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http://dx.doi.org/10.5423/PPJ.OA.05.2022.0067

Microbiota Communities of Healthy and Bacterial Pustule Diseased Soybean  

Kim, Da-Ran (Resarch Institute of Life Science, Gyeongsang National University)
Kim, Su-Hyeon (Division of Applied Life Science (BK21Plus), Gyeongsang National University)
Lee, Su In (Division of Applied Life Science (BK21Plus), Gyeongsang National University)
Kwak, Youn-Sig (Resarch Institute of Life Science, Gyeongsang National University)
Publication Information
The Plant Pathology Journal / v.38, no.4, 2022 , pp. 372-382 More about this Journal
Abstract
Soybean is an important source of protein and for a wide range of agricultural, food, and industrial applications. Soybean is being affected by Xanthomonas citri pv. glycines, a causal pathogen of bacterial pustule disease, result in a reduction in yield and quality. Diverse microbial communities of plants are involved in various plant stresses is known. Therefore, we designed to investigate the microbial community differentiation depending on the infection of X. citri pv. glycines. The microbial community's abundance, diversity, and similarity showed a difference between infected and non-infected soybean. Microbiota community analysis, excluding X. citri pv. glycines, revealed that Pseudomonas spp. would increase the population of the infected soybean. Results of DESeq analyses suggested that energy metabolism, secondary metabolite, and TCA cycle metabolism were actively diverse in the non-infected soybeans. Additionally, Streptomyces bacillaris S8, an endophyte microbiota member, was nominated as a key microbe in the healthy soybeans. Genome analysis of S. bacillaris S8 presented that salinomycin may be the critical antibacterial metabolite. Our findings on the composition of soybean microbiota communities and the key strain information will contribute to developing biological control strategies against X. citri pv. glycines.
Keywords
biotic stress; microbial community; Streptomyces; Xanthomonas citri pv. glycines;
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1 Yoon, S.-H., Ha, S.-M., Kwon, S., Lim, J., Kim, Y., Seo, H. and Chun, J. 2017. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int. J. Syst. Evol. Microbiol. 67:1613-1617.   DOI
2 Xiong, C., Singh, B. K., He, J.-Z., Han, Y.-L., Li, P.-P., Wan, L.-H., Meng, G.-Z., Liu, S.-Y., Wang, J.-T., Wu, C.-F., Ge, A.-H. and Zhang, L.-M. 2021. Plant developmental stage drives the differentiation in ecological role of the maize microbiome. Microbiome 9:171.   DOI
3 Blin, K., Shaw, S., Kloosterman, A. M., Charlop-Powers, Z., van Wezel, G. P., Medema, M. H. and Weber, T. 2021. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res. 49:W29-W35.   DOI
4 Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A. and Holmes, S. P. 2016. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13:581-583.   DOI
5 Colombo, E. M., Kunova, A., Pizzatti, C., Saracchi, M., Cortesi, P. and Pasquali, M. 2019. Selection of an endophytic Streptomyces sp. strain DEF09 from wheat roots as a biocontrol agent against Fusarium graminearum. Front. Microbiol. 10:2356.   DOI
6 Hwang, H.-H., Chien, P.-R., Huang, F.-C., Hung, S.-H., Kuo, C.-H., Deng, W.-L., Chiang, E.-P. I. and Huang, C.-C. 2021. A plant endophytic bacterium, Burkholderia seminalis strain 869T2, promotes plant growth in Arabidopsis, Pak Choi, Chinese Amaranth, Lettuces, and other vegetables. Microorganisms 9:1703.   DOI
7 Dang, H., Zhang, T., Li, G., Mu, Y., Lv, X., Wang, Z. and Zhuang, L. 2020. Root-associated endophytic bacterial community composition and structure of three medicinal licorices and their changes with the growing year. BMC Microbiol. 20:291.   DOI
8 Deng, S., Caddell, D. F., Xu., G., Dahlen, L., Washington, L., Yang, J. and Coleman-Derr, D. 2021. Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome. ISME J. 15:3181-3194.   DOI
9 Dewangan, J., Srivastava, S. and Rath, S. K. 2017. Salinomycin: a new paradigm in cancer therapy. Tumour Biol. 39:1010428317695035.
