DOI QR코드

DOI QR Code

Comparison of Microbial Community of Rhizosphere and Endosphere in Kiwifruit

  • Kim, Min-Jung (Department of Plant Medicine and Institute of Agriculture & Life Science, Gyeongsang National University) ;
  • Do, Heeil (Division of Applied Life Science and Research Institute of Life Science, Gyeongsang National University) ;
  • Cho, Gyeongjun (Division of Applied Life Science and Research Institute of Life Science, Gyeongsang National University) ;
  • Jeong, Rae-Dong (Department of Applied Biology, Chonnam National University) ;
  • Kwak, Youn-Sig (Department of Plant Medicine and Institute of Agriculture & Life Science, Gyeongsang National University)
  • Received : 2019.08.06
  • Accepted : 2019.09.08
  • Published : 2019.12.01

Abstract

Understanding the microbial community and function are crucial knowledge for crop management. In this study, bacterial and fungal community structures both rhizosphere and endosphere in kiwifruit were analyzed to gain our knowledge in kiwifruit microbiome. Microbial community in rhizosphere was less variation than endosphere community. Functional prediction results demonstrated that abundance of saprotrophic fungi was similar in both rhizosphere and endosphere, but potential pathogenic fungi was more abundance in endosphere than in rhizosphere. This finding suggested that maintain healthy soil is the first priority to protect the host plant against biotic stresses.

