Effect of above-ground plant species on soil microbial community structure and its impact on suppression of Rhizoctonia solani AG3

Environmental Microbiology

Volumn 8, Issue 2, 2006, Pages 233-246

  Garbeva, P ^a,b   Postma, J ^c   Van Veen, J A ^a   Van Elsas, J D ^b  

^a NETHERLANDS INSTITUTE OF ECOLOGY NIOO KNAW   (Netherlands)

^b UNIVERSITY OF GRONINGEN   (Netherlands)

^c WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BACILLUS (BACTERIUM); BACTERIA (MICROORGANISMS); HYPHOMYCETES; PSEUDOMONAS; THANATEPHORUS CUCUMERIS; ZEA MAYS;

BACTERIAL DNA; FUNGAL DNA;

AGRICULTURE; ARTICLE; GROWTH, DEVELOPMENT AND AGING; HYPHOMYCETES; MAIZE; METHODOLOGY; MICROBIOLOGY; POACEAE; POLYMERASE CHAIN REACTION; STANDARD;

AGRICULTURE; DNA, BACTERIAL; DNA, FUNGAL; POACEAE; POLYMERASE CHAIN REACTION; RHIZOCTONIA; SOIL MICROBIOLOGY; ZEA MAYS;

EID: 33644862479     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2005.00888.x     Document Type: Article

References (49)

