Advertisement

World Journal of Microbiology and Biotechnology

, Volume 18, Issue 7, pp 661–671 | Cite as

Microbial studies of compost: bacterial identification, and their potential for turfgrass pathogen suppression

  • Jeanine I. Boulter
  • Jack T. Trevors
  • Greg J. Boland
Article

Abstract

Composting is the degradation of organic materials through the activities of diverse microorganisms. This research examined microbial community dynamics, population levels and identification of bacteria throughout the composting process and in storage. In addition, an evaluation was performed to determine the potential for dominant bacterial isolates to suppress selected turfgrass pathogens: Sclerotinia homoeocarpa, Pythium graminicola, Typhula ishikariensis, and Microdochium nivale, responsible for causing the turfgrass diseases dollar spot, pythium blight, typhula blight, and fusarium patch, respectively. Composts supported high population levels of bacteria with 78% of cultures tested being Gram-negative. Proteolytic activity, found in 29% of cultures tested is a potential mechanism of suppression or competition with other microorganisms. Although the Biolog system did not identify a wide range of bacteria, the main Gram-negative genera identified in mature compost were Pseudomonas (28%), Serratia (20%), Klebsiella (11%), and Enterobacter (5%). Twenty-one percent of isolates tested were not identified by Biolog, and many more had similarity indexes < 0.50. The microbial identification system, based on whole cell fatty acid analysis, identified a wide range of bacteria, with a higher proportion of similarities than the Biolog system. Genera common to both testing procedures included Pseudomonas, Serratia, and Enterobacter. All Gram-positives were identified as Bacillus spp. Phospholipid fatty acid analysis, used to estimate the diversity of microbial communities, was useful in monitoring changes in microbial population in storage and during composting, as well as estimating levels of compost maturity. Plate challenge experiments revealed a number of cultures with antagonistic activity against turfgrass pathogens. There were 52, 31, 32 and 19% of the bacterial isolates tested that exhibited antagonistic activity against S. homoeocarpa, P. graminicola, T. ishikariensis, and M. nivale, respectively. Improved understanding of microbial populations and their dynamics in composts will expand their potential to act as suppressants on pathogenic fungi or turfgrass.

