Comparison on the structure and function of the rhizosphere microbial community between healthy and root-rot Panax notoginseng

Abstract Root-rot disease, the main catastrophic disease of Panax notoginseng (Burk.) F.H. Chen, causes yield reduction and serious economic losses. However, knowledge of the relationship between rhizosphere microbial community and root-rot disease is limited. Therefore, the objective of this study was to evaluate the changes in the rhizosphere microbial community following the occurrence of P. notoginseng root-rot disease using three different techniques: phospholipid fatty acid (PLFA) profiling, 16S rRNA gene sequencing and functional-inference-based approaches (PICRUSt: phylogenetic investigation of communities by reconstruction of unobserved states). With paired comparison design, we studied the rhizosphere microbial community structure of healthy and root-rot P. notoginseng plants in Wenshan region of Yunnan province, southwest China. Microbial PLFA profiles showed that the abundance of total microbes, bacteria, fungi and the proportion of gram-negative bacteria in the rhizosphere soil of diseased plants were significantly higher than those of healthy plants. Furthermore, the proportion of gram-positive bacterial, actinomycetal and arbuscular mycorrhizal fungal PLFAs were significantly lower in the rhizosphere soil of diseased plants, and Proteobacteria was identified to be the marker phylum in rhizosphere soil of diseased P. notoginseng . By PICRUSt analysis, bacterial community function was predicted based on 16S rRNA sequencing. It was found that the potential function of microbial community from rhizosphere soil of diseased P. notoginseng differed significantly from that of healthy plants. Moreover, soil variables including soil texture and soil organic carbon significantly correlated with PLFA profiles, and were identified as important abiotic factors in shaping microbial communities.