PUB - Publikationen an der Universität Bielefeld

ARB: a software environment for sequence data.
Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar , Buchner A, Lai T, Steppi S, Jobb G, Forster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, Konig A, Liss T, Lussmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer KH., Nucleic Acids Res. 32(4), 2004
PMID: 14985472

Kinetics of decolourisation and biotransformation of direct black 38 by C. hominis and P. stutzeri.
Bafana A, Devi SS, Krishnamurthi K, Chakrabarti T., Appl. Microbiol. Biotechnol. 74(5), 2007
PMID: 17318544

Quantifying the biodegradation of phenanthrene by Pseudomonas stutzeri P16 in the presence of a nonionic surfactant.
Grimberg SJ, Stringfellow WT, Aitken MD., Appl. Environ. Microbiol. 62(7), 1996
PMID: 8779577

Genomic analysis of polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1.
Kim SJ, Kweon O, Jones RC, Edmondson RD, Cerniglia CE., Biodegradation 19(6), 2008
PMID: 18421421

Metagenomics for studying unculturable microorganisms: cutting the Gordian knot.
Schloss PD, Handelsman J., Genome Biol. 6(8), 2005
PMID: 16086859

A polyphasic approach for assessing the suitability of bioremediation for the treatment of hydrocarbon-impacted soil.
Adetutu EM, Smith RJ, Weber J, Aleer S, Mitchell JG, Ball AS, Juhasz AL., Sci. Total Environ. 450-451(), 2013
PMID: 23454909

Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis.
Suenaga H, Koyama Y, Miyakoshi M, Miyazaki R, Yano H, Sota M, Ohtsubo Y, Tsuda M, Miyazaki K., ISME J 3(12), 2009
PMID: 19587775

Metagenomics: application of genomics to uncultured microorganisms.
Handelsman J., Microbiol. Mol. Biol. Rev. 68(4), 2004
PMID: 15590779

Pyrosequencing investigation into the bacterial community in permafrost soils along the China-Russia Crude Oil Pipeline (CRCOP).
Yang S, Wen X, Jin H, Wu Q., PLoS ONE 7(12), 2012
PMID: 23300754

Extraction of inhibitor-free metagenomic DNA from polluted sediments, compatible with molecular diversity analysis using adsorption and ion-exchange treatments.
Desai C, Madamwar D., Bioresour. Technol. 98(4), 2006
PMID: 16806911

Accurate taxonomic assignment of short pyrosequencing reads.
Clemente JC, Jansson J, Valiente G., Pac Symp Biocomput (), 2010
PMID: 19908352

New insights into the activation of o-xylene biodegradation in Pseudomonas stutzeri OX1 by pathway substrates.
Arenghi FL, Barbieri P, Bertoni G, de Lorenzo V., EMBO Rep. 2(5), 2001
PMID: 11375933

Discovery of a novel styrene monooxygenase originating from the metagenome.
van Hellemond EW, Janssen DB, Fraaije MW., Appl. Environ. Microbiol. 73(18), 2007
PMID: 17644649

Metabolic networks, microbial ecology and 'omics' technologies: towards understanding in situ biodegradation processes.
Vilchez-Vargas R, Junca H, Pieper DH., Environ. Microbiol. 12(12), 2010
PMID: 20860734

The Pfam protein families database.
Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A., Nucleic Acids Res. 38(Database issue), 2009
PMID: 19920124

Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.
Venkateswaran K, Moser DP, Dollhopf ME, Lies DP, Saffarini DA, MacGregor BJ, Ringelberg DB, White DC, Nishijima M, Sano H, Burghardt J, Stackebrandt E, Nealson KH, Nealson KH., Int. J. Syst. Bacteriol. 49 Pt 2(), 1999
PMID: 10319494

DNA Probe Method for the Detection of Specific Microorganisms in the Soil Bacterial Community.
Holben WE, Jansson JK, Chelm BK, Tiedje JM., Appl. Environ. Microbiol. 54(3), 1988
PMID: 16347582

Generation and initial characterization of Pseudomonas stutzeri KC mutants with impaired ability to degrade carbon tetrachloride.
Sepulveda-Torres LC, Rajendran N, Dybas MJ, Criddle CS., Arch. Microbiol. 171(6), 1999
PMID: 10369898

Bacterial metabolism of polychlorinated biphenyls.
Pieper DH, Seeger M., J. Mol. Microbiol. Biotechnol. 15(2-3), 2008
PMID: 18685266

