Genomically-selected antifungal Bacillaceae strains improve wheat yield and baking quality

Abstract

Soil microbial diversity degradation through agricultural intensification necessitates sustainable alternatives. This study employed genomic and phenotypic approaches to characterize wheat rhizosphere-associated Bacillaceae for agricultural applications. Initial screening of 576 sporulating isolates for antifungal activity against Fusarium graminearum, followed by RAPD analysis, identified 39 distinct genetic profiles, out of which 15 were classified in Bacillus amyloliquefaciens or Priestia megaterium groups by 16S RNA sequence. Whole-genome sequencing of selected strains enabled precise taxonomic classification and comprehensive trait prediction using in silico tools. Genomic mining revealed strain-specific distributions of beneficial traits, including antimicrobial compound production pathways and plant growth-promoting characteristics. Phenotypic validation confirmed key predicted traits while uncovering additional functionalities not detected in silico. Integration of kernel bioassays, pot experiments, and field trials identified Bacillus velezensis ZAV-W70 and P. megaterium ZAV-W64 as promising biofertilizer and biocontrol candidates, demonstrating enhanced yield without fungicides and improved bread-making quality, respectively. These findings highlight the value of combining genomic analysis with traditional screening methods for developing effective agricultural biologicals, contributing to sustainable wheat production practices. KEY POINTS: • Rhizosphere Bacillaceae strains show dual plant growth promotion and biocontrol • B. velezensis ZAV-W70 and P. megaterium ZAV-W64 increase wheat yield • ZAV-W64 increases bread-making quality including total gluten and alveograph W.

Keywords: Bacillus velezensis; Priestia megaterium; Comparative genomics; Field assays; Gene mining; Grain wheat quality; Plant-growth promoting rhizobacteria.

Fig. 1

Antifungal activity of selected Bacillaceae strains on wheat seeds. Quantification of antifungal activity using bacterial-free supernatants. Wheat seeds were treated with supernatants, sterile distilled water and PD broth (negative fungicide control), or Metalaxyl® solution (positive fungicide control), followed by inoculation with F. graminearum (1.0 × 105 spores/mL). Infection symptoms were quantified at 5 days post-inoculation using ImageJ, expressed as the percentage of mycelial growth relative to the total seed surface. Values are means ± SEM (n = 3). Bars not sharing the same letter are significantly different according to ANOVA and LSD multiple comparison test (p < 0.05)

Fig. 2

Plant growth promotion of selected Bacillaceae strains in seedlings assays growth under controlled conditions. The figure summarizes the results obtained in trials of seedlings growth under controlled conditions across three repetitions. Values are expressed as means ± SEM (n = 36). Values not sharing any letter are significantly different according to ANOVA LSD multiple comparison test (p < 0.05). Measured variables included shoot parameters (greenness index = GI, the length of the first leaf = LH1, and the second leaf = LH2, total foliar area = TFA), root parameters (total length = RTL; average diameter = RAD; surface = RS; volume = RV), and seedling weights (shoot fresh weight = RFW, root fresh weight = SFW, shoot dry weight = SDW, root dry weight = RDW). The root tip number (RNT) parameter was excluded, as it showed no significant differences. In the statistical notation, the letter c indicates a significant increase, compared to the control across all three replicates (p < 0.01); b denotes a significant increase in one replicate (p < 0.01), while a shows no significant difference from the control in any replicate. The parameters further describe in the results section were those with significant differences in the three experimental replicates

Fig. 3

Effects of P. megaterium ZAV-W64 and B. velezensis ZAV-W70 on wheat yield under field conditions. Yield results from the 2022 (left panel) and 2023 (right panel) growing seasons. Wheat seeds were treated with ZAV-W64, ZAV-W70, or controls (water and fungicide). Yield values are expressed as means ± SEM (n = 3 for 2022; n = 4 for 2023). Bars not sharing any letter are significantly different according to ANOVA and LSD multiple comparison test (p < 0.05)

Fig. 4

Effects of P. megaterium ZAV-W64 and B. velezensis ZAV-W70 on wheat seed quality parameters. Wet gluten content (left panel) and alveograph W parameter (right panel), indicating dough strength, in seeds produced from plants grown from seeds treated with ZAV-W64, ZAV-W70, or controls (water and fungicide) prior to sowing. Values are expressed as means ± SEM (n = 3). Bars not sharing any letter are significantly different according to ANOVA and LSD multiple comparison test (p < 0.05)