Bacillus species suppress Pratylenchus in roots and shape the bacterial community in the rhizosphere of lima bean

Abstract

Bacillus species are known to effectively control root-lesion nematodes such as Pratylenchus spp. However, the efficacy of control may vary between Bacillus species. In addition to their direct effects on nematodes, Bacillus species can modulate rhizosphere microbial communities, potentially enhancing biocontrol outcomes. In this study, we investigated the effects of B. subtilis and B. amyloliquefaciens, applied individually and in combination, on the suppression of Pratylenchus spp. and shifts in rhizosphere bacterial communities associated with lima bean (Phaseolus lunatus) landraces and advanced lines. We quantified Pratylenchus populations in soil and root samples following inoculation and assessed changes in rhizosphere bacterial communities using 16S rRNA gene profiling. Both Bacillus strains significantly reduced Pratylenchus populations in roots, with B. subtilis showing greater efficacy, particularly in the landrace genotype. The rhizosphere bacteriome was primarily composed of Actinobacteria, Proteobacteria, and Firmicutes, and inoculation with Bacillus strains altered the abundance of specific bacterial genera. Moreover, predicted microbial functions related to nitrogen cycling and organic matter degradation were affected, with genotype-specific responses observed. Our findings demonstrate that B. subtilis and B. amyloliquefaciens are effective biocontrol agents against Pratylenchus spp. and differentially modulate rhizosphere microbial communities in lima bean, depending on plant genotype.