10 Bintarti, A. F., Sulesky-Grieb, A., Stopnisek, N. and Shade, A. 2022. Endophytic microbiome variation among single plant seeds. Phytobiomes J. 6:45-55.   DOI
11 Jeon, C.-W., Kim, D.-R. and Kwak, Y.-S. 2019. Valinomycin, produced by Streptomyces sp. S8, a key antifungal metabolite in large patch disease suppressiveness. World J. Microbiol. Biotechnol. 35:128.   DOI
12 Dong, L., Cheng, R., Xiao, L., Wei, F., Wei, G., Xu, J., Wang, Y., Guo, X., Chen, Z. and Chen, S. 2018. Diversity and composition of bacterial endophytes among plant parts of Panax notoginseng. Chin. Med. 13:41.   DOI
13 Han, Q., Ma, Q., Chen, Y., Tian, B., Xu, L., Bai, Y., Chen, W. and Li, X. 2020. Variation in rhizosphere microbial communities and its association with the symbiotic efficiency of rhizobia in soybean. ISME J. 14:1915-1928.   DOI
14 Xu, T., Cao, L., Zeng, J., Franco, C. M. M., Yang, Y., Hu, X., Liu, Y., Wang, X., Gao, Y., Bu, Z., Shi, L., Zhou, G., Zhou, Q., Liu, X. and Zhu, Y. 2019a. The antifungal action mode of the rice endophyte Streptomyces hygroscopicus OsiSh-2 as a potential biocontrol agent against the rice blast pathogen. Pestic. Biochem. Physiol. 160:58-69.   DOI
15 Kim, D.-R., Cho, G., Jeon, C.-W., Weller, D. M., Thomashow, L. S., Paulitz, T. C. and Kwak, Y.-S. 2019a. A mutualistic interaction between Streptomyces bacteria, strawberry plants and pollinating bees. Nat. Commun. 10:4802.   DOI
16 Kim, M.-J., Chae, D.-H., Cho, G., Kim, D.-R. and Kwak, Y.-S. 2019b. Characterization of antibacterial strains against kiwifruit bacterial canker pathogen. Plant Pathol. J. 35:473-485.   DOI
17 Mingma, R., Pathom-aree, W., Trakulnaleamsai, S., Thamchaipenet, A. and Duangmal, K. 2014. Isolation of rhizospheric and roots endophytic actinomycetes from Leguminosae plant and their activities to inhibit soybean pathogen, Xanthomonas campestris pv. glycine. World J. Microbiol. Biotechnol. 30:271-280.   DOI
18 de Almeida Lopes, K. B., Carpentieri-Pipolo, V., Oro, T. H., Stefani Pagliosa, E. and Degrassi, G. 2016. Culturable endophytic bacterial communities associated with field-grown soybean. J. Appl. Microbiol. 120:740-755.   DOI
19 Dini-Andreote, F. and Raaijmakers, J. M. 2018. Embracing community ecology in plant microbiome research. Trends Plant Sci. 23:467-469.   DOI
20 Hannula, S. E., Zhu, F., Heinen, R. and Bezemer, T. M. 2019. Foliar-feeding insects acquire microbiomes from the soil rather than the host plant. Nat. Commun. 10:1254.   DOI
21 Kang, I.-J., Kim, K. S., Beattie, G. A., Chung, H., Heu, S. and Hwang, I. 2021. Characterization of Xanthomonas citri pv. glycines population genetics and virulence in a national survey of bacterial pustule disease in Korea. Plant Pathol. J. 37:652-661.   DOI
22 Kruskal, W. H. and Wallis, W. A. 1952. Use of ranks in one-criterion variance analysis. J. Am. Stat. Assoc. 47.260:583-621.   DOI
23 Kim, D.-R., Jeon, C.-W., Cho, G., Thomashow, L. S., Weller, D. M., Paik, M.-J., Lee, Y. B. and Kwak, Y.-S. 2021a. Glutamic acid reshapes the plant microbiota to protect plants against pathogens. Microbiome 9:244.   DOI
24 Kim, D.-R. and Kwak, Y.-S. 2021. A genome-wide analysis of antibiotic producing genes in Streptomyces globisporus SP6C4. Plant Pathol. J. 37:389-395.   DOI
25 Orozco-Mosqueda, M. D. C. and Santoyo, G. 2021. Plant-microbial endophytes interactions: scrutinizing their beneficial mechanisms from genomic explorations. Curr. Plant Biol. 25:100189.   DOI
26 Jagermeyr, J., Robock, A., Elliott, J., Muller, C., Xia, L., Khabarov, N., Folberth, C., Schmid, E., Liu, W., Zabel, F., Rabin, S. S., Puma, M. J., Heslin, A., Franke, J., Foster, I., Asseng, S., Bardeen, C. G., Toon, O. B. and Rosenzweig, C. 2020. A regional nuclear conflict would compromise global food security. Proc. Natl. Acad. Sci. U. S. A. 117:7071-7081.   DOI
27 Longley, R., Noel, Z. A., Benucci, G. M. N., Chilvers, M. I., Trail, F. and Bonito, G. 2020. Crop management impacts the soybean (Glycine max) microbiome. Front. Microbiol. 11:1116.   DOI
