Real-time quantitative PCR analysis of diesel-degrading genes of acinetobacter calcoaceticus isolates.

Abstract

The diesel-degrading capabilities of Acinetobacter calcoaceticus isolates LT1, LT1A and V2 were established in previous studies. LT1 and LT1A were isolated from diesel-contaminated soil and V2 was from soil contaminated with used engine oil. Isolates were grown in Bushnell-Haas medium supplemented with 1% sterile diesel. Determination of diesel-degradation patterns by gravimetric analysis and harvesting of cells for RNA extraction were performed at regular time intervals over a 60 day period. The involvement of genes alkM, alkR, rubA, rubB, estB, lipA, lipB, and xcpR in hydrocarbon degradation has been reported in previous studies. LT1, LT1A, and V2 were compared in terms of gene expression levels by real-time quantitative PCR. Expression levels were assessed by relative quantification and normalized against the 16S rRNA reference gene using the Relative Expression Software Tool - XL (REST-XL). Amplification of all genes, except rubB, was achieved with a high degree of efficiency. The expression of rubA, alkM, alkR, xcpR, and lipB based on pair-wise randomization, was all down-regulated in LT1A in relation to LT1. Highest expression levels of the aforementioned genes were documented during the initial stages of incubation for LT1 while LT1A showed highest expression levels midway through the study period. LT1, LT1A, and V2 achieved 58.6%, 51.7%, and 48.3% diesel degradation after 5 days of incubation, respectively. The higher percentage of diesel degradation achieved by LT1 can be attributed to higher levels of overall gene expression in the initial stages of degradation. Amplification of alkane hydroxylase alkM of V2 revealed a possible second hydroxylase gene that was expressed after 20 days of incubation. Amplification of alkR and xcpR in V2 isolates also resulted in multiple product formation. Very low lipB and lipA expression was detected in LT1 and LT1A and the absence of lipA expression in V2 suggests that lipases were not involved in diesel degradation. In contrast, estB was predominantly expressed in V2, and suspected to be involved in the release of a bioemulsifier that was only observed in V2 samples. Although all three isolates were comparably efficient in degrading diesel, the results of this study suggest that different mechanisms may be employed in the degradation process.