Investigations into the microbial community structure and functionality within the rhizosphere microbiome of both healthy and diseased Coptis chinensis.

Root rot, a devastating disease caused by multiple pathogens, significantly impacts numerous crops, including the economically important medicinal plant Coptis chinensis. Harnessing plant-associated microbiomes for disease prevention, yield enhancement, and accurate prediction of soil health status has emerged as a promising sustainable agricultural strategy. However, the rhizosphere microbiome assembly dynamics, successional patterns, and functional profiles during C. chinensis root rot progression remain largely uncharted, with diagnostic biomarkers for early detection in diseased soils/seedlings still unavailable, limiting microbiome-based intervention development. The amplicon data analyses revealed that root rot infection significantly altered the rhizosphere microbiome assembly of C. chinensis, increasing the influence of deterministic processes on microbial community structure. Two potential pathogenic taxa, Paraboeremia and Didymella, significantly enriched in diseased rhizospheres and positively correlated with disease severity, were identified as the causal agents of C. chinensis root rot. Notably, we found that the host plant could recruit diverse beneficial microbes (e.g., Chryseobacterium, Mesorhizobium, Sphingomonas, Bosea) and form larger and more complex microbial networks under pathogen pressure, to enhance disease resistance through functional modules involved in antimicrobial synthesis and immune regulation. Most significantly, three fungal biomarkers (Cladosporium, Fusidium, and Codinaea) were discovered to be strongly associated with root rot occurrence, and demonstrated consistent predictive capacity across multiple independent datasets, indicating their potential utility for risk assessment of C. chinensis root rot in field soils.