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DISEASE CONTROL

Real-time PCR quantification of Colletotrichum coccodes DNA in soils from bioherbicide field-release assays, with normalization for PCR inhibition

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Pages 42-51 | Accepted 15 Nov 2005, Published online: 01 Apr 2010

References

  • Atkins , S. D. , Clark , I. M. , Sosnowska , D. , Hirsch , P. R. and Kerry , B. R. 2003 . Detection and quantification of Plectosphaerella cucumerina, a potential biological control agent of potato cyst nematodes, by using conventional PCR, real-time PCR, selective media, and baiting . Appl. Environ. Microbiol. , 69 : 4788 – 4793 .
  • Bates , J. A. , Taylor , E. J. A. , Kenyon , D. M. and Thomas , J. E. 2001 . The application of real-time PCR to the identification, detection and quantification of Pyrenophora species in barley seed . Mol. Plant Pathol. , 2 : 49 – 57 .
  • Bell , K. S. , Roberts , J. , Verrall , S. , Cullen , D. W. , Williams , N. A. , Harrison , J. G. , Toth , I. K. , Cooke , D. E. L. , Duncan , J. M. and Claxton , J. R. 1999 . Detection and quantification of Spongo spora subterranea f. sp. subterranea in soils and on tubers using specific PCR primers . Eur. J. Plant Pathol. , 105 : 905 – 915 .
  • Bohm , J. , Hahn , A. , Schubert , R. , Bahnweg , G. , Adler , N. , Nechwatal , J. , Oehlmann , R. and Osswald , W. 1999 . Real-time quantitative PCR: DNA determination in isolated spores of the mycorrhizal fungus Glomus mosseae and monitoring of Phyto phthora infestans and Phytophthora citricola in their respective host plants . Phytopathol. Z. , 147 : 409 – 416 .
  • Braid , M. D. , Daniels , L. M. and Kitts , C. L. 2003 . Removal of PCR inhibitors from soil DNA by chemical flocculation . J. Microbiol. Methods , 52 : 389 – 393 .
  • Bridge , P. and Spooner , B. 2001 . Soil fungi: diversity and detection . Plant Soil , 232 : 147 – 154 .
  • Broccolo , F. , Locatelli , G. , Sarmati , L. , Piergiovanni , S. , Veglia , F. , Andreoni , M. , Butto , S. , Ensoli , B. , Lusso , P. and Malnati , M. S. 2002 . Calibrated real-time PCR assay for quantitation of human herpesvirus 8 DNA in biological fluids . J. Clin. Microbiol. , 40 : 4652 – 4658 .
  • Bruce , K. D. , Hiorns , W. D. , Hobman , J. L. , Osborn , A. M. , Strike , P. and Ritchie , D. A. 1992 . Amplification of DNA from native populations of soil bacteria by using the polymerase chain reaction . Appl. Environ. Microbiol. , 58 : 3413 – 3416 .
  • Burgmann , H. , Widmer , F. , Sigler , W. V. and Zeyer , J. 2003 . mRNA extraction and reverse transcription – PCR protocol for detection of nifH gene expression by Azotobacter vinelandii in soil . Appl. Environ. Microbiol. , 69 : 1928 – 1935 .
  • Cullen , D. W. , Lees , A. K. , Toth , I. K. and Duncan , J. M. 2001 . Conventional PCR and real-time quantitative PCR detection of Helminthosporium solani in soil and on potato tubers . Eur. J. Plant Pathol. , 107 : 387 – 398 .
  • Cullen , D. W. , Lees , A. K. , Toth , I. K. and Duncan , J. M. 2002 . Detection of Colletotrichum coccodes from soil and potato tubers by conventional and quantitative real-time PCR . Plant Pathol. (London) , 51 : 281 – 292 .
