Genomic and biochemical characterization of Bacillus siamensis CIS52 reveals its potential to control phytopathogenic fungi.

Abstract

Genome sequencing of Bacillus siamensis CIS52 confirmed its identity and revealed gene clusters involved in the biosynthesis of antifungal compounds, including fengycin, surfactin, and bacillaene. Biochemical characterization showed its ability to solubilize phosphate (121.27 ± 0.05 mg/L), produce indole acetic acid (36.93 ± 0.01 mg/L), and exhibit ACC deaminase activity, supporting its role as a plant growth-promoting rhizobacterium. The cell-free supernatant of B. siamensis CIS52 completely inhibited the growth of Sclerotium rolfsii and Rhizoctonia solani and partially suppressed Phytophthora sp. (53.25 ± 3.44%), Colletotrichum gloeosporioides (35.11 ± 2.04%), Alternaria alternata (35.09 ± 5.32%), and Fusarium oxysporum (16.44 ± 3.36%). Extracts of the cell-free supernatant retained antifungal activity, consistent with the presence of lipopeptide-type compounds as confirmed by Fourier-transform infrared (FTIR) spectroscopy. PCR analysis confirmed the presence of biosynthetic genes for iturin (ituA, ituB, ituC, and ituD), fengycin (fenB and fenD), and surfactin (srfAB) in the genome of B. siamensis CIS52. In sealed plate assays, volatile organic compounds from B. siamensis CIS52 reduced the growth of R. solani (73.78 ± 0.77%), S. rolfsii (62.22 ± 0.77%), and A. alternata (61.78 ± 2.04%). GC-MS analysis identified antifungal VOCs, including 2,5-dimethylpyrazine, 2-methyl-3-isopropylpyrazine, and 2-dodecanone. These results demonstrate that B. siamensis CIS52 suppresses phytopathogenic fungi through the combined action of lipopeptides and VOCs, highlighting its potential as a biocontrol agent and plant growth-promoting rhizobacterium for sustainable agriculture.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04539-4.