Exposure of soil microbial communities to chromium and arsenic alters their diversity and structure.
Sheik CS, Mitchell TW, Rizvi FZ, Rehman Y, Faisal M, Hasnain S, McInerney MJ, Krumholz LR., PLoS ONE 7(6), 2012
PMID: 22768219

The molecular basis for adaptive evolution in novel extradiol dioxygenases retrieved from the metagenome.
Suenaga H, Mizuta S, Miyazaki K., FEMS Microbiol. Ecol. 69(3), 2009
PMID: 19566698

Identification of bacteria utilizing biphenyl, benzoate, and naphthalene in long-term contaminated soil.
Uhlik O, Wald J, Strejcek M, Musilova L, Ridl J, Hroudova M, Vlcek C, Cardenas E, Mackova M, Macek T., PLoS ONE 7(7), 2012
PMID: 22808223

Genetic and genomic insights into the role of benzoate-catabolic pathway redundancy in Burkholderia xenovorans LB400.
Denef VJ, Klappenbach JA, Patrauchan MA, Florizone C, Rodrigues JL, Tsoi TV, Verstraete W, Eltis LD, Tiedje JM., Appl. Environ. Microbiol. 72(1), 2006
PMID: 16391095

Decolorization of azo dyes by Rhodobacter sphaeroides.
Song ZY, Zhou JT, Wang J, Yan B, Du CH., Biotechnol. Lett. 25(21), 2003
PMID: 14677704

Decolorization of methyl red by a mixed culture of Bacillus sp. and Pseudomonas stutzeri.
Itoh K, Kitade Y, Nakanishi M, Yatome C., J Environ Sci Health A Tox Hazard Subst Environ Eng 37(3), 2002
PMID: 11929077

The COG database: new developments in phylogenetic classification of proteins from complete genomes.
Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV., Nucleic Acids Res. 29(1), 2001
PMID: 11125040

Shewanella--the environmentally versatile genome.
Tiedje JM., Nat. Biotechnol. 20(11), 2002
PMID: 12410251

Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products.
Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM., Chem. Biol. 5(10), 1998
PMID: 9818143

Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.
Wang Q, Garrity GM, Tiedje JM, Cole JR., Appl. Environ. Microbiol. 73(16), 2007
PMID: 17586664

Metagenomics reveals diversity and abundance of meta-cleavage pathways in microbial communities from soil highly contaminated with jet fuel under air-sparging bioremediation.
Brennerova MV, Josefiova J, Brenner V, Pieper DH, Junca H., Environ. Microbiol. 11(9), 2009
PMID: 19575758

Degradation of p-nitrophenol by the phototrophic bacterium Rhodobacter capsulatus.
Roldan MD, Blasco R, Caballero FJ, Castillo F., Arch. Microbiol. 169(1), 1998
PMID: 9396833

The University of Minnesota Biocatalysis/Biodegradation Database: improving public access.
Gao J, Ellis LB, Wackett LP., Nucleic Acids Res. 38(Database issue), 2009
PMID: 19767608

MEGAN analysis of metagenomic data.
Huson DH, Auch AF, Qi J, Schuster SC., Genome Res. 17(3), 2007
PMID: 17255551

Methods for microbial DNA extraction from soil for PCR amplification.
Yeates C, Gillings MR, Davison AD, Altavilla N, Veal DA., Biol Proced Online 1(), 1998
PMID: 12734590

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis.
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM., Nucleic Acids Res. 37(Database issue), 2008
PMID: 19004872

Metabolic reconstruction of aromatic compounds degradation from the genome of the amazing pollutant-degrading bacterium Cupriavidus necator JMP134.
Perez-Pantoja D, De la Iglesia R, Pieper DH, Gonzalez B., FEMS Microbiol. Rev. 32(5), 2008
PMID: 18691224

MetaSAMS--a novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets.
Zakrzewski M, Bekel T, Ander C, Puhler A, Rupp O, Stoye J, Schluter A, Goesmann A., J. Biotechnol. 167(2), 2012
PMID: 23026555

Identification of nitrogen-incorporating bacteria in petroleum-contaminated arctic soils by using [15N]DNA-based stable isotope probing and pyrosequencing.
Bell TH, Yergeau E, Martineau C, Juck D, Whyte LG, Greer CW., Appl. Environ. Microbiol. 77(12), 2011
PMID: 21498745

Intrinsic bioremediability of an aromatic hydrocarbon-polluted groundwater: diversity of bacterial population and toluene monoxygenase genes.
Cavalca L, Dell'Amico E, Andreoni V., Appl. Microbiol. Biotechnol. 64(4), 2003
PMID: 14624316

