Diversity analysis and function prediction of rhizo- and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range
- Published
- Accepted
- Subject Areas
- Biodiversity, Ecology, Microbiology, Plant Science
- Keywords
- endophytic bacteria, invasive plant, bacterial community, 16S rRNA gene, plant-microbe interactions
- Copyright
- © 2018 Cheng et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 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.26701v1
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.
Author Comment
This is a submission to PeerJ for review.
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:
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.
Hinić V, Lang C, Weisser M, Straub C, Frei R, and Goldenberger D. 2012. Corynebacterium tuberculostearicum: a potentially misidentified and multiresistant corynebacterium species isolated from clinical specimens. Journal of Clinical Microbiology 50:2561-2567.
Kumar VA, Augustine D, Panikar D, Nandakumar A, Dinesh KR, Karim S, and Philip R. 2011. Brevibacterium casei as a cause of brain abscess in an immunocompetent patient. Journal of Clinical Microbiology 49:4374-4376.
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.