Evaluation of PCR primers for denaturing gradient gel electrophoresis analysis of fungal communities in compost

Journal of Applied Microbiology

Volumn 95, Issue 5, 2003, Pages 934-948

  Marshall, M N ^a   Cocolin, L ^b   Mills, D A ^c   VanderGheynst, J S ^a  

^a University of California   (United States)

^b UNIVERSITY OF UDINE   (Italy)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Compost; DGGE; Fungi; PCR; Primers; rDNA

Indexed keywords

COMPOSTING; ELECTROPHORESIS; MICROORGANISMS; POLYMERASE CHAIN REACTION; REGRESSION ANALYSIS;

COLONISATION; COMPOST; DENATURING GRADIENT GEL ELECTROPHORESIS; FUNGAL COMMUNITY; GEL ELECTROPHORESIS ANALYSIS; PCR; PCR PRIMERS; PRIMER; PRIMER SETS; RDNA;

FUNGI;

DNA; DNA 18S; DNA 28S; RIBOSOME DNA; UNCLASSIFIED DRUG;

COMMUNITY STRUCTURE; COMPOST; FUNGUS; POLYMERASE CHAIN REACTION;

ARTICLE; ARTIFACT; COMPOST; DENATURING GRADIENT GEL ELECTROPHORESIS; FUNGAL DETECTION; FUNGUS CULTURE; GRAPE; INOCULATION; LOGISTIC REGRESSION ANALYSIS; MICROFLORA; NONHUMAN; POLYMERASE CHAIN REACTION; RICE;

FUNGI; VITIS SP.;

EID: 0242383517     PISSN: 13645072     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2672.2003.02062.x     Document Type: Article

References (51)

