This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169
Avrahami S, Conrad R, Braker G (2002) Effect of soil ammonium concentration on NO2 release and on the community structure of ammonia oxidizers and denitrifiers. Appl Environ Microbiol 68:5685–5692
Baker GC and Cowan DA (2004) 16S rDNA primers and the unbiased assessment of thermophile diversity. Biochem Soc Transact 32:218–221
Baker GC, Smith JJ, Cowan DA (2003) Review and re-analysis of domain-specific 16 Sprimers. J Microbiol Methods 55:541–555
Barns SM, Takala SL, Kuske CR (1999) Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment. Appl Environ Microbiol 65:1731–1737
Beja O, Suzuki MT, Koonin EV, Aravind L, Hadd A, Nguyen LP, Villacorta R, Amjadi M, Garrigues C, Jovanovich SB, Feldman RA, DeLong EF (2000) Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ Microbiol 2:516–529
Boon N, De Windt W, Verstraete W, Top EM (2002) Evaluation of nested PCR-DGGE (denaturing gradient gel electrophoresis) with group-specific 16S rRNA primers for the analysis of bacterial communities from different wastewater treatment plants. FEMS Microbiol Ecol 39:101–112
Borneman J, Triplett EW (1997) Molecular microbial diversity in soils from eastern Amazonia — evidence for unusual microorganisms and microbial population shifts associated with deforestation. Appl Environ Microbiol 63:2647–2653
Borneman J, Skroch PW, O’Sullivan 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
Braker G, Fesefeldt A, Witzel KP (1998) Development of PCR primer systems for amplification of nitrite reductase genes (nirK and nirS) to detect denitrifying bacteria in environmental samples. Appl Environ Microbiol 64:3769–3775
Brüggemann J, Stephen JR, Chang Y-J, Macnaughton SJ, Kowalchuk GA, Kline E, White DC (2000) Competitive PCR-DGGE analysis of bacterial mixtures: an internal standard and an appraisal of template enumeration accuracy. J Microbiol Methods 40:111–123
Buchan A, Neidle EL, Moran MA (2001) Diversity of the ring-cleaving dioxygenase gene pcaH in a salt marsh bacterial community. Appl Environ Microbiol 67:5801–5809
Castro H, Reddy KR, Ogram A (2002) Composition and function of sulfate-reducing prokaryotes in eutrophic and pristine areas of the Florida Everglades. Appl Environ Microbiol 68:6129–6137
Chang YJ, Stephen JR, Richter AP, Venosa AD, Brüggemann J, Macnaughton SJ, Kowalchuk GA, Haines JR, Kline E, White DC (2000) Phylogenetic analysis of aerobic freshwater and marine enrichment cultures efficient in hydrocarbon degradation: effect of profiling method. J Microbiol Methods 40:19–31
Clapp JP (1999) The identification of root-associated fungi by polymerase chain reaction-single-strand conformational polymorphism (PCR-SSCP). In: Akkermans ADL, Van Elsas JD, De Bruijn FJ (eds) Molecular microbial ecology manual, vol 3.4.7. Kluwer Academic Publishers, Dordrecht, pp 1–18
Clayton RA, Sutton G, Hinkle PS, Bult C, Fields C (1995) Intraspecific variation in small-subunit ribosomal-RNA sequences in Genbank: why single sequences may not adequately represent prokaryotic taxa. Int J Syst Bacteriol 45:595–599
Cole JR, Chai B, Marsh TL, Farris RJ, Wang Q, Kulam SA, Chandra S, McGarrell DM, Schmidt TM, Garrity GM, Tiedje JM (2003) The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31:442–443
Cook KL, Sayler GS (2003) Environmental application of array technology: promise, problems and practicalities. Curr Opin Biotechnol 14:311–318
Curtis TP, Sloan WT, Scannell JW (2002) Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci USA 99:10494–10499
Dahllöf I, Baillie H, Kjelleberg S (2000) rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity. Appl Environ Microbiol 66:3376–3380
