Bacterial community shifts in Fusarium-induced avocado root rot and the antagonistic potential of Bacillus siamensis NB92

Avocado root rot, driven by soil-borne fungi such as <i>Fusarium</i> spp., poses a major challenge to global avocado production. The rhizosphere microbiome is critical for plant health, yet the impact of root rot on bacterial community structure and its implications for disease management remain poorly understood. Here, we combined culture-independent 16S rDNA amplicon sequencing with culture-dependent isolation to characterize bacterial communities in healthy and <i>Fusarium</i>-infested avocado bulk and rhizosphere soils. Key beneficial taxa, notably <i>Bacillus</i>, were then isolated and evaluated for their antagonistic potential. Results showed that root rot significantly reduced rhizosphere bacterial α-diversity, altered community structure, and depleted phyla such as Actinobacteriota and Firmicutes that contain beneficial taxa. Beneficial genera such as <i>Bacillus</i> and <i>Streptomyces</i> declined, while cultivable <i>Fusarium</i> counts increased. Negative correlations between <i>Fusarium</i> abundance, the bacteria-to-fungi ratio, and the relative abundance of beneficial bacteria further underscore their suppressive role. Guided by these findings, we isolated <i>Bacillus</i> strain NB92, identified as <i>Bacillus siamensis</i> through morphological, biochemical, and 16S rRNA and <i>gyrA</i> gene analyses. NB92 exhibited strong antagonistic activity against the root rot pathogen (<i>Fusarium</i> sp. St7) via both direct antagonism and volatile organic compound production. Inoculating NB92 into diseased rhizosphere soil boosted <i>Bacillus</i> counts and reduced <i>Fusarium</i> abundance. Moreover, NB92 effectively inhibited the pathogen's necrotizing ability. <i>B. siamensis</i> NB92 thus represents a promising, sustainable biocontrol agent and contributes to the development of microbiome-based strategies for managing avocado root rot.