1. Agrios, G.N. (1991) Plant Pathology. San Diego, CA: Academic Press.
2. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Research 25, 3389-3402.
3. Amann, R.I., Ludwig, W. and Schleifer, K. (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiological Reviews 59, 143-169.
4. Ben-Yephet, Y. and Nelson, E.B. (1999) Differential suppression of damping-off caused by Pythium aphanidermatum, P. irregulare, and P. myriotylum in composts at different temperatures. Plant Disease 83, 356-360.
5. Borneman, J. and Hartin, R.J. (2000) PCR primers that amplify fungal rRNA genes from environmental samples. Applied and Environmental Microbiology 66, 4356-5360.
6. de Brito Alvarez, M.A., Gagne, S. and Antoun, H. (1995) Effect of compost on rhizosphere microflora of the tomato and on the incidence of plant growth-promoting rhizobacteria. Applied and Environmental Microbiology 61, 194-199.
7. Cocolin, L., Bisson, L.F. and Mills, D.A. (2000) Direct profiling of the yeast dynamics in wine fermentations. FEMS Microbiology Letters 189, 81-87.
8. Craft, C.M. and Nelson, E.B. (1996) Microbial properties of composts that suppress damping-off and root rot of creeping bentgrass caused by Pythuim graminicola. Applied and Environmental Microbiology 62, 1550-1557.
9. Debosz, K., Petersen, S.O., Kure, L.K. and Ambus, P. (2002) Evaluating effects of sewage sludge and household compost on soil physical, chemical and microbiological properties. Applied Soil Ecology 19, 237-248.
10. van Elsas, J.D., Duarte, G.F., Keijzer-Wolters, A. and 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. Journal of Microbiological Methods 43, 133-151.
11. Erhart, E., Burian, K., Hartl, W. and Stich, K. (1999) Suppression of Pythium ultimum by biowaste composts in relation to compost microbial biomass, activity and content of phenolic compounds. Journal of Phytopathology 147, 299-305.
12. Ferris, M.J., Muyzer, G. and Ward, D.M. (1996) Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Applied and Environmental Microbiology 62, 340-346.
13. Frostegard, A., Courtois, S., Ramisse, V., Clerc, S., Bernillon, D., Gall, F.L., Jeannin, P., Nesme, X., et al. (1999) Quantification of bias related to the extraction of DNA directly from soils. Applied and Environmental Microbiology 65, 5409-5420.
14. Head, I.M., Saunders, J.R. and Pickup, R.W. (1998) Microbial evolution, diversity, and ecology: a decade of ribosomal RNA analysis of uncultivated microorganisms. Microbial Ecology 35, 1-21.
15. Hoitink, H.A.J. and Boehm, M.J. (1993) Mechanisms of suppression of soil-borne plant pathogens in compost-amended substrates. In Science and Engineering of Composting: Design, Environmental, Microbiological and Utilization Aspects ed. Hoitink, H.A.J. and Keener, H.M. pp. 601-621. Worthington, OH: Renaissance Publications.
16. Hoitink, H.A.J. and Boehm, M.J. (1999) Biocontrol within the context of soil microbial communities: a substrate-dependent phenomenon. Annual Review of Phytopathology 37, 427-446.
17. Ibekwe, A.M., Papiernik, S.K., Gan, J., Yates, S.R., Crowley, D.E. and Yang, C.-H. (2001) Microcosm enrichment of 1,3-dichloropropene-degrading soil microbial communities in a compost-amended soil. Journal of Applied Microbiology 91, 668-676.
18. Ishii, K., Fukui, M. and Takii, S. (2000) Microbial succession during a composting process as evaluated by denaturing gradient gel electrophoresis analysis. Journal of Applied Microbiology 89, 768-777.
19. Kowalchuk, G.A., Gerards, S. and Woldendorp, J.W. (1997) Detection and characterization of fungal infections of Ammophila arenaria (marram grass) roots by denaturing gradient gel electrophoresis of specifically amplified 18S rDNA. Applied and Environmental Microbiology 63, 3858-3865.
20. Kowalchuk, G.A., Naoumenko, Z.S., Derikx, P.J.L., Felske, A., Stephen, J.R. and Arkhipchenko, I.A. (1999) Molecular analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in compost and composted materials. Applied and Environmental Microbiology 65, 396-403.
21. Krsek, M. and Wellington, E.M.H. (1999) Comparison of different methods for the isolation and purification of total community DNA from soil. Journal of Microbiological Methods 39, 1-16.
22. Kuske, C.R., Banton, K.L., Adorada, D.L., Stark, P.C., Hill, K.K. and Jackson, P.J. (1998) Small-scale DNA sample preparation method for field PCR detection of microbial cells and spores in soil. Applied and Environmental Microbiology 64, 2463-2472.
23. LaMontagne, M.G., Michel, Jr. F.C., Holden, P.A. and Reddy, C.A. (2002) Evaluation of extraction and purification methods for obtaining PCR-amplifiable DNA from compost for microbial community analysis. Journal of Microbiological Methods 49, 255-264.
24. Malik, M., Kain, J., Pettigrew, C. and Ogram, A. (1994) Purification and molecular analysis of microbial DNA from compost. Journal of Microbiological Methods 20, 183-196.
25. Mathur, S.P. (1991) Composting processes. In Bioconversion of Waste Materials to Industrial Products ed. Martin, A.M. pp. 147-183. London, UK: Elsevier Applied Science.