28 Lu, T., Ke, M., Lavoie, M., Jin, Y., Fan, X., Zhang, Z., Fu, Z., Sun, L., Gillings, M., Penuelas, J., Qian, H. and Zhu, Y.-G. 2018. Rhizosphere microorganisms can influence the timing of plant flowering. Microbiome 6:231.   DOI
29 Chen, S., Chen, X. and Xu, J. 2016. Impacts of climate change on agriculture: evidence from China. J. Environ. Econ. Manage. 76:105-124.   DOI
30 Kim, S.-H., Cho, G., Lee, S. I., Kim, D.-R. and Kwak, Y.-S. 2021b. Comparison of bacterial community of healthy and Erwinia amylovora infected apples. Plant Pathol. J. 37:396-403.   DOI
31 Lau, J. A., Lennon, J. T. and Heath, K. D. 2017. Trees harness the power of microbes to survive climate change. Proc. Natl. Acad. Sci. U. S. A. 114:11009-11011.   DOI
32 Lopez-Velasco, G., Carder, P. A., Welbaum, G. E. and Ponder, M. A. 2013. Diversity of the spinach (Spinacia oleracea) spermosphere and phyllosphere bacterial communities. FEMS Microbiol. Lett. 346:146-154.   DOI
33 Lundberg, D. S., Yourstone, S., Mieczkowski, P., Jones, C. D. and Dangl, J. L. 2013. Practical innovations for high-throughput amplicon sequencing. Nat. Methods 10:999-1002.   DOI
34 Murali, A., Bhargava, A. and Wright, E. S. 2018. IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences. Microbiome 6:140.   DOI
35 Villalobos, J. A., Yi, B. R. and Wallace, I. S. 2015. 2-Fluoro-Lfucose is a metabolically incorporated inhibitor of plant cell wall polysaccharide fucosylation. PLoS ONE 10:e0139091.   DOI
36 Park, D. S., Kim, J. S., Han. C. H., Ko, S. J. and Kim, H. K. 2007. (Korea) The primer set for sensitive and specific detection of Xanthomonas axonopodis pv. glycines by polymerase chain reaction. KB101834763B1. 9 May 2007.
37 Reverchon, F. and Mendez-Bravo, A. 2021. Plant-mediated above-belowground interactions: a phytobiome story. In: Plant-animal interactions: source of biodiversity, eds. by K. Del-Claro and H. M. Torezan-Sillingardi, pp. 205-231. Springer, Cham, Switzerland.
38 Jeong, N., Kim, K.-S., Jeong, S., Kim, J.-Y., Park, S.-K., Lee, J. S., Jeong, S.-C., Kang, S.-T., Ha, B.-K., Kim, D.-Y., Kim, N., Moon, J.-K. and Choi, M. S. 2019. Korean soybean core collection: genotypic and phenotypic diversity population structure and genome-wide association study. PLoS ONE 14:e0224074.   DOI
39 Simonin, M., Briand, M., Chesneau, G., Rochefort, A., Marais, C., Sarniguet, A. and Barret, M. 2022. Seed microbiota revealed by a large-scale meta-analysis including 50 plant species. New Phytol. 234:1448-1463.   DOI
40 Teeling, H. and Glockner, F. O. 2012. Current opportunities and challenges in microbial metagenome analysis: a bioinformatic perspective. Brief Bioinform. 13:728-742.   DOI
41 Aziz, R. K., Bartels, D., Best, A. A., DeJongh, M., Disz, T., Edwards, R. A., Formsma, K., Gerdes, S., Glass, E. M., Kubal, M., Meyer, F., Olsen, G. J., Olson, R., Osterman, A. L., Overbeek, R. A., McNeil, L. K., Paarmann, D., Paczian, T., Parrello, B., Pusch, G. D., Reich, C., Stevens, R., Vassieva, O., Vonstein, V., Wilke, A. and Zagnitko, O. 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75.   DOI
42 Rodriguez, R. and Duran, P. 2020. Natural holobiome engineering by using native extreme microbiome to counteract the climate change effects. Front. Bioeng. Biotechnol. 8:568.   DOI
43 Teheran-Sierra, L. G., Funnicelli, M. I. G., de Carvalho, L. A. L., Ferro, M. I. T., Soares, M. A. and Pinheiro, D. G. 2021. Bacterial communities associated with sugarcane under different agricultural management exhibit a diversity of plant growth-promoting traits and evidence of synergistic effect. Microbiol. Res. 247:126729.   DOI
44 Wilson, K. 2001. Preparation of genomic DNA from bacteria. Curr. Protoc. Mol. Biol. 56:2.4.   DOI
45 Xu, Y., Ge, Y., Song, J. and Rensing, C. 2019b. Assembly of root-associated microbial community of typical rice cultivars in different soil types. Biol. Fertil. Soils 56:249-260.   DOI
46 Ikeda, S., Rallos, L. E. E., Okubo, T., Eda, S., Inaba, S., Mitsui, H. and Minamisawa, K. 2008. Microbial community analysis of field-grown soybeans with different nodulation phenotypes. Appl. Environ. Microbiol. 74:5704-5709.   DOI