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 <i>Phomopsis liquidambaris</i> 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 <i>Ph. liquidambaris</i> colonization on the rhizosphere microbial community, soil nitrogen forms, and peanut physiology were analyzed. (3) Results: Colonization by <i>Ph. liquidambaris</i> 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 <i>Bradyrhizobium</i> 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-<i>Bradyrhizobium</i> 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 <i>Ph. liquidambaris</i> 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.