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References
Akkermans ADL, Elsas van JD, Bruijn de FJ (1995) Molecular microbial ecology manual. Kluwer, Dordrecht, pp 1–488
Anderson IC, Cairney JWG (2004) Diversity and ecology of soil fungal communities: increased understanding through the application of molecular techniques. Environ Microbiol 6:796–779
Anderson IC, Campbell CD, Prosser JI (2003a) Potential bias of fungal 18S rDNA and internal transcribed spacer polymerase chain reaction primers for estimating fungal biodiversity in soil. Environ Microbiol 5:36–47
Anderson IC, Campbell CD, Prosser JI (2003b) Diversity of fungi in organic soils under a moorland-Scots pine (Pinus sylvestris L) gradient. Environ Microbiol 5:1121–1132
Baek JM, Kenerley CM (1998) Detection and enumeration of a genetically modified fungus in soil environments by quantitative competitive polymerase chain reaction. FEMS Microbiol Ecol 25:419–428
Baschien C, Manz W, Neu RN, Szewzyk U (2001) Fluorescence in situ hybridization of freshwater fungi. Int Rev Hydrobiol 86:371–381
Berney C, Fahrni J, Pawlowski J (2004) How many novel eukaryotic kingdoms? Pitfalls and limitations of environmental DNA surveys. BMC Biol 2:13
Borneman J, Hartin RJ (2000) PCR primers that amplify fungal rRNA genes from environmental samples. Appl Environ Microbiol 66:4356–4360
Bougoure DS, Cairney JWG (2005) Fungi associated with hair roots of Rhododendron lochiae (Ericaceae) in an Australian tropical cloud forest revealed by culturing and culture-independent molecular methods. Environ Microbiol 7:1743–1754
Bridge P, Spooner B (2003) Soil fungi: diversity and detection. Plant Soil 232:147–154
Bruns TD, White TJ, Taylor JW (1991) Fungal molecular systematics. Annu Rev Ecol Syst 22:525–564
Buckley DH, Schmidt TM (2002) Exploring the diversity of soil — a microbial rain forest. In: Staley JT, Reysenbach Al (eds) Biodiversity of microbial life: foundation of Earth’s biosphere. Wiley, New York, pp 183–208
Cabello M, Arambarri A (2002) Diversity in soil fungi from undisturbed and disturbed Celtis tala and Scutia buxifolia forests in the eastern Buenos Aires province. Argentina, Microbiol Res 157:115–125
Cahill D, Mohr P (2004) Plant-pathogen interactions (Plant biology 2004: abstracts of the annual meeting of the American Society of Plant Biologists). American Society of Plant Biologists, New York, p 134
Cai L, Jeewon R, Hyde KD (2005) Phylogenetic evaluation and taxonomic revision of Schizothecium based on ribosomal DNA and protein coding genes. Fungal Divers 19:1–17
Cho JH, Rupe JC, Cummings MS, Gubur EE (2001) Isolation and identification of F solani f sp From soil and modified Nash and Syder’s medium. Plant Dis 85:256–260
Davet P, Rouxel F (1997) Détection et isolement des champignons du sol. INRA, Paris, p 203
Dixon MT, Hillis DM (1993) Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis. Mol Biol Evol 10:256–267
Duong LM, Lumyong S, Hyde KD, Jeewon R (2004) Emarcea castanopsicola gen. et sp. nov. from Thailand, a new xylariaceous taxon based on morphology and DNA sequences. Stud Mycol 50:253–260
Duong LM, Lumyong S, Jeewon R, Hyde KD (2006) DGGE coupled with ribosomal DNA phylogenies reveal uncharacterized fungal phylotypes on living leaves of Magnolia liliifera. Fungal Divers 23:121–138
Egger KN (1995) Molecular analysis of ectomycorrhizal fungal communities. Can J Bot 73:1415–1422
Elmholt S, Labouriau R, Hestbjerg H, Nielsen LM (1999) Detection and estimation of conidial abundance of Penicillium verrucosum in soil by dilution plating on a selective and diagnostic agar medium (DYSG). Mycol Res 103:887–895
Elsas van JD, Overbeck van LS (1993) Bacterial responses to soil stimuli. In: Kjelleberg S (ed) Starvation in bacteria. Plenum, New York, pp 55–79
Elsas van 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
Fromin N, Hamelin J, Tarnawski S, Roesti D, Miserez KJ, Forestier N (2002) Statistical analysis of denaturing gel electrophoresis (DGGE) fingerprinting patterns. Environ Microbiol 4:634–643
