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. 2019 Jul 17;9(1):10389.
doi: 10.1038/s41598-019-46863-9.

Diversity of culture-independent bacteria and antimicrobial activity of culturable endophytic bacteria isolated from different Dendrobium stems

Shan-Shan Wang  1   2 , Jia-Meng Liu  3   4 , Jing Sun  1   2 , Yu-Feng Sun  1   2 , Jia-Ni Liu  1   2 , Ning Jia  1   2 , Bei Fan  5   6 , Xiao-Feng Dai  7   8
Affiliations

Diversity of culture-independent bacteria and antimicrobial activity of culturable endophytic bacteria isolated from different Dendrobium stems

Shan-Shan Wang et al. Sci Rep. .

Abstract

Dendrobium is known for its pharmacological actions including anti-cancer effect, anti-fatigue effect, gastric ulcer protective effect, and so on. At present, only studies on endophytic fungi of Dendrobium affecting the metabolites of host plants have been reported, very little research has been done on endophytic bacteria. In this study, we have demonstrated the great diversity of endophytic bacteria in 6 Dendrobium samples from different origins and cultivars. According to the results of the culture-independent method, the endophytic bacterial community in Dendrobium stems showed obvious different in the 6 samples and was influenced by origin and cultivar. Some bacteria including Ralstonia, Comamonas and Lelliottia were first detected in Dendrobium in this study. Based on the culture-dependent method, a total of 165 cultivable endophytic bacteria isolates were isolated from the sterilized Dendrobium stems, and were classified into 43 species according to the 16S rRNA gene sequence analysis. Moreover, 14 of the 43 strains showed antimicrobial activity against phytopathogen using the Kirby-Bauer method. Strain NA-HTong-7 (Bacillus megaterium, 99.12%) showed the highest antimicrobial activity. This study was the first comprehensive study on endophytic bacteria of Dendrobium from different origins and cultivars, which provides new insights into the endophytic bacteria from Dendrobium.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Composition and relative abundance of endophytic bacterial in different samples on the genus level (The color of the column represents the different genera, and the length of the column represents the proportion size of the genus. Sequences that could not be classified into any known group were assigned as “unclassified”. Genera making up less than 1% of total composition in each sample were classified as “other”).
Figure 2
Figure 2
The differences among the samples in the grouping (a- Partial Least Squares Discriminant Analysis (PLS-DA) illustrates differences between bacterial communities in the 6 samples; b- Heatmap of the top 50 most abundant genera in bacterial communities detected in the 6 samples. Dendrograms for hierarchical cluster analysis grouping genera and sample locations are shown at the left and at the top, respectively).
Figure 3
Figure 3
The phylogenetic tree of the 43 species identified in this study (GenBank accession numbers are given in parentheses. Strain name: medium type-sample type- strain number. For example: GP-HM-1 means that the bacterial strain No. 1 isolated from D. huoshanense collected from Huoshan using M-WA agar (GP) culture medium).
Figure 4
Figure 4
Diversity of endophytic bacteria composition of cultivable endophytes (a -Percent of cultivable endophytes on Genus level on the whole; b - Comparison of Genus level distributions for the 6 samples).
Figure 5
Figure 5
Composition and relative abundance of endophytic bacterial phyla in different samples (a -Percent of the culture-independent endophytic bacteria on phylum level on the whole; b - Percent of the cultivable endophytic bacteria on phylum level on the whole).
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