The rhizospheric soil physicochemical properties of sweet potato
After sweet potato continuous cropping two years, the content of available Mn in the rhizospheric soil of X18 and Y138 respectively decreased by 32.68% and 31.14% at the early stage of planting , and decreased by27.35% and 31.10% at the early stage of harvest. (Table 1). The soil pH of X18 and Y138 respectively decreased by 2.72% and 3.11% at the early stage of planting, the change was not significant at the early stage of harvest. The content of available Ca in the rhizospheric soil of X18 and Y138 respectively increased by29.80% and 38.97% , available Zn increased by 56.11% and 43.19% at the early stage of planting, and available Ca respectively increased by 30.75% and 26.47%, available Zn increased by 29.46% and 30.81% at the early stage of harvest. Available Fe of X18 and Y138 respectively decreased by 18.61% and 17.08% at the early stage of harvest, the change was not significant at the early stage of planting. The content of available B in the rhizospheric soil of X18 decreased by 20.63% at the early stage of planting, while the change of Y138 was not significant.
α-diversity of bacteria in rhizospheric soil of sweet potato
The average coverage of all samples was 96.19% (Table 2). The rarefaction curve of each sample had already approached a saturation plateau (Fig. 1), which indicated that the sequencing had reached saturation, and the results were thought to truly reflect the sample conditions. The reads of per sample ranged from 24695 to 37688. The OTUs of per sample ranged from 3137 to 3734. Richness index (Chao) and diversity index (Shannon and Simpson) of X18 and Y138 were calculated based on the number of bacterial OTUs. Unlike the Shannon index, the larger the Simpson index value, the lower the community diversity. The Chao and Shannon index values of X18 and Y138 were higher at the early stage of harvest than that at the early stage of planting, and they were the opposite of the Simpson index, indicating that species richness and diversity of the two communities at the early stage of harvest were higher. At the same time, the Chao and Shannon indexes of X18 were higher than those of Y138, which were contrary to the Simpson index. In other words, the richness and diversity of bacteria in the rhizospheric soil of X18 were higher than those of Y138.
Community composition analysis of bacteria in rhizospheric soil of sweet potato
At the phylum level (Fig. 2), X18 and Y138 rhizospheric soil bacteria mainly belonged to Proteobacteria (28.5%-34.9%), Acidobacteria (10.4%-21.1%), Actinobacteria (11.3%-18.1%), Planctomycetes (5.2%-9.9%), Chloroflexi (4.6%-9.1%), Bacteroidetes (3.4%-6.1%), Gemmatimonadetes (3.0%-7.4%), and Firmicutes (1.4%-10.9%). Among them, Proteobacteria was the most prevalent, and Acidobacteria and Actinobacteria were next.
After sweet potato continuous cropping two years, the content of Proteobacteria in the rhizospheric soil of X18 and Y138 decreased by 17.30% and 8.05% at the early stage of harvest, respectively. Acidobacteria in the rhizospheric soil of X18 and Y138 showed a decreasing trend and finally increased slightly, while Actinobacteria showed the opposite trend. The content of Firmicutes in the rhizospheric soil of X18 and Y138 was higher at the early stage of planting than that at the early stage of harvest. while the change of Planctomycetes was opposite. Further, the content of Chloroflexi and Gemmatimonadetes in the rhizospheric soil of X18 and Y138 showed an increasing trend, Chloroflexi respectively increased by 81.09% and 96.69%, and Gemmatimonadetes increased by 103.11% and 122.56%, respectively. In addition, the content of Gemmatimonadetes in the rhizospheric soil of Y138 was higher than that of X18, especially in 2016.
At the genus level (Fig. 3), the relative abundance of Subgroup 6_norank (6.59% - 14.74%), Nitrosomonadaceae_uncultured (1.83%-6.40%), Anaerolineaceae_uncultured (1.75%-3.63%) were the top three dominant bacteria genus in all rhizospheric soils of X18 and Y138, other major genus included Bacillus (0.65%-4.14%), MSB-1E8_norank (0.87%-3.83%), Tepidisphaeraceae_norank (1.71%-2.56% ), Xanthomonadales_norank (0.62%-2.08%), and Lysobacter (0.55%-2.06%). After two years of continuous cropping, the content of Subgroup 6_norank in the rhizospheric soil of X18 and Y138 showed a decreasing trend, respectively decreased by 54.34% and 52.66%, and then increased slightly at the early stage of harvest in 2016. However, Nitrosomonadaceae-uncultured and Anaerolineaceae-uncultured in the rhizospheric soil of X18 and Y138 were present at low levels at the early stage of planting but increased at the early stage of harvest. while Bacillus and Lysobacter showed the opposite trend. Moreover, in every sampling period, the content of Lysobacter in the rhizospheric soil of X18 was higher than that of Y138. Bacillus was the same as Lysobacter, except for the early stage of planting in 2015. In addition, In the second year of continuous cropping, the reduction of Lysobacter in the rhizospheric soil of X18 and Y138 was 1.3 times and 2.4 times of the reduction in the first year.
