Solid-state fermentation of Streptomyces sp. IPV2742: characterisation of a new potential biocontrol agent and its metabolites

Plant pathogens pose a significant threat to global crop production and food security. Generally, phytopathogens are controlled by fungicides. However, fungicides can often be environmental polluting and have negative effects on the biosphere. The sustainability of the agricultural sector is strongly linked to the development of new biological strategies as an alternative to fungicides. Streptomyces species play a key role in biocontrol of phytopathogens thanks to the high number of secondary metabolites produced. Moreover, growing Streptomyces spp. on unconventional substrates like agri-food waste could re-valorise agricultural waste and, at the same time, improve food security by reducing crop loss and the production of mycotoxins. In this study, Streptomyces sp. IPV2742, isolated from Vitis vinifera, was characterised for its activity against phytopathogens in vitro. Genome mining combined with solid state fermentation (SSF) were carried out to investigate the biosynthetic potential of IPV2742 to produce secondary metabolites applicable as new active molecules. The genome of IPV2742 has been sequenced and annotated. Through genomic analysis, several putative compounds, and untargeted metabolites, including RiPPs, RiPPs-like compounds, and polyketides with antimicrobial properties had been identified. Dual culture assays confirmed the IPV2742 antagonistic activity against a wide range of phytopathogens, and the most promising results were observed against Botrytis cinerea and Sclerotinia sclerotiorum, with an inhibitory activity respectively of 65% and 64%. SSF was developed to trigger cryptic natural product biosynthesis with antifungal activity. The crude extract obtained from fermented substrates showed growth inhibitory activity against S. sclerotiorum, Fusarium culmorum and B. cinerea. These results suggest that IPV2742 may be considered a candidate biocontrol agent against pathogens and as a source of new bioactive molecules.