Environmental genomics: exploring the unmined richness of microbes to degrade xenobiotics (original) (raw)

• Abraham WR, Nogales B, Golyshin PN, Pieper DH, Timmis KN (2002) Polychlorinated biphenyl-degrading microbial communities in soils and sediments. Curr Opin Microbiol 5:246–253
  Article CAS PubMed Google Scholar
• Adamczyk J, Hesselsoe M, Iversen N, Horn M, Lehner A, Nielsen PH, Schloter M, Rosvel P, Wagner M (2003) The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial structure and function. Appl Environ Microbiol 69:6875–6887
  Article CAS PubMed Google Scholar
• Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual cells without cultivation. Microbiol Rev 59:143–169
  CAS PubMed Google Scholar
• Beja O, Aravind L, Koonin EV, Suzuki MT, Hadd A, Nguyen LP, Jovanovich SB, Gates CM, Feldman RA, Spudich JL, Spudich EN, DeLong EF (2000) Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289:1902–1906
  Article CAS PubMed Google Scholar
• Blehert DS, Fox BG, Chambliss GH (1999) Cloning and sequence analysis of two Pseudomonas flavoprotein xenobiotic reductases. J Bacteriol 181:6254–6263
  CAS PubMed Google Scholar
• Burgmann H, Widmer F, Sigler WV, Zeyer J (2003) mRNA extraction and reverse transcription-PCR protocol for detection of nifH gene expression by Azotobacter vinelandii in soil. Appl Environ Microbiol 69:1928–1935
  Article CAS PubMed Google Scholar
• Celis JE, Kruhoffer M, Gromova I, Frederiksen C, Ostergaard M, Thykjaer T, Gromov P, Yu H, Palsdottir H, Magnusson N, Orntoft TF (2000) Gene expression profiling: monitoring transcription and translation products using DNA microarrays and proteomics. FEBS Lett 480:2–16
  Google Scholar
• Dennis P, Edwards EA, Liss SN, Fulthorpe R (2003) Monitoring gene expression in mixed microbial communities by using DNA microarrays. Appl Environ Microbiol 69:769–778
  Article CAS PubMed Google Scholar
• El Fantroussi S, Naveau H, Agathos SN (1998) Anaerobic dechlorinating bacteria. Biotechnol Prog 14:167–188
  Article CAS PubMed Google Scholar
• El Fantroussi S, Urakawa H, Bernhard AE, Kelly JJ, Noble PA, Smidt H, Yershov GM, Stahl DA (2003) Direct profiling of environmental microbial populations by thermal dissociation analysis of native rRNAs hybridized to oligonucleotide microarrays. Appl Environ Microbiol 69:2377–2382
  Article CAS PubMed Google Scholar
• Entcheva P, Liebl W, Johann A, Hartsch T, Streit WR (2001) Direct cloning from enrichment cultures, a reliable strategy for isolation of complete operons and genes from microbial consortia. Appl Environ Microbiol 67:89–99
  Article CAS PubMed Google Scholar
• Esteve-Nunez A, Caballero A, Ramos JL (2001) Biological degradation of 2,4,6-trinitrotoluene. Microbiol Mol Biol Rev 65:335–352
  Article CAS PubMed Google Scholar
• Eyers L, Stenuit B, El Fantroussi S, Agathos SN (2004) Microbial characterization of TNT-contaminated soils and anaerobic TNT degradation: high and unusual denitration activity. In: Verstraete W (ed) Eur Symp Environ Biotechnol 5, Oostende, Belgium, pp 51–54
• Guschin DY, Mobarry BK, Proudnikov D, Stahl DA, Rittman BE, Mirzabekov AD (1997) Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology. Appl Environ Microbiol 63:2397–2402
  CAS PubMed Google Scholar
• Heiss G, Hofmann KW, Trachtmann N, Walters DM, Rouviere P, Knackmuss H-J (2002) npd gene functions of Rhodococcus (opacus) erythropolis HL PM-1 in the initial steps of 2,4,6-trinitrophenol degradation. Microbiology 148:799–806
  Google Scholar
• Heiss G, Trachtmann N, Abe Y, Takeo M, Knackmuss H-J (2003) Homologous npdGI genes in 2,4-dinitrophenol- and 4-nitrophenol-degrading Rhodococcus spp. Appl Environ Microbiol 69:2748–2754
  Article CAS PubMed Google Scholar
• Hughes MA, Williams PA (2001) Cloning and characterization of the pnb genes, encoding enzymes for 4-nitrobenzoate catabolism in Pseudomonas putida TW3. J Bacteriol 183:1225–1232
  Article CAS PubMed Google Scholar
• James KD, Williams PA (1998) ntn genes determining the early steps in the divergent catabolism of 4-nitrotoluene and toluene in Pseudomonas sp. strain TW3. J Bacteriol 180:2043–2049
  CAS PubMed Google Scholar
• James KD, Hughes MA, Williams PA (2000) Cloning and expression of ntnD, encoding a novel NAD(P)+-independent 4-nitrobenzyl alcohol dehydrogenase from Pseudomonas sp. strain TW3. J Bacteriol 182:3136–3141
  Article CAS PubMed Google Scholar
