Response of maize root endophytes to carbon-nitrogen coupling in the irrigated area of the West Liaohe Plain, Inner Mongolia

Stover return and nitrogen management are key agricultural practices influencing crop root-associated microbial communities. However, how their coupling affects the community structure, absolute abundance, and functional potential of maize root endophytes remains poorly understood. This study was based on a five-year stationary field experiment in the West Liaohe Plain irrigation area, a two-factor split-plot design was established with two stover return levels (no return; half return at 4500 kg/ha; full return at 9000 kg/ha) and two nitrogen application rates (conventional 450 kg/ha; reduced 300 kg/ha), resulting in six treatments. Root samples were collected at the silking stage (R1). High-throughput sequencing of the 16 S rRNA gene V4-V5 region and the ITS gene ITS2 region, combined with an internal standard-based absolute quantification method, was used to characterize root endophytic bacterial and fungal community structure, diversity, absolute abundance, and their correlations with environmental factors. Results showed that the dominant bacterial phylum was Pseudomonadota, and the dominant genus was Pseudomonas. Compared with NN, NR significantly increased the relative abundance of Pseudomonas but reduced bacterial diversity. Although the total absolute abundance of the fungal community in NR was high, its species composition was homogeneous with strong homogeneity. In HN, Pseudomonadota dominated the bacterial community, with enrichment of organic matter-degrading taxa, while the abundance of potential pathogens such as Fusarium increased in fungi. HR significantly enriched Bacteroidota and suppressed Pseudomonas, containing the highest number of unique bacterial ASVs; its fungal community exhibited the strongest heterogeneity, with increased abundance of beneficial saprotrophs such as Mortierella. The bacterial community structure in TN was conservative, still dominated by Pseudomonadota, with the lowest total fungal abundance but enrichment of yeast taxa. TR significantly weakened the dominance of Pseudomonas and increased the abundance of Rhizobium, Agrobacterium, and Actinomycetota, maintaining high functional differentiation potential, while fungi enriched saprotrophs including Mortierella and Penicillium. Correlation analysis indicated that alkali-hydrolyzable nitrogen and available potassium were the core environmental factors driving changes in root endophytic microbial community structure. In conclusion, full stover return combined with reduced nitrogen application (TR) facilitates the construction of a multifunctional community with both nitrogen-fixing potential and organic matter transformation capacity, providing a microbiological basis for the synergistic realization of maize stover resource utilization and nitrogen fertilizer reduction in the West Liaohe Plain irrigation area.