Dark septate endophyte colonization exceeds arbuscular mycorrhizal colonization across winter wheat production systems

Abstract Background and aims Dark septate endophytes (DSE) are widespread root-associated fungi, yet their colonization and responses to agricultural production practices remain poorly characterized relative to arbuscular mycorrhizal fungi (AMF). We quantified DSE and AMF root colonization in winter wheat and evaluated their responses to production environment, nitrogen fertilization, variety, and crop stage, and their associations with soil chemistry and grain yield. Methods Ten winter wheat varieties were evaluated across three production environments under two nitrogen treatments (N0 and N150) at Heading and Harvest. DSE and AMF percent root length colonization (%RLC) were quantified microscopically. Soil chemistry and grain yield were evaluated using multivariate and mixed-effects approaches, including direct statistical comparisons between fungal guilds. Results DSE colonization ranged from 8.6–73.2% and AMF from 4.7–68.5%. Overall, DSE colonization exceeded AMF colonization (33.8% vs. 23.5%). DSE colonization exceeded AMF colonization across all three environments, both nitrogen treatments, at Harvest, and in seven varieties, whereas AMF colonization exceeded DSE colonization at Heading and in one variety. DSE, but not AMF, colonization was significantly reduced under N150 relative to N0. Soil chemistry explained little additional variation in fungal colonization, although exploratory analyses identified stronger individual soil associations for DSE than AMF. Neither fungal guild was significantly associated with grain yield. Conclusions DSE are a substantial and responsive component of winter wheat root colonization and exhibit patterns distinct from AMF. Simultaneous evaluation of both guilds provides a comparative framework for understanding root fungal ecology across integrated wheat production systems.