Potential Utility of Bacillus amyloliquefaciens SFB-1 as a Biocontrol Agent for Sweetpotato Black Rot Caused by Ceratocystis fimbriata

Abstract

Background/Objectives: Sweetpotato black rot, caused by Ceratocystis fimbriata, is a severe fungal disease in sweetpotato production. Biological control strategies represent a promising, environmentally sustainable approach to managing this disease. This study investigates the biocontrol potential of Bacillus amyloliquefaciens SFB-1 against C. fimbriata. Methods: The antagonistic activities of strain SFB-1 on C. fimbriata were assessed through in vitro assays, including evaluations of mycelial inhibition, spore germination, and mycelial morphology. Pathogenicity assays on harvested sweetpotato roots assessed lesion diameter and depth. A transcriptomic analysis of C. fimbriata exposed to strain SFB-1 was performed to explore the underlying antifungal mechanism of SFB-1 on C. fimbriata. The qRT-PCR was employed to validate the RNA-seq results. Results: In vitro assays demonstrated that strain SFB-1 inhibited C. fimbriata mycelial growth by up to 81.01%, caused mycelial swelling, and completely suppressed spore germination at 10⁸ CFU/mL. The cell-free supernatant of strain SFB-1 also suppressed C. fimbriata growth. Pathogenicity assays revealed that strain SFB-1 treatments reduced lesion diameter and depth on harvested sweetpotato roots by over 50% compared to untreated controls. Transcriptomic analysis of C. fimbriata treated with strain SFB-1 identified 1164 differentially expressed genes, with significant alterations in genes associated with cell wall integrity, cell membrane stability, spore germination, detoxification, and antioxidant responses. The qRT-PCR validation of 16 genes confirmed the consistency with the RNA-seq results. Conclusions: B. amyloliquefaciens SFB-1 demonstrates significant biocontrol efficacy against C. fimbriata through multiple mechanisms, positioning it as a promising solution for the sustainable management of sweetpotato black rot.

Keywords: Bacillus amyloliquefaciens; Ceratocystis fimbriata; biocontrol; sweetpotato; transcriptome.

Figure 1

Antagonistic activity of strain SFB-1 against C. fimbriata in vitro. (A) Dual-culture assay of C. fimbriata and strain SFB-1 on PDA medium. (B) Effect of strain SFB-1 on C. fimbriata mycelia. C. fimbriata mycelia were treated with strain SFB-1, and without strain SFB-1, and micrographs were obtained. (C) Diameter of C. fimbriata mycelial growth and inhibition of mycelial growth. (D) Visual representation of inhibition rate of strain SFB-1 on mycelial diameter. Significance levels: *** p < 0.001.

Figure 2

Effect of B. amyloliquefaciens SFB-1 on the morphology of C. fimbriata mycelia at different times. Mycelia of C. fimbriata were treated with sterile water and strain SFB-1 at the concentration of 1 × 10⁷ CFU/mL. Arrows indicate mycelial swelling. Scale bar indicates 50 μm.

Figure 3

Effects of B. amyloliquefaciens SFB-1 at various concentrations on spore germination of C. fimbriata at 16 hpi. (A) Effects of strain SFB-1 on spore germination rates. (B,C) Spore germination rates and inhibition rates of C. fimbriata treated with strain SFB-1 at different concentrations (1 × 10³, 1 × 10⁴, 1 × 10⁵, 1 × 10⁶, 1 × 10⁷, 1 × 10⁸ CFU/mL) at 16 hpi. Untreated spores served as the control. Means with different letters for each strain SFB-1 concentration denote significant differences (p < 0.001).

Figure 4

Antagonism capacity of strain SFB-1 VOCs and CFS against C. fimbriata. (A) The growth inhibition results of strain SFB-1 VOCs on C. fimbriata on PDA plate. (B) The mycelial diameters of the control groups and treatment groups on day 7. “ns” represented no significant difference. (C) The growth inhibition results of strain SFB-1 CFS to C. fimbriata on PDA plate. (D) Inhibition rate of the CFS on mycelia on the third and seventh days.

Figure 5

Biocontrol efficacy of strain SFB-1 against C. fimbriata on sweetpotato storage roots. (A,B) The symptoms of black rot disease on sweetpotato in control samples and in strain SFB-1-treated samples on day 10. (C,D) Statistics of disease spot diameter and depth. Significance levels: *** p < 0.001.

Figure 6

DEGs analysis of C. fimbriata after SFB-1 treatment. (A) Number of upregulated and downregulated DEGs after SFB-1 treatment. (B) Enriched GO terms significantly enriched (p < 0.05) with DEGs. (C) KEGG pathways significantly enriched (p < 0.05) with DEGs.

Figure 7

Heatmaps showing the relative expression of selected DEGs in C. fimbriata following SFB-1 treatment. The log₂ (fold-change) was colored and standardized. Colors indicate DEGs in strain SFB-1-treated C. fimbriata mycelia versus the control. Red, upregulated; blue, downregulated. (A–D) DEGs involved in (A) cell wall, (B) cell membrane, (C) spore development, and (D) detoxification.

Figure 8

Relative expression levels of 16 DEGs involved in cell membrane integrity, cell wall biosynthesis, spore development, and detoxification processes assessed using RNA-seq and qRT-PCR.