Rhizosphere and bulk soil bacterial community succession is influenced more by changes in soil properties than in rhizosphere metabolites across a maize growing season

The rhizosphere microbiome composition shifts across plant developmental stages. In addition, the bulk soil microbiome also changes during the growing season. However, the factors governing the rhizosphere and bulk soil microbiome succession across plant development are still not well identified. In this study we analyzed the changes in rhizosphere and bulk soil bacterial community structure through 16S rRNA amplicon sequencing across three maize growth stages (vegetative leaf 5 [V5], vegetative leaf 10 [V10] and reproductive stage 2 [R2]), as well as their correlations with temporal shifts in soil physicochemical properties and in root metabolites quantified in rhizosphere soils by LC/GC–MS. Twelve maize genotypes were used in a replicated field experiment for a comprehensive study. Results indicated significant correlations between the rhizosphere and bulk soil bacterial community succession with the temporal changes in rhizosphere metabolites and soil physicochemical properties. The changes in soil properties (mainly soil N and moisture) across stages explained more of the variation in the rhizosphere and bulk soil bacterial communities than the rhizosphere metabolites. However, shifts in rhizosphere metabolites (mainly sugars and gibberellins) across stages also strongly affected the rhizosphere bacterial community succession, but this effect was weaker on the bulk soil bacterial community. In addition to the changes in microbiome composition and diversity, we also detected changes in soil microbial respiration between plant developmental stages, with greater microbial activity at the V10 stage. In sum, our study showed that changes in soil properties have a great influence on both rhizosphere and bulk soil bacterial community succession across a growing season. The changes in plant root metabolites across the cropping season also affected the succession of the belowground bacterial communities, but the impact was much larger on the rhizosphere than on the bulk soil microbiome. Understanding the ecological processes shaping the belowground microbiomes through time is pivotal to develop future strategies for the most appropriate crop management across the whole growing season.