Diversity of Bacillaceae on rice grown in acid sulfate soils in Vietnam: taxonomy, specialized metabolites, and inhibitory effects on fungal pathogens

Acid sulfate soils pose significant challenges to rice production due to their negative impact on root development and nutrient uptake, reducing rice yield and quality. The excessive use of fungicides by farmers to control rice diseases has exacerbated the issue, as it contributes to environmental pollution and poses health risks. Our study aimed to isolate indigenous bacteria from rice grown in acid sulfate soils with potential biocontrol activity against common fungal pathogens in Vietnam. Using 16S rRNA amplicon sequencing, a total of 91 bacterial strains were identified up to the genus level. Bacillaceae were predominant on healthy rice plants, whereas Pseudomonas spp. also occurred on plants infested with the rice blast pathogen Pyricularia oryzae. Genome sequencing, protein orthology, and multilocus sequence analyses revealed the presence of six taxonomic groups of Bacillaceae: Rossellomorea marisflavi (basionym: Bacillus marisflavi), Priestia megaterium (basionym: Bacillus megaterium), Priestia koreensis (basionym: Bacillus koreensis), Bacillus thuringiensis, Bacillus altitudinis, and Bacillus siamensis. Dual-culture assays showed that most strains had antifungal activity against Pyricularia oryzae, Rhizoctonia solani AG2-1, and Bipolaris oryzae, whereas only B. siamensis and two B. thuringiensis strains were active against Rhizoctonia solani AG1-IA. R. marisflavi strains were in general inactive. Genome mining identified various biosynthetic gene clusters associated with specialized metabolite production, some of which were linked to potential antimicrobial activity. Production of these metabolites was confirmed by chemical analysis. These results suggest that indigenous Bacillaceae strains from acid sulfate soils could be used as biocontrol agents for the sustainable management of rice diseases under acidic conditions.