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http://dx.doi.org/10.5423/PPJ.OA.03.2018.0047

Taxonomic and Functional Changes of Bacterial Communities in the Rhizosphere of Kimchi Cabbage After Seed Bacterization with Proteus vulgaris JBLS202  

Bhattacharyya, Dipto (Division of Biotechnology, Chonbuk National University)
Duta, Swarnalee (Division of Biotechnology, Chonbuk National University)
Yu, Sang-Mi (Freshwater Bioresources Utilization Division, Nakdonggang National Institute of Biological Resources)
Jeong, Sang Chul (Freshwater Bioresources Utilization Division, Nakdonggang National Institute of Biological Resources)
Lee, Yong Hoon (Division of Biotechnology, Chonbuk National University)
Publication Information
The Plant Pathology Journal / v.34, no.4, 2018 , pp. 286-296 More about this Journal
Abstract
Maintenance of a beneficial microbial community, especially in the rhizosphere, is indispensable for plant growth and agricultural sustainability. In this sense, plant growth-promoting rhizobacteria (PGPR) have been extensively studied for their role in plant growth promotion and disease resistance. However, the impact of introducing PGPR strains into rhizosphere microbial communities is still underexplored. We previously found that the Proteus vulgaris JBLS202 strain (JBLS202) promoted growth of Kimchi cabbage and altered the relative abundance of total bacteria and Pseudomonas spp. in the treated rhizosphere. To extend these findings, we used pyrosequencing to analyze the changes in bacterial communities in the rhizosphere of Kimchi cabbage after introduction of JBLS202. The alterations were also evaluated by taxon-specific realtime PCR (qPCR). The pyrosequencing data revealed an increase in total bacteria abundance, including specific groups such as Proteobacteria, Acidobacteria, and Actinobacteria, in the treated rhizosphere. Time-course qPCR analysis confirmed the increase in the abundance of Acidobacteria, Actinobacteria, Alphaproteobacteria, and Betaproteobacteria. Furthermore, genes involved in nitrogen cycling were upregulated by JBLS202 treatment indicating changes in ecological function of the rhizosphere soil. Overall, these results indicate that introduction of JBLS202 alters both the composition and function of the rhizosphere bacterial community, which can have direct and indirect effects on plant growth. Therefore, we propose that long-term changes in bacterial composition and community-level function need to be considered for practical use of PGPRs.
Keywords
microbiome; PGPR; pyrosequencing; rhizosphere;
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1 Burgmann, H., Meier, S., Bunge, M., Widmer, F. and Zeyer, J. 2005. Effects of model root exudates on structure and activity of a soil diazotroph community. Environ. Microbiol. 7:1711-1724.   DOI
2 Chowdhury, S. P., Dietel, K., Rändler, M., Schmid, M., Junge, H., Borriss, R., Hartmann, A. and Grosch, R. 2013. Effects of Bacillus amyloliquefaciens FZB42 on lettuce growth and health under pathogen pressure and its impact on the rhizosphere bacterial community. PloS One 8:e68818.   DOI
3 Chun, J. and Goodfellow, M. 1995. A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int. J. Syst. Bacteriol. 45:240-245.   DOI
4 Chun, J., Lee, J. H., Jung, Y., Kim, M., Kim, S., Kim, B. K. and Lim, Y. W. 2007. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int. J. Syst. Evol. Microbiol. 57:2259-2261.   DOI
5 Dutta, S. and Podile, A. R. 2010. Plant growth promoting rhizobacteria (PGPR): Bugs to debug the root zone. Crit. Rev. Microbiol. 36:232-244.   DOI
6 Dutta, S., Rani, T. S. and Podile, A. R. 2013. Root exudate-induced alterations in Bacillus cereus cell wall contribute to root colonization and plant growth promotion. Plos One 8:e78369.   DOI
