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Molecular ecology of fungal entomopathogens: molecular genetic tools and their applications in population and fate studies

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Abstract

The power of molecular genetic techniques to address ecological research questions has opened a distinct interdisciplinary research area collectively referred to as molecular ecology. Molecular ecology combines aspects of diverse research fields like population and evolutionary genetics, as well as biodiversity, conservation biology, behavioural ecology, or species-habitat interactions. Molecular techniques detect specific DNA sequence characteristics that are used as genetic markers to discriminate individuals or taxonomic groups, for instance in analyses of population and community structures, for elucidation of phylogenetic relationships, or for the characterization and monitoring of specific strains in the environment. Here, we summarize the PCR-based molecular techniques used in molecular ecological research on fungal entomopathogens and discuss novel techniques that may have relevance to the studies of entomopathogenic fungi in the future. We discuss the flow chart of the molecular ecology approaches and we highlight some of the critical steps involved. There are still many unresolved questions in the understanding of the ecology of fungal entomopathogens. These include population characteristics and relations of genotypes and habitats as well as host-pathogen interactions. Molecular tools can provide substantial support for ecological research and offer insight into this far inaccessible systems. Application of molecular ecology approaches will stimulate and accelerate new research in the field of entomophathogen ecology.

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References

  • Agboton BV, Delalibera I, Hanna R, von Tiedemann A (2009) Molecular detection and differentiation of Brazilian and African isolates of the entomopathogen Neozygites tanajoae (Entomophthorales: Neozygitaceae) with PCR using specific primers. Biocontrol Sci Technol 19:67–79

    Google Scholar 

  • Aghajanzadeh S, Prasad DT, Mallik B (2007) Genetic diversity in Hirsutella thompsonii isolates based on random amplified polymorphic DNA analysis. BioControl 52:375–383

    CAS  Google Scholar 

  • Akkermans ADL, Van Elsas JD, DeBruijn FJ (1995) Molecular microbial ecology manual. Kluwer, Dordrecht

    Google Scholar 

  • Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial-cells without cultivation. Microbiol Rev 59:143–169

    CAS  PubMed  Google Scholar 

  • Amann R, Fuchs BM, Behrens S (2001) The identification of microorganisms by fluorescence in situ hybridisation. Curr Opin Biotechnol 12:231–236

    CAS  PubMed  Google Scholar 

  • Anderson IC, Cairney JWG (2004) Diversity and ecology of soil fungal communities: increased understanding through the application of molecular techniques. Environ Microbiol 6:769–779

    CAS  PubMed  Google Scholar 

  • Aquino de Muro M, Mehta S, Moore D (2003) The use of amplified fragment length polymorphism for molecular analysis of Beauveria bassiana isolates from Kenya and other countries, and their correlation with host and geographical origin. FEMS Microbiol Lett 229:249–257

    CAS  PubMed  Google Scholar 

  • Aquino de Muro M, Elliott S, Moore D, Parker BL, Skinner M, Reid W, El Bouhssini M (2005) Molecular characterisation of Beauveria bassiana isolates obtained from overwintering sites of Sunn Pests (Eurygaster and Aelia species). Mycol Res 109:294–306

    CAS  PubMed  Google Scholar 

  • Arbeli Z, Fuentes CL (2007) Improved purification and PCR amplification of DNA from environmental samples. FEMS Microbiol Lett 272:269–275

    CAS  PubMed  Google Scholar 

  • Avis JC (2004) Molecular markers, natural history, and evolution. Sinauer Associates, Sunderland

    Google Scholar 

  • Bain JM, Tavanti A, Davidson AD, Jacobsen MD, Shaw D, Gow NAR, Odds FC (2007) Multilocus sequence typing of the pathogenic fungus Aspergillus fumigatus. J Clin Microbiol 45:1469–1477

    CAS  PubMed  Google Scholar 

  • Beebee T, Rowe G (2008) An introduction to molecular ecology. Oxford University Press, Oxford

    Google Scholar 

  • Bell AS, Blanford S, Jenkins N, Thomas MB, Read AF (2009) Real-time quantitative PCR for analysis of candidate fungal biopesticides against malaria: technique validation and first applications. J Invertebr Pathol 100:160–168

    CAS  PubMed  Google Scholar 

  • Bidochka MJ, Walsh SRA, Ramos ME, St Leger RJ, Silver JC, Roberts DW (1995) Pathotypes in the Entomophaga grylli species complex of grasshopper pathogens differentiated with random amplification of polymorphic DNA and cloned-DNA probes. Appl Environ Microbiol 61:556–560

    CAS  PubMed  Google Scholar 

  • Bidochka MJ, St Leger RJ, Stuart A, Gowanlock K (1999) Nuclear rDNA phylogeny in the fungal genus Verticillium and its relationship to insect and plant virulence, extracellular proteases and carbohydrases. Microbiology 145:955–963

    CAS  PubMed  Google Scholar 

  • Bidochka MJ, Kamp AM, Lavender TM, Dekoning J, De Croos JN (2001) Habitat association in two genetic groups of the insect-pathogenic fungus Metarhizium anisopliae: uncovering cryptic species? Appl Environ Microbiol 67:1335–1342

    CAS  PubMed  Google Scholar 

  • Bidochka MJ, Small CLN, Spironello M (2005) Recombination within sympatric cryptic species of the insect pathogenic fungus Metarhizium anisopliae. Environ Microbiol 7:1361–1368

    CAS  PubMed  Google Scholar 

  • Bischoff JF, Rehner SA, Humber RA (2009) A multilocus phylogeny ofthe Metarhizium anisopliae lineage. Mycologia 101:512–530

    CAS  PubMed  Google Scholar 

  • Blackwell M (2009) Fungal evolution and taxonomy. BioControl. doi:10.1007/s10526-009-9243-8 (this SI)

  • Borneman J, Hartin RJ (2000) PCR primers that amplify fungal rRNA genes from environmental samples. Appl Environ Microbiol 66:4356–4360

    CAS  PubMed  Google Scholar 

  • Boucias DG, Tigano MS, Sosa-Gomez DR, Glare TR, Inglis PW (2000) Genotypic properties of the entomopathogenic fungus Nomuraea rileyi. Biol Control 19:124–138

    CAS  Google Scholar 

  • Bridge PD, Prior C, Sagbohan J, Lomer CJ, Carey M, Buddie AG (1997) Molecular characterization of isolates of Metarhizium from locusts and grasshoppers. Biodivers Conserv 6:177–189

    Google Scholar 

  • Brookes AJ (1999) The essence of SNPs. Gene 234:177–186

    CAS  PubMed  Google Scholar 

  • Bruck D (2009) Fungal entomopathogens in the rhizosphere. BioControl. doi:10.1007/s10526-009-9236-7 (this SI)

  • Brugmans B, van der Hulst RGM, Visser RGF, Lindhout P, van Eck HJ (2003) A new and versatile method for the successful conversion of AFLP markers into simple single locus markers. Nucleic Acids Res 31:e55

