Genomic and metabolomic insights into the antimicrobial compounds and plant growth-promoting potential of Bacillus velezensis B115
Abstract The B115 strain, isolated from the inter-root soil of healthy plants in a continuous cropping site of Panax notoginseng, was identified as Bacillus velezensis B115 by 16S rDNA sequence comparison and comparative genomic analysis. B115 is a strain of beneficial microorganisms present in the...
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Nature Portfolio
2025-03-01
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| Online Access: | https://doi.org/10.1038/s41598-025-92322-z |
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| author | Jili Chen Yuzhou Feng Junchi Ma Qing Zhang Yumei Dong Dongjie Li Xuemei Duan Lequn Zhou Zhihua Li Ying Yang Bo Cai Ze Liu Jialong Yu Bo Zhou Tao Liu |
| author_facet | Jili Chen Yuzhou Feng Junchi Ma Qing Zhang Yumei Dong Dongjie Li Xuemei Duan Lequn Zhou Zhihua Li Ying Yang Bo Cai Ze Liu Jialong Yu Bo Zhou Tao Liu |
| author_sort | Jili Chen |
| collection | DOAJ |
| description | Abstract The B115 strain, isolated from the inter-root soil of healthy plants in a continuous cropping site of Panax notoginseng, was identified as Bacillus velezensis B115 by 16S rDNA sequence comparison and comparative genomic analysis. B115 is a strain of beneficial microorganisms present in the inter-root zone of plants, with favorable plant growth-promoting properties and antagonistic effects against the plant pathogen Fusarium oxysporum. However, the whole genome of B115 remains unclear, thus restricting its potential applications. To address this gap, the whole genome of B115 has been sequenced and annotated to elucidate the molecular mechanisms underlying its plant growth-promoting and antimicrobial activities. The genome analysis revealed that B115 comprises a single circular chromosome of 4,200,774 bp and a plasmid region 16,878 bp long, possessing a GC content of 45.95%. Moreover, 4349 protein-coding genes were predicted. Notably, the B115 genome contains a substantial number of genes (103) involved in the biosynthesis, transport, and catabolism of secondary metabolites. Through genome mining, 13 BGCs and 540 genes encoding secondary metabolites with predicted roles were identified, including members of the surfactin and fengycin families. Utilizing LC–MS/MS technologies, 2318 metabolites were detected in the fermentation broth of B. velezensis B115, encompassing compounds such as Corynebactin, Gamabufotalin, Pracinostat, Indoleacetic acid, (8)-Gingerol, Luteolin, Liquiritigenin, and other metabolites with antimicrobial, growth-promoting, antioxidant, and antitumor properties. By exploring secondary metabolite-related genes and predicting potential secondary metabolites from the B115 genome based on the whole-genome sequence results, we further elucidate the genomic basis for its ability to promote plant growth and inhibit pathogen activity. |
| format | Article |
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| issn | 2045-2322 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Nature Portfolio |
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| series | Scientific Reports |
| spelling | doaj-art-b423f8c1936d4d79a42bfcfa9507c6c52025-08-20T02:10:20ZengNature PortfolioScientific Reports2045-23222025-03-0115111310.1038/s41598-025-92322-zGenomic and metabolomic insights into the antimicrobial compounds and plant growth-promoting potential of Bacillus velezensis B115Jili Chen0Yuzhou Feng1Junchi Ma2Qing Zhang3Yumei Dong4Dongjie Li5Xuemei Duan6Lequn Zhou7Zhihua Li8Ying Yang9Bo Cai10Ze Liu11Jialong Yu12Bo Zhou13Tao Liu14College of Agronomy and Biotechnology, Yunnan Agricultural UniversityCollege of Resources and Environment, Yunnan Agricultural UniversityCollege of Agronomy and Biotechnology, Yunnan Agricultural UniversityCollege of Agronomy and Biotechnology, Yunnan Agricultural UniversityCollege of Agronomy and Biotechnology, Yunnan Agricultural UniversityRaw Material Center of China Tobacco Yunnan Industrial Co., Ltd.Tobacco Leaf Quality Inspection