Development of real-time PCR technique for the estimation of population density of Pythium intermedium in forest soils

Microbiological Research

Volumn 165, Issue 8, 2010, Pages 695-705

  Li, Mingzhu ^a   Senda, Masako ^a   Komatsu, Tsutomu ^b   Suga, Haruhisa ^a   Kageyama, Koji ^a  

^a GIFU UNIVERSITY   (Japan)

^b Hokkaido Kamikawa Agricultural Experiment Station   (Japan)

Author keywords

DNA extraction; Internal transcribed spacer regions; Pythium intermedium; Real time PCR; SYBR Green

Indexed keywords

DNA EXTRACTION; INTERNAL TRANSCRIBED SPACERS; PYTHIUM; REAL-TIME PCR; SYBR GREEN;

DNA; ECOSYSTEMS; POPULATION DYNAMICS; SOILS; TRANSCRIPTION;

POLYMERASE CHAIN REACTION;

PRIMER DNA;

AGRICULTURAL ECOSYSTEM; CARBON CYCLE; EUKARYOTE; FOREST ECOSYSTEM; FOREST SOIL; GENETIC ANALYSIS; POLYMERASE CHAIN REACTION; POPULATION DENSITY; POPULATION ESTIMATION; REAL TIME; SOIL MICROORGANISM;

ARTICLE; BACTERIAL COUNT; COMPARATIVE STUDY; EVALUATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; JAPAN; METHODOLOGY; MICROBIOLOGY; MYCOLOGY; POLYMERASE CHAIN REACTION; PYTHIUM; SENSITIVITY AND SPECIFICITY; TREE;

COLONY COUNT, MICROBIAL; DNA PRIMERS; JAPAN; MYCOLOGY; POLYMERASE CHAIN REACTION; PYTHIUM; SENSITIVITY AND SPECIFICITY; SOIL MICROBIOLOGY; TREES;

CHUBU; GIFU; HONSHU; JAPAN; TAKAYAMA;

PYTHIUM; PYTHIUM INTERMEDIUM;

EID: 78049449456     PISSN: 09445013     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.micres.2009.11.010     Document Type: Article

References (38)

