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) |
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 | 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 |
13 | 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 |
14 | 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 |
15 | 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 |
16 | 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 |
17 | 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 |
18 | 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 |
19 | 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 |
20 | 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 |
21 | 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 |
22 | 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 |
23 | 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 |
24 | Dini-Andreote, F. and Raaijmakers, J. M. 2018. Embracing community ecology in plant microbiome research. Trends Plant Sci. 23:467-469. DOI |
25 | 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 |
26 | 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 |
27 | 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 |
28 | 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 |
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 |