Metagenomic sequencing reveals structural and functional differentiation of rhizosphere bacterial communities driven by nitrogen and potassium deficiency associated with root rot of Schisandra chinensis

Background Frequent incidence of root rot in Schisandra chinensis impairs its yield and quality, yet the rhizosphere microecological mechanism driving this incidence remains unclear. Methods To clarify this mechanism, healthy and root rot-infected S. chinensis plants were analyzed in this study. The plant growth, rhizosphere soil physicochemical properties, and the structural and functional differences in rhizosphere bacterial communities under both conditions were analyzed. Results Our results showed that root rot significantly inhibited S. chinensis growth and pathogen colonization-induced rhizosphere acidification, with reduced hydrolyzable nitrogen (HN) and available potassium (AK). Analysis of the intergroup differences in bacterial species revealed that the healthy rhizosphere was enriched with Acidobacteriota, Luteitalea , Pseudomonadota, Pseudolabrys , and Methylomirabilota, whereas infected rhizosphere was dominated by Gaiella (Actinomycetota), Gemmatimonas (Gemmatimonadota), Bradyrhizobium , and Sphingomicrobium (Pseudomonadota). Functional annotation based on COG, KEGG, and CAZy databases revealed that the bacteria of the healthy rhizosphere were enriched in defensive-cooperative functions (synergistic metabolism, secondary metabolite synthesis, complex carbon metabolism), while those of the infected rhizosphere exhibited simplified survival functions (individual metabolism, ABC transport, simple carbohydrate metabolism). Redundancy analysis identified HN and AK as key nutrients driving community differentiation in the rhizosphere. Conclusion This study revealed that root rot in S. chinensis is closely associated with an imbalance in the rhizosphere environment–bacterial community–function system, with healthy plants exhibiting specific core bacterial biomarkers and more complex synergistic metabolic networks, while HN and AK are key nutrients influencing rhizosphere bacterial communities. This study clarifies the rhizosphere microecological mechanism associated with S. chinensis root rot, providing a theoretical basis for its control.