Section, Raw Material Department, Hongyun Honghe Tobacco (Group) Co., Ltd.Tobacco Leaf Quality Inspection Section, Raw Material Department, Hongyun Honghe Tobacco (Group) Co., Ltd.Tobacco Leaf Quality Inspection Section, Raw Material Department, Hongyun Honghe Tobacco (Group) Co., Ltd.Technology Center of China Tobacco Yunnan Industrial Co., Ltd.Technology Center of China Tobacco Yunnan Industrial Co., Ltd.Technology Center of China Tobacco Yunnan Industrial Co., Ltd.Yunnan Tobacco CompanyTechnology Center of China Tobacco Yunnan Industrial Co., Ltd.College of Agronomy and Biotechnology, Yunnan Agricultural UniversityAbstract The B115 strain, isolated from the inter-root soil of healthy plants in a continuous cropping site of Panax notoginseng, was identified as Bacillus velezensis B115 by 16S rDNA sequence comparison and comparative genomic analysis. B115 is a strain of beneficial microorganisms present in the inter-root zone of plants, with favorable plant growth-promoting properties and antagonistic effects against the plant pathogen Fusarium oxysporum. However, the whole genome of B115 remains unclear, thus restricting its potential applications. To address this gap, the whole genome of B115 has been sequenced and annotated to elucidate the molecular mechanisms underlying its plant growth-promoting and antimicrobial activities. The genome analysis revealed that B115 comprises a single circular chromosome of 4,200,774 bp and a plasmid region 16,878 bp long, possessing a GC content of 45.95%. Moreover, 4349 protein-coding genes were predicted. Notably, the B115 genome contains a substantial number of genes (103) involved in the biosynthesis, transport, and catabolism of secondary metabolites. Through genome mining, 13 BGCs and 540 genes encoding secondary metabolites with predicted roles were identified, including members of the surfactin and fengycin families. Utilizing LC–MS/MS technologies, 2318 metabolites were detected in the fermentation broth of B. velezensis B115, encompassing compounds such as Corynebactin, Gamabufotalin, Pracinostat, Indoleacetic acid, (8)-Gingerol, Luteolin, Liquiritigenin, and other metabolites with antimicrobial, growth-promoting, antioxidant, and antitumor properties. By exploring secondary metabolite-related genes and predicting potential secondary metabolites from the B115 genome based on the whole-genome sequence results, we further elucidate the genomic basis for its ability to promote plant growth and inhibit pathogen activity.https://doi.org/10.1038/s41598-025-92322-zGenome miningBacillus velezensisB115GenesSecondary metabolitesGenome |
| spellingShingle | Jili Chen Yuzhou Feng Junchi Ma Qing Zhang Yumei Dong Dongjie Li Xuemei Duan Lequn Zhou Zhihua Li Ying Yang Bo Cai Ze Liu Jialong Yu Bo Zhou Tao Liu Genomic and metabolomic insights into the antimicrobial compounds and plant growth-promoting potential of Bacillus velezensis B115 Scientific Reports Genome mining Bacillus velezensis B115 Genes Secondary metabolites Genome |
| title | Genomic and metabolomic insights into the antimicrobial compounds and plant growth-promoting potential of Bacillus velezensis B115 |
| title_full | Genomic and metabolomic insights into the antimicrobial compounds and plant growth-promoting potential of Bacillus velezensis B115 |
| title_fullStr | Genomic and metabolomic insights into the antimicrobial compounds and plant growth-promoting potential of Bacillus velezensis B115 |
| title_full_unstemmed | Genomic and metabolomic insights into the antimicrobial compounds and plant growth-promoting potential of Bacillus velezensis B115 |
| title_short | Genomic and metabolomic insights into the antimicrobial compounds and plant growth-promoting potential of Bacillus velezensis B115 |
| title_sort | genomic and metabolomic insights into the antimicrobial compounds and plant growth promoting potential of bacillus velezensis b115 |
| topic | Genome mining Bacillus velezensis B115 Genes Secondary metabolites Genome |
| url | https://doi.org/10.1038/s41598-025-92322-z |
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