Effects of plant cultivars on the structure of bacterial and fungal communities associated with ginseng

There is an increasing awareness of the importance of root-associated bacteria and fungi to plant growth. At present, little is known about whether different ginseng cultivars affect the soil rhizosphere microbial community. Here, we examined the changes in the microorganismal diversity and composition of the rhizospheres of different ginseng cultivars. The rhizosphere soil of four ginseng cultivars, namely CBGL (GAOLI ginseng), JYSH (COMMON ginseng) and SZSZ (SHIZHU ginseng) and TSBT (BIANTIAO ginseng) were obtained. The 16S rRNA genes and internal transcribed spacer (ITS) regions from the total ginseng rhizosphere microorganism community were analyzed to investigate the diversity and structure of the bacterial and fungal communities of the different ginseng cultivars. We found that fungal communities were more influenced by the cultivars than bacterial communities, and we revealed differences in the microbial community composition and diversity among the different ginseng cultivars. We found that fungal diversity was negatively correlated with bacterial diversity in CBGL, JYSH and SZSZ, but, TSBT had the lowest bacterial and fungal diversity, which may be related to the agricultural management for BIANTIAO ginseng. We also discovered certain rhizosphere microorganisms that may be associated with pathogenicity and the long survival time of ginseng cultivars, including Bacillus, Alternaria alternata and Cladosporium sp. agrAR069. We conclude that the microbial diversity and community structures under different ginseng cultivars are significantly different and are related to the host cultivar. This result provides information that can be used for the breeding of Panax ginseng.


Introduction
Increasing evidence indicates that rhizosphere microorganisms have a significant influence on plant growth, root structure and nutrient uptake (Berendsen et al. 2012;Vacheron et al. 2013), and the diversity and composition of rhizosphere microbial communities are essential for maintaining soil quality and plant health. Plant roots can promote or prevent the recruitment of rhizosphere microorganisms by secreting root exudates and volatile compounds (Berendsen et al. 2012;Schmidt et al. 2019). A variety of root exudates, including sugars and amino acids, as well as proteins, organic acids and various secondary metabolites, are released into the rhizosphere and thus become nutrients for rhizosphere microbes, affecting the composition and diversity of rhizosphere microbial communities (Aira et al. 2010;Babalola 2010). This effect might largely depend on the plant species or genotype (Rengel and Marschner 2005). By comparing wheat (Triticum aestivum L.) seedling root exudates, Qu et al. (2021) suggested that organic acids might promote beneficial microorganisms, such as Rhizobiaceae and Burkholderiaceae. Rootsecreted malic acid recruits Bacillus subtilis FB17 in Arabidopsis thaliana (Rudrappa et al. 2008). Different plants interact through plant roots and microbes to form an underground environment that is beneficial to plant growth and development (Turner et al. 2013). Thus, understanding the effect of plant cultivars (plant genotypes) on soil microbial communities is useful for the cultivation of crops.
Rhizosphere microorganisms not only affect the growth of annual crops but also seriously affect the growth of perennial crops (Lugtenberg and Kamilova 2009;Marques et al. 2014). Ginseng, a traditional Chinese medicine, has long been used in clinics for the treatment of various diseases, such as diabetes, hypertension and Alzheimer's disease (Wei 2016;Zheng et al. 2012). There is a wide variety of microorganisms in the rhizosphere soil, including beneficial, harmful and neutral microorganisms, which may interact with the roots of ginseng, thereby affecting the growth and health of ginseng (Bian et al. 2020;Qu et al. 2021;Tong et al. 2021). In recent years, wild ginseng germplasm resources have been made scarce due to excessive exploitation. Thus, wild ginseng has been gradually displaced by cultivated ginseng on the market (Wu et al. 2013). In general, the growth period of cultivated ginseng is only 4-5 years, and studies have suggested yield losses of up to 30%-60% in cultivated ginseng due to soil-borne diseases (Kim et al. 2012). Ginseng is usually not grown continuously for many years on the same field (Ying et al. 2012). Dong et al. (2018) suggested that the bacterial diversity decreased and fungal diversity increased in the rhizosphere soils of cultivated ginseng under continuous growing. Long-term cultivation of ginseng leads to the prevalence of pathogenic microbes, such as Fusarium in rhizosphere soil, which is the reason for the failure of ginseng cultivation over many years (Dong et al. 2018). These problems hinder the development of the ginseng industry (Xiao et al. 2016).
