(A) Bacterial taxonomic composition of root, stem, and leaf endophytes from intermediate wheatgrass and annual wheat at phylum level. Samples from three different field sites and two time points (n = 114–120 per plant and compartment) were merged. The category “other” was merged from ASVs with a relative abundance below 0.01. (B) Bacterial community composition of intermediate wheatgrass and annual wheat visualized as NMDS plots divided by the main influencing factors field site and plant compartment. The plant genotype is a major source of bacterial community variation in the roots, but to a lesser extent in the aboveground materials (detailed statistics in Table 1). (C) Bacterial alpha diversity in different plant genotypes and compartments depicted as Shannon H′, species richness, and Faith’s phylogenetic diversity. Three sampling sites and two sampling time points were merged (n = 114–120). The Kruskal–Wallis test, followed by pairwise comparisons with Wilcoxon testing and “fdr” adjustments, was used to assess significant differences, indicated by asterisks (^**P < .01 and ^***P < .001).