    PubMed  Google Scholar 

  • Bulat SA, Mironenko N (1990) Species identity of the phytopathogenic fungi Pyrenophora teres Drechsler and P. graminea Ito & Kuribayashi. Mikol Fitopatol 24:435–441

    Google Scholar 

  • Bürgmann H, Pesaro M, Widmer F, Zeyer J (2001) A strategy for optimizing quality and quantity of DNA extracted from soil. J Microbiol Methods 45:7–20

    PubMed  Google Scholar 

  • Cariello NF, Thilly WG, Swenberg JA, Skopek TR (1991) Deletion mutagenesis during polymerase chain-reaction—dependence on DNA-polymerase. Gene 99:105–108

    CAS  PubMed  Google Scholar 

  • Castrillo LA, Vandenberg JD, Wraight SP (2003) Strain-specific detection of introduced Beauveria bassiana in agricultural fields by use of sequence-characterized amplified region markers. J Invertebr Pathol 82:75–83

    CAS  PubMed  Google Scholar 

  • Castrillo LA, Thomsen L, Juneja P, Hajek AE (2007) Detection and quantification of Entomophaga maimaiga resting spores in forest soil using real-time PCR. Mycol Res 111:324–331

    CAS  PubMed  Google Scholar 

  • Castrillo L, Griggs MH, Vandenberg JD (2008) Quantitative detection of Beauveria bassiana GHA (Ascomycota: Hypocreales), a potential microbial control agent of the emerald ash borer, by use of real-time PCR. Biol Control 45:163–169

    CAS  Google Scholar 

  • Chew JSK, Strongman DB, MacKay RM (1998) Comparisons of twenty isolates of the entomopathogen Paecilomyces farinosus by analysis of RAPD markers. Mycol Res 102:1254–1258

    Google Scholar 

  • Christen R (2008) Global sequencing: a review of current molecular data and new methods available to assess microbial diversity. Microbes Environ 23:253–268

    Google Scholar 

  • Coates BS, Hellmich RL, Lewis LC (2002a) Beauveria bassiana haplotype determinatin based on nuclear rDNA internal transcribed spacer PCR-RFLP. Mycol Res 106:40–50

    CAS  Google Scholar 

  • Coates BS, Hellmich RL, Lewis LC (2002b) Nuclear small subunit rRNA group I intron variation among Beauveria spp. provide tools tor strain identification and evidence of horizontal transfer. Curr Genet 41:414–424

    CAS  PubMed  Google Scholar 

  • Cox-Foster DL, Conlan S, Holmes EC, Palacios G, Evans JD, Moran NA, Quan PL, Briese T, Hornig M, Geiser DM, Martinson V, van Engelsdorp D, Kalkstein AL, Drysdale A, Hui J, Zhai JH, Cui LW, Hutchison SK, Simons JF, Egholm M, Pettis JS, Lipkin WI (2007) A metagenomic survey of microbes in honey bee colony collapse disorder. Science 318:283–287

    CAS  PubMed  Google Scholar 

  • Cravanzola F, Piatti P, Bridge PD, Ozino OI (1997) Detection of genetic polymorphism by RAPD-PCR in strains of the entomopathogenic fungus Beauveria brongniartii isolated from the European cockchafer (Melolontha spp.). Lett Appl Microbiol 25:289–294

    CAS  Google Scholar 

  • Dalleau-Clouet C, Gauthier N, Risterucci AM, Bon MC, Fargues J (2005) Isolation and characterization of microsatellite loci from the entomopathogenic hyphomycete, Paecilomyces fumosoroseus. Mol Ecol Notes 5:496–498

    CAS  Google Scholar 

  • 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

    PubMed  Google Scholar 

  • Destefano RHR, Destefano SAL, Messias CL (2004) Detection of Metarhizium anisopliae var. anisopliae within infected sugarcane borer Diatraea saccharalis (Lepidoptera, Pyralidae) using specific primers. Genet Mol Biol 27:245–252

    CAS  Google Scholar 

  • Devi UK, Reineke A, Rao UCM, Reddy NRN, Khan APA (2007) AFLP and single-strand conformation polymorphism studies of recombination in the entomopathogenic fungus Nomuraea rileyi. Mycol Res 111:716–725

    CAS  PubMed  Google Scholar 

  • Enkerli J, Widmer F, Gessler C, Keller S (2001) Strain-specific microsatellite markers in the entomopathogenic fungus Beauveria brongniartii. Mycol Res 105:1079–1087

    CAS  Google Scholar 

  • Enkerli J, Widmer F, Keller S (2004) Long-term field persistence of Beauveria brongniartii strains applied as biocontrol agents against European cockchafer larvae in Switzerland. Biol Control 29:115–123

    Google Scholar 

  • Enkerli J, Kölliker R, Keller S, Widmer F (2005) Isolation and characterization of microsatellite markers from the entomopathogenic fungus Metarhizium anisopliae. Mol Ecol Notes 5:384–386

    CAS  Google Scholar 

  • Enkerli J, Ghormade V, Oulevey C, Widmer F (2009) PCR-RFLP analysis of chitinase genes enables efficient genotyping of Metarhizium anisopliae var. anisopliae. J Invertebr Pathol 102:185–188

    CAS  PubMed  Google Scholar 

  • Entz SC, Johnson DL, Kawchuk LM (2005) Development of a PCR-based diagnostic assay for the specific detection of the entomopathogenic fungus Metarhizium anisopliae var. acridum. Mycol Res 109:1302–1312

    CAS  PubMed  Google Scholar 

  • Estrada ME, Camacho MV, Benito C (2007) The molecular diversity of different isolates of Beauveria bassiana (Bals.) Vuill. as assessed using intermicrosatellites (ISSRs). Cell Mol Biol Lett 12:240–252

    CAS  PubMed  Google Scholar 

  • Fang WG, Leng B, Xiao YH, Jin K, Ma JC, Fan YH, Feng J, Yang XY, Zhang YJ, Pei Y (2005) Cloning of Beauveria bassiana chitinase gene Bbchit1 and its application to improve fungal strain virulence. Appl Environ Microbiol 71:363–370

    CAS  PubMed  Google Scholar 

  • Fargues J, Bon MC, Manguin S, Couteaudier Y (2002) Genetic variability among Paecilomyces fumosoroseus isolates from various geographical and host insect origins based on the rDNA-ITS regions. Mycol Res 106:1066–1074

    CAS  Google Scholar 

  • Fegan M, Manners JM, Maclean DJ, Irwin JAG, Samuels KDZ, Holdom DG, Li DP (1993) Random amplified polymorphic DNA markers reveal a high degree of genetic diversity in the entomopathogenic fungus Metarhizium anisopliae var. anisopliae. J Gen Microbiol 139:2075–2081

    CAS  PubMed  Google Scholar 

  • Feinstein LM, Sul WJ, Blackwood CB (2009) Assessment of bias associated with incomplete extraction of microbial DNA from soil. Appl Environ Microbiol 75:5428–5433

