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References

  • Alexander DC, Costanzo MA, Guzzo J, Cai J, Charoensri N, Diorio C, Dubow MS (2000) Blazing towards the next millennium: luciferase fusions to identify genes responsive to environmental stress. Water Air Soil Pollut 123:81–94

    Article  CAS  Google Scholar 

  • Alfreider A, Vogt C, Babel W (2003) Expression of chlorocatechol 1,2-dioxygenase and chlorocatechol 2,3-dioxygenase genes in chlorobenzene-contaminated subsurface samples. Appl Environ Microbiol 69:1372–1376

    Article  CAS  Google Scholar 

  • Amann R, Kühl M (1998) In situ methods for assessment of microorganisms and their activities. Curr Opin Microbiol 1: 352–358

    Article  CAS  Google Scholar 

  • Amann R, Ludwig W (2000) Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology. FEMS Microbiol Rev 24:555–565

    Article  CAS  Google Scholar 

  • Amann R, Snaidr J, Wagner M, Ludwig W, Schleifer KH (1996) In situ visualization of high genetic diversity in a natural microbial community. J Bacteriol 178:3496–3500

    CAS  Google Scholar 

  • Amann R, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA (1990) Combination of 16S ribosomal-RNA-targeted oligonucleotide probes with flow-cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 56:1919–1925

    CAS  Google Scholar 

  • Amarger N (2002) Genetically modified bacteria in agriculture. Biochimie 84:1061–1072

    Article  CAS  Google Scholar 

  • Applegate BM, Kehrmeyer SR, Sayler GS (1998) A chromosomally based tod-luxCDABE whole-cell reporter for benzene, toluene, ethylbenzene, and xylene (BTEX) sensing. Appl Environ Microbiol 64:2730–2735

    CAS  Google Scholar 

  • Assmus B, Hutzler P, Kirchhof G, Amann R, Lawrence JR, Hartmann A (1995) In-Situ localization of Azospirillum brasilense in the rhizosphere of wheat with fluorescently labeled, ribosomal-RNA-targeted oligonucleotide probes and scanning confocal laser microscopy. Appl Environ Microbiol 61:1013–1019

    CAS  Google Scholar 

  • Auman AJ, Lidstrom ME (2002) Analysis of sMMO-containing Type I methanotrophs in Lake Washington sediment. Environ Microbiol 4: 517–524

    Article  CAS  Google Scholar 

  • Bae YS, Knudsen GR (2000) Cotransformation of Trichoderma harzianum with betaglucuronidase and green fluorescent protein genes provides a useful tool formonitoring fungal growth and activity in natural soils. Appl Environ Microbiol 66:810–815

    Article  CAS  Google Scholar 

  • Baker PW, Futamata H, Harayama S, Watanabe K (2001) Molecular diversity of pMMO and sMMO in a TCE-contaminated aquifer during bioremediation. FEMS Microbiol Ecol 38:161–167

    CAS  Google Scholar 

  • Barkay T, Olson BH (1986) Phenotypic and genotypic adaptation of aerobic heterotrophic sediment bacterial communities to mercury stress. Appl Environ Microbiol 52:403–406

    CAS  Google Scholar 

  • Barkay T, Fouts DL, Olson BH (1985) Preparation of a DNA gene probe for detection of mercury resistance genes in gram-negative bacterial communities. Appl Environ Microbiol 49:686–692

    CAS  Google Scholar 

  • Behrens S, Ruhland C, Inacio J, Huber H, Fonseca A, Spencer-Martins I, Fuchs BM, Amann R (2003) In situ accessibility of small-subunit rRNA of members of the domains Bacteria, Archaea, and Eucarya to Cy3-labeled oligonucleotide probes. Appl Environ Microbiol 69:1748–1758

    CAS  Google Scholar 

  • Bergero R, Harrier LA, Franken P (2003) Reporter genes: applications to the study of arbuscular mycorrhizal (AM) fungi and their symbiotic interactions with plant. Plant Soil 255:143–155