1. Akkermans ADL. Van Elsas JD. De Bruijn FJ. 1995 Molecular Microbial Ecology Manual Dordrecht, the Netherlands Kluwer Academic Publishers.
2. Baar J. ter Braak CJF. 1996 Ectomycorrhizal sporocarp occurrence as affected by manipulation of litter and humus layers in Scots pine stands of different age Appl Soil Ecol 4 61 73
3. Berg G. Roskot N. Steidle A. Eberl L. Zock A. Smalla K. 2002 Plant-dependent genotypic and phenotypic diversity of antagonistic rhizobacteria isolated from different Verticillium host plants Appl Environ Microb 68 3328 3338
4. Bloem J. Schouten T. Didden W. Akkerhuis GJ. Keidel H. Rutgers M. Breure T. 2004 Measuring soil biodiversity: experiences, impediments and research need Proceedings of the OECD Expert Meeting on Soil Erosion Biodiversity Indicators, March 2003, Rome, Italy, pp. 109 120 Paris OECD
5. Broughton LC. Gross KL. 2000 Patterns of diversity in plant and soil microbial communities along a productivity gradient in a Michigan old-field Oecologia 125 420 427
6. Chiarini L. Bevivino A. Dalmastri C. Nacamulli C. Tabacchioni S. 1998 Influence of plant development, cultivar and soil type on microbial colonization of maize root Appl Soil Ecol 8 11 18
7. Cook RJ. Baker KF. 1983 The Nature and Practice of Biological Control of Plant Pathogens St Paul, MN, USA APS
8. Da Silva KRA. Salles JF. Seldin L. van Elsas JD. 2003 Application of a novel Paenibacillus-specific PCR-DGGE method and sequence analysis to assess the diversity of Paenibacillus spp. in the maize rhizosphere J Microbiol Methods 54 213 231
9. De Leij FAAM. Whipps JM. Lynch JM. 1993 The use of colony development for the characterization of bacterial communities in soils and roots Microb Ecol 27 81 97
10. Garbeva P. 2005 The significance of microbial diversity in agricultural soil for disease suppressiveness PhD Thesis Leiden, the Netherlands
11. Garbeva P. Van Veen JA. Van Elsas JD. 2003 Predominant Bacillus spp. in agricultural soil under different management regimes detected via PCR-DGGE Microb Ecol 45 302 316
12. Garbeva P. Van Veen JA. Van Elsas JD. 2004 Assessment of the diversity, and antagonism towards Rhizoctonia solani AG3, of Pseudomonas species in soil from different agricultural regimes FEMS Microbiol Ecol 47 51 64
13. Grayston SJ. Campbell CD. Bardgett RD. Mawdsley JL. Clegg CD. Ritz K. et al. 2004 Assessing shifts in microbial community structure across a range of grasslands of different management using CLPP, PLFA and community DNA techniques Appl Soil Ecol 25 63 84
14. Heuer H. Krsek M. Baker P. Smalla K. Wellington EMH. 1997 Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients Appl Environ Microbiol 63 3233 3241
15. Johnson NC. Tilman D. Wedin DA. 1992 Plant and soil controls on mycorrhizal fungal communities Ecology 73 2034 2042
16. Kennedy AC. Smith KL. 1995 Soil microbial diversity and the sustainability of agricultural soil Plant Soil 170 75 86
17. Kirk JL. Beaudette LA. Hart M. Moutoglis P. Klironomos JN. Lee H. Trevors JT. 2004 Methods of studying soil microbial diversity J Microbiol Methods 58 169 188
18. Kowalchuk GA. Buma DS. de Boer W. Klinkhamer PGL. van Veen JA. 2002 Effects of above-ground plant species composition and diversity on the soil-borne microorganisms Antonie Van Leeuwenhoek 81 509 520
19. McCaig AE. Glover LA. Prosser JI. 2001 Numerical analysis of grassland bacterial community structure under different land management regimes by using 16S ribosomal DNA sequencing data and denaturing gradient gel electrophoresis banding patterns Appl Environ Microbiol 67 4554 4559
20. Mader P. Fliessbach A. Dubois D. Gunts L. Fried P. Niggli U. 2002 Soil fertility and biodiversity in organic farming Science 296 1694 1697
21. Mazzola M. Gu Y-H. 2002 Wheat genotype-specific induction of soil microbial communities suppressive to Rhizoctonia solani AG5 and AG8 Phytopathology 92 1300 1307
22. Miller HJ. Liljeroth E. Henken G. van Veen JA. 1990 Fluctuations in the fluorescent pseudomonad and actinomycete population of rhizosphere and rhizoplane during the growth of spring wheat Can J Microbiol 36 254 258
23. Muyzer G. Smalla K. 1998 Application of denaturing gradient gel electrophoresis (DGGE) and the temperature gradient gel electrophoresis (TGGE) in microbial ecology Antonie Van Leeuwenhoek 73 127 141
24. Nitta T. 1991 Diversity of root fungal floras: its applications for soil-borne diseases and crop growth J Agric Res 25 6 11
25. Pankhurst CE. McDonald HJ. Hawke BG. Kirkby CA. 2002 Effect of tillage and stubble management on chemical and microbiological properties and the development of suppression towards cereal root disease in soils from two sites in NSW, Australia Soil Biol Biochem 34 833 840
26. Prosser JI. 2002 Molecular and functional diversity in soil micro-organisms Plant Soil 244 9 17
27. Raaijmakers JM. Weller DM. 1998 Natural plant protection by 2,4-diacetyl phloroglucinol-producing Pseudomonas spp. in take-all decline soils Molec Plant-Microb Interact 11 144 152
28. Read DJ. 1998 Plants on the web Nature 396 22 23
29. Rodriguez-Kabana R. Canullo GH. 1992 Cropping systems for the management of phytonematodes Phytoparasitica 20 211 224
30. Salles JF. De Souza FA. Van Elsas JD. 2002 Molecular method to assess the diversity of Burkholderia species in environmental samples Appl Environ Microbiol 68 1595 1603
31. Salles JF. Van Elsas JD. Van Veen JA. 2004 Multivariate analyses of Burkholderia species in soil: effect of crop and land use history Appl Environ Microbiol 70 4012 4020
32. Salles JF. Samyn E. Vandamme P. Van Veen JA. van Elsas JD. 2005 Changes in agricultural management drive the diversity of Burkholderia species isolated on PCAT medium Soil Biol Biochem in press ).
33. Sambrook J. Fritsch EF. Maniatis T. 1998 Molecular Cloning: A Laboratory Manual 2nd edn Cold Spring Harbor, NY, USA Cold Spring Harbor Laboratory Press.
34. Schippers B. 1992 Prospects for management of natural suppressiveness to control soil-borne pathogens. In Biological Control of Plant Diseases Tjamos EC. Papavizas GC. Cook RJ. (eds) New York, USA Plenum Press, pp. 1 12
35. Sivapalan A. Morgan WC. Franz RP. 1993 Monitoring populations of soil microorganisms during a conversion from a conventional to an organic system of vegetable growing Biol Agric Hortic 10 9 27
36. Smalla K. Wieland G. Buchner A. Zock A. Parzy J. Kaiser S. et al. 2001 Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed Appl Environ Microbiol 67 4742 4751
37. Smiley RW. 1978 Colonization of wheat roots by Gaeumannomyces graminis inhibited by specific soils, microorganisms and ammonium nitrogen Soilbiol Biochem 10 175 179
38. Stirling GR. 1991 Biological Control of Plant Parasitic Nemathodes - Progress, Problems and Prospects Wallingford, Oxon, UK CAB International.
39. Ter Braak CJF. 1994 Canonical community ordination. Part I: basic theory and linear methods Ecoscience 1 127 140
40. Tiedje JM. Asuming-Brempong S. Nusslein K. Marsh TL. Flynn SJ. 1999 Opening the black box of soil microbial diversity Appl Soil Ecol 13 109 122
41. Torsvik V. Goksoyr J. Daae FL. 1990 High diversity in DNA of soil bacteria Appl Environ Microbiol 56 782 787
42. Vainio EJ. Hantula J. 2000 Direct analysis of wood-inhabiting fungi using denaturing gradient gel electrophoresis of amplified ribosomal DNA Mycol Res 104 927 936
43. Van Bruggen AHC. 1995 Plant disease in high-input compared to reduced-input and organic farming systems Plant Dis 79 976 983
44. Van der Putten WH. Mortimer S. Hedlund K. Van Dijk C. Brown VK. Leps J. et al. 2000 Plant species diversity as a driver of early succession in abandoned fields: multi-site approach Oecologia 124 91 99
45. Van Elsas JD. Garbeva P. Salles J. 2002 Effects of agronomical measures on the microbial diversity of soils as related to the suppression of soil-borne plant pathogens Biodegradation 13 29 40
46. Wardle DA. Nicholson S. 1996 Synergistic effects of grassland plant species on soil microbial biomass and activity: implications for ecosystem-level effects of enriched plant diversity Func Ecol 10 410 416
47. Wardle DA. Bonner KI. Barker GM. Yeates GW. Nicolson KS. Bardgett RD. et al. 1999 Plant removals in perennial grassland: vegetation dynamics, decomposers, soil biodiversity, and ecosystem properties Ecol Monogr 69 535 568
48. Wieland G. Neumann R. Backhaus H. 2001 Variation of microbial communities in soil, rhizosphere and rhizoplane in response to crop species, soil type and crop development Appl Environ Microbiol 67 5849 5854
49. Workneh F. van Bruggen AHC. Drinkwater LE. Shennan C. 1993 Variables associated with corky root and Phytophthora root rot of tomatoes in organic and conventional farms Phytopathology 83 581 589