bug bottles vs qpcr

Bug Bottles vs qPCR – What’s the Difference?

What are ‘Bug Bottles’?

As highlighted in a previous blog, microbes can cause a range of microbiological problems in oil and gas extraction processes. By controlling microbial growth, operators can prevent issues such as:

Various methods are available for monitoring levels of problematic groups of bacteria, like acid-producers and sulfate-reducers. One method that has a well-established history, is the serial dilution most probable number (MPN) culture test, often referred to as “Bug Bottles.” This is a visual method, where the sample is serially diluted in a number of bottles containing growth media, allowed to incubate, and then the MPN is estimated based on the number of bottles that change colour.


The MPN culture test method is simple and easy to interpret, but there are a few limitations:

  • incubation times can be significant, requiring up to 28 days depending on the microbe that’s being targeted.
  • approximately <1% of microorganisms are culturable, so culture-based results can significantly underestimate the total concentration or overestimate biocide efficacy.


What is qPCR?

A great alternative that has recently gained in popularity is quantitative Polymerase Chain Reaction (qPCR). This is a DNA-based method that can be used to rapidly detect and quantify microorganisms in environmental or industrial samples. Like with serial dilution culture tests, different qPCR assays can be used to identify concentrations of key groups, such as total prokaryotes, sulfate-reducing prokaryotes, or iron-reducing bacteria.


Unlike culture-based methods, qPCR has the advantage of being:

  • fast, sensitive, and highly specific.
  • results can be obtained within 2.5 hours of sample collection and it does not rely on microbial growth, so it is not limited to only detecting culturable microorganisms.
  • it can also be used to process a variety of sample types, such as liquids, solids, and coupons.

Historically, qPCR testing could be relatively complex compared to culture-based tests, but LuminUltra’s GeneCountTM qPCR provides a complete off-the-shelf solution with assay kits that were designed and optimized for identifying key target organisms in contaminated samples from industrial, oil & gas, and wastewater facilities. The GeneCount qPCR test also provides an excellent complement to 2nd Generation ATP testing, as ATP can be used for routine, day-to-day monitoring, while GeneCount qPCR can be used for weekly or monthly monitoring, with additional testing for diagnosing any identified issues.


Be sure to check out our GeneCount brochure to learn more about our DNA-based products and services.

Brad Mcilwain

Brad McIlwain has over eight years of experience in the water and wastewater industry. Prior to joining LuminUltra, he worked for several years as a consulting engineer, where he helped solve complex water and wastewater treatment process issues. He has a particular interest in water system corrosion. During his Master’s, his research focused on water quality and corrosion in premise plumbing. Brad enjoys being outdoors, spending as many weekends as possible camping, hiking, and cycling.

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