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Effects of agronomical measures on the microbial diversity of soils as related to the suppression of soil-borne plant pathogens

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Abstract

The diversity of soil microbial communities can be key to the capacity of soils tosuppress soil-borne plant diseases. As agricultural practice, as well as directedagronomical measures, are known to be able to affect soil microbial diversity, it isplausible that the soil microflora can be geared towards a greater suppressivity ofsoil-borne diseases as a result of the selection of suitable soil management regimes.In the context of a programme aimed at investigating the microbial diversity of soilsunder different agricultural regimes, including permanent grassland versus arableland under agricultural rotation, we assessed how soil microbial diversity is affectedin relation to the suppression of the soil-borne potato pathogen Rhizoctoniasolani AG3. The diversity in the microbial communities over about a growingseason was described by using cultivation-based – plating on different media – and cultivation-independent – soil DNA-based PCR followed by denaturing gradient gel electrophoresis (DGGE) community fingerprinting – methods. The results showed great diversity in the soil microbiota at both the culturable and cultivation-independent detection levels. Using cultivation methods, various differences between treatments with respect to sizes of bacterial and fungal populations were detected, with highest population sizes generally found in rhizospheres. In addition, the evenness of eco-physiologically differing bacterial types was higher in grassland than in arable land under rotation. At the cultivation-independent level, clear differences in the diversities of several microbial groups between permanent grassland and arable land under rotation were apparent. Bio-assays that assessed the growth of R. solani AG3 hyphae through soil indicated a greater growth suppression in grassland than in arable land soils. Similarly, an experiment performed in the glasshouse showed clear differences in both microbial diversities and suppressiveness of R. solani growth in soil, depending on the presence of either maizeor oats as the crop. The significance of these findings for designing soil managementstrategies is discussed.

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References

  • Abawi GS & Widmer TL (2000) Impact of soil health management practices on soil-borne pathogens, nematodes and root diseases of vegetable crops. Appl. Soil Ecol. 15: 37-47

    Google Scholar 

  • Akkermans ADL, Van Elsas JD & De Bruijn FJ (1995) Molecular Microbial Ecology Manual. Kluwer Academic Publishers, Dordrecht, The Netherlands

    Google Scholar 

  • Alef K & Nannipieri P 1995. Methods in Applied SoilMicrobiology and Biochemistry. Acad. Press, London

    Google Scholar 

  • Ball K & Trevors JT (2002) Bacterial genomics: the use of DNA microarrays and bacterial artificial chromosomes. J. Microbiol. Methods 49: 275-284

    Google Scholar 

  • Borneman J, Skroch PW, O'Sullivan KM, Palus JA, Rumjanek, NG, Jansen JL, Nienhuis J & Triplett, E (1996) Molecular microbial diversity of an agricultural soil in Wisconsin. Appl. Environ. Microbiol. 62: 1935-1943

    Google Scholar 

  • De Boer W, Klein Gunnewiek PJA & Woldendorp JW (1998) Suppression of hyphal growth of soil-borne fungi by dune soils from vigorous and declining stands of Ammophila arenaria. New Phytol. 138: 107-116

    Google Scholar 

  • De Leij FAAM, Whipps JM & Lynch JM (1993) The use of colony development for the characterization of bacterial communities in soils and on roots. Microb. Ecol. 27: 81-97

    Google Scholar 

  • Garbeva P, van Elsas JD & van Veen JA (2002a) Diversity within Bacillus sp. in agricultural land under different management regimes. Proceed. Bageco-7, Bergen, NO

  • Garbeva P, van Veen JA & van Elsas JD (2002b) Assessment of the diversity of Pseudomonas species in soil by using specific PCR followed by denaturing gradient gel electrophoresis and sequencing analysis. FEMS Microbiol. Ecol. (subm.)

  • Gelsomino A, Keijzer-Wolters AC, Cacco G & van Elsas JD (1999) Assessment of bacterial community structure in soil by polymerase chain reaction and denaturing gradient gel electrophoresis. J. Microbiol. Meth. 38: 1-15

    Google Scholar 

  • Hagedorn C, Gould WD, Bardinelli TR & Gustavson DR (1987) A selective medium for enumeration and recovery of Pseudomonas cepacia biotypes from soil. Appl. Environ. Microbiol. 53: 2265-2268

    Google Scholar 

  • 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

    Google Scholar 

  • Hurt RA, Qiu X, Wu L, Roh, Y, Palumbo AV, Tiedje JM & Zhou J (2001) Simultaneous recovery of RNA and DNA from soils and sediments. Appl. Environ. Microbiol. 67: 4495-4503

    Google Scholar 

  • Kennedy AC & Smith KL 1995. Soil microbial diversity and the sustainability of agricultural soils. Plant Soil 170: 75-86

    Google Scholar 

  • Kuske CR, Barns SM & Busch JD (1997) Diverse uncultivated bacterial groups from soils of the arid Southwestern United States that are present in many geographic regions. Appl. Environ. Microbiol. 63: 3614-3621

    Google Scholar 

  • Mazzola M (1999) Transformation of soil microbial community structure and Rhizoctonia-suppressive potential in response to apple roots. Phytopathol. 89: 920-927

    Google Scholar 

  • Miller HJ, Liljeroth E, Henken G & van Veen JA (1990) Fluctuations in the fluorescent pseudomonad and actinomycete populations of rhizosphere and rhizoplane during the growth of spring wheat. Can. J. Microbiol. 36: 254-258

    Google Scholar 

  • Nüsslein K & Tiedje JM (1999) Soil bacterial community shift correlated with change from forest to pasture vegetation in a tropical soil. Appl. Environ. Microbiol. 65: 3622-3626

