Microorganisms in the oilfield – wanted dead or alive?

28 Nov 2024

How can oil and gas operators prevent microbial damage to their systems?

Monitoring methods, from culture-based to DNA-based techniques, help detect microbial threats that can disrupt flow or harm materials. By testing diverse samples, setting KPIs, and tracking trends, operators can manage risks and protect system integrity.

How different microbial monitoring methods can help catch the culprit

Many microorganisms encountered in oil and gas installations can have negative effects on operations, such as disrupting flow assurance and impacting material integrity. In the last decade, a suite of microbiological and molecular methods has become available to help monitor microorganisms in these systems. The challenge, however, is to understand the output of these different techniques to appropriately gauge the associated risks and act accordingly. Although all these methods aim to achieve the same goal, they all measure slightly different sub-sections of the microbial community which can make the interpretation of the results challenging if unfamiliar.

What type of samples are routinely tested?

Unsurprisingly, the samples available to aid monitoring are very diverse given the variety of systems and complexity of issues encountered in the oil and gas industry. Testing can be conducted on either planktonic samples, including seawater, produced water, oily emulsions, and crude oils, or sessile samples, such as sludge, corrosion products, general solids, and swab samples isolated from pipelines and corrosion coupons.  Looking at this list of different sample types and considering the different process systems (water injection, production, separation, effluent, drainage, etc.), it becomes very clear that using one single method is not usually suitable for all the different scenarios.

Using cultures-based techniques

When using standard growth-based microbiological methods, we rely on the microorganisms present within the sample to flourish in the selected culture medium to confirm their presence as well as estimate their abundance. Certain factors and parameters need to be considered when detecting the microbes of interest using culture-based methods, such as the triplicate MPN (Most Probable Number) method, as outlined below.

• The targeted microbes can grow within the chosen culture medium, based on the formulation of a specific culture medium including the appropriate growth substrates (carbon sources, minerals, etc.)
• Matching the salinity of the medium with the conditions at the sampling site.
• Selecting the correct incubation temperature so that the organisms of interest can grow at the temperature that matches the sampling site.
• Identifying the atmospheric redox conditions (e.g. aerobic, anaerobic or microaerophilic).
• Setting an incubation period that allows recovery of the target microbe, e.g. allow the targeted microbes to grow sufficiently for enumeration.

With the above in mind and taking into account any potential flaws due to sampling procedures, we can conclude with reasonable confidence that the cells (type and numbers) detected are indicative of what was present at the sample location. Indeed, a good understanding of where and when to use the triplicate MPN method and how to interpret results has been gained through years of experience and continuous monitoring of various systems. This method is easy to use in the field and has helped users build data trends and guided mitigation actions to improve control and safeguard their systems from microbiological threats.

But not all microorganisms are culturable

However, it is well known that only a small percentage of all microorganisms are culturable, and the question arises: how do we ensure important information on microbial growth is not missed?  No detection by culture-based methods can have several potential reasons, such as simply choosing the incorrect culture conditions (e.g. wrong medium type, wrong incubation temperature, etc.)  However, some microorganisms simply cannot be cultured in growth media, or they are functional but not culturable, e.g. dormant, for example due to environmental stress (this includes stress due to biocide treatment); or they are not present at all in the sample taken. As such, failure to positively grow certain microorganisms does not necessarily indicate the organisms we are interested in are not present, or indeed dead.

Using DNA-based techniques

Alternative approaches such as using DNA-based methods like qPCR analysis or Next Generation Sequencing (NGS) will overcome the hurdle of detecting non-culturable microorganisms and provide quantification (or estimated enumeration) of the living, dead and 'active but unculturable' microorganism of interest.

These techniques offer more targeted detection of microbes and overcome the issue of culturing by removing the requirement to match the culture conditions to the sampling site. However, there are still certain factors which need to be considered when applying these technologies:

• Determine the target and design the correct primer pair.
• Optimize DNA extraction methods as different sample types might require different consideration, and this is not necessarily easy to standardize.
• Sample preservation: as these are predominately lab-based methods they require special sample handling during transportation.

Nowadays, these technologies, especially true for qPCR analysis, are well established and are used routinely to monitor microbial numbers. Due to their frequent use, the sampling procedures, DNA extraction, and certain qPCR primer combinations are well established in specific systems. In contrast, NGS, a more specialized technique, is mostly used in failure investigation; for example, in cases where more in-depth knowledge on the microbiological community is required.

Living or dead?

When using DNA-based technology the common critique is that we are detecting living, dead and dormant cells, which without using a different set of analysis (such as MPN) we cannot differentiate between. 

Whilst it is vitally important to differentiate between these states in some circumstances such as medical environments for example, the environments in the oil and gas  industry are ever-changing and complex, with many different factors influencing microbial growth and the effects of these on the growth of cells.

Understanding the presence of certain microorganisms in oil and gas operations can give an indication of potential risk. For example, detecting a target of concern, even if a portion of these detected microbes were dead at the time of sampling, will give information that these have been present recently and could have been responsible for a failure observed or could become an issue in future. Thus, continued monitoring is vitally important to develop trends which will allow for timely action when the numbers change and may allow prediction of a worsening scenario.

What does this mean?

Considering the above, it becomes apparent that monitoring microbiological numbers in the oil and gas industry can be quite complex but if monitoring methods are selected carefully to suit the systems at a risk from microbiological growth there are a few 'tools' to choose from. Once a set of tests are selected it is important to set meaningful key performance indicators (KPI), regularly conduct sampling and analysis, and trend the data to highlight any changes. It is important to remember that in a complex system, like in the oil and gas industry, we are looking for indicator organisms which, like a canary in the mine, can act as a warning sign.

Our expert microbiology team can advise on oilfield microorganism monitoring programmes and assist with the surveys of oilfield samples.

Learn more

Boost your own knowledge in oilfield microbiology with our Microbiology Courses in Aberdeen, UK.