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Rapid identification of bacteria associated with Acute Oak Decline by high‐resolution melt analysis
Author(s) -
Brady C.,
Allainguillaume J.,
Denman S.,
Arnold D.
Publication year - 2016
Publication title -
letters in applied microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.698
H-Index - 110
eISSN - 1472-765X
pISSN - 0266-8254
DOI - 10.1111/lam.12593
Subject(s) - phylogenetic tree , biology , subspecies , high resolution melt , 16s ribosomal rna , enterobacteriaceae , sequence analysis , population , bacteria , identification (biology) , gene , microbiology and biotechnology , genetics , botany , escherichia coli , zoology , polymerase chain reaction , demography , sociology
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. Significance and Impact of the Study 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.