Long-Term Organic-Mineral Fertilization Reshapes Soil Microbiomes, Nitrogen Cycling, and Tea Quality

Continuous fertilization may modify soil nutrient pools and microbial communities in tea plantations, but their joint relationships with nitrogen-cycling genes and tea-leaf composition remain incompletely characterized. Soil properties, tea quality, and shotgun metagenomic profiles were examined after 16 years of four field management regimes: no fertilization (CK), chemical fertilization (CF), organic manure (OM), and combined organic–mineral fertilization (OMN). Relative to CK, OMN had higher soil organic matter (73.30%), total nitrogen (76.12%), total phosphorus (140.45%), alkali-hydrolyzable nitrogen (128.20%), available phosphorus (182.35%), available potassium (93.89%), and nitrate nitrogen (313.86%). OMN also increased tea-shoot free amino acids (29.60%) and catechins (21.96%) relative to CK, whereas caffeine (13.45%) and water-extract content (6.73%) were lower. Microbial richness indices (ACE, Chao1, and observed species) were higher under OMN than CK by 22.46%, 18.24%, and 22.90%, respectively. Community composition differed among treatments (ANOSIM: R = 1, p = 0.001). Of 32,733 annotated nitrogen-cycling genes, 21,874 were shared among treatments, while OMN had the largest treatment-specific gene set (1912). Soil nutrient properties covaried with nitrogen-cycling gene profiles. These endpoint observations indicate distinct soil, microbial, and tea-chemical characteristics under sustained fertilizer regimes; metagenomic gene profiles describe functional potential rather than measured nitrogen-transformation rates.