Metagenomic analysis of wolfberry branch substrates under tomato cultivation without additional nitrogen fertilization

Under conditions without additional nitrogen fertilization, nitrogen availability in organic substrate–based horticultural systems depends largely on microbially mediated mineralization processes within the plant–substrate system. Woody agricultural wastes such as wolfberry (Lycium barbarum L.) branches contain substantial organic nitrogen pools and are increasingly used as cultivation substrates. However, how crop cultivation, particularly tomato as a representative horticultural crop, influences rhizosphere nitrogen cycling and microbial functional structure in such substrates remains poorly understood. A wolfberry branch-derived organic substrate was used without additional nitrogen fertilization; nitrogen supply relied entirely on mineralization of substrate-derived organic nitrogen. Two treatments were established: tomato cultivation (NZP) and no cultivation (NZNP). Tomato cultivation significantly increased ammonium nitrogen (NH₄⁺–N), organic nitrogen, and net nitrogen mineralization rates, while suppressing nitrate (NO₃⁻–N) accumulation. Urease activity was enhanced, whereas protease and sucrase activities declined, indicating a shift away from inorganic nitrogen dependence toward sustained organic nitrogen mineralization. Metagenomic analysis indicated shifts in community functional potential, with higher relative abundances of copiotrophic taxa (e.g., Proteobacteria and Bacteroidota) and increased relative abundance of nitrogen-transforming genera such as Thauera. The relative abundances of nirA and amoA showed statistically significant differences between treatments, whereas other nitrogen-cycling genes exhibited non-significant trends. Redundancy and correlation analyses identified pH, NH₄⁺–N, and microbial biomass nitrogen as key drivers shaping microbial community structure and nitrogen cycling functions. Tomato cultivation significantly altered rhizosphere microbial community structure and nitrogen cycling functional profiles in wolfberry branch substrates under conditions without additional nitrogen fertilization. The observed increase in organic nitrogen mineralization and reduced nitrate accumulation suggest a potential shift in nitrogen transformation patterns; however, these findings reflect functional potential inferred from metagenomic analysis rather than directly measured nitrogen retention processes. These findings provide mechanistic insight into plant–microbe interactions that support efficient nitrogen use in organic substrate-based horticultural systems.