Rapid detection and identification of the metabolically diverse genus Gordonia by 16S rRNA-gene-targeted genus-specific primers.
The importance of the emerging genus Gordonia in industrial and environmental biotechnology is evidenced by the recent increase in associated publications and patents. But, investigations into potentially valuable Gordonia members are restricted by the limitations of current isolation and detection techniques. This motivated us to design a genus-specific oligonucleotide primer pair which could assist in rapid detection of species of the genus Gordonia by means of PCR-specific amplification. The Gordonia-specific 16S rDNA fragment (829 bp) was successfully amplified for all the reference Gordonia species with the designed primer pair G268F/G1096R. No amplification was noted for closely related species from other genera. The genus specificity was validated with 47 strains including wild-type isolates. Interestingly, two strains assigned earlier as Gordonia nitida (DSM 777) and Gordonia rubripertinctus (ATCC 21930) failed to produce a Gordonia-specific fragment with this primer pair. Further analysis of these two isolates based on 16S rDNA sequencing and phylogenetic analysis classified them to the genus Rhodococcus. Preliminary screening of soil samples with the Gordonia-specific primers was successful in terms of the rapid detection of nine Gordonia wild-type isolates.
Shen
Fo-Ting
FT
Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 250 Kuo Kuang Road, Taichung 40227, Taiwan, ROC.
Young
Chiu-Chung
CC
D017931:DNA Primers; D004269:DNA, Bacterial / Q000032:analysis* / Q000235:genetics; D004275:DNA, Ribosomal / Q000032:analysis* / Q000235:genetics; D033601:Gordonia Bacterium / Q000235:genetics / Q000302:isolation & purification*; D008828:Microbiological Techniques; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA
D017931:DNA Primers; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S