Isooctane-based DNA extraction method from crude oil

Microbes from oil reservoirs shape petroleum composition through processes such as biodegradation or souring. Such processes are considered economically detrimental and might pose health and safety hazards. It is therefore crucial to understand the composition of a reservoir's microbial community and its metabolic capabilities. However, such analyses are hindered by difficulties in extracting DNA from such complex fluids as crude oil. Here we present a novel DNA extraction method from oils with a wide API gravity (density) range. We investigated the ability to extract cells from oils with different solvents and surfactants, the latter both non-ionic and ionic. Furthermore, we evaluated three DNA extraction methods. Overall, the best DNA yields and the highest number of 16S rRNA reads were achieved with isooctane as a solvent, followed by an ionic surfactant treatment with sodium dodecyl sulfate (SDS) and DNA extraction via the PowerSoil Pro kit (Qiagen). The final method was then applied to various oils from oil reservoirs collected in aseptic conditions. Despite the expected low cell density of 101-103cells/ml, the new method yielded reliable results with average 16S rRNA sequencing reads in the order of 41431(±8860) per sample. Thermophilic, halophilic, and anaerobic taxa, which are most likely to be indigenous to the oil reservoir, were found in all samples. API gravity and DNA yield, despite the sufficient DNA obtained, did not show a correlation.