Structure, Function, Diversity, and Composition of Fungal Communities in Rhizospheric Soil of Coptis chinensis Franch under a Successive Cropping System

Mohammad Murtaza Alami¹, Jinqi Xue², Yutao Ma³, Dengyan Zhu⁴, Aqleem Abbas⁵, Zedan Gong⁶, Xuekui Wang⁶

Affiliations

¹ Department of Crop cultivation and Farming system, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
² Department of Crop Science, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
³ Department of pharmaceutical botany, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
⁴ Department of Agronomy and seed science and technology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
⁵ The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
⁶ College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.

PMID: 32070003
PMCID: PMC7076387
DOI: 10.3390/plants9020244

Structure, Function, Diversity, and Composition of Fungal Communities in Rhizospheric Soil of Coptis chinensis Franch under a Successive Cropping System

Mohammad Murtaza Alami et al. Plants (Basel). 2020.

. 2020 Feb 13;9(2):244.

doi: 10.3390/plants9020244.

Authors

Mohammad Murtaza Alami¹, Jinqi Xue², Yutao Ma³, Dengyan Zhu⁴, Aqleem Abbas⁵, Zedan Gong⁶, Xuekui Wang⁶

Affiliations

¹ Department of Crop cultivation and Farming system, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
² Department of Crop Science, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
³ Department of pharmaceutical botany, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
⁴ Department of Agronomy and seed science and technology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
⁵ The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
⁶ College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.

PMID: 32070003
PMCID: PMC7076387
DOI: 10.3390/plants9020244

Abstract

Soil types and cropping systems influence the diversity and composition of the rhizospheric microbial communities. Coptis chinensis Franch is one of the most important medicinal plants in China. In the current study, we provide detailed information regarding the diversity and composition of rhizospheric fungal communities of the C. chinensis plants in continuous cropping fields and fallow fields in two seasons (winter and summer), using next-generation sequencing. Alpha diversity was higher in the five-year C. chinensis field and lower in fallow fields. Significant differences analysis confirmed more fungi in the cultivated field soil than in fallow fields. Additionally, PCoA of beta diversity indices revealed that samples associated with the cultivated fields and fallow fields in different seasons were separated. Five fungal phyla (Ascomycota, Basidiomycota, Chytridiomycota, Glomeromycota and Mucoromycota) were identified from the soil samples in addition to the unclassified fungal taxa and Cryptomycota, and among these phyla, Ascomycota was predominantly found. FUNGuild fungal functional prediction revealed that saprotroph was the dominant trophic type in all two time-series soil samples. Redundancy analysis (RDA) of the dominant phyla data and soil physiochemical properties revealed the variations in fungal community structure in the soil samples. Knowledge from the present study could provide a valuable reference for solving the continuous cropping problems and promote the sustainable development of the C. chinensis industry.

Keywords: C. chinensis; composition; continuous cropping; fungi diversity; rhizosphere; structure.

PubMed Disclaimer

Conflict of interest statement

The authors have no conflict of interest in this manuscript.

Figures

**Figure 1**
Alpha diversity indices of the fungal community in *C. chinensis* rhizosphere soils and fallow fields. Observed species richness (A), Shannon diversity index accounting for species abundance and evenness of distribution (B), Inverse Simpson diversity (C), Chao that estimates the actual species richness of sample (D), and the phylogenetic diversity (E) of FF, that is, the fallow field soil, where Y1 represents when one-year *C. chinensis* cultivated the soil, Y3 where three-year *C. chinensis* cultivated the soil, and Y5 indicates that five-year *C. chinensis* cultivated the soil. There were four independent replicates of each treatment.

**Figure 2**
Bray–Curtis dissimilarity hierarchical cluster tree of soil fungal community; in winter (A) and summer (B); FF: fallow field soil; Y1: one-year *C. chinensis* cultivated the soil; Y3: three-year *C. chinensis* cultivated the soil; and Y5: five-year *C. chinensis* cultivated the soil.

**Figure 3**
Principle coordinate analysis (PcoA); in winter (A) and summer (B); FF: fallow field soil; Y1: one-year *C. chinensis* cultivated the soil; Y3: three-year *C. chinensis* cultivated the soil; and Y5: five-year *C. chinensis* cultivated the soil.

