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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
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
Amann R, Kühl M (1998) In situ methods for assessment of microorganisms and their activities. Curr Opin Microbiol 1: 352–358
Amann R, Ludwig W (2000) Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology. FEMS Microbiol Rev 24:555–565
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
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
Amarger N (2002) Genetically modified bacteria in agriculture. Biochimie 84:1061–1072
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
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
Auman AJ, Lidstrom ME (2002) Analysis of sMMO-containing Type I methanotrophs in Lake Washington sediment. Environ Microbiol 4: 517–524
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
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
Barkay T, Olson BH (1986) Phenotypic and genotypic adaptation of aerobic heterotrophic sediment bacterial communities to mercury stress. Appl Environ Microbiol 52:403–406
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
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
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
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
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
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
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
Boschker HTS, Middelburg JJ (2002) Stable isotopes and biomarkers in microbial ecology. FEMS Microbiol Ecol 40:85–95
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
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
Burlage RS, Palumbo AV, Heitzer A, Sayler G (1994) Bioluminescent reporter bacteria detect contaminants in soil samples. Appl Biochem Biotechnol 45/46:731–740
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
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
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
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
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
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
Czarnetzki AB, Tebbe CC (2004) Detection and phylogenetic analysis of Wolbachia in Collembola. Environ Microbiol 6:35–44
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
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
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
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
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
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
Dollard MA, Billard P (2003) Whole-cell bacterial sensors for the monitoring of phosphate bioavailability. J Microbiol Methods 55: 221–229
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
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
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
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
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
Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60–63
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
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
Hansen LH, Sorensen SJ (2000) Versatile biosensor vectors for detection and quantification of mercury. FEMS Microbiol Lett 193:123–127
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
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
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
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
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
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
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
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
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
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
Jansson JK (2003) Marker and reporter genes: illuminating tools for environmental microbiologists. Curr Opin Microbiol 6:310–316
Jansson JK, van Elsas JD, Bailey MJ (2000) Tracking genetically engineered microorganisms. Landes Bioscience, Georgetown, Texas
Killham K, Yeomans C (2001) Rhizosphere carbon flow measurement and implications: from isotopes to reporter genes. Plant Soil 232: 91–96
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
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
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
Leveau JHJ, Lindow SE (2002) Bioreporters in microbial ecology. Curr Opin Microbiol 5:259–265
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
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
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
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
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
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
Manefield M, Turner SL (2002) Quorum sensing in context: out of molecular biology and into microbial ecology. Microbiol SGM 148: 3762–3764
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
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
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
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
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
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
Norton JM, Alzerreca JJ, Suwa Y, Klotz MG (2002) Diversity of ammonia monooxygenase operon in autotrophic ammonia-oxidizing bacteria. Arch Microbiol 177:139–149
Ogram A, Sayler GS, Barkay T (1987) DNA extraction and purification from sediments. J Microbiol Methods 7:57–66
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
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
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
Pace N, Stahl DA, Lane DJ, Olsen GJ (1986) The analysis of natural microbial populations by rRNA sequences. Adv Microb Ecol 9:1–55
Paerl HW, Steppe TF (2003) Scaling up: the next challenge in environmental microbiology. Environ Microbiol 5:1025–1038
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
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
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
Prachayasittikul V, Ayudhya CIN, Bulow L (2001) Lighting E. coli cells as biological sensors for Cd2(+). Biotechnol Lett 23: 1285–1291
Prosser JI (2002) Molecular and functional diversity in soil micro-organisms. Plant Soil 244:9–17
Radajewski S, Ineson P, Parekh NR, Murrell JC (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403:646–649
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
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
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
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
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
Sayler GS, Ripp S (2000) Field applications of genetically engineered microorganisms for bioremediation processes. Curr Opin Biotechnol 11: 286–289
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
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
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
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
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
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
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
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
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
Stahl DA, Lane DJ, Olsen GJ, Pace NR (1984) Analysis of hydrothermal vent-associated symbionts by ribosomal RNA sequences. Science 224: 409–411
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
Steffan RJ, Goksoyr J, Bej AK, Atlas RM (1988) Recovery of DNA from soils and sediments. Appl Environ Microbiol 54:2908–2915
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
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
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
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
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
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
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
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
Torsvik V, Ovreas L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5:240–245
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
Tunlid A (1999) Molecular biology: a linkage between microbial ecology, general ecology and organismal biology. Oikos 85:177–189
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
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
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
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
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
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
Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 95:6578–6583
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
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
Williamson N, Brian P, Wellington EMH (2000) Molecular detection of bacterial and streptomycete chitinases in the environment. Antonie Van Leeuwenhoek 78:315–321
Woese C, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74:5088–5090
Yinon J (2002) Field detection and monitoring of explosives. Trac Trends Anal Chem 21:292–301
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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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