    CAS  PubMed  Google Scholar 

  • Felsenstein J (2009) PHYLIP (Phylogeny Inference Package) version 3.69. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle

    Google Scholar 

  • Fernandes EKK, Costa GL, Moraes AML, Zahner V, Bittencourt V (2006) Study on morphology, pathogenicity, and genetic variability of Beauveria bassiana isolates obtained from Boophilus microplus tick. Parasitol Res 98:324–332

    PubMed  Google Scholar 

  • Field D, Wills C (1996) Long, polymorphic microsatellites in simple organisms. Proc R Soc Lond B Biol Sci 263:209–215

    CAS  Google Scholar 

  • Fisher MM, Triplett EW (1999) Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol 65:4630–4636

    CAS  PubMed  Google Scholar 

  • Fournier A, Widmer F, Enkerli J (2009) Development of a single nucleotide polymorphism (SNP) assay for genotyping of Pandora neoaphidis. (submitted)

  • Fournier A, Enkerli J, Keller S, Widmer F (2008) A PCR-based tool for the cultivation-independent monitoring of Pandora neoaphidis. J Invertebr Pathol 99:49–56

    CAS  PubMed  Google Scholar 

  • Francis C, Anagnou-Veroniki N, Rouffaud MA, De Bievre C, Papierok B (2004) Morphometric and genetic variation among strains of two related species of Erynia (Zygomycota, Entomophthorales) isolated from aphids or Diptera in a limited geographical area lngreece. J Mycol Med 14:171–180

    Google Scholar 

  • Freimoser FM, Hu G, Leger RJ (2005) Variation in gene expression patterns as the insect pathogen Metarhizium anisopliae adapts to different host cuticles or nutrient deprivation in vitro. Microbiology 151:361–371

    CAS  PubMed  Google Scholar 

  • Frey JC, Angert ER, Pell AN (2006) Assessment of biases associated with profiling simple, model communities using terminal-restriction fragment length polymorphism-based analyses. J Microbiol Methods 67:9–19

    CAS  PubMed  Google Scholar 

  • 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 extraciton of DNA directly form soils. Appl Environ Microbiol 65:5409–5420

    PubMed  Google Scholar 

  • Gauthier N, Dalleau-Clouet C, Fargues J (2007) Microsatellite variability in the entomopathogenic fungus Paecilomyces fumosoroseus: genetic diversity and population structure. Mycologia 99:693–704

    CAS  PubMed  Google Scholar 

  • George MLC, Nelson RJ, Zeigler RS, Leung H (1998) Rapid population analysis of Magnaporthe grisea by using rep-PCR and endogenous repetitive DNA sequences. Phytopathology 88:223–229

    CAS  PubMed  Google Scholar 

  • Ghikas DV, Kouvelis VN, Typas MA (2006) The complete mitochondrial genome of the entomopathogenic fungus Metarhizium anisopliae var. anisopliae: gene order and trn gene clusters reveal a common evolutionary course for all Sordariomycetes, while intergenic regions show variation. Arch Microbiol 185:393–401

    CAS  PubMed  Google Scholar 

  • Glare TR, Reay SD, Nelson TL, Moore R (2008) Beauveria caledonica is a naturally occurring pathogen of forest beetles. Mycol Res 112:352–360

    CAS  PubMed  Google Scholar 

  • Goldstein DB, Schlötterer C (1999) Microsatellites: evolution and applications. Oxford University Press, New York

    Google Scholar 

  • Green SJ, Freeman S, Hadar Y, Minz D (2004) Molecular tools for isolate and community studies of Pyrenomycete fungi. Mycologia 96:439–451

    CAS  Google Scholar 

  • Groppe K, Sanders I, Wiemken A, Boller T (1995) A microsatellite marker for studying the ecology and diversity of fungal endophytes (Epichloe spp.) in grasses. Appl Environ Microbiol 61:3943–3949

    CAS  PubMed  Google Scholar 

  • Guzman-Franco AW, Atkins SD, Alderson PG, Pell JK (2008) Development of species-specific diagnostic primers for Zoophthora radicans and Pandora blunckii; two co-occurring fungal pathogens of the diamondback moth, Plutella xylostella. Mycol Res 112:1227–1240

    CAS  PubMed  Google Scholar 

  • Hajek AE, Delalibera I (2009) Fungal pathogens as classical biological control agents against arthropods. BioControl. doi:10.1007/s10526-009-9253-6 (this SI)

  • Hajek AE, Hodge KT, Liebherr JK, Day WH, Vandenberg JD (1996) Use of RAPD analysis to trace the origin of the weevil pathogen Zoophthora phytonomi in North America. Mycol Res 100:349–355

    Google Scholar 

  • Hajek AE, Jensen AB, Thomsen L, Hodge KT, Eilenberg J (2003) PCR-RFLP is used to investigate relations among species in the entomopathogenic genera Eryniopsis and Entomophaga. Mycologia 95:262–268

    CAS  Google Scholar 

  • Hartmann M, Widmer F (2006) Community structure analyses are more sensititive to differences in soil bacterial communities than anonymous diversity indices. Appl Environ Microbiol 72:7804–7812

    CAS  PubMed  Google Scholar 

  • Hartmann M, Widmer F (2008) Reliability for detecting composition and changes of microbial communities by T-RFLP genetic profiling. FEMS Microbiol Ecol 63:249–260

    CAS  PubMed  Google Scholar 

  • Hartmann M, Fliessbach A, Oberholzer H-R, Widmer F (2006) Ranking the magnitude of crop and farming system effects on soil microbial biomass and genetic structure of bacterial communities. FEMS Microbiol Ecol 57:378–388

    CAS  PubMed  Google Scholar 

  • Hartmann M, Enkerli J, Widmer F (2007) Residual polymerase activity-induced bias in terminal restriction fragment length polymorphism analysis. Environ Microbiol 9:555–559

    CAS  PubMed  Google Scholar 

  • He JZ, Xu ZH, Hughes J (2005) Analyses of soil fungal communities in adjacent natural forest and hoop pine plantation ecosystems of subtropical Australia using molecular approaches based on 18S rRNA genes. FEMS Microbiol Lett 247:91–100

    CAS  PubMed  Google Scholar 

  • Hegedus DD, Khachatourians GG (1996) Identification and differentiation of the entomopathogenic fungus Beauveria bassiana using polymerase chain reaction and singel-strand conformation polymorphism analysis. J Invertebr Pathol 67:289–299

    CAS  PubMed  Google Scholar 

  • Hernan-Gomez S, Espinosa JC, Ubeda JF (2000) Characterization of wine yeasts by temperature gradient gel electrophoresis (TGGE). FEMS Microbiol Lett 193:45–50

    Article  CAS  PubMed  Google Scholar 

  • Hesketh H, Roy HE, Eilenberg J, Hails RS (2009) Challenges in modelling complexity of fungal entomopathogens in semi-natural populations of insects. BioControl. doi:10.1007/s10526-009-9249-2 (this SI)