    Article  CAS  Google Scholar 

  • Bertilsson S, Cavanaugh CM, Polz MF (2002) Sequencing-independent method to generate oligonucleotide probes targeting a variable region in bacterial 16S rRNA by PCR with detachable primers. Appl Environ Microbiol 68:6077–6086

    Article  CAS  Google Scholar 

  • Bintrim SB, Donohue TJ, Handelsman J, Roberts GP, Goodman RM (1997) Molecular phylogeny of Archaea from soil. Proc Natl Acad Sci USA 94:277–282

    Article  CAS  Google Scholar 

  • Bogan BW, Schoenike B, Lamar RT, Cullen D (1996) Expression of lip genes during growth in soil and oxidation of anthracene by Phanerochaete chrysosporium. Appl Environ Microbiol 62:3697–3703

    CAS  Google Scholar 

  • Borneman J, Skroch PW, Osullivan KM, Palus JA, Rumjanek NG, Jansen JL, Nienhuis J, Triplett EW (1996) Molecular microbial diversity of an agricultural soil in Wisconsin. Appl Environ Microbiol 62: 1935–1943

    CAS  Google Scholar 

  • Boschker HTS, Middelburg JJ (2002) Stable isotopes and biomarkers in microbial ecology. FEMS Microbiol Ecol 40:85–95

    CAS  Google Scholar 

  • Brennerova MV, Crowley DE (1994) Direct detection of rhizosphere-colonizing Pseudomonas sp. using an Escherichia coli ribosomal RNA promoter in a Tn7-lux system. FEMS Microbiol Ecol 14:319–330

    CAS  Google Scholar 

  • Britz ML, Simonov N, Chun UK (1997) Stabilization of bioluminescence of immobilized Photobacterium phosphoreum and monitoring of environmental pollutants. J Microbiol Biotechnol 7:242–249

    CAS  Google Scholar 

  • Burlage RS, Palumbo AV, Heitzer A, Sayler G (1994) Bioluminescent reporter bacteria detect contaminants in soil samples. Appl Biochem Biotechnol 45/46:731–740

    Article  Google Scholar 

  • Casavant NC, Beattie GA, Phillips GJ, Halverson LJ (2002) Site-specific recombination based genetic system for reporting transient or low-level gene expression. Appl Environ Microbiol 68:3588–3596

    Article  CAS  Google Scholar 

  • Cho JC, Tiedje JM (2001) Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays. Appl Environ Microbiol 67:3677–3682

    Article  CAS  Google Scholar 

  • Choi HY, Ryder MH, Gillings MR, Stokes HW, Ophel-Keller KM, Veal DA (2003) Survival of a lacZY-marked strain of Pseudomonas corrugata following a field release. FEMS Microbiol Ecol 43:367–374

    CAS  Google Scholar 

  • Christensen BB, Sternberg C, Molin S (1996) Bacterial plasmid conjugation on semi-solid surfaces monitored with the green fluorescent protein (GFP) from Aequorea victoria as a marker. Gene 173:59–65

    Article  CAS  Google Scholar 

  • Christensen BB, Sternberg C, Andersen JB, Eberl L, Moller S, Givskov M, Molin S (1998) Establishment of new genetic traits in a microbial biofilm community. Appl Environ Microbiol 64:2247–2255

    CAS  Google Scholar 

  • Corich V, Giacomini A, Vian P, Vendramin E, Carlot M, Basaglia M, Squartini A, Casella S, Nuti MP (2001) Aspects of marker/reporter stability and selectivity in soil microbiology. Microbial Ecol 41: 333–340

    CAS  Google Scholar 

  • Czarnetzki AB, Tebbe CC (2004) Detection and phylogenetic analysis of Wolbachia in Collembola. Environ Microbiol 6:35–44

    Article  CAS  Google Scholar 

  • Dahlberg C, Bergstrom M, Hermansson M (1998) In situ detection of high levels of horizontal plasmid transfer in marine bacterial communities. Appl Environ Microbiol 64:2670–2675

