Diversity and distribution of biosynthetic gene clusters in agricultural soil microbiomes

作者：Zhiguo Zhang, Lu Zhang, Lihan Zhang, Haiyan Chu, Jizhong Zhou, Feng Ju · 发表于：mSystems · 年份：2024 · DOI：10.1128/msystems.01263-23 · 被引用次数：33 · 研究领域：Microbial Community Ecology and Physiology、Probiotics and Fermented Foods、Microbial Metabolites in Food Biotechnology

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 potenti...