Marker Genes in Soil Microbiology

  • Christoph C. Tebbe
Part of the Soil Biology book series (SOILBIOL, volume 3)


Marker Gene Appl Environ Soil Microbiology Methane Monooxygenase 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 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 123:81–94CrossRefGoogle Scholar
  2. 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 69:1372–1376CrossRefGoogle Scholar
  3. Amann R, Kühl M (1998) In situ methods for assessment of microorganisms and their activities. Curr Opin Microbiol 1: 352–358CrossRefGoogle Scholar
  4. Amann R, Ludwig W (2000) Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology. FEMS Microbiol Rev 24:555–565CrossRefGoogle Scholar
  5. 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 178:3496–3500Google Scholar
  6. 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 56:1919–1925Google Scholar
  7. Amarger N (2002) Genetically modified bacteria in agriculture. Biochimie 84:1061–1072CrossRefGoogle Scholar
  8. 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 64:2730–2735Google Scholar
  9. 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 61:1013–1019Google Scholar
  10. Auman AJ, Lidstrom ME (2002) Analysis of sMMO-containing Type I methanotrophs in Lake Washington sediment. Environ Microbiol 4: 517–524CrossRefGoogle Scholar
  11. 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 66:810–815CrossRefGoogle Scholar
  12. 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 38:161–167Google Scholar
  13. Barkay T, Olson BH (1986) Phenotypic and genotypic adaptation of aerobic heterotrophic sediment bacterial communities to mercury stress. Appl Environ Microbiol 52:403–406Google Scholar
  14. 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 49:686–692Google Scholar
  15. 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 69:1748–1758Google Scholar
  16. 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 255:143–155CrossRefGoogle Scholar
  17. 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 68:6077–6086CrossRefGoogle Scholar
  18. Bintrim SB, Donohue TJ, Handelsman J, Roberts GP, Goodman RM (1997) Molecular phylogeny of Archaea from soil. Proc Natl Acad Sci USA 94:277–282CrossRefGoogle Scholar
  19. 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 62:3697–3703Google Scholar
  20. 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: 1935–1943Google Scholar
  21. Boschker HTS, Middelburg JJ (2002) Stable isotopes and biomarkers in microbial ecology. FEMS Microbiol Ecol 40:85–95Google Scholar
  22. 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 14:319–330Google Scholar
  23. Britz ML, Simonov N, Chun UK (1997) Stabilization of bioluminescence of immobilized Photobacterium phosphoreum and monitoring of environmental pollutants. J Microbiol Biotechnol 7:242–249Google Scholar
  24. Burlage RS, Palumbo AV, Heitzer A, Sayler G (1994) Bioluminescent reporter bacteria detect contaminants in soil samples. Appl Biochem Biotechnol 45/46:731–740CrossRefGoogle Scholar
  25. 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 68:3588–3596CrossRefGoogle Scholar
  26. Cho JC, Tiedje JM (2001) Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays. Appl Environ Microbiol 67:3677–3682CrossRefGoogle Scholar
  27. 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 43:367–374Google Scholar
  28. 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 173:59–65CrossRefGoogle Scholar
  29. 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 64:2247–2255Google Scholar
  30. 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: 333–340Google Scholar
  31. Czarnetzki AB, Tebbe CC (2004) Detection and phylogenetic analysis of Wolbachia in Collembola. Environ Microbiol 6:35–44CrossRefGoogle Scholar
  32. Dahlberg C, Bergstrom M, Hermansson M (1998) In situ detection of high levels of horizontal plasmid transfer in marine bacterial communities. Appl Environ Microbiol 64:2670–2675Google Scholar
  33. 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: 5273–5284Google Scholar
  34. 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 67:5810–5818Google Scholar
  35. Daly K, Sharp RJ, McCarthy AJ (2000) Development of nucleotide probes and PCR primers for detecting phylogenetic subgroups of sulfate-reducing bacteria. Microbiology UK 146:1693–1705Google Scholar
  36. 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, SwedenGoogle Scholar
  37. 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 64:3869–3877Google Scholar
  38. Dollard MA, Billard P (2003) Whole-cell bacterial sensors for the monitoring of phosphate bioavailability. J Microbiol Methods 55: 221–229CrossRefGoogle Scholar
  39. 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: 439–444CrossRefGoogle Scholar
  40. 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 17:7843–7853Google Scholar
  41. Fitts R, Diamond M, Hamilton C, Neri M (1983) DNA-DNA hybridization assay for detection of Salmonella spp. in foods. Appl Environ Microbiol 46:1146–1151Google Scholar
  42. 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 179:7089–7097Google Scholar
  43. 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: 446–453Google Scholar
