Effect of a bioformulation with native Bacillus subtilis and Bacillus thuringiensis strains on the control of Fusarium oxysporum and the rhizosphere microbiome of strawberry (Fragaria × ananassa)

Introduction Strawberry ( Fragaria × ananassa ) is an economically important fruit crop whose production has increased substantially in recent years. However, its productivity is severely affected by a wide range of pathogens, including Fusarium oxysporum , the causal agent of wilt. Although chemical control remains widely used, biological strategies have gained increasing attention because of their environmental benefits and contribution to sustainable agriculture. The objective of this study was to evaluate the biocontrol potential of native bacterial bioformulations against F. oxysporum in strawberry under field conditions. Methods Bacteria isolated from rhizosphere soil and root samples collected from eight producing farms in Cauca, Colombia, were screened for antagonistic activity, and the most effective isolates were identified by 16S rRNA gene sequencing. Bioformulations based on Bacillus subtilis UCBF11 and Bacillus thuringiensis UCBF2 were developed as microbial “bioinputs” and evaluated under open-field conditions in strawberry crops inoculated with F. oxysporum . Agronomic variables such as root growth and biomass, biomass promotion indexes, and the bioinput efficiency index were determined. Additionally, the effect of the treatments on the rhizosphere microbiota was analyzed using high-throughput sequencing of the 16S rRNA and ITS regions. Results and Discussion A total of 350 isolates were obtained. B. subtilis UCBF11 and B. thuringiensis UCBF2 showed high antagonistic activity against F. oxysporum , with inhibition percentages of 79.72% and 84.95%, respectively. Field application of these bioinputs significantly increased root length and biomass compared to the control treatments, with B. subtilis UCBF11 showing the most outstanding performance. Metataxonomic analysis showed modifications in the structure of bacterial and fungal communities among treatments, and bioinput application was associated with a lower increase in the relative abundance of F. oxysporum . These results demonstrate the potential of B. subtilis UCBF11 and B. thuringiensis UCBF2 as biological control agents against F. oxysporum in strawberry crops.