Physicochemical properties of sweet potato rhizospheric soil
Available Mn in the Xushu 18 (X18) and Yizi 138 (Y138) rhizospheric soils decreased by 32.68% and 31.14%, respectively, at the beginning of planting in 2016 than in 2015, and by 27.35% and 31.10% in the pre-harvest period (Table 1). The soil pH of the X18 and Y138 were decreased by 2.72% and 3.11%, respectively, at the beginning of planting in 2016 than in 2015; change in pH were not significant in the pre-harvest period. At the beginning of planting, available Ca in the X18 and Y138 rhizospheric soils increased by 29.80% and 38.97%, respectively; available Zn increased by 56.11% and 43.19% ,respectively in 2016 than in 2015. And available Ca increased by 30.75% and 26.47%, respectively, while available Zn increased by 29.46% and 30.81%, respectively, in the pre-harvest period in 2016 than in 2015. Available Fe in the X18 and Y138 soils decreased by 18.61% and 17.08%, respectively, in the pre-harvest period in 2016 than in 2015, but was not significantly different at the beginning of planting. Available B in the X18 rhizospheric soil decreased by 20.63% at the beginning of planting, while the change in the Y138 soil was not significant.
Rhizospheric soil bacterial α-diversity
The average coverage of all samples was 96.19% (Table 2). Rarefaction curves were close to plateau (Fig. 1), indicating that our sequencing depth was good. The reads ranged from 24,695 – 37,688 for samples, and the operational taxonomic units (OTUs) ranged from 3,137 – 3,734. Chao, Shannon, and Simpson indexes were computed based on the bacterial OTUs. Unlike the Shannon index, the larger the Simpson value, the lower the community diversity. The Chao and Shannon values of the X18 and Y138 soils were higher in the pre-harvest period than at the beginning of planting, while the opposite was true of the Simpson index, indicating that two communities had higher species richness and diversity in the pre-harvest period.
After X18 continuous cropping, the Chao index decreased by 2.53% and the Shannon and Simpson indices were basically unchanged at the beginning of planting in 2016 than in 2015; in the pre-harvest period, the Chao and Shannon indices increased by 5.95% and 1.59%, respectively, and the Simpson index decreased by 17.86%. After Y138 continuous cropping, the Chao and Shannon indices increased by 2.80% and 1.66%, respectively, and the Simpson indices decreased by 22.22% at the beginning of planting in 2016 than in 2015; in the pre-harvest period, the Chao and Shannon indices increased by 2.53% and 1.16%, respectively, and the Simpson index decreased by 14.29%. These indicated that the diversity and richness of rhizosphere soil bacteria of X18 and Y138 also increased after continuous cropping.
X18 had higher Chao and Shannon indices than Y138, which were contrary to the Simpson index. In other words, the bacterial richness and diversity were higher in X18 rhizospheric soil than in Y138 soil.
Community composition analysis of rhizospheric soil bacteria
At the phylum level (Fig. 2), the dominant bacterial phyla of all samples were 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 abundant phylum, followed by Acidobacteria and Actinobacteria.
After X18 and Y138 continuous cropping, Proteobacteria decreased by 17.30% and 8.05% , respectively, in the pre-harvest period. Acidobacteria showed a decreasing trend and finally increased slightly, while Actinobacteria showed the opposite trend. After continuous cropping, the Firmicutes content of X18 soil increased by 71.54% and 97.66% in the early planting and early harvest stages, respectively, and by 4.10% and 129.57%, respectively in Y138 soil. Moreover, In both varieties, the Firmicutes contents was higher at the beginning of planting than in the early harvest period of the same year. However, the opposite trend was observed for Planctomycetes. The Planctomycetes content of X18 in the early planting and early harvest stages decreased by 30.36% and 7.35%, respectively, while that of Y138 decreased by 40.51% and 19.04%, respectively. Further, the Chloroflexi and Gemmatimonadetes contents showed increasing trends. In X18 and Y138 rhizospheric soils, Chloroflexi increased by 81.09% and 96.69%, respectively ,and Gemmatimonadetes increased by 103.11% and 122.56%, respectively. Gemmatimonadetes was higher in Y138 rhizospheric soil than in X18 soil, especially in 2016.