da Silva KRA, Salles JF, Seldin L, Van Elsas JD (2003) Application of a novel Paenibacillus specific PCR-DGGE methodand sequence analysis to assess the diversity of Paenibacillus spp. in the maize rhizosphere. J Microbiol Methods 54:213–231
de Souza FA, Kowalchuk GA, Leeflang P, Van Veen JA, Smit E (2004) PCR-denaturing gradient gel electrophoresis profiling of inter-and intraspecies 18S rRNA gene sequence heterogeneity is an accurate and sensitive method to assess species diversity of arbuscular mycorrhizal fungi of the genus Gigaspora. Appl Environ Microbiol 70:1413–1424
Diallo MD, Willems A, Vloemans N, Cousin S, Vandekerckhove TT, de Lajudie P, Neyra M, Vyverman W, Gillis M, Van der Gucht K (2004) Polymerase chain reaction denaturing gradient gel electrophoresis analysis of the N2-fixing bacterial diversity in soil under Acacia tortilis ssp. raddiana and Balanites aegyptiaca in the dryland part of Senegal. Environ Microbiol 6:400–415
Dickie IA, Xu B, Koide RT (2002) Vertical niche differentiation of ectomycorrhizal hyphae in soil as shown by T-RFLP analysis. New Phytol 156:527–535
Duineveld BM, Kowalchuk GA, Keijzer A, Van Elsas JD, Van Veen JA (2001) Analysis of bacterial communities in the rhizosphere of chrysanthemum via denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA as well as DNA fragments coding for 16S rRNA. Appl Environ Microbiol 67:172–178
Dunbar J, Barns SM, Ticknor LO, Kuske CR (2002) Empirical and theoretical bacterial diversity in four Arizona soils. Appl Environ Microbiol 68:3035–3045
Engebretson JJ, Moyer CL (2003) Fidelity of select restriction endonucleases in determining microbial diversity by terminal-restriction fragment length polymorphism. Appl Environ Microbiol 69:4823–4829
Fromin N, Hamelin J, Tarnawski S, Roesti D, Jourdain-Miserez K, Forestier N, Teyssier-Cuvelle S, Gillet F, Aragno M, Rossi P (2002) Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns. Environ Microbiol 4:634–643
Frostegård A, Courtois S, Ramisse V, Clerc S, Bernillon D, Le Gall F, Jeannin P, Nesme X, Simonet P (1999) Quantification of bias related to the extraction of DNA directly from soils. Appl Environ Microbiol 65:5409–5420
Garbeva P, Van Veen JA, Van Elsas JD (2003) Predominant Bacillus spp. in agricultural soil under different management regimes detected via PCR-DGGE. Microb Ecol 45:302–316
Garbeva P, Van Veen JA, Van Elsas JD (2004) Assessment of the diversity, and antagonism towards Rhizoctonia solani AG3, of Pseudomonas species in soil from different agricultural regimes. FEMS Microbiol Ecol 47:51–64
Garcia-Martinez J, Acinas SG, Anton AI, Rodriguez-Valera F (1999) Use of the 16S–23S ribosomal genes spacer region in studies of prokaryotic diversity. J Microbiol Methods 36:55–64
Gardener BBM, Mavrodi DV, Thomashow LS, Weller DM (2001) A rapid polymerase chain reaction-based assay characterizing rhizosphere populations of 2,4-diacetylphloroglucinol-producing bacteria. Phytopathology 91:44–54
Gardes M, Bruns TD (1993) ITS primers with enhanced specificity for Basidiomycetes: application to the identification of mycorrhizae and rusts. Mol Ecol 2:113–118
Giovannoni SJ, Delong EF, Olsen GJ, Pace NR (1988) Phylogenetic group-specific oligodeoxynucleotide probes for identification of single microbial-cells. J Bacteriol 170:720–726
Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso sea bacterioplankton. Nature 345:60–63
Gollotte A, Van Tuinen D, Atkinson D (2004) Diversity of arbuscular mycorrhizal fungi colonising roots of the grass species Agrostis capillaris and Lolium perenne in a field experiment. Mycorrhiza 14:111–117
Gomes NCM, Heuer H, Schönfeld J, Costa R, Mendonça-Hagler L, Smalla K (2001) Bacterial diversity of the rhizosphere of maize (Zea mays) grown in tropical soil studied by temperature gradient gel electrophoresis. Plant Soil 232:167–180