Development of an oligonucleotide microarray to detect di- and monooxygenase genes for benzene degradation in soil.
Iwai S, Kurisu F, Urakawa H, Yagi O, Kasuga I, Furumai H., FEMS Microbiol. Lett. 285(1), 2008
PMID: 18547327

Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples.
Miller DN, Bryant JE, Madsen EL, Ghiorse WC., Appl. Environ. Microbiol. 65(11), 1999
PMID: 10543776

Diversity, abundance, and consistency of microbial oxygenase expression and biodegradation in a shallow contaminated aquifer.
Yagi JM, Madsen EL., Appl. Environ. Microbiol. 75(20), 2009
PMID: 19700556

Tracking the influence of long-term chromium pollution on soil bacterial community structures by comparative analyses of 16S rRNA gene phylotypes.
Desai C, Parikh RY, Vaishnav T, Shouche YS, Madamwar D., Res. Microbiol. 160(1), 2008
PMID: 18996186

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers.
Liu Z, DeSantis TZ, Andersen GL, Knight R., Nucleic Acids Res. 36(18), 2008
PMID: 18723574

Comparative genomics and functional analysis of niche-specific adaptation in Pseudomonas putida.
Wu X, Monchy S, Taghavi S, Zhu W, Ramos J, van der Lelie D., FEMS Microbiol. Rev. 35(2), 2011
PMID: 20796030

Hyperthermophilic phosphotriesterases/lactonases for the environment and human health.
Mandrich L, Merone L, Manco G., Environ Technol 31(10), 2010
PMID: 20718294

High aromatic ring-cleavage diversity in birch rhizosphere: PAH treatment-specific changes of I.E.3 group extradiol dioxygenases and 16S rRNA bacterial communities in soil.
Sipila TP, Keskinen AK, Akerman ML, Fortelius C, Haahtela K, Yrjala K., ISME J 2(9), 2008
PMID: 18563190

DNA recovery from soils of diverse composition.
Zhou J, Bruns MA, Tiedje JM., Appl. Environ. Microbiol. 62(2), 1996
PMID: 8593035

Growth substrate- and phase-specific expression of biphenyl, benzoate, and C1 metabolic pathways in Burkholderia xenovorans LB400.
Denef VJ, Patrauchan MA, Florizone C, Park J, Tsoi TV, Verstraete W, Tiedje JM, Eltis LD., J. Bacteriol. 187(23), 2005
PMID: 16291673

Advances in molecular and "-omics" technologies to gauge microbial communities and bioremediation at xenobiotic/anthropogen contaminated sites.
Desai C, Pathak H, Madamwar D., Bioresour. Technol. 101(6), 2009
PMID: 19962886

Dynamics of bacterial communities in two unpolluted soils after spiking with phenanthrene: soil type specific and common responders.
Ding GC, Heuer H, Smalla K., Front Microbiol 3(), 2012
PMID: 22934091

New directions and interactions in metagenomics research.
Ward N., FEMS Microbiol. Ecol. 55(3), 2006
PMID: 16466373

Genome sequencing in microfabricated high-density picolitre reactors.
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM., Nature 437(7057), 2005
PMID: 16056220

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G., Nat. Genet. 25(1), 2000
PMID: 10802651

Phylogenetic classification of short environmental DNA fragments.
Krause L, Diaz NN, Goesmann A, Kelley S, Nattkemper TW, Rohwer F, Edwards RA, Stoye J., Nucleic Acids Res. 36(7), 2008
PMID: 18285365

KEGG: Kyoto Encyclopedia of Genes and Genomes.
Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M., Nucleic Acids Res. 27(1), 1999
PMID: 9847135

Assessment of toluene/biphenyl dioxygenase gene diversity in benzene-polluted soils: links between benzene biodegradation and genes similar to those encoding isopropylbenzene dioxygenases.
Witzig R, Junca H, Hecht HJ, Pieper DH., Appl. Environ. Microbiol. 72(5), 2006
PMID: 16672497

Soil washing improves the recovery of total community DNA from polluted and high organic content sediments.
Fortin N, Beaumier D, Lee K, Greer CW., J. Microbiol. Methods 56(2), 2004
PMID: 14744447

Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment.
Iwai S, Chai B, Sul WJ, Cole JR, Hashsham SA, Tiedje JM., ISME J 4(2), 2009
PMID: 19776767

Biotechnological prospects from metagenomics.
Schloss PD, Handelsman J., Curr. Opin. Biotechnol. 14(3), 2003
PMID: 12849784