Sugar accumulation stage in sugar beets is a key stage in response to continuous cropping soil microbial community assembly

Continuous cropping effects are a major constraint to the sugar beet industry. Although the microbial community of continuously cropped sugar beets has been studied, the effect of continuous cropping on microbial symbiotic networks and their function during plant development is unclear.

We analyzed bulk soil and rhizosphere from continuously cropped sugar beet at four growth stages using amplicon and metagenome sequencing and explored the microbial composition, co-occurrence networks, and potential functions of the microbiome at each plant developmental stage. Soil metrics were correlated with microbial communities, and sugar beet from fields with a maize-beet crop rotation acted as a control group.

Continuous cropping and the plant developmental stage had far-reaching effects on plant compartment microbial diversity, composition, and cross-kingdom networks, with the strongest effects observed in the rhizosphere of plants at the sugar accumulation stage. Metagenomic analyses further showed that continuous cropping profoundly affects the assembly and function of the soil microbiome at the host developmental stage. Significant changes in the compositions of the fungal and bacterial communities were observed as the plants developed especially during the sugar accumulation stage, as disease-associated pathogens increased and became the core microbial population in the continuously cropped group.

Continuous cropping alters the structure of the microbial core population and resulting in very strong selective regulation of the composition and potential function of the soil microbiome during plant development.