- Volume 46 Issue 6
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Analysis of Community Structure of Metabolically Active Bacteria in a Rice Field Subjected to Long-Term Fertilization Practices
- Ahn, Jae-Hyung (Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration) ;
- Choi, Min-Young (Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration) ;
- Lee, Hye-Won (Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration) ;
- Kim, Byung-Yong (Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration) ;
- Song, Jaekyeong (Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration) ;
- Kim, Myung-Sook (Soil & Ferilization Division, National Academy of Agricultural Science, Rural Development Administration) ;
- Weon, Hang-Yeon (Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration)
- Received : 2013.10.28
- Accepted : 2013.11.29
- Published : 2013.12.31
To estimate the effect of long-term fertilization on metabolically active bacterial communities in a rice field, RNA was extracted from endosphere (rice root), rhizosphere, and bulk soil that had been subjected to different fertilization regimes for 59 years, and the 16S rRNAs were analyzed using the pyrosequencing method. The richness and diversity of metabolically active bacteria were higher in bulk soil than in the endosphere and rhizosphere, and showed no significant difference between non-fertilized and fertilized plots. Weighted UniFrac analysis showed that each compartment had characteristic bacterial communities and that the effect of long-term fertilization on the structure of bacterial community was more pronounced in bulk soil than in the endosphere and rhizosphere. The 16S rRNAs affiliated with Alphaproteobacteria and Firmicutes were more abundant in the endosphere than in bulk soil while those affiliated with Chloroflexi and Acidobacteria were more abundant in bulk soil than in the endosphere. Several dominant operational taxonomic units (clustered at a 97% similarity cut-off) showed different frequencies between non-fertilized and fertilized plots, suggesting that the fertilization affected their activities in the rice field.
RNA;Bacterial community;Rice field;Fertilization
Grant : Research Program for Agricultural Science & Technology Development
Supported by : National Academy of Agricultural Science
- Ahn, J.H., J. Song, B.Y. Kim, M.S. Kim, J.H. Joa, and H.Y. Weon. 2012. Characterization of the bacterial and archaeal communities in rice field soils subjected to long-term fertilization practices. J. Microbiol. 50:754-765. https://doi.org/10.1007/s12275-012-2409-6
- Ahn, J.H., M.Y. Choi, B.Y. Kim, J.S. Lee, J. Song, G.Y. Kim, and H.Y. Weon. 2013. Effects of water-saving irrigation on the emission of greenhouse gases and the prokaryotic communities in rice paddy soils. Microb. Ecol. in press.
- Chun, J., K. Kim, J.H. Lee, and Y. Choi. 2010. The analysis of oral microbial communities of wild-type and toll-like receptor 2-deficient mice using a 454 GS FLX Titanium pyrosequencer. BMC Microbiol. 10:101. https://doi.org/10.1186/1471-2180-10-101
- Cole, J.R., Q. Wang, E. Cardenas, J. Fish, B. Chai, R.J. Farris, A.S. Kulam-Syed-Mohideen, D.M. McGarrell, T. Marsh, G.M. Garrity, and J.M. Tiedje. 2009. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37:D141-D145. https://doi.org/10.1093/nar/gkn879
- Cui, J., H. Meng, M. Nie, X. Chen, Z. Li, N. Bu, B. Li, J. Chen, Z. Quan, and C. Fang. 2012. Bacterial succession during 500 years of soil development under agricultural use. Ecol. Res. 27:793-807. https://doi.org/10.1007/s11284-012-0955-3
- Edgar, R.C., B.J. Haas, J.C. Clemente, C. Quince, and R. Knight. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 27:2194-2200. https://doi.org/10.1093/bioinformatics/btr381
- Fierer, N., M.A. Bradford, and R.B. Jackson. 2007. Toward an ecological classification of soil bacteria. Ecology. 88:1354-1364. https://doi.org/10.1890/05-1839
- Flessa, H. and W.R. Fischer. 1992. Plant-induced changes in the redox potentials of rice rhizospheres. Plant Soil. 143:55-60. https://doi.org/10.1007/BF00009128
- Frenzel, P., F. Rothfuss, and R. Conrad. 1992. Oxygen profiles and methane turnover in a flooded rice microcosm. Biol. Fert. Soils. 14:84-89. https://doi.org/10.1007/BF00336255
- Hardoim, P.R., F.D. Andreote, B. Reinhold-Hurek, A. Sessitsch, L.S. van Overbeek, and J.D. van Elsas. 2011. Rice root-associated bacteria: Insights into community structures across 10 cultivars. FEMS Microbiol. Ecol. 77:154-164. https://doi.org/10.1111/j.1574-6941.2011.01092.x
- He, Q. and R.A. Sanford. 2003. Characterization of Fe(III) reduction by chlororespiring Anaeromxyobacter dehalogenans. Appl. Environ. Microbiol. 69:2712-2718. https://doi.org/10.1128/AEM.69.5.2712-2718.2003
- Hengstmann, U., K.-J. Chin, P.H. Janssen, and W. Liesack. 1999. Comparative phylogenetic assignment of environmental sequences of genes encoding 16S rRNA and numerically abundant culturable bacteria from an anoxic rice paddy soil. Appl. Environ. Microbiol. 65:5050-5058.
