Direct colony PCR-SSCP for detection of multiple pythiaceous oomycetes in environmental samples

Journal of Microbiological Methods

Volumn 61, Issue 1, 2005, Pages 25-32

  Kong, Ping ^a   Richardson, Patricia A ^a   Hong, Chuanxue ^a  

^a Physiology   (United States)

Author keywords

Direct colony PCR; Irrigation water; ITS 1 SSCP; Phytophthora; Plant tissues; Pythium; Soil

Indexed keywords

AGAR; WATER;

ALGA; ANALYTIC METHOD; ARTICLE; CONTROLLED STUDY; DNA EXTRACTION; ENVIRONMENT; FUNGAL COLONIZATION; FUNGAL DETECTION; GENE AMPLIFICATION; MICROBIAL POPULATION DYNAMICS; MYCELIUM; NONHUMAN; OOMYCETES; PLANT TISSUE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PYTHIACEAE; SINGLE STRAND CONFORMATION POLYMORPHISM; SOIL;

DAPHNE; DNA, FUNGAL; LYCOPERSICON ESCULENTUM; PHYTOPHTHORA; PLANT DISEASES; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE-STRANDED CONFORMATIONAL; PYTHIUM; RHODODENDRON; SOIL MICROBIOLOGY; TOBACCO; VINCA;

OOMYCETES; PHYTOPHTHORA; PYTHIUM;

EID: 12844288950     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2004.10.019     Document Type: Article

References (41)

