The Effect of Biological Control Agents on Paddy Soil Bacterial Community Structure

Aisyah Surya Bintang(1*), Arif Wibowo(2), Achmadi Priyatmojo(3), Siti Subandiyah(4)

(1) Department of Agriculture, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro Jln. Prof. Sudarto, SH, Tembalang, Semarang, Central Java 50275 Indonesia
(2) Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada Jln. Flora No. 1, Bulaksumur, Sleman, Yogyakarta 55281 Indonesia
(3) Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada Jln. Flora No. 1, Bulaksumur, Sleman, Yogyakarta 55281 Indonesia
(4) Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada Jln. Flora No. 1, Bulaksumur, Sleman, Yogyakarta 55281 Indonesia
(*) Corresponding Author


Biodiversity has been defined as the range of significantly different types of organisms and their relative abundance in an assemblage of community. The aim of this research was to understand about soil bacterial community after on biological control agents (BCA) treatments with various formulations. This research was conducted at Sleman Regency, Special Region of Yogyakarta and Faculty Agriculture of Universitas Gadjah Mada. The research conducted with culture dependent and culture independent methods to assess soil bacterial diversity. The results showed that soil bacterial diversity before and after treatment of biological control agent were different. Results from this research suggested different molecular methods regarding soil bacterial diversity based on their benefits and challenges. 


bacteria; culture dependent; culture independent; diversity; soil

Full Text:



Bååth, E. (1998). Growth Rates of Bacterial Communities in Soils at Varying pH: A Comparison of the Thymidine and Leucine Incorporation Techniques. Microbial Ecology, 36(3), 316‒327. DOI

Bappeda Daerah Istimewa Yogyakarta. (2021). Jenis Tanah DIY. Retrieved from URL

Bolton, H., Jr., Smith, J. L., & Link, S. O. (1993). Soil Microbial Biomass and Activity of a Disturbed and Undisturbed Shrub-steppe Ecosystem. Soil Biology and Biochemistry, 25(5), 545‒552. DOI

Cardinale, M., Brusetti, L., Quatrini, P., Borin, S., Puglia, A. M., Rizzi, A., Zanardini, E., Sorlini, C., Corselli, C., & Daffonchio, D. (2004). Comparison of Different Primer Sets for Use in Automated Ribosomal Intergenic Spacer Analysis of Complex Bacterial Communities. Applied and Environmental Microbiology, 70(10), 6147–6156. DOI

Cardinale, B. J., Duffy, J. E., Gonzalez, A., Hooper, D. U., Perrings, C., Narwani, A., Mace, G. M., Tilman, D., Wardle, D. A., Kinzig, A. P., Daily, G. C., Loreau, M. I., Grace, J. B., Larigaudarie, A., Srivastava, D. S., & Naeem, S. (2012). Biodiversity Loss and its Impact on Humanity. Nature, 486(7401), 59‒67. DOI

Clarholm, M. (1994). The Microbial Loop in Soil. In K. Ritz, J. Dighton, & K. E. Giller (eds.), Beyond the Biomass: Compositional and Functional Analysis of Soil Microbial Communities (pp. 221‒230). Chichester, United Kingdom: John Wiley & Sons.

Fenchel, T. (2005). Cosmopolitan Microbes and Their ‘Çryptic’ Species. Aquatic Microbial Ecology, 41(1), 49–54. DOI

Fisher, M. M. & Triplett, E. W. (1999). Automated Approach for Ribosomal Intergenic Spacer Analysis of Microbial Diversity and Its Application to Freshwater Bacterial Communities. Applied and Environmental Microbiology, 65(10), 4630‒4636. DOI

Flight, W. G., Smith, A., Palsey, C., Marchesi, J. R., Bull, M. J., Norville, P. J., Mutton, K. J., Webb, K. A., Thomas, R. J. B., Jines, A. M., & Mahenthiralingam, M. (2015). Rapid Detection of Emerging Pathogens and Loss of Microbial Diversity Associated with Severe Lung Disease in Cystic Fibrosis. Journal of Clinical Microbiology, 53(7), 2022‒2029. DOI

Garbeva, P., van Veen, J. A., & van Elsas, J. D. (2004). Microbial Diversity in Soil: Selection of Microbial Populations by Plant and Soil Type and Implications for Disease Suppressiveness. Annual Review of Phytopathology, 42, 243‒270. DOI

Garbeva, P., Postma, J., van Veen, J. A., & van Elsas, J. D. (2006). Effect Above-Ground Plant Species on Soil Microbial Community Structure and its Impact on Suppression of Rhizoctonia solani AG3. Environmental Microbiology, 8(2), 233‒246. DOI

Giovannoni, S. J., Britschgi, T. B., Moyer, C. L., & Field, K. G. (1990). Genetic Diversity in Sargasso Sea Bacterioplankton. Nature, 345(6270), 60‒63. DOI

Harpole, W. (2010). Neutral Theory of Species Diversity. Nature Education Knowledge, 3(10), 60. Retrieved from URL

He, J. Z., Zheng, Y., Chen, C. R., He, Y. G., & Zhang, L. M. (2008). Microbial Composition and Diversity of an Upland Red Oil under Long-Term Fertilization Treatments as Revealed by Culture-Dependent and Culture-Independent Approaches. Journal of Soils and Sediments, 8(5), 349‒358. DOI

Hugenholtz, P., Goebel, B. M., & Pace, N. (1998). Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity. Journal of Bacteriology, 180(18), 4765‒4774. DOI

Istiqomah, D. (2015). Seleksi Rizobakteri Bawang Merah untuk Mengendalikan Penyakit Moler [Master’s thesis]. Yogyakarta, Indonesia: Universitas Gadjah Mada.

