Diversity analysis and function prediction of rhizo- and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range
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Abstract
Because increasing evidence has confirmed the importance of plant-associated bacteria for plant growth and productivity, it is believed that interactions between bacteria and alien plants play an important role in plant invasions. However, the diversity of bacterial communities associated with invasive plants is poorly understood. Therefore, we investigated the diversity of rhizo- and endophytic bacteria associated with the invasive annual plant Senecio vulgaris L (Asteraceae) based on bacterial 16S rRNA gene data obtained from 57 samples of four S. vulgaris populations in a subtropical mountainous area in central China. Significant differences in diversity were observed between plant compartments. Rhizosphere harbored much more bacterial OTUs and showed higher alpha diversity than the leaf and root endosphere. Bacterial community composition differed substantially between compartments and locations in relative abundance profiles, especially at phyla and family level. However, the top five phyla (Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Acidobacteria) comprised more than 90% of abundance in all the bacterial communities. And similar endophytic communities with a shared core set of bacteria were observed from different S. vulgaris populations. According to the function prediction based on the identification and abundance information of the OTU, bacteria characterized as plant pathogens, as well as those involved in ureolysis and nitrate reduction, were rich in endophytic communities. This study reveals the microbiomes and their putative function in the invasive S. vulgaris plants and is also the first step for future studies on the role of interactions between bacteria and alien plants in plant invasions.
Cite this as
2018. Diversity analysis and function prediction of rhizo- and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range. PeerJ Preprints 6:e26701v1 https://doi.org/10.7287/peerj.preprints.26701v1note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
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This is a submission to PeerJ for review.
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Supplemental Information
Minimum and Maximum temperature in March and April 2016 in Shennongjia
Data of temperature were obtained from the local meteorological office.
The ten most abundant functional groups of bacterial communities associated with all samples and each compartment of Senecio vulgaris plants
Number of 16S rRNA gene sequences amplified from different plant compartments and sampling location
* contamination was from chloroplasts and mitochondria in the host plants
Number of 16S rRNA gene sequences annotated to different levels amplified from different plant compartments and sampling location
Core bacterial OTUs in leaf endosphere of Senecio vulgaris plants
/=unidentified taxa
Core bacterial OTUs in root endosphere of Senecio vulgaris plants
/=unidentified taxa
Function of Core bacterial OTUs in leaf endosphere of Senecio vulgaris plants
Reference:
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FAPROTAX: Downloaded from website http://www.zoology.ubc.ca/louca/FAPROTAX/lib/php/index.php?section=Home[p]
Function of Core bacterial OTUs in root endosphere of Senecio vulgaris plants
Reference:
Busse HJ, Denner EB, Buczolits S, Salkinoja-Salonen M, Bennasar A, and Kampfer P. 2003. Sphingomonas aurantiaca sp. nov., Sphingomonas aerolata sp. nov. and Sphingomonas faeni sp. nov., air- and dustborne and Antarctic, orange-pigmented, psychrotolerant bacteria, and emended description of the genus Sphingomonas. Int J Syst Evol Microbiol 53:1253-1260.
Zamora L, Vela AI, Palacios MA, Domínguez L, and Fernández-Garayzábal JF. 2012. First isolation and characterization of Chryseobacterium shigense from rainbow trout. BMC Veterinary Research 8:77. FAPROTAX: Downloaded from website http://www.zoology.ubc.ca/louca/FAPROTAX/lib/php/index.php?section=Home[p]
Sample name
Explanation for names of the samples used in this study
absolute abundunce of each OTU
This dataset shows number of reads annotated to OTUs. The rows are OTUs and the variables are samples. See explanations for them in the dataset "Sample name".
Relative abundunce of each OTU
This dataset shows abundunce percentage of each OTU in each sample. The rows are OTUs and the variables are samples. See explanations for them in the dataset "Sample name". The OTUs matching chloroplasts, mitochondrial or Viridiplantae were not in this dataset.
relative abundance of OTUs associated with each function annotated by FAPROTAX
DNA sequence data of the bacteria OTUs identified from rhizospere and endosphere of Senecio vulgaris plants
Additional Information
Competing Interests
The authors declare there are no competing interests.
Author Contributions
Dandan Cheng conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Zhongsai Tian performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Liang Feng authored or reviewed drafts of the paper, approved the final draft.
Lin Xu performed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.
Hongmei Wang authored or reviewed drafts of the paper, approved the final draft.
DNA Deposition
The following information was supplied regarding the deposition of DNA sequences:
We have submitted the sequence data in NCBI GenBank and the data can been see on https://www.ncbi.nlm.nih.gov/nuccore/?term=MG274323:MG279042[accn]
The data is also uploaded as a Supplemental File.
Data Deposition
The following information was supplied regarding data availability:
1) NCBI GenBank
2)URL https://www.ncbi.nlm.nih.gov/nuccore/?term=MG274323:MG279042[accn]
Funding
This work is supported by National Natural Science Foundation of China (31570537 and 31200425) and the Fundamental Research Funds for the Central Universities (CUG130411) granted to Dandan Cheng. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
