Species-specific detection of hydrocarbon-utilizing bacteria

Journal of Microbiological Methods - Tập 39 - Trang 59-78 - 1999
Vincent L Wilson1,2, Brent C Tatford1, Xiuqin Yin1,2, Sean C Rajki1, Maud M Walsh1, Paul LaRock3
1Institute of Environmental Studies, Louisiana State University, Baton Rouge, LA 70803, USA
2Institute for Mutagenesis, Louisiana State University, Baton Rouge, LA 70803, USA
3Department of Oceanography and Coastal Studies, Louisiana State University, Baton Rouge, LA 70803, USA

Tài liệu tham khảo

Barany, 1991, The ligase chain reaction in a PCR world, PCR Methods Appl., 1, 5, 10.1101/gr.1.1.5 Bochner, 1989, Sleuthing out bacterial identities, Nature, 339, 157, 10.1038/339157a0 Bossio, 1998, Impacts of carbon and flooding on soil microbial communities: phospholipid fatty acid profiles and substrate utilization, Microb. Ecol., 35, 265, 10.1007/s002489900082 Bossio, 1998, Determinants of soil microbial communities: effects of agricultural management, season, and soil type on phospholipid fatty acid profiles, Microb. Ecol., 36, 1, 10.1007/s002489900087 Braun-Howland, 1993, Use of a simplified cell blot technique and 16S rRNA-directed probes for identification of common environmental isolates, Appl. Environ. Microbiol., 59, 3219, 10.1128/AEM.59.10.3219-3224.1993 Brosius, 1981, Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli, J. Mol. Biol., 148, 107, 10.1016/0022-2836(81)90508-8 Chatelut, 1995, Epidemiological typing of Stenotrophomonas (Xanthomonas) maltophilia by PCR, J. Clin. Microbiol., 33, 912, 10.1128/JCM.33.4.912-914.1995 Davies, 1997, CFTR gene transfer reduces the binding of Pseudomonas aeruginosa to cystic fibrosis respiratory epithelium, Am. J. Respir. Cell Mol. Biol., 16, 657, 10.1165/ajrcmb.16.6.9191467 DeBruijn, 1992, Use of repetitive (repetitive extragenic palindromic and enterobacterial repetitive intergenic consensus) sequences and the polymerase chain reaction to fingerprint the genomes of Rhizobium meliloti isolates and other soil bacteria, Appl. Environ. Microbiol., 58, 2180, 10.1128/AEM.58.7.2180-2187.1992 DeLong, 1985, Phylogenetic stains: ribosomal-based probes for the identification of single cells, Science, 243, 1360, 10.1126/science.2466341 Deziel, 1996, Biosurfactant production by a soil Pseudomonas strain growing on polycyclic aromatic hydrocarbons, Appl. Environ. Microbiol., 62, 1908, 10.1128/AEM.62.6.1908-1912.1996 Farmer, 1973, Isolation of Serratia marcescens on deoxyribonuclease–toluidine blue–cephalothin agar, Appl. Microbiol., 25, 151, 10.1128/AEM.25.1.151-152.1973 Hu, 1994, Evolutionary trail of the mitochondrial genome as based on human 16S rDNA pseudogenes, Gene, 147, 197, 10.1016/0378-1119(94)90065-5 Hugenholtz, 1996, Identifying microbial diversity in the natural environment: a molecular phylogenetic approach, TIBTECH, 14, 190, 10.1016/0167-7799(96)10025-1 Lane, 1985, Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses, Proc. Natl. Acad. Sci. USA, 82, 6955, 10.1073/pnas.82.20.6955 Liang, 1996, Mitochondrial DNA copy number changes in human gliomas, Cancer Lett., 105, 167, 10.1016/0304-3835(96)04276-0 Lindstrom, 1991, Microbial populations and hydrocarbon biodegradation potentials in fertilized shoreline sediments affected by the T/V Exxon Valdez oil spill, Appl. Environ. Microbiol., 57, 2514, 10.1128/AEM.57.9.2514-2522.1991 Marchesi, 1998, Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA, Appl. Environ. Microbiol., 64, 795, 10.1128/AEM.64.2.795-799.1998 Marmur, 1961, A procedure for the isolation of deoxyribonucleic acid from micro-organisms, J. Mol. Biol., 3, 208, 10.1016/S0022-2836(61)80047-8 