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Background  A major facilitator superfamily transporter Dehp2 was recently shown to be playing an important role in transport and biodegradation of haloacids in  Paraburkholderia caribensis  MBA4, and Dehp2 is phylogenetically conserved in  Burkholderia  sensu lato.    Results  We designed both  Burkholderia  sensu stricto-specific and  Paraburkholderia -specific qPCR assays based on  dehp2  and 16S rRNA, and validated the qPCR assays in 12 bacterial strains. The qPCR assays could detect single species of  Burkholderia  sensu stricto or  Paraburkholderia  with high sensitivity and discriminate them in mixtures with high specificity over a wide dynamic range of relative concentrations. At relatively lower cost compared with sequencing-based approach, the qPCR assays will facilitate discrimination of  Burkholderia  sensu stricto and  Paraburkholderia  in a large number of samples.    Conclusions  For the first time, we report the utilization of a haloacids transporter gene for discriminative purpose in  Burkholderia  sensu lato. This enables not only quick decision on proper handling of putative pathogenic samples in  Burkholderia  sensu stricto group but also future exploitation of relevant species in  Paraburkholderia  group for haloacids biodegradation purposes.    Electronic supplementary material  The online version of this article (10.1186/s12866-019-1411-0) contains supplementary material, which is available to authorized users.

Application of qPCR assays based on haloacids transporter gene dehp2 for discrimination of Burkholderia and Paraburkholderia