Bioorganic fertilizers promote plant health by activating phagotrophic protists at different plant growth stages

Protists have gradually become recognized to play important roles in suppressing plant pathogens and as key regulators of microbiome assembly. However, how dynamics at different growth stages impact rhizosphere protists and their interactions with bacteria, as well as their links with plant disease suppression, remains under investigated. In this study, we used a long-term field experiment (with different fertilization treatments) as a model to investigate the variation in protists during all growth stages and their interactions with bacteria, as well as their role in with plant disease suppression. We found that different fertilization treatments at different growth stages induced different rhizosphere protist communities and protist–bacterial interactions. Phagotrophic protists are negatively associated with disease incidence at all growth stages. Bioorganic fertilizer increased the abundance of phagotrophic protists, especially Allapsidae _X, Cercomonas , and Hartmannella , at the seeding stage, flowering stage, and fruiting stage. These beneficial phagotrophic protists alternate at different growth stages, constantly activating beneficial microorganisms and promoting a continuous increase in the abundance of bacteria beneficial to plants (such as Lybacter , Klebsiella , and Bacillus ), thereby enhancing plant disease suppression. Together, our findings demonstrate that phagotrophic protists exhibit dynamic changes across different growth stages. These phagotrophic protists constantly activate distinct disease-suppressive bacteria to effectively reduce the incidence of bacterial wilt disease at different growth stages. Our research on disease-suppressive phagotrophic protists and bacteria at different growth stages provides an effective and novel strategy for suppressing bacterial wilt disease. • Protists effectively reduce the incidence of bacterial wilt disease at different growth stages. • Phagotrophic protists exhibit dynamic changes across different growth stages. • Beneficial bacteria were enriched by phagotrophic protists, enhancing disease suppression.