  • Dauch , A. L. , Watson , A. K. and Jabaji-Hare , S. H. 2003 . Detection of the biocontrol agent Colletotrichum coccodes (183088) from the target weed velvetleaf and from soil by strain-specific PCR markers . J. Microbiol. Methods , 55 : 51 – 64 .
  • Dillard , H. R. and Cobb , A. C. 1998 . Survival of Colletotrichum coccodes in infected tomato tissue and in soil . Plant Dis. , 82 : 235 – 238 .
  • DiTommaso , A. and Watson , A. K. 1995 . Impact of a fungal patho gen, Colletotrichum coccodes on growth and competitive ability of Abutilon theophrasti . New Phytol. , 131 : 51 – 60 .
  • Filion , M. , St-Arnaud , M. and Jabaji-Hare , S. H. 2002 . Direct quantification of fungi from soil substrate using real-time PCR . J. Microbiol. Methods , 53 : 67 – 76 .
  • Frostegard , A. , Courtois , S. , Ramisse , V. , Clerc , S. , Bernillon , D. , Le Gall , F. , Jeannin , P. , Nesme , X. and Simonet , P. 1999 . Quantification of bias related to the extraction of DNA directly from soils . Appl. Environ. Microbiol , 65 : 5409 – 5420 .
  • Gardes , M. and Bruns , T. D. 1993 . ITS primers with enhanced specificity for basidiomycetes – application to the identification of mycorrhizae and rusts . Mol. Ecol. , 2 : 113 – 118 .
  • Hietala , A. M. , Eikenes , M. , Kvaalen , H. , Solheim , H. and Fossdal , C. G. 2003 . Multiplex real-time PCR for monitoring Heterobasidion annosum colonization in Norway spruce clones that differ in disease resistance . Appl. Environ. Microbiol. , 69 : 4413 – 4420 .
  • Lee , S. B. and Taylor , J. W. 1990 . “ Isolation of DNA from fungal mycelial and single spores ” . In PCR protocols: a guide to methods and applications , Edited by: Innis , M. A. , Gelfand , D. H. , Sninsky , J. S. and White , T. J. 283 – 287 . San Diego, Calif : Academic Press Inc .
  • Lee , S. Y. , Bollinger , J. , Bezdicek , D. and Ogram , A. 1996 . Estimation of the abundance of an uncultured soil bacterial strain by a competitive quantitative PCR method . Appl. Environ. Microbiol. , 62 : 3787 – 3793 .
  • Lees , A. K. , Cullen , D. W. , Sullivan , L. and Nicolson , M. J. 2002 . Development of conventional and quantitative real-time PCR assays for the detection and identification of Rhizoctonia solani AG-3 in potato and soil . Plant Pathol. (London) , 51 : 293 – 302 .
  • Martin-Laurent , F. , Philippot , L. , Hallet , S. , Chaussod , R. , Germon , J. C. , Soulas , G. and Catroux , G. 2001 . DNA extraction from soils: old bias for new microbial diversity analysis methods . Appl. Environ. Microbiol. , 67 : 2354 – 2359 .
  • McGregor , D. P. , Forster , S. , Steven , J. , Adair , J. , Leary , S. E. C. , Leslie , D. L. , Harris , W. J. and Titball , R. W. 1996 . Simultaneous detection of microorganisms in soil suspension based on PCR amplification of bacterial 16S rRNA fragments . Biotechniques , 21 : 463 – 471 .
  • Meijerink , J. , Mandigers , C. , van de Locht , L. , Tonnissen , E. , Goodsaid , F. and Raemaekers , J. 2001 . A novel method to compensate for different amplification efficiencies between patient DNA samples in quantitative real-time PCR . J. Mol. Diagn. , 3 : 55 – 61 .
  • Mendum , T. A. , Sockett , R. E. and Hirsch , P. R. 1998 . The detection of Gram-negative bacterial mRNA from soil by RT-PCR . FEMS (Fed. Eur. Microbiol. Soc.) Microbiol. Lett. , 164 : 369 – 373 .