Cultivated ginseng is mainly divided into four cultivars in China according to their cultivation regions and root morphology, namely, COM-MON, BIANTIAO, SHIZHU and GAOLI ginseng. GAOLI ginseng, COMMON ginseng, BIANTIAO ginseng and SHIZHU ginseng are mainly cultivated in Korean Autonomous County of Jilin Province, Fusong County in Jilin Province, Kuandian Manchu Autonomous County in Liaoning Province and Ji'an city of Jilin Province, respectively. In addition, all ginseng seedlings are planted directly in the fields, except BIANTIAO ginseng seedlings. In general, ginseng plantations typically grow young BIANTIAO ginseng seedlings for three years and then transplant them to another field for their growth. Different ginseng cultivars show different levels of stress resistance. Among the four ginseng cultivars, SHIZHU ginseng has high stress resistance, and BIANTIAO ginseng has a long survival time (Liu 1993;Su et al. 2008). These characteristics may be related to rhizosphere microorganisms. We hypothesized that (1) the diversity and structure of the bacterial and fungal communities of the different ginseng cultivar rhizospheres are different, and this difference is probably caused by the ginseng cultivars, (2) the pathogenicity and survival time of different ginseng cultivars may be related to the abundance of some rhizosphere microbial taxa.
To our knowledge, however, no study has investigated the contributions of different ginseng cultivars to shaping the rhizosphere microbial community. Therefore, to explore the rhizosphere microbial community of different ginseng cultivars. we used the 16S rRNA gene and ITS regions (1) to investigate the diversity and structure of the bacterial and fungal communities of the different ginseng cultivar rhizospheres and (2) to identify the dominant bacterial and fungal communities in the rhizosphere soil of different ginseng cultivars. This study provides insight into the variations in the rhizosphere soil microbial community of different ginseng cultivars, which provides a theoretical basis for the cultivation of ginseng and promotes the development of ginseng as well as medicinal plants in the ginseng genus.
All ginseng were planted directly in the field for six years, and only BIANTIAO ginseng was grown for three years in ginseng plantations and then transplanted to the field for another three years. All rhizosphere soil samples were collected in August 2018. The rhizosphere soil of ginseng was collected and sampled from a 20 cm depth using a shovel. The ginseng plants were carefully removed from the ground, keeping the root system intact. The large clumps of soil on the roots were removed, and the soil samples of tightly attaching roots were passed through a 2 mm sieve and placed into a sterile EP tube. In total, the sample of CBGL, JYSH, SZSZ and TSBT were set up with 8, 7, 6 and 6 biological replicates, respectively (Table S1). The soil samples from each ginseng cultivars were collected from at least three healthy, disease-free ginseng roots (one to three biological replicates of rhizosphere soil samples were collected from the roots of each ginseng plant). All samples were immediately transferred into the liquid nitrogen and they were stored at − 80 °C until genomic DNA extraction using the E.Z.N.A.® Stool DNA Kit. Soil characteristics and biogeographic data of the sampling sites are provided in Table S1.

PCR, amplicon quantification and sequencing
The 341F (5'-ACT CCT ACG GGA GGC AGC AG-3') / 806R (5' -GGA CTA CHVGGG TWT CTAAT-3') and ITS1-1 (5'-CTT GGT CAT TTA GAG GAA GTAA-3') / ITS1-2 (5'-GCT GCG TTC TTC ATC GAT GC-3') primer pairs were used to amplify V3-V4 regions of the bacterial 16S rRNA gene and the fungal ITS1 gene, respectively. All PCRs were performed using NEB Phusion High-Fidelity PCR Master Mix following the manufacturer's recommendations with 30 ng of DNA, 4μL of PCR primer cocktail and 25μL of PCR Master Mix. Moreover, negative controls (no templates) were included in this step to check for primer or sample DNA contamination. PCR products were verified by electrophoresis on a 1% agarose gel and purified using AMPure_XP_Beads Kit (AGEN-COURT) to remove unspecific products. The library quality was evaluated by an Agilent 2100 bioanalyzer instrument (Agilent DNA 1, 000 Reagents). The libraries were sequenced using an Illumina HiSeq platform (HiSeq SBS Kit V2, Illumina) platform. Sequence data were deposited in the NCBI SRA database under accession number PRJNA715960.

