Comparative Transcriptomics Reveals Distinct Adaptation Mechanisms for Degradation of n-Alkane and Branched Alkane in the Salt-Tolerant Bacterium Dietzia sp. CN-3.

Although hydrocarbon-degrading bacteria utilize a wide range of alkanes, the global metabolic features and regulatory mechanisms governing their growth on alkanes with different chain lengths remain incompletely elucidated. In this study, we analyzed the comparative transcriptomics of a salt-tolerant bacterium, Dietzia sp. CN-3, to investigate molecular adaptations and metabolic processes when grown on n-hexadecane (C₁₆), branched alkane (pristane), and glucose. A total of 1766 differentially expressed genes (DEGs) were identified in the C₁₆ group compared to the glucose control, with 1024 (58.0%) being upregulated and 742 (42.0%) being downregulated. Notably, the pristane group exhibited 1542 DEGs, of which 488 (31.6%) were upregulated and 1054 (68.4%) were downregulated. Our results demonstrate that C₁₆ and pristane induced common genes of alkane hydroxylation in the core alkane degradation pathway, while eliciting distinct transcriptional patterns of genes involved in lipid metabolism, energy metabolism, metal ion transportation, cell surface composition biosynthesis, and transcription regulation. The findings reveal that CN-3 employs diverse metabolic strategies to adapt to alkanes with different chain lengths, displaying considerable metabolic plasticity. This study significantly enhances our understanding of molecular adaptation of bacteria to hydrocarbon-containing environments and may provide valuable information for further studies of petroleum hydrocarbon bioremediation.