Efficiency of nitrogen and phosphorus cycling in paddy soils is directly driven by functional gene-microbe...

Rice productivity in karst regions is often constrained by low nitrogen (N) and phosphorus (P) use efficiency, yet the attributes associated with reduced nutrient cycling function in medium- and low-yield paddy fields remain unclear. We selected five representative paddy soil profiles in Qianxi City, Guizhou Province, comprising one high-yield field, one medium-yield field and three low-yield fields characterised by sandy soil, water deficit or waterlogging. These profiles contained 23 diagnostic horizons, yielding 23 composite soil samples for analyses of soil physicochemical properties, enzyme activities, metagenome-derived functional gene abundance and microbial community composition. Integrative analyses, including redundancy analysis, co-occurrence networks, random forest modelling and structural equation modelling (SEM), were used to evaluate attributes associated with nitrogen and phosphorus cycling functional potential. Across paddy field types, N- and P-cycling functional genes showed distinct abundance patterns. In the waterlogged low-yield field, the abundance value of nifH reached 525.33 reads, 5.3-fold higher than that in the high-yield field. Genes associated with organic P mineralisation and regulation, including phoD, phoU and ppnK, ranged from 608 to 2,480 reads across field types. Microbial taxonomic profiles associated with N- and P-cycling functions also differed among paddy fields. Available phosphorus showed the strongest association with P-cycling functional profiles (Mantel r = 0.72). SEM showed that gene-related variables were positively associated with integrated N and P cycling functional potential (path coefficient = 0.567, P < 0.01), whereas soil microbial variables were negatively associated with this potential (- 0.619, P < 0.01). These results identify attributes associated with nutrient cycling constraints in karst paddy fields and provide a basis for targeted nutrient management.