Korean Journal of Microbiology (미생물학회지)

The Microbiological Society of Korea (한국미생물학회)
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Bacterial core community in soybean rhizosphere

콩 근권의 핵심 세균 군집

  • Lee, Youngmi (Agricultural Microbiology Division, National Academy of Agricultural Science, RDA) ;
  • Ahn, Jae-Hyung (Agricultural Microbiology Division, National Academy of Agricultural Science, RDA) ;
  • Choi, Yu-Mi (RDA-Genebank, National Academy of Agricultural Science, RDA) ;
  • Weon, Hang-Yeon (Agricultural Microbiology Division, National Academy of Agricultural Science, RDA) ;
  • Yoon, Jung-Hoon (Department of Food Science and Biotechnology, Sungkyunkwan University) ;
  • Song, Jaekyeong (Agricultural Microbiology Division, National Academy of Agricultural Science, RDA)
  • 이영미 (국립농업과학원 농업미생물과) ;
  • 안재형 (국립농업과학원 농업미생물과) ;
  • 최유미 (국립농업과학원 농업유전자원센터) ;
  • 원항연 (국립농업과학원 농업미생물과) ;
  • 윤정훈 (성균관대학교 식품생명공학과) ;
  • 송재경 (국립농업과학원 농업미생물과)
  • Received : 2015.10.30
  • Accepted : 2015.11.12
  • Published : 2015.12.31
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Abstract

Soybean is well known to be originated from Korea and far-east Asian countries, and studies of many root nodule bacteria associated with soybean have mainly-focused on nitrogen fixation, but much less study was carried out on bacterial community in the rhizosphere of soybean. In this study, we analyzed the bacterial community in rhizosphere of Korean soybean, Daepungkong using the pyrosequencing method based on the 16S rRNA gene to characterize the change of the rhizosphere community structure according to the growth stages of soybeans and to elucidate bacterial core community in rhizosphere of soybean. Our results revealed that bacterial community of rhizosphere soil differed from that of bulk soil and was composed of a total of 21 bacterial phyla. The predominant phylum in the rhizosphere of soybean was Proteobacteria (36.6-42.5%) and followed by Acidobacteria (8.6-9.4%), Bacteroidetes (6.1-10.9%), Actinobacteria (6.4-9.8%), and Firmicutes (5.7-6.3%). The bacterial core community in soybean rhizosphere was mainly composed of the operational taxonomic units (OTUs) belonging to the phylum Proteobacteria throughout all growth stages. The OTU00006 belonged to the genus Bradyrhizobium had the highest abundance and Steroidobacter, Streptomyces, Devosia were followed. These results show that bacterial core community in soybean rhizosphere was mainly composed of OTUs associated with plant growth promotion and nutrient cycles.

콩은 우리나라와 극동아시아가 원산지로 알려져 있으나 국산 콩의 근권 세균 군집에 대한 연구는 미흡하다. 따라서 본 연구에서는 국산 재배콩을 대상으로 차세대 염기서열 분석 방법인 파이로시퀀싱 방법을 사용하여 콩 근권 세균 군집 구조를 해석하고 생육단계별 군집의 변화 및 콩 근권의 핵심 세균 군집을 구명하고자 하였다. 세균 군집 분석 결과, 근권 세균의 군집은 근권과 비근권간에 뚜렷한 차이를 보였으며, 총 21개의 문으로 구성되었다. Proteobacteria가 가장 우점(36.6-42.5%)하였고, Acidobacteria (8.6-9.4%), Bacteroidetes (6.1-10.9%), Actinobacteria (6.4-9.8%), Firmicutes (5.7-6.3%) 등의 순으로 상대풍부도가 감소하였다. 모든 생육단계에 걸쳐 콩 근권의 핵심 세균 군집에는 Proteobacteria에 속한 OTU들이 가장 많이 분포하였으며, 이들 중 Bradyrhizobium에 속한 OTU의 상대 풍부도가 가장 높았다. 본 연구결과는 콩 근권의 핵심 세균 군집은 주로 생육 촉진 기능과 유기물 순환에 관련된 OTU로 구성되어 있다는 것을 보여주었다.

