Microbial diversity of ginseng rhizosphere soil treated with Pp-7250 co-bacterial agent
OTUs of bacteria groups BS, PS, PB and CK were 4618, 4386, 4197,and 5132, 4 OTUs were common to all samples, OTUs unique to groups PS and PB is 2440, 2959 (Fig. 4C1). OTUs of fungi groups BS, PS, PB and CK were 3009, 2753, 3101, 3061, 566 OTUs were common to all samples, 1479, 1252 unique to the groups PS and PB (Fig. 4C2). To further investigate the composition communities, all bacterial and fungi sequences were classified from phylum to species level (Table S8, 9).
The number of valid sequences and OTUs of the samples were significantly different between the BS, PS and PB treatment groups and the CK control group (P < 0.05) (Fig. 4D, E). Based on 16S rRNA sequences analysis, at 97% similarity level, it can be seen that the diversity and richness of bacteria in ginseng rhizosphere soil were reduced sequentially in the groups CK, BS, PS and PB, but the differences were not significant (P > 0.05) (Fig. 4D1-D4). Fungi ITS rDNA sequence analysis, Shannon index in groups PB and BS were lower than those in group CK (P < 0.05), and in group PB was significantly lower than in group BS (P < 0.05). Simpson index in group PB were both significantly lower than in groups CK and BS (P < 0.05) (Fig. 4E1-E4). It suggests that the Pp-7250 co-bacterial agent inhibited the growth of pathogenic fungi in the soil, thus reducing the species diversity of the ginseng rhizosphere soil microbial communities, but further analysis is required to determine which fungi were reduced.
The difference in ginseng rhizosphere soil microbial communities treated with Pp-7250 co-bacterial agent
PCoA analyses of the bacterial communities showed significant differences between groups, and the differences between groups were greater than that within groups (R > 0, P < 0.05). In the results of PCoA analysis based on bacterial OTUs, it can be seen that the bacterial communities in both PS and PB treatment groups were significantly separated from the groups CK and BS, as well as between the groups PS and PB, and significantly between the BS and CK groups (Fig. 5A). Combined with UPGMA cluster analysis, microbial agents BS, PS, and PB all had significant effects on soil microbial communities, and microbial agents PS and PB had greater effects (Fig. 5C). The differences in fungi Community Structure Similar to the bacterial community results, but there was a partial overlap between the groups CK and BS (Fig. 5B, D). These results suggested that the microbial communities have significantly changed after inoculation with different microbial agents.
Microbial community composition and dominant communities in ginseng rhizosphere soil microbial communities treated with Pp-7250 co-bacterial agent
Microbial taxa were identified on the basis of ASV. Relative abundance of the top 15 bacterial community at the phylum level in the ginseng rhizosphere soil (Fig. 6A, Table S10). Among them, Proteobacteria and Acidobacteria were the dominant bacterial taxa in the ginseng rhizosphere soil, with relative abundances of 49.31–69.49%. The relative abundance of Gemmatimonadota (5.65%) and Firmicutes (1.34%) in the group PB was significantly higher than that of the group CK (P < 0.05), and the relative abundance of Chloroflexi (10.33%, 12.99%) in the groups PB and PS was higher than that of the other treatment groups. Proteobacteria (29.94%, 21.29%) had higher abundance in groups PB and PS than in groups BS and CK (P < 0.05).
Relative abundance of the top 15 fungi community at the phylum level in the ginseng rhizosphere soil (Fig. 6B, Table S11), Basidiomycota and Ascomycota were the dominant fungi taxa in the ginseng rhizosphere soil, with relative abundances of 84.40 ~ 93.49%. The relative abundance of Basidiomycota (54.10%) in the group PB was significantly higher than that of the group CK (P < 0.05), and Ascomycota(39.39%)was the lowest in the group PB. The relative abundance of Mortierellomycota and Chytridiomycota in the groups PB and PS was significantly higher than that of the group CK (P < 0.05).
Based on abundance clustering heatmap of the top 80 bacterial community genus in ginseng rhizosphere soil and Table of the top 20 genus (Fig. 6C,E, Table S12). Among the bacterial genus with significant differences between groups were Rhodanobacter (3.52%), Candidatus_Solibacter (3.04%), Gemmatimonas (1.73%), Pseudolabrys (1.71%), Ellin6067 (1.55%), Acidibacter (0.58%), Bacillus (0.56%), etc, and Paenibacillus (0.02%) outside the top 20. The results of ANOVA analysis showed that, Rhodanobacter, Gemmatimonas, Pseudolabrys, Bacillus and Paenibacillus had the highest abundance in the group PB, which increased by 252.37%, 279.43%, 3146.68%, 602.59%, and 1537.07%, respectively, compared with CK (P < 0.05). Whereas Ellin6067 and Acidibacter had the lowest abundance in the group PB, decreasing by 40.50%, and 35.66%, respectively, compared to the group CK (P < 0.05). Furthermore, Candidatus_Solibacte (1.03%) in the group PS obtained significant enrichment (P < 0.05). Differences between the groups BS and CK were small.