Keywords

References

  1. Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A. and Holmes, S. P. 2016. DADA2: highresolution sample inference from Illumina amplicon data. Nat. Methods 13:581-583. https://doi.org/10.1038/nmeth.3869
  2. Chen, Q., Jiang, J. R., Zhang, G. Z., Cai, L. and Crous, P. W. 2015. Resolving the Phoma enigma. Stud. Mycol. 82:137-217. https://doi.org/10.1016/j.simyco.2015.10.003
  3. Chi, F., Shen, S.-H., Cheng, H.-P., Jing, Y.-X., Yanni, Y. G. and Dazzo, F. B. 2005. Ascending migration of endophytic rhizobia, from roots to leaves, inside rice plants and assessment of benefits to rice growth physiology. Appl. Environ. Microbiol. 71:7271-7278. https://doi.org/10.1128/AEM.71.11.7271-7278.2005
  4. Cho, G., Kim, M.-J., Kwon, Y. and Kwak, Y.-S. 2018. Comparison of endophytic microbial community in kiwifruit plant cultivars. Plant Pathol. J. 34:341-346. https://doi.org/10.5423/PPJ.NT.12.2017.0284
  5. Coleman-Derr, D., Desgarennes, D., Fonseca-Garcia, C., Gross, S., Clingenpeel, S., Woyke, T., North, G., Visel, A., Partida-Martinez, L. P. and Tringe, S. G. 2015. Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species. New Phytol. 209:798-811. https://doi.org/10.1111/nph.13697
  6. Cregger, M. A., Veach, A. M., Yang, Z. K., Crouch, M. J., Vilgalys, R., Tuskan, G. A. and Schadt, C. W. 2018. The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome. Microbiome 6:31. https://doi.org/10.1186/s40168-018-0413-8
  7. Daniel, R. 2005. The metagenomics of soil. Nat. Rev. Microbiol. 3:470-478. https://doi.org/10.1038/nrmicro1160
  8. Garrido, L. M., Alves, J. M. P., Oliveria, L. S., Gruber, A., Padilla, G. and Araujo, W. L. 2016. Draft genome sequence of Curtobacterium sp. strains ER1/6, and endophytic strain isolated from Citrus sinensis with potential to be used as a biocontrol agent. Genome Announc. 4:e01264-16.
  9. Hulikere, M. M., Joshi, C. G., Danagoudar, A., Poyya, J., Kudva, A. K. and Dhanajaya, B. L. 2017. Biogenic synthesis of gold nanoparticles by marine endophytic fungus-Cladosporium cladosporioides isolated from seaweed and evaluation of their antioxidant and antimicrobial properties. Process Biochem. 63:137-144. https://doi.org/10.1016/j.procbio.2017.09.008
  10. Khan, A. L., Waqas, M., Kang, S.-M., Al-Harrasi, A., Hussain, J., Al-Rawahi, A., Al-Khiziri, S., Ullah, I., Ali, L., Jung, H.-Y. and Lee, I.-J. 2014. Bacterial endophyte Sphingomonas sp. LK11 produces gibberellins and IAA and promotes tomato plant growth. J. Microbiol. 52:689-695. https://doi.org/10.1007/s12275-014-4002-7
  11. Koljalg, U., Nilsson, R. H., Abarenkov, K., Tedersoo, L., Taylor, A. F. S., Bahram, M., Bates, S. T., Bruns, T. D., Bengtsson-Palme, J., Callaghan, T. M., Douglas, B., Drenkhan, T., Eberhardt, U., Duenas, M., Grebenc, T., Griffith, G. W., Hartmann, M., Kirk, P. M., Kohout, P., Larsson, E., Lindahl, B. D., Lucking, R., Martin, M. P., Matheny, P. B., Nguyen, N. H., Niskanen, T., Oja, J., Peay, K. G., Peintner, U., Peterson, M., Poldmaa, K., Saag, L., Saar, I., Schussler, A., Scott, J. A., Senes, C., Smith, M. E., Suija, A., Taylor, D. L., Telleria, M. T., Weiss, M. and Larsson, K. H. 2013. Towards a unified paradigm for sequence-based identification of fungi. Mol. Ecol. 22:5271-5277. https://doi.org/10.1111/mec.12481
  12. Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., Clemente, J. C., Burkepile, D. E., Vega Thurber, R. L., Knight, R., Beiko, R. G. and Huttenhower, C. 2013. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat. Biotechnol. 31:814-821. https://doi.org/10.1038/nbt.2676
  13. Love, M. I., Huber, W. and Anders, S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15:550. https://doi.org/10.1186/s13059-014-0550-8
  14. Lumactud, R., Shen, S. Y., Lau, M. and Fulthorpe, R. 2016. Bacterial endophytes isolated from plants in natural oil seep soils with chronic hydrocarbon contamination. Front. Microbiol. 7:755.
  15. McMurdie, P. J. and Holmes, S. 2013. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8:e61217. https://doi.org/10.1371/journal.pone.0061217
  16. Miao, L.-Y., Mo, X.-C., Xi, X.-Y., Zhou, L., De, G., Ke, Y.-S., Liu, P., Song, F.-J., Jin, W.-W. and Zhang, P. 2018. Transcriptome analysis of a taxol-producing endophytic fungus Cladosporium cladosporioides MD2. AMB Expr. 8:21. https://doi.org/10.1186/s13568-018-0555-x
  17. Miao, Y.-Y., Shi, S.-L., Zhang, J.-G. and Mohamad, O. A. 2017. Migration, colonization and seedling growth of rhizobia with matrine treatment in alfalfa (Medicago sativa L.). Acta Agric. Scand. B. Soil Plant Sci. 68:26-38.
  18. Miliute, I., Buzaite, O., Baniulis, D. and Stanys, V. 2015. Bacterial endophytes in agricultural crops and their role in stress tolerance: a review. Zemdirbyste 102:465-478. https://doi.org/10.13080/z-a.2015.102.060
  19. Montel, E., Bridge, P. D. and Sutton, B. C. 1991. An integrated approach to Phoma systematics. Mycopathologia 115:89-103. https://doi.org/10.1007/BF00436797
  20. Nguyen, N. H., Song, Z., Bates, S. T., Branco, S., Tedersoo, L., Menke, J., Schilling J. S. and Kennedy, P. G. 2016. FUNGuild: an open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecol. 20:241-248. https://doi.org/10.1016/j.funeco.2015.06.006
  21. Qin, Y., Pan, X. and Yuan, Z. 2016. Seed endophytic microbiota in a coastal plant and phytobeneficial properties of the fungus Cladosporium cladosporioides. Fungal Ecol. 24:53-60. https://doi.org/10.1016/j.funeco.2016.08.011
  22. Ottesen, A. R., Pena, A. G., White, J. R., Pettengill, J. B., Li, C., Allard, S., Rideout, S., Allard, M., Hill, T., Evans, P., Strain, E., Musser, S., Knight, R. and Brown, E. 2013. Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato). BMC Microbiol. 13:114. https://doi.org/10.1186/1471-2180-13-114
  23. Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J. and Glockner, F. O. 2012. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41:D590-D596. https://doi.org/10.1093/nar/gks1219
  24. Quiza, L., St-Arnaud, M. and Yergeau, E. 2015. Harnessing phytomicrobiome signaling for rhizosphere microbiome engineering. Front. Plant Sci. 6:507.
  25. Rodriguez, R. J., White, J. F. Jr., Arnold, A. E. and Redman, R. S. 2008. Fungal endophytes: diversity and functional roles. New Phytol. 182:314-330. https://doi.org/10.1111/j.1469-8137.2009.02773.x
  26. Santoyo, G., Moreno-Hagelsieb, G., del Carmen Orozco-Mosqueda, M. and Glick, B. R. 2016. Plant growth-promoting bacterial endophytes. Microbiol. Res. 183:92-99. https://doi.org/10.1016/j.micres.2015.11.008
  27. Torres, D. E., Rojas-Martinez, R. I., Zavaleta-Mejia, E., Guevara-Fefer, P., Marquez-Guzman, G. J. and Perez-Martinez, C. 2017. Cladosporium cladosporioides and Cladosporium pseudocladosporioides as potential new fungal antagonists of Puccinia horiana Henn., the causal agent of chrysanthemum white rust. PLoS ONE 12:e0170782. https://doi.org/10.1371/journal.pone.0170782
  28. Vandenkoornhuyse, P., Quaiser, A., Duhamel, M., Le Van, A. and Dufresne, A. 2015. The importance of the microbiome of the plant holobiont. New Phytol. 206:1196-1206. https://doi.org/10.1111/nph.13312
  29. Wickham, H. 2016. ggplot2: elegant graphics for data analysis. 2nd ed. Springer International Publishing, Cham, Switzerland. 260 pp.