Precipitation gradients restructure rhizosphere and bulk soil microbial communities and potential nitrogen-cycling gene profiles in a desert steppe.

Precipitation change can restructure microbially mediated soil nitrogen (N) cycling in water-limited grasslands, yet whether rhizosphere and bulk soils respond differently remains unclear. An in situ precipitation-gradient experiment in the desert steppe of Inner Mongolia combined soil physicochemical measurements, shotgun metagenomic sequencing, and piecewise structural equation modelling. Treatments included 50% reduced precipitation (W-50%), ambient precipitation (CK), 50% increased precipitation (W+50%), and 100% increased precipitation (W+100%). Soil water content was 37.2% higher under W+100% than under W-50%, whereas NO3--N was 55.5% lower under W+50% than under W-50%. Microbial α-diversity showed a significant treatment × soil compartment interaction, whereas N-cycling functional α-diversity did not differ significantly among precipitation treatments or soil compartments. Precipitation treatment explained 48.35% of microbial community variation and 38.41% of N-cycling gene variation, while soil compartment explained 8.88% and 11.16%, respectively. From W-50% to W+50%, Sphingomonas increased from 2.93% to 13.66% in bulk soil and from 5.14% to 16.87% in rhizosphere soil. Relative to CK, W-50% increased the relative abundances of narZ and norB by 152.5% and 46.6% but decreased those of nrfC and gltD by 27.2% and 7.9%. W+50% increased the relative abundance of ureC by 23.1% while decreasing those of amoB, nirD, and nirK by 56.9%, 31.3%, and 17.8%, respectively. Compared with bulk soil, rhizosphere soil had higher relative abundances of nrfA, ureB, gltB, and nifD. Piecewise SEM explained 86.8% of the variation in N-cycling functional profiles, with microbial community composition showing the strongest association (β = 0.710, P < 0.001). These findings show that precipitation gradients primarily reorganize microbial community composition and potential N-cycling functions, with distinct N-cycling gene profiles between rhizosphere and bulk soils.