1. A. Aufuavre-Brown, C.M. Tang, and D.W. Holden Detection of gene-disruption events in Aspergillus transformants by polymerase chain reaction direct from conidiospores Curr. Genet. 24 1993 177 178
2. A.M. Bailey, D.J. Mitchell, K.L. Manjunath, G. Nolasco, and C.L. Niblett Identification to the species level of the plant pathogens Phytophthora and Pythium by using unique sequences of ITS1 region of ribosomal DNA as capture probes for PCR ELISA FEMS Microbiol. Lett. 207 2002 153 158
3. M. Briard, M. Dutertre, F. Rouxel, and Y. Brygoo Ribosomal RNA sequence divergence within the Pythiaceae Mycol. Res. 99 1995 1119 1127
4. D.E.L. Cooke, A. Drebth, J.M. Duncan, G. Wagels, and C.M. Brasier A molecular phylogeny of Phytophthora and related oomycetes Fungal Genet. Biol. 30 2000 17 32
5. M.M. Dick Keys to Pythium 1990 University of Reading Reading, UK 64 pp.
6. D. Ercolini PCR-DGGE fingerprinting: novel strategies for detection of microbes in food J. Microbiol. Methods 56 2004 297 314
7. T. Ersek, J.E. Schoelz, and J.T. English PCR amplification of species-specific DNA sequences can distinguish among Phytophthora species Appl. Environ. Microbiol. 60 1994 2616 2621
8. D.C. Erwin, and O.K. Ribeiro Phytophthora Diseases Worldwide 1996 APS Press St. Paul, MN
9. A.J. Ferguson, and S.N. Jeffers Detecting multiple species of Phytophthora in container mixes from ornamental crop nurseries Plant Dis. 83 1999 1129 1136
10. K.A. Fode-Vaughan, C.F. Wimpee, C.C. Remsen, and M.L.P. Collins Detection of bacteria in environmental samples by direct PCR without DNA extraction BioTechniques 31 2001 598 607
11. H. Förster, and M.D. Coffey Approaches to the taxonomy of Phytophthora using polymorphisms in mitochondrial and nuclear DNA J.A. Lucas R.C. Shattock D.S. Shaw L.R. Cooke Phytophthora 1991 Cambridge University Press Cambridge, UK 164 183
12. D. Güssow, and T. Clackson Direct clone characterization from plaques and colonies by the polymerase chain reaction Nucleic Acids Res. 17 1989 4000
13. J.B. Herrick, E.L. Madsen, C.A. Batt, and W.C. Ghiorse Polymerase chain reaction amplification of naphthalene-catabolic and 16S rDNA gene sequences from indigenous sediment bacteria Appl. Environ. Microbiol. 59 1993 687 694
14. A. Hiraishi Direct automated sequencing of 16S rDNA amplified by polymerase chain reaction from bacterial culture without DNA purification Lett. Appl. Microbiol. 15 1992 210 213
15. C.X. Hong, P.A. Richardson, and P. Kong Comparison of filter membranes as tools for monitoring pythiaceous species in irrigation water Phytopathology 92 2002 610 616
16. Y. Hongoh, H. Yuzawa, M. Ohkuma, and T. Kudo Evaluation of primers and PCR conditions for the analysis of 16S rRNA genes from a natural environment FEMS Microbiol. Lett. 221 2003 299 304
17. K. Ishii, and M. Fukui Optimization of annealing temperature to reduce bias caused by a primer mismatch in multitemplate PCR Appl. Environ. Microbiol. 67 2001 3753 3755
18. L.F. Johnson, and E.A. Curl Methods for Research on the Ecology of Soil-Borne Plant Pathogens 1972 Burgess Publ. Minneapolis, MN 247 pp.
19. A.K. Joshi, V. Baichwal, and G.F.L. Ames Rapid polymerase chain reaction amplification using intact bacterial cells BioTechniques 10 1991 42 44
20. H.S. Judelson, and P.W. Tooley Enhanced polymerase chain reaction methods for detecting and quantifying Phytophthora infestans in plants Phytopathology 90 2000 1112 1119
21. K. Kageyama, A. Ohyama, and M. Hyakumachi Detection of Pythium ultimum using polymerase chain reaction with species-specific primers Plant Dis. 81 1997 1155 1160
22. P. Kong, C.X. Hong, S.A. Jeffers, and P.A. Richardson A species-specific polymerase chain reaction assay for detection of Phytophthora nicotianae in irrigation water Phytopathology 93 2003 822 831
23. P. Kong, C.X. Hong, P.A. Richardson, and M.E. Gallegly Single-strand-conformation polymorphism of ribosomal DNA for species differentiation within genus Phytophthora Fungal Genet. Biol. 39 2003 238 249
24. P. Kong, C.X. Hong, and P.A. Richardson Rapid detection of Phytophthora cinnamomi using PCR and primers derived from Lpv putative storage protein genes Plant Pathol. 52 2003 681 693
25. P. Kong, P.A. Richardson, G.W. Moorman, and C.X. Hong Single-strand conformational polymorphism analysis of the ribosomal internal transcribed spacer 1 for rapid species identification within the genus Pythium FEMS Microbiol. Lett. 240 2004 229 236
26. C.A. Lévesque, C.E. Harlton, and A.W.A.M. de Cock Identification of some oomycetes by reverse dot blot hybridization Phytopathology 88 1998 213 222
27. C.A. Lichtensteiger, S.M. Steenbergen, R.M. Lee, D.D. Polson, and E.R. Vimr Direct PCR analysis for toxigenic Pasteurella multocida J. Clin. Microbiol. 34 1996 3035 3039
28. F.N. Martin Phylogenetic relationships among some Pythium species inferred from sequence analysis of the mitochondrially encoded cytochrome oxidase II gene Mycologia 92 2000 711 727
29. C. Matsumoto, K. Kageyama, H. Suga, and M. Hyakumachi Phylogenetic relationships of Pythium species based on ITS and 5.8S sequences of the ribosomal DNA Mycoscience 40 1999 321 331
30. G. Muyzer DGGE/TGGE a method for identifying genes from natural ecosystems Curr. Opin. Microbiol. 2 1999 317 322
31. J.B. Ristaino, M. Madritch, C.L. Trout, and G. Parra PCR amplification of ribosomal DNA for species identification in the plant pathogen genus Phytophthora Appl. Environ. Microbiol. 64 1998 948 954
32. N.W. Schaad, D. Opgenorth, and P. Gaush Real time polymerase chain reaction for one hour on site diagnosis of Pierce's disease of grape in early season asymptomatic vines Phytopathology 92 2002 721 728
33. D.S. Sheu, Y.T. Wong, and C.Y. Lee Rapid detection of polyhydroxyalkanoate-accumulating bacteria isolated from the environment by colony PCR Microbiology 146 2000 2019 2025
34. P.W. Tooley, B.A. Bunyard, M.A. Carras, and E. Hatziloukas Development of PCR primers from internal transcribed spacer region 2 for detection of Phytophthora species infecting potatoes Appl. Environ. Micobiol. 63 1997 1467 1475
35. A.J. Van der Plaats-Niterink Monograph of the genus Pythium Stud. Mycol. Baarn 21 1981 1 242
36. C.M.J. van Zeijl, E.H.M. van de Kamp, P.J. Punt, G.C.M. Selten, B. Hauer, R.F.M. van Gorcom, and C.A.M.J.J. van de Hondel An improved colony-PCR method for filamentous fungi for amplification of PCR-fragments of several kilobases J. Biotechnol. 59 1997 221 224
37. P.H. Wang, and J.G. White Molecular characterization of Pythium species based on RFLP analysis of the internal transcribed spacer region of ribosomal DNA Physiol. Mol. Plant Pathol. 51 1997 129 143
38. P.H. Wang, Y.T. Wang, and J.G. White Species-specific PCR primers for Pythium developed from ribosomal ITS1 region Lett. Appl. Microbiol. 37 2003 127 132
39. T. Wangsomboondee, and J.B. Ristaino Optimization of sample size and DNA extraction methods to improve PCR detection of different propagules of Phytophthora infestans Plant Dis. 86 2002 247 253
40. G.M. Waterhouse Key to the species of Phytophthora de Bary Mycol. Pap. vol. 92 1963 Commonwealth Mycological Institute Kew, UK
41. I.G. Wilson Inhibition and facilitation of nucleic acid amplification Appl. Environ. Microbiol. 63 1997 3741 3751