- Kogel-Knabner, I., W. Amelung, Z. Cao, S. Fiedler, P. Frenzel, R. Jahn, K. Kalbitz, A. Kolbl, and M. Schloter. 2010. Biogeochemistry of paddy soils. Geoderma. 157:1-14. https://doi.org/10.1016/j.geoderma.2010.03.009
- Kelly, D., A. Wood, and E. Stackebrandt. 2005. Genus II. Thiobacillus, p. 764-769. In D. J. Brenner, N. R. Krieg, G. M. Garrity, J. T. Staley, D. R. Boone, P. Vos, M. Goodfellow, F. A. Rainey and K. H. Schleifer (eds.), Bergey's manual of systematic bacteriology, Springer, USA.
- Kim, M.S., J.H. Ahn, M.K. Jung, J.H. Yu, D. Joo, M.C. Kim, H.Y. Shin, T. Kim, T.H. Ryu, S.J. Kweon, D.H. Kim, and J.O. Ka. 2005. Molecular and cultivation-based characterization of bacterial community structure in rice field soil. J. Microbiol. Biotechn. 15:1087-1093.
- Kim, M.S., Y.H. Kim, S.S. Kang, H.B. Yun, and B.K. Hyun. 2012. Long-term application effects of fertilizers and amendments on changes of soil organic carbon in paddy soil. Korean J. Soil. Sci. Fert. 45:1108-1113. https://doi.org/10.7745/KJSSF.2012.45.6.1108
- Kuykendall, L.D. 2005. Genus I. Bradyrhizobium, p. 438-443. In D. J. Brenner, N. R. Krieg, G. M. Garrity, J. T. Staley, D. R. Boone, P. Vos, M. Goodfellow, F. A. Rainey and K. H. Schleifer (eds.), Bergey's manual of systematic bacteriology, Springer US, New York, USA.
- Letunic, I. and P. Bork. 2011. Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res. 39:W475-W478. https://doi.org/10.1093/nar/gkr201
- Liesack, W., S. Schnell, and N.P. Revsbech. 2000. Microbiology of flooded rice paddies. FEMS Microbiol. Rev. 24:625-645. https://doi.org/10.1111/j.1574-6976.2000.tb00563.x
- Lozupone, C. and R. Knight. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71:8228-8235. https://doi.org/10.1128/AEM.71.12.8228-8235.2005
- Lu, Y., D. Rosencrantz, W. Liesack, and R. Conrad. 2006. Structure and activity of bacterial community inhabiting rice roots and the rhizosphere. Environ. Microbiol. 8:1351-1360. https://doi.org/10.1111/j.1462-2920.2006.01028.x
- Ludwig, W., O. Strunk, R. Westram, L. Richter, H. Meier, Yadhukumar, A. Buchner, T. Lai, S. Steppi, G. Jobb, W. Forster, I. Brettske, S. Gerber, A.W. Ginhart, O. Gross, S. Grumann, S. Hermann, R. Jost, A. Konig, T. Liss, R. Lussmann, M. May, B. Nonhoff, B. Reichel, R. Strehlow, A. Stamatakis, N. Stuckmann, A. Vilbig, M. Lenke, T. Ludwig, A. Bode, and K.H. Schleifer. 2004. ARB: a software environment for sequence data. Nucleic Acids Res. 32:1363-1371. https://doi.org/10.1093/nar/gkh293
- Ma, K. and Y. Lu. 2011. Regulation of microbial methane production and oxidation by intermittent drainage in rice field soil. FEMS Microbiol. Ecol. 75:446-456. https://doi.org/10.1111/j.1574-6941.2010.01018.x
- Ma, K., R. Conrad, and Y. Lu. 2012. Responses of methanogen mcrA genes and their transcripts to an alternate dry/wet cycle of paddy field soil. Appl. Environ. Microbiol. 78:445-454. https://doi.org/10.1128/AEM.06934-11
