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European Journal of Plant Pathology

, Volume 155, Issue 4, pp 1211–1223 | Cite as

Assessing the potential of culture-independent 16S rRNA microbiome analysis in disease diagnostics: the example of Dianthus gratianopolitanus and Robbsia andropogonis

  • Marco Enrique Mechan-Llontop
  • Long Tian
  • Vivian Bernal-Galeano
  • Ella Reeves
  • Mary Ann Hansen
  • Elizabeth Ann Bush
  • Boris Alexander VinatzerEmail author
Article

Abstract

The goal of this study was to determine if culture-independent 16S rRNA sequencing of plant-associated microbiomes could facilitate disease diagnosis of cheddar pinks (Dianthus gratianopolitanus) with symptoms of leaf spotting at a Virginia nursery. The microbiome composition of cheddar pinks at the same nursery and at a second nursery in the absence of any disease outbreak was determined as well. After the pathogen was identified as Burkholderia andropogonis (synonym: Robbsia andropogonis) in a parallel culture-dependent study, the microbiome of plants artificially inoculated with R. andropogonis was also analyzed. The genus Robbsia was found to be ubiquitously present on all Dianthus gratianopolitanus nursery plants. However, because of the low resolution of 16S rRNA sequencing, it was not possible to determine the presence or absence of the pathogen at the species level. While relative abundance of Robbsia sequences had slightly increased during the disease outbreak, symptomatic plants did not have a significantly higher abundance of Robbsia than asymptomatic plants. Only microbiomes of artificially inoculated plants were dominated by Robbsia. We conclude that culture-independent microbiome analysis using 16S rRNA sequencing was unable to aid disease diagnosis in this specific case. Limitations and potential of the approach in disease diagnosis in general are discussed.

Keywords

16S rRNA amplicon sequencing Dianthus Robbsia andropogonis Pathogen identification Disease diagnostics 

Notes

Funding information

This work was supported by the Virginia Agricultural Experiment Station and the Hatch Program of the National Institute of Food and Agriculture, US Department of Agriculture, the College of Agriculture and Life Sciences, Virginia Tech, and by the National Science Foundation, grant IOS-1354215. Funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Research involving human participants and/or animals

Not applicable. The study did not involve either humans or animals.

Informed consent

Not applicable. The study did not involve human participants.

Supplementary material

10658_2019_1850_MOESM1_ESM.pdf (771 kb)
Figure S1 Rarefaction curves of all individual samples drawn from raw data. (PDF 771 kb)
10658_2019_1850_MOESM2_ESM.pdf (3.4 mb)
ESM 2 (PDF 3470 kb)
10658_2019_1850_MOESM3_ESM.xlsx (655 kb)
ESM 3 (XLSX 655 kb)

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Copyright information

© Koninklijke Nederlandse Planteziektenkundige Vereniging 2019

Authors and Affiliations

  1. 1.School of Plant and Environmental SciencesVirginia TechBlacksburgUSA

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