Abstract
<title>Abstract</title> <p> <bold>Background:</bold> Wild <italic>Fritillaria cirrhosa</italic> is a slow-growing alpine medicinal geophyte for which harvest age is assumed to influence bulb quality, yet it is not known whether consecutive growth years are accompanied by concordant changes in bulb chemistry, bulb-associated microbiota, and root transcription. We profiled 1- to 4-year-old wild plants by untargeted bulb LC-MS, bacterial 16S and fungal ITS amplicon sequencing of bulb-adhering soil, and root RNA sequencing, using three biological replicates per growth year and data layer. <bold>Results:</bold> Of 2,117 retained LC-MS features, 11 (0.5%) were associated with growth year after false-discovery-rate correction and application of an absolute Spearman threshold of |ρ| ≥ 0.60. Bacterial richness, Shannon diversity, and Bray-Curtis composition did not differ significantly among years (PERMANOVA R² = 0.294, P = 0.339). Fungal alpha diversity was also nonsignificant, whereas fungal community composition differed among years (R² = 0.401, P = 0.002). Adjacent-year root transcriptome contrasts contained 157, 157, and 318 differentially expressed genes for years 1-2, 2-3, and 3-4, respectively; protein processing in the endoplasmic reticulum was the only KEGG pathway that remained significant after multiple-testing correction, specifically in the year 3-4 contrast (adjusted P = 1.98 × 10⁻⁴). <bold>Conclusions:</bold> Growth-year responses were layer specific rather than synchronous. Fungal community turnover and the late root transcriptional response enriched for endoplasmic-reticulum protein processing were the strongest signals, complemented by 11 age-associated bulb metabolite features. Together, these results define the year 3-4 interval as a priority developmental window and provide focused molecular, chemical, and microbial candidates for validation across independent <italic>Fritillaria</italic> populations. </p>