- Nakayama, N., A. Okabe, K. Toyota, M. Kimura, and S. Asakawa. 2006. Phylogenetic distribution of bacteria isolated from the floodwater of a Japanese paddy field. Soil Sci. Plant Nutr. 52:305-312. https://doi.org/10.1111/j.1747-0765.2006.00039.x
- Podosokorskaya, O.A., E.A. Bonch-Osmolovskaya, A.A. Novikov, T.V. Kolganova, and I.V. Kublanov. 2013. Ornatilinea apprima gen. nov., sp. nov., a novel cellulolytic representative of class Anaerolineae. Int. J. Syst. Evol. Microbiol. 63:86-92. https://doi.org/10.1099/ijs.0.041012-0
- Price, M.N., P.S. Dehal, and A.P. Arkin. 2009. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol. Biol. Evol. 26:1641-1650. https://doi.org/10.1093/molbev/msp077
- Pruesse, E., J. Peplies, and F.O. Glockner. 2012. SINA: accurate high throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics. 28:1823-1829. https://doi.org/10.1093/bioinformatics/bts252
- Qin, S., J. Li, H.-H. Chen, G.-Z. Zhao, W.-Y. Zhu, C.-L. Jiang, L.-H. Xu, and W.-J. Li. 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. https://doi.org/10.1128/AEM.01034-09
- Quince, C., A. Lanzen, R. Davenport, and P. Turnbaugh. 2011. Removing noise from pyrosequenced amplicons. BMC Bioinformatics. 12:38. https://doi.org/10.1186/1471-2105-12-38
- Revsbech, N.P., O. Pedersen, W. Reichardt, and A. Briones. 1999. Microsensor analysis of oxygen and pH in the rice rhizosphere under field and laboratory conditions. Biol. Fert. Soils. 29:379-385. https://doi.org/10.1007/s003740050568
- Sanford, R.A., J.R. Cole, and J.M. Tiedje. 2002. Characterization and description of Anaeromyxobacter dehalogenans gen. nov., sp. nov., an aryl-halorespiring facultative anaerobic Myxobacterium. Appl. Environ. Microbiol. 68:893-900. https://doi.org/10.1128/AEM.68.2.893-900.2002
- Schloss, P.D., S.L. Westcott, T. Ryabin, J.R. Hall, M. Hartmann, E.B. Hollister, R.A. Lesniewski, B.B. Oakley, D.H. Parks, C.J. Robinson, J.W. Sahl, B. Stres, G.G. Thallinger, D.J. Van Horn, and C.F. Weber. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75:7537-7541. https://doi.org/10.1128/AEM.01541-09
- Sessitsch, A., P. Hardoim, J. Doring, A. Weilharter, A. Krause, T. Woyke, B. Mitter, L. Hauberg-Lotte, F. Friedrich, M. Rahalkar, T. Hurek, A. Sarkar, L. Bodrossy, L. van Overbeek, D. Brar, J.D. van Elsas, and B. Reinhold-Hurek. 2011. Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis. Mol. Plant Microbe In. 25:28-36.
- Yeon, B.Y., H.K. Kwak, B.L. Huh, C.W. Hong, and J.H. Lee. 1997. Influence of long term application of compost, lime and silicate fertilizer on some properties of paddy soil. RDA. J. Agro-Envir. Sci. 39:9-15.
- Yeon, B.Y., H.K. Kwak, Y.S. Song, H.J. Jun, H.J. Cho, and C.H. Kim. 2007. Changes in rice yield and soil organic matter content under continued application of rice straw compost for 50 years in paddy soil. Korean J. Soil. Sci. Fert. 40:454-459.
- Dynamics of bacterial communities in rice field soils as affected by different long-term fertilization practices vol.54, pp.11, 2016, https://doi.org/10.1007/s12275-016-6463-3