7 Eddy, S. R. 2011. Accelerated profile HMM Searches. PLoS Comput. Biol. 7:e1002195.   DOI
8 Glick, B. R., Todorovic, B., Czarny, J., Cheng, Z., Duan, J. and McConkey, B. 2007. Promotion of plant growth by bacterial ACC deaminase. Crit. Rev. Plant Sci. 26:227-242.   DOI
9 Hai, B., Diallo, N. H., Sall, S., Haesler, F., Schauss, K., Bonzi, M., Assigbetse, K., Chotte, J. L., Munch, J. C. and Schloter, M. 2009. Quantifcation of key genes steering the microbial nitrogen cycle in the rhizosphere of sorghum cultivars in tropical agroecosystems. Appl. Environ. Microbiol. 75:4993-5000.   DOI
10 Heck, K. L. Jr., Van Belle, G. and Simberloff, D. 1975. Explicit calculation of the rarefaction diversity measurement and the determination of sufficient sample size. Ecology 56:1459-1461.   DOI
11 Hirsch, P. R., Mauchline, T. H. and Clark, I. M. 2010. Culture-independent molecular techniques for soil microbial ecology. Soil Biol. Biochem. 42:878-887.   DOI
12 Hou, J., Liu, W., Wang, B., Wang, Q., Luo, Y. and Franks, A. E. 2015. PGPR enhanced phytoremediation of petroleum contaminated soil and rhizosphere microbial community response. Chemosphere 138:592-598.   DOI
13 Huang, X. F., Chaparro, J. M., Reardon, K. F., Zhang, R., Shen, Q. and Vivanco, J. M. 2014. Rhizosphere interactions: root exudates, microbes, and microbial communities. Botany 92:267-275.   DOI
14 Kamilova, F., Kravchenko, L. V., Shaposhnikov, A. I., Azarova, T., Makarova, N. and Lugtenberg, B. 2006. Organic acids, sugars, and L-tryptophane in exudates of vegetables growing on stonewool and their effects on activities of rhizosphere bacteria. Mol. Plant-Microbe Interact. 19:250-256.   DOI
15 LaSala, P. R., Segal, J., Han Faye, S., Tarrand Jeffrey, J. and Han Xiang, Y. 2007. First reported infections caused by three newly described genera in the family Xanthomonadaceae. J. Clin. Microbiol. 45:641-644.   DOI
16 Kang, Y., Shen, M., Wang, H. and Zhao, Q. 2013. A possible mechanism of action of plant growth promoting rhizobacteria (PGPR) strain Bacillus pumilus WP8 via regulation of soil bacterial community structure. J. Gen. Appl. Microbiol. 59:267-277.   DOI
17 Kim, M., Yoon, H., Kim, Y. E., Kim, Y. J., Kong, W. S. and Kim, J. G. 2014. Comparative analysis of bacterial diversity and communities inhabiting the fairy ring of Tricholoma matsutake by barcoded pyrosequencing. J. Appl. Microbiol. 117:699-710.   DOI
18 Kim, O. S., Cho, Y. J., Lee, K., Yoon, S. H., Kim, M., Na, H., Park, S. C., Jeon, Y. S., Lee, J. H., Yi, H., Won, S. and Chun, J. 2012. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultures species. Int. J. Syst. Evol. Microbiol. 62:716-721.   DOI
19 Kozdroj, J. 2008. Microbial community in the rhizosphere of young maize seedlings is susceptible to the impact of introduced pseudomonads as indicated by FAME analysis. J. Gen. Appl. Microbiol. 54:205-210.   DOI
20 Kwon, S., Kim, T. S., Yu, G. H., Jung, J. H. and Park, H. D. 2010. Bacterial community composition and diversity of a full-scale integrated fxed-flm activated sludge system as investigated by pyrosequencing. J. Microbiol. Biotechnol. 20:1717-1723.
21 Li, W. Z. and Godzik, A. 2006. Cd-hit: a fast program for clustering and comparing large setsof protein or nucleotide sequences. Bioinformatics 22:1658-1659.   DOI
22 Mendes, R., Kruijt, M., de Bruijn, I., Dekkers, E., van der Voort, M., Schneider, J. H., Piceno, Y. M., DeSantis, T. Z., Anderson, G. L., Bakker, P. A. and Raaijmakers, J. M. 2011. Deciphering the rhizosphere microbiome. Science 332:1097-1100.   DOI
23 Liu, D., Liu, Y., Fang, S. and Tian, Y. 2015. Tree species composition influenced microbial diversity and nitrogen availability in rhizosphere soil. Plant Soil Environ. 61:438-443.