  • Hibbett DS, Binder M, Bischoff JF, Blackwell M, Cannon PF, Eriksson OE, Huhndorf S, James T, Kirk PM, Lucking R, Lumbsch HT, Lutzoni F, Matheny PB, McLaughlin DJ, Powell MJ, Redhead S, Schoch CL, Spatafora JW, Stalpers JA, Vilgalys R, Aime MC, Aptroot A, Bauer R, Begerow D, Benny GL, Castlebury LA, Crous PW, Dai YC, Gams W, Geiser DM, Griffith GW, Gueidan C, Hawksworth DL, Hestmark G, Hosaka K, Humber RA, Hyde KD, Ironside JE, Koljalg U, Kurtzman CP, Larsson KH, Lichtwardt R, Longcore J, Miadlikowska J, Miller A, Moncalvo JM, Mozley-Standridge S, Oberwinkler F, Parmasto E, Reeb V, Rogers JD, Roux C, Ryvarden L, Sampaio JP, Schussler A, Sugiyama J, Thorn RG, Tibell L, Untereiner WA, Walker C, Wang Z, Weir A, Weiss M, White MM, Winka K, Yao YJ, Zhang N (2007) A higher-level phylogenetic classification of the Fungi. Mycol Res 111:509–547

    PubMed  Google Scholar 

  • Hodge KT, Sawyer AJ, Humber RA (1995) RAPD-PCR for identification of Zoophthora radicans isolates in biological control of the potato leafhopper. J Invertebr Pathol 65:1–9

    CAS  PubMed  Google Scholar 

  • Hughes JB, Hellmann JJ (2005) The application of rarefaction techniques to molecular inventories of microbial diversity. Methods Enzymol 397:292–308

    CAS  PubMed  Google Scholar 

  • Hughes JB, Hellmann JJ, Ricketts TH, Bohannan BJM (2001) Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Microbiol 67:4399–4406

    CAS  PubMed  Google Scholar 

  • Hunt J, Boddy L, Randerson PF, Rogers HJ (2004) An evaluation of 18S rDNA approaches for the study of fungal diversity in grassland soils. Microb Ecol 47:385–395

    CAS  PubMed  Google Scholar 

  • Inglis GD, Duke GM, Goettel MS, Kabaluk JT (2008) Genetic diversity of Metarhizium anisopliae var. anisopliae in southwestern British Columbia. J Invertebr Pathol 98:101–113

    CAS  PubMed  Google Scholar 

  • Jackson CR, Harper JP, Willoughby D, Roden EE, Churchill PF (1997) A simple, efficient method for the separation of humic substances and DNA from environmental samples. Appl Environ Microbiol 63:4993–4995

    CAS  PubMed  Google Scholar 

  • James TY, Kauff F, Schoch CL, Matheny PB, Hofstetter V, Cox CJ, Celio G, Gueidan C, Fraker E, Miadlikowska J, Lumbsch HT, Rauhut A, Reeb V, Arnold AE, Amtoft A, Stajich JE, Hosaka K, Sung GH, Johnson D, O’Rourke B, Crockett M, Binder M, Curtis JM, Slot JC, Wang Z, Wilson AW, Schussler A, Longcore JE, O’Donnell K, Mozley-Standridge S, Porter D, Letcher PM, Powell MJ, Taylor JW, White MM, Griffith GW, Davies DR, Humber RA, Morton JB, Sugiyama J, Rossman AY, Rogers JD, Pfister DH, Hewitt D, Hansen K, Hambleton S, Shoemaker RA, Kohlmeyer J, Volkmann-Kohlmeyer B, Spotts RA, Serdani M, Crous PW, Hughes KW, Matsuura K, Langer E, Langer G, Untereiner WA, Lucking R, Budel B, Geiser DM, Aptroot A, Diederich P, Schmitt I, Schultz M, Yahr R, Hibbett DS, Lutzoni F, McLaughlin DJ, Spatafora JW, Vilgalys R (2006) Reconstructing the early evolution of fungi using a six-gene phylogeny. Nature 443:818–822

    CAS  PubMed  Google Scholar 

  • Jensen AB, Eilenberg J (2001) Genetic variation within the insect-pathogenic genus Entomophthora, focusing on the E. muscae complex, using PCR-RFLP of the ITS II and the LSU rDNA. Mycol Res 105:307–312

    CAS  Google Scholar 

  • Jensen AB, Gargas A, Eilenberg J, Rosendahl S (1998) Relationships of the insect-pathogenic order entomophthorales (Zygomycota, Fungi) based on phylogenetic analyses of nuclear small subunit ribosomal DNA sequences (SSU rDNA). Fungal Genet Biol 24:325–334

    CAS  PubMed  Google Scholar 

  • Jensen AB, Thomsen L, Eilenberg J (2001) Intraspecific variation and host specificity of Entomophthora muscae sensu stricto isolates revealed by random amplified polymorphic DNA, universal primed PCR, PCR-restriction fragment length polymorphism, and conidial morphology. J Invertebr Pathol 78:251–259

    CAS  PubMed  Google Scholar 

  • Kabir S, Rajendran N, Amemiya T, Itoh T (2003) Quantitative measurement of fungal DNA extracted by three different methods using real-time polymerase chain reaction. J Biosci Bioeng 96:337–343

    CAS  PubMed  Google Scholar 

  • Kanagawa T (2003) Bias and artifacts in multitemplate polymerase chain reactions (PCR). J Biosci Bioeng 96:317–323

    CAS  PubMed  Google Scholar 

  • Kim S, Misra A (2007) SNP genotyping: technologies and biomedical applications. Annu Rev Biomed Eng 9:289–320

    CAS  PubMed  Google Scholar 

  • Kirk JL, Beaudette LA, Hart M, Moutoglis P, Khironomos JN, Lee H, Trevors JT (2004) Methods of studying soil microbial diversity. J Microbiol Methods 58:169–188

    CAS  PubMed  Google Scholar 

  • Klamer M, Hedlund K (2004) Fungal diversity in set-aide agricultural soil investigated using terminal-restriction fragment length polymorphism. Soil Biol Biochem 36:983–988

    CAS  Google Scholar 

  • Kouvelis VN, Ghikas DV, Edgington S, Typas MA, Moore D (2008a) Molecular characterization of isolates of Beauveria bassiana obtained from overwintering and summer populations of Sunn Pest (Eurygaster integriceps). Lett Appl Microbiol 46:414–420

    CAS  PubMed  Google Scholar 

  • Kouvelis VN, Sialakouma A, Typas MA (2008b) Mitochondrial gene sequences alone or combined with ITS region sequences provide firm molecular criteria for the classification of Lecanicillium species. Mycol Res 112:829–844

    CAS  PubMed  Google Scholar 

  • Kowalchuk GA, deBruijn FJ, Head IM, Akkermans ADL, Van Elsas JD (2004) Molecular microbial ecolgy manual. Kluwer, Dordrecht

    Google Scholar 

  • Kreader CA (1996) Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein. Appl Environ Microbiol 62:1102–1106