Based on abundance clustering heatmap of the top 80 fungi community genus in ginseng rhizosphere soil and Table of the top 20 genus (Fig. 6D,F, Table S13). The fungi genus with significant differences between groups were Cortinarius (29.73%), Sebacina (7.47%), Tetracladium (7.41%), Fusarium (7.12%), and Russula (1.71%), Paecilomyces (2.35%), Trechispora (1.82%), Alternaria (1.05%), Saitozyma (0.51%), Ilyonectria (0.46%), etc. The abundance of Cortinarius, Russula, Paecilomyces, Trechispora in the group PB increased by 30.27%, 20.98%, 39.50%, 583.81% compared to the group CK (P < 0.05), whereas Fusarium, Tetracladium, Alternaria, and Ilyonectria had the lowest abundance in the group PB, which decreased by 27.60%, 91.81%, 45.43%, and 26.15% (P < 0.05), respectively, compared to the group CK. Saitozyma (0.14%) in the group PS obtained significant enrichment (P < 0.05). Differences between the groups BS and CK were small. It suggests that Pp-7250 co-bacterial agent had a significant effect on the ginseng rhizosphere soil microbial communities, promoting a decrease in beneficial bacteria and an increase in harmful bacteria.
Correlation analysis of rhizosphere soil microbial with disease index, agronomic traits, efficacy components and pesticides residue in ginseng treated with Pp-7250 co-bacterial agent
We conducted the Pearson correlation analysis to predict the relationship between microorganisms and disease indices, agronomic traits, efficacy components, and pesticide residue. The Pearson correlation coefficients showed that ginseng survival rates and disease prevention were significant positively correlated with the beneficial microorganism Gemmatimonas, Bacillus, Paenibacillus, Cortinarius, Paecilomyces and Trechispora (P < 0.05), and were significant negatively correlated with the fungal genera Fusarium, Mortierella, Tetracladium, Alternaria, and Ilyonectria (P < 0.05) (Fig. 7A). Ginseng plant length and root weight were significant positively correlated with the beneficial microorganism Paenibacillus, Cortinarius, Sebacina, Russula, Paecilomyces, and Trechispora (P < 0.05), and with the fungal genera Fusarium, Tetracladium, Alternaria, and Ilyonectria were significant negatively correlated (P < 0.05) (Fig. 7B). It was shown that ginseng diseases and growth are related to the species of rhizosphere soil microbial, and that Pp-7250 co-bacterial agent to increase the beneficial bacteria and reduce the harmful bacteria is a good strategy to improve ginseng production performance.
According to RDA analysis, nine ginsenoside monomers in ginseng in each treatment group showed significant positive correlation with group PB. The nine ginsenoside monomers showed significant positive correlation with the beneficial bacteria Bacillus, Paenibacillus, and Cortinarius in group PB (Fig. 7C1, C2). It indicated that Pp-7250 co-bacterial agent promoted the accumulation of ginsenosides by enriching ginseng rhizosphere soil beneficial microorganisms Bacillus, Paenibacillus, and Cortinarius. The degradation rates of pesticides PCNB, heptachlor and aldrin in ginseng showed significant positive correlation with group PB, PCNB and heptachlor showed significant positive correlation with the beneficial bacteria Paenibacillus and Cortinarius (P < 0.01), and aldrin showed significant positive correlation with Paenibacillus (P < 0.01) (Fig. 7D1, D2). It indicated that Pp-7250 co-bacterial agent promoted the degradation of ginseng pesticide residue by enriching by enriching ginseng rhizosphere soil beneficial microorganisms Bacillus, Paenibacillus, and Cortinarius.
Microbial community function in ginseng rhizosphere soil treated with Pp-7250 co-bacterial agent
Bacterial community function in ginseng rhizosphere soil treated with Pp-7250 co-bacterial agent
To gain insights into the direct effects of different treatment conditions on soil microbial function, 16S rRNA gene sequences were predicted using PICRUSt. Eight classes of biometabolic pathways were analysed, which were systematically classified into two or three layers within each broad class of metabolic pathways. The results, show a comparison of KEGG pathway abundance between the three treatment groups, indicating that the PB treatment group exhibited higher metabolism, environmental information processing, global and overview map function and lower human diseases (Fig. 8A, Table S14). Analysed at level 3, abundance of seven related functions including metabolic pathways (16.56%), biosynthesis of secondary metabolites (7.90%), biosynthesis of antibiotics (5.87%), biosynthesis of amino acids (3.56%), carbon fixation pathways in prokaryotes (1.02%), DNA replication (0.52%), and terpenoid backbone biosynthesis (0.48%) in ginseng rhizosphere soil, these seven functions were significantly higher in the group PB than in the control group (P < 0.05) (Fig. 8B). The Pp-7250 co-bacterial agent promoted ginseng growth, ginsenoside accumulation, pesticides residue degradation, and reduced ginseng disease rate by regulating the function of ginseng rhizosphere soil bacterial communities.
Fungi community function in ginseng rhizosphere soil treated with Pp-7250 co-bacterial agent
FUNGuild was used to predict the nutritional and functional groups of the fungal communities with different treaments. The four treatments had different trophic modes, including pathotroph, saprotroph and symbiotroph (Fig. 8C). The relative abundance of pathotroph was significantly reduced in the group PB compared to the group CK (P < 0.05), whereas the differences in the relative abundance of saprotroph and symbiotroph were not significantamong the groups (P > 0.05). Further analysing the 27 categories of the three nutritional patterns, plant pathogen and animal pathogen were significantly lower in the group PB than in the other groups(P < 0.05). plant pathogen and animal pathogen were significantly positively correlated with disease (P < 0.05), and were significantly negatively correlated with growth potential (plant height, fresh weight, etc.) (P < 0.05). (Fig. 8D, Table S15). The Pp-7250 co-bacterial agent promoted ginseng growth, ginsenoside accumulation, pesticides residue degradation, and reduced ginseng disease rate by regulating the function of ginseng rhizosphere soil fungi communities.