**Figure 4**
Venn diagrams showed shared and unique species of fungi in winter (A) and summer (B); FF: fallow field soil; Y1: one-year *C. chinensis* cultivated the soil; Y3: three-year *C. chinensis* cultivated the soil; Y5: five-year *C. chinensis* cultivated the soil.

**Figure 5**
Multiple comparisons between the relative abundance of eight top fungal phyla: in winter (A) and summer (B); FF: fallow field soil; Y1: one-year *C. chinensis* cultivated the soil; Y3: three-year *C. chinensis* cultivated the soil; Y5: five-year *C. chinensis* cultivated the soil. * shows significant difference (p-value<0.05), ** shows significant difference (p-value<0.01), *** shows significant difference (p-value<0.001).

**Figure 6**
The relative abundance of three trophic modes in rhizosphere soil (A) relative abundance functional guild winter (B) and summer (C); FF: fallow field soil; Y1: one-year *C. chinensis* cultivated soil; Y3: three-year *C. chinensis* cultivated soil; Y5: five-year *C. chinensis* cultivated soil.

**Figure 7**
The length and angle of lines represent redundancy analysis (RDA) of the abundant fungal phyla and environmental variables in winter (A) and summer (B); Correlations between RDA axes and the environmental variables. Correlations between RDA axes and the rhizosphere fungal phyla are represented by words (i.e., the fungal phylum names). FF: fallow field soil; Y1: one-year *C. chinensis* cultivated soil; Y3: three-year *C. chinensis* cultivated soil; Y5: five-year *C. chinensis* cultivated soil; TCN: total content of Nitrogen; TCP: total content of phosphorus; TCK: total content of potassium; TOC: total organic carbon and pH.

**Figure 8**
The heatmap of the correlation between fungal phyla and physicochemical characteristics of rhizospheric soil (A) in winter and (B) in summer. This heatmap was created according to the result of Spearman’s correlation analysis. Positive relationships are represented in red, while negative relationships are represented in blue. The significant correlations are presented as asterisks (*, p < 0.05; **, p < 0.01; ***, p < 0.001).

See this image and copyright information in PMC

References

1. Teng H., Choi Y.H. Optimization of ultrasonic-assisted extraction of bioactive alkaloid compounds from Rhizoma coptidis (Coptis chinensis Franch.) using response surface methodology. Food Chem. 2014;142:299–305. doi: 10.1016/j.foodchem.2013.06.136. - DOI - PubMed
1. Song X., Pan Y., Li L., Wu X., Wang Y. Composition and diversity of rhizosphere fungal community in Coptis chinensis Franch. continuous cropping fields. PLoS ONE. 2018;13:e0193811. doi: 10.1371/journal.pone.0193811. - DOI - PMC - PubMed
1. Wang L., Zhang S.-Y., Chen L., Huang X.-J., Zhang Q.-W., Jiang R.-W., Yao F., Ye W.-C. New enantiomeric isoquinoline alkaloids from Coptis chinensis. Phytochem. Lett. 2014;7:89–92. doi: 10.1016/j.phytol.2013.10.007. - DOI
1. Fierer N., Lauber C.L., Ramirez K.S., Zaneveld J., Bradford M.A., Knight R. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J. 2012;6:1007–1017. doi: 10.1038/ismej.2011.159. - DOI - PMC - PubMed
1. Sun L., Gao J., Huang T., Kendall J.R.A., Shen Q., Zhang R. Parental material and cultivation determine soil bacterial community structure and fertility. Fems Microbiol. Ecol. 2015;91:1–10. doi: 10.1093/femsec/fiu010. - DOI - PubMed

Grants and funding

2017YFC1701000/This research was financially supported by the National Key R&D Program. Specialized Research on Modernization of Traditional Chinese Medicine. Large-scale cultivation of Huanglian (Coptis chinensis Franch) and two other Chinese medicinal plants with high

LinkOut - more resources

Full Text Sources

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Structure, Function, Diversity, and Composition of Fungal Communities in Rhizospheric Soil of Coptis chinensis Franch under a Successive Cropping System

Affiliations

Structure, Function, Diversity, and Composition of Fungal Communities in Rhizospheric Soil of Coptis chinensis Franch under a Successive Cropping System

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

Grants and funding

LinkOut - more resources

Full Text Sources