Antifungal mechanism of Bacillus amyloliquefaciens strain GKT04 against Fusarium wilt revealed using genomic and transcriptomic analyses

Abstract

The application of endophytic bacteria, particularly members of the genus Bacillus , offers a promising strategy for the biocontrol of plant fungal diseases, owing to their sustainability and ecological safety. Although multiple secondary metabolites that demonstrate antifungal capacity have been identified in diverse endophytic bacteria, the regulatory mechanisms of their biosynthesis remain largely unknown. To elucidate this, we sequenced the entire genome of Bacillus amyloliquefaciens GKT04, a strain isolated from banana root, which showed high inhibitory activity against Fusarium oxysporum f. sp. cubense race 4 (FOC4). The GKT04 genome consists of a circular chromosome and a circular plasmid, which harbors 4,087 protein‐coding genes and 113 RNA genes. Eight gene clusters that could potentially encode antifungal components were identified. We further applied RNA‐Seq analysis to survey genome‐wide changes in the gene expression of strain GKT04 during its inhibition of FOC4. In total, 575 upregulated and 242 downregulated genes enriched in several amino acid and carbohydrate metabolism pathways were identified. Specifically, gene clusters associated with difficidin, bacillibactin, and bacilysin were significantly upregulated, and their gene regulatory networks were constructed. Our work thereby provides insights into the genomic features and gene expression patterns of this B . amyloliquefaciens strain, which presents an excellent potential for the biocontrol of Fusarium wilt.

Digital gene expression profiling of the transcriptional response to Sclerotinia sclerotiorum and its antagonistic bacterium Bacillus amyloliquefaciens in soybean

“…(termed induced systemic resistance, ISR) ( Lugtenberg and Kamilova, 2009 ; Chen et al, 2020 ). The metabolites of B. amyloliquefaciens can be used to control root, leaf, and post-harvest diseases of major cash crops, such as sugarcane, tobacco, and tomato ( Liu et al, 2020 ; Tian et al, 2021 ; Zhao, 2021 ). B. amyloliquefaciens can promote crop growth or inhibit pathogens by producing and secreting secondary metabolites ( Salazar et al, 2017 ).…”

Broad-spectrum resistance mechanism of serine protease Sp1 in Bacillus licheniformis W10 via dual comparative transcriptome analysis

“…Amino acids are indispensable components in the formation of cell structures and various enzymes. The degradation of valine, leucine and isoleucine might be related to propanoate metabolism, which enters the TCA cycle ( Tian et al, 2021 ). DEGs of valine, leucine and isoleucine degradation were all upregulated in this work, indicating that some cell structures and enzymatic activities might be damaged, similar to the hyphal morphological changes in P. amygdali .…”

“…Chitinase and glucanase were reported to be major mucolytic enzymes that dissolve fungal cell walls ( Ji et al, 2020b ). Lipopeptides such as iturins and surfactin from Bacillus are widely known for targeting the host cell wall that causes its collapse and the membrane through pore formation, ultimately leading to cell death and inhibiting fungal growth ( Someya, 2008 ; Tian et al, 2021 ). Wang et al (2014) identified a 55 kDa antifungal protein produced by the B. licheniformis HS10 strain that was a carboxypeptidase and had significant inhibitory effects on eight different plant pathogenic fungi.…”

A Thermotolerant Marine Bacillus amyloliquefaciens S185 Producing Iturin A5 for Antifungal Activity against Fusarium oxysporum f. sp. cubense

“…More than 20,000 distinct bioactive chemicals have been found in marine fauna and flora to date [34,35]. Previously, different species of Bacillus with confirmed biocontrol activity against Foc have been reported, including B. amyloliquefaciens GKT04 [36,37], W19 [38], NIN-6 [39], and NJN-6 [40], B. velezensis HN03 [41], and (iii) B. subtilis strains B26 [42], B04, B05 and B10 [43], and N11 [44]. However, an extensive screening of the biocontrol strains from marine bacteria to control FWB pathogen is limited.…”