Interactions of PGPR from the phylum bacillota with native rhizosphere microbiota: current insights and future perspectives

The intensive use of synthetic fertilizers and pesticides has increased crop productivity but also contributed to soil degradation and biodiversity loss, highlighting the need for more sustainable agricultural strategies. Among emerging solutions, plant growth-promoting rhizobacteria (PGPR), particularly members of the Bacillota phylum, are gaining attention as effective bioinoculants that enhance plant growth and tolerance to biotic and abiotic stresses. However, introduced strains do not function in isolation. They enter complex microbial communities, shaped by plant type and developmental stage, influenced by soil properties and environmental conditions. While the positive effects of PGPR on plant performance are well documented, their impact on indigenous rhizosphere microbiota remains less studied. This review synthesizes current knowledge on how Bacillota-based inoculants influence native microbial communities in cereals, vegetables, orchard crops, and fiber plants. Most studies report shifts toward plant-beneficial taxa and reduced abundance of potential pathogens following Bacillota application. Frequently enriched genera include Bacillus, Pseudomonas, Lysobacter, Sphingomonas, Streptomyces, Azotobacter, Arthrobacter, Pseudarthrobacter, Bradyrhizobium, Devosia, Flavobacterium, Klebsiella, Herbaspirillum, and Rhodanobacter. These changes are often associated with improved plant growth and yield, and stress resilience. However, responses strongly depend on strain, plant and methodological approach. We summarize commonly applied approaches used to assess these interactions. Despite technological advances, limitations remain, such as single time-point sampling, simplified experimental systems, and insufficient integration of inoculant persistence with community analyses. Standardized, multi-site experimental frameworks, with multiple sampling terms are needed to improve predictability and ensure the safe implementation of PGPR-based solutions in sustainable agriculture.