26. May, B.A. and VanderGheynst, J.S. (2001) A predictor variable for efficacy of Lagenidium giganteum produced in solid-state cultivation. Applied and Industrial Microbiology 27, 203-207.
27. May, L.A., Smiley, B. and Schmidt, M.G. (2001) Comparative denaturing gradient gel electrophoresis analysis of fungal communities associated with whole plant corn silage. Canadian Journal of Microbiology 47, 829-841.
28. Miller, D.N., Bryant, J.E., Madsen, E.L. and Ghiorse, W.C. (1999) Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Applied and Environmental Microbiology 65, 4715-4724.
29. Mohlenhoff, P., Muller, L., Gorbushina, A.A. and Petersen, K. (2001) Molecular approach to the characterization of fungal communities: methods for DNA extraction, PCR amplification and DGGE analysis of painted art objects. FEMS Microbiology Letters 195, 169-173.
30. More, M.I., Herrick, J.B., Silva, M.C., Ghiorse, W.C. and Madsen, E.L. (1994) Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment. Applied and Environmental Microbiology 60, 1572-1580.
31. Muyzer, G., Waal, E.C.D. and Uitterlinden, A.G. (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied and Environmental Microbiology 59, 695-700.
32. Nakasaki, K., Hiraoka, S. and Nagata, H. (1998) A new operation for producing disease-suppressive compost from grass clippings. Applied and Environmental Microbiology 64, 4015-4020.
33. O'Donnell, K. (1993) Fusarium and its near relatives. In The Fungal Holomorph: Mitotic, Meiotic and Pleomorphic Speciation in Fungal Systematics ed. Reynolds, D.R. and Taylor, J.W. pp. 225-233. Wallingford, CT: CAB International.
34. Ogram, A. (1998) Isolation of nucleic acids from environmental samples. In Techniques in Microbial Ecology ed. Burlage, R.S., Atlas, R., Stahl, D., Sayler, G. and Geesey, G. pp. 273-288. New York, NY: Oxford University Press.
35. ben Omar, N. and Ampe, F. (2000) Microbial community dynamics during production of the Mexican fermented maize dough pozol. Applied and Environmental Microbiology 66, 3664-3673.
36. Pennanen, T., Paavolainen, L. and Hantula, J. (2001) Rapid PCR-based method for the direct analysis of fungal communities in complex environmental samples. Soil Biology and Biochemistry 33, 697-699.
37. Qiu, X., Wu, L., Huang, H., McDonel, P.E., Palumbo, A.V., Tiedje, J.M. and Zhou, J. (2001) Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning. Applied and Environmental Microbiology 67, 880-887.
38. Roling, W.F.M., Kerler, J., Braster, M., Apriyantono, A., Stam, H. and van Verseveld, H.W. (2001) Microorganisms with a taste for vanilla: microbial ecology of traditional Indonesian vanilla curing. Applied and Environmental Microbiology 67, 1995-2003.
39. Sambrook, J., Fritsch, E.F. and Maniantis, T. (1989) Molecular Cloning: a Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
40. Schabereiter-Gurtner, C., Pinar, G., Lubitz, W. and Rolleke, S. (2001) Analysis of fungal communities on historical church window glass by denaturing gradient gel electrophoresis and phylogenetic 18S rDNA sequence analysis. Journal of Microbiological Methods 47, 345-354.
41. Smit, E., Leeflang, P., Glandorf, B., van Elsas, J.D. and 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. Applied and Environmental Microbiology 65, 2614-2621.
42. Strom, P.F. (1985a) Effect of temperature on bacterial species diversity in thermophilic solid-waste composting. Applied and Environmental Microbiology 50, 899-905.
43. Strom, P.F. (1985b) Identification of thermophilic bacteria in solid-waste composting. Applied and Environmental Microbiology 50, 906-913.
44. 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 yeast. Applied and Environmental Microbiology 59, 2657-2665.
45. Tuitert, G., Szczech, M. and Bollen, G.J. (1998) Suppression of Rhizoctonia solani in potting mixtures amended with compost made from organic household waste. Phytopathology 88, 764-773.
46. Ueno, Y., Haruta, S., Ishii, M. and Igarashi, Y. (2001) Microbial community in anaerobic hydrogen-producing microflora enriched from sludge compost. Applied Microbiology and Biotechnology 57, 555-562.
47. Vainio, E.J. and Hantula, J. (2000) Direct analysis of wood-inhabiting fungi using denaturing gradient gel electrophoresis of amplified ribosomal DNA. Mycological Research 104, 927-936.
48. VanderGheynst, J.S. and Lei, F. (2003) Microbial community structure dynamics during aerated and mixed composting. Transactions of the ASAE, 46, 577-587.
49. 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 ed. Innis, M.A., Gelfand, D.H., Sninsky, J.J. and White, T.J. pp. 315-322. San Diego, CA: Academic Press.
50. Wilson, I.G. (1997) Inhibition and facilitation of nucleic acid amplification. Applied and Environmental Microbiology 63, 3741-3751.
51. Zhou, J., Bruns, M.A. and Tiedje, J.M. (1996) DNA recovery from soils of diverse composition. Applied and Environmental Microbiology 62, 316-322.