ABSTRACT: Paeonia lactiflora Pall (P. lactiflora) is a plant with medicinal and economic value; during its growth, root secondary metabolism and rhizosphere microbes interact, but no systematic study has examined microbiome and metabolome changes under different planting and harvest times; to address this, we used amplicon sequencing for microbial diversity and untargeted metabolomics for metabolite profiling, then integrated and correlated the datasets. We measured paeoniflorin (PC) by HPLC, total phenolic content (TPC) by the Folin-Ciocalteu method, total flavonoid content (TFC) by the NaNO2-Al(NO3)3 method, and antioxidant activity by DPPH, ABTS, hydroxyl radical scavenging, and FRAP assays. From bacterial results, Proteobacteria was the dominant phylum, and Subgroup_2 was the most abundant genus; for fungi, Ascomycota dominated, and Coniosporium was the top genus. Metabolomic PCA separated all treatment groups, and we identified 447, 471, 493, and 453 differential metabolites from four pairwise comparisons, including lipids, phenylpropanoids, polyketides, and benzenoids. Enrichment analysis indicated these differences were mostly related to amino acid metabolism, secondary metabolite biosynthesis, and ABC transporter pathways. Notably, CS-4 had higher PC, TPC, and TFC, and also stronger radical-scavenging activity than other groups. Overall, our findings suggest planting pattern and harvest time both affect plant phenotype and metabolic profiles, providing a solid theoretical basis for improving cultivation.
