Variation in rhizosphere microbial communities and nitrogen- and phosphorus-cycling functional genes among rubber plantations in Yunnan, China

Introduction Rhizosphere microorganisms are important participants in soil nutrient transformation. However, variation in rhizosphere microbial community composition and nitrogen (N)- and phosphorus (P)-cycling functional gene profiles among rubber plantations in Yunnan Province remains unclear. Methods Metagenomic sequencing was used to compare rhizosphere microbial community composition and N- and P-cycling functional gene profiles among the rubber plantations located in five major natural rubber-producing areas in Yunnan Province, China: Gengma (MD), Ximeng (XM), Mengla (ML), Jinghong (JH), and Jiangcheng (JC). Results Bacterial and fungal community composition and N- and P-cycling functional gene profiles differed significantly among the five rubber plantations. JC exhibited higher fungal diversity and richness, but its bacterial diversity was significantly lower than that in MD. The bacterial communities were dominated by Pseudomonadota, Acidobacteriota, and Actinomycetota, and the relative abundance of Acidobacteria was significantly enriched in JC compared to JH. Furthermore, Mucoromycota, Ascomycota, and Basidiomycota were the dominant phyla in the fungal community. At the functional level, compared to JC, key genes associated with N cycling were significantly enriched in ML, including N assimilation ( glnA , gltB , gltD ), dissimilatory nitrate reduction to ammonium ( narG , narH , nirB ), nitrification ( nxrA , nxrB ), and denitrification ( napA , napB ). Furthermore, the nosZ gene was also significantly enriched in MD compared to JC. Regarding the P cycle, compared to JC, genes associated with high-affinity phosphate transporters ( pstA , pstB , pstC ) and polyphosphate degradation ( ndk ) were significantly enriched in MD, whereas the organic phosphorus mineralization-related gene phnX exhibited the opposite trend. Meanwhile, compared to MD, the polyphosphate degradation-related gene ppk2 was significantly enriched in ML, whereas the inorganic phosphorus solubilization-related gene pqqC exhibited the opposite pattern. Hierarchical partitioning identified soil pH, total phosphorus (TP), and total potassium (TK) as the primary factors significantly associated with variations in bacterial community composition and P-cycling functional gene profiles. Conclusion In summary, the composition of rhizosphere bacterial and fungal communities, as well as the functional gene profiles related to N and P cycling, differed significantly among the investigated rubber plantations. These variations were closely associated with soil physicochemical factors. These findings may provide a microbiological basis for further developing site-specific nutrient management strategies in rubber plantations.