    CAS  Google Scholar 

  • Daims H, Nielsen JL, Nielsen PH, Schleifer KH, Wagner M (2001a) In situ characterization of Nitrospira-like nitrite-oxidizing bacteria active in wastewater treatment plants. Appl Environ Microbiol 67: 5273–5284

    CAS  Google Scholar 

  • Daims H, Ramsing NB, Schleifer KH, Wagner M (2001b) Cultivation-independent, semi-automatic determination of absolute bacterial cell numbers in environmental samples by fluorescence in situ hybridization. Appl Environ Microbiol 67:5810–5818

    CAS  Google Scholar 

  • Daly K, Sharp RJ, McCarthy AJ (2000) Development of nucleotide probes and PCR primers for detecting phylogenetic subgroups of sulfate-reducing bacteria. Microbiology UK 146:1693–1705

    CAS  Google Scholar 

  • De Lorenzo V, Glover A, Hill P, Jansson JK, Jorgenson K, Lindström K, Mergeay M, Molin S, Morgan A, Nybroe O, Oliver J, Prosser J, Romantshuk M, Selbitschka W, Tebbe C, Top E (1998) Marker genes as tags for monitoring microorganisms in nature — an opinion. Centraltryckeriet AB, Boras, Sweden

    Google Scholar 

  • Dojka MA, Hugenholtz P, Haack SK, Pace NR (1998) Microbial diversity in a hydrocarbon and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl Environ Microbiol 64:3869–3877

    CAS  Google Scholar 

  • Dollard MA, Billard P (2003) Whole-cell bacterial sensors for the monitoring of phosphate bioavailability. J Microbiol Methods 55: 221–229

    Article  CAS  Google Scholar 

  • Drahos SJ, Hemming BC, McPherson S (1986) Tracking recombinant organisms in the environment: β-galactosidase as a selectable non-antibiotic marker for fluoresecent pseudomonads. Bio/Technology 4: 439–444

    Article  CAS  Google Scholar 

  • Edwards U, Rogall T, Blöcker H, Emde M, Böttger EC (1990) Isolation and direct sequencing of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 17:7843–7853

    Google Scholar 

  • Fitts R, Diamond M, Hamilton C, Neri M (1983) DNA-DNA hybridization assay for detection of Salmonella spp. in foods. Appl Environ Microbiol 46:1146–1151

    CAS  Google Scholar 

  • Flavier AB, Ganova Raeva LM, Schell MA, Denny TP (1997) Hierarchical autoinduction in Ralstonia solanacearum: control of acyl-homoserine lactone production by a novel autoregulatory system responsive to 3-hydroxypalmitic acid methyl ester. J Bacteriol 179:7089–7097

    CAS  Google Scholar 

  • Fredrickson JK, Bezdicek DF, Brockman FJ, Li SW (1988) Enumeration of Tn5 mutant bacteria in soil by using a most-probable-number-DNA hybridization procedure and antibiotic resistance. Appl Environ Microbiol 54: 446–453

    CAS  Google Scholar 

  • Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60–63

    Article  CAS  Google Scholar 

  • Grunstein M, Hogness DS (1975) Colony hybridization: a method for the isolation of cloned DNAs that contain a specific gene. Proc Natl Acad Sci USA 72:3961–3965

    CAS  Google Scholar 

  • Hakkila K, Maksimow M, Karp M, Virta M (2002) Reporter genes lucFF, luxCDABE, gfp, and dsred have different characteristics in whole-cell bacterial sensors. Anal Biochem 301:235–242

    Article  CAS  Google Scholar 

  • Hansen LH, Sorensen SJ (2000) Versatile biosensor vectors for detection and quantification of mercury. FEMS Microbiol Lett 193:123–127

