Altitudinal changes induce responses in Coptis chinensis Franch. rhizomes: endophytic communities, metabolite types, and alkaloid contents

<i>Coptis chinensis</i> Franch. is a perennial medicinal plant with huge economic and social benefits, but how altitude affects the accumulation of bioactive compounds through microbial ecosystems remains unexplored. This study examined how microbial communities at different altitudes influence the bioactive components of <i>Coptis chinensis</i>, to help identify beneficial microorganisms for application to its rhizomes. Samples of <i>Coptis chinensis</i> were cultivated at four different altitudes in Shizhu, Chongqing. To characterize the phytochemical profile of <i>Coptis chinensis</i>, nine specific alkaloids were quantified by High Performance Liquid Chromatography (HPLC) and Ultraviolet-Visible Spectrophotometry (UV-Vis), with Liquid Chromatography-Mass Spectrometry (LC-MS) subsequently employed to characterize differential metabolite accumulation at each altitude. Microbial community structure in the rhizomes was analyzed by metagenomic sequencing. Results indicated that the contents of groenlandicine, coptisine, berberine, and total alkaloids increased with altitude, with the total alkaloid content rising from 15.97% at 907 m to 17.82% at 1698 m (<i>P</i> < 0.01). Analysis revealed 912 differential metabolites, with distinct accumulation patterns at different altitudes. Microbial diversity in the rhizomes also varied by altitude, with significant shifts in Mucoromycota, Pseudomonadota, <i>Rhizophagus</i>, and <i>Mesorhizobium</i> populations. Moreover, the relative abundance of these microorganisms was intricately linked to alkaloid content. High altitude significantly enhances alkaloid accumulation in <i>C. chinensis</i>, and this effect is primarily mediated by the enrichment of beneficial endophytes, which promote the biosynthesis of target alkaloids via optimizing nitrogen utilization and inducing the expression of key enzymes.