Molecular detection and phylogenetic characterization of Gordonia species in heavily oil-contaminated soils

This study was undertaken to assess genetic diversity among Gordonia species present in heavily oil-contaminated sites using both a culture-dependent and a culture-independent (PCR-denaturing gradient gel electrophoresis (DGGE)) approach. Soil samples for this purpose were collected from 8 different heavily (crude) oil-contaminated industrial park sites located around Kaohsiung County, Taiwan. Using Gordonia-specific PCR-DGGE, a significant increase in Gordonia species diversity was noted in 1% heavily oil-enriched soil. A total of 67 strains were scored and identified as Gordonia after genus-specific PCR amplification and sequencing. BOX-PCR fingerprinting of culturable Gordonia showed wide strain diversity. A total of 33 different strains were identified from most of the sampling sites. Based on gyrB gene sequence analysis, all Gordonia strains could be segregated into five major clusters. Gordonia amicalis was the predominant species in all oil-amended soil samples. Isolates sharing <98.5% gyrB gene sequence similarities with Gordonia type strains represent indigenous novel Gordonia species. Variations in phenotypic characteristics further confirm the presence of a wide range of species and strain diversity among Gordonia isolates. Based on the genotypic and phenotypic details obtained here, we conclude that heavily oil-contaminated soil supports diverse indigenous Gordonia strains.