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Composition of prokaryotic and viral community in continuously cropped field of Coptis chinensis Franch

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Abstract

Purpose

The important role of viral communities in various environments is being continuously revealed. However, the current understanding of viruses in soil ecosystem remains poor, especially in plant continuous cropping soils.

Methods

Here, we provide detailed information about prokaryotic and viral diversity, the functional classes of viral ORFs and virus-host linkage in Coptis chinensis continuously cropped fields and uncultivated fields by analyzing physiochemical characteristics, 16S rRNA gene sequencing and viromic data.

Results

Among prokaryotes, some specific bacteria, especially plant pathogens of the order Burkholderiales, were enriched in soil due to the continuous cropping of C. chinensis. For viruses, we recovered 1,029 viral contigs from continuous cropping and uncultivated soil samples. Continuous cropping of C. chinensis significantly influenced the diversity and abundance of soil viral communities and viral protein functions. Furthermore, we linked 9.06% of viral contigs to putative hosts, spanning 7 bacterial phyla and 2 archaeal phyla. Unfortunately, the specific bacteria enriched in C. chinensis continuous cropping soils were not predicted to be prokaryotic hosts of the recovered viruses.

Conclusion

Overall, these findings reveal the effects of C. chinensis continuous cropping on the diversity and composition of the prokaryotic and viral communities, and indicated how virus-host interactions influence the soil microbes in continuous cropping systems.

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Abbreviations

OTU:

Operational taxonomic unit

ORF:

Open reading frame

PCR:

Polymerase chain reaction

DNA:

Deoxyribonucleic acid

RNA:

Ribonucleic acid

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Acknowledgements

This work is supported by the National Key Research and Development Program of China for Traditional Chinese Medicine Modernization (2017YFC1702600), the National Natural Science Foundation (31600148), and the Natural Science Foundation of Shandong Province (ZR2021MC018). We would like to thank James Voordeckers for English language editing.

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Authors and Affiliations

  1. School of Biological Science and Technology, University of Jinan, Jinan, 250022, China

    Xiangyu Fan, Mengzhi Ji, Kaili Sun, Zhen Tian, Rongfeng Gao & Yang Liu

  2. Medical Research Institute, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China

    Muyuan Li, Guojian Liao & Changhua Hu

Authors
  1. Xiangyu Fan
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  2. Mengzhi Ji
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  3. Muyuan Li
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  7. Yang Liu
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  8. Guojian Liao
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  9. Changhua Hu
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Contributions

Xiangyu Fan and Changhua Hu designed the research; Xiangyu Fan, Mengzhi Ji, Muyuan Li, Kaili Sun, Zhen Tian, Rongfeng Gao and Yang Liu performed research and analyzed the data; Xiangyu Fan wrote the paper. Guojian Liao helped to modify the manuscript.

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Correspondence to Xiangyu Fan or Changhua Hu.

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The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. The authors declare no conflict of interest.

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Supplementary Information

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Figure S1.

The picture of experimental settings. (a) Original soil. (b) Continuous cropping soil. (PNG 4987 kb)

Supplementary file1 (TIF 12946 kb)

Figure S2.

The refraction curve with maximum read depth for the 16S rRNA gene sequences. (PNG 158 kb)

Supplementary file2 (TIF 9289 kb)

Figure S3.

Virus-host interaction network in genus level. Hexagons represent viruses and circles represent hosts. Blue hexagons represent viruses which lie in both soil types. Cyan hexagons represent viruses which lie in Original_soil sample. Purple hexagons represent viruses which lie in CC_soil sample. Line represents interaction between virus and its host(s). (PNG 124 kb)

Supplementary file3 (TIF 637 kb)

Supplementary file4 (XLSX 10 kb)

Supplementary file5 (XLSX 11 kb)

Supplementary file6 (XLSX 18 kb)

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Fan, X., Ji, M., Li, M. et al. Composition of prokaryotic and viral community in continuously cropped field of Coptis chinensis Franch. Plant Soil 481, 97–109 (2022). https://doi.org/10.1007/s11104-022-05620-0

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