Browse > Article
http://dx.doi.org/10.5423/PPJ.SI.01.2013.0015

Sampling and Selection Factors that Enhance the Diversity of Microbial Collections: Application to Biopesticide Development  

Park, Jun-Kyung (Environmentally-Friendly Agricultural Research Institute and WCU Center for Development of Core Technology for Bio- Environment Control, Chonnam National University)
Lee, Seung-Hwan (Environmentally-Friendly Agricultural Research Institute and WCU Center for Development of Core Technology for Bio- Environment Control, Chonnam National University)
Lee, Jang-Hoon (Environmentally-Friendly Agricultural Research Institute and WCU Center for Development of Core Technology for Bio- Environment Control, Chonnam National University)
Han, Songhee (Environmentally-Friendly Agricultural Research Institute and WCU Center for Development of Core Technology for Bio- Environment Control, Chonnam National University)
Kang, Hunseung (Environmentally-Friendly Agricultural Research Institute and WCU Center for Development of Core Technology for Bio- Environment Control, Chonnam National University)
Kim, Jin-Cheol (Chemical Biotechnology Research Center, Korea Research Institute of Chemical Technology)
Kim, Young Cheol (Environmentally-Friendly Agricultural Research Institute and WCU Center for Development of Core Technology for Bio- Environment Control, Chonnam National University)
McSpadden Gardener, Brian (Environmentally-Friendly Agricultural Research Institute and WCU Center for Development of Core Technology for Bio- Environment Control, Chonnam National University)
Publication Information
The Plant Pathology Journal / v.29, no.2, 2013 , pp. 144-153 More about this Journal
Abstract
Diverse bacteria are known to colonize plants. However, only a small fraction of that diversity has been evaluated for their biopesticide potential. To date, the criteria for sampling and selection in such bioprospecting endeavors have not been systematically evaluated in terms of the relative amount of diversity they provide for analysis. The present study aimed to enhance the success of bioprospecting efforts by increasing the diversity while removing the genotypic redundancy often present in large collections of bacteria. We developed a multivariate sampling and marker-based selection strategy that significantly increase the diversity of bacteria recovered from plants. In doing so, we quantified the effects of varying sampling intensity, media composition, incubation conditions, plant species, and soil source on the diversity of recovered isolates. Subsequent sequencing and high-throughput phenotypic analyses of a small fraction of the collected isolates revealed that this approach led to the recovery of over a dozen rare and, to date, poorly characterized genera of plant-associated bacteria with significant biopesticide activities. Overall, the sampling and selection approach described led to an approximately 5-fold improvement in efficiency and the recovery of several novel strains of bacteria with significant biopesticide potential.
Keywords
ARDRA; biocontrol; microbial diversity; plant growth promotion;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Fierer, N. and Jackson, R. B. 2006. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. USA 103:626−663.
2 Fravel, D. 2005. Commercialization and implementation of biocontrol. Ann. Rev. Phytopathol. 43:337−359.
3 Garbeva P., van Veen J. A. and van Elsas J. D. 2004. Microbial diversity in soils, selection of microbial populations by plant and soil type and implications for disease suppressiveness. Ann. Rev. Phytopathol. 42:243−270.
4 Harman, G. E., Obregon, M. A., Samuels, G. J. and Lorito, M. 2010. Changing models for commercialization and implementation of biocontrol in the developed and developing world. Plant Dis. 94:928−939.   DOI   ScienceOn
5 Hoitink, H. A. J. and Boehm, M. J. 1999. Biocontrol within the context of soil microbial communities, a substrate dependent phenomenon. Ann. Rev. Phytopathol. 37:427−446.
6 Ibekwe, A. M., Poss, J. A., Grattan, S. R., Grieve, C. M. and Suarez, D. 2010. Bacterial diversity in cucumber (Cucumis sativus) rhizosphere in response to salinity, soil pH, and boron. Soil Biol. Biochem. 42:567−575.
7 Kim, J.-C., Choi, G. J., Park, J.-H., Kim, H. T. and Cho, K. Y. 2001. Activity against plant pathogenic fungi of phomalactone isolated from Nigrospora sphaerica. Pest Manag. Sci. 57:554-559.   DOI   ScienceOn
8 Kim, Y. C., Leveau, J., McSpadden Gardener, B. B., Pierson, E. A., Pierson, L. S. and Ryu, C.-M. 2011. The multifactorial basis for plant health promotion by plant-associated bacteria. Appl. Environ. Microbiol. 77:1548−1555.