Gray ND, Head IM (2001) Linking genetic identity and function in communities of uncultured bacteria. Environ Microbiol 3:481–492
Griffiths RI, Whiteley AS, O’Donnell AG, Bailey MJ (2000) Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA-and rRNA-based microbial community composition. Appl Environ Microbiol 66:5488–5491
Hansen MC, Tolker-Nielsen T, Givskov M, Molin S (1998) Biased 16S rDNA PCR amplification caused by interference from DNA flanking the template region. FEMS Microbiol Ecol 26:141–149
Heilig HGHJ, Zoetendal EG, Vaughan EE, Marteau P, Akkermans ADL, de Vos WM (2002) Molecular diversity of Lactobacillus spp. and other lactic acid bacteria in the human intestine as determined by specific amplification of 16S ribosomal DNA. Appl Environ Microbiol 68:114–123
Helgason T, Daniell TJ, Husband R, Fitter AH, Young JPW (1998) Ploughing up the wood-wide web. Nature 394:431
Henckel T, Friedrich M, Conrad R (1999) Molecular analyses of the methane-oxidizing microbial community in rice field soil by targeting the genes of the 16S rRNA, particulate methane monooxygenase, and methanol dehydrogenase. Appl Environ Microbiol 65:1980–1990
Heuer H, Krsek M, Baker P, Smalla K, Wellington EMH (1997) Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl Environ Microbiol 63:3233–3241
Heuer H, Hartung K, Wieland G, Kramer I, Smalla K (1999) Polynucleotide probes that target a hypervariable region of 16S rRNA genes to identify bacterial isolates corresponding to bands of community fingerprints. Appl Environ Microbiol 63:1045–1049
Hilario E, Thomas RB, Young JM (2004) Improved resolution on phylogenetic relationships among Pseudomonas by the combined analysis of atpD, carA, recA and 16S rDNA. Antonie Van Leeuwenhoek 86:51–64
Holben WE, Feris KP, Kettunen A, Apajalahti JHA (2004) GC fractionation enhances microbial community diversity assessment and detection of minority populations of bacteria by denaturing gradient gel electrophoresis. Appl Environ Microbiol 70:2263–2270
Horner-Devine MC, Leibold MA, Smith VH, Bohannan BJM (2003) Bacterial diversity patterns along a gradient of primary productivity. Ecol Lett 6:613–622
Horz HP, Rotthauwe JH, Lukow T, Liesack W (2000) Identification of major subgroups of ammonia-oxidizing bacteria in environmental samples by T-RFLP analysis of amoA PCR products. J Microbiol Methods 39:197–204
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
Hughes JB, Hellmann JJ, Ricketts TH, Bohannan BJM (2001) Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Microbiol 67:4399–4406
Hurt RA, Qiu XY, Wu LY, Roh Y, Palumbo AV, Tiedje JM, Zhou JH (2001) Simultaneous recovery of RNA and DNA from soils and sediments. Appl Environ Microbiol 67:4495–4503
Johnsen K, Jacobsen CS, Torsvik V, Sørensen J (2001) Pesticide effects on bacterial diversity in agricultural soils — a review. Biol Fertil Soils 33:443–453
Jurgens G, Lindstrom K, Saano A (1997) Novel group within the kingdom Crenarchaeota from boreal forest soil. Appl Environ Microbiol 63:803–805
Klamer M, Roberts MS, Levine LH, Drake BG, Garland JL (2002) Influence of elevated CO2 on the fungal community in a coastal scrub oak forest soil investigated with terminal-restriction fragment length polymorphism analysis. Appl Environ Microbiol 68:4370–4376
Klappenbach JA, Saxman PR, Cole JR, Schmidt TM (2001) RRNDB: the ribosomal RNA operon copy number database. Nucleic Acids Res 29:181–184
Kopczynski ED, Bateson MM, Ward DM (1994) Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms. Appl Environ Microbiol 60:746–748
Kowalchuk GA, Gerards S, Woldendorp JW (1997a) Detection and characterization of fungal infections of Ammophila arenaria (marram grass) roots by denaturing gradient gel electrophoresis of specifically amplified 18S rDNA. Appl Environ Microbiol 63:3858–3865
