Diversity of the rhizosphere microbial community of different cultivars
In total, we obtained 727476 and 1452196 high-quality reads from all samples, and 4242 and 4830 OTUs were identified for bacteria and fungi with 97% sequence similarity, respectively (Table S2). The number of OTUs of bacterial and fungal communities detected for CBGL, JYSH, SZSZ and TSBT were 3093, 3288, 2937, 2541 and 2261, 1652, 2372, 1113, respectively (Fig 1). Intriguingly, the proportion of shared OTUs for the fungal community was relatively smaller than that for the bacterial community between every two soil groups.
There were no significant differences in bacterial diversity in the rhizosphere soil between CBGL and SZSZ according to the alpha diversity indices (i.e., observed species, Chao 1, Ace and Shannon indexes) (ANOVA, p > 0.05, Table 1). Among these groups, the highest bacterial richness was detected in JYSH (2212.1429 of observed species). Moreover, the fungal diversity varied considerably across the rhizosphere soil of the different ginseng cultivars (ANOVA, p < 0.05, Table 1), and SZSZ had a significantly higher species richness than the other samples (1116.5000 of observed species) (Table 1). Furthermore, JYSH had a lower level of fungal richness (673.4286 of observed species) than the other groups (Table 1). TSBT had the lowest microbial richness for both fungi and bacteria (the observed species was 548.6667 for fungi and 1661.0000 for bacteria). In addition, we also found that fungal diversity was negatively correlated with bacterial diversity in CBGL, JYSH and SZSZ.
Composition of the bacterial community
We assessed the taxonomic distributions of bacterial OTUs at different 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 made up 95% of the entire bacterial community. Proteobacteria, Acidobacteria and Verrucomicrobia were the most abundant phyla across all samples, accounting for 22.41% ~ 26.99%, 18.14% ~ 34.07% and 5.99% ~ 17.64% of the total valid reads in all samples, respectively (Fig 2a). Among them, Acidobacteria was the most abundant phylum in CBGL, and its relative abundance was significantly higher than that in the other groups (ANOVA, p < 0.05, Fig S1a), while Proteobacteria was the most abundant phylum across the other groups. The relative abundance of Proteobacteria was not different across the rhizospheres of the four ginseng cultivars (ANOVA, p > 0.05, Fig S1a). Moreover, there were significant differences among the four samples in their 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 (13.5682%), Spartobacteria (averaging 11.8407%), Acidobacteriia (averaging 8.4706%), Solibacteres (averaging 4.7707%) and Actinobacteria (averaging 4.5109%) (Fig 2c). 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, Fig 3a; 4a).
Composition of the fungal community
We also explored the fungal community by ITS sequencing with the same analysis method used for the 16S above. There were three dominant fungal phyla in the rhizosphere soil of all four ginseng cultivars. The relative abundances of Basidiomycota (range 19.2685% ~ 29.2577%), Ascomycota (range 26.0865% ~ 62.2524%, and Zygomycota (range 13.6333% ~ 45.7716%) accounted for more than 90% of the relative abundance across JYSH, CBGL, SZSZ, and TSBT (Fig 2b). However, the relative abundances of these dominant fungal phyla showed some differences across the four ginseng cultivars. The relative abundance of Ascomycota in SZSZ was significantly higher than that in the other samples (ANOVA, p < 0.05, Fig S1b). In addition, the relative abundance of Zygomycota in SZSZ was significantly lower than that in other ginseng cultivar rhizosphere soils (ANOVA, p < 0.05, Fig S1b).
At the class level, based on the average relative abundance, the main classes were Sordariomycetes (16.83%), Agaricomycetes (10.57%), Eurotiomycetes (9.29%), Dothideomycetes (8.81%) and Tremellomycetes (6.40%). Among them, Sordariomycetes was the dominant class in all groups except for TSBT, in which the main class was Agaricomycetes (15.54%) (Fig 2d). At the genus level, Mortierella was the most abundant genus among the four ginseng cultivars (Fig 3b). However, the distribution of dominant fungal genera showed differences across the four cultivars. Mortierella was more abundant in TSBT than in other samples (ANOVA, p < 0.05, Fig 4b), while Alternaria_alternata and Cladosporium_sp_agrAR069 were significantly more abundant in CBGL, JYSH and SZSZ than in TSBT (ANOVA, p < 0.05, Fig 5).
We performed beta diversity analysis for the rhizosphere bacterial and fungal communities to reflect the similarities among the different ginseng cultivars. The clustering results of the beta diversity analysis performed using the weighted UniFrac distance matrix and the Bray-Curtis distance matrix revealed a similar microbial community structure for the replicates in each group. We found that the bacterial and fungal compositions were obviously different among the four ginseng cultivars (Fig 6).
Linear Discriminant Analysis Effect Size (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 an LDA score higher than 2.0 (Fig S2a). The LEfSe analysis of the rhizosphere bacterial community showed that there were 47 distinctly abundant taxa among the four ginseng cultivars. 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 classes Chloracidobacteria, Acidobacteria_6 and Thermoleophilia. The distinctly abundant taxa in the rhizosphere soils of SZSZ were the classes Actinobacteria, Spartobacteria and Deltaproteobacteria and the Rhizobiales order. The Bacteroidetes, Ktedonobacteria, AD3, Verrucomicrobia and TM7 phyla and the Gammaproteobacteria class were enriched in TSBT (Fig 6a).
A total of 79 abundant fungal taxa were significantly different across CBGL, JYSH, SZSZ and TSBT (Fig S2b). Among the 79 fungal taxa, 20 taxa were enriched in CBGL, principally the Nectriaceae and Pleosporaceae families and the Tremellomycetes class. The abundant fungal taxa in the rhizosphere of JYSH were the Sordariales order and the Leotiomycetes and Capnodiales classes. The most distinctly abundant fungal taxa were Eurotiomycetes, Dothideomycetes and Agaricales in the SZSZ. The enriched fungal taxa in TSBT were the Zygomycota phylum and the Boletales order (Fig 6b).