Effects of cultivation soils and ages on microbiome in the rhizosphere soil of Panax ginseng

To protect the limited forest resources, forestry soils for Panax ginseng cultivation is gradually replaced by farmland, but the extent to which soil type and cultivation age affects soil microbiome in the ginseng rhizosphere is not well known. By using Illumina MiSeq sequencing of the 16S and ITS2 rRNA genes, we tested the effects of two soil types (forest, and farmland) and three cultivation ages (four, five, and six years) on soil microbiome in the ginseng rhizosphere from nine locations in Jilin Province, China. Relative abundance and diversity of rhizosphere microbes differed among soil samples, and Ascomycota, Acidobacteria, Proteobacteria, Actinobacteria and Chloroflexi were the dominant phyla. Soil type positively influenced fungal community, while cultivation age had more positive effect on bacterial than on fungal community. Richness and diversity of fungal community was greater in forest than in farmland soils, while these parameters for bacterial communities were lower in forest than in farmland soils. A deterioration of soil fertility and continuous cultivation increased the proportion of pathogens such as Fusarium, Cylindrocarpon, but reduced the proportion of beneficial and neutral fungi and bacteria. The observed changes in soil properties (pH, organic matter, total nitrogen, total phosphorus, and total potassium) caused by soil type and cultivation age could be explained by the variations in the microbiome. A network analysis indicated that farmland and increasing cultivation age augmented the proportion of pathogens but diminished the proportion of beneficial and neutral fungi and bacteria. The present study showed that the rhizosphere microbiome differed between forest and farmland soils. Cultivation age had a stronger influence on bacterial than on fungal community. These findings suggested that soil microbiome dynamics may be a bioindicator of soil quality, and defining the microbial players involved in various cultivation ages will promote the selection and adoption of favorable ginseng cultivation lands.