    CAS  PubMed  Google Scholar 

  • Kristensen R, Berdal KG, Holst-Jensen A (2007) Simultaneous detection and identification of trichothecene- and moniliformin-producing Fusarium species based on multiplex SNP analysis. J Appl Microbiol 102:1071–1081

    CAS  PubMed  Google Scholar 

  • Kuske CR, Banton KL, Adorada DL, Stark PC, Hill KK, Jackson PJ (1998) Small-scale DNA sample preparation method for field PCR detection of microbial cells and spores in soil. Appl Environ Microbiol 64:2463–2472

    CAS  PubMed  Google Scholar 

  • Lambreghts R, Shi M, Belden WJ, de Caprio D, Park D, Henn MR, Galagan JE, Bastürkmen M, Birren BW, Sachs MS, Dunlap JC, Loros JJ (2009) A high-density single nucleotide polymorphism map for Neurospora crassa. Genetics 181:767–781

    CAS  PubMed  Google Scholar 

  • LaMontagne MG, Michel FC, Holden PA, Reddy CA (2002) Evaluation of extraction and purification methods for obtaining PCR-amplifiable DNA from compost for microbial community analysis. J Microbiol Methods 49:255–264

    CAS  PubMed  Google Scholar 

  • Leal SCM, Bertioli DJ, Butt TM, Peberdy JF (1994) Characterization of isolates of the entomopathogenic fungus Metarhizium anisopliae by RAPD-PCR. Mycol Res 98:1077–1081

    CAS  Google Scholar 

  • Leal SCM, Bertioli DJ, Butt TM, Carder JH, Burrows PR, Peberdy YF (1997) Amplification and restriction endonuclease digestion of the Pr1 gene for the detection and characterization of Metarhizium strains. Mycol Res 101:257–265

    CAS  Google Scholar 

  • Leland JE, McGuire MR, Grace JA, Jaronski ST, Ulloa M, Park YH, Plattner RD (2005) Strain selection of a fungal entomopathogen, Beauveria bassiana, for control of plant bugs (Lygus spp.) (Heteroptera: Miridae). Biol Control 35:104–114

    Google Scholar 

  • Lihme M, Jensen AB, Rosendahl S (2009) Local scale population genetic structure of Entomophthora muscae epidemics. Fungal Ecol 2:81–86

    Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Liu ZY, Liang ZQ, Liu AY, Yao YJ, Hyde KD, Yu ZN (2002) Molecular evidence for teleomorph-anamorph connections in Cordyceps based on ITS-5.8S rDNA sequences. Mycol Res 106:1100–1108

    CAS  Google Scholar 

  • Lloyd-Jones G, Hunter DWF (2001) Comparison of rapid DNA extraction methods applied to contrasting New Zealand soils. Soil Biol Biochem 33:2053–2059

    CAS  Google Scholar 

  • Lord NS, Kaplan CW, Shank P, Kitts CL, Elrod SL (2002) Assessment of fungal diversity using terminal restriction fragment (TRF) pattern analysis: comparison of 18S and ITS ribosomal regions. FEMS Microbiol Ecol 42:327–337

    CAS  PubMed  Google Scholar 

  • Lynch MJM, Thorn RG (2006) Diversity of basidiomycetes in Michigan agricultural soils. Appl Environ Microbiol 72:7050–7056

    CAS  PubMed  Google Scholar 

  • Manzano M, Cocolin L, Iacumin L, Cantoni C, Comi G (2005) A PCR-TGGE (temperature gradient gel electrophoresis) technique to assess differentiation among enological Saccharomyces cerevisiae strains. Int J Food Microbiol 101:333–339

    CAS  PubMed  Google Scholar 

  • Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen ZT, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu PG, Begley RF, Rothberg JM (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380

    CAS  PubMed  Google Scholar 

  • Martin-Laurent F, 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

    CAS  PubMed  Google Scholar 

  • Maurer P, Couteaudier Y, Girard PA, Bridge PD, Riba G (1997) Genetic diversity of Beauveria bassiana and relatedness to host insect range. Mycol Res 101:159–164

    Google Scholar 

  • McGuire MR, Ulloa M, Park YH, Hudson N (2005) Biological and molecular characteristics of Beauveria bassiana isolates from California Lygus hesperus (Hemiptera: Miridae) populations. Biol Control 33:307–314

    Google Scholar 

  • Meudt HM, Clarke AC (2007) Almost forgotten or latest practice? AFLP applications, analyses and advances. Trends Plant Sci 12:106–117

    CAS  PubMed  Google Scholar 

  • Meyling NV, Eilenberg J (2006) Isolation and characterisation of Beauveria bassiana isolates from phylloplanes of hedgerow vegetation. Mycol Res 110:188–195

    CAS  PubMed  Google Scholar 

  • Meyling NV, Eilenberg J (2007) Ecology of the entomopathogenic fungi Beauveria bassiana and Metarhizium anisopliae in temperate agroecosystems: potential for conservation biological control. Biol Control 43:145–155

    Google Scholar 

  • Meyling NV, Hajek AE (2009) Principles from community and metapopulation ecology: application to fungal entomopathogens BioControl. doi:10.1007/s10526-009-9246-5 (this SI)

  • Meyling NV, Lubeck M, Buckley EP, Eilenberg J, Rehner SA (2009) Community composition, host range and genetic structure of the fungal entomopathogen Beauveria in adjoining agricultural and seminatural habitats. Mol Ecol 18:1282–1293

    CAS  PubMed  Google Scholar 

  • Midgley DJ, Saleeba JA, Stewart MI, Simpson AE, McGee PA (2007) Molecular diversity of soil basidiomycete communities in northern-central New South Wales, Australia. Mycol Res 111:370–378

    CAS  PubMed  Google Scholar 

  • Miller DN, Bryant JE, Madsen EL, Ghiorse WC (1999) Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl Environ Microbiol 65:4715–4724

    CAS  PubMed  Google Scholar 

  • Mitina GV, Mikhailova LA, Yli-Mattila T (2007) RAPD-PCR, UP-PCR and rDNA sequence analyses of the entomopathogenic fungus Verticillium lecanii and its pathogenicity towards insects and phytopathogenic fungi. Arch Phytopathol Pflanzenschutz 41:113–128

    Google Scholar 

  • Mor H, Gindin G, BenZeev IS, Raccah B, Geschtovt NU, Ajtkhozhina N (1996) Diversity among isolates of Verticillium lecanii as expressed by DNA polymorphism and virulence towards Bemisia tabaci. Phytoparasitica 24:111–118

    Google Scholar 

  • Morin PA, Luikart G, Wayne RK (2004) SNPs in ecology, evolution and conservation. Trends Ecol Evol 19:208–216

    Google Scholar 

  • Mozes-Koch R, Edelbaum O, Livneh O, Sztejnberg A, Uziel A, Gerson U, Sela I (1995) Identification of Hirsutella species, isolates within a species and intraspecific heterokaryons by random amplified polymorphic DNA (RAPD). J Plant Dis Protect 102:284–290