Kowalchuk GA, Stephen JR, de Boer W, Prosser JI, Embley TM, Woldendorp JW (1997b) Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments. Appl Environ Microbiol 63:1489–1497
Kowalchuk GA, de Souza FA, Van Veen JA (2002) Community analysis of arbuscular mycorrhizal fungi associated with Ammophila arenaria in Dutch coastal sand dunes. Mol Ecol 11:571–581
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
Loy A, Lehner A, Lee N, Adamczyk J, Meier H, Ernst J, Schleifer KH, Wagner M (2002) Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl Environ Microbiol 68:5064–5081
Ludwig W, Schleifer KH (1999) Phylogeny of bacteria beyond the 16S rRNA standard. ASM News 65:752–757
Ludwig W, Strunk O, Klugbauer S, Klugbauer N, Weizenegger M, Neumaier J, Bachleitner M, Schleifer KH (1998) Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19:554–568
Lyons JI, Newell SY, Buchan A, Moran MA (2003) Diversity of ascomycete laccase gene sequences in a southeastern US salt marsh. Microb Ecol 45:270–281
Marchesi JR, Sato T, Weightman AJ, Martin TA, Fry JC, Hiom SJ Wade WG (1998) Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol 64:795–799
Martinez-Murcia AJ, Acinas SG, Rodriguez-Valera F (1995) Evaluation of the prokaryotic diversity by restrictase digestion of 16S rDNA directly amplified from hypersaline environments. FEMS Microbiol Ecol 17:247–256
May LA, Smiley B, Schmidt MG (2001) Comparative denaturing gradient gel electrophoresis analysis of fungal communities associated with whole plant corn silage. Can J Microbiol 47:829–841
McCaig AE, Glover LA, Prosser JI (1999) Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures. Appl Environ Microbiol 65:1721–1730
McDonald I, Murrell J (1997a) The methanol dehydrogenase structural gene mxaF and its use as a functional gene probe for methanotrophs and methylotrophs. Appl Environ Microbiol 63:3218–3224
McDonald IR, Murrell JC (1997b) The particulate methane monooxygenase gene pmoA and its use as a functional gene probe for methanotrophs. FEMS Microbiol Lett 156:205–210
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
Möhlenhoff P, Muller L, Gorbushina AA, Petersen K (2001) Molecular approach to the characterisation of fungal communities: methods for DNA extraction, PCR amplification and DGGE analysis of painted art objects. FEMS Microbiol Lett 195:169–173
Moyer CL, Tiedje JM, Dobbs FC, Karl DM (1996) A computer-simulated restriction fragment length polymorphism analysis of bacterial small-subunit rRNA genes: efficacy of selected tetrameric restriction enzymes for studies of microbial diversity in nature? Appl Environ Microbiol 62:2501–2507
Muyzer G, Smalla K (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leeuwenhoek 73:127–141
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, Teske A, Wirsen CO, Jannasch HW (1995) Phylogenetic-relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel-electrophoresis of 16S rDNA fragments. Arch Microbiol 164:165–172
Nannipieri P, Ascher J, Ceccherini MT, Landi L, Pietramellara G, Renella G (2003) Microbial diversity and soil functions. Eur J Soil Sci 54:655–670
Neufeld JD, Yu ZT, Lam W, Mohn WW (2004) Serial analysis of ribosomal sequence tags (SARST): a high-throughput method for profiling complex microbial communities. Environ Microbiol 6:131–144
Nicolaisen MH, Ramsing NB (2002) Denaturing gradient gel electrophoresis (DGGE) approaches to study the diversity of ammonia-oxidizing bacteria. J Microbiol Methods 50:189–203
Nold SC, Zhou J, Devol AH, Tiedje JM (2000) Pacific Northwest marine sediments contain ammonia-oxidizing bacteria in the beta subdivision of the Proteobacteria. Appl Environ Microbiol 66:4532–4535
