Advanced SearchSearch Tips
Comparative Analysis of Endophytic Bacterial Communities in the Roots of Rice Grown under Long-term Fertilization Practice using Pyrosequencing Method
facebook(new window)  Pirnt(new window) E-mail(new window) Excel Download
 Title & Authors
Comparative Analysis of Endophytic Bacterial Communities in the Roots of Rice Grown under Long-term Fertilization Practice using Pyrosequencing Method
Kim, Byung-Yong; Ahn, Jae-Hyung; Song, Jaekyeong; Kim, Myung-Sook; Weon, Hang-Yeon;
  PDF(new window)
Bacterial endophytes may be important factors in plant growth and ecologically relevant functions in rice. Using pyrosequencing technology, we analyzed the composition of endophytic bacterial communities that colonized the roots of rice cultivated in long-term fertilized (APK) and non-fertilized (NF) paddy soils. A total of 1,900 reads were obtained from 2 samples. All sequences were classified into 177 OTUs (APK sample) or 72 OTUs (NF sample) at a 97% similarity cut-off. Twenty-two OTUs were shared between the 2 samples, and these were also the most dominant OTUs in both samples. Proteobacteria was the most dominant phylum with 90.2%, followed by Actinobacteria (7.1%) and Bacteroidetes (1.1%). Furthermore, Pseudomonas was the most abundant genus in both samples. We observed clear differences in the structure of the endophytic bacterial community structure between the 2 samples. Notably, the distributions of Alphaproteobacteria and Gammaproteobacteria were markedly different. The diversity index of the APK sample was higher than that of the NF sample. These findings showed that the endophytic bacterial community of rice roots was affected by the presence of fertilizers in the rice field soil.
Pyrosequencing;Bacterial community;Rice;Endophytic;Long-term fertilization;
 Cited by
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. crossref(new window)

Babalola, O.O. 2010. Beneficial bacteria of agricultural importance. Biotechnol. Lett. 32:1559-1570. crossref(new window)

Berg, G., A. Krechel, M. Ditz, R.A. Sikora, A. Ulrich, and J. Hallmann. 2005. Endophytic and ectophytic potato-associated bacterial communities differ in structure and antagonistic function against plant pathogenic fungi. FEMS Microbiol. Ecol. 51:215-229. crossref(new window)

Chun, J., K.Y. 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. crossref(new window)

Compant, S., C. Clement, and A. Sessitsch. 2010. Plant growthpromoting bacteria in the rhizo- and endosphere of plants: Their role, colonization, mechanisms involved and prospects for utilization. Soil Biol. Biochem. 42:669-678. crossref(new window)

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. crossref(new window)

Jones, R.T., M.S. Robeson, C.L. Lauber, M. Hamady, R. Knight, and N. Fierer. 2009. A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J. 3:442-453. crossref(new window)

Kim, J.H. and J.K. Lee. 2011. Identification and characterization of an endophytic strain of Streptomyces from rice roots (Orysa sativa L.). Kor. J. Microbiol. 47:375-380.

Kim, M.S., Y.H. Kim, B.K. Hyun, J.E. Yang, Y.S. Zhang, H.B. Yun, Y.K. Sonn, Y.J. Lee, and S.K. Ha. 2011. Rice yield and changes of available silicate in paddy soils from long-term application of chemical fertilizers and soil amendments. Korean J. Soil Sci. Fert. 44:1118-1123. crossref(new window)

Kim, O.S., Y.J. Cho, K. Lee, S.H. Yoon, M. Kim, H. Na, S.C. Park, Y.S. Jeon, J.H. Lee, H. Yi, S. Won, and J. Chun. 2012. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int. J. Syst. Evol. Microbiol. 62:716-721. crossref(new window)

Lian, J., Z. Wang, and S. Zhou. 2008. Response of endophytic bacterial communities in banana tissue culture plantlets to Fusarium wilt pathogen infection. J. Gen. Appl. Microbiol. 54:83-92. crossref(new window)

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. crossref(new window)

Manter, D.K., J.A. Delgado, D.G. Holm, and R.A. Stong. 2010. Pyrosequencing reveals a highly diverse and cultivarspecific bacterial endophyte community in potato roots. Microb. Ecol. 60:157-166. crossref(new window)

Mercado-Blanco, J. and P.A. Bakker. 2007. Interactions between plants and beneficial Pseudomonas spp.: exploiting bacterial traits for crop protection. Antonie van Leeuwenhoek. 92:367-389. crossref(new window)

Park, M., H. Lee, S.G. Hong, and O.S. Kim. 2012. Endophytic bacterial diversity of antartic moss, Sanionia uncinata. Antarct. Sci. 4:1-4.

Park, S.Y., S.H. Yang, S.K. Choi, J.G. Kim, and S.H. Park. 2007. Isolation and characterization of endophytic bacteria from rice root cultivated in Korea. Kor. J. Microbiol. Biotechnol. 35:1-10.

Pruesse, E., C. Quast, K. Knittel, B.M. Fuchs, W. Ludwig, J. Peplies, and F.O. Glockner. 2007. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35:7188-7196. crossref(new window)

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. crossref(new window)

Quince, C., A. Lanzen, R.J. Davenport, and P.J. Turnbaugh. 2011. Removing noise from pyrosequenced amplicons. BMC Bioinformatics. 12:38. crossref(new window)

Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.

Saravanakumar, D. and R. Samiyappan. 2007. ACC deaminase from Pseudomonas fluorescens mediated saline resistance in groundnut (Arachis hypogea) plants. J. Appl. Microbiol. 102:1283-1292. crossref(new window)

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, communitysupported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75:7537-7541. crossref(new window)

Shin, D.S., M.S. Park, S. Jung, M.S. Lee, K.H. Lee, K.S. Bae, and S.B. Kim. 2007. Plant growth-promoting potential of endophytic bacteria isolated from roots of coastal sand dune plants. J. Microbiol. Biotechnol. 17:1361-1368.

Stockwell, V.O. and J.P. Stack. 2007. Using Pseudomonas spp. for integrated biological control. Phytopathology. 97:244-249. crossref(new window)

Strobel, G., B. Daisy, U. Castillo, and J. Harper. 2004. Natural products from endophytic microorganisms. J. Nat. Prod. 67:257-268. crossref(new window)

Taghavi, S., D. van der Lelie, A. Hoffman, Y.B. Zhang, M.D. Walla, J. Vangronsveld, L. Newman, and S. Monchy. 2010. Genome sequence of the plant growth promoting endophytic bacterium Enterobacter sp. 638. PLoS Genet. 6:e1000943. crossref(new window)

Tamura, K., D. Peterson, N. Peterson, G. Stecher, M. Nei, and S. Kumar. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28:2731-2739. crossref(new window)

Ulrich, K., A. Ulrich, and D. Ewald. 2008. Diversity of endophytic bacterial communities in poplar grown under field conditions. FEMS Microbiol. Ecol. 63:169-180. crossref(new window)