    Article  CAS  Google Scholar 

  • Head IM, Saunders JR, Pickup RW (1998) Microbial evolution, diversity, and ecology: a decade of ribosomal RNA analysis of uncultivated microorganisms. Microb Ecol 35:1–21

    Article  CAS  Google Scholar 

  • Hill WE, Payne WL, Aulisio CCG (1983) Detection and enumeration of virulent Yersinia enterolitica in food by DNA colony hybridization. Appl Environ Microbiol 46:636–641

    CAS  Google Scholar 

  • Hoffmann A, Thimm T, Dröge M, Moore ERB, Munch JC, Tebbe CC (1998) Intergeneric transfer of conjugative and mobilizable plasmids harbored by Escherichia coli in the gut of the soil microarthropod Folsomia candida (Collembola). Appl Environ Microbiol 64: 2652–2659

    CAS  Google Scholar 

  • Holben WE, Jansson JK, Chelm BK, Tiedje JM (1988) DNA probe method for the detection of specific microorganisms in the soil bacterial community. Appl Environ Microbiol 54:703–711

    CAS  Google Scholar 

  • Holden PA, LaMontagne MG, Bruce AK, Miller WG, Lindow SE (2002) Assessing the role of Pseudomonas aeruginosa surface-active gene expression in hexadecane biodegradation in sand. Appl Environ Microbiol 68:2509–2518

    Article  CAS  Google Scholar 

  • Huber R, Burggraf S, Mayer T, Barns SM, Rossnagel P, Stetter KO (1995) Isolation of a hyperthermophilic archeum predicted by in situ RNA analysis. Nature 376:57–58

    Article  CAS  Google Scholar 

  • Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774

    CAS  Google Scholar 

  • Ivask A, Virta M, Kahru A (2002) Construction and use of specific luminescent recombinant bacterial sensors for the assessment of bioavailable fraction of cadmium, zinc,mercury and chromium in the soil. Soil Biol Biochem 34:1439–1447

    Article  CAS  Google Scholar 

  • Jacob GBA, Colin DCB, Paton GI (2001) Comparison of response of six different luminescent bacterial bioassays to bioremediation of five contrasting oils. J Environ Monit 3:404–410

    Google Scholar 

  • Jaeger CH, Lindow SE, Miller S, Clark E, Firestone MK (1999) Mapping of sugar and amino acid availability in soil around roots with bacterial sensors of sucrose and tryptophan. Appl Environ Microbiol 65: 2685–2690

    CAS  Google Scholar 

  • Jansson JK (2003) Marker and reporter genes: illuminating tools for environmental microbiologists. Curr Opin Microbiol 6:310–316

    CAS  Google Scholar 

  • Jansson JK, van Elsas JD, Bailey MJ (2000) Tracking genetically engineered microorganisms. Landes Bioscience, Georgetown, Texas

    Google Scholar 

  • Killham K, Yeomans C (2001) Rhizosphere carbon flow measurement and implications: from isotopes to reporter genes. Plant Soil 232: 91–96

    Article  CAS  Google Scholar 

  • Kostrzynska M, Leung KT, Lee H, Trevors JT (2002) Green fluorescent protein-based biosensor for detecting SOS-inducing activity of genotoxic compounds. J Microbiol Methods 48:43–51

    Article  CAS  Google Scholar 

  • Kowalchuk GA, Stienstra AW, Heilig GHJ, Stephen JR, Woldendorp JW (2000) Changes in the community structure of ammonia-oxidizing bacteria during secondary succession of calcareous grasslands. Environ Microbiol 2: 99–110

    Article  CAS  Google Scholar 

  • Kluepfel DA, Kline EL, Skipper HD, Hughes TA, Gooden DT, Drahos DJ, Barry GF, Hemming BC, Brandt EJ (1991) The release and tracking of genetically engineered bacteria in the environment. Phytopathol 81: 348–352

    Google Scholar 

  • Leveau JHJ, Lindow SE (2002) Bioreporters in microbial ecology. Curr Opin Microbiol 5:259–265