Data analysis
Raw reads with ambiguous bases, an average Phred score less than 20 and a length less than 10 bp were filtered out using Trimmomatic software (v 0.36) (Bolger et al. 2014). Additionally, the chimeric sequences were identified and removed using UCHIME software (v 4.2.40) (Edgar et al. 2011). The operational taxonomic units (OTUs) of bacteria and fungi were clustered at 97% sequence similarity using UPARSE (v 7.0.1090) (Edgar 2013). OTUs identified as chloroplast, mitochondria or singleton OTUs were removed. Subsequently, the bacterial and fungal OTUs were determined using RDP Classifier v 2.2 (Ribosomal Database Project) against the Greengenes (v 201,304) database and the UNITE (v 7.2) database. In brief, a Venn plot was used to show the number of unique and common OTUs in different groups by the 'VennDiagram' package in R (v 3.1.1). The alpha diversity of the bacterial and fungal communities was characterized by the Chao 1 (species richness), Pielou (species evenness) and Shannon (species diversity) indices to analyze the phylogenetic diversity of each group using MOTHUR (v 1.31.2). Moreover, principal coordinate analyses (PCoA) were performed in QIIME software (v 1.80) to reflect the beta diversity of the microbial community, evaluating the similarity in community among the different groups along with the Bray-Curtis distance matrix (Caporaso et al. 2010). Furthermore, linear discriminant analysis (LDA) effect size (LEfSe) was also used to detect significantly different taxa (LDA scores greater than 2.0 at a P < 0.01) with differential abundance in the Galaxy online analytics platform (http:// hutte nhower. sph. havard. edu/ galaxy).
Statistical analysis of the alpha diversity indices of the bacteria and fungi were performed with Tukey's honestly significant difference test in R package (v 3.5.3) (P < 0.05). The correlation analysis of alpha diversity indices between bacteria and fungi was used by the function 'cor. test' in R package (v 3.5.3) (P < 0.05). One-way analysis of variance (ANOVA) was performed to analyze the impacts of the cultivars on the rhizosphere microbial composition using SPSS. Mantel tests were used to assess the correlation between rhizosphere microbial communities and soil physical and chemical properties (N, P, K, PH and physical properties), as well as temperature using 'vegan' package in R (v 3.5.3) (P < 0.05), respectively (Dixon 2003). In addition, PERMANOVAs was used to assess the effects of ginseng cultivars on bacterial and fungal community based on the Bray-Curtis distance using the 'vegan' package in R (v 3.5.3) (P < 0.05) (Dixon 2003).

Factors driving microbial communities in ginseng cultivars
We investigated the effect of all factors, including soil physical and chemical properties, temperature and ginseng cultivars on microbial communities. The Mantel tests showed that the soil physical and chemical properties and temperature were not correlated with microbial communities (Table S4, P > 0.05), whereas the ginseng cultivars explained 86% and 82% of variance in bacteria and fungi, respectively (Table 1, PERMANOVAs, P < 0.01). The PCoA of Bray-Curtis distance matrix demonstrated that samples from the four groups showed clear separation, suggesting that the bacterial and fungal communities were obviously different among the four ginseng cultivars (Fig. 1).
There were no significant differences in bacterial diversity between CBGL and SZSZ according to  Fig. 3a, b, c). Among these groups, the highest bacterial diversity was detected in JYSH. Moreover, the fungal diversity varied considerably across the rhizosphere soil of the different ginseng cultivars (ANOVA, P < 0.05, Fig. 3d, e, f). Compared to the other the groups, SZSZ had the highest fungal diversity, and JYSH had the lowest level of fungal diversity. TSBT had the lowest microbial diversity for both fungi and bacteria (ANOVA, P < 0.05, Fig. 3). Furthermore, the Chao 1 (species richness) index of fungi was lower than that of bacteria (ANOVA, P < 0.01, Fig. 3a, d). In addition, we found that fungal diversity was negatively correlated with bacterial diversity in CBGL, JYSH and SZSZ (Table S5).

