Combined use of a specific probe and PCAT medium to study Burkholderia in soil

Due to its pathogenic traits and agricultural benefits, there is some chall enge in detecting Burkholderia in the soil environment. In this perspective , an existing semi-selective medium, (PCAT), was combined with a Burkholder ia specific molecular probe. Using the complete 16S rRNA sequences of all a vailable Burkholderia series type strains, we selected the p following sequ ence: 5 ' -ACCCTCTGTTCCGACCATTGTATGA-3 '. The probe was validated against G enBank sequences, with dot blots and colony hybridization tests. A diversit y study of all strains growing on a PCAT plate after plating a soil dilutio n (75 strains) was carried out with ARDRA analysis and colony hybridization tests. All the hybridizing strains belonged to genus Burkholderia. The maj or type of non-hybridizing isolates belonged to Pseudomonas (16S rRNA seque ncing). Both tools were combined to compare the Burkholderia populations in a rhizosphere (maize) and a non-rhizosphere soil, Based on hybridizing PCA T isolates, we were able to show an increase in Burkholderia populations in the maize rhizosphere. This genus represented 2% and 16% of the total cult ivable microflora in the non-rhizosphere and rhizosphere soils, respectivel y. Although PCAT was shown not to be appropriate to routinely enumerate Bur kholderia populations in soil, it allowed environmental investigations at t he genus level, when combined with a molecular specific probe. (C) 2001 Els evier Science B.V. All rights reserved.