Genomic and metabolomic insights into potential mechanisms of plant growth promotion by Streptomyces rochei S32 in various crops

Abstract Aims The use of plant growth-promoting rhizobacteria in crop production necessitates an understanding of the underlying mechanisms. We investigated the potential mechanisms of plant growth promotion by Streptomyces rochei S32 in wheat and tomato crops. Methods The effects of S. rochei S32 on plant growth and its antagonistic activity against soil-borne pathogenic fungi were tested in petri dishes. The underlying molecular mechanisms were identified based on whole-genome sequencing and bioinformatics analysis. The results of genomic analysis were verified by widely targeted metabolomics and mechanism studies of plant growth promotion. Results The growth of crop seedlings treated with the cell-free fermentation broth of S. rochei S32 was markedly improved in 15 d. This effect was demonstrated by increased plant height (24.7%) and root length (17.4%) of wheat (400-fold dilution), as well as extended root length (40.9%) of tomato (200-fold dilution). S. rochei S32 showed antagonistic activity against multiple pathogenic fungi, especially Macropoma kawatsukai. The bacterial genome contains an 8,041,158-bp chromosome and two plasmids. A total of 7486 annotated genes were classified into 31 Gene Ontology functional categories. Genomic analysis revealed the potential for the production of indole-3-acetic acid, fungal cell wall hydrolases, antibiotics (e.g., candicidin, streptothricin, borrellin, albaflavenone), and siderophores. Thirty-nine phytohormones and 2205 secondary metabolites were detected, including indole-3-acetic acid, phytosphingosine, haloprogin, acivicin, and corynebactin. Normal bacterial growth occurred on a nitrogen-free medium. Conclusion S. rochei S32 can promote plant growth directly or indirectly through nitrogen fixation and production of phytohormones, extracellular hydrolases, antibiotics, and siderophores.