24 Lo, C. C. 2010. Effect of pesticides on soil microbial community. J. Environ. Sci. Health B 45:348-359.
25 Lugtenberg, B. and Kamilova, F. 2009. Plant-growth promoting rhizobacteria. Annu. Rev. Microbiol. 63:541-556.   DOI
26 Myers, E. W. and Miller, W. 1988. Optimal alignments in linear space. Comput. Appl. Biosci. 4:11-17.
27 Nannipieri, P., Ascher, J., Ceccherini, M. T., Landi, L., Pietramellara, G. and Renella, G. 2003. Microbial diversity and soil functions. Eur. J. Soil Sci. 54:655-670.   DOI
28 Sanguin, H., Sarniguet, A., Gazengel, K., Moenne-Loccoz, Y. and Grundmann, G. 2009. Rhizosphere bacterial communities associated with disease suppressiveness stages of take-all decline in wheat monoculture. New Phytol. 184:694-707.   DOI
29 Piromyou, P., Buranabanyat, B., Tantasawat, P., Tittabutr, P., Boonkerd, N. and Teaumroong, N. 2011. Effect of plant growth promoting rhizobacteria (PGPR) inoculation on microbial community structure in rhizosphere of forage corn cultivated in Thailand. Eur. J. Soil. Biol. 47:44-54.   DOI
30 Qiu, M., Zhang, R., Xue, C., Zhang, S., Li, S., Zhang, N. and Shen, Q. 2012. Application of a novel bio-organic fertilizer can control Fusarium wilt by regulating the microbial community of cucumber rhizosphere soils. Biol. Fert. Soils 48:807-816.   DOI
31 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., Robinson, C. J., Sahl, J. W., Stres, B., Thallinger, G. G., Van Horn, D. J. and Weber, C. F. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75:7537-7541.   DOI
32 Shen, Z., Ruan, Y., Chao, X., Zhang, J., Li, R. and Shen, Q. 2015. Rhizosphere microbial community manipulated by 2 years of consecutive biofertilizer application associated with banana Fusarium wilt disease suppression. Biol. Fert. Soils 51:553-562.   DOI
33 Somers, E., Vanderleyden, J. and Srinivasan, M. 2004. Rhizosphere bacterial signalling: a love parade beneath our feet. Crit. Rev. Microbiol. 30:205-240.   DOI
34 Sugiyama, A., Ueda, Y., Zushi, T., Takase, H. and Yazaki, K. 2014. Changes in the bacterial community of soybean rhizospheres during growth in the feld. PLoS One 9:e100709.   DOI
35 Trivedi, P., He, Z., Van Nostrand, J. D., Albrigo, G., Zhou, J. and Wang, N. 2012. Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere. ISME J. 6:363-383.   DOI
36 Trabelsi, D. and Mhamdi, R. 2013. Microbial inoculants and their impact on soil microbial communities: A review. Biomed. Res. Int. 2013:863240.
37 Bais, H. P., Broeckling, C. D. and Vivanco, J. M. 2008. Root exudates modulate plant-microbe interactions in the rhizosphere. In: Soil Biol., ed. by P. Karlovsky, pp. 241-252. Springer, Berlin, Germany.
38 Bending, G. D., Rodriguez-Cruz, M. S. and Lincoln, S. D. 2007. Fungicide impacts on microbial communities in soils with contrasting management histories. Chemosphere 69:82-88.   DOI
39 Bhattacharyya, D. and Lee, Y. H. 2016. The bacterial community in the rhizosphere of Kimchi cabbage restructured by volatile compounds emitted from rhizobacterium Proteus vulgaris JBLS202. Appl. Soil Ecol. 105:48-56.   DOI
40 Bhattacharyya, D., Garladinne, M. and Lee, Y. H. 2015. Volatile indole produced by rhizobacterium Proteus vulgaris JBLS202 stimulates growth of Arabidopsis thaliana through auxin, cytokinin, and brassinosteroid pathways. J. Plant. Growth. Regul. 34:158-168.   DOI
41 Unno, T., Jang, J., Han, D., Kim, J. H., Sadowsky, M. J., Kim, O. S., Chun, J. and Hur, H. G. 2010. Use of barcoded pyrosequencing and shared OTUs to determine sources of fecal bacteria in watersheds. Environ. Sci. Technol. 44:7777-7782.   DOI
42 Wang, F., Liang, Y., Jiang, Y., Yang, Y., Xue, K., Xiong, J., Zhou, J. and Sun, B. 2015. Planting increases the abundance and structure complexity of soil core functional genes relevant to carbon and nitrogen cycling. Sci. Rep. 5:14345.   DOI
43 Yu, S. M. and Lee, Y. H. 2013. Plant growth promoting rhizobacterium Proteus vulgaris JBLS202 stimulates the seedling growth of Chinese cabbage through indole emission. Plant Soil 370:485-495.   DOI
44 Zinger, L., Shanhavaz, B., Baptist, F., Geremia, R. A. and Choler, P. 2009. Microbial diversity in alpine tundra soils correlates with snow cover dynamics. ISME J. 3:850-859.   DOI
45 Bulgarelli, D., Schlaeppi, K., Spaepen, S., van Themaat, E. V. L. and Schulze-Lefert, P. 2013. Structure and functions of the bacterial microbiota of plants. Annu. Rev. Plant Biol. 64:807-838.   DOI