Background Root-associated microbiomes are important for plant nutrient uptake, disease suppression and plant growth. It is important to reveal wheat-root associated microbial community assembly and dominant drivers determining their variability. Methods Using 16S rRNA gene profiling, we investigated the effects of sample type, location, growth stage and variety on prokaryotic communities in the root endosphere and rhizosphere of wheat and bulk soil based on the field samples including 5 varieties from 4 locations along similar latitude with the distance about 157 to 800 km apart between any two locations.Results Prokaryotic communities were more diverse in the bulk soil and rhizosphere than in root endosphere. Wheat-root associated prokaryotic community assembly was shaped predominantly by sample type, while within each sample type, location had stronger effects on the variation in prokaryotic community than growth stage or variety. Wheat variety effects varied substantially among different locations and growth stages in root endosphere and rhizosphere samples, and the variety effects were location-specific and growth stage-specific. Root endosphere specially enriched Pseudomonas, relative to other two sample types, while rhizosphere mainly enriched Bacillus. Conclusions This study characterized prokaryotic communities of wheat-root endosphere and rhizosphere and their relationships, and demonstrated significant interactive effects between wheat variety, location and growth stage on prokaryotic community assembly in field condition.

The root-associated microbiomes play important roles in plant growth. However, it is largely unknown how wheat variety evolutionary relatedness shapes each sub-community in root microbiome, and in turn, how these microbes affect wheat yield and quality. Here we studied the prokaryotic communities associated with the rhizosphere and root endosphere in 95 wheat varieties at regreening and heading stages. The results indicated that the less diverse but abundant core prokaryotic taxa occurred among all varieties. Among these core taxa, we identified 49 and 108 heritable ASVs (amplicon sequence variants), whose variations in relative abundances across the root endosphere and rhizosphere samples were significantly affected by wheat variety. The significant correlations between phylogenetic distance of wheat varieties and prokaryotic community dissimilarity were only observed in non-core and abundant sub-communities in the endosphere samples. Again, wheat yield was only significantly associated with root endosphere microbiota at heading stage. Additionally, wheat yield could be predicted using total abundance of 94 prokaryotic taxa as an indicator. Our results demonstrated that the prokaryotic communities in root endosphere had higher correlations with wheat yield and quality than those in rhizosphere, thus, managing root endosphere microbiota, especially core taxa, through agronomic practices and crop breeding, is important for promoting wheat yield and quality.

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