  • Moreira , D. 1998 . Efficient removal of PCR inhibitors using agarose-embedded DNA preparations . Nucleic Acids Res. , 26 : 3309 – 3310 .
  • Roche Diagnostics . 2000 . Overview of LightCycler quantification methods , Mannheim, , Germany : Roche Molecular Biochemicals . Technical Note No. LC 10/2000
  • SAS Institute Inc . 1989 . SAS/STAT user's guide. , 4th ed. , Vol. 2 , Cary, N.C. : SAS Institute Inc . Version 6 [computer program]
  • Steffan , R. J. and Atlas , R. M. 1988 . DNA amplification to enhance detection of genetically engineered bacteria in environmental samples . Appl. Environ. Microbiol. , 54 : 2185 – 2191 .
  • Stocher , M. and Berg , J. 2002 . Normalized quantification of human cytomegalovirus DNA by competitive real-time PCR on the LightCycler instrument . J. Clin. Microbiol. , 40 : 4547 – 4553 .
  • Stubner , S. 2002 . Enumeration of 16S rDNA of Desulfo tomaculum lineage 1 in rice field soil by real-time PCR with SybrGreen(tm) detection . J. Microbiol. Methods , 50 : 155 – 164 .
  • Taylor , G. , Wang , X. and Jabaji-Hare , S. H. 2003 . Detection of the mycoparasite Stachybotrys elegans, using primers with sequence-characterized amplification regions in conventional and real-time PCR . Can. J. Plant Pathol. , 25 : 49 – 61 .
  • Tebbe , C. C. and 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 .
  • Torsvik , V. L. 1980 . Isolation of bacterial DNA from soil . Soil Biol. Biochem. , 12 : 15 – 22 .
  • Tsai , Y.-L. and Olson , B. H. 1991 . Rapid method for direct extraction of DNA from soil and sediments . Appl. Environ. Micro biol. , 57 : 1070 – 1074 .
  • Tsai , Y.-L. and Olson , B. H. 1992 . Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction . Appl. Environ. Microbiol. , 58 : 754 – 757 .
  • van de Graaf , P. V. , Lees , A. K. , Cullen , D. W. and Duncan , J. M. 2003 . Detection and quantification of Spongospora subterranea in soil, water and plant tissue samples using real-time PCR . Eur. J. Plant Pathol. , 109 : 589 – 597 .
  • Weller , S. A. , Elphinstone , J. G. , Smith , N. C. , Boonham , N. and Stead , D. E. 2000 . Detection of Ralstonia solanacearum strains with a quantitative, multiplex, real-time, fluorogenic PCR (TaqMan) assay . Appl. Environ. Microbiol. , 66 : 2853 – 2858 .
  • White , T. J. , Bruns , T. , Lee , S. and Taylor , J. 1990 . “ Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics ” . In PCR protocols: a guide to methods and applications , Edited by: Innis , M. A. , Gelfand , D. H. , Sninsky , J. S. and White , T. J. 315 – 322 . San Diego, Calif : Academic Press, Inc .
  • Wilhelm , J. and Pingoud , A. 2003 . Real-time polymerase chain reaction . ChemBioChem , 4 : 1120 – 1128 .
  • Wilson , I. G. 1997 . Inhibition and facilitation of nucleic acid amplification . Appl. Environ. Microbiol. , 63 : 3741 – 3751 .
  • Young , C. C. , Burghoff , R. L. , Keim , L. G. , Minak-Bernero , V. , Lute , J. R. and Hinton , S. M. 1993 . Polyvinylpyrrolidone – agarose gel electrophoresis purification of polymerase chain reaction – amplifiable DNA from soils . Appl. Environ. Microbiol. , 59 : 1972 – 1974 .
  • Zolan , M. E. and Pukkila , P. J. 1986 . Inheritance of DNA methylation in Coprinus cinereus . Mol. Cell. Biol. , 6 : 195 – 200 .

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