Fungal Endophyte Comprehensively Orchestrates Nodulation and Nitrogen Utilization of Legume Crop (Arachis hypogaea L.)

(1) Background: Improving nitrogen use efficiency in peanuts is essential for achieving a high yield with reduced nitrogen fertilizer input. This study investigates the role of the fungal endophyte Phomopsis liquidambaris in regulating nitrogen utilization throughout the entire growth cycle of peanuts. (2) Methods: Field pot experiments and a two-year plot trial were conducted. The effects of Ph. liquidambaris colonization on the rhizosphere microbial community, soil nitrogen forms, and peanut physiology were analyzed. (3) Results: Colonization by Ph. liquidambaris significantly suppressed the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the rhizosphere at the seedling stage. This led to a transient decrease in nitrate and an increase in ammonium availability, which enhanced nodulation-related physiological responses. Concurrently, the peanut-specific rhizobium Bradyrhizobium sp. was enriched in the rhizosphere, and the root exudates induced by the fungus further stimulated nodulation activity. These early-stage effects promoted the establishment of peanut–Bradyrhizobium symbiosis. During the mid-to-late growth stages, the fungus positively reshaped the composition of key functional microbial groups (including diazotrophs, AOA, and AOB), thereby increasing rhizosphere nitrogen availability. (4) Conclusions: Under low nitrogen fertilization, inoculation with Ph. liquidambaris maintained yield stability in long-term monocropped peanuts by enhancing early nodulation and late-stage rhizosphere nitrogen availability. This study provides a promising microbe-based strategy to support sustainable legume production with reduced nitrogen fertilizer application.