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Changes in the soil microbial community are associated with the occurrence of Panax quinquefolius L. root rot diseases

  • Jinglong JiangEmail author
  • Miao Yu
  • Ruping Hou
  • Li Li
  • Xuming Ren
  • Chengjin Jiao
  • Lingjuan Yang
  • Hao Xu
Regular Article

Abstract

Background and aims

Root-rot disease, a catastrophic disease of Panax quinquefolium L. causes yield reduction and serious economic losses. However, knowledge of the relationship between rhizosphere microbial community and root-rot disease is limited. This study is aim to test whether the bacteria and fungi community differed between the soil attached to healthy and rotten roots of American ginseng. Moreover, the effects of American ginseng cultivation for 4 years on changes of soil physiochemical properties and microbial community were also investigated.

Methods

High-throughput sequencing (Illumina MiSeq) was used to investigate the difference of microbial communities in the soils of new farmland (C) and the rhizosphere soils around healthy (H) and root rot diseased ginseng (R).

Results

Cultivation of American ginseng for 4 years not only changed the soil physicochemical properties, but also significantly increased the richness of the soil bacteria and decreased the fungal richness and diversity. Compared with other genera, the bacterial genera Nitrospira and the fungal genera Gibberella and Podospora were strongly enriched in the soil of new farmland. However, the relative abundance of Janthinobacterium, Nitrospira and Pedomicrobium in bacterial community, and Mrakia, Paradendryphiella, Sporopachydermia, Myrothecium and Racocetra in fungal community were significantly decreased after culture of American ginseng. The results also showed that the bacteria and fungi community differs between the soil attached to healthy and rotten roots of American ginseng. The richness indices of fungal community showed a significant decrease in rhizosphere soils of R comparing with H. The bacteria Rhodoplanes and Kaistobacter were the dominant genera in the H sample, whereas Sphingobium was dominant in the R sample. Notably, Monographella was significantly higher in the R sample (23.13%) than that of H sample (2.90%). In addition, the fungi Melanophyllum and Staphylotrichum were the most differently abundant in the H sample, whereas Mortierella and Cistella were the differently abundant genera in the R sample.

Conclusions

Our results indicate that cultivation of American ginseng changed the edaphic factors and the soil microbial community, and there are significant differences in the microbial community between the soil attached to healthy and rotten roots of American ginseng.

Keywords

American ginseng Root rot diseases Community diversity Illumina MiSeq sequencing 

Abbreviations

ACE

Abundance based coverage estimator

ANOSIM

Analysis of similarities

ANOVA

Analysis of variance

CAG

Cultivate American ginseng

EC

Electrical conductivity

HCN

Hydrogen cyanide

ITS

Internal transcribed spacer

LDA

Linear discriminant analysis

LEfSe

Linear discriminant analysis effect size

OM

Organic material

OTUs

Operational taxonomic units

PCoA

Principal co-ordinates analysis

PCR

Polymerase chain reaction

Phl

2,4-diacetylphloroglucinol

QIIME

Quantitative insights into microbial ecology

SRA

Sequence Read Archive

SPSS

Statistical product and service solutions

UNITE

unite.ut.ee

WPGMA

Weighted pair group method with arithmetic averages

Notes

Acknowledgements

We thank Anita K. Snyder, M.Sc. for the helpful suggestions and language polishing on this manuscript. This research was supported by the National Natural Science Foundation of China (31660153), Shaanxi Province Key Research and Development Project (2018NY-042), China, Shaanxi Key Projects of International Cooperation in Science and Technology Innovation (2015KTTSSF01-02), China.

Compliance with ethical standards

Conflict of interest

The authors declare no conflicts of interest.

Supplementary material

11104_2018_3928_MOESM1_ESM.doc (30 kb)
ESM 1 (DOC 30 kb)
11104_2018_3928_Fig5_ESM.png (412 kb)
Fig. S1

The flow chart of the experimental procedure (PNG 412 kb)

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High Resolution Image (TIF 840 kb)
11104_2018_3928_Fig6_ESM.png (124 kb)
Fig. S2

Length distribution of bacterial and fungal sequences. (PNG 123 kb)

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High Resolution Image (TIF 375 kb)
11104_2018_3928_Fig7_ESM.png (583 kb)
Fig. S3

Rarefaction curves measuring the observed species in bacterial and fungal communities. (PNG 583 kb)

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High Resolution Image (TIF 795 kb)
11104_2018_3928_Fig8_ESM.png (134 kb)
Fig. S4

Weighted Pair-Group Method with Arithmetic Averages (WPGMA) dendrogram constructed from ThetaYC distances of bacterial and fungal communities in each sample. (PNG 133 kb)

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High Resolution Image (TIF 343 kb)
11104_2018_3928_Fig9_ESM.png (826 kb)
Fig. S5

Hierarchical clustering of the bacterial and fungal communities based on the top 50 genera in the different soil samples. (PNG 825 kb)

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High Resolution Image (TIF 1179 kb)
11104_2018_3928_Fig10_ESM.png (19.4 mb)
Fig. S6

Spearman’s correlation network analysis of dominant bacterial (top) and fungal (bottom) species interactions. Nodes represent dominant genera. A line between two nodes indicates that there is a correlation between the two genera. A negative correlation is indicated by a green line, while a positive correlation is indicated by orange. The more connections to a node, the more associations this genus has with other members of the flora. (PNG 19899 kb)

11104_2018_3928_MOESM7_ESM.tif (25.5 mb)
High Resolution Image (TIF 26127 kb)

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© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.School of Biological Science and EngineeringShaanxi University of TechnologyHanzhongChina
  2. 2.School of Chemical and Environmental SciencesShaanxi University of TechnologHanzhongChina
  3. 3.School of Bioengineering and BiotechnologyTianshui Normal UniversityTianshuiChina

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