Phylogenetic and Metabolic Responses of Rhizosphere Microbes to the Cultivation of Panax notoginseng

Replanting diseases are thought to be a bottleneck hampering the sustainable cultivation of Panax notoginseng, a rare medicinal plant. To elucidate the contribution of microbes to the obstacle, microbial diversities in rhizospheres of P. notoginseng were investigated using illumina sequencing technology and metabolic profile analysis. Significant alterations were observed in phylogenetic and metabolic levels. For the phylogenetic diversity, bacteria had the highest diversity for the 1st year cultivation and decreased gradually, whereas fungi showed the opposite trend. For bacteria, 34 phyla and 630 genera were detected, and the dominant Proteobacteria (Pseudomonas and Sulfurospirillum) and Actinobacteria decreased but Acidobacteria (Gp1 and Gp2) increased with the cultivation time. For fungi, 6 phyla and 169 genera were identified, and the dominant Ascomycota (Clathrosphaerina, Pestalotiopsis) decreased with the cultivation time, while Fusarium and unidentified genera increased to be the most dominant in the 2nd-3rd year cultivated soils. Metabolic profiles indicated that the rhizosphere bacteria had higher utilization values of carbon sources and diversity indices in comparison with the control. The utilized carbon sources varied with cultivation, indicating the changing profile of carbon sources in rhizospheres that may induce microbial fluctuation. The alteration of microbial communities could be both a reflection and a cause of continuous cropping obstacle of P. notoginseng.