Discovery of functional gene markers for monitoring hydrocarbon pollution in the marine environment using a metatranscriptomics approach

DNA-based monitoring instruments targeting microbial genes involved in hydrocarbon degradation pathways have emerged as next generation tools for detection of oil pollution in the marine environment. However, the knowledge about microbial hydrocarbon degradation genes is still limited and there is no functional marker adapted for use with such devices. The DNA-based Environmental Sample Processor (ESP) instrument was used in the laboratory to collect seawater samples during an oil exposure experiment, designed to mimic a realistic oil spill scenario at sea at an early stage (7 days). Extracted RNA from samples collected at the start of experiment, as well as from day 4 and day 7 was used for RNA-seq sequencing using Illumina NextSeq500 sequencing technology. Metatranscriptomic sequencing revealed that KEGG pathways involved in carbohydrate metabolism, amino acid metabolism, energy metabolism, membrane transport and xenobiotics biodegradation and metabolism were the most abundant significantly enriched pathways in samples exposed to oil. Identification of the expressed genes involved in key processes of hydrocarbons degradation was done based on the KEGG database annotation and 342 genes were identified. These genes encode enzymes participating in degradation of alkane, benzoate, aminobenzoate, fluorobenzoate, chloroalkane and chloroalkene, chlorocyclohexane and chlorobenzene, toluene, xylene, ethylbenzene, styrene, atrazine, caprolactam, dioxin, naphthalene and PAH. The identified genes serve as potential candidates for developing quantitative assays to detect microbial genes involved in early stages of oil degradation.