Nübel U, Engelen B, Felske A, Snaidr J, Wieshuber A, Amann RI, Ludwig W, Backhaus H (1996) Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J Bacteriol 178:5636–5643
Nübel U, Garcia-Pichel F, Muyzer G (1997) PCR primers to amplify 16S rRNA genes from cyanobacteria. Appl Environ Microbiol 63:3327–3332
Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR, Stahl DA (1986) Microbial ecology and evolution: a ribosomal RNA approach. Ann Rev Microbiol 40:337–365
Øvreås L, Forney L, Daae FL, Torsvik V (1997) Distribution of bacterioplankton in meromictic lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl Environ Microbiol 63:3367–3373
Pace NR (1997) A molecular view of microbial diversity and the biosphere. Science 276:734–740
Pace NR, Stahl DA, Lane DJ, Olsen GJ (1986) The analysis of natural microbial populations by ribosomal RNA sequences. Adv Microb Ecol 9:1–55
Peixoto RS, Coutinho HLD, Rumjanek NG, Macrae A, Rosado AS (2002) Use of rpoB and 16S rRNA genes to analyse bacterial diversity of a tropical soil using PCR and DGGE. Lett Appl Microbiol 35:316–320
Polz MF, Cavanaugh CM (1998) Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol 64:3724–3730
Porteous LA, Widmer F, Seidler RJ (2002) Multiple enzyme restriction fragment length polymorphism analysis for high resolution distinction of Pseudomonas (sensu stricto) 16S rRNA genes. J Microbiol Methods 51:337–348
Poulsen LK, Ballard G, Stahl DA (1993) Use of ribosomal-RNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms. Appl Environ Microbiol 59:1354–1360
Raaijmakers JM, Weller DM, Thomashow LS (1997) Frequency of antibiotic-producing Pseudomonas spp. in natural environments. Appl Environ Microbiol 63:881–887
Rasmussen LD, Ekelund F, Hansen LH, Sorensen SJ, Johnsen K (2001) Group-specific PCR primers to amplify 24S alpha-subunit rRNA genes from Kinetoplastida (Protozoa) used in denaturing gradient gel electrophoresis. Microb Ecol 42:109–115
Reysenbach AL, Wickham GS, Pace NR (1994) Phylogenetic analysis of the hyperthermophilic pink filament community in Octopus Spring, Yellowstone National Park. Appl Environ Microbiol 60:2113–2119
Rhee SK, Liu X, Wu L, Chong SC, Wan X, Zhou JH (2004) Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl Environ Microbiol 70:4303–4317
Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA, MacNeil IA, Minor 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
Rösch C, Mergel A, Bothe H (2002) Biodiversity of denitrifying and dinitrogen-fixing bacteria in an acid forest soil. Appl Environ Microbiol 68:3818–3829
Rosling A, Landeweert R, Lindahl BD, Larsson KH, Kuyper TW, Taylor AFS, Finlay RD (2003) Vertical distribution of ectomycorrhizal fungal taxa in a podzol soil profile. New Phytol 159:775–783
Rotthauwe JH, Witzel KP, Liesack W (1997) The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammoniaoxidizing populations. Appl Environ Microbiol 63:4704–4712
Rudi K, Skulberg OM, Larsen F, Jakobsen KS (1997) Strain characterization and classification of oxyphotobacteria in clone cultures on the basis of 16S rRNA sequences from the variable regions V6, V7, and V8. Appl Environ Microbiol 63:2593–2599
Sakai M, Matsuka A, Komura T, Kanazawa S (2004) Application of a new PCR primer for terminal restriction fragment length polymorphism analysis of the bacterial communities in plant roots. J Microbiol Methods 59:81–89
Salles JF, De Souza FA, Van Elsas JD (2002) Molecular method to assess the diversity of Burkholderia species in environmental samples. Appl Environ Microbiol 68:1595–1603
Schabereiter-Gurtner C, Pinar G, Lubitz W, Rolleke S (2001) Analysis of fungal communities on historical church window glass by denaturing gradient gel electrophoresis and phylogenetic 18S rDNA sequence analysis. J Microbiol Methods 47:345–354
