Diversity, community structure and potential functions of root-associated bacterial communities of different wheat (Triticum aestivum) cultivars under field conditions

Abstract

Abstract Aim Wheat (Triticum aestivum) microbiome is essential to its growth and adaptation under the current climatic crisis. Wheat breeding programs are mainly focused on developing pest and stress resistant cultivars; thus, plant genotype-by-microbiome interactions have gained attention. Thus, local wheat cultivars represent an opportunity to examine recruited and supporting bacterial communities under field conditions. Method In this study, we used Illumina MiSeq to explore the diversity, community structure and potential functions of root-associated bacterial communities of four wheat cultivars under field conditions. Results Proteobacteria was the most abundant phylum in root endosphere (51.1 to 74.4%) and rhizosphere samples (39.3 to 44.9%) across cultivars. Differences in alpha and beta diversity were observed in root endosphere and rhizosphere, independently of cultivar. Potassium was identified as the main factor driving rhizosphere microbiomes of wheat. Higher proportion of shared OTUs were found in rhizosphere (mainly Pseudomonas, Flavobacterium, and Janthinobacterium) compared with root-endosphere (dominated by Delftia, Acinetobacter, Stenotrophomonas, Kaistobacter) across cultivars. General predicted functional activities revealed chemoheterotrophy and aerobic chemoheterotrophy as more observed in the root endosphere environment, whereas nitrogen cycling was the more predicted in rhizosphere. Co-occurrence analysis revealed complex bacterial interactions in niche microbiomes identifying three (Comamonadaceae, Enterobacteraceae, Micrococcaceae) and four (Corynebacteraceae, Dermabacteraceae, Xanthomonadaceae, Staphylococcaceae) families as keystone taxa for root endosphere and rhizosphere, respectively. Conclusions Our findings suggest that under the same field conditions community differences are driven by niche, rather than cultivar. This might contribute to the development of new cultivars able to recruit specific bacterial communities.