Leite, N. A., Alves-Pereira, A., Corrêa, A. S., Zucchi, M. I., & Omoto, C. (2014). Demographics and Genetic Variability of the New Bollworm (Helicoverpa zea) and the Old World Bollworm (Helicoverpa armigera) in Brazil. PLoS ONE, 9(11), e113286. DOI

Lopes, A. R., Faria, C., Prieto-Fernández, Á., Trasa-Cepeda, C., Manaia, C. M., & Nunes, O. C. (2011). Comparative Study of the Microbial Diversity a Bulk Paddy Soil of Two Rice Fields Subjected to Organic and Conventional Farming. Soil Biology and Chemistry, 43(1), 115‒125. DOI

Marschner, P., Crowley, D., & Yang, C. H. (2004). Development of Specific Rhizosphere Bacterial Communities in Relation to Plant Species, Nutrition, and Soil Type. Plant and Soil, 261(1‒2), 199‒208. DOI

Ranjard, L., Brothier, E., & Nazaret. S. (2000). Sequencing Bands of Ribosomal Intergenic Spacer Analysis Fingerprints for Characterization and Microscale Distribution of Soil Bacterium Populations Responding to Mercury Spiking. Applied and Environmental Microbiology, 66(12), 5334‒5339. DOI

Roman, D. L., Voiculescu, D. I., Filip, M., Ostafe, V., & Isvoran, A. (2021). Effects of Triazole Fungicides on Soil Microbiota and on the Activities of Enzymes Found in Soil: A Review. Agriculture, 11(9), 893-911. DOI

Schlegel, H. G., & Jannasch, H. W. (1992). Prokaryotes and Their Habitats. In A. Balows, H. G. Trüper, M. Dworkin, W. Harder, & K-H. Schleifer (Eds.), The Prokaryotes I (pp. 75–125.) New York, United States: Springer-Verlag.

Sheng, Z. L., Min, L., Yong, H. C., & Abid, S. (2005). Effect of Nutrient and Pest Management in Soil Microorganism in Hybrid Rice Double-Annual Cropping System. Communications in Soil Science and Plant Analysis, 36(11‒12), 1525‒1536. DOI

Song, Y. N., Su, J., Chen, R., Lin. Y., & Wang, F. (2014). Diversity of Microbial Community in a Paddy Soil with cry1Ac/cpti Transgenic Rice. Pedosphere, 24(3), 349‒358. DOI

Torsvik, V., Daae, F., Sandaa, R. A., & Øvreảs, L. (1998). Novel Techniques for Analyzing Microbial Diversity in Natural and Perturbed Environments. Journal of Biotechnology, 64(1), 53‒62. DOI

Turco, R. F., Kennedy, A. C., & Jawson, M. D. (1994). Microbial Indicators of Soil Quality. In J.W. Doran, D.C. Coleman, D.F. Bezdicek, & B.A. Stewart (Eds.), Defining Soil Quality for a Sustainable Environment (Vol. 35, pp. 73‒90). Madison, W.I., United States: Soil Science Society of America and American Society of Agronomy. DOI

Xuan, D. T. (2012). Microbial Communities in Paddy Fields in the Mekong Delta of Vietnam [Doctoral thesis]. Uppsala, Sweden: Swedish University of Agricultural Sciences. Retrieved from URL

Yang, C-H., & Crowley, D. E. (2000). Rhizosphere Microbial Community Structure in Relation to Root Location and Plant Iron Nutritional Status. Applied and Environmental Microbiology, 66(1), 345‒351. DOI

Yang, D., & Zhang, M. (2014). Effects of Land-Use Conversion from Paddy Field to Orchard Farm on Soil Microbial Genetic Diversity and Community Structure. European Journal of Soil Biology, 64, 30‒39. DOI

Yao, R-J., Yang, J-S., Zhang, T-J., Gao, P., Yu, S-P., & Wang, X-P. (2013). Short-Term Effect of Cultivation and Crop Rotation Systems on Soil Quality Indicators in a Coastal Newly Reclaimed Farming Area. Journal of Soils and Sediments, 13(8), 1335‒1350. DOI

Zhao, L., Ma, T., Gao, M., Gao, P., Cao, M., Zhu, X., & Li, G. (2012). Characterization of Microbial Diversity and Community in Water Flooding Oil Reservoirs in China. World Journal of Microbiology and Biotechnology, 28(10), 3039‒3052. DOI


Article Metrics

Abstract views : 681 | views : 374


  • There are currently no refbacks.

Copyright (c) 2022 Jurnal Perlindungan Tanaman Indonesia

Creative Commons License
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.


Jurnal Perlindungan Tanaman Indonesia ISSN 1410-1637 (print)ISSN 2548-4788 (online) is published by Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada in collaboration with Indonesian Entomological Society (Perhimpunan Entomologi Indonesia, PEI) and Indonesian Phytopathological Society (Perhimpunan Fitopatologi Indonesia, PFI). The content of this website is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.  

View website statistics