Specific detection of Lysobacter antibioticus strains in agricultural soil using PCR and real-time PCR

Abstract

Lysobacter antibioticus is an important biocontrol bacteria against phytopathogens in soil and with the ability to produce nonvolatile antimicrobial metabolites has been extensively characterised. It's important to estabilish application techniques to detect and monitor L. antibioticus directly and acurately in soil samples. We developed and tested 13 primer sets according to phenazine gene (phzA, phzB, phzD, phzF, phzS) and cyclohexanone monooxygenase gene (phzNO1), a pair of primer phzNO1 F1/phzNO1 R1 based on cyclohexanone monooxygenase (phzNO1) gene of L. antibioticus strain OH13 was selected and optimized PCR amplification conditions for rapid and accurate detection. After screening 8 strains of L. antibioticus, 2 strains of L. enzymogenes, 1 strains of L. capsici, Arthrobacterium, Bacillus, Microbacterium, Burkholderia, Pseudomonas and other bacteria strains isolated from different agricultural soils, the phzNO1 F1/phzNO1 R1 primers amplified a single PCR band about 229 bp from L. antibioticus. The detection sensitivity with primers phzNO1 F1/phzNO1 R1 was 5.14×104 fg/25μL of genomic DNA and 2.254×1010 - 2.254×1011 CFU/mL for the soil samples. Real-time fluorescent qPCR assays were to develope a specific method to monitor L. antibioticus in edatope as well as guide soil micro-ecological management.