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Characteristics and Diversity of Endophytic Bacteria in Endangered Chinese Herb Glehnia littoralis Based on Illumina Sequencing

XIAOWEI HUO

XIAOWEI HUO

College of Pharmaceutical Science, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Hebei UniversityBaoding, China
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HUO, XIAOWEI
, 
YUE WANG

YUE WANG

College of Traditional Chinese Medicine, Hebei UniversityBaoding, China
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WANG, YUE
, 
DAWEI ZHANG

DAWEI ZHANG

Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of TechnologyChangzhou, China
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ZHANG, DAWEI
, 
TING GAO

TING GAO

  • Key Laboratory of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural UniversityQingdao, China
  • Shanghai Key Laboratory of Plant Functional Genomics and Resources (Shanghai Chenshan Botanical Garden)Shanghai, China
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GAO, TING
 and 
MENGMENG LIU

MENGMENG LIU

  • College of Traditional Chinese Medicine, Hebei UniversityBaoding, China
  • Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of TechnologyChangzhou, China
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LIU, MENGMENG
  
Sep 08, 2020
Characteristics and Diversity of Endophytic Bacteria in Endangered Chinese Herb Glehnia littoralis Based on Illumina Sequencing's Cover Image
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Article Category: original-paper
Published Online: Sep 08, 2020
Page range: 283 - 291
Received: Apr 17, 2020
Accepted: Jun 19, 2020
DOI: https://doi.org/10.33073/pjm-2020-031
Keywords
© 2020 Xiaowei Huo et al., published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Fig. 1.

Rarefaction curves based on the Shannon index OUT level. Error bars represent the standard error of four replicates.
Rarefaction curves based on the Shannon index OUT level. Error bars represent the standard error of four replicates.

Fig. 2.

Venn diagram showing the OTUs shared among different samples associated with G. littoralis.
Venn diagram showing the OTUs shared among different samples associated with G. littoralis.

Fig. 3.

The bacterial abundance of different tissues at the phylum level.
The bacterial abundance of different tissues at the phylum level.

Fig. 4.

Heatmap displaying the relative abundances of the most dominant genera (top 50) in each sample. The dendrogram represents complete-linkage agglomerative clustering, based on Euclidean dissimilarities.
Heatmap displaying the relative abundances of the most dominant genera (top 50) in each sample. The dendrogram represents complete-linkage agglomerative clustering, based on Euclidean dissimilarities.

Fig. 5.

Statistical comparison of the relative abundance at the family level by the Kruskal-Wallis H test. P < 0.05 was considered statistically significant.
Statistical comparison of the relative abundance at the family level by the Kruskal-Wallis H test. P < 0.05 was considered statistically significant.

Fig. 6.

Hierarchical cluster analysis of different microbiota in different samples using pairwise weighted UniFrac distances. L1, L2, L3, L4, four repetitions of the leaf; S1, S2, S3, S4, four repetitions of the stem; R1, R2, R3, R4, four repetitions of the root.
Hierarchical cluster analysis of different microbiota in different samples using pairwise weighted UniFrac distances. L1, L2, L3, L4, four repetitions of the leaf; S1, S2, S3, S4, four repetitions of the stem; R1, R2, R3, R4, four repetitions of the root.

Fig. 7.

Principal coordinate analysis (PCoA) based on Bray-Curtis dissimilarity between different samples.
Principal coordinate analysis (PCoA) based on Bray-Curtis dissimilarity between different samples.

Characteristics of effective tags from samples of endophytic bacteria and rhizosphere bacteria associated with G_ littoralis_

SampleSample siteNumber of tagsTotal length (bp)Average length (bp)Effective (%)
Leaf1161,49124,250,81639486.74
Leaf2270,53927,826,64739487.38
Leaf3372,50228,614,92639480.78
Leaf4456,67922,401,39339571.51
Stem1174,17629,259,67039485.41
Stem2271,88328,374,40839479.27
Stem3373,23228,877,13839466.46
Stem4468,97127,201,00639481.54
Root1174,70529,478,19139479.50
Root2270,45627,847,10539570.56
Root3353,18321,019,55039572.88
Root4472,01728,464,45939573.40

Operational taxonomic unit (OTU) richness and diversity indices of different samples associated with G_ littoralis with a 97% similarity cut-off_

Sample nameOTUs observedShannonChao1ACECoverage (%)
Leaf526 ± 34 b3.58 ± 0.43 b600 ± 66 b599 ± 69 b99.6
Steam555 ± 22 b3.73 ± 0.39 b613 ± 82 b616 ± 77 b99.6
Root694 ± 19 a4.60 ± 0.19 a803 ± 40 a818 ± 42 a99.6

The Adonis analysis of the difference among samples associated with G_ littoralis_

TissuesLeafStem
RootR2 = 0.68, p = 0.027R2 = 0.46, p = 0.041
StemR2 = 0.09, p = 0.748
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