    Article  Google Scholar 

  • Liesack W, Stackebrandt E (1992) Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. J Bacteriol 174:5072–5078

    CAS  Google Scholar 

  • Liu WT, Marsh TL, Cheng H, Forney LJ (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63: 4516–4522

    CAS  Google Scholar 

  • Loper JE, Lindow SE (1994) A biological sensor for iron available to bacteria in their habitats on plant surfaces. Appl Environ Microbiol 60:1934–1941

    CAS  Google Scholar 

  • Lueders T, Friedrich MW (2003) Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Appl Environ Microbiol 69:320–326

    Article  CAS  Google Scholar 

  • Lueders T, Chin KJ, Conrad R, Friedrich M (2001) Molecular analyses of methyl-coenzyme M reductase alpha-subunit (McrA) genes in rice field soil and enrichment cultures reveal the methanogenic phenotype of a novel archaeal lineage. Environ Microbiol 3:194–204

    Article  CAS  Google Scholar 

  • Luton PE, Wayne JM, Sharp RJ, Riley PW (2002) The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. Microbiol SGM 148:3521–3530

    CAS  Google Scholar 

  • Manefield M, Turner SL (2002) Quorum sensing in context: out of molecular biology and into microbial ecology. Microbiol SGM 148: 3762–3764

    CAS  Google Scholar 

  • Manefield M, Whiteley AS, Griffiths RI, Bailey MJ (2002) RNA stable isotope probing, a novel means of linking microbial community function to Phylogeny. Appl Environ Microbiol 68:5367–5373

    Article  CAS  Google Scholar 

  • Marchesi JR, Weightman AJ (2003) Comparing the dehalogenase gene pool in cultivated alpha-halocarboxylic acid-degrading bacteria with the environmental metagene pool. Appl Environ Microbiol 69:4375–4382

    Article  CAS  Google Scholar 

  • Metcalfe AC, Krsek M, Gooday GW, Prosser JI, Wellington EMH (2002) Molecular analysis of a bacterial chitinolytic community in an upland pasture. Appl Environ Microbiol 68:5042–5050

    Article  CAS  Google Scholar 

  • Miller WG, Brandl MT, Quinones B, Lindow SE (2001) Biological sensor for sucrose availability: relative sensitivities of various reporter genes. Appl Environ Microbiol 67:1308–1317

    CAS  Google Scholar 

  • Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700

    CAS  Google Scholar 

  • Muyzer G, Brinkhoff T, Nübel U, Santegoeds C, Schäfer H, Wawer C (1998) Denaturing gradient gel electrophoresis (DGGE) in microbial ecology. In: Akkermans ADL, van Elsas JD, de Bruijn FJ (eds) Molecular microbial ecology manual. Kluwer, Dordrecht, pp 1–27

    Google Scholar 

  • Norton JM, Alzerreca JJ, Suwa Y, Klotz MG (2002) Diversity of ammonia monooxygenase operon in autotrophic ammonia-oxidizing bacteria. Arch Microbiol 177:139–149

    Article  CAS  Google Scholar 

  • Ogram A, Sayler GS, Barkay T (1987) DNA extraction and purification from sediments. J Microbiol Methods 7:57–66

    Article  CAS  Google Scholar 

  • Okuta A, Ohnishi K, Harayama S (1998) PCR isolation of catechol 2,3-dioxygenase gene fragments from environmental samples and their assembly into functional genes. Gene 212:221–228

    Article  CAS  Google Scholar 

  • Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR, Stahl DA (1986) Microbial ecology and evolution: a ribosomal RNA approach. Annu Rev Microbiol 40:337–365

    Article  CAS  Google Scholar 

  • Otsuka J, Terai G, Nakano T (1999) Phylogeny of organisms investigated by the base-pair changes in the stem regions of small and large ribosomal subunit RNAs. J Mol Evol 48:218–235

    CAS  Google Scholar 

  • Pace N, Stahl DA, Lane DJ, Olsen GJ (1986) The analysis of natural microbial populations by rRNA sequences. Adv Microb Ecol 9:1–55