Keywords

References

  1. Amann, R.I., Ludwig, W., and Schleifer, K.H. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143-169.
  2. Bakker, P.A.H.M., Berendsen, R.L., Doornbos, R.F., Wintermans, P.C.A., and Pieterse, C.M.J. 2013. The rhizosphere revisited: Root microbiomics. Front Plant Sci 4, 165.
  3. Barbour, W., Hattermann, D., and Stacey, G. 1991. Chemotaxis of Bradyrhizobium japonicum to soybean exudates. Appl. Environ. Microbiol. 57, 2635-2639.
  4. Barns, S.M., Takala, S.L., and Kuske, C.R. 1999. Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment. Appl. Environ. Microbiol. 65, 1731-1737.
  5. Baudoin, E., Benizri, E., and Guckert, A. 2002. Impact of growth stage on the bacterial community structure along maize roots, as determined by metabolic and genetic fingerprinting. Appl. Soil Ecol. 19, 135-145. https://doi.org/10.1016/S0929-1393(01)00185-8
  6. Berendsen, R.L., Pieterse, C.M.J., and Bakker, P.A.H.M. 2012. The rhizosphere microbiome and plant health. Trends Plant Sci. 17, 478-486. https://doi.org/10.1016/j.tplants.2012.04.001
  7. Chaparro, J.M., Badri, D.V., Bakker, M.G., Sugiyama, A., Manter, D.K., and Vivanco, J.M. 2013. Root exudation of phytochemicals in Arabidopsis follows specific patterns that are developmentally programmed and correlate with soil microbial functions. PLoS One 8, e55731. https://doi.org/10.1371/journal.pone.0055731
  8. Chaparro, J.M., Badri, D.V., and Vivanco, J.M. 2014. Rhizosphere microbiome assemblage is affected by plant development. ISME J. 8, 790-803. https://doi.org/10.1038/ismej.2013.196
  9. Clough, S.J. and Bent, A.F. 1998. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16, 735-743. https://doi.org/10.1046/j.1365-313x.1998.00343.x
  10. Cole, J.R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R.J., Kulam-Syed-Mohideen, A., McGarrell, D., Marsh, T., and Garrity, G.M. 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
  11. Edgar, R.C., Haas, B.J., Clemente, J.C., Quince, C., and Knight, R. 2011. Uchime improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194-2200. https://doi.org/10.1093/bioinformatics/btr381
  12. Faoro, H., Alves, A., Souza, E., Rigo, L., Cruz, L., Al-Janabi, S., Monteiro, R., Baura, V., and Pedrosa, F. 2010. Influence of soil characteristics on the diversity of bacteria in the southern brazilian atlantic forest. Appl. Environ. Microbiol. 76, 4744-4749. https://doi.org/10.1128/AEM.03025-09
  13. Fehr, W.R. and Caviness, C.E. 1977. Stages of soybean development, Cooperative Extension Service; Agriculture and Home Economics Experiment Station, Iowa State University of Science and Technology.
  14. Fierer, N. and Jackson, R.B. 2006. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. USA 103, 626-631. https://doi.org/10.1073/pnas.0507535103
  15. Foster, R. 1988. Microenvironments of soil microorganisms. Biol. Fert. Soils 6, 189-203.
  16. Frey, S.D., Knorr, M., Parrent, J.L., and Simpson, R.T. 2004. Chronic nitrogen enrichment affects the structure and function of the soil microbial community in temperate hardwood and pine forests. Forest Ecol. Manag. 196, 159-171. https://doi.org/10.1016/j.foreco.2004.03.018
  17. Girvan, M.S., Bullimore, J., Pretty, J.N., Osborn, A.M., and Ball, A.S. 2003. Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Appl. Environ. Microbiol. 69, 1800-1809. https://doi.org/10.1128/AEM.69.3.1800-1809.2003
