Microbiological Testing as Part of Well Maintenance

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A better understanding of the conditions downhole is key to managing a well more effectively.

By Michael Schnieders, PG, PH-GW

I received a question on bacteria during a presentation on wells and their vulnerabilities. A gentleman posing the question pointed out he had been led to believe any occurrence of bacteria within a well was a sure sign of contamination.

Many in the water well industry believe this, and many more of our customers share this same misunderstanding too.

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Thousands of Species

As our abilities as a science expand, we are identifying levels of bacteria in parts of the world we never knew or assumed existed. Bacteria have been identified at the bottom of the trench systems within the ocean and at the top of Mount Everest.

In their book, The Microbiology of the Terrestrial Deep Subsurface, Doctors Penny S. Amy and Dana L. Haldeman state bacteria have a “universal presence…and that there remain thousands of species of