbiol 4:291. doi:10.3389/fmicb.2013.00291 PMID:24101916 PMCID:PMC3787254
• Penton C, Johnson TA, Quensen JF, Iwai S, Cole JR, Tiedje JM. 2013. Functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter. Front Microbiol 4:279. doi:10.3389/fmicb.2013.00279 PMID:24062736 PMCID:PMC3775264

2012

• Baushke SW, Stedtfeld RD, Tourlousse DM, Ahmad F, Wick LM, Gulari E, Tiedje JM, Hashsham SA. 2012. Identification of non-specific hybridization using an empirical equation fitted to non-equilibrium dissociation curves. J Microbiol Methods 90(1):29-35. doi:10.1016/j.mimet.2012.04.003 PMID:22537822 PMCID:PMC3366151

2011

• 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
• 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

2010

• Chang H, Zylstra GJ. 2010. Xanthomonads. In: Handbook of Hydrocarbon and Lipid Microbiology. Springer Verlag GmbH, Heidelberg, Germany. pp.1805-1811.
• Iwai S, Chai B, Sul WJ, Cole JR, Hashsham SA, Tiedje JM. 2010. Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment. ISME J 4(2):279-285. doi:10.1038/ismej.2009.104 PMID:19776767 PMCID:PMC2808446
• Ni Chadhain SM, Zylstra GJ. 2010. Functional Gene Diversity, Biogeography, and Dynamics. In: Handbook of Hydrocarbon and Lipid Microbiology. Springer Verlag GmbH, Heidelberg, Germany. pp.2413-2422.
• Parnell JJ, Denef VJ, Park J, Tsoi TV, Tiedje JM. 2010. Environmentally relevant parameters affecting PCB degradation: carbon source- and growth phase-mitigated effects of the expression of the biphenyl pathway and associated genes in Burkholderia xenovorans LB400. Biodegradation 21(1):147-156. doi:10.1007/s10532-009-9289-4 PMID:19672561

2009

• Schuler L, Jouanneau Y, Ni Chadhain SM, Meyer C, Pouli M, Zylstra GJ, Hols P, Agathos SN. 2009. Characterization of a ring-hydroxylating dioxygenase from phenanthrene-degrading Sphingomonas sp strain LH128 able to oxidize benz[a]anthracene. Appl Microbiol Biotechnol 83(3):465-475. doi:10.1007/s00253-009-1858-2 PMID:19172265
• 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

2008

• Cardenas E, Tiedje JM. 2008. New tools for discovering and characterizing microbial diversity. Curr Opin Biotechnol 19(6):544-549. doi:10.1016/j.copbio.2008.10.010 PMID:18984052
• 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

2007

• Leigh MB, Pellizari VH, Uhlik O, Sutka R, Rodrigues JM, Ostrom N, Zhou J, Tiedje JM. 2007. Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs). ISME J 1(2):134-148. doi:10.1038/ismej.2007.26 PMID:18043623

2006

• Chain PS, Denef VJ, Konstantinidis KT, Vergez LM, Agullo L, Reyes VL, Hauser L, Cordova M, Gomez L, Gonzalez M, Land M, Lao V, Larimer FW, LiPuma JJ, Mahenthiralingam E, Malfatti SA, Marx CJ, Parnell JJ, Ramette A, Richardson PM, Seeger M, Smith D, Spilker T, Sul WJ, Tsoi TV, Ulrich LE, Zhulin IB, Tiedje JM. 2006. Burkholderia xenovorans LB400 harbors a multi-replicon, 973-Mbp genome shaped for versatility. Proc Natl Acad Sci U S A 103(42):15280-15287. doi:10.1073/pnas.0606924103 PMID:17030797 PMCID:PMC1622818
• 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

2004

• 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
• Goris J, De Vos P, Caballero-Mellado J, Park J, Falsen E, Quensen JF, Tiedje JM, Vandamme P. 2004. Classification of the biphenyl- and polychlorinated biphenyl-degrading strain LB400(T) and relatives as Burkholderia xenovorans sp nov. Int J Syst Evol Microbiol 54(5):1677-1681.
• Smithwick LA, Quensen JF, Smith A, Kurtz DT, London L, Morris PJ. 2004. The inhibition of LPS-induced splenocyte proliferation by ortho-substituted and microbially dechlorinated polychlorinated biphenyls is associated with a decreased expression of cyclin D2. Toxicology 204(1):61-74. PMID:15369849
• Tiedje JM, Konstantinidis KT. 2004. Trends between gene content and genome size in prokaryotic species with larger genomes. Proc Natl Acad Sci U S A 101(9):3160-3165. PMID:14973198

