Microecological recombination of <i>Angelica sinensis</i> driven by the transplanting of “alpine seedling–cellar planting–dam cultivation”

Transplanting is important for obtaining and maintaining excellent germplasm of cultivated plants. During plant transplantation, the endophytic microbial community regularly reorganizes, which may be crucial for plant germplasm rejuvenation. <i>Angelica sinensis</i>, a widely used medicinal and edible plant, relies on transplanting for its exceptional quality. To explore the microecological recombination of <i>A. sinensis</i> during the transplanting process of "alpine seedling-cellar planting-dam cultivation", this study analyzed shifts in endophytic and soil microbial communities across the three transplanting stages in Min County, Gansu Province, China. High-throughput sequencing revealed significant changes, with 82.27% to 84.65% of bacteria and 93.19% to 93.49% of fungi species altering in transplanted <i>Angelica</i>. Main findings indicate that Mortierellomycota, Actinobacteriota, and Myxococcota were dominant in cellar planting root and cellar rhizosphere soil, contrasting with Firmicutes predominance in alpine and dam areas. Notably, potentially pathogenic endophytes like <i>Fusarium</i> and <i>Xanthomonas</i> decreased post-alpine seedling and cellar planting, favoring a healthier plant environment. Cellar planting root exhibited a rich accumulation of psychrophilic flora, including <i>Tetracladium</i>, <i>Pseudomonas</i>, and <i>Flavobacterium</i>, alongside a unique dominance of <i>Mortierella</i> fungi. Microbial co-occurrence network analysis highlighted cellar planting root as pivotal, suggesting its importance in microbial interactions. In conclusion, transplanting significantly reshaped <i>A. sinensis</i>'s endophytic flora, with fungi showing more pronounced recombination than bacteria. Soil microbial communities emerged as crucial drivers of this recombination, facilitating the overwintering of <i>A. sinensis</i>, reducing diseases, and rejuvenating the germplasm. Transplanting-driven microecological reorganization is an important scientific mechanism for the high-quality production of cultivated medicinal plants.