Wheat cultivar replacement drives soil microbiome and microbial cooccurrence patterns

While wheat domestication is reported to influence the soil microbial community, few studies have evaluated the influence of cultivar replacement in modern breeding on both bacterial and fungal communities. Especially, few studies reported the bacterial-fungal interkingdom association by analysis of taxa co-occurrence or co-exclusion between different wheat growth stages. In this study, we selected major wheat cultivars from different decades to investigate their genetic relatedness, plant traits, soil bacterial and fungal communities in the rhizosphere and proximal root zone, and the relationships between them. Our results indicated that host selection had the greatest impact on bacterial and fungal communities compared to growth stage and sampling location (P<0.001). At flowering, the soil microbial community in the genotype group consisting of the 1950 s (W_50 s) and 1960 s (W_60 s) cultivars could be clearly distinguished from those in later genotype groups. Plant traits explained the largest source of variation in microbial β-diversity (12.8–20.6%) (P=0.01), with plant height, aboveground dry matter, leaf area per plant and specific root length being associated with the divergence in microbial composition or quantity among cultivars. The cultivar from the 1970 s (W_70 s) enriched a greater number of microbial taxa with the highest relative abundance, suggesting that old cultivar could be considered as a source of cultivar-microbe interaction. The cultivar from the 2000 s (W_00 s) enriched taxa from the bacterial genus Nocardioides and increased the fungal phylum Glomeromycota in the rhizosphere. At three growth stages, W_00 s root-zone exhibited the highest bacteria/fungi ratio (B/F) and contained more phosphorus cycle-related bacterial phoD-genes than W_50 s and W_60 s. The co-occurrence network revealed more operational taxonomic units (OTUs) from the bacterial order Rhizobiales in the largest module of W_00 s. The increased B/F ratio and the aforementioned taxa are reported to be involved in soil nitrogen and phosphorus availability, suggesting that contemporary cultivar may recruit beneficial bacteria and fungi while weaken the association with other fungi. These findings contribute to the development of microbiome-based breeding strategies for sustainable wheat farming.