Bacillus drives functional states in synthetic plant root bacterial communities

Abstract Background Plant roots release root exudates to attract microbes that form root communities, which in turn promote plant health and growth. Root community assembly arises from millions of interactions between microbes and the plant, leading to robust and stable microbial networks. To manage the complexity of natural root microbiomes for research purposes, scientists have developed reductionist approaches using synthetic microbial inocula (SynComs). Recently, an increasing number of studies employed SynComs to investigate root microbiome assembly and dynamics under various conditions or with specific plant mutants. These studies have identified bacterial traits linked to root competence, but if and how these traits shape root microbiome dynamics across conditions is not well understood. Results To explore whether bacterial trait selection follows recurrent patterns, we conducted a meta-analysis of nine SynCom studies involving plant roots. Surprisingly, we observed that root communities frequently assemble into two distinct functional states. Further analysis revealed that these states are characterized by differences in the abundance of Bacilli. We propose that these Bacilli-associated functional states are driven by microbial interactions such as quorum sensing and biofilm formation and that host activities, including root exudation and immune responses, influence these functional states. Conclusions Whether natural root communities also organize into distinct functional states remains unclear, but the implications could be significant. Functional diversification within root communities may influence the effectiveness of plant-beneficial bioinoculants, particularly Bacilli-based inoculants. To optimize microbiome-driven plant benefits, a deeper understanding of the mechanisms underlying functional state differentiation in root microbiomes is needed.