Bacteria compost biocontrol disease suppression grey snow mould diversity fungi pathogen pink snow mould phospholipid analysis plant microorganism turfgrass 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Adani, F., Genevini, P.L., Gasperi, F. & Zorzi, G. 1997 Organic matter evolution index (OMEI) as a measure of composting efficiency. Compost Science and Utilization 5, 53–62.Google Scholar
  2. Atkinson, C.F., Jones, D.D. & Gauthier, J.J. 1997 Microbial activities during composting of pulp and paper-mill primary solids. World Journal of Microbiology and Biotechnology 13, 519–525.Google Scholar
  3. Bagnasco, P., De La Fuente, L., Gualtieri, G., Noya, F. & Arias, A. 1998 Fluorescent Pseudomonas spp. as biocontrol agents against forage legume root pathogenic fungi. Soil Biology and Biochemistry 30, 1317–1322.Google Scholar
  4. Becker, P.M. & Stottmeiser, U. 1998 General (Biolog GN) versus siterelevant (pollutant-dependent) sole-carbon-source utilization patterns as a means to approaching community functioning. Canadian Journal of Microbiology 44, 913–919.Google Scholar
  5. Beffa, T., Blanc, M., Lyon, P., Vogt, G. & Aragno, M. 1999a Isolation of Thermus strains from hot composts (60 °C to 80 °C). Applied and Environmental Microbiology 62, 1723–1727.Google Scholar
  6. Beffa, T., Blanc, M., Marilley, L., Fisher, J.L., Lyon, P.F. & Aragno, M. 1996b Taxonomic and metabolic microbial diversity during composting. In The Science of Composting, Part 1, eds. de Bertoldi, M., Sequi, P., Lemmes, B. & Papi, T. pp. 149–161. London, England: Chapman and Hall. ISBN 0751403830.Google Scholar
  7. Bossio, D.A. & Scow, K.M. 1998 Impacts of carbon and flooding on soil microbial communities: phospholipid fatty acid profiles and substrate utilization patterns. Microbial Ecology 35, 265–278.Google Scholar
  8. Bossio, D.A., Scow, K.M. & Graham, K.J. 1998 Determinants of soil microbial communities: effects of agricultural management, season, and soil type on phospholipid fatty acid profiles. Microbial Ecology 36, 1–12.Google Scholar
  9. Boulter, J.I., Boland, G.J. & Trevors, J.T. 2000 Compost: a study of the development process and end-product potential for suppression of turfgrass disease. World Journal of Microbiology and Biotechnology 16, 115–134.Google Scholar
  10. Boulter, J.I., Boland, G.J. & Trevors, J.T. 2002 Evaluation of composts for suppression of dollar spot (Sclerotinia homoeocarpa) of turfgrass. Plant Disease, 86, 405–410.Google Scholar
  11. Burpee, L.L., Kaye, L.M., Goulty, L.G. & Lawton, M.B. 1987 Suppression of gray snow mold on creeping bentgrass by an isolate of Typhula phacorrhiza. Plant Disease 71, 97–100.Google Scholar
  12. Carpenter-Boggs, L., Kennedy, A.C. & Reganold, J.P. 1998 Use of phospholipid fatty acids and carbon source utilization patterns to track microbial community succession in developing compost. Applied and Environmental Microbiology 64, 4062–4064.Google Scholar
  13. Chen, W., Hoitink, H.A.J. & Madden, L.V. 1988a Microbial activity and biomass in container media for predicting suppressiveness to damping-off caused by Pythium ultimum. Phytopathology 78, 1447–1450.Google Scholar
  14. Chen, W., Hoitink, H.A.J., Schmitthenner, F. & Tuovinen, O.H. 1988b The role of microbial activity in suppression of damping-off caused by Pythium ultimum. Phytopathology 78, 314–322.Google Scholar
  15. Chung, Y.C. & Neethling, J.B. 1988 ATP as a measure of anaerobic sludge digester activity. Journal of Water Pollution Control Federation 60, 197–112.Google Scholar
  16. De Meyer, G. & Hofte, M. 1997 Salicylic acid produced by the Rhizobacterium Pseudomonas aeruginosa 7NSK2 induces resistance to leaf infection by Botrytis cinerea on bean. Phytopathology 87, 588–593.Google Scholar
  17. Dunne, C., Crowley, J.J., Moenne-Loccoz, Y., Dowling, D.N., De Bruijn, F.J. & O'Gara, F. 1997 Biological control of Pythium ultimum by Stenotrophomonas maltophilia W81 is mediated by an extracellular proteolytic activity. Microbiology 143, 3921–3931.Google Scholar
  18. Dunne, C., Moenne-Loccoz, Y., McCarthy, J., Higgins, P., Powell, J., Dowling, D.N. & O'Gara, F. 1998 Combining proteolytic and phloroglucinol-producing bacteria for improved biocontrol of Pythium-mediated damping-off of sugar beet. Plant Pathology 47, 299–307.Google Scholar
  19. Edwards, S.G. & Seddon, B., eds. 1994 Interaction of Bacillus species with phytopathogenic fungi - methods of analysis and manipulation for biocontrol purposes, pp. 101–118. Wallingford: CAB International.Google Scholar
  20. Elad, Y. & Chet, I. 1987 Possible role of competition for nutrients in biocontrol of pythium damping-off by bacteria. Phytopathology 77, 190–195.Google Scholar
  21. Fokkema, N.J. 1993 Opportunities and problems of control of foliar pathogens with micro-organisms. Pesticide Science 37, 411–416.Google Scholar