1. Ali-Shtayeh MS, Lim-Ho CL, Dick MW An improved method and medium for quantitative estimates of populations of Pythium species from soil. Trans Br Mycol Soc 1986, 86:39-47.
2. Interpretation of PCR methods for species definition. Applications of PCR in mycology 1998, CAB International, New York. P.D. Bridge, D.K. Arora, D.K. Reddy, R.P. Elander (Eds.).
3. Chen W. Restriction fragment length polymorphisms in enzymatically amplified ribosomal DNAs of three heterothallic Pythium species. Phytopathology 1992, 82:1467-1472.
4. Chilvers MI, du Toit LJ, Akamatsu H, Peever TL A real-time, quantitative PCR seed assay for Botrytis spp. that cause neck rot of onion. Plant Dis 2007, 91:599-608.
5. Conway KE Selective medium for isolation of Pythium spp. from soil. Plant Dis 1985, 69:393-395.
6. Polymerase chain reaction in mycology. Applications of PCR in mycology 1998, CAB international, New York, pp. 1-20. V. Edel, P.D. Bridge, D.K. Arora, C.A. Reddy, R.P. Elander (Eds.).
7. Filion M, St-Arnaud M, Jabaji-Hare SH Direct quantification of fungal DNA from soil substrate using real-time PCR. J Microbiol Methods 2003, 53:67-76.
8. Giglio S, Monis PT, Saint CP Legionella confirmation using real-time PCR and SYTO9 is an alternative to current methodology. Appl Environ Microbiol 2005, 71:8944-8948.
9. Kageyama K, Komatsu T, Suga H Refined PCR protocol for detection of plant pathogens in soil. J Gen Plant Pathol 2003, 69:153-160.
10. Kageyama K, Ohyama A, Hyakumachi M Detection of Pythium ultimum using polymerase chain reaction with species-specific primers. Plant Dis 1997, 81:1155-1160.
11. Kageyama K, Senda M, Asano T, Suga H, Ishiguro K Intra-isolate heterogeneity of the ITS region of rDNA in Pythium helicoides. Mycol Res 2007, 111:416-423.
12. Klassen GR, Balcerzak M, de Cock WAM 5S ribosomal RNA gene spacers as species-specific probes for eight species of Pythium. Phytopathology 1996, 86:581-587.
13. Kontanis EJ, Reed FA Evaluation of real-time PCR amplification efficiencies to detect PCR inhibitors. J Forensic Sci 2006, 51(4):795-804.
14. Krsek M, Wellington EMH Comparison of different methods for the isolation and purification of total community DNA from soil. J Microbiol Methods 1999, 39:1-16.
15. Liles MR, Williamson LL, Rodbumrer J, Torsvik V, Goodman RM, Handelsman J Recovery, purification, and cloning of high-molecular-weight DNA from soil microorganisms. Appl Environ Microbiol 2008, 74:3302-3305.
16. Lévesque CA, de Cock WAM Molecular phylogeny and taxonomy of the genus Pythium. Mycol Res 2004, 108:1363-1383.
17. Martin FN Electrophoretic karyotype polymorphisms in the genus Pythium. Mycologia 1995, 87:333-353.
18. Martin FN Importance of selfing and outcrossing in the population biology of Pythium. Phytopathology 2006, 96:S146.
19. Martin-Laurent F, Philippot L, Hallet S, Chaussod R, Germon JC, Soulas G, Catroux G DNA extraction from soils: old bias for new microbial diversity analysis methods. Appl Environ Microbiol 2001, 67:2354-2359.
20. McCartney HA, Foster SJ, Fraaije BA, Ward E Molecular diagnostics for fungal plant pathogens. Pest Manage Sci 2003, 59:129-142.
21. Miller DN, Bryant JE, Madsen EL, Ghiorse WC Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl Environ Microbiol 1999, 65:4715-4724.
22. Mircetich SM, Kraft JM Efficiency of various selective media in determining Pythium population in soil. Mycopathol Mycol Appl 1973, 50:151-161.
23. Morita Y, Tojo M Modifications of PARP medium using fluazinam, miconazole, and nystatin for detection of Pythium spp. in soil. Plant Dis 2007, 91:1591-1599.
24. Morrison TB, Ma Y, Weis JH, Weis JJ Rapid and sensitive quantification of Borrelia burgdorferi-infected mouse tissues by continuous fluorescent monitoring of PCR. J Clin Microbiol 1999, 37:987-992.
25. Nitsche A, Steuer N, Schmidt CA, Landt O, Siegert W Different real-time PCR formats compared for the quantitative detection of human cytomegalovirus DNA. Clin Chem 1999, 45:1932-1937.
26. Picard C, Ponsonnet C, Paget E, Nesme X, Simonet P Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Appl Environ Microbiol 1992, 58:2717-2722.
27. Sagova-Mareckova M, Cermak L, Novotna J, Plhackova K, Forstova J, Kopecky J Innovative methods for soil DNA purification tested in soils with widely differing characteristics. Appl Environ Microbiol 2008, 74:2902-2907.
28. Schnerr H, Niessen L, Vogel RF Real time detection of the Tri5 gene in Fusarium species by LightCycler PCR using SYBR Green I for continuous fluorescence monitoring. Int J Food Microbiol 2001, 71:53-61.
29. Schroeder KL, Okubara PA, Tambong JT, Le'vesque CA, Paulitz TC Identification and quantification of pathogenic Pythium spp. from soils in eastern Washington using real-time polymerase chain reaction. Phytopathology 2006, 96:637-647.
30. Senda, M and Kageyama, K Pythium species in cool-temperate forest soil. The 8th international mycological congress, Cains, Australia, 2006.
31. Soejima T, Iida K, Qin T, Taniai H, Seki M, Yoshida S-I Method to detect only live bacteria during PCR amplification. J Clin Microbiol 2008, 46:2305-2313.
32. Szalanski AL, Sui DD, Harris TS, Powers TO Identification of cyst nematodes of agronomic and regulatory concern with PCR-RFLP of ITS 1. J Nematol 1997, 29:255-267.
33. Tan, BS, Senda, M and Kageyama, K Respiration properties of Pythium species from cool-temperate forest soil. The 8th international mycological congress, Cains, Australia, 2006.
34. Van der Plaats-Niterink, AJ Monograph of the genus Pythium. No. 21, Studies in mycology. Centraalbureau Voor Schimmelcultures, Baarn, The Netherlands, 1981.
35. Vincelli P, Tisserat N Nucleic acid-based pathogen detection in applied plant pathology. Plant dis 2008, 92(5):660-669.
36. Wang PH, Chang CW Detection of the low-germinationrate resting oospores of Pythium myriotylum from soil by PCR. Lett Appl Microbiol 2003, 36:157-161.
37. White TJ, Bruns T, Lee S, Taylor JW Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR protocols: 315-322. A guide to methods and applications 1990, Academic Press, New York. M.A. Innis, D.H. Gelgard, J.J. Sninsky, T.J. White (Eds.).
38. Wittwer CT, Ririe KM, Andrew RV, David DA, Gundry RA, Balis UJ The LightCyclerk: a microvolume multisample fluorimeter with rapid temperature control. Bio-Techniques 1997, 22:176-1181.