    CAS  Google Scholar 

  • Paerl HW, Steppe TF (2003) Scaling up: the next challenge in environmental microbiology. Environ Microbiol 5:1025–1038

    Article  Google Scholar 

  • Peplies J, Glökner FO, Amann R (2003) Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes. Appl Environ Microbiol 69:1397–1407

    Article  CAS  Google Scholar 

  • Philippot L, Piutti S, Martin-Laurent F, Hallet S, Germon JC (2002) Molecular analysis of the nitrate-reducing community from unplanted and maize-planted soils. Appl Environ Microbiol 68:6121–6128

    Article  CAS  Google Scholar 

  • Porteous F, Killham K, Meharg A (2000) Use of a lux-marked rhizobacterium as a biosensor to assess changes in rhizosphere C flow due to pollutant stress. Chemosphere 41:1549–1554

    Article  CAS  Google Scholar 

  • Prachayasittikul V, Ayudhya CIN, Bulow L (2001) Lighting E. coli cells as biological sensors for Cd2(+). Biotechnol Lett 23: 1285–1291

    Article  CAS  Google Scholar 

  • Prosser JI (2002) Molecular and functional diversity in soil micro-organisms. Plant Soil 244:9–17

    Article  CAS  Google Scholar 

  • Radajewski S, Ineson P, Parekh NR, Murrell JC (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403:646–649

    CAS  Google Scholar 

  • Ranjard L, Richaume A, Jocteur-Monrozier L, Nazaret S (1997) Response of soil bacteria to Hg(II) in relation to soil characteristics and cell location. FEMS Microbiol Ecol 24:321–331

    CAS  Google Scholar 

  • Rasmussen LD, Sorensen SJ, Turner RR, Barkay T (2000) Application of a mer-lux biosensor for estimating bioavailable mercury in soil. Soil Biol Biochem 32:639–646

    Article  CAS  Google Scholar 

  • Ripp S, Nivens DE, Ahn Y, Werner C, Jarrell J, Easter JP, Cox CD, Burlage RS, Sayler GS (2000) Controlled field release of a bioluminescent genetically engineered microorganism for bioremediation process monitoring and control. Environ Sci Technol 34:846–853

    CAS  Google Scholar 

  • Rossbach S, Kukuk ML, Wilson TL, Feng SF, Pearson MM, Fisher MA (2000) Cadmium regulated gene fusions in Pseudomonas fluorescens. Environ Microbiol 2:373–382

    Article  CAS  Google Scholar 

  • Saiki RK, Scharf S, Faloona F, Mullis KB, Horn GT, Erlich HA, Arnheim N (1985) Enzymatic amplification of β-globin genomic sequences and restriction site analysis for the diagnosis of sickle-cell anemia. Science 230:1350–1354

    CAS  Google Scholar 

  • Sayler GS, Ripp S (2000) Field applications of genetically engineered microorganisms for bioremediation processes. Curr Opin Biotechnol 11: 286–289

    Article  CAS  Google Scholar 

  • Sayler GS, Shields MS, Tedford E, Breen A, Hooper S, Sirotkin K, Davis JW (1985) Application of DNA-DNA colony hybridization to the detection of catabolic genotypes in environmental samples. Appl Environ Microbiol 49:1295–1303

    CAS  Google Scholar 

  • Schwieger F, Tebbe CC (1998) A new approach to utilize PCR-single-strand-conformation polymorphism for 16S rRNA gene-based microbial community analysis. Appl Environ Microbiol 64:4870–4876

    CAS  Google Scholar 

  • Selbitschka W, Pühler A, Simon R (1992) The construction of recA deficient containment. Rhizobium meliloti and R. leguminosarum strains marked with gusA or luc cassettes for use in risk assessment studies. Mol Ecol 1:9–19