  22. Forster, J.C., Zech, W. & Wiirdinger, E. 1993 Comparison of chemical and microbial methods for the characterization of the maturity of composts from contrasting sources. Biology and Fertility of Soils 16, 93–99.Google Scholar
  23. Fulthorpe, R.R., Liss, S.N. & Allen, D.G. 1993 Characterization of bacteria isolated from a bleached kraft paper mill wastewater treatment system. Canadian Journal of Microbiology 39, 13–24.Google Scholar
  24. Garland, J.L. 1997 Analysis and interpretation of community-level physiological profiles in microbial ecology. FEMS Microbiology Ecology 24, 289–300.Google Scholar
  25. Goodman, D.M. & Burpee, L.L. 1991 Biological control of dollar spot disease of creeping bentgrass. Phytopathology 81, 1438–1446.Google Scholar
  26. Henis, Y. & Chet, I. 1975 Microbial control of plant pathogens. Advances in Applied Microbiology 19, 85–111.Google Scholar
  27. Herrmann, R.F. & Shann, J.F. 1997 Microbial community changes during the composting of municipal solid waste. Microbial Ecology 33, 78–85.Google Scholar
  28. Hodges, C.F., Campbell, D.A. & Christians, N. 1994 Potential biocontrol of Sclerotinia homoeocarpa and Bipolaris sorokiniana on the phylloplane of Poa pratensis with strains of Pseudomonas spp. Plant Pathology 43, 500–506.Google Scholar
  29. Hoitink, H.A.J. & Fahy, P.C. 1986 Basis for the control of soilborne plant pathogens with composts. Annual Reviews of Phytopathology 24, 93–114.Google Scholar
  30. Hoitink, H.A.J., Inbar, Y. & Boehm, M.J. 1993 Compost can suppress soil-borne diseases in container media. American Nurseryman 178, 91–94.Google Scholar
  31. Hoitink, H.A.J., Stone, A.G. & Han, D.Y. 1997 Suppression of plant disease by composts. HortScience 32, 184–187.Google Scholar
  32. Insam, H., Amor, K., Renner, M. & Crepaz, C. 1996 Changes in functional abilities of the microbial community during composting of manure. Microbial Ecology 31, 77–87.Google Scholar
  33. Keel, C., Voisard, C., Berling, C.H., Kahr, G. & Defago, G. 1989 Iron sufficiency, a prerequisite for the suppression of tobacco black root rot by Pseudomonas fluorescens strain CHA0 under gnotobiotic conditions. Phytopathology 79, 584–589.Google Scholar
  34. Kersters, I., van Nooren, L., Verschuere, L., Vauterin, L., Wouters, A., Mergaert, J., Swings, J. & Verstraete, W. 1997 Utility of the Biolog system for the characterization of heterotrophic microbial communities. Systematic and Applied Microbiology 20, 439–447.Google Scholar
  35. Klamer, M. & Baath, E. 1998 Microbial community dynamics during composting of straw material studied using phospholipid fatty acid analysis. FEMS Microbiology Ecology 27, 9–20.Google Scholar
  36. Ko, W. & Lockwood, J.L. 1970 Mechanism of lysis of fungal mycelia in soil. Phytopathology 60, 148–154.Google Scholar
  37. Kwok, O.C.H., Fahy, P.C., Hoitink, H.A.J. & Kuter, G.A. 1987 Interactions between bacteria and Trichoderma hamatum in suppression of Rhizoctonia damping-off in bark compost media. Phytopathology 77, 1206–1212.Google Scholar
  38. Lawton, M.B. & Burpee, L.L. 1990 Effect of rate and frequency of application of Typhula phacorrhiza on biological control of typhula blight of creeping bentgrass. Phytopathology 80, 70–73.Google Scholar
  39. Li, H., White, D., Lamza, K.A., Berger, F. & Liefert, C. 1998 Biological control of Botrytis, Phytophthora and Pythium by Bacillus subtilis Cot1 and CL27 of micropropagated plants in highhumidity fogging glasshouses. Plant Cell, Tissue and Organ Culture 52, 109–112.Google Scholar
  40. Lockwood, J.L. & Filonow, A.B. 1981 Responses of fungi to nutrient-limiting conditions and to inhibitory substances in natural habitats. Advances in Microbial Ecology 5, 1–61.Google Scholar
  41. Lorito, M., Peterbauer, C., Hayes, C.K. & Harman, G.E. 1994 Synergistic interaction between fungal cell wall degrading enzymes and different antifungal compounds enhances inhibition of spore germination. Microbiology 140, 623–629.Google Scholar
  42. Lucas, J.A. 1998 Plant pathology and plant pathogens, 3rd edn. 247 pp. Osney Mead, Oxford: Blackwell Science, Ltd. ISBN 0632030461.Google Scholar
  43. Madigan, M.T., Martinko, J.M. & Parker, J. 1997 Biology of Microorganisms, 8th edn. 1038 pp. Upper Saddle River, NJ, USA: Prentice-Hall. ISBN 0130819220.Google Scholar
  44. McKinley, V.L., Vestal, J.R. & Eralp, A.E. 1985 Microbial activity in composting: part I. Biocycle 26, 39–43.Google Scholar
  45. Nelson, E.B. 1991 Introduction and establishment of strains of Enterobacter cloacae in golf course turf for the biological control of dollar spot. Plant Disease 75, 510–514.Google Scholar
  46. Nelson, E.B. 1992 The biological control of turfgrass diseases. In Golf Course Management. pp. 10. March 1992.Google Scholar
  47. Nielsen, M.N., Sorensen, J., Fels, J. & Pedersen, H.C. 1998 Secondary metabolite-and endochitinase-dependent antagonism toward plant-pathogenic microfungi of Pseudomonas fluorescens isolated from sugar beet rhizosphere. Applied and Environmental Microbiology 64, 3563–3569.Google Scholar
