What is the best way to monitor oilfield microbes?

NCIMB’s consultant microbiologist Dr Carol Devine considers the challenges and the options available

NCIMB has worked with biofilms from various locations and in a number of different ways over the years, but the main area that we have focused on is the monitoring of microbial populations in biofilms that influence microbiologically influenced corrosion (MIC) in offshore oil and gas production facilities. It is important that oil and gas operators monitor the location, prevalence and diversity of these populations in order to generate data to aid the mitigation of the effects of pitting corrosion. Such localised corrosion is difficult to predict and detect – and can lead to sudden failures that may cause major disruption to operations – as well as detrimental effects to the marine environment.

NCIMB works in collaboration with leading corrosion monitoring specialists ICR Integrity to offer full microbiology surveys of offshore facilities, helping the industry assess the threat of MIC so informed decisions can be made regarding the remedial action required. 

So how exactly do you sample biofilms from within an oil and gas production system or a seawater injection system? Obtaining samples of fluids from within the pipelines or vessels is relatively straightforward but, while there will always be planktonic cells in fluids, the samples of great importance to an oilfield microbiologist are sessile samples – that is samples of the biofilm attached to the pipework, flowlines or growing in the vessels themselves.

Consequently, samples of biofilm containing complex populations of microorganisms can be taken from corrosion coupons. These corrosion monitoring devices are located around the topsides facilities to give an indication of the prevalence of corrosive biofilm and are used to calculate general corrosion and pitting corrosion rates for that particular area. Corrosion coupon retrieval operations, coupon weight loss analysis and biofilm sampling from the coupons, is undertaken by ICR’s multi-skilled technicians who then ship the samples to NCIMB for microbiological analysis.

The challenge is then for the lab is to enumerate the microbes growing within these biofilms. The populations present are complex – but the tools that are available for monitoring oilfield microbes have changed and developed over the years.

The Most Probable Number method (MPNs) uses serial dilutions to estimate the number of living microbes present. It remains a popular approach, as it has several advantages. The majority of historical data from the North Sea was obtained using MPNs and so the technique remains a popular option. The disadvantages are that only certain microorganisms will grow in the particular conditions provided by the test kits, and incubation periods can be lengthy.

We can also use qPCR, a method based on the detection and quantification of DNA. There is no growth requirement, and qPCR may enumerate microbes that are not detected using MPNs. Specific primers can be used to detect archaebacteria and methanogens which are now known to play an important role in MIC but may not be included in an MPN count. However, qPCR is not a perfect solution either! It counts both living and dead cells and the relationship between the amount of DNA detected and the number of bacteria present is not always straightforward, as some cells may have multiple copies of the same gene – so three copies of the gene may be one cell with three genes or three cells with one gene.

An alternative approach is the use of metagenomics where the whole microbial community is analysed. This can give information on the types of bacteria present and help determine if they are problem. Metagenomics has allowed scientists to understand much more about the different groups and species of bacteria that are present in the biofilms that grow on oil and gas production pipework, revealing greater diversity than was once thought to exist in this environment. However, as with qPCR, it assays the living and the dead. And it is semi-quantitative – in other words it calculates relative abundance in the total population present rather than the definitive number present.  

We are often asked which of these methods is the best solution for monitoring populations in the biofilms within oil and gas facilities. This is not a straightforward question to answer! It is important to understand that the different methods available for monitoring microorgansims are not different ways of measuring the same thing – they all measure different things. Consequently, the most comprehensive picture may be obtained with a combination of methods, i.e., combining MPNs and a molecular technique. Also, integrating qPCR and 16S metagenomic analysis delivers an improved method of biomonitoring for the purpose of assessing the threat of MIC. It offers accurate detection and enumeration of the microbial community present in each sample for:

  • Identification of production areas with a high threat of MIC allowing early targeted remediation.
  • Monitoring and trend analysis of changes in microbial communities over time and in response to treatments and interventions.
  • Improved visual data reporting.
  • The ability to generate data in order to set more effective Key Performance Indicators (KPIs) for monitoring and management.
  • Allowing the improved selection of effective biocides based on analysis of the microbial community pre and post biocide treatments.

At NCIMB, we can advise on appropriate methodologies, undertake the analysis and interpret results. We work with our partners at ICR Integrity to access appropriate samples and provide optimal data to assist our clients make informed decisions regarding the threat of MIC.

To find out more about the work we have done with the oil and gas sector, watch our video or contact enquries@ncimb.com

Dr Carol Devine, Consultant Microbiologist

“It is important to understand that the different methods available for monitoring microorganisms are not different ways of measuring the same thing – they all measure different things.”