9 Sloan, W. T., Quince, C. and Curtis, T. P. 2008. The uncountables. Pg 35-54. Chapter 3 in Accessing Uncultivated Microorganisms, from the Environment to Organisms and Genomes and Back. K. Zengler ed. ASM Press:Washington D.C.
10 Yang, C., Crowley, D. E., Borneman, J. and Keen, N. T. 2001. Microbial phyllosphere populations are more complex than previously realized. Proc. Natl. Acad. Sci. USA 98:3889−389.
11 Zengler, K. 2009. The central role of the cell in microbial ecology. Microbiol. Mol. Biol. Rev. 73:712−719.
12 Cho, J. C. and Tiedje, J. M. 2000. Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil. Appl. Environ. Microbiol. 66:5448−5456.   DOI   ScienceOn
13 Cho, J.-Y., Choi, G. J., Lee, S.-W., Jang, K. S., Kim, H. K., Kim, C. H., Cho, C. H., Lee, S. O., Cho, K. Y. and Kim, J.-C. 2006. Antifungal activity against Collectotrichum spp. of curcuminoids isolated from Curcuma longa L. rhizomes. J. Microbiol. Biotechnol. 16:280-285.
14 Benitez, M. S. and McSpadden Gardener, B. B. 2009. Linking sequence to function in soil bacteria, sequence-directed isolation of novel bacteria contributing to soilborne plant disease suppression. Appl. Envirol. Microbiol. 75:915−924.
15 Borneman, J. and Becker, J. O. 2007. Identifying microorganisms involved in specific pathogen suppression in soil. Ann. Rev. Phytopathol. 45:153−172.   DOI   ScienceOn
16 Copping, L. G. and Duke, S. O. 2007. Natural products that have been used commercially as crop protection agents. Pest Manag. Sci. 63:524−554.   DOI   ScienceOn
17 McSpadden Gardener, B., Gutierrez, L. J., Joshi, R., Edema, R. and Lutton, E. 2005. Distribution and biocontrol potential of phlD+ Pseudomonas species in corn and soybean fields. Phytopathology 95:715−724.   DOI   ScienceOn
18 Copping, L. G. 2004. The Manual of Biocontrol Agents. 3rd ed of the BioPesticide Manual. British Crop Protection Council, Alton, England. p 1-171.
19 Fahlgren, C., Hagstrom, A., Nilsson, D. and Zweifel, U. L. 2010. Annual variations in the diversity, viability, and origin of airborne bacteria. Appl. Environ. Microbiol. 76:3015−3025.
20 Marrone, P. G. 2007. Barriers to adoption of biological control agents and biological pesticides. In, CAB Review: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources. CABI, published online, ISSN 1749-8848, 2, No. 051.
21 McSpadden Gardener, B. B., Schroeder, K. L., Kalloger, S. E., Raaijmakers, J. M., Thomahsow, L. S. and Weller, D. M. 2000. Genotypic and Phenotypic diversity of phlD-containing Pseudomonas strains isolated from the rhizosphere of wheat. Appl. Environ. Microbiol. 66:1939−1946.
22 Nunes da Rocha, U., van Overbeek, L. and van Elsas, J. D. 2009. Exploration of the hitherto-uncultured bacteria from the rhizosphere. FEMS Microbiol. Ecol. 69:313−328.   DOI   ScienceOn
23 Qin, S., Li, J., Chen, H.-H., Zhao, G.-Z., Zhu, W.-Y., Jiang, C.-L. and Li, W.-J. 2009. Isolation, diversity, and antimicrobial activity of rare actinobacteria from medicinal plants of tropical rain forests in Xishuangbanna, China. Appl. Environ. Microbiol. 75:6176−6186.
24 Ramette, A. and Tiedje, J. M. 2007. Multiscale responses of microbial life to spatial distance and environmental heterogeneity in a patchy ecosystem. Proc. Natl. Acad. Sci. USA 104:2761−276.
25 Rodriguez-Diaz, M., Rodeles-Gonzales, B., Pozo-Clemente, C., Martinez-Toledo, M. V. and Gonzalez-Lopez, J. 2008. A review on the taxonomy and possible screening of traits of plant growth promoting rhizobacteria. Pg 55-80, Chapter 4 in Plant Bacteria Interactions, Strategies and Techniques to Promote Plant Growth. I. Ahmad, J Pichtel, and S. Hayat eds. Wiley- VCH: Weinhem.
26 Sachs, J. L., Kembel, S. W., Lau, A. H. and Simms, E. L. 2009. In situ phylogenetics structure and diversity of wild Bradyrhizobium communities. Appl. Environ. Microbiol. 75:4727−4735.