Precipitation changes exert a fundamental effect on the nitrogen (N) cycle in water-limited grasslands. Soil microbes are essential drivers of N cycle, and the rates and their stabilities of interrelated N-cycling processes are reflected by the abundance and diversity of N-cycling genes. Yet, little is known about how altered precipitation affects the genes involved in the entire N-cycling pathways.

By combining a 6-year precipitation manipulation experiment (−30%, ambient, +30%, +50%) with metagenomic sequencing, we investigated the responses of N-cycling gene abundance and diversity to altered precipitation at two soil depths (0–10 and 30–50 cm).

We found that increased precipitation enhanced the abundance of numerous key genes, leading to an acceleration of N turnover, but decreased the diversity of ammonium assimilation genes. Decreased precipitation did not reduce abundance or diversity of N-cycling genes. Most N-cycling genes showed generally consistent responses to altered precipitation in the topsoil (0–10 cm) and subsoil (30–50 cm), albeit with clear distinctions in both abundance and diversity by soil depth. These precipitation-specific responses and depth-dependent variabilities of functional genes were attributed to the distinct taxonomic composition of each N-cycling gene. Furthermore, we quantified gross N transformation rates and found that they were well predicted by the abundance of most N-cycling genes (e.g. genes involved in ammonium assimilation and nitrification).

Our study sheds new light on the soil N cycle under precipitation alterations from the perspective of individual gene abundance and diversity and shows that future increases in precipitation could accelerate soil N turnover in arid and semi-arid lands.