Moyer, 1994, Estimation of diversity and community structure through restriction length polymorphism distribution analysis of bacterial 16S rRNA genes from a microbial mat at an active hydrothermal vent system, Loihi Seamount, Hawaii, Appl. Environ. Microbiol., 60, 871, 10.1128/AEM.60.3.871-879.1994 Muyzer, 1993, Profiling of microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction amplified genes coding for 16S rRNA, Appl. Environ. Microbiol., 59, 695, 10.1128/AEM.59.3.695-700.1993 Olsen, 1991, The ribosomal RNA database project, Nucleic Acids Res., 19, 2017, 10.1093/nar/19.17.4817 Pennanen, 1998, Structure of a microbial community in soil after prolonged addition of low levels of simulated acid rain, Appl. Environ. Microbiol., 64, 2173, 10.1128/AEM.64.6.2173-2180.1998 Pier, 1997, Cystic fibrosis transmembrane conductance regulator is an epithelial cell receptor for clearance of Pseudomonas aeruginosa from the lung, Proc. Natl. Acad. Sci. USA, 4, 12088, 10.1073/pnas.94.22.12088 Sattler, D.L., 1997. Bioremediation of contaminated groundwater at two former wood preserving facilities. Louisiana State University Master’s Thesis, Baton Rouge, LA. Shen, 1998, Identification of hydrocarbon-degrading bacteria in soil by reverse sample genome probing, Appl. Environ. Microbiol., 64, 637, 10.1128/AEM.64.2.637-645.1998 Suzuki, 1996, Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR, Appl. Environ. Microbiol., 62, 625, 10.1128/AEM.62.2.625-630.1996 Tani, 1998, Development of a direct in situ PCR method for detection of specific bacteria in natural environments, Appl. Environ. Microbiol., 64, 1536, 10.1128/AEM.64.4.1536-1540.1998 Teske, 1996, Molecular identification of bacteria from a coculture by denaturing gradient gel electrophoresis of 16S ribosomal DNA fragments as a tool for isolation in pure cultures, Appl. Environ. Microbiol., 62, 4210, 10.1128/AEM.62.11.4210-4215.1996 van Couwenberghe, 1995, Genomic fingerprinting of epidemic and endemic strains of Stenotrophomonas maltophilia (formerly Xanthomonas maltophilia) by arbitrarily primed PCR, J. Clin. Microbiol., 33, 1289, 10.1128/JCM.33.5.1289-1291.1995 Wang, 1996, PCR detection and quantitation of predominant anaerobic bacteria in human and animal fecal samples, Appl. Environ. Microbiol., 62, 1242, 10.1128/AEM.62.4.1242-1247.1996 Welsh, 1990, Fingerprinting genomes using PCR with arbitrary primers, Nucleic Acids Res., 18, 7213, 10.1093/nar/18.24.7213 Wheeler, 1996, The oligonucleotide probe database, Appl. Environ. Microbiol., 62, 3557, 10.1128/AEM.62.10.3557-3559.1996 Wiedmann, 1992, Discrimination of Listeria monocytogenes from other Listeria species by ligase chain reaction, Appl. Environ. Microbiol., 58, 3443, 10.1128/AEM.58.11.3443-3447.1992 Williams, 1990, DNA polymorphisms amplified by arbitrary primers are useful as genetic markers, Nucleic Acids Res., 18, 6531, 10.1093/nar/18.22.6531 Wilson, 1996, Human colonic biota studied by ribosomal DNA sequence analysis, Appl. Environ. Microbiol., 62, 2273, 10.1128/AEM.62.7.2273-2278.1996 Wilson, 1989, Alkyl and aryl carcinogen adducts detected in human peripheral lung, Carcinogenesis, 10, 2149, 10.1093/carcin/10.11.2149 Wilson, 1999, Lee. W.R., Needle-in-a-Haystack detection and identification of base substitution mutations in human tissues, Mutat. Res. Genom., 406, 79, 10.1016/S1383-5726(99)00005-9 Winn-Deen, 1993, High density multiplex mutation analysis using the oligonucleotide ligation assay (OLA) and sequence-coded separation, Am. J. Hum. Genet., 53, 1512 Woese, 1987, Bacterial evolution, Microbiol. Rev., 51, 221, 10.1128/MR.51.2.221-271.1987