  18. Gomez-Pereira, P.R., Schuler, M., Fuchs, B.M., Bennke, C., Teeling, H., Waldmann, J., Richter, M., Barbe, V., Bataille, E., Glockner, F.O., et al. 2012. Genomic content of uncultured bacteroidetes from contrasting oceanic provinces in the north atlantic ocean. Environ. Microbiol. 14, 52-66. https://doi.org/10.1111/j.1462-2920.2011.02555.x
  19. Gottel, N.R., Castro, H.F., Kerley, M., Yang, Z., Pelletier, D.A., Podar, M., Karpinets, T., Uberbacher, E., Tuskan, G.A., Vilgalys, R., et al. 2011. Distinct microbial communities within the endosphere and rhizosphere of populus deltoides roots across contrasting soil types. Appl. Environ. Microbiol. 77, 5934-5944. https://doi.org/10.1128/AEM.05255-11
  20. Graham, P.H. 2008. Ecology of the root-nodule bacteria of legumes, pp. 23-58. In Dilworth, M., James, E., Sprent, J., and Newton, W. (eds.), Nitrogen-fixing leguminous symbioses, Springer Netherlands.
  21. Houlden, A., Timms-Wilson, T.M., Day, M.J., and Bailey, M.J. 2008. Influence of plant developmental stage on microbial community structure and activity in the rhizosphere of three field crops. FEMS Microbiol. Ecol. 65, 193-201. https://doi.org/10.1111/j.1574-6941.2008.00535.x
  22. Isanga, J. and Zhang, G.N. 2008. Soybean bioactive components and their implications to health-a review. Food Rev. Int. 24, 252-276. https://doi.org/10.1080/87559120801926351
  23. Kirchman, D.L. 2002. The ecology of cytophaga-flavobacteria in aquatic environments. FEMS Microbiol. Ecol. 39, 91-100.
  24. Lauber, C.L., Strickland, M.S., Bradford, M.A., and Fierer, N. 2008. The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biol. Biochem. 40, 2407-2415. https://doi.org/10.1016/j.soilbio.2008.05.021
  25. Lozupone, C. and Knight, R. 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
  26. Mendes, L.W., Kuramae, E.E., Navarrete, A.A., van Veen, J.A., and Tsai, S.M. 2014. Taxonomical and functional microbial community selection in soybean rhizosphere. ISME J. 8, 1577-1587. https://doi.org/10.1038/ismej.2014.17
  27. Mougel, C., Offre, P., Ranjard, L., Corberand, T., Gamalero, E., Robin, C., and Lemanceau, P. 2006. Dynamic of the genetic structure of bacterial and fungal communities at different developmental stages of Medicago truncatula Gaertn. Cv. Jemalong line J5. New Phytol. 170, 165-175. https://doi.org/10.1111/j.1469-8137.2006.01650.x
  28. Ofek, M., Hadar, Y., and Minz, D. 2012. Ecology of root colonizing Massilia (Oxalobacteraceae). PLoS One 7, e40117. https://doi.org/10.1371/journal.pone.0040117
  29. Philippot, L., Raaijmakers, J.M., Lemanceau, P., and van der Putten, W.H. 2013. Going back to the roots: The microbial ecology of the rhizosphere. Nat. Rev. Microbiol. 11, 789-799. https://doi.org/10.1038/nrmicro3109
  30. Prashar, P., Kapoor, N., and Sachdeva, S. 2014. Rhizosphere: its structure, bacterial diversity and significance. Rev. Environ. Sci. Biotechnol. 13, 63-77. https://doi.org/10.1007/s11157-013-9317-z
  31. Pruesse, E., Peplies, J., and Glockner, F.O. 2012. Sina: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28, 1823-1829. https://doi.org/10.1093/bioinformatics/bts252
  32. Quince, C., Lanzen, A., Davenport, R.J., and Turnbaugh, P.J. 2011. Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12, 38. https://doi.org/10.1186/1471-2105-12-38
  33. Raaijmakers, J., Paulitz, T., Steinberg, C., Alabouvette, C., and Moenne-Loccoz, Y. 2009. The rhizosphere: A playground and battlefield for soilborne pathogens and beneficial microorganisms. Plant Soil 321, 341-361. https://doi.org/10.1007/s11104-008-9568-6
