Diversity and composition of bacterial endophytes among plant parts of Panax notoginseng

Dong, Lixin; Cheng, Ruiyang; Xiao, Liang; Wei, Fang; Wei, Guangfei; Xu, Jiang; Wang, Yong; Guo, Xiaotong; Chen, Zhongjian; Chen, Shilin

doi:10.1186/s13020-018-0198-5

Cited by 60 publications

(56 citation statements)

References 40 publications

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“…Contrary to the order of bacterial endophytes observed in this study, Dong et al [39] observed relative abundances of bacterial endophytes, such Conexibacter, Gemmatimonas, Holophaga, Luteolibacter, Methylophilus, Prosthecobacter, Solirubrobacter, Bradyrhizobium, Novosphingobium, Phenylobacterium, Sphingobium, and Steroidobacter, in the above-ground parts of Panaxnoto ginseng. This showed that the diversity of endophytes varies, depending on the plant species.…”

Section: Discussioncontrasting

confidence: 99%

Seasonal Diversity of Endophytic Bacteria Associated with Cinnamomum camphora (L.) Presl.

2019

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Investigations on the density, diversity, and distribution of endophytic bacterial community associated with leaves of Cinnamomum camphora (L.) Presl. were carried out during three seasons using 16s rDNA high-throughput sequencing technology. Samples were collected from five species in Nanping (A, B, C, D, and E) and one from Fuqin (F) in the Fujian province, China in the months of April, July, and October (represented by 1, 2 and 3), indicating spring, summer, and early winter, respectively. Results from 16s rDNA sequences revealed 10,844,124 effective sequences. The highest OTUs (Operational taxonomic units) was highest in the A1 sample (1086), while the lowest was in C2 (509). Our observations showed that samples taken in October had the highest diversity of endophytes as indicated by the Shannon index (B3 = 5.3337), Chao1 (E3 = 1233.10), abundance-based coverage estimator (ACE) (A3 = 1764.72), and the Simpson indices of diversity (C3 = 0.1655) irrespective of the species. The order of the endophytes richness in the samples was April > July > October. The Ribosomal Database Project (RDP) classifier showed that the obtained sequences belonged to nine major phyla: Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Acidobacteria, Planctomycetes, Chloroflexi, and Fusobacteria. Proteobacteria accounted for the highest proportion in each sample, ranging from 35.15% to 89.72%. These sequences belonged mainly to 10 orders: Rhizobiales, Clostridiales, Peseudomonadales, Burkholderiales, Bacteroidales, Enterobacteriales, Rhodocyclales, Sphingomonadales, Lactobacillales, and Bacillales. Also, other taxa with possible taxonomic statuses, which were unclassified, were present.

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Section: Discussioncontrasting

confidence: 99%

Seasonal Diversity of Endophytic Bacteria Associated with Cinnamomum camphora (L.) Presl.

2019

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“…Illumina based sequencing were employed for the screening of endophytic bacterial diversity in the medicinal plant tree Peony and they reported Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and acidobacteria as dominat groups of bacterial endophytes (Yang et al, 2017). Panax notoginseng a medicinal plant with antihypertensive, antithrombic and neuroprotective bioactivities were screened for the diversity analysis of bacterial endophytes associated with the plant using the QUIIME Pineline and indicated the presence of Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes as major communities of bacterial endophytes in this plant (Dong et al,2018). Previous works on endophytes by Sessitsch et al, (2012) reported in the present study were also reported by various researchers with special mention to the endophyte-host interactive growth promotion (Brigido et al, 2019).…”

Section: Otu and Taxonomic Composition Analysissupporting

confidence: 76%

Diversity Analysis of Endophytic Bacterial Microflora in Emilia sonchifolia (Linn.) DC on Illumina Mi Seq Platforms

Urumbil¹,

Kumar²

2020

J. Pure Appl. Microbiol.

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Bacterial endophytes inhabiting medicinal plants are less explored, but are diverse and play crucial roles in regulating growth and development of the host. Metagenomics using Illumina MiSeq platform facilitate whole community level characterization. The present study reports the diversity of bacterial endophytic microflora from the medicinal plant Emilia sonchifolia (Linn.) DC. Metagenomic analysis of medicinal plants leads to the identification of novel organisms or genes which will help the correlative elucidation of plant-microbe interactions. Effective sequences were amplified from 16S rRNA gene V3-V4 variable region. OTU analysis at different taxonomic level clearly catalogues two Phyla viz. Proteobacteria and Firmicutes which belonged to Gammaproteobacteria and Bacilli. In these classes five orders such as Enterobacteriales, Pseudomonadales, Xanthomonadales, Bacillales and Betaproteobacteriales were detected. Among these orders five families were identified in which the most predominant was Enterobacteriaceae and Pseudomonadeaceae while the other three families viz. Xanthomanadaceae, Planococcaceae and Burkholderiaceae were less represented. At genus level very less number of bacteria were identified while a bulk majority remained unclassified. Of the seven identified genus the most prominent one was Pseudomonas followed by Stenotrophomonas, Cronobacter, Lysinibacillus, Pantoea, Kluyvera and Pseudorhodoferax. At species level only two were identified vz. Pseudomonas otitidis and P.geniculate. Alpha diversity analysis using various statistical indices like Simpson and Shannon explains the diversity of microbiome. Next generation sequencing survey of DNA sample extracted from host plant through metagenomic data screening identified different endophytic bacteria which are difficult to grow in culture conditions.

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“…and Corynebacterium sp. were found sporadically in the endophytic community of the in vitro cultured wheat varieties, but all of them were reported to be a part of endomicrobiome [45][46][47][48].…”

Section: Resultsmentioning

confidence: 99%

Endophytic Bacterial Microbiome Diversity in Early Developmental Stage Plant Tissues of Wheat Varieties

Žiarovská

Medo

Kyseľ

et al. 2020

Plants

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Endophytic bacteria are an important part of different functions in plants that lead to plants’ production characteristics as well as their stress response mechanisms. Endophytic bacterial diversity was analyzed in this study to describe 16S rRNA variability and changes in the leaves of drought-tolerant and drought-susceptible wheat when growth under in vitro conditions. A metagenomic analysis was applied and a pilot exploratory study was performed to prove this type of analysis as applicable to tracking endophytic bacterial diversity changes when a drought stress is applied to an in vitro culture of wheat. The study showed that the changes in the bacterial endophytes’ variabilities associated preferentially with the drought stress varietal characteristics of the analyzed wheat instead of the applied stress conditions.

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Diversity and composition of bacterial endophytes among plant parts of Panax notoginseng

Cited by 60 publications

References 40 publications

Seasonal Diversity of Endophytic Bacteria Associated with Cinnamomum camphora (L.) Presl.

Seasonal Diversity of Endophytic Bacteria Associated with Cinnamomum camphora (L.) Presl.

Diversity Analysis of Endophytic Bacterial Microflora in Emilia sonchifolia (Linn.) DC on Illumina Mi Seq Platforms

Endophytic Bacterial Microbiome Diversity in Early Developmental Stage Plant Tissues of Wheat Varieties

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