At the genus level (Fig. 3), Subgroup 6_norank (6.59% – 14.74%), Nitrosomonadaceae_uncultured (1.83%–6.40%), and Anaerolineaceae_uncultured (1.75%–3.63%) were the top three dominant bacteria genera in all rhizospheric soils of X18 and Y138. Other major genera were 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, Subgroup 6_norank displayed decreasing trends in the X18 and Y138 rhizospheric soils, decreasing by 54.34% and 52.66%, respectively, and then increased slightly in the 2016 pre-harvest period. However, Nitrosomonadaceae-uncultured and Anaerolineaceae-uncultured were present at low levels at the beginning of planting, then were increased in the pre-harvest period of the same year. Bacillus and Lysobacter showed the opposite trend. Moreover, in every sampling period, Lysobacter was higher in the rhizospheric soil of X18 than in that of Y138. This was also true of Bacillus, except for the beginning of planting in 2015. Furthermore, in2016, the reduction of Lysobacter in X18 and Y138 rhizosphere soil was 1.3 and 2.4 times greater than in 2015.
Venn analysis of rhizospheric soil bacteria
Venn diagram revealed the overlapped and unique OTUs of all samples (Fig. 4). After two years of continuous cropping, the OTUs shared by all samples was 507. In the four sampling periods, there were 95, 158, 127, and 202 unique OTUs in the rhizospheric soils of X18, and 89, 124,141, and 159 unique OTUs in the rhizospheric soils of Y138 . As continuous cropping year increased, the specific OTUs in X18 soil increased by 33.68% and 27.85% in the early planting and early harvest periods, while the OTUs in Y138 soil increased by 58.43% and 28.23% in these periods.
The number of OTUs specific to X18 was greater than that specific to Y138 (except for the beginning of planting in 2016), indicating that continuous cropping led to changes in the bacterial communities in X18 and Y138 rhizosphere soil. These differences were largest during the early harvest period of 2016.
Heatmap, clustering, and principal component analysis (PCA) of rhizospheric soil bacteria
The results of heatmap and clustering analysis of 40 phyla in all samples are illustrated in Fig. 5, and clearly demonstrate the differences in rhizospheric soil bacterial composition between the X18 and Y138 varieties. The samples grouped into two clusters and samples from the same consecutive cropping times clustered together. In addition, X18 and Y138 samples from the same sampling periods grouped together.
The OTUs of X18 and Y138 were subjected to PCA. The extracted two principal components explained 72.48% of the total variation (Fig. 6). As continuous cropping time increased, samples from different sampling times became farther apart. However, at the same sampling times, X18 and Y138 samples were relatively close to each other. With continuous cropping, the distance between these samples also gradually increased, which indicated that differences between their bacterial communities were also increasing. These results were consistent with the results of the heatmap and cluster analyses in Fig. 5. Overall, the results suggested that (i) continuous cropping led to bacterial community structure changes in X18 and Y138 rhizosphere soil; (ii) rhizospheric soil bacterial community structures of X18 and Y138 were similar in the same sampling period.
Relationship between bacterial phyla and physicochemical characteristics of sweet potato rhizospheric soil
The results of redundancy analysis (RDA) on top ten bacterial phyla and environmental factors of X18 and Y138 rhizospheric soil are showed in Fig. 7. RDA1 and RDA2 explained 56.57% and 28.05% of the total variation, respectively. The magnitude of the effects of soil properties on bacterial community structure had the following order, soil pH > Ca > Mn > Zn > B > Fe. The results showed that soil pH (r2=0.9737, Pr=0.004) and available Ca (r2=0.8815, Pr=0.011) were significantly correlated with the bacterial community. It indicated that pH was a strong predictor of the X18 and Y138 rhizospheric soil bacterial community compositions.
In addition, the results of Spearman’s correlation coefficient analysis were as follows (Fig. 8). pH was positively correlated with Planctomycetes (R=0.97) and Acidobacteria (R=0.93), but had negative correlations with Actinobacteria (R = −0.79) and Firmicutes (R = −0.72); available Ca was positively related to Actinobacteria (R=0.89) and Gemmatimonadetes (R=0.86), and was inversely correlated with Acidobacteria (R = −0.79), Planctomycetes (R= −0.75), and Nitrospirae (R= −0.72). At the same time, it can be seen from 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 similar effects on the bacteria, which were different from the rest.