Cultural bacterial diversity on rice grown in acid sulfate soils in Vietnam
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 ninety-one bacterial strains were identified up to the genus level. Bacillaceae were predominant in healthy field, while Pseudomonas spp. dominated in blast-infested fields. Genome sequencing, protein orthology, and multilocus sequence analyses revealed five taxonomic groups of Bacillaceae: Rossellomorea marisflavi (basionym: Bacillus marisflavi), Priestia megaterium (basionym: Bacillus megaterium), Bacillus thuringiensis, Bacillus altitudinis, and Bacillus velezensis. Dual-culture assays showed antifungal activity of B. thuringiensis, B. altitudinis, and B. velezensis isolates against Pyricularia oryzae, Rhizoctonia solani, and Cochliobolus miyabeanus. Genome mining identified various biosynthetic gene clusters associated with secondary metabolites production, some of which were linked to potential antimicrobial activity. These results suggest that indigenous Bacillus strains from acid sulfate soils could be used as biocontrol agents for the sustainable management of rice diseases under acidic conditions.