Unravelling the secondary metabolome and biocontrol potential of the recently described species Bacillus nakamurai

In the prospect of novel potential biocontrol agents, a new strain BDI-IS1 belonging to the recently described Bacillus nakamurai was selected for its strong in vitro antimicrobial activities against a range of bacterial and fungal phytopathogens. Genome mining coupled with metabolomics revealed that BDI-IS1 produces multiple non-ribosomal secondary metabolites including surfactin, iturin A, bacillaene, bacillibactin and bacilysin, together with some some ribosomally-synthesized and post-translationally modified peptides (RiPPs) such as plantazolicin, and potentially amylocyclicin, bacinapeptin and LCI. Reverse genetics further showed the specific involvement of some of these compounds in the antagonistic activity of the strain. Comparative genomics between the five already sequenced B. nakamurai strains showed that non-ribosomal products constitute the core metabolome of the species while RiPPs are more strain-specific. Although the secondary metabolome lacks some key bioactive metabolites found in B. velezensis, greenhouse experiments show that B. nakamurai BDI-IS1 is able to protect tomato and maize plants against early blight and northern leaf blight caused by Alternaria solani and Exserohilum turcicum, respectively, at levels similar to or better than B. velezensis QST713. The reduction of these foliar diseases, following root or leaf application of the bacterial suspension demonstrates that BDI-IS1 can act by direct antibiosis and by inducing plant defence mechanisms. These findings indicate that B. nakamurai BDI-IS1 can be considered as a good candidate for biocontrol of plant diseases prevailing in tropical regions, and encourage further research into its spectrum of activity, its requirements and the conditions needed to ensure its efficacy.