    Google Scholar 

  • Picard C, Di Cello F, Ventura M, Fani R & Guckert A (2000) Frequency and biodiversity of 2,4-diacetylphloroglucinol-producing bacteria isolated from the maize rhizosphere at different stages of plant growth. Appl. Environ. Microbiol. 66: 948-955

    Google Scholar 

  • Raaijmakers JM, Weller DM & Thomashow LS (1997) Frequency of antibiotic-producing Pseudomonas spp. in natural environments. Appl. Environ. Microbiol. 63: 881-887

    Google Scholar 

  • Raaijmakers JM & Weller DM (1998) Natural plant protection by 2,4-diacetyl phloroglucinol-producing Pseudomonas spp. in take-all decline soils. Molec. Plant-Microbe Interact. 11: 144-152

    Google Scholar 

  • Rondon MR, August PR, Betterman AD, Brady SF, Grossman TH, Liles MR. Loiacono K, Lynch BA, MacNeil IA, Minor C, Tiong CL, Gilman M, Osburne MS, Clardy J, Handelsman J & Goodman RM (1999) Cloning a soil metagenome-bacterial artificial chromosome libraries to harvest microbial diversity in natural environments. Appl. Environ. Microbiol. 66: 2541-2547

    Google Scholar 

  • Salles JF, De Souza FA & van Elsas JD (2002) A molecular method to assess the diversity of Burkholderia species in environmental samples. Appl. Environ. Microbiol. 68: 1595-1603

    Google Scholar 

  • Sambrook J, Fritsch EF & Maniatis T (1989) Molecular Cloning; A Laboratory Manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y

    Google Scholar 

  • Schönfeld J, Gelsomino A, van Overbeek LS, Smalla K & van Elsas JD (2002) Effects of compost addition and simulated solarisation on the fate of Ralstonia solanacearum biovar 2 and indigenous bacteria in soil. FEMS Microbiol. Ecol. (in press)

  • Smalla K, Cresswell N, Mendonca-Hagler LC, Wolters A & van Elsas JD (1993) Rapid DNA extraction protocol from soil for polymerase chain reaction mediated amplification. J. Appl. Bacteriol. 74: 78-85

    Google Scholar 

  • Smalla K, Wieland G, Buchner A, Zock A, Parzy J, Kaiser S, Roskot N, Heuer H & Berg G (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

    Google Scholar 

  • Staley JT & Konopka A (1985) Measurement of in situ activities of non-photosynthetic microorganisms in aquatic and terrestrial habitats. Ann. Rev. Microbiol. 39: 321-346

    Google Scholar 

  • Tiedje JM, Asuming-Brempong S, Nüsslein K, Marsh TL & Flynn SJ (1999) Opening the black box of soil microbial diversity. Appl. Soil Ecol. 13: 109-122

    Google Scholar 

  • Turco RF, Kennedy AC & Jawson MD (1994) Microbial indicators of soil quality. In: Doran JW, Coleman DC, Bezdicek DF & Stewart BA (Eds) Defining soil quality for a sustainable environment. Soil Sc. Soc Am., Madison, WI, USA, pp. 73-90

    Google Scholar 

  • Yang CH & Crowley DE (2000) Rhizosphere microbial community structure in relation to root location and plant iron nutritional status. Appl. Environ. Microbiol. 66: 345-351

    Google Scholar 

  • Van Bruggen AHC & Semenov AM (2000) In search of biological indicators for soil health and disease suppression. Appl. Soil Ecol. 15: 13-24

    Google Scholar 

  • Van Elsas JD, Dijkstra AF, Govaert JM & van Veen JA (1986) Survival of Pseudomonas fluorescens and Bacillus subtilis introduced into two soils of different texture in field microplots. FEMS Microbiol. Ecol. 38: 151-160

    Google Scholar 

  • Van Elsas JD, Trevors JT & Wellington EMH (1997) Modern Soil Microbiology. Marcel Dekker, Inc., New York

    Google Scholar 

  • Van Elsas JD, Mäntynen V & Wolters AC (1997) Soil DNA extraction and assessment of the fate of Mycobacterium chlorophenolicum strain PCP-1 in different soils via 16S ribosomal RNA gene sequence based most-probable-number PCR and immuno-fluorescence. Biol. Fertil. Soils 24: 188-195

    Google Scholar 

  • Van Elsas JD, Duarte GF, Rosado AS & Smalla K (1998) Microbiological and molecular biology methods for monitoring microbial inoculants and their effects in the environment. J. Microbiol. Methods 32: 133-154

    Google Scholar 

  • Van Elsas JD, Duarte GF, Keijzer-Wolters AC & Smit E (2000) Analysis of the dynamics of fungal communities in soil via fungalspecific PCR of soil DNA followed by denaturing gradient gel electrophoresis. J. Microbiol. Methods 43: 133-151

    Google Scholar 

  • Van Veen JA, van Overbeek LS & van Elsas JD (1997) Fate and activity of microorganisms following release into soil. Microb. Mol. Biol. Rev. 61: 121-135

    Google Scholar 

  • Ward N, Rainey FA, Goebel B & Stackebrandt E (1995) Identifying and culturing the "unculturables": a challenge for microbiologists. In: Allsopp D, Colwell RR & Hawksworth DL (Eds) Microbial Diversity and Ecosystem Functioning (pp. 89-110) CAB International

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  1. P.O. Box 16, 6700AA, Wageningen, The Netherlands

    Jan Dirk van Elsas, Paolina Garbeva & Joana Salles

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  1. Jan Dirk van Elsas
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  2. Paolina Garbeva
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  3. Joana Salles
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van Elsas, J.D., Garbeva, P. & Salles, J. Effects of agronomical measures on the microbial diversity of soils as related to the suppression of soil-borne plant pathogens. Biodegradation 13, 29–40 (2002). https://doi.org/10.1023/A:1016393915414

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