Abstract
A culture-independent survey of the bacterial diversity in rhizosphere soils of diseased (scab) and disease-free apple trees was conducted to assess the role of bacteria in disease suppression. Community DNA was extracted from soil samples and amplified by PCR using primers specific for bacterial 16S rRNA gene sequences. Clone libraries were constructed with the PCR products and analysed based on amplified rDNA restriction analysis (ARDRA) patterns. The phylotypes and their frequency distribution in both libraries indicated that the phylotype did not represent a single group. Rarefaction curve, and Shannon and Simpson diversity indices exhibited insignificant diversity differences between the samples in terms of bacterial community composition, whereas more chitinase and β-1,3 glucanase activities were recorded in samples from disease-free trees than from diseased trees. Based on the operational taxonomic units identified in ARDRA, 80 representative clones were selected from the libraries and partially sequenced. Sequence similarity searches with the resulting sequences identified the dominance of uncultured bacteria to the extent of 70% and 72.5% in disease free and diseased rhizospheres, respectively. The foregoing studies conclude a possible role for enhanced microbial activity in terms of enzyme production in tree (apple) health, although no distinct partitioning of composition or significant diversity of bacterial communities inhabiting diseased and disease-free rhizosphere soils was observed at any given time.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Amann RL, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169
Borneman J, Skroch PW, O’Sullivan KM, Palus JA, Rumjanek NG, Jansen JL, Niehnuis J, Triplett EW (1996) Molecular microbial diversity of an agricultural soil in Wisconsin. Appl Environ Microbiol 62(6):1935–1943
Carisse O, Phillion V, Rolland D, Bernier J (2000) Effect of fall application of fungal antagonists on spring ascospore production of the apple scab pathogen Venturia inaequalis. Phytopathology 90:31–37
Chow ML, Radomski CC, Mcdermott JM, Davies J, Axelrood PE (2002) Molecular characterization of bacterial diversity in lodge pole pine (Pinus contorta) rhizosphere soils from British Columbia forest soils differing in disturbance and geographic source. FEMS Microbiol Ecol 42:347–357
Filion M, Hamelin RC, Bernier L, St-Arnaud M (2004) Molecular profiling of rhizosphere microbial communities associated with healthy and diseased black spruce (Picea mariana) seedlings grown in a nursery. Appl Environ Microbiol 70(6):3541–3551
Garbeva P (2005) The significance of microbial diversity in agricultural soil for disease suppressiveness. PhD Thesis, Leiden University, Leiden, The Netherlands
Garbeva P, van Veen JA, van Elsas JD (2004) Microbial diversity in soil: selection of microbial populations by plant and soil type and implications for disease suppressiveness. Annu Rev Phytopathol 42:243–270
Gupta GK (1989) Apple scab-economics and technology. Pesticides 23:33–39
Harvell CD, Kim K, Burkholder JM, Colwell RR, Epstein PR, Grimes DJ, Hofmann EE, Lipp EK, Osterhause ADME, Overstreet RM, Porter JW, Smith GW, Vasta GR (1999) Emerging marine diseases-climate links and anthropomorphic factors. Science 285:1505–1510
Hong TY, Meng M (2003) Biochemical characterization and antifungal activity of an endo-1,3-β-glucanase of Paenibacillus sp. isolated from garden soil. Appl Microbiol Biotechnol 61:472–478
Huang CJ, Wang TK, Chung SC, Chen CY (2005) Identification of an antifungal chitinase from a potential biocontrol agent, Bacillus cereus 29-9. J Biochem Mol Biol 38:82–88
Jeffries P, Gianinazzi S, Perotto S, Turnau K, Barea JM (2003) The contribution of arbuscular mycorrhizal fungi in sustainable maintenance of plant health and soil fertility. Biol Fertil Soils 37:1–16
Jetiyanon K (2007) Defensive-related enzyme response in plants treated with a mixture of Bacillus strains (IN937a and IN937b) against different pathogens. Biol Control 42:178–185
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
Lukow T, Dunfield PF, Liesack W (2000) Use of the T-RFLP technique to assess spatial and temporal changes in the bacterial community structure within an agricultural soil planted with transgenic and non-transgenic potato plants. FEMS Microbiol Ecol 32:241–247
Machardy WE (1996) Apple scab: biology, epidemiology, and management. American Phytopathological Society, St. Paul, MN
Maidak BL, Cole JR, Parker CTJR, Garrity GM, Larsen N, Li B, Lilburn TG, Mccaughey MJ, Olsen GJ, Overbeek R, Pramanik S, Schmidt TM, Tiedje JM, Woese CR (1999) A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res 27(1):171–173
Mohammadi M, Kazemi H (2002) Changes in peroxidase and polyphenol oxidase activities in susceptible and resistant wheat heads inoculated with Fusarium graminearum and induced resistance. Plant Sci 162:491–498
Nannipieri P, Ascher J, Ceccherini MT, Landi L, Pietramellara G, Renella G, Valori F (2007) Microbial diversity and microbial activity in the rhizosphere. Ci Suelo 25(1):89–97
Nunan N, Daniell TJ, Singh BK, Papert A, McNicol JW, Prosser JI (2005) Links between plant and rhizoplane bacterial communities in grassland soils, characterized using molecular techniques. Appl Environ Microbiol 71:6784–6792
Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in excel. Population genetic software for teaching and research. Mol Ecol 6:288–295, Notes
Rodriguez-Kabana R, Godoy G, Morgan-Jones G, Shelby RA (1983) The determination of soil chitinase activity: conditions for assay and ecological studies. Plant Soil 75:95–106
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74(12):5463–5467
Sessitsch A, Weilharter A, Gerzabek MH, Kirchmann H, Kandeler E (2001) Microbial population structures in soil particle size fractions of a long-term fertilizer field experiment. Appl Environ Microbiol 67:4215–4224
Sharma IM, Bhardwaj SS (2003) Efficacy and economics of different fungicide spray schedules in controlling premature defoliation disease in apple. Plant Dis Res 18(1):21–24
Sotolova I, Jandera A (1985) Activity of l, 3-β-d-glucanases in soil. Folia Microbiol 30:521–524
Thakur VS, Sharma N, Verma S (2005) Present scenario of apple scab in various apple orchards of Himachal Pradesh. Hortic J 18(3):134–136
Ward DM, Weller R, Bateson MM (1990) 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345:63–65
Yang CH, Crowley DE, Menge JA (2001) 16S rDNA fingerprinting of rhizosphere bacterial communities associated with healthy and Phytophthora infected avocado roots. FEMS Microbiol Ecol 35:129–136
Acknowledgements
The authors are thankful to the Director, Institute of Himalayan Bioresource Technology (IHBT, Palampur, India), for support and encouragement during the course of this investigation. This work was supported by the Council of Scientific and Industrial Research, Government of India through co-ordinated network program (SMM 002). IHBT Publication No. 0951.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Shanmugam, V., Verma, R., Rajkumar, S. et al. Bacterial diversity and soil enzyme activity in diseased and disease free apple rhizosphere soils. Ann Microbiol 61, 765–772 (2011). https://doi.org/10.1007/s13213-010-0193-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s13213-010-0193-2