Phenology-dependent assembly and functional potential of the Artemisia lavandulifolia rhizosphere microbiome

Plant developmental stages represent important endogenous drivers shaping rhizosphere microbiome assembly and functional potential. However, how rhizosphere microbial communities of Artemisia lavandulifolia shift across distinct phenological stages remains largely unexplored. To address this knowledge gap, we employed high-throughput sequencing to comprehensively characterize the rhizosphere bacterial and fungal communities of A. lavandulifolia during the early vegetative stage (EVS) and late vegetative stage (LVS). Additionally, quantitative PCR was used to determine the absolute abundance of bacterial 16S rRNA, fungal ITS genes, and key functional genes related to carbon, nitrogen, and phosphorus cycling. The results revealed significantly higher α-diversity in both bacterial and fungal communities at LVS compared to EVS (p < 0.05). Co-occurrence network analysis revealed that microbial co-occurrence patterns became increasingly complex with plant development, as evidenced by greater numbers of nodes and edges in both bacterial (1189 vs. 1049 nodes; 98,550 vs. 76,390 edges) and fungal (373 vs. 230 nodes; 6932 vs. 4509 edges) networks during LVS. Notably, absolute abundances of functional genes mediating carbon fixation (cbbLR), nitrogen cycling (amoA), and phosphorus mineralization (phoD) were significantly elevated at LVS relative to EVS (p < 0.05). Collectively, these findings demonstrate that plant ontogeny is associated with stage-dependent shifts in the functional potential of the A. lavandulifolia rhizosphere microbiome, suggesting adaptive adjustments in microbially mediated nutrient cycling to meet heightened host metabolic demands during late vegetative growth.

The online version contains supplementary material available at https://doi.org/10.1007/s13205-026-05024-2.