Soil organisms are affected by the presence of predatory protists. However, it remains poorly understood how predatory protists can affect plant disease incidence and how fertilization regimes can affect these interactions. Here, we characterise the rhizosphere bacteria, fungi and protists over eleven growing seasons of tomato planting under three fertilization regimes, i.e conventional, organic and bioorganic, and with different bacterial wilt disease incidence levels. We find that predatory protists are negatively associated with disease incidence, especially two ciliophoran Colpoda OTUs, and that bioorganic fertilization enhances the abundance of predatory protists. In glasshouse experiments we find that the predatory protist Colpoda influences disease incidence by directly consuming pathogens and indirectly increasing the presence of pathogen-suppressive microorganisms in the soil. Together, we demonstrate that predatory protists reduce bacterial wilt disease incidence in tomato plants via direct and indirect reductions of pathogens. Our study provides insights on the role that predatory protists play in plant disease, which could be used to design more sustainable agricultural practices.

Conventional chemical-based control methods for soil-borne diseases often degrade soil quality. The recycling of organic wastes offers a promising solution to simultaneously alleviate environmental pollution and restore soil health. As a beneficial fungus, Trichoderma plays a crucial role in enhancing plant performance. However, knowledge of the mechanisms through which organic wastes and Trichoderma interact to influence plant performance remains limited. We investigated how the combined application of organic wastes (chitin and straw) and a biocontrol fungus (Trichoderma) influenced the rhizosphere microbiome to improve plant performance. Compared with the control, organic waste alone, and Trichoderma alone treatments, the combined application of organic wastes and Trichoderma significantly (p < 0.05) increased cucumber yield and reduced pathogen density. Increased yield and reduced pathogen density were associated with changes in bacterial and fungal communities induced by this combined application treatment. Indeed, this combined application treatment enabled plants to recruit certain potentially beneficial core bacterial (e.g., Streptomyces and Flavisolibacter) and fungal taxa (e.g., Trichoderma), increasing their positive interactions in the rhizosphere. We demonstrate that the combined application of organic wastes and Trichoderma can shape distinct rhizosphere bacterial and fungal communities, promoting an increase in beneficial microorganisms and their positive interactions, which contribute to enhanced plant performance.

Infections with Ralstonia solanacearum have caused considerable agricultural and economic losses. Complex interactions among pathogens, the soil microbiome and soil properties determine health status; however, their interactions have not been explored thoroughly. Here, we collected soils from local naturally healthy and diseased tobacco fields, used Illumina amplicon sequencing to analyze the soil microbial community, determined the physicochemical properties of the soils, and explored the disease-suppressive mechanism of the healthy soil. We found that the microbial structure significantly differed and that the microbial network was more complex in healthy soils than in diseased soils. The key indicator species of the microbial community are also different; those of healthy soil included Sphingomonas and Pseudomonas , which are potentially beneficial bacteria. We further isolated culturable bacterial strains from healthy soil and obtained two indicator strains, Pseudomonas sp. strain R3 and Sphingomonas sp. strain S75. With respect to the soil physicochemical properties, hydrolysable nitrogen was closely related to the microbial community, positively correlated with the indicators of healthy soils and negatively correlated with Ralstonia solanacearum . We further investigated the inhibitory effects of healthy soil indicator species and hydrolysable nitrogen on tobacco bacterial wilt in laboratory and pot experiments, and the results revealed that the greenhouse experiment demonstrated that higher nitrate nitrogen availability enhanced the disease suppression provided by the inoculated indicator strains. We demonstrated that healthy soils presented relatively low pathogen abundance and had more beneficial bacterial indicator species. Hydrolysable nitrogen was the soil property most strongly associated with bacterial community composition and pathogen abundance. In greenhouse experiments, increased nitrate nitrogen enhanced the disease-suppressive effects of the beneficial indicator strains. However, the direct effect of hydrolysable nitrogen on microbial interactions requires further investigation.