Endophytic bacteria modulate rhizosphere microbiota and nitrogen transformations in Paulownia fortunei (Seem.) Hemsl

Non-leguminous trees, such as Paulownia fortunei (P. fortunei), rely on soil microbial nitrate transformation to meet their high nitrogen (N) demand. Understanding how these plants influence rhizosphere N cycling is critical for sustainable forest management. This study aimed to explore the potential metabolite-linked route by which root-associated endophytic bacteria enhance N availability in P. fortunei via rhizosphere modulation.

A five-year field trial was conducted on a Ferralic Cambisol using P. fortunei inoculated with selected endophytes. Plant performance (foliar N, photosynthesis) and soil N pools (Total nitrogen, TN; nitrate nitrogen, NO₃⁻-N; ammonium nitrogen, NH₄⁺-N) were assessed. We combined amplicon sequencing, metagenomics, and untargeted soil metabolomics to profile the rhizosphere community, N-cycling genes, and metabolite shifts.

Endophytic inoculation, specifically with PG7, significantly increased foliar N and improved photosynthetic traits. This promotion was concurrent with a marked reshaping of the rhizosphere microbiota, characterized by the enrichment of specific nucleoside metabolites (e.g., uridine) and an elevated relative abundance of nitrate-reduction genes (nasD/k26139). Culture assays confirmed that these metabolites could modulate bacterial growth and influence the nitrate-to-ammonium conversion potential, supporting a functional shift toward microbial assimilatory nitrate reduction (ANR) in the field trial.

Our findings suggest a potential metabolite-linked route in which non-leguminous trees may utilize endophytes to engineer the rhizosphere niche, thereby promoting microbial ANR and potentially conserving N in soil. This mechanism provides microbial and metabolic targets for managing N cycling and improving N-use efficiency in forest nurseries and plantations.