Abstract: The present disclosure relates generally to methods and/or means for generating and analyzing gene expression profiles of a microorganism isolated from an environment contaminated with toxic organic compounds. In particular, the disclosure relates to methods and/or means of identifying genes, enzymes, and metabolic pathways involved in naphthenic acids compounds (NAFC) or naphthenic acid (NA) degradation activity. Engineered microorganisms with increased naphthenic acid (NA) degradation activity and their use for biodegradation of toxic organic compounds in contaminated environments are further provided.