Bacillus velezensis SQR9 sways the rhizosphere community and its sociality toward cooperation and plant growth promotion

According to the Lotka-Volterra competition model, intraspecific competition in plant-associated microbial communities should be stronger than interspecific competition. However, there is limited information on whether microbial communities follow this pattern and how disturbance by a newcomer affects them. Given the increasing popularity of probiotics, filling this knowledge gap could help guide future coexistence research. Here, we show that inoculation with a known probiotic, B. velezensis SQR9 shifts species co-occurrence patterns by decreasing the diversity of more distant species and promoting the growth of more closely related species, especially within the Bacillus community. By testing the sociality of Bacillus rhizosphere isolates, we then demonstrated that SQR9 increases the frequency of cooperative interactions in the Bacillus community, which may contribute to the promotion of plant growth. Finally, we provide an ecosystem framework comprising the strains genetic relatedness, metabolic niche space and social compatibility for the efficient and reliable assembly of Bacillus consortia. These findings shed new light on the ecological mechanisms underlying the beneficial effects of probiotics on host fitness.