Composition of the bacterial community
We assessed the taxonomic distributions of bacterial OTUs at different classification levels. Whether at the phylum level or at the order level, no significant differences in the composition of bacterial communities were detected among the rhizosphere soils of the different ginseng cultivars. At the phylum level, 10 dominant bacterial phyla were assigned, which comprised 95% of the entire bacterial community. Proteobacteria, Acidobacteria and Verrucomicrobia were the most abundant phyla across all groups, accounting for 22.41% ~ 26.99%, 18.14% ~ 34.07% and 5.99% ~ 17.64% of the total sequences in all groups, respectively (Fig. 4a). Among them, Acidobacteria was the most abundant phylum in CBGL, and its relative abundance was significantly higher in CBGL than in the other groups (ANOVA, P < 0.05, Fig. S1a). Proteobacteria was the most abundant phylum across the other groups. The relative abundance of Proteobacteria was not different across the rhizospheres of the four groups. Moreover, there were significant differences among the four groups in the other main bacterial phyla, such as AD3, Nitrospirae, and TM7 (ANOVA, P < 0.05, Fig. S1a). At the class level, the abundant classes were Alphaproteobacteria (averaging 13.57%), Spartobacteria (averaging 11.84%), Acidobacteria (averaging 8.47%), Solibacteres (averaging 4.78%) and Actinobacteria (averaging 4.51%) (Fig. 4b).
Bacillus is a kind of rhizosphere and endophytic bacteria promoting plant growth (PGPR/ PGPB). At the genus level, the relative abundance of Bacillus was significantly higher in SZSZ and TSBT than in CBGL and JYSH (ANOVA, P < 0.05, Figs. 4c and 5a). We also explored the fungal community by ITS sequencing with the same analysis method used for the 16S rRNA genes above. There were three dominant fungal phyla in the four groups. The relative abundances of Basidiomycota (range 19.27% ~ 29.26%), Ascomycota (range 26.09% ~ 62.29%, and Zygomycota (range 13.63% ~ 45.77%) accounted for more than 90% of the relative abundance across JYSH, CBGL, SZSZ, and TSBT (Fig. 4d). However, the relative abundances of these dominant fungal phyla showed some differences across the four groups. The relative abundance of Ascomycota in SZSZ was significantly higher than that in the other groups. In addition, the relative abundance of Zygomycota in SZSZ was significantly lower than that in other rhizosphere soils of ginseng cultivar (ANOVA, P < 0.05, Fig. S1b). At the class level, the main classes were Sordariomycetes (16.83%), Agaricomycetes (10.57%), Eurotiomycetes (9.29%), Dothideomycetes (8.81%) and Tremellomycetes (6.40%) based on the average relative abundance. Among them, Sordariomycetes was the dominant class in all groups except for TSBT, in which the main class was Agaricomycetes (15.54%) (Fig. 4e). At the genus level, Mortierella was the most abundant genus among the four groups (Fig. 4f). However, the distribution of dominant fungal genera showed differences across the four groups. Mortierella was more abundant in TSBT than in other groups (ANOVA, P < 0.05, Fig. 5b). Alternaria alternata, Cladosporium spp. and Fusarium spp. are potential pathogens causing root rot. Alternaria alternata and Cladosporium sp. agrAR069 were significantly more abundant in CBGL, JYSH and SZSZ than in TSBT (ANOVA, P < 0.05, Fig. 5c, d).

LEfSe of the bacterial and fungal communities in the rhizosphere of the four ginseng cultivars
To provide more information on the rhizosphere bacterial and fungal communities of the different cultivars, we used LEfSe to identify differentially abundant taxa among CBGL, JYSH, SZSZ and TSBT with a LDA score higher than 2.0. The LEfSe analysis of the rhizosphere bacterial community showed that there were 47 distinctly abundant taxa among the four groups. Of the 47 taxa, 11 were differentially abundant in CBGL, notably, Solibacteres, Acidobacteriia, DA052 and Gemmatimonadetes. The enriched taxa in JYSH were the phylum Nitrospirae and the Chloracidobacteria, Acidobac-teria_6 and Thermoleophilia classes. The distinctly abundant taxa in SZSZ were the Actinobacteria, Spartobacteria and Deltaproteobacteria classes as well as the order Rhizobiales. The Bacteroidetes, Ktedonobacteria, AD3, Verrucomicrobia and TM7 phyla, and the class Gammaproteobacteria were enriched in TSBT (Fig. 6a, S2a).
A total of 79 abundant fungal taxa significantly differed across CBGL, JYSH, SZSZ and TSBT. Among the 79 fungal taxa, 20 taxa were enriched in CBGL, The enriched fungal taxa in TSBT were the Zygomycota phylum and the Boletales order (Fig. 6b, S2b). In this study, we investigated bacterial and fungal communities that assemble on ginseng cultivars. The physical and chemical properties of soils as well as the temperature used to grow by various ginseng cultivars are different, but the soil physical and chemical properties and temperature were not significantly correlated with both bacterial and fungal communities. In addition, the PERMANOVAs result showed that the ginseng cultivars explained 86% and 82% of the variance in bacteria and fungi, respectively. In addition, Huang et al. (2017) demonstrated that the rhizosphere microbial community was obviously different in two cultivars of Brassica parachinensis L. Zhou et al. (2015) indicated that the microbial communities in rhizosphere of four cucumber cultivars varied significantly. Therefore, we inferred that the ginseng cultivars are the main factor affecting the bacterial and fungal community in this study.

