DNA sequencing of oilfield samples: impact of protocol choices on the microbiological conclusions

摘要

In the last decade, molecular microbiology techniques have significantly expanded the understanding of the resident microflora in hydrocarbon reservoirs and production systems. These methods have been steadily accepted by the industry and are widely viewed as accurate, comprehensive and highly valuable tools that augment or may eventually replace conventional methods. The resulting information has helped operators and service companies to develop better monitoring programs, assess risks and tailor mitigation strategies to control undesired microbial activities in wells, flowlines and separation facilities. Nonetheless, many molecular procedures cannot be performed onsite and samples are typically sent offsite for specialized analyses. The lack of standard procedures hinders comparison of findings between laboratories. Operators currently use dissimilar sampling and preservation protocols, different methods for DNA extraction, separate sequencing platforms and varied approaches for the analyses of the resulting molecular data. In this study, we retrieved multiple samples from several wells in an onshore oilfield and submitted them for 16S rDNA taxonomic analysis in two different laboratories. The results showed significant differences between laboratories in the total abundance of organisms, their taxonomic composition and the presence/absence of certain diagnostic bacteria. Close examination of the protocols revealed that the sample preservation techniques and specific 16S rDNA gene primer sets likely had a significant impact on the resulting information. Collectively, this experience suggests that while molecular techniques are extremely powerful tools to analyze oilfield microbiology, the lack of consensus on an industry wide protocol may lead to discrepancies that could negatively impact the exploitation of these promising methods.