Garbeva P, Veen van JA, Elsas van JD (2004) Microbial diversity in soil: selection of microbial populations by plant and soil type and implications for disease suppressiveness. Annu Rev Phytopathol 42:243–270
Garrett, SD (1981) Soil fungi and soil fertility: an introduction to soil mycology. Pergamon, Oxford, pp 141–145
Gomes NCM, Fagbola O, Costa R, Rumjanek NG, Buchner A, Mendona-Hagler L, Smalla K (2003) Dynamics of fungal communities in bulk and maize rhizosphere soil in the tropics. Appl Environ Microbiol 69:3758–3766
Gouy M, Li WH (1989) Molecular phylogeny of the kingdoms Animalia, Plantae and Fungi. Mol Biol Evol 6:109–122
Gurtner SC, 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
Hawskworth DL, Rossman AY (1997) Where are all the undescribed fungi? Phytopathology 87:888–891
Hillis DM, Dixon MT (1991) Ribosomal DNA: molecular evolution and phylogenetic inference. Q Rev Biol 66:411–453
Janssen PH, Yates PS, Grinton BE, Taylor PM, Sait M (2002) Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl Environ Microbiol 68:2391–2396
Jaworski CA, McCarter SM, Johnson AW, Williamson RE (1978) Response of onions grown for transplants to soil fumigation. J Am Soc Hortic Sci 103:385–388
Jeewon R, Liew ECY, Hyde KD (2002) Phylogenetic relationships of Pestalotiopsis and allied genera inferred from ribosomal DNA sequences and morphological characters. Mol Phylogenet Evol 25:378–392
Jeewon R, Liew ECY, Simpson JA, Hodgkiss IJ, Hyde KD (2003a) Phylogenetic significance of morphological characters in the taxonomy of Pestalotiopsis species. Molecular Phylogenet Evol 27:372–383
Jeewon R, Liew ECY, Hyde KD (2003b) Molecular systematics of the Amphisphaeriaceae based on cladistic analyses of partial LSU rDNA sequences. Mycol Res 107:1392–1402
Jeewon R, Liew ECY, Hyde KD (2004) Phylogenetic evaluation of species nomenclature of Pestalotiopsis in relation to host association. Fungal Divers 17:39–55
Kirk JL, Beaudette LA, Hart M, Moutoglis P (2004) Methods of studying soil microbial diversity. J Microbiol Methods 58:169–188
Kouichi S, Yoshihisa S, Masanori S, Kazuo S (2005) A new primer for discrimination of arbuscular mycorrhizal fungi with polymerase chain reaction-denature gradient gel electrophoresis. Grassl Sci 51:179–181
Kowalchuk GA, Gerards S, Woldendorp JW (1997) 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
Landeweert R, Hoffland E, Finlay RD, Kuyper TW, Breemen van N (2001) Linking plants to rocks: ectomycorrhizal fungi mobilise nutrients from minerals. Trends Ecol Evol 16:248–254
Laurent FM, Philippot L, Hallet S, Chaussod R, Germon JC, Soulas G, Catroux G (2001) DNA extraction from soils: old bias for new microbial diversity analysis methods. Appl Environ Microbiol 67:2354–2359
Liew ECY, Aptroot A, Hyde KD (2000) Phylogenetic significance of the pseudoparaphyses in loculoascomycete taxonomy. Mol Phylogenet Evol 16:392–402
Lowell JL, Klein DA (2001) Comparative single-strand conformation polymorphism (SSCP) and microscopy-based analysis of nitrogen cultivation interactive effects on the fungal community of a semiarid steppe soil. FEMS Microbiol Ecol 1239:1–8
Maarit-Niemi R, Heiskanen I, Wallenius K, Lindstrom K (2001) Extraction and purification of DNA in rhizosphere soil samplesfor PCR-DGGE analysis of bacterial consortia. J Microbiol Methods 45:155–165
MacNaughton SJ, Stephen JR, Venosa AD, Davis GA, Chang YJ, White DC (1999) Microbial population changes during bioremediation of an experimental oil spill. Appl Environ Microbiol 65:3566–3574
May LA, Smiley B, Schmidt MG (2001) Comparative denaturing gradient gel electrophoresis analyses of fungal communities associated with whole plant corn silage. Can J Bot 47:829–841
Mitchell JI, Roberts PJ, Moss ST (1995) Sequence or structure? A short review on the application of nucleic acid sequence information to fungal taxonomy. Mycologist 9:67–75
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
Muyzer G, Waal de EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analyses of polymerase chain reaction-amplified genes coding for 16S rDNA. Appl Environ Microbiol 59:695–700