  44. Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60–63CrossRefGoogle Scholar
  45. 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 72:3961–3965Google Scholar
  46. 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 301:235–242CrossRefGoogle Scholar
  47. Hansen LH, Sorensen SJ (2000) Versatile biosensor vectors for detection and quantification of mercury. FEMS Microbiol Lett 193:123–127CrossRefGoogle Scholar
  48. Head IM, Saunders JR, Pickup RW (1998) Microbial evolution, diversity, and ecology: a decade of ribosomal RNA analysis of uncultivated microorganisms. Microb Ecol 35:1–21CrossRefGoogle Scholar
  49. Hill WE, Payne WL, Aulisio CCG (1983) Detection and enumeration of virulent Yersinia enterolitica in food by DNA colony hybridization. Appl Environ Microbiol 46:636–641Google Scholar
  50. 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: 2652–2659Google Scholar
  51. 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 54:703–711Google Scholar
  52. 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 68:2509–2518CrossRefGoogle Scholar
  53. 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 376:57–58CrossRefGoogle Scholar
  54. Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774Google Scholar
  55. 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 34:1439–1447CrossRefGoogle Scholar
  56. 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 3:404–410Google Scholar
  57. 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: 2685–2690Google Scholar
  58. Jansson JK (2003) Marker and reporter genes: illuminating tools for environmental microbiologists. Curr Opin Microbiol 6:310–316Google Scholar
  59. Jansson JK, van Elsas JD, Bailey MJ (2000) Tracking genetically engineered microorganisms. Landes Bioscience, Georgetown, TexasGoogle Scholar
  60. Killham K, Yeomans C (2001) Rhizosphere carbon flow measurement and implications: from isotopes to reporter genes. Plant Soil 232: 91–96CrossRefGoogle Scholar
  61. 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 48:43–51CrossRefGoogle Scholar
  62. 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: 99–110CrossRefGoogle Scholar
  63. 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: 348–352Google Scholar
  64. Leveau JHJ, Lindow SE (2002) Bioreporters in microbial ecology. Curr Opin Microbiol 5:259–265CrossRefGoogle Scholar
  65. 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 174:5072–5078Google Scholar
  66. 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: 4516–4522Google Scholar
  67. Loper JE, Lindow SE (1994) A biological sensor for iron available to bacteria in their habitats on plant surfaces. Appl Environ Microbiol 60:1934–1941Google Scholar
  68. 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 69:320–326CrossRefGoogle Scholar
  69. 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 3:194–204CrossRefGoogle Scholar
  70. 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 148:3521–3530Google Scholar
  71. Manefield M, Turner SL (2002) Quorum sensing in context: out of molecular biology and into microbial ecology. Microbiol SGM 148: 3762–3764Google Scholar
  72. 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 68:5367–5373CrossRefGoogle Scholar
  73. 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 69:4375–4382CrossRefGoogle Scholar
  74. 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 68:5042–5050CrossRefGoogle Scholar
  75. Miller WG, Brandl MT, Quinones B, Lindow SE (2001) Biological sensor for sucrose availability: relative sensitivities of various reporter genes. Appl Environ Microbiol 67:1308–1317Google Scholar
  76. 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 59:695–700Google Scholar
  77. 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 1–27Google Scholar
  78. Norton JM, Alzerreca JJ, Suwa Y, Klotz MG (2002) Diversity of ammonia monooxygenase operon in autotrophic ammonia-oxidizing bacteria. Arch Microbiol 177:139–149CrossRefGoogle Scholar
  79. Ogram A, Sayler GS, Barkay T (1987) DNA extraction and purification from sediments. J Microbiol Methods 7:57–66CrossRefGoogle Scholar
  80. 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 212:221–228CrossRefGoogle Scholar
  81. Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR, Stahl DA (1986) Microbial ecology and evolution: a ribosomal RNA approach. Annu Rev Microbiol 40:337–365CrossRefGoogle Scholar
  82. 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 48:218–235Google Scholar
  83. Pace N, Stahl DA, Lane DJ, Olsen GJ (1986) The analysis of natural microbial populations by rRNA sequences. Adv Microb Ecol 9:1–55Google Scholar
  84. Paerl HW, Steppe TF (2003) Scaling up: the next challenge in environmental microbiology. Environ Microbiol 5:1025–1038CrossRefGoogle Scholar
  85. 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 69:1397–1407CrossRefGoogle Scholar
  86. 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 68:6121–6128CrossRefGoogle Scholar
  87. 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 41:1549–1554CrossRefGoogle Scholar
