Identification and onion pathogenicity of Burkholderia cepacia complex isolates from the onion rhizosphere and onion field soil

Appl Environ Microbiol. 2008 May;74(10):3121-9. doi: 10.1128/AEM.01941-07. Epub 2008 Mar 14.


Burkholderia cepacia complex strains are genetically related but phenotypically diverse organisms that are important opportunistic pathogens in patients with cystic fibrosis (CF,) as well as pathogens of onion and banana, colonizers of the rhizospheres of many plant species, and common inhabitants of bulk soil. Genotypic identification and pathogenicity characterization were performed on B. cepacia complex isolates from the rhizosphere of onion and organic soils in Michigan. A total of 3,798 putative B. cepacia complex isolates were recovered on Pseudomonas cepacia azelaic acid tryptamine and trypan blue tetracycline semiselective media during the 2004 growing season from six commercial onion fields located in two counties in Michigan. Putative B. cepacia complex isolates were identified by hybridization to a 16S rRNA gene probe, followed by duplex PCR using primers targeted to the 16S rRNA gene and recA sequences and restriction fragment length polymorphism analysis of the recA sequence. A total of 1,290 isolates, 980 rhizosphere and 310 soil isolates, were assigned to the species B. cepacia (160), B. cenocepacia (480), B. ambifaria (623), and B. pyrrocinia (27). The majority of isolates identified as B. cepacia (85%), B. cenocepacia (90%), and B. ambifaria (76%) were pathogenic in a detached onion bulb scale assay and caused symptoms of water soaking, maceration, and/or necrosis. A phylogenetic analysis of recA sequences from representative B. cepacia complex type and panel strains, along with isolates collected in this study, revealed that the B. cenocepacia isolates associated with onion grouped within the III-B lineage and that some strains were closely related to strain AU1054, which was isolated from a CF patient. This study revealed that multiple B. cepacia complex species colonize the onion rhizosphere and have the potential to cause sour skin rot disease of onion. In addition, the onion rhizosphere is a natural habitat and a potential environmental source of B. cenocepacia.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / genetics
  • Burkholderia cepacia complex / classification
  • Burkholderia cepacia complex / isolation & purification*
  • Burkholderia cepacia complex / pathogenicity*
  • Culture Media / chemistry
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / genetics
  • Genotype
  • Michigan
  • Molecular Sequence Data
  • Nucleic Acid Hybridization
  • Onions / microbiology*
  • Phylogeny
  • Plant Diseases / microbiology
  • Plant Roots / microbiology*
  • Polymerase Chain Reaction
  • Polymorphism, Restriction Fragment Length
  • RNA, Ribosomal, 16S / genetics
  • Rec A Recombinases / genetics
  • Sequence Analysis, DNA
  • Soil Microbiology*


  • Bacterial Proteins
  • Culture Media
  • DNA, Bacterial
  • RNA, Ribosomal, 16S
  • Rec A Recombinases

Associated data

  • GENBANK/EU078998
  • GENBANK/EU078999
  • GENBANK/EU079000
  • GENBANK/EU079001
  • GENBANK/EU079002
  • GENBANK/EU079003
  • GENBANK/EU079004
  • GENBANK/EU079005
  • GENBANK/EU079006
  • GENBANK/EU079007
  • GENBANK/EU079008
  • GENBANK/EU079009
  • GENBANK/EU079010
  • GENBANK/EU079011
  • GENBANK/EU079012
  • GENBANK/EU079013
  • GENBANK/EU079014
  • GENBANK/EU079015
  • GENBANK/EU079016
  • GENBANK/EU079017
  • GENBANK/EU079018
  • GENBANK/EU079019
  • GENBANK/EU079020
  • GENBANK/EU079021
  • GENBANK/EU079022
  • GENBANK/EU079023