Schleifer KH (2004) Microbial diversity: facts, problems and prospects. Syst ApplMicrobiol 27:3–9
Schmalenberger A, Schwieger F, Tebbe CC (2001) Effect of primers hybridizing to different evolutionarily conserved regions of the small-subunit rRNA gene in PCR-based microbial community analyses and genetic profiling. Appl Environ Microbiol 67:3557–3563
Sekiguchi H, Tomioka N, Nakahara T, Uchiyama H (2001) A single band does not always represent single bacterial strains in denaturing gradient gel electrophoresis analysis. Biotechnol Lett 23:1205–1208
Sigler PB, Xu ZH, Rye HS, Burston SG, Fenton WA, Horwich AL (1998) Structure and function in GroEL-mediated protein folding. Annu Rev Biochem 67:581–608
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
Smit E, Leeflang P, Glandorf B, Van Elsas JD, Wernars K (1999) Analysis of fungal diversity in thewheat rhizosphere by sequencing of cloned PCR-amplified genes encoding 18S rRNA and temperature gradient gel electrophoresis. Appl Environ Microbiol 65:2614–2621
Sneath PHA (1993) Evidence from Aeromonas for genetic crossing-over in ribosomal sequences. Int J Syst Bacteriol 43:626–629
Speksnijder AGCL, Kowalchuk GA, De Jong S, Kline E, Stephen JR, Laanbroek HJ (2001) Microvariation artifacts introduced by PCR and cloning of closely related 16S rRNA gene sequences. Appl Environ Microbiol 67:469–472
Stephen JR, Chang YJ, Macnaughton SJ, Kowalchuk GA, Leung KT, Flemming CA, White DC (1999) Effect of toxic metals on indigenous soil β-subgroup Proteobacterium ammonia oxidizer community structure and protection against toxicity by inoculated metalresistant bacteria. Appl Environ Microbiol 65:95–101
Stephen JR, Kowalchuk GA (2002) Ribotyping methods for assessment of in situ microbial community structure. In: Bitton G (ed) Encyclopedia of environmental microbiology, vol 5. John Wiley and Sons, New York, pp 2728–2741
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
Thomas CM (2000) The horizontal gene pool: bacterial plasmids and gene spread. Harwood Academic Publishers, Amsterdam
Torsvik V, Goksøyr J, Daae FL (1990) High diversity in DNA of soil bacteria. Appl Environ Microbiol 56:782–787
Torsvik V, Daae FL, Sandaå RA, Øvreås L (1998) Novel techniques for analysing microbial diversity in natural and perturbed environments. J Biotechnol 64:53–62
Torsvik V, Øvreås L, Thingstad TF (2002) Prokaryotic diversity: magnitude, dynamics, and controlling factors. Science 296:1064–1066
Trevors JT (1996) DNA in soil — adsorption, genetic transformation, molecular evolution and genetic microchip. Antonie Van Leeuwenhoek 70:1–10
Vainio EJ, Hantula J (2000) Direct analysis of wood-inhabiting fungi using denaturing gradient gel electrophoresis of amplified ribosomal DNA. Mycol Res 104:927–936
Valinsky L, Della Vedova G, Jiang T, Borneman J (2002a) Oligonucleotide fingerprinting of rRNA genes for analysis of fungal community composition. Appl Environ Microbiol 68:5999–6004
Valinsky L, Della Vedova G, Scupham AJ, Alvey S, Figueroa A, Yin B, Hartin J, Chrobak M, Crowley DE, Jiang T, Borneman J (2002b) Analysis of bacterial community composition by oligonucleotide fingerprinting of rRNA genes. Appl Environ Microbiol 68:3243–3250
Van de Peer Y, Robbrecht E, de Hoog S, Caers A, de Rijk P, de Wachter R (1999) Database on the structure of small subunit ribosomal RNA. Nucleic Acids Res 27:179–183
Van Elsas JD, Duarte GF, Keijzer-Wolters A, Smit E (2000) Analysis of the dynamics of fungal communities in soil via fungal-specific PCR of soil DNA followed by denaturing gradient gel electrophoresis. J Microbiol Methods 43:133–151
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
von Wintzingerode F, Göbel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21:213–229