  34. Rivas, R., Velazquez, E., Willems, A., Vizcaino, N., Subba-Rao, N.S., Mateos, P.F., Gillis, M., Dazzo, F.B., and Martinez-Molina, E. 2002. A new species of Devosia that forms a unique nitrogen-fixing root-nodule symbiosis with the aquatic legume Neptunia natans (L.f.) druce. Appl. Environ. Microbiol. 68, 5217-5222. https://doi.org/10.1128/AEM.68.11.5217-5222.2002
  35. Rousk, J., Baath, E., Brookes, P.C., Lauber, C.L., Lozupone, C., Caporaso, J.G., Knight, R., and Fierer, N. 2010. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 4, 1340-1351. https://doi.org/10.1038/ismej.2010.58
  36. Sakai, M., Hosoda, A., Ogura, K., and Ikenaga, M. 2014. The growth of Steroidobacter agariperforans sp. nov., a novel agardegrading bacterium isolated from soil, is enhanced by the diffusible metabolites produced by bacteria belonging to rhizobiales. Microb. Environ. 29, 89-95. https://doi.org/10.1264/jsme2.ME13169
  37. Schloss, P.D. and Handelsman, J. 2006. Toward a census of bacteria in soil. PLoS Comput Biol. 2, e92. https://doi.org/10.1371/journal.pcbi.0020092
  38. Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B., Lesniewski, R.A., Oakley, B.B., Parks, D.H., and Robinson, C.J. 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
  39. Schmutz, J., Cannon, S.B., Schlueter, J., Ma, J., Mitros, T., Nelson, W., Hyten, D.L., Song, Q., Thelen, J.J., Cheng, J., et al. 2010. Genome sequence of the palaeopolyploid soybean. Nature 463, 178-183. https://doi.org/10.1038/nature08670
  40. Shade, A. and Handelsman, J. 2012. Beyond the venn diagram: The hunt for a core microbiome. Environ. Microbiol. 14, 4-12. https://doi.org/10.1111/j.1462-2920.2011.02585.x
  41. Sohn, J.H., Kwon, K.K., Kang, J.H., Jung, H.B., and Kim, S.J. 2004. Novosphingobium pentaromativorans sp. nov., a high-molecularmass polycyclic aromatic hydrocarbon-degrading bacterium isolated from estuarine sediment. Int. J. Syst. Evol. Microbiol. 54, 1483-1487. https://doi.org/10.1099/ijs.0.02945-0
  42. Su, C., Lei, L., Duan, Y., Zhang, K.Q., and Yang, J. 2012. Culture-independent methods for studying environmental microorganisms: methods, application, and perspective. Appl. Microbiol. Biotechnol. 93, 993-1003. https://doi.org/10.1007/s00253-011-3800-7
  43. Sugiyama, A., Ueda, Y., Zushi, T., Takase, H., and Yazaki, K. 2014. Changes in the bacterial community of soybean rhizospheres during growth in the field. PLoS One 9, e100709. https://doi.org/10.1371/journal.pone.0100709
  44. Van Spanning, R., Delgado, M., and Richardson, D. 2005. The nitrogen cycle: Denitrification and its relationship to $N_2$ fixation, pp. 277-342. Nitrogen fixation in agriculture, forestry, ecology, and the environment, Springer.
  45. Ward, N.L., Challacombe, J.F., Janssen, P.H., Henrissat, B., Coutinho, P.M., Wu, M., Xie, G., Haft, D.H., Sait, M., and Badger, J. 2009. Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Appl. Environ. Microbiol. 75, 2046-2056. https://doi.org/10.1128/AEM.02294-08
  46. Xu, Y., Wang, G., Jin, J., Liu, J., Zhang, Q., and Liu, X. 2009. Bacterial communities in soybean rhizosphere in response to soil type, soybean genotype, and their growth stage. Soil Biol. Biochem. 41, 919-925. https://doi.org/10.1016/j.soilbio.2008.10.027
  47. Yousuf, B., Keshri, J., Mishra, A., and Jha, B. 2012. Application of targeted metagenomics to explore abundance and diversity of $CO_2$-fixing bacterial community using cbbL gene from the rhizosphere of Arachis hypogaea. Gene 506, 18-24. https://doi.org/10.1016/j.gene.2012.06.083

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