Bacteria-protists-fungi interaction network of sugar beet and potato rhizospheres

The rhizosphere microbiome (RM) is one of the plant-associated microbiomes, including bacteria, fungi, protists, and other microorganisms. Microorganism-microorganism interactions play important roles on plant growth and health, while the bacterial-protist-fungal interaction has not been explored in detail. In this study, the rhizosphere microbiomes (RMs) of sugar beet and potato in experimental fields were compared during six growth stages. The results showed that the phyla compositions of the rhizosphere microbiome were similar in two crops, but the temporal dynamics of structures and functions were different. The bacterial-protist-fungal interaction network was the structural-functional core of RM. Protists in rare networks were the main driver of the interaction network assembly. The correlation of bacteria and protists was stronger than that of bacteria and fungi. Bacteria in abundant networks were correlated with basic nutrient functions, fungi mainly affected the crop health-associated traits, and protists were positively correlated with most nutritional functions, but negatively correlated with many crop diseases. The taxonomy of soil protists and their direct independent ecological functions need to be further investigated. The bacterial-protist-fungal interaction network and associated environmental factors form a soil microecosystem, which can be used to predict crop health and soil ecological functions and regulate field management.