Co-inoculation of protist and Bacillus enhances plant growth via reshaping rhizosphere bacterial community composition and function

Abstract

Plant growth-promoting rhizobacteria (PGPR) have been widely used for the promotion of plant performance. Predatory protists can influence the taxonomic and functional composition of rhizosphere bacteria. However, research on the impact of the interaction between protist and PGPR on plant performance remains at a very early stage. Here, we examined the impacts of individual inoculation of protist (Colpoda inflata, Dimastigella trypaniformis, or Vermamoeba vermiformis) or the PGPR strain Bacillus velezensis SQR9 as well as the co-inoculation of the protist C. inflata and B. velezensis SQR9 on the growth of tomato plants. We found that all individual protists and Bacillus could promote plant growth compared to the control with no microbe inoculation, with the co-inoculation of C. inflata and B. velezensis SQR9 achieving the greatest performance, including plant height, fresh weight, and dry weight. Different protists harbored distinct rhizosphere bacterial communities, with the co-inoculation of protist and Bacillus resulting in the lowest bacterial diversity and driving significant changes in community structure and composition, particularly by increasing the relative abundance of Proteobacteria. Random forest model highlighted Cellvibrio as the most important bacterial predictor of plant growth, which was enriched after protist inoculation, especially after the mixed inoculation of protist and Bacillus. We further found that bacterial functional genes of nitrogen metabolism were the key determinants of plant growth. These results indicate that the interaction between protists and Bacillus can support plant growth by reshaping rhizosphere bacterial community composition and function. Understanding the interaction mechanisms between protist and PGPR is crucial for their effective utilization in sustainable agriculture.