Identification of bacteria pathogenic to or associated with onion (Allium cepa) based on sequence differences in a portion of the conserved gyrase B gene

• Published in: Journal of microbiological methods 2014-08, Vol.103, p.138-143
• Main Authors: Bonasera, Jean M., Asselin, Jo Ann E., Beer, Steven V.
• Format: Article
• Language: English
• Subjects: Allium cepa; Amino Acid Sequence; Bacteria; Bacteria - classification; Bacteria - genetics; Bacteria - isolation & purification; Bacteria - pathogenicity; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Biodiversity; Conserved Sequence; DNA Gyrase - chemistry; DNA Gyrase - genetics; Enterobacteriaceae; Gyrase B; High-Throughput Screening Assays; Identification-bacteria; Molecular Sequence Data; Molecular Typing - methods; Onion; Onions - microbiology; Pathogenic-bacteria; PCR; Protein Interaction Domains and Motifs; Sensitivity and Specificity; Sequence Analysis, DNA
• ISSN: 0167-7012; 1872-8359
• DOI: 10.1016/j.mimet.2014.06.002

We have developed a method for the identification of Gram-negative bacteria, particularly members of the Enterobacteriaceae, based on sequence variation in a portion of the gyrB gene. Thus, we identified, in most cases to species level, over 1000 isolates from onion bulbs and leaves and soil in which onions were grown. •High throughput method was developed to identify bacteria associated with onions (Allium cepa).•The method is based on sequence diversity in C-terminal portion of the gyrase B gene.•The method requires equipment for PCR and agarose-gel electrophoresis.•The limit of detection of this method is species dependent.•The method is cost-effective for use in large-scale surveys.