    CAS  Google Scholar 

  • Shaw PD, Ping G, Daly SL, Cha C, Cronan JE, Rinehart KL, Farrand SK (1997) Detecting and characterizing N-acyl-homoserine lactone signal molecules by thin-layer chromatography. Proc Natl Acad Sci USA 94: 6036–6041

    CAS  Google Scholar 

  • Simpson ML, Sayler GS, Applegate BM, Ripp S, Nivens DE, Paulus MJ, Jellison GE (1998) Bioluminescent-bioreporter integrated circuits form novel whole-cell biosensors. Trends Biotechnol 16:332–338

    Article  CAS  Google Scholar 

  • Small J, Call DR, Brockman FJ, Straub TM, Chandler DP (2001) Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays. Appl Environ Microbiol 67:4708–4716

    Article  CAS  Google Scholar 

  • Smalla K, Krögerrecklenfort E, Heuer H, Dejonghe W, Top E, Osborn M, Niewint J, Tebbe C, Barr M, Bailey M, Greated A, Thomas C, Turner S, Young P, Nikolakopoulou D, Karagouni A, Wolters A, van Elsas JD, Dronen K, Sandaa R, Borin S, Brabhu J, Grohmann E, Sobecky P (2000) PCR-based detection of mobile genetic elements in total community DNA. Microbiology UK 146:1256–1257

    CAS  Google Scholar 

  • Smit E, van Elsas JD, van Veen JA, Devos WM (1991) Detection of plasmid transfer from Pseudomonas fluorescens to indigenous bacteria in soil by using bacteriophage Phi-R2f for donor counterselection. Appl Environ Microbiol 57:3482–3488

    CAS  Google Scholar 

  • Sorensen J, Jensen LE, Nybroe O (2001) Soil and rhizosphere as habitats for Pseudomonas inoculants: new knowledge on distribution, activity and physiological state derived from micro-scale and single-cell studies. Plant Soil 232:97–108

    CAS  Google Scholar 

  • Stahl DA, Lane DJ, Olsen GJ, Pace NR (1984) Analysis of hydrothermal vent-associated symbionts by ribosomal RNA sequences. Science 224: 409–411

    CAS  Google Scholar 

  • Stahl DA, Lane DJ, Olsen GJ, Pace NR (1985) Characterization of a Yellowstone hot spring microbial community by 5S rRNA sequences. Appl Environ Microbiol 49:1379–1384

    CAS  Google Scholar 

  • Steffan RJ, Goksoyr J, Bej AK, Atlas RM (1988) Recovery of DNA from soils and sediments. Appl Environ Microbiol 54:2908–2915

    CAS  Google Scholar 

  • Suarez A, Güttler A, Strätz M, Staendner LH, Timmis KN, Guzman CA (1997) Green fluorescent protein-based reporter systems for genetic analysis of bacteria including monocopy applications. Gene 196:69–74

    Article  CAS  Google Scholar 

  • Suzuki MT, Giovannoni SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62:625–630

    CAS  Google Scholar 

  • Tebbe CC (2000) Use of luc-tagged genetically modified microorganisms (GMMs) to study rhizobial ecology in soil columns, field lysimeters and field plots. In: Jansson JK, vanElsas JD, Bailey MJ (eds) Tracking genetically engineered microorganisms. Landes Bioscience, Georgetown, Texas, pp 127–137

    Google Scholar 

  • Tebbe CC, Vahjen W (1993) Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant-DNA from bacteria and a yeast. Appl Environ Microbiol 59:2657–2665

    CAS  Google Scholar 

  • Tebbe CC, Schmalenberger A, Peters S, Schwieger F (2001) Single-strand conformation polymorphism (SSCP) for microbial community analysis. In: Rochelle PA (ed) Environmental molecular microbiology: protocols and applications. Horizon Scientific, Wymondham, UK, pp 161–175

    Google Scholar 

  • Thimm T, Hoffmann A, Fritz I, Tebbe CC (2001) Contribution of the earthworm Lumbricus rubellus (Annelida, Oligochaeta) to the establishment of plasmids in soil bacterial communities. Microbial Ecol 41: 341–351