    CAS  Google Scholar 

  • Mullis K, Falcoma F, Scharf S, Snikl R, Horn G, Erlich H (1986) Specific amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harbor Symp Quant Biol 51:280

    Google Scholar 

  • Mullis KB, Ferré F, Gibbs RA (1994) The polymerase chain reaction. Birkhäuser, Boston

    Google Scholar 

  • Munoz C, Talquenca SG, Volpe ML (2009) Tetra primer ARMS-PCR for identification of SNP in beta-tubulin of Botrytis cinerea, responsible of resistance to benzimidazole. J Microbiol Methods 78:245–246

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Nagahama T, Sato H, Shimazu M, Sugiyama J (1995) Phylogenetic divergence of the entomophthoralean fungi: evidence from nuclear 18S ribosomal RNA gene sequences. Mycologia 87:203–209

    CAS  Google Scholar 

  • Neuvéglise C, Brygoo Y, Vercambre B, Riba G (1994) Comparative analysis of molecular and biological characteristics of strains of Beauveria brongniartii isolated form insects. Mycol Res 98:322–328

    Google Scholar 

  • Neuvéglise C, Brygoo Y, Riba G (1997) 28S rDNA group-I introns: a powerful tool for identifying strains of Beauveria brongniartii. Mol Ecol 6:373–381

    PubMed  Google Scholar 

  • Nielsen C, Sommer C, Eilenberg J, Hansen KS, Humber RA (2001) Characterization of aphid pathogenic species in the genus Pandora by PCR techniques and digital image analysis. Mycologia 93:864–874

    CAS  Google Scholar 

  • Nielsen C, Milgroom MG, Hajek A (2005) Genetic diversity in the gypsy moth fungal pathogen Entomophaga maimaiga from founder populations in North America and source populations in Asia. Mycol Res 109:941–950

    CAS  PubMed  Google Scholar 

  • Nikoh N, Fukatsu T (2000) Interkingdom host jumping underground: phylogenetic analysis of entomoparasitic fungi of the genus Cordyceps. Mol Biol Evol 17:629–638

    CAS  PubMed  Google Scholar 

  • O’Brien HE, Parrent JL, Jackson JA, Moncalvo JM, Vilgalys R (2005) Fungal community analysis by large-scale sequencing of environmental samples. Appl Environ Microbiol 71:5544–5550

    PubMed  Google Scholar 

  • Oliveira CA, Sá NMH, Gomes EA, Marriel IE, Scotti MR, Guimarães CT, Schaffert RE, Alves VMC (2009) Assessment of the mycorrhizal community in the rhizosphere of maize (Zea mays L.) genotypes contrasting for phosphorus efficiency in the acid savannas of Brazil using denaturing gradient gel electrophoresis (DGGE). Appl Soil Ecol 41:249–258

    Google Scholar 

  • Oulevey C, Widmer F, Kölliker R, Enkerli J (2009) An optimized microsatellite marker set for detection of Metarhizium anisopliae genotype diversity on field and regional scales. Mycol Res 113:1016–1024

    CAS  PubMed  Google Scholar 

  • Ownley B, Gwinn KD, Vega FE (2009) Endophytic fungal entomopathogens with activity against plant pathogens: ecology and evolution. BioControl. doi:10.1007/s10526-009-9241-x (this SI)

  • Pantou MP, Mavridou A, Typas MA (2003) IGS sequence variation, group-I introns and the complete nuclear ribosomal DNA of the entomopathogenic fungus Metarhizium: excellent tools for isolate detection and phylogenetic analysis. Fungal Genet Biol 38:159–174

    CAS  PubMed  Google Scholar 

  • Perez T, Albornoz J, Dominguez A (1998) An evaluation of RAPD fragment reproducibility and nature. Mol Ecol 7:1347–1357

    CAS  PubMed  Google Scholar 

  • Pesaro M, Widmer F (2006) Identification and specific detection of a novel Pseudomonadaceae cluster associated with soils from winter wheat plots of a long-term agricultural field experiment. Appl Environ Microbiol 72:37–43

    CAS  PubMed  Google Scholar 

  • Petrosino JF, Highlander S, Luna RA, Gibbs RA, Versalovic J (2009) Metagenomic pyrosequencing and microbial identification. Clin Chem 55:856–866

    CAS  PubMed  Google Scholar 

  • Piatti P, Cravanzola F, Bridge PD, Ozino OI (1998) Molecular characterization of Beauveria brongniartii isolates obtained from Melolontha melolontha in Valle d’Aosta (Italy) by RAPD-PCR. Lett Appl Microbiol 26:317–324

    CAS  Google Scholar 

  • Poussier S, Cheron JJ, Couteau A, Luisetti J (2002) Evaluation of procedures for reliable PCR detection of Ralstonia solanacearum in common natural substrates. J Microbiol Methods 51:349–359

    CAS  PubMed  Google Scholar 

  • Qin X, Evans JD, Aronstein KA, Murray KD, Weinstock GM (2006) Genome sequences of the honey bee pathogens Paenibacillus larvae and Ascosphaera apis. Insect Mol Biol 15:715–718

    CAS  PubMed  Google Scholar 

  • Qiu XY, Wu LY, Huang HS, McDonel PE, Palumbo AV, Tiedje JM, Zhou JZ (2001) Evaluation of PCR-generated chimeras: mutations, and heteroduplexes with 16S rRNA gene-based cloning. Appl Environ Microbiol 67:880–887

    CAS  PubMed  Google Scholar 

  • Rakotonirainy M, Cariou M, Brygoo Y, Riba G (1994) Phylogenetic relationships within the genus Metarhizium based on 28S rRNA sequences and isozyme comparison. Mycol Res 98:225–230

    CAS  Google Scholar 

  • Ramette A (2007) Multivariate analyses in microbial ecology. FEMS Microbiol Ecol 62:142–160

    CAS  PubMed  Google Scholar 

  • 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 analysis fingerprints: biological and methodological variability. Appl Environ Microbiol 67:4479–4487

    CAS  PubMed  Google Scholar 

  • R Development Core Team (2008) R: a language and environment for statistical computing. http://www.R-project.org

  • Rees GN, Baldwin DS, Watson GO, Perryman S, Nielsen DL (2004) Ordination and significance testing of microbial community composition derived from terminal restriction fragment length polymorphisms: application of multivariate statistics. Antonie Van Leeuwenhoek 86:339–347

    PubMed  Google Scholar 

  • Rehner SA, Buckley EP (2003) Isolation and characterization of microsatellite loci from the entomopathogenic fungus Beauveria bassiana (Ascomycota: Hypocreales). Mol Ecol Notes 3:409–411

    CAS  Google Scholar 

  • Rehner SA, Buckley E (2005) A Beauveria phylogeny inferred from nuclear ITS and EF1-alpha sequences: evidence for cryptic diversification and links to Cordyceps teleomorphs. Mycologia 97:84–98

