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Genomic and Functional Characterization of the Endophytic Bacillus subtilis 7PJ-16 Strain, a Potential Biocontrol Agent of Mulberry Fruit Sclerotiniose

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Abstract

Bacillus sp. 7PJ-16, an endophytic bacterium isolated from a healthy mulberry stem and previously identified as Bacillus tequilensis 7PJ-16, exhibits strong antifungal activity and has the capacity to promote plant growth. This strain was studied for its effectiveness as a biocontrol agent to reduce mulberry fruit sclerotiniose in the field and as a growth-promoting agent for mulberry in the greenhouse. In field studies, the cell suspension and supernatant of strain 7PJ-16 exhibited biocontrol efficacy and the lowest disease incidence was reduced down to only 0.80%. In greenhouse experiments, the cell suspension (1.0 × 106 and 1.0 × 105 CFU/mL) and the cell-free supernatant (100-fold and 1000-fold dilution) stimulated mulberry seed germination and promoted mulberry seedling growth. In addition, to accurately identify the 7PJ-16 strain and further explore the mechanisms of its antifungal and growth-promoting properties, the complete genome of this strain was sequenced and annotated. The 7PJ-16 genome is comprised of two circular plasmids and a 4,209,045-bp circular chromosome, containing 4492 protein-coding genes and 116 RNA genes. This strain was ultimately designed as Bacillus subtilis based on core genome sequence analyses using a phylogenomic approach. In this genome, we identified a series of gene clusters that function in the synthesis of non-ribosomal peptides (surfactin, fengycin, bacillibactin, and bacilysin) as well as the ribosome-dependent synthesis of tasA and bacteriocins (subtilin, subtilosin A), which are responsible for the biosynthesis of numerous antimicrobial metabolites. Additionally, several genes with function that promote plant growth, such as indole-3-acetic acid biosynthesis, the production of volatile substances, and siderophores synthesis, were also identified. The information described in this study has established a good foundation for understanding the beneficial interactions between endophytes and host plants, and facilitates the further application of B. subtilis 7PJ-16 as an agricultural biofertilizer and biocontrol agent.

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Acknowledgments

The authors acknowledge the financial support of the National Natural Science Foundation of China (31601678) to Jie Xie, the Fundamental Research Funds for the Central Universities (XDJK2018D020) to Ting Ou, and the Natural Science Foundation of Chongqing (cstc2015jcyjys80001) to Jie Xie.

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Authors and Affiliations

  1. State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, 400715, People’s Republic of China

    Wei-fang Xu, Hui-shuang Ren, Ting Ou, Jun-hong Wei, Tian Li, Ze-yang Zhou & Jie Xie

  2. Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing, 400715, People’s Republic of China

    Wei-fang Xu, Hui-shuang Ren, Ting Ou, Jun-hong Wei, Tian Li, Ze-yang Zhou & Jie Xie

  3. Institute of Sericulture Science and Technology Research, Chongqing, 400700, People’s Republic of China

    Ting Lei & Chuan-shu Huang

  4. Department of Plant Sciences, Montana State University, Bozeman, MT, 59717, USA

    Gary Strobel

  5. College of Life Science, Chongqing Normal University, Chongqing, 400047, People’s Republic of China

    Ze-yang Zhou

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  1. Wei-fang Xu
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  2. Hui-shuang Ren
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  3. Ting Ou
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  4. Ting Lei
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  9. Ze-yang Zhou
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Correspondence to Ze-yang Zhou or Jie Xie.

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Xu, Wf., Ren, Hs., Ou, T. et al. Genomic and Functional Characterization of the Endophytic Bacillus subtilis 7PJ-16 Strain, a Potential Biocontrol Agent of Mulberry Fruit Sclerotiniose. Microb Ecol 77, 651–663 (2019). https://doi.org/10.1007/s00248-018-1247-4

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