    CAS  Google Scholar 

  • Tiedje JM, Asuming-Brempong S, Nusslein K, Marsh TL, Flynn SJ (1999) Opening the black box of soil microbial diversity. Appl Soil Ecol 13:109–122

    Article  Google Scholar 

  • Tom-Petersen A, Hosbond C, Nybroe O (2001) Identification of copper-induced genes in Pseudomonas fluorescens and use of a reporter strain to monitor bioavailable copper in soil. FEMS Microbiol Ecol 38: 59–67

    CAS  Google Scholar 

  • Torsvik V, Ovreas L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5:240–245

    Article  CAS  Google Scholar 

  • Tourasse NJ, Gouy M (1997) Evolutionary distances between nucleotide sequences based on the distribution of substitution rates among sites as estimated by parsimony. Mol Biol Evol 14:287–298

    CAS  Google Scholar 

  • Tunlid A (1999) Molecular biology: a linkage between microbial ecology, general ecology and organismal biology. Oikos 85:177–189

    CAS  Google Scholar 

  • Van Elsas JD, Trevors JT (1990) Plasmid transfer to indigenous bacteria in soil and rhizospheres: problems and perspectives. In: Fry JC, Day MJ (eds) Bacterial genetics in natural environments. Chapman and Hall, London, pp 188–199

    Google Scholar 

  • Van Overbeek LS, van Elsas JD (1995) Root exudate-induced promoter activity in Pseudomonas fluorescens mutants in the wheat rhizosphere. Appl Environ Microbiol 61:890–898

    Google Scholar 

  • Watanabe K, Teramoto M, Futamata H, Harayama S (1998) Molecular detection, isolation, and physiological characterization of functionally dominant phenol-degrading bacteria in activated sludge. Appl Environ Microbiol 64:4396–4402

    CAS  Google Scholar 

  • Weilbo J, Skorupska A (2001) Construction of improved vectors and cassettes containing gusA and antibiotic resistance genes for studies of transcriptional activity and bacterial localization. J Microbiol Methods 45:197–205

    Google Scholar 

  • Weller R, Ward DM (1989) Selective recovery of 16S rRNA sequences from natural microbial communities in the form of cDNA. Appl Environ Microbiol 55:1818–1822

    CAS  Google Scholar 

  • Wellington EMH, Berry A, Krsek M (2003) Resolving functional diversity in relation to microbial community structure in soil: exploiting genomics and stable isotope probing. Curr Opin Microbiol 6:295–301

    Article  CAS  Google Scholar 

  • Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 95:6578–6583

    Article  CAS  Google Scholar 

  • Widmer F, Shaffer BT, Porteous LA, Seidler RJ (1999) Analysis of nifH gene pool complexity in soil and litter at a Douglas fir forest site in the Oregon Cascade Mountain Range. Appl Environ Microbiol 65: 374–380

    CAS  Google Scholar 

  • Willardson BM, Wilkins JF, Rand TA, Schupp JM, Hill KK, Keim P, Jackson PJ (1998) Development and testing of a bacterial biosensor for toluene-based environmental contaminants. Appl Environ Microbiol 64: 1006–1012

    CAS  Google Scholar 

  • Williamson N, Brian P, Wellington EMH (2000) Molecular detection of bacterial and streptomycete chitinases in the environment. Antonie Van Leeuwenhoek 78:315–321

    Article  CAS  Google Scholar 

  • Woese C, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74:5088–5090

    CAS  Google Scholar 

  • Yinon J (2002) Field detection and monitoring of explosives. Trac Trends Anal Chem 21:292–301

    Article  CAS  Google Scholar 

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Tebbe, C.C. (2005). Marker Genes in Soil Microbiology. In: Varma, A., Buscot, F. (eds) Microorganisms in Soils: Roles in Genesis and Functions. Soil Biology, vol 3. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-26609-7_17

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