    CAS  PubMed  Google Scholar 

  • Rehner SA, Evans JD (2009) Microsatellite loci for the fungus Ascosphaera apis: cause of honey bee chalkbrood disease. Mol Ecol Resour 9:855–858

    CAS  Google Scholar 

  • Rieseberg L (1996) Homology among RAPD fragments in interspecific comparisons. Mol Ecol 5:99–105

    CAS  Google Scholar 

  • Roh C, Villatte F, Kim BG, Schmid RD (2006) Comparative study of methods for extraction and purification of environmental DNA from soil and sludge samples. Appl Biochem Biotechnol 134:97–112

    CAS  PubMed  Google Scholar 

  • Rohel E, Couteaudier Y, Papierok B, Cavelier N, Dedryver CA (1997) Ribosomal internal transcribed spacer size variation correlated with RAPD-PCR pattern polymorphisms in the entomopathogenic fungus Erynia neoaphidis and some closely related species. Mycol Res 101:573–579

    CAS  Google Scholar 

  • Romanowski G, Lorenz MG, Wackernagel W (1993) Use of polymerase chain-reaction and electroporation of Escherichia coli to monitor the persistence of extracellular plasmid DNA introduced into natural soils. Appl Environ Microbiol 59:3438–3446

    CAS  PubMed  Google Scholar 

  • Ronaghi M, Uhlen M, Nyren P (1998) A sequencing method based on real-time pyrophosphate. Science 281:363–365

    CAS  PubMed  Google Scholar 

  • Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor

    Google Scholar 

  • Schadt CW, Martin AP, Lipson DA, Schmidt SK (2003) Seasonal dynamics of previously unknown fungal lineages in tundra soils. Science 301:1359–1361

    CAS  PubMed  Google Scholar 

  • Schneider S, Enkerli J, Widmer F (2009) A generally applicable assay for the quantification of inhibitory effects on PCR. J Microbiol Methods 78:351–353

    CAS  PubMed  Google Scholar 

  • Schwarzenbach K, Enkerli J, Widmer F (2007a) Objective criteria to assess representativity of soil fungal community profiles. J Microbiol Methods 68:358–366

    CAS  PubMed  Google Scholar 

  • Schwarzenbach K, Widmer F, Enkerli J (2007b) Cultivation-independent analysis of fungal genotypes in soil by using simple sequence repeat markers. Appl Environ Microbiol 73:6519–6525

    CAS  PubMed  Google Scholar 

  • Schwarzenbach K, Enkerli J, Widmer F (2009) Effects of biological and chemical insect control agents on fungal community structures in soil microcosms. Appl Soil Ecol 42:54–62

    Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Sessitsch A, Hackl E, Wenzl P, Kilian A, Kostic T, Stralis-Pavese N, Sandjong BT, Bodrossy L (2006) Diagnostic microbial microarrays in soil ecology. New Phytol 171(4):719–735

    CAS  PubMed  Google Scholar 

  • Smit E, Leeflang P, Glandorf B, van Elsas JD, Wernars K (1999) Analysis 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

    CAS  PubMed  Google Scholar 

  • Sosa-Gomez DR, Humber RA, Hodge KT, Binneck E, da Silva-Brandao KL (2009) Variability of the mitochondrial SSU rDNA of Nomuraea species and other entomopathogenic fungi from Hypocreales. Mycopathologia 167:145–154

    CAS  PubMed  Google Scholar 

  • Sudisha J, Kumar SA, Niranjana SR, Shetty NP, Shetty HS (2009) Cloning and development of pathotype-specific SCAR marker associated with Sclerospora graminicola isolates from pearl millet. Australas Plant Pathol 38:216–221

    CAS  Google Scholar 

  • Sugimoto M, Koike M, Hiyama N, Nagao H (2003) Genetic, morphological, and virulence characterization of the entomopathogenic fungus Verticillium lecanii. J Invertebr Pathol 82:176–187

    CAS  PubMed  Google Scholar 

  • Suzuki M, Rappe MS, Giovannoni SJ (1998) Kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity. Appl Environ Microbiol 64:4522–4529

    CAS  PubMed  Google Scholar 

  • Swofford DL (2002) PAUP*: phylogenetic analysis using parsimony (* and other methods). Version 4.0b10. Sinauer Associates, Sunderland

    Google Scholar 

  • Takatsuka J (2007) Specific PCR assays for the detection of DNA from Beauveria bassiana F-263, a highly virulent strain affecting the Japanese pine sawyer, Monochamus alternaturs (Coleoptera: Cerambycidae), by a sequence-characterized amplified region (SCAR) marker. Appl Entomol Zool 42:619–628

    CAS  Google Scholar 

  • Taylor JW, Fisher MC (2003) Fungal multilocus sequence typing—it’s not just for bacteria. Curr Opin Microbiol 6:351–356

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Thomsen L, Jensen AB (2002) Application of nested-PCR technique to resting spores from the Entomophthora muscae species complex: implications for analyses of host-pathogen population interactions. Mycologia 94:794–802

    CAS  Google Scholar 

  • Tigano MS, Adams B, Maimala S, Boucias D (2006) Genetic diversity of Hirsutella thompsonii isolates from Thailand based on AFLP analysis and partial β-tubulin gene sequences. Genet Mol Biol 29:715–721

    CAS  Google Scholar 

  • Tominaga T (2006) Rapid discrimination of Listeria monocytogenes strains by microtemperature gradient gel electrophoresis. J Clin Microbiol 44:2199–2206

    CAS  PubMed  Google Scholar 

  • Tringe SG, Rubin EM (2005) Metagenomics: DNA sequencing of environmental samples. Nat Rev Genet 6:805–814

    CAS  PubMed  Google Scholar 

  • Tun CC, Ikenaga M, Asakawa S, Kimura M (2002) Community structure of bacteria and fungi responsible for rice straw decomposition in a paddy field estimated by PCR-RFLP analysis. Soil Sci Plant Nutri 48:805–813

    Google Scholar 

  • Tymon AM, Pell JK (2005) ISSR, ERIC and RAPD techniques to detect genetic diversity in the aphid pathogen Pandora neoaphidis. Mycol Res 109:285–293

    CAS  PubMed  Google Scholar 

  • Tymon AM, Shah PA, Pell JK (2004) PCR-based molecular discrimination of Pandora neoaphidis isolates from related entomopathogenic fungi and development of species-specific diagnostic primers. Mycol Res 108:419–433

    CAS  PubMed  Google Scholar 

  • 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

    PubMed  Google Scholar 

  • Vandenkoornhuyse P, Baldauf SL, Leyval C, Straczek J, Young JPW (2002) Evolution—extensive fungal diversity in plant roots. Science 295:2051

    PubMed  Google Scholar 

  • Vargas LRB, Rossato M, Ribeiro RTD, de Barros NM (2003) Characterization of Nomuraea rileyi strains using polymorphic DNA, virulence and enzyme activity. Braz Arch Biol Technol 46:13–18

