Efficacy of species-specific recA PCR tests in the identification of Burkholderia cepacia complex environmental isolates.
In this study, we evaluated if recA species-specific PCR assays could be successfully applied to identify environmental isolates of the widespread Burkholderia cepacia complex (Bcc) species. A total of 729 Bcc rhizosphere isolates collected in different samplings were assigned to the species B. cepacia genomovar I (61), B. cenocepacia recA lineage IIIB (514), B. ambifaria (124) and B. pyrrocinia (30), by means of recA (RFLP) analysis, and PCR tests were performed to assess sensitivity and specificity of recA species-specific primers pairs. B. cepacia genomovar I specific primers produced the expected amplicon with all isolates of the corresponding species (sensitivity, 100%), and cross-reacted with all B. pyrrocinia isolates. On the contrary, B. cenocepacia IIIB primers did not give the expected amplicon in 164 B. cenocepacia IIIB isolates (sensitivity, 68.1%), and isolates of distinct populations showed different sensitivity. B. ambifaria primers failed to amplify a recA-specific fragment only in a few isolates of this species (sensitivity, 93.5%). The absence of specific amplification in a high number of B. cenocepacia rhizosphere isolates indicates that recA specific PCR assays can lead to an underestimation of environmental microorganisms belonging to this bacterial species.
Dalmastri
Claudia
C
Ente Nazionale per le Nuove Tecnologie, l'Energia e l'Ambiente (ENEA), C.R. Casaccia Department of Biotechnologies, Protection of Health and Ecosystems, Plant Genetics and Genomics Section, Rome, Italy. claudia.dalmastri@casaccia.enea.it
Pirone
Luisa
L
Tabacchioni
Silvia
S
Bevivino
Annamaria
A
Chiarini
Luigi
L
D001426:Bacterial Proteins / Q000235:genetics; D042602:Burkholderia cepacia complex / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D016172:DNA Fingerprinting; D018517:Plant Roots / Q000382:microbiology; D016133:Polymerase Chain Reaction / Q000379:methods*; D012150:Polymorphism, Restriction Fragment Length; D011938:Rec A Recombinases / Q000235:genetics*; D012680:Sensitivity and Specificity; D012988:Soil Microbiology; D003313:Zea mays / Q000382:microbiology*
D001426:Bacterial Proteins; D011938:Rec A Recombinases