Wagner M, Erhart R, Manz W, Amann R, Lemmer H, Wedi D, Schleifer KH (1994) Development of an ribosomal-RNA-targeted oligonucleotide probe specific for the genus Acinetobacter and its application for in situ monitoring in activated-sludge. Appl Environ Microbiol 60:792–800
Waite IS, O’Donnell AG, Harrison A, Davies JT, Colvan SR, Ekschmitt K, Dogan H, Wolters V, Bongers T, Bongers M (2003) Design and evaluation of nematode 18S rDNA primers for PCR and denaturing gradient gel electrophoresis (DGGE) of soil community DNA. Soil Biol Biochem 35:1165–1173
Wang GCY, Wang Y (1997) Frequency of formation of chimeric molecules is a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes. Appl Environ Microbiol 63:4645–4650
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
Watanabe K, Kodama Y, Harayama S (2001a) Design and evaluation of PCR primers to amplify bacterial 16S ribosomal DNA fragments used for community fingerprinting. J Microbiol Methods 44:253–262
Watanabe K, Nelson JS, Harayama S, Kasai H (2001b) ICB database: the gyrB database for identification and classification of bacteria. Nucleic Acids Res 29:344–345
Watanabe T, Asakawa S, Nakamura A, Nagaoka K, Kimura M (2004) DGGE method for analyzing 16S rDNA of methanogenic archaeal community in paddy field soil. FEMS Microbiol Lett 232:153–163
Wawer C, Muyzer G (1995) Genetic diversity of Desulfovibrio spp. in environmental samples analyzed by denaturing gradient gel-electrophoresis of [NiFe] hydrogenase gene fragments. Appl Environ Microbiol 61:2203–2210
White TJ, Bruns TD, Lee S, Taylor JW (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols: a guide to methods and applications. Academic Press, San Diego, pp 315–322
Widmer F, Seidler RJ, Gillevet PM, Watrud LS, Di Giovanni GD (1998) A highly selective PCR protocol for detecting 16S rRNA genes of the genus Pseudomonas (sensu stricto) in environmental samples. Appl Environ Microbiol 64:2545–2553
Williamson N, Brian P, Wellington EMH (2000) Molecular detection of bacterial and streptomycete chitinases in the environment. Antonie Van Leeuwenhoek 78:315–321
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
Yamamoto S, Harayama S (1995) PCR amplification and direct sequencing of gyrb genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl Environ Microbiol 61:1104–1109
Yin B, Crowley D, Sparovek G, De Melo WJ, Borneman J (2000) Bacterial functional redundancy along a soil reclamation gradient. Appl Environ Microbiol 66:4361–4365
Zarda B, Hahn D, Chatzinotas A, Schonhuber W, Neef A, Amann RI, Zeyer J (1997) Analysis of bacterial community structure in bulk soil by in situ hybridization. Arch Microbiol 168:185–192
Zhou JH (2003) Microarrays for bacterial detection and microbial community analysis. Curr Opin Microbiol 6:288–294
Zhou JZ, Xia BC, Treves DS, Wu LY, Marsh TL, O’Neill RV, Palumbo AV, Tiedje JM (2002) Spatial and resource factors influencing high microbial diversity in soil. Appl Environ Microbiol 68:326–334
Zhou JZ, Xia BC, Huang H, Palumbo AV, Tiedje JM (2004) Microbial diversity and heterogeneity in sandy subsurface soils. Appl Environ Microbiol 70:1723–1734
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Kowalchuk, G.A., Drigo, B., Yergeau, E., van Veen, J.A. (2006). Assessing Bacterial and Fungal Community Structure in Soil Using Ribosomal RNA and Other Structural Gene Markers. In: Nannipieri, P., Smalla, K. (eds) Nucleic Acids and Proteins in Soil. Soil Biology, vol 8. Springer, Berlin, Heidelberg . https://doi.org/10.1007/3-540-29449-X_8
Download citation
DOI: https://doi.org/10.1007/3-540-29449-X_8
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-29448-1
Online ISBN: 978-3-540-29449-8
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)