    CAS  Google Scholar 

  • Vega FE, Goettel M, Blackwell M, Chandler D, Jackson MA, Keller S, Koike M, Maniania NK, Monzon A, Ownley BH, Pell J, Rangel DEN, Roy HE (2009) Fungal entomopathogens: new insights on their ecology. Fungal Ecol 2:149–159

    Google Scholar 

  • Vekemans X, Beauwens T, Lemaire M, Roldan-Ruiz I (2002) Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size. Mol Ecol 11:139–151

    CAS  PubMed  Google Scholar 

  • Velásquez VB, Carcamo MP, Merino CR, Iglesias AF, Duran JF (2007) Intraspecific differentiation of Chilean isolates of the entomopathogenic fungi Metarhizium anisopliae var. anisopliae as revealed by RAPD, SSR and ITS markers. Genet Mol Biol 30:89–99

    Google Scholar 

  • Versalovic J, Schneider M, DeBruijn FJ, Lupski JR (1994) Genomic fingerprinting of bacteria using repetitive sequence-base polymerase chain reaction. Methods Mol Cell Biol 5:25–40

    CAS  Google Scholar 

  • Viebahn M, Veenman C, Wernars K, van Loon LC, Smit E, Bakker P (2005) Assessment of differences in ascomycete communities in the rhizosphere of field-grown wheat and potato. FEMS Microbiol Ecol 53:245–253

    CAS  PubMed  Google Scholar 

  • Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414

    CAS  PubMed  Google Scholar 

  • Wada S, Horita M, Hirayae K, Shimazu M (2003) Discrimination of Japanese isolates of Beauveria brongniartii (Deuteromycotina: Hyphomycetes) by RFLP of the rDNA-ITS regions. Appl Entomol Zool 38:551–557

    CAS  Google Scholar 

  • Wagner-Dobler I, Lunsdorf H, Lubbehusen T, von Canstein HF, Li Y (2000) Structure and species composition of mercury-reducing biofilms. Appl Environ Microbiol 66:4559–4563

    CAS  PubMed  Google Scholar 

  • Wang CS, St Leger RJ (2007) The MAD1 adhesin of Metarhizium anisopliae links adhesion with blastospore production and virulence to insects, and the MAD2 adhesin enables attachment to plants. Eukaryotic Cell 6:808–816

    CAS  PubMed  Google Scholar 

  • Wang CS, Li ZZ, Typas MA, Butt TM (2003a) Nuclear large subunit rDNA group I intron distribution in a population of Beauveria bassiana strains: phylogenetic implications. Mycol Res 107:1189–1200

    CAS  PubMed  Google Scholar 

  • Wang CS, Shah FA, Patel N, Li ZZ, Butt TM (2003b) Molecular investigation on strain genetic relatedness and population structure of Beauveria bassiana. Environ Microbiol 5:908–915

    CAS  PubMed  Google Scholar 

  • Wang C, Fan M, Li Z, Butt TM (2004) Molecular monitoring and evaluation of the application of the insect-pathogenic fungus Beauveria bassiana in southeast China. J Appl Microbiol 96:861–870

    CAS  PubMed  Google Scholar 

  • Wang CS, Hu G, St Leger RJ (2005a) Differential gene expression by Metarhizium anisopliae growing in root exudate and host (Manduca sexta) cuticle or hemolymph reveals mechanisms of physiological adaptation. Fungal Genet Biol 42:704–718

    CAS  PubMed  Google Scholar 

  • Wang SB, Miao XX, Zhao WG, Huang B, Fan MZ, Li ZZ, Huang YP (2005b) Genetic diversity and population structure among strains of the entomopathogenic fungus, Beauveria bassiana, as revealed by inter-simple sequence repeats (ISSR). Mycol Res 109:1364–1372

    CAS  PubMed  Google Scholar 

  • Watson RJ, Blackwell B (2000) Purification and characterization of a common soil component which inhibits the polymerase chain reaction. Can J Microbiol 46:633–642

    CAS  PubMed  Google Scholar 

  • Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18:7213–7218

    CAS  PubMed  Google Scholar 

  • White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetic studies. In: Innis M, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols—a guide to methods and applications. Academic Press, San Diego, pp 315–322

    Google Scholar 

  • Whitehouse CA, Hottel HE (2007) Comparison of five commercial DNA extraction kits for the recovery of Francisella tularensis DNA from spiked soil samples. Mol Cell Biochem 21:92–96

    CAS  Google Scholar 

  • Widmer F, Seidler RJ, Watrud LS (1996) Sensitive detection of transgenic plant marker gene persistence in soil microcosms. Mol Ecol 5:603–613

    CAS  Google Scholar 

  • Widmer F, Fliessbach A, Laczko E, Schulze-Aurich J, Zeyer J (2001) Assessing soil biological characteristics: a comparison of bulk soil community DNA-, PLFA-, and Biolog (TM)-analyses. Soil Biol Biochem 33:1029–1036

    CAS  Google Scholar 

  • Widmer F, Hartmann M, Frey B, Kölliker R (2006) A novel strategy to extract specific phylogenetic sequence information from community T-RFLP. J Microbiol Methods 66:512–520

    CAS  PubMed  Google Scholar 

  • Williams JK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphism amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535

    CAS  PubMed  Google Scholar 

  • Wilson IG (1997) Inhibition and facilitation of nucleic acid amplification. Appl Environ Microbiol 63:3741–3751

    CAS  PubMed  Google Scholar 

  • Xu JP, Guo H, Yang ZL (2007) Single nucleotide polymorphisms in the ectomycorrhizal mushroom Tricholoma matsutake. Microbiology 153:2002–2012

    CAS  PubMed  Google Scholar 

  • Yergeau E, Filion M, Vujanovic V, St-Arnaud M (2005) A PCR-denaturing gradient gel electrophoresis approach to assess Fusarium diversity in asparagus. J Microbiol Methods 60:143–154

    CAS  PubMed  Google Scholar 

  • Yergeau E, Vujanovic V, St-Arnaud M (2006) Changes in communities of Fusarium and arbuscular mycorrhizal fungi as related to different asparagus cultural factors. Microb Ecol 52:104–113

    PubMed  Google Scholar 

  • Zare R, Kouvelis VN, Typas MA, Bridge PD (1999) Presence of a 20 bp insertion/deletion in the ITS1 region of Verticillium lecanii. Lett Appl Microbiol 28:258–262

    CAS  PubMed  Google Scholar 

  • Zhou J, Bruns MA, Tiedje JM (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62:316–322

    CAS  PubMed  Google Scholar 

  • Zhou G, Whong W-Z, Ong T, Chen B (2000) Development of a fungus-specific PCR assay for detecting low-level fungi in an indoor environment. Mol Cell Probes 14:339–348

    CAS  PubMed  Google Scholar 

  • Zietkiewicz E, Rafalskim A, Labuda D (1994) Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20:176–183

    CAS  PubMed  Google Scholar 

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Enkerli, J., Widmer, F. Molecular ecology of fungal entomopathogens: molecular genetic tools and their applications in population and fate studies. BioControl 55, 17–37 (2010). https://doi.org/10.1007/s10526-009-9251-8

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