Ginseng cultivars affect rhizosphere microbial diversity
We found that the different ginseng cultivars had significantly different microbial diversity in the rhizosphere soil. The microbial diversity may have been affected by a wide variety of factors, such as plant genotype and growth stage et al. (Chen et al. 2019;Wu et al. 2018). In our study, all soil samples of the four ginseng cultivars were collected at the same growth stage, which was the fruiting stage of ginseng cultivated for six years, thereby allowing us to exclude the impact of growth stage on the microbial community. Therefore, we inferred that ginseng cultivars were the main factor affecting rhizosphere microbial diversity. The root growth rate of four ginseng cultivars was different, which may have led to the inconsistency of root exudate composition. Different root exudates may promote or inhibit specific rhizosphere microbial taxa, thereby affecting the diversity of rhizosphere microorganisms. For instance, faster-growing durum wheat (Triticum turgidum ssp. durum) cultivar (PR22D89) showed lower root exudation and higher microbial diversity than seven other cultivars (Iannucci et al. 2021).
Furthermore, we found that fungal diversity was negatively correlated with bacterial diversity in all groups except for TSBT, which may be explained by the fact that long-term cultivation depleted the soil of nutrients such as carbon. Ginseng grown continuously for six years might result in nutrient deficiency stress in the microbial community of rhizosphere soil, which would lead to an imbalance in microbial diversity. A similar phenomenon has been found to occur in Rehmannia glutinosa rhizosphere microbes under consecutive monoculture ). In the present study, TSBT had the lowest bacterial diversity and fungal diversity of all the ginseng cultivar rhizosphere soils, which may have been caused by artificial factors, but the sampling methods for all rhizosphere soils were consistent, allowing us to rule out this possibility. However, the low diversity might be related to the agricultural management for BIAN-TIAO ginseng. COMMON ginseng, GAOLI ginseng and SHIZHU ginseng were planted directly in the field for six years, but BIANTIAO ginseng seedlings were grown for three years before transplanting them to another field (Zhao et al. 2007). The rhizosphere microbial community might be assembled early in plant development, and later transplantation may alter the natural microbial community diversity (Coleman-Derr et al. 2016). Therefore, the different method of agricultural management may influence the rhizosphere microbial diversity.
Ginseng cultivars change the composition of the microbial community in the ginseng rhizosphere Although no significant differences in the composition of bacterial and fungal communities were detected among the ginseng cultivars in the examination of different taxonomic levels, the abundance of certain dominant bacterial groups showed significant differences among the groups. These findings demonstrated that ginseng cultivars affected the composition of the rhizospheric microbial community. The different cultivars might not result in different specific taxa in the community and may lead to changes in the dominance of only certain taxa in the microbial community. Some microorganisms had a special affinity for certain plant cultivars, which is in accordance with previous studies showing the effect of plant cultivars on rhizosphere communities (Bressan et al. 2009;Meyer et al. 2010;Wang et al. 2019b).
Significant differences in the abundances of dominant bacterial phyla were found. For example, Proteobacteria was significantly enriched in SZSZ, and Acidobacteria had a high abundance in JYSH. Ying et al. (2012) also showed that Proteobacteria and Acidobacteria are the dominant phyla in the ginseng rhizosphere (Ying et al. 2012). Furthermore, Ascomycota was significantly abundant in SZSZ, and Agaricomycetes (belonging to the Basidiomycota phylum) was also more abundant in TSBT than in the other groups. Ascomycota and Basidiomycota are known to promote resistance to pathogens and tolerance to abiotic stresses, and they are widely found in the rhizosphere soils of plants (Mardanova et al. 2019). These taxa that were significantly present in the soils of the different ginseng cultivars indicate the specificity of the rhizosphere microorganisms of the different ginseng cultivars, and these microorganisms may participate in the growth of different ginseng cultivars. Furthermore, ginseng cultivars can affect the composition of rhizosphere microorganism communities.
