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Zhang Z, Zhang L, Zhang L, Chu H, Zhou J, Ju F. Diversity and distribution of biosynthetic gene clusters in agricultural soil microbiomes. mSystems 2024; 9:e0126323. [PMID: 38470142 PMCID: PMC11019929 DOI: 10.1128/msystems.01263-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/26/2024] [Indexed: 03/13/2024] Open
Abstract
Bacterial secondary metabolites serve as an important source of molecules for drug discovery. They also play an important function in mediating the interactions of microbial producers with their living environment and surrounding organisms. However, little is known about the genetic novelty, distribution, and community-level impacts of soil bacterial biosynthetic potential on a large geographic scale. Here, we constructed the first catalog of 11,149 biosynthetic gene clusters (BGCs) from agricultural soils across China and unearthed hidden biosynthetic potential for new natural product discovery from the not-yet-cultivated soil bacteria. Notably, we revealed soil pH as the strongest environmental driver of BGC biogeography and predicted that soil acidification and global climate change could damage the biosynthetic potential of the soil microbiome. The co-occurrence network of bacterial genomes revealed two BGC-rich species, i.e., Nocardia niigatensis from Actinobacteriota and PSRF01 from Acidobacteriota, as the module hub and connector, respectively, indicating their keystone positions in the soil microbial communities. We also uncovered a dominant role of BGC-inferred biotic interactions over environmental drivers in structuring the soil microbiome. Overall, this study achieved novel insights into the BGC landscape in agricultural soils of China, substantially expanding our understanding of the diversity and novelty of bacterial secondary metabolism and the potential role of secondary metabolites in microbiota assembly.IMPORTANCEBacterial secondary metabolites not only serve as the foundation for numerous therapeutics (e.g., antibiotics and anticancer drugs), but they also play critical ecological roles in mediating microbial interactions (e.g., competition and communication). However, our knowledge of bacterial secondary metabolism is limited to only a small fraction of cultured strains, thus restricting our comprehensive understanding of their diversity, novelty, and potential ecological roles in soil ecosystems. Here, we used culture-independent metagenomics to explore biosynthetic potentials in agricultural soils of China. Our analyses revealed a high degree of genetic diversity and novelty within biosynthetic gene clusters in agricultural soil environments, offering valuable insights for biochemists seeking to synthesize novel bioactive products. Furthermore, we uncovered the pivotal role of BGC-rich species in microbial communities and the significant relationship between BGC richness and microbial phylogenetic turnover. This information emphasizes the importance of biosynthetic potential in the assembly of microbial communities.
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Affiliation(s)
- Zhiguo Zhang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Coastal Environment and Resources Research of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang, China
- Center of Synthetic Biology and Integrated Bioengineering, Westlake University, Hangzhou, Zhejiang, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Lu Zhang
- Key Laboratory of Coastal Environment and Resources Research of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang, China
- Center of Synthetic Biology and Integrated Bioengineering, Westlake University, Hangzhou, Zhejiang, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Lihan Zhang
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- Department of Chemistry, Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, Hangzhou, Zhejiang, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources Research of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang, China
- Center of Synthetic Biology and Integrated Bioengineering, Westlake University, Hangzhou, Zhejiang, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
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Alajlani MM. Characterization of subtilosin gene in wild type Bacillus spp. and possible physiological role. Sci Rep 2022; 12:10521. [PMID: 35732659 PMCID: PMC9217942 DOI: 10.1038/s41598-022-13804-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/27/2022] [Indexed: 11/09/2022] Open
Abstract
In a designed study to screen for antimicrobial exhibiting bacteria using molecular aspects, Bacillus species were considered to investigate antibiotic biosynthesis genes. 28 bacterial strains and 3 induced mutants were screened for the presence of subtilosin gene (sbo) and subtilosin through PCR and Mass spectrometry respectively. Sbo gene was detected in 16 out of 28 Bacillus strains. The results from gene sequences deliberated by multiple sequence alignments revealed high-level homology to the sequences of the sbo-alb gene locus of B. subtilis 168 and the other limited reported strains. Hence, this report provided additional strains to support the idea of subtilosin gene predominance amongst Bacillus strains isolated from environment and to find different species containing homologous genes, furthermore the utilization of its conserved region as a means of identifying Bacillus spp. that produce subtilosin. This is the first report to confirm the detection of subtilosin production from B. amyloliquefaciens.
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Affiliation(s)
- Muaaz Mutaz Alajlani
- Department of Pharmaceutical Biology/Pharmacognosy, Institute of Pharmacy, University of Halle-Wittenberg, Hoher Weg 8, 06120, Halle (Saale), Germany.
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Alajlani MM. Characterization of subtilosin gene in wild type Bacillus spp. and possible physiological role. Sci Rep 2022; 12:10521. [DOI: https:/doi.org/10.1038/s41598-022-13804-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/27/2022] [Indexed: 08/08/2023] Open
Abstract
AbstractIn a designed study to screen for antimicrobial exhibiting bacteria using molecular aspects, Bacillus species were considered to investigate antibiotic biosynthesis genes. 28 bacterial strains and 3 induced mutants were screened for the presence of subtilosin gene (sbo) and subtilosin through PCR and Mass spectrometry respectively. Sbo gene was detected in 16 out of 28 Bacillus strains. The results from gene sequences deliberated by multiple sequence alignments revealed high-level homology to the sequences of the sbo-alb gene locus of B. subtilis 168 and the other limited reported strains. Hence, this report provided additional strains to support the idea of subtilosin gene predominance amongst Bacillus strains isolated from environment and to find different species containing homologous genes, furthermore the utilization of its conserved region as a means of identifying Bacillus spp. that produce subtilosin. This is the first report to confirm the detection of subtilosin production from B. amyloliquefaciens.
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