title: Rapid identification of bacteria associated with Acute Oak Decline by high-resolution melt analysis.
abstract: Two Gram-negative Enterobacteriaceae, Gibbsiella quercinecans and Brenneria goodwinii, are frequently isolated from oak suffering from Acute Oak Decline. These two species are difficult to identify based on colony morphology, carbohydrate utilization or 16S rRNA gene sequence, and identification using gyrB gene sequencing is time-consuming and laborious. A rapid identification technique, based on high-resolution melt analysis of the atpD gene, was designed to efficiently process numerous isolates from an increasing number of affected woodlands and parks. Principal component analysis of the resulting melt curves from strains of G. quercinecans, B. goodwinii and their close phylogenetic relatives allowed differentiation into distinct clusters based on species or subspecies identity.
  
  
  CONCLUSIONS
  Acute Oak Decline is an increasing threat to Britain's native oak population. Two novel bacterial species both belonging to the family Enterobacteriaceae, Gibbsiella quercinecans and Brenneria goodwinii, are thought to play an important role in symptom development. Here, we describe a rapid identification technique using high-resolution melt analysis of the atpD gene able to assign isolates to either G. quercinecans or B. goodwinii in a single assay, greatly reducing the time taken to identify if either or both of these species are present in symptomatic oak.
authors.affiliation: Faculty of Health and Applied Sciences, Centre for Research in Bioscience, University of the West of England, Bristol, UK.
authors.forename: C
authors.identifier: http://orcid.org/0000-0001-8035-9491
authors.initials: C
authors.lastname: Brady
authors.affiliation: Faculty of Health and Applied Sciences, Centre for Research in Bioscience, University of the West of England, Bristol, UK.
authors.forename: J
authors.initials: J
authors.lastname: Allainguillaume
authors.affiliation: Forest Research, Centre for Ecosystems Society and Biosecurity, Farnham, UK.
authors.forename: S
authors.initials: S
authors.lastname: Denman
authors.affiliation: Faculty of Health and Applied Sciences, Centre for Research in Bioscience, University of the West of England, Bristol, UK.
authors.forename: D
authors.initials: D
authors.lastname: Arnold
mesh_terms: D015373:Bacterial Typing Techniques; D027081:DNA Gyrase / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics; D004755:Enterobacteriaceae / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D009691:Nucleic Acid Denaturation; D010802:Phylogeny; D010935:Plant Diseases / Q000382:microbiology*; D025341:Principal Component Analysis; D029963:Quercus / Q000382:microbiology*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics*; D006113:United Kingdom
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D014157:Transcription Factors; D027081:DNA Gyrase
keywords: Acute Oak Decline; Brenneria goodwinii; Gibbsiella quercinecans; High-resolution melt; identification