title: Soil bacterial and fungal community dynamics in relation to Panax notoginseng death rate in a continuous cropping system.
abstract: Notoginseng (Panax notoginseng), a valuable herbal medicine, has high death rates in continuous cropping systems. Variation in the soil microbial community is considered the primary cause of notoginseng mortality, although the taxa responsible for crop failure remains unidentified. This study used high-throughput sequencing methods to characterize changes in the microbial community and screen microbial taxa related to the death rate. Fungal diversity significantly decreased in soils cropped with notoginseng for three years. The death rate and the fungal diversity were significantly negatively correlated, suggesting that fungal diversity might be a potential bioindicator of soil health. Positive correlation coefficients revealed that Burkholderiales, Syntrophobacteraceae, Myrmecridium, Phaeosphaeria, Fusarium, and Phoma were better adapted to colonization of diseased plants. The relative abundance of Fusarium oxysporum (R = 0.841, P < 0.05) and Phaeosphaeria rousseliana (R = 0.830, P < 0.05) were positively associated with the death rate. F. oxysporum was a pathogen of notoginseng root-rot that caused seedling death. Negative correlation coefficients indicated that Thermogemmatisporaceae, Actinosynnemataceae, Hydnodontaceae, Herpotrichiellaceae, and Coniosporium might be antagonists of pathogens, and the relative abundance of Coniosporium perforans was negatively correlated with the death rate. Our findings provide a dynamic overview of the microbial community and present a clear scope for screening beneficial microbes and pathogens of notoginseng.
authors.affiliation: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
authors.forename: Linlin
authors.initials: L
authors.lastname: Dong
authors.affiliation: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
authors.forename: Jiang
authors.initials: J
authors.lastname: Xu
authors.affiliation: Wenshan Prefecture Sanqi Science and Technology Research Institute, Sanqi Research department, Yunnan province 663000, China.
authors.forename: Guangquan
authors.initials: G
authors.lastname: Feng
authors.affiliation: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
authors.forename: Xiwen
authors.initials: X
authors.lastname: Li
authors.affiliation: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
authors.forename: Shilin
authors.initials: S
authors.lastname: Chen
mesh_terms: D000383:Agriculture / Q000379:methods; D001203:Ascomycota / Q000235:genetics; D044822:Biodiversity; D004271:DNA, Fungal; D005658:Fungi / Q000235:genetics; D005670:Fusarium / Q000235:genetics; D053723:Panax notoginseng / Q000382:microbiology / Q000502:physiology*; D010802:Phylogeny; D010935:Plant Diseases / Q000382:microbiology; D018517:Plant Roots / Q000382:microbiology; D016133:Polymerase Chain Reaction; D058441:Rhizosphere; D012984:Software; D012987:Soil; D012988:Soil Microbiology
chemical_list: D004271:DNA, Fungal; D012987:Soil