• Johnson GR, Jain RK, Spain JC (2002) Origins of the 2,4-dinitrotoluene pathway. J Bacteriol 184:4219–4232
  Article CAS PubMed Google Scholar
• Kumar A, Larsson O, Parodi D, Liang Z (2000) Silinized nucleic acids: a general platform for DNA immobilization. Nucleic Acids Res 28:E71
  Article CAS PubMed Google Scholar
• Leadbetter JR (2003) Cultivation of recalcitrant microbes: cells are alive, well and revealing their secrets in the 21st century laboratory. Curr Opin Microbiol 6:274–281
  Article CAS PubMed Google Scholar
• Liles MR, Manske BF, Bintrim SB, Handelsman J, Goodman RM (2003) A census of rRNA genes and linked genomic sequences within a soil metagenomic library. Appl Environ Microbiol 69:2684–2691
  Article CAS PubMed Google Scholar
• Parales JV, Kumar A, Parales RE, Gibson DT (1996) Cloning and sequencing of the genes encoding 2-nitrotoluene dioxygenase from Pseudomonas sp. JS42. Gene 181:57–61
  Article CAS PubMed Google Scholar
• Parro V, Moreno-Paz M (2003) Gene function analysis in environmental isolates: the nif regulon of the strict iron oxidizing bacterium Leptospirillum ferrooxidans. Proc Natl Acad Sci USA 100:7883–7888
  Article CAS PubMed Google Scholar
• Pas BA van de, Jansen S, Dijkema C, Schraa G, Vos WM de, Stams AJ (2001) Energy yield of respiration on chloroaromatic compounds in Desulfitobacterium dehalogenans. Appl Environ Microbiol 67:3958–3963
  Article PubMed Google Scholar
• Quaiser A, Ochsenreiter T, Lanz C, Schuster SC, Treusch AH, Eck J, Schleper C (2003) Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics. Mol Microbiol 50:563–575
  Article CAS PubMed Google Scholar
• Radajewski S, Ineson P, Parekh NR, Murrell JC (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403:646–649
  Article CAS PubMed Google Scholar
• Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA, MacNeil IA, Micor C, Tiong CL, Gilman M, Osburne MS, Clardy J, Handelsman J, Goodman RM (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66:2541–2547
  Article CAS PubMed Google Scholar
• Rosselló-Mora R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39–67
  Google Scholar
• Schloss PD, Handelsman J (2003) Biotechnological prospects from metagenomics. Curr Opin Microbiol 14:303–310
  Article CAS Google Scholar
• Schut G, Zhou J, Adams MW (2001) DNA microarray analysis of the hyperthermophilic archaeon Pyrococcus furiosus: evidence for a new type of sulfur-reducing enzyme complex. J Bacteriol 183:7027–7036
  Article CAS PubMed Google Scholar
• Sebat JL, Colwell FS, Crawford RL (2003) Metagenomic profiling: microarray analysis of an environmental genomic library. Appl Environ Microbiol 69:4927–4934
  Article CAS PubMed Google Scholar
• Shizuya H, Simon M (1992) Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an _F_-factor-based vector. Proc Natl Acad Sci USA 89:8794–8797
  CAS PubMed Google Scholar
• Torsvik V, Øvreås L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5:240–245
  Article CAS PubMed Google Scholar
• Urakawa H, El Fantroussi S, Smidt H, Smoot JC, Tribou EH, Kelly JJ, Noble PA, Stahl DA (2003) Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays. Appl Environ Microbiol 69:2848–2856
  Article CAS PubMed Google Scholar
• Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu DY, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74
  Article CAS PubMed Google Scholar
• Walters DM, Russ R, Knackmuss H, Rouviere PE (2001) High-density sampling of a bacterial operon using mRNA differential display. Gene 273:305–315
  Article CAS PubMed Google Scholar
• Ward DM, Weller R, Bateson MM (1990) 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 344:63–65
  Article Google Scholar
• Wu L, Thompson DK, Li G, Hurt RA, Tiedje JM, Zhou J (2001) Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl Environ Microbiol 67:5780–5790
  Article CAS PubMed Google Scholar
• Ye RW, Tao W, Bedzyk L, Young T, Chen M, Li G (2000) Global gene expression profiles of Bacillus subtilis grown under anaerobic conditions. J Bacteriol 182:4458–4465
  Article CAS PubMed Google Scholar
• Ye RW, Wang T, Bedzyk L, Croker KM (2001) Applications of DNA microarrays in microbial systems. J Microbiol Methods 47:257–272
  Article CAS PubMed Google Scholar
• Zhou J, Thompson DK (2002) Challenges in applying microarrays to environmental studies. Curr Opin Biotechnol 13:204–207
  Article CAS PubMed Google Scholar