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

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.