Soil-dwelling Naegleria enhances plant performance by stimulating beneficial bacterial functions in the rhizosphere

Soil protists play vital roles in influencing plant performance, yet their interactions with plant-beneficial bacteria are still poorly understood. Here, we examine how two soil protists (Naegleria sp. and Cercomonas sp.) affect the pathogen Ralstonia solanacearum, both on individual beneficial bacteria and within a synthetic microbial community (SynCom). Combining in vitro and pot experiments, we find that the SynCom together with Naegleria provided significantly greater suppression of the pathogen (enhanced suppressiveness by 74.29% compared to SynCom alone). Additionally, Naegleria increases SynCom biofilm biomass by 2.44 times. Population dynamics tracking revealed that Naegleria enriched Bacillus populations, leading to a positive correlation between Bacillus and Pseudomonas. Metatranscriptomics analysis shows upregulation of genes related to biofilm formation (such as epsA-O and tapA-sipW-tasA operon) and secondary metabolite biosynthesis (e.g., macrolactin H, bacillaene, and difficidin) in the presence of Naegleria. Our study demonstrates that Naegleria enhances plant health by predating on pathogens, promoting beneficial bacteria, and stimulating protective microbial functions in the rhizosphere.