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Background   Panax notoginseng  is a highly valuable medicinal plant. Reduced  P. notoginseng  yield is a common and serious problem that arises in a continuous cropping system. Variation in the composition and function of soil microbial community is considered the primary cause of yield reduction.    Methods  This study used shotgun metagenomic sequencing approaches to describe the taxonomic and functional features of  P. notoginseng  rhizosphere microbiome and screen microbial taxa and functional traits related to yields.    Results  At the family and genus level, a total of 43 families and 45 genera (relative abundance > 0.1%) were obtained, and the correlation with the yield of  P. notoginseng  was further analyzed. Nitrosomonadaceae, Xanthomonadaceae,  Mycobacterium  and  Arthrobacter  that were enriched in soils with higher yields were positively correlated with  P. notoginseng  yields, thereby suggesting that they might increase yields. Negative correlation coefficients indicated that Xanthobacteraceae, Caulobacteraceae, Oxalobacteraceae, Chitinophagaceae,  Sphingomonas ,  Hyphomicrobium ,  Variovora x and  Phenylobacterium  might be detrimental to  P. notoginseng  growth. A total of 85 functional traits were significantly ( P  < 0.05) correlated with  P. notoginseng  yields. Functional traits, likely steroid biosynthesis and MAPK signaling pathway were positively correlated with  P. notoginseng  yields. In contrast, functional traits, such as bacterial secretion system, ABC transporters, metabolism of xenobiotics by cytochrome P450 and drug metabolism–cytochrome P450, were negatively associated with yields.    Conclusions  This study describes an overview of the rhizosphere microbiome of  P. notoginseng  with discrepant yields and identifies the taxa and functional traits related to yields. Our results provide valuable information to guide the isolation and culture of potentially beneficial microorganisms and to utilize the power of the microbiome to increase plant yields in a continuous cropping system.

Composition and function of rhizosphere microbiome of Panax notoginseng with discrepant yields