2003

• Denef VJ, Park J, Rodrigues JM, Tsoi TV, Hashsham SA, Tiedje JM. 2003. Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities. Environ Microbiol 5(10):933-943. PMID:14510847
• Park J. 2003. Expanded applicability of DNA microarray technology in environmental microbiology. In: Proceedings of the International Meeting of the Federation of Korean Microbiological Societies. October 24-25. College of Science, Yonsei University, Seoul, Korea, Republic Of.
• Park J, Li H, Tiedje JM. 2003. Determination of gene-dependent sorption of DNA on clays using a microarray technique. In: Proceedings of the 103^rd General Meeting of the American Society for Microbiology, May 18-22. Washington, DC.
• Park J, Ramsburg A, Abriola LM, Tiedje JM. 2003. Biofilm-associated utilization of biphenyl on organo-coated sand by Burkholderia sp. LB400. In: Proceedings of the General Meeting, American Society for Microbiology, May 23-27. New Orleans, LA.
• Smithwick LA, Smith A, Quensen JF, Stack A, London L, Morris PJ. 2003. Inhibition of LPS-induced splenocyte proliferation by orthosubstituted polychlorinated biphenyl congeners. Toxicology 188(2-3):319-333. PMID:12767701
• Tiedje JM. 2003. Molecular windows into microbial communities. In: Proceedings of the International Meeting of the Federation of Korean Microbiological Societies. October 24-25. College of Science, Yonsei University, Seoul, Korea, Republic Of.
• Tiedje JM. 2003. Molecular windows into microbial communities. In: Proceedings of the International Meeting of the Federation of Korean Microbiological Societies. October 24-25. College of Science, Yonsei University, Seoul, Korea, Republic Of.

2001

• Rodrigues JM, Aiello MR, Quensen JF, Maltseva OV. 2001. Degradation of products from anerobic dechlorination of Aroclor 1242 in contaminated sediment using two recombinant bacteria. In: Proceedings of the American Society for Microbiology, 101st General Meeting. Orlando, FL.
• Rodrigues JM, Maltseva OV, Tsoi TV, Helton RR, Quensen JF, Fukuda M, Tiedje JM. 2001. Development of a Rhodococcus recombinant strain for degradation products from anaerobic dechlorination of PCBs. Environ Sci Technol 35(4):663-668. PMID:11349275

2000

• Maltseva OV, Rodrigues JM, Quensen JF, Tsoi TV, Tiedje JM. 2000. Growth of Burkholderia sp. LB400 and recombinant LH400(ohb) on simulated anaerobic dechlorination products from Aroclor 1242. In: Proceedings of the American Society for Microbiology 100^th general meeting. pp.149.
• Quensen JF, Tsoi TV, Maltseva OV, Rodrigues JM, Zwiernik MJ, Tiedje JM. 2000. Strategies for the anaerobic/aerobic biotreatment of polychlorinated biphenyls. In: Proceedings of the Society of Environmental Toxicology and Chemistry, 21st Annual Meeting, 12-16 November. Nashville, TN. pp.56.
• Rodrigues JM, Aiello MR, Maltseva OV, Tsoi TV, Tiedje JM. 2000. A flourescent PCR-based method to quantify the recombinant Rhodococcus sp. strain RHA1 in soil. In: Proceedings of the American Society for Microbiology, 100th General Meeting, 21-25 May. Los Angeles, CA. pp.170.
• Tiedje JM. 2000. Putting novel microbes to work on industry wastes. In: Proceedings of the Symposium for Japan Bioindustry Association. pp.47-54.
• Tsoi TV, Cole JR, Rech S, Tiedje JM. 2000. Molecular Analysis Implicates Existence Of Two Differing Mechanisms Of Aryl Reductive Ortho-Dehalogenation In Coryneform Bacterium Strain KZ-4. In: Proceedings of the American Society for Microbiology 100^th general meeting.

1999

• Maltseva OV, Tsoi TV, Quensen JF, Fukuda M, Tiedje JM. 1999. Degradation of anaerobic reductive dechlorination products of Aroclor 1242 by four aerobic bacteria. Biodegradation 10(5):363-371. PMID:10870552
• Tsoi TV, Cole JR, Maltseva OV, Rech S, Quensen JF, Rodrigues JM, Spain J, Tiedje JM. 1999. Promiscuous Dehalogenating Dioxygenase (ISP) From Pseudomonas aeruginosa 142: Evolutionary Model And Metabolic Engineering Tool. In: Proceedings of the International Symposium Pseudomonas. Maui, HI.