Effect of crop rotation on the diversity of the bacterial community colonizing rice straw residues in paddy rice cultured soil in the Mekong Delta of Vietnam

Tran Van Dung * and Cao Ngoc Diep

* Corresponding author (tvandung@ctu.edu.vn)

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Received: 29 Jan 2016
Revised: 25 Apr 2016
Accepted: 30 Mar 2017
Published: 31 Mar 2017
DOI: 10.22144/ctu.jen.2017.018
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Tran, V. D., & Cao, N. D. (2017). Effect of crop rotation on the diversity of the bacterial community colonizing rice straw residues in paddy rice cultured soil in the Mekong Delta of Vietnam. CTU Journal of Innovation and Sustainable Development , (05), 150-157. https://doi.org/10.22144/ctu.jen.2017.018
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No. 05 (2017)

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Abstract

In this study, the influence of crop rotation on the microbial diversity was investigated over a three crops. The studied crop rotation systems were rice-rice-rice (CRS1), rice-rice-baby corn (CRS2), rice-rice-mungbean (CRS3) and baby corn-rice-mungbean (CRS4).Litter bags containing rice stems were inserted into the soil and recollected at different time points for analysis and they were used to compare with the diversity of the bacterial community colonizing the rice straw by means of 16S rRNA gene based Denaturing Gradient Gel Electrophoresis (DGGE), UPGMA analysis and Shannon index (H) comparision. The results showed that the bacterial diversity colonizing rice straw residues were significantly different in composition in the (CRS4) rotation systemcompared to those in the 3 other systems.There were not significant differences in bacterial Shannon index during cultivation of crop I . In crop II and crop III, the CRS4 rotation system showed a H index higher than this of recorded in the CRS1, CRS2 and CRS3 treatments. The average H over the whole experiment was highest for the CRS4 system( H=1.13) and significantly different compared to the overall average H calculated for the other 2 systems CRS2(H=1.03) and CRS3( H=1.05) ,indicating that crop rotation with two upland crops was a vital key to the improvement of the Shannon index
Keywords: Bacterial community, crop rotation systems, DGGE, litter bags, rice straw residues, Shannon diversity index

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References

Akasaka, H., Izawa, T., Ueki, K., Ueki, A., 2003. Phylogeny of numerically abundant culturable anaerobic bacteria associated with degradation of rice plant residue in Japanese paddy field soil. FEMS Microbiology Ecology 43:149-161.

Asakawa, S., Kimura, M., 2008. Comparison of bacterial community structure at main habitats in paddy field ecosystem on DGGE analysis. Soil Biology and Biochemistry 40: 1322-1329.

Asari, N., Ishihara, R., Nakajima, Y., Kimura, M., Asakawa, S., 2008. Cyanobacterial communities of rice straw left on the soil surface of a paddy field. Biology and Fertility of Soils 44: 605-612.

Boon, N., Goris, J., De Vos, P., Verstraete, W., Top, E.M., 2000. Bioaugmentation of activated sludge by an indigenous 3-chloroaniline degrading Comamonastestosteroni strain I2gfp. Applied and Environmental Microbiology 66: 2906-2913.

Boon, N., Windt, W., Verstraete, W., Top, E.M., 2002. Evaluation of nested PCR-DGGE (denaturing gradient gel electrophoresis) with group-specific 16S rRNA primers for the analysis of bacterial communities from different wastewater treatment plants. FEMS Microbiology Ecology 39:101-112.

Carrera, L.M., Buyer, J.S., Vinyard, B., Abdul-Baki, A.A., Sikora, L.J., Teasdale, J.R., 2007. Effects of cover crops, compost, and manure amendments on soil micro- bial community structure in tomato production systems. Applied Soil Ecology 37:247–255.

Christensen, M .,1989. A view of fungal ecology. Mycology 81:1–19.

Drenovsky, R.E., Vo, D., Graham, K.J., Scow, K.M., 2004. Soil water content and organic carbon availability are major determinants of soil microbial community composition. Microbial Ecology 48:424–430.

Eichner, C. A., Erb, R. W., Timmis, K. N., Wagner-Dobler, I., 1999. Thermal gradient gelelectrophoresis analysis of bioprotection from pollutant shocks in the activated sludge microbial community. Applied and Environmental Microbiology 65:102–109.

Feng, Y., Motta, A.C., Burmester, C.H., Reeves, D.W., van Santen, E., Osborne, J.A., 2002. Effects of tillage systems on soil microbial community structure under a continuous cotton cropping system. In: van Santen E (eds.) Making conservation tillage conventional: building a future on 25 years of research. Proceedings of 25th Annual southern conservation tillage conference for sustainable agriculture, pp.222–226.