Fungi are more susceptible to ginseng cultivars than bacteria By comparing the rhizosphere bacterial and fungal communities of the four ginseng cultivars, we found that the proportion of shared fungal OTUs was much smaller than that of bacterial OTUs between any two pairs of groups, suggesting that the fungal communities were more influenced by the cultivars than the bacterial communities. Previous studies have reported that bacterial communities are more resistant and resilient to environmental disturbances in terms of structure and diversity than fungal communities (Uroz et al. 2016). One explanation for this phenomenon is that bacteria metabolize a range of compounds, suggesting that bacterial communities are relatively stable (Wang et al. 2019a). In addition, bacteria and fungi reproduce differently and bacteria generally grow faster than fungi, which may also result in relatively stable bacterial communities that are not easily affected (Zheng et al. 2020). In a recent study of three Agave species, Coleman-Derr et al. (2016) also found that there was a larger fraction of shared bacterial OTUs than fungal OTUs. Furthermore, the Chao 1 index reflectes the species richness of community (Puig and Kokonendji 2018). In our study, the Chao 1 (species richness) index of fungi was lower than that of bacteria, which may have caused the numbers of shared fungal OTUs to be less than that of bacterial OTUs.
Rhizosphere microorganisms associated with pathogenicity and the survival time of ginseng In our research, we also found correlations the potentially pathogenic microorganisms and ginseng cultivars. For bacteria at the genus level, Bacillus was more abundant in SZSZ than in TSBT, CBGL and JYSH. Bacillus are Gram-positive, sporulating aerobes or facultative anaerobes that are widely distributed in the soil environment, and many isolates possess antifungal effects, promoting plant growth (Araújo et al. 2005;Phae and Shoda 1991). The enrichment of the Bacillus genus in SZSZ may be related to the high stress resistance of SHIZHU ginseng. Bacillus species produce antimicrobial substances (AMS) to prevent the deleterious effects of phytopathogens (Felske and Akkermans 1998;Tiwari et al. 2010).
For fungi, Mortierella was the most abundant genus in the rhizosphere of all ginseng cultivars, accounting for 26.67% of the total fungal sequences. Previous studies have suggested that some species of Mortierella produce antibiotics, and several isolates have been demonstrated as potential antagonistic agents against various plant pathogens (Somers et al. 2004). This taxon might also be regarded as an important indicator of Fusarium disease control in ginseng cultivation. In general, cultivated ginseng can grow for only 4-5 years. However, BIANTIAO ginseng has long survival time (Liu 1993). Mortierella was obviously enriched in TSBT, accounting for 44.93%. The long survival time of BIANTIAO ginseng may be related to the high abundance of Mortierella. Moreover, the relative abundances of Alternaria alternata and Cladosporium sp. agrAR069 were significantly higher in CBGL, JYSH and SZSZ than in TSBT in our study. Root rot is a common and severe disease caused by many pathogens, such as Alternaria alternata and Cladosporium spp., and occurs under the continuous growing of watermelon (Huang et al. 2020;Liu et al. 2019). In summary, BIANTIAO ginseng was not easily infected compared to the other ginseng cultivars, which may be related to specific microbial taxa. Understanding the potential relationships between the different ginseng cultivars and rhizosphere microorganisms is important for the development of the ginseng industry.

Conclusion
In this study, we reported the first comprehensive investigation of the rhizosphere soil bacterial and fungal communities of four ginseng cultivars, CBGL (GAOLI ginseng), JYSH (COMMON ginseng) and SZSZ (SHIZHU ginseng) and TSBT (BIANTIAO ginseng). The present study suggested that the ginseng cultivars were the main factors affecting the composition and diversity of the rhizosphere microbial community. We also discovered certain rhizosphere microorganisms that may be associated with pathogenicity and the long survival time of ginseng cultivars, including Bacillus, Alternaria alternata and Cladosporium sp. agrAR069. This discovery is benefits to the agricultural development of ginseng and provides a theoretical basis for the control of ginseng diseases and insect pests. In the future cultivation of ginseng, perhaps we can artificially increase or decrease the abundance of certain microorganisms to increase the survival time of cultivated ginseng. Because, the soil samples were collected from only one growing stage of ginseng (fruiting) in our study, our results do not represent the dynamic changes in the rhizosphere microbial community throughout the development stage of ginseng. Therefore, the rhizosphere soil from distinct growing stages of ginseng should be selected in future research, such as seedling and flowering, to clearly understand the dynamic changes in ginseng rhizospheric microorganisms and provide a scientific basis for the development of ginseng industry.