Genomic and metabolomic profiling reveal Streptomyces rochei S32 contributes to plant growth by nitrogen fixation and production of bioactive substances

To unfold the full potential of plant growth-promoting rhizobacteria in crop production it is desirable to explore the mechanisms through which they promote growth. We investigated the potential mechanisms of plant growth promotion by Streptomyces rochei S32 in two crops.

The effects of S. rochei S32 on plant growth and its antagonistic activity against soil-borne pathogenic fungi were tested. 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.

S. rochei S32 significantly improved the growth of wheat and tomato. The shoot length (24.7%) and root length (25.3%) of wheat (400-fold dilution of cell-free fermentation filtrate) were increased, and the root length of tomato (200-fold dilution) was prolonged (40.9%), and the field yield was also increased. 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, acivicin, and corynebactin. Normal bacterial growth occurred on a nitrogen-free medium.

S. rochei S32 can promote plant growth directly or indirectly through nitrogen fixation and production of phytohormones, extracellular hydrolases, antibiotics, and siderophores.