Ferris, H., Venette, R.C., Scow, K.M., 2004. Soil management to enhance bacterivore and fungivore nematode populations and their nitrogen mineralization function. Applied Soil Ecology 25:19–35.

Gans, J., Wolinsky, M., Dunbar, J., 2005. Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309:1387–1389.

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.

Garbeva, P., van Elsas, J.D., van Veen, J.A., 2008. Rhizosphere microbial community and its response to plant species and soil history. Plant and Soil 302:19–32.

Govaerts, B., Mezzalama, M., Unno, Y., Sayre, K.D., Luna-Guido,M., Vanherck, K., Dendooven, L., Deckers, J., 2007. Influence of tillage, residue management, and crop rotation on soil microbial biomass and catabolic diversity. Applied soil ecology 37:18-30.

Henckel, D., Chin, K.-J., Janssen, P.H., Liesack, W., 1999. Comparative phylogenetic assignment of environmental sequences of genes encoding 16S rRNA and numerically abundant culturable bacteria from an anoxic rice paddy soil. Applied and Environmental Microbiology 65: 5050-5058.

Henckel, T., Jäckel, U., Conrad, R., 2001. Vertical distribution of the methanotrophic community after drainage of rice field soil. FEMS microbiology ecology 34: 279-291.

Kikuchi, H., Watanabe, T., Jia, Z., Kimura, M., Asakawa, S., 2007. Molecular analyses reveal stability of bacterial communities in bulk soil of a Japanese paddy field: Estimation by denaturing gradient gel electrophoresis of 16S rRNA genes amplified from DNA accompanied with RNA. Soil Science and Plant Nutrition 53:448-458.

Kimura, M., Asakawa, S., 2006. Comparison of community structures of microbiota at main habitats in rice field ecosystems based on phospholipid fatty acid analysis. Biology and Fertility of Soils 43: 20-29.

Lu, Y., Watanabe, A., Kimura, M., 2002. Contribution of plant-derived carbon to soil microbial biomass dynamics in a paddy rice microcosm. Biology and Fertility of Soils 36:136-142.

Lueders, T., Friedrich, M., 2000. Archaeal population dynamics during sequential reduction processes in rice field soil. Applied and Environmental Microbiology 66:2732-2742.

Mazzola, M., 2004. Assessment and management of soil microbial community structure for disease suppression. Annual Review of Phytopathology 42: 35–59.

Mengel, K., 1985. Dynamics and availability of major nutrients in soils. Advances in soil sciences 2: 65–131.

Miethling, R., Wieland, G., Backhaus, H., Tebbe, C.C., 2000. Variation of microbial rhizosphere communities in response to crop species, soil origin, and inoculation with Sinorhizobium meliloti L33. Microbial Ecology 41: 43–56.

Mittal, S., Johri, B.N., 2008. Influence of management practices on the diversity of pseudomonads in rhizosphere soil of wheat cropping system. Biology and Fertility of Soils 44:823-831.

Nubel, U., Engelen, B., Felske, A., Snaidr, J., Wieshuber, A., Amann, R. I., Ludwig, W., Backhaus, H., 1996. Sequence heterogeneities of genes encoding16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. Journal of Bacteriology 178:5636–5643.

Saison, C., Degrange, V., Oliver, R., Millard, P., Commeaux, C., Montange, D., LeRoux, X., 2006. Alteration and resilience of the soil microbial community following compost amendment: effects of compost level and compost-borne microbial community. Environmental Microbiology 8: 247–257.

Shannon, C.E., Weaver, W., 1963. The Mathematical Theory of Communication. University of Illinois Press, Urbana, IL. pp: 7-24

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. Applied and Environmental Microbiology 67:4742– 4751.

Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G., Zuberer, D.A., 2005. Principles and Applications of Soil Microbiology. Prentice Hall, Upper Saddle River, NJ. pp: 183

Weber, S., Stunber, S., Conrad, R., 2001. Bacterial populations colonizing and degrading rice straw in anoxic paddy soil. Applied and Environmental Microbiology 67:1318-1327.

WRB, 2006. World Reference for Soil Resoures 2006. Report No.103. Food and Agriculture Organization of the United Nation, Rome, Italy. ISBN 978-92-5-108369-4

Zak, J. C., Willig, M. R., Moorhead, D. L., Wildman, H. G., 1994. Functional diversity of microbial communities: a quantitative approach. Soil Biology and Biochemistry 26:1101-1108