  48. Odumeru, J.A., Steele, M., Fruhner, L., Larkin, C., Jiang, J., Mann, E. & McNab, W.B. 1999 Evaluation of accuracy and repeatability of identification of food-borne pathogens by automated bacterial identification systems. Journal of Clinical Microbiology 37, 944–949.Google Scholar
  49. Ongena, M., Daayf, F., Jacques, P., Thonart, P., Benhamou, N., Paulitz, T. C., Cornelis, P., Koedam, N. & Belanger, R.R. 1999 Protection of cucumber against Pythium root rot by fluorescent pseudomonas: predominant role of induced resistance over siderophores and antibiosis. Plant Pathology 48, 66–76.Google Scholar
  50. O'sullivan, D. & O'Gara, F. 1992 Traits of fluorescent Pseudomonas spp. involved in suppression of plant root pathogens. Microbiological Reviews 56, 662–676.Google Scholar
  51. Parkinson, D.T., Gray, R.G. & Williams, S.T. 1971 Methods for Studying the Ecology of Soil Microorganisms. Oxford IBP Handbook no. 19, Blackwell Scientific Publications, Ltd. ISBN 0632082607.Google Scholar
  52. Phae, C.G. & Shoda, M. 1990 Expression of the suppressive effect of Bacillus subtilis on phytopathogens in inoculated composts. Journal of Fermentation and Bioengineering 70, 409–414.Google Scholar
  53. Phae, C.G., Sasaki, M., Shoda, M. & Kubota, H. 1990 Characteristics of Bacillus subtilis isolated from composts suppressing phytopathogenic microorganisms. Soil Science, Plant Nutrition 4, 575–586.Google Scholar
  54. Richard, D. & Zimmerman, R. 1995 Respiration rate - reheating potential: a comparison of measures of compost stability. Compost Science and Utilization 3, 74–79.Google Scholar
  55. Shanahan, P., O'sullivan, D.J., Simpson, P., Glennon, J.D. & O'Gara, F. 1992 Isolation of 2,4-diacetylphloroglucinol from a fluorescent pseudomonad and investigation of physiological parameters influencing its production. Applied and Environmental Microbiology 58, 353–358.Google Scholar
  56. Tunlid, A., Hoitink, H.A., Low, C. & White, D.C. 1989 Characterization of bacteria that suppress Rhizoctonia damping-off in bark compost media by analysis of fatty acid biomarkers. Applied and Environmental Microbiology 55, 1368–1374.Google Scholar
  57. Van Dijk, K. & Nelson, E.B. 1998 Inactivation of seed exudate stimulants of Pythium ultimum sporangium germination by biocontrol strains of Enterobacter cloacae and other seed-associated bacteria. Soil Biology and Biochemistry 30, 183–192.Google Scholar
  58. Verschuere, L., Fievez, V., van Vooren, L., Rombaut, G. & Verstraete, W. 1999. Modelling the color development in Biolog microtiter plates by the Gompertz function. Systemic and Applied Microbiology 21, 609–617.Google Scholar
  59. Verschuere, L., Fievez, V., van Vooren, L. & Verstraete, W. 1997 The contribution of individual populations to the Biolog pattern of model microbial communities. FEMS Microbial Ecology 24, 353–362.Google Scholar
  60. Vestal, J.R. & White, D.C. 1989 Lipid analysis in microbial ecology: quantitative approaches to the study of microbial communities. BioScience 39, 535–541.Google Scholar
  61. Walker, R., Powell, A.A. & Seddon, B. 1998 Bacillus isolates from the spermosphere of peas and dwarf French beans with antifungal activity against Botrytis cinerea and Pythium species. Journal of Applied Microbiology 84, 791–801.Google Scholar
  62. Weltzien, H.C. 1991 Biocontrol of foliar fungal diseases with compost extracts. In Microbial Ecology of Leaves, eds. Andrews, J.H. & Hirano, S.S. pp. 430–450. New York: Springer-Verlag, Inc. ISBN 038975799.Google Scholar
  63. Whipps, J.M. 1997a Developments in the biological control of soilborne plant pathogens. Advances in Botanical Research 26, 1–134.Google Scholar
  64. Whipps, J.M. 1997b Ecological considerations involved in commercial development of biological control agents for soil-borne diseases. In Modern Soil Microbiology, eds. Dirk van Elsas, J., Trevors, J.T. & Wellington, E.M.H. pp. 683. ISBN 0824794362.Google Scholar
  65. White, D.C. 1988 Validation of quantative analysis of microbial biomass, community structure, and metabolic activity. Arch. Hydrobiol. Beih. Ergeben Limnol 31, 1–18.Google Scholar
  66. Whitney, P.J. & Lynch, J.M. 1996 Importance of lignocellulosic compounds in composting. In The Science of Composting, Part 1, eds. De Bertoldi, M., Sequi, P., Lemmes, B. & Papi, T. pp. 531–541. London, England: Chapman and Hall. ISBN 0751403830.Google Scholar
  67. Wollum, A.G.I. 1982 Cultural methods for soil microorganisms. In Methods of Soil Analysis, Part 2: Chemical and Microbiological Properties9, eds. Miller, R.H. & Keeney, D.R. pp. 781–802. Madison, Wisconsin, USA: Soil Science Society of America, Inc. ISBN 0891180729.Google Scholar

Copyright information

© Kluwer Academic Publishers 2002

Authors and Affiliations

  • Jeanine I. Boulter
    • 1
  • Jack T. Trevors
    • 1
  • Greg J. Boland
    • 1
  1. 1.Department of Environmental BiologyUniversity of GuelphGuelphCanada

Personalised recommendations