Diversity and Predicted Functional Profiles of Wheat Seed Endophytic Microbiota Associated with Grain Nutritional Quality Traits

Abstract

Wheat seed endophytic microbiota may be associated with seed nutritional quality, yet systematic studies on this relationship remain limited. In this study, nine representative wheat cultivars were selected from more than 600 wheat accessions based on starch and protein contents and classified into three groups: high-starch and low-protein (HL), medium-starch and medium-protein (MM), and low-starch and high-protein (LH). Amplicon sequencing, LEfSe differential analysis, co-occurrence network analysis, Spearman correlation analysis, and PICRUSt2 v2.6.3 and FUNGuild v1.1 functional prediction were integrated to systematically investigate the relationship between seed endophytic microorganisms and wheat nutritional quality. The results showed that Massilia, Exiguobacterium, and Vishniacozyma were among the key endophytic genera detected in wheat seeds. The composition, co-occurrence network characteristics, and predicted functional profiles of endophytic microbial communities differed markedly among wheat quality groups. The HL group exhibited higher relative abundance of predicted functions related to carbon metabolism and relatively high network modularity, whereas the MM group showed intermediate network characteristics and distinct bacterial and fungal taxa. The LH group exhibited higher network connectivity and more extensive co-occurrence associations, together with higher relative abundances of predicted functions related to nitrogen metabolism, secondary metabolism, and phytohormone-related metabolism. Spearman correlation analysis further revealed significant associations between specific endophytic genera and nutritional quality traits, including starch, protein, wet gluten, and amylose-to-amylopectin ratio. FUNGuild analysis also revealed group-specific differences in predicted fungal trophic modes. Collectively, these findings demonstrate distinct associations between seed endophytic microbial community characteristics and wheat nutritional quality profiles, providing a basis for further investigation of the potential contribution of seed microbiota to wheat quality variation.