Metagenomics insights into the functional profiles of soil carbon, nitrogen, and phosphorus cycles in a walnut orchard under various regimes of long-term fertilisation

Soil microbial functional potential is important for productivity and sustainable agricultural development; however, the potential response of soil nutrient cycling to different fertilisation regimes remains unclear, especially in perennial tree soils. Here, metagenomic sequencing was applied to investigate the soil microbial functional profiles of carbon (C), nitrogen (N), and phosphorus (P) cycling after seven years of chemical, organic, and biofertiliser fertilisation in walnut (Juglans regia L.) orchard. Microbial communities balanced their elemental requirements through selective degradation. The highest relative abundance of genes for labile C-degradation (amyA, malZ, and xylH) was found under chemical fertilisation (F), whereas the metabolic potential for soil N and P cycling was less affected by F. Compared with CK and F, the addition of organic and/or biofertiliser significantly reduced the relative abundances of labile and recalcitrant C-degradation genes (e.g., chi, and xylH) but promoted the processes of N degradation (GDH1, GDH2, ureA, glnA, and arcC), DNRA (nrfA, napB, and napC), organic P mineralisation (phy), P solubilisation (gcd), and P uptake and transport (phnD) in walnut soils. At the phylum level, most C, N, and P cycle-related microbes were similar, and applying biofertiliser remarkably improved the relative abundances of Proteobacteria and Firmicutes involved in C, N, and P cycling processes. Furthermore, soil TN and AP were key limiting macronutrients for regulating the pathways of soil C, N, and P cycles and microbial taxa. C, N, and P cycle-related genes were tightly coupled through synergetic or antagonistic interactions, especially metabolic pathways encoded by glnA, mmsA, phy, and appA. Overall, our results provide a biological perspective on the microbial genetic potential of soil C, N, and P cycles in perennial crops and explore their interactions under different long-term fertilisation regimes in a walnut orchard.