Diversity patterns of soil microbial communities in the Sophora flavescens rhizosphere in response to continuous monocropping

Abstract

Background: Continuous monocropping can affect the physicochemical and biological characteristics of cultivated soil. Sophora flavescens is a valuable herbal medicine and sensitive to continuous monocropping. Currently, diversity patterns of soil microbial communities in soil continuous monocropping with S. flavescens have not been extensively elucidated.

Results: In this study, comparative 16S rDNA and internal transcribed spacer (ITS) MiSeq sequencing analyses were used to examine the taxonomic community structure and microbial diversity in nonrhizosphere soil (CK) and rhizosphere soils (SCC, TCC, and FCC) sampled from fields that had undergone two, three, and five years of continuous monocropping, respectively. Among the microbial communities, a decreased abundance of Acidobacteria and increased abundances of Proteobacteria and Bacteroidetes were found with the increase in monocropping years of S. flavescens. As the continuous monocropping time increased, the diversity of the bacterial community decreased, but that of fungi increased. Redundancy analysis also showed that among the properties of the rhizosphere soil, the available phosphorus, organic matter, total nitrogen, and sucrase had the greatest impacts on the diversity of the rhizosphere microbial community. Moreover, a biomarker for S. flavescens soil was also identified using the most differentially abundant bacteria and fungi in soil samples.

Conclusions: Our study indicates that long-term monocropping exerted great impacts on microbial community distributions and soil physicochemical properties. The relationship between microbial community and physicochemical properties of rhizosphere soil would help clarify the side effects of continuous S. flavescens monocropping. Our study may aid in uncovering the theoretical basis underlying obstacles to continuous monocropping and provide better guidance for crop production.

Keywords: Continuous monocropping; Microbial community; Rhizosphere soil; Soil physicochemical property; Sophora flavescens.

Fig. 1

Distribution of the ten most abundant bacterial (a) and fungal (b) phyla of rhizosphere soil after various years of continuous monocropping with S. flavescens. The bar length on the outer ring represents the percentage of each phylum in each sample

Fig. 2

OTUs of microbial communities in rhizosphere and CK soils. a Flower plots showing the number of sample-specific OTUs (in the petals) and core OTUs (in the center) for all samples. b Venn diagram of OTUs observed as unique or shared among the four sites. The number of each site contains all the identified OTUs from all replicates. The above description also applies to c and d

Fig. 3

Alpha diversity of soil microbial communities at sites after various years of continuous monocropping with S. flavescens. The top and bottom panels show the estimates of bacterial and fungal alpha diversity of each sample, respectively. Different lowercase letters above the boxplots indicate significant differences between different samples according to one-way ANOVA with Duncan’s multiple range test (P < 0.05)

Fig. 4

Unweighted UniFrac clustering and NMDS of microbial communities in S. flavescens rhizosphere and CK soils. A and B show the unweighted UniFrac heatmaps for all samples, demonstrating the similarity of the microbial community structure between rhizosphere and CK soils. C and D show two-dimensional, nonmetric multidimensional scaling (NMDS) results representing the bacterial and fungal communities present in the four S. flavescens sampling sites

Fig. 5

RDA plots of the bacterial (a) and fungal (b) communities with respect to environmental variables in the root zone of S. flavescens. AP (mg/kg), OM (g/kg), sucrase (mg/g), TN (g/kg), urease (mg/g)

Fig. 6

LEfSe analysis of bacterial 16S rDNA (a) and fungal ITS rDNA (b) sequences with different abundances between soil samples. The circles radiating from inside to outside represent the taxonomic level from phylum to genus. Each small circle at a different classification level represents a classification at that level, and the diameter of the small circle is proportional to the relative abundance of that taxon. The nonsignificantly different species are uniformly colored yellow, and the different species biomarkers are colored the same as the groups. Green nodes represent the microbial groups that play an important role in the control group, and red, blue, and purple nodes represent the microbial groups that play an important role in the SCC, TCC, and FCC groups, respectively. The names of species represented by letters are shown in the legend on the right