Transcriptomic Analysis Reveals the Time-Dependent Mechanism of Antifungal Activity in Bacillus velezensis GHZJ-1

Frequent outbreaks of bacterial and fungal diseases in aquaculture cause severe economic losses, making biological control using probiotics a crucial strategy. Bacillus velezensis synthesizes diverse antimicrobial secondary metabolites; however, its biocontrol potential is tightly regulated by environmental signals such as cultivation time. In this study, we investigated the effect of growing time on the antifungal activity of B. velezensis GHZJ-1, isolated from an aquatic environment. It was found that GHZJ-1 shows obvious antifungal activity against the aquatic pathogen Metschnikowia bicuspidata upon 48 h growth but no such activity for 24 h via the agar-diffusion method. We further compared the transcriptomes of GHZJ-1 cells collected at 24 h and 48 h through RNA-Seq. Our results revealed that compared with 24 h, 1821 genes were differentially expressed at 48 h, with 903 upregulated and 918 downregulated. Downregulated genes were enriched in primary metabolic pathways (e.g., ribosome assembly and carbon metabolism), whereas upregulated genes were enriched in secondary metabolite biosynthesis and transmembrane transport. Importantly, 35 upregulated genes directly associated with antimicrobial activity were identified, notably including the ones encoding core elements of a large polyketide synthase (e.g., pksN, log₂FC = 2.24), the petrobactin siderophore system (highest log₂FC = 3.39), and various antimicrobial peptide export systems. Furthermore, the degU gene was activated at 48 h. These data suggest that facing continuously increased environmental stress over time, GHZJ-1 undergoes global transcriptional reprogramming and resource reallocation, downregulating basal metabolism to construct a synergistic antagonistic system coupling chemical defense with nutritional competition. This study elucidates the time-dependent mechanism for antifungal activity in GHZJ-1, providing a molecular theoretical basis for its green biocontrol application in aquaculture diseases caused by fungi.