  88. Prachayasittikul V, Ayudhya CIN, Bulow L (2001) Lighting E. coli cells as biological sensors for Cd2(+). Biotechnol Lett 23: 1285–1291CrossRefGoogle Scholar
  89. Prosser JI (2002) Molecular and functional diversity in soil micro-organisms. Plant Soil 244:9–17CrossRefGoogle Scholar
  90. Radajewski S, Ineson P, Parekh NR, Murrell JC (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403:646–649Google Scholar
  91. 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 24:321–331Google Scholar
  92. Rasmussen LD, Sorensen SJ, Turner RR, Barkay T (2000) Application of a mer-lux biosensor for estimating bioavailable mercury in soil. Soil Biol Biochem 32:639–646CrossRefGoogle Scholar
  93. 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 34:846–853Google Scholar
  94. Rossbach S, Kukuk ML, Wilson TL, Feng SF, Pearson MM, Fisher MA (2000) Cadmium regulated gene fusions in Pseudomonas fluorescens. Environ Microbiol 2:373–382CrossRefGoogle Scholar
  95. 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 230:1350–1354Google Scholar
  96. Sayler GS, Ripp S (2000) Field applications of genetically engineered microorganisms for bioremediation processes. Curr Opin Biotechnol 11: 286–289CrossRefGoogle Scholar
  97. 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 49:1295–1303Google Scholar
  98. 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 64:4870–4876Google Scholar
  99. 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 1:9–19Google Scholar
  100. 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: 6036–6041Google Scholar
  101. 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 16:332–338CrossRefGoogle Scholar
  102. 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 67:4708–4716CrossRefGoogle Scholar
  103. 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 146:1256–1257Google Scholar
  104. 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 57:3482–3488Google Scholar
  105. 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 232:97–108Google Scholar
  106. Stahl DA, Lane DJ, Olsen GJ, Pace NR (1984) Analysis of hydrothermal vent-associated symbionts by ribosomal RNA sequences. Science 224: 409–411Google Scholar
  107. Stahl DA, Lane DJ, Olsen GJ, Pace NR (1985) Characterization of a Yellowstone hot spring microbial community by 5S rRNA sequences. Appl Environ Microbiol 49:1379–1384Google Scholar
  108. Steffan RJ, Goksoyr J, Bej AK, Atlas RM (1988) Recovery of DNA from soils and sediments. Appl Environ Microbiol 54:2908–2915Google Scholar
  109. 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 196:69–74CrossRefGoogle Scholar
  110. Suzuki MT, Giovannoni SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62:625–630Google Scholar
  111. 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 127–137Google Scholar
  112. 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 59:2657–2665Google Scholar
  113. 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 161–175Google Scholar
  114. 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: 341–351Google Scholar
  115. Tiedje JM, Asuming-Brempong S, Nusslein K, Marsh TL, Flynn SJ (1999) Opening the black box of soil microbial diversity. Appl Soil Ecol 13:109–122CrossRefGoogle Scholar
  116. 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: 59–67Google Scholar
  117. Torsvik V, Ovreas L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5:240–245CrossRefGoogle Scholar
  118. 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 14:287–298Google Scholar
  119. Tunlid A (1999) Molecular biology: a linkage between microbial ecology, general ecology and organismal biology. Oikos 85:177–189Google Scholar
  120. 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 188–199Google Scholar
  121. Van Overbeek LS, van Elsas JD (1995) Root exudate-induced promoter activity in Pseudomonas fluorescens mutants in the wheat rhizosphere. Appl Environ Microbiol 61:890–898Google Scholar
  122. 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 64:4396–4402Google Scholar
  123. 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 45:197–205Google Scholar
  124. Weller R, Ward DM (1989) Selective recovery of 16S rRNA sequences from natural microbial communities in the form of cDNA. Appl Environ Microbiol 55:1818–1822Google Scholar
  125. 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 6:295–301CrossRefGoogle Scholar
  126. Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 95:6578–6583CrossRefGoogle Scholar
  127. 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: 374–380Google Scholar
  128. 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: 1006–1012Google Scholar
  129. Williamson N, Brian P, Wellington EMH (2000) Molecular detection of bacterial and streptomycete chitinases in the environment. Antonie Van Leeuwenhoek 78:315–321CrossRefGoogle Scholar
  130. Woese C, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74:5088–5090Google Scholar
  131. Yinon J (2002) Field detection and monitoring of explosives. Trac Trends Anal Chem 21:292–301CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Christoph C. Tebbe
    • 1
  1. 1.Institut für AgrarökologieBundesforschungsanstalt für Landwirtschaft (FAL)BraunschweigGermany

Personalised recommendations