Nikolcheva LG, Bärlocher F (2005) Molecular approaches to estimate fungal diversity. II. Denaturing gradient gel electrophoresis (DGGE). In: Graça MAS, Bärlocher F, Gessner MO (eds) Methods to study litter decomposition. Springer, Berlin Heidelberg New York, pp 177–183
Nikolcheva LG, Cockshutt AM, Bärlocher F (2003) Determining diversity of freshwater fungi on decaying leaves: comparison of traditional and molecular approaches. Appl Environ Microbiol 69:2548–2554
Nikolcheva LG, Bourque T, Bärlocher F (2005) Fungal diversity during initial stages of leaf decomposition in a stream. Mycol Res 109:246–253
Omar B, Ampe NF (2000) Microbial community dynamics during production of the Mexican fermented maize dough pozol. Appl Environ Microbiol 66:3664–3673
Parkinson D (1983) Functional relationships between soil organisms. Proc Int Colloq Soil Zool 8:153–165
Prosser JI (2002) Molecular and functional diversity in soil microorganisms. Plant Sci 244:9–17
Ranjard L, Poly F, Lata JC, Mougel C, Thioulouse J, Nazaret S (2001) Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analyses fingerprints: biological and methodological variability. Appl Environ Microbiol 67:4479–4487
Rosado AS, Duarte GF, Seldin L, Elsas van JD (1998) Genetic diversity of nifH gene sequences in Paenibacillus azotofixans strains and soil samples analyzed by denaturing gradient gel electrophoresis of PCR-amplified gene fragments. Appl Environ Microbiol 64:2770–2779
Schadt CW, Martin AP, Lipson DA, Steven K (2003) Seasonal dynamics of previously unknown fungal lineages in Tundra soils. Science 301:1359–1361
Sekiguchi H, Tomioka N, Nakahara T, Uchiyama H (2001) A single band does not always represent single bacterial strains in denaturing gradient gel electrophoresis. Biotechnol Lett 23:1205–1208
Smit E, Leeflang P, Glandorf B, Elsas van JD, Wernars K (1999) Analyses of fungal diversity in the wheat rhizosphere by sequencing of cloned PCR-amplified genes encoding 18S rRNA and temperature gradient gel electrophoresis. Appl Environ Microbiol 65:2614–2621
Spatafora JW (1995) Ascomal evolution of filamentous ascomycetes: evidence from molecular data. Can J Bot 73:S811–S815
Stackebrandt E, Goebel BM (1994) A place for DNA-DNA reassociation and 16S ribosomal-RNA sequence analyses in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849
Torsvik V, Øvreås L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5:240–245
Valinsky L, Vedova GD, Jiang T, Borneman J (2002) Oligonucleotide fingerprinting of rRNA genes for analyses of fungal community composition. Appl Environ Microbiol 68:5999–6004
Viaud M, Pasquier A, Brygoo Y (2000) Diversity of soil fungi studied by PCR-RFLP of ITS. Mycol Res 104:1027–1032
Vilgalys R, Hester M (1990) Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J Bacteriol 172:4238–4246
Vinokurova NG, Khmel’nitskaya II, Baskunov BP, Arinbasarov MU (2003) Occurrence of indole alkaloids among secondary metabolites of soil Aspergillus spp. Appl Biochem Microbiol 39:192–196
White TJ, Bruns TL, Lee S, Taylor JW (1990) Amplication and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis M (ed) PCR protocols, a guide to methods and applications, Academic, San Diego, pp 315–322
Williams ST, Parkinson D, Burges NB (1965) An examination of the soil washing technique by its application to several soils. Plant Soil 22:167–186
Wintzingerode FV, Göbel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21:213–229
Yu X, Cheng J, Wong MH (2005) Earthworm-mycorrhiza interaction on Cd uptake and growth of ryegrass. Soil Biol Biochem 37:195–201
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Jeewon, R., Hyde, K.D. (2007). Detection and Diversity of Fungi from Environmental Samples: Traditional Versus Molecular Approaches. In: Varma, A., Oelmüller, R. (eds) Advanced Techniques in Soil Microbiology. Soil Biology, vol 11. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-70865-0_1
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