Venn analysis of bacteria in rhizospheric soil of sweet potato
Venn diagrams directly showed the overlapped and unique OTUs of all samples. (Fig. 4). After two years of continuous cropping, the number of OTUs shared by all samples were 507. In the four sampling periods, there were 95, 158, 127, and 202 unique OTUs in the rhizospheric soils of X18. However, the unique OTUs in the rhizospheric soils of Y138 were 89, 124,141, and 159, respectively. With the increase in continuous cropping time, the number of OTUs specific to X18 and Y138 showed an increasing trend. The number of OTUs specific to X18 was more than that of Y138 (except for the early stage of planting in 2016), indicating that continuous cropping led to changes in the rhizospheric soil bacterial communities of X18 and Y138. Further, the differences were largest during the early harvest period of 2016.
Heatmap and clustering analysis and PCA of bacteria in rhizospheric soil of sweet potato
Heatmap and clustering analysis results for the 40 phyla from the different samples were shown in Fig. 5. Based on the relative abundance value of the heatmap and color changes, the difference in bacteria composition in the rhizospheric soil of X18 and Y138 could be seen more clearly. Furthermore, the clustering results showed that all samples grouped into two large clusters and the samples of the same continuous cropping years were gathered together. In addition, X18 and Y138 from the same sampling period grouped together.
The OTUs of X18 and Y138 were subjected to PCA. The extracted two principal components explained 72.48% of the variation in total (Fig. 6). With an increase in continuous cropping years, the distribution of X18 samples at different sampling times was relatively discrete. A similar trend was observed for Y138. It indicated that bacterial community structure in rhizospheric soil of X18 and Y138 changed with the extension of continuous cropping time. However, in the same sampling period, X18 and Y138 samples were relatively close to each other. With the increase in continuous cropping time, the distance between these samples also gradually increased, which indicated that differences between their bacterial communities were also increasingly large. These results were consistent with the results of heatmap and cluster analysis in Fig. 5. Overall, these results indicated that (i) continuous cropping resulted in the changes of bacterial community structure in rhizospheric soil of X18 and Y138; (ii) bacterial community compositions in rhizospheric soil of X18 and Y138 were relatively similar in the same sampling period.
Relationship between dominant bacterialphyla and rhizospheric soil properties of sweet potato
RDA performed on the top 10 bacterial phyla and rhizospheric soil properties of X18 and Y138 showed that the first and second RDA components explained 56.57% and 28.05% of the total variation, respectively (Fig. 7). The effect of soil properties on bacterial community structure was found to occur in the following order: soil pH > Ca > Mn > Zn > B > Fe. To investigate the significances of the effects of soil environmental factors on bacterial community composition, we calculated the r2 and Pr. The results showed that soil pH (r2=0.9737, Pr=0.004), available Ca (r2=0.8815, Pr=0.011) were significantly correlated with the bacterial community. It indicated that soil pH was a strong predictor of bacterial community in the rhizospheric soil of X18 and Y138.
Moreover, Spearman’s correlation coefficient was used to evaluate the relationship between soil physicochemical properties and bacterial phyla abundance (Fig. 8). Results showed the following correlations between bacterial phyla and soil properties: pH was positively correlated with Planctomycetes (R = 0.97) and Acidobacteria (R = 0.93) and negatively correlated with Actinobacteria (R = −0.79) and Firmicutes (R = −0.72); available Ca was positively correlated with Actinobacteria (R=0.89) and Gemmatimonadetes (R=0.86), and negatively correlated with Acidobacteria (R = −0.79), Planctomycetes (R= −0.75) and Nitrospirae (R= −0.72); available Mn was positively correlated with Planctomycetes (R = 0.81) and Acidobacteria (R = 0.78), and negatively correlated with Gemmatimonadetes (R = −0.81) and Actinobacteria (R = −0.80). At the same time, it can be seen from the Fig.8 that the soil physicochemical properties were divided into two groups, with available Ca and available Zn clustered into one group and the rest clustered into another, indicating that available Ca and available Zn had a similar effect on the bacteria but different from the rest.