Impact of sample preservation protocols for metagenomics analysis in the oilfield

The lack of standardized protocols and the remote nature of oilfields are major concerns when it comes to sample preservation to maintain the integrity of the microbial population during transport.  Those concerns led Jordan Schmidt, Ph.D., and his team to do a research project where the focus was to discuss a major deficiency with the application of metagenomics in the oil & gas industry.

Metagenomics in the oil and gas industry

The implementation of metagenomics in the oil and gas industry has drastically increased in the last several years. It is being used for a host of applications, including:

  • microbially influenced corrosion (MIC) origin detection,
  • biocide efficacy studies, and
  • microbial content evaluations of injection water and water used for hydraulic fracturing.

Metagenomic protocols

One major deficiency with the application of metagenomics is the lack of standardized protocols. Due to the remote nature of oilfields, sample preservation and maintaining the integrity of the microbial population during transport is of particular concern. If not preserved properly, the microbial community composition can change between sample collection and DNA extraction.

Several studies have been conducted recently on DNA preservation of environmental samples. However, no consensus has been reached on the best practice. Results are often dependent on the preservation techniques tested, the types of samples, and the target organisms examined. Furthermore, most studies were focused on samples from the natural environment, with very few studies examining oilfield associated samples.

Purpose of the research

The objective of this study was to evaluate several common preservation techniques for both liquids and solids that would be suitable for remote oilfield locations. Techniques tested included:

  1. filtration followed by air drying,
  2. storage of sample at low temperatures (refrigeration or on-ice),
  3. freezing, and
  4. chemical preservation.

The air-dried and chemically preserved samples were exposed to different storage temperatures (20-50°C) and transportation times. Comparative data analysis was conducted on the preserved samples against unpreserved sample used for DNA sample preparation immediately after collection.  All DNA samples prepared were sequenced using Illumina 16S rRNA sequencing.

The comprehensive study started to fill the gap pertaining to oilfield sample preservation and will contribute towards the development of standard protocols for metagenomics analysis.

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Jordan Schmidt

Jordan has a PhD in Civil Engineering specializing in biological wastewater treatment. During his PhD, Jordan contributed to full-scale field evaluations of municipal waste stabilization ponds in the Canadian territory of Nunavut. He has a diverse background of expertise including data science, experimental design, statistical programming and full-scale municipal wastewater treatment. When he’s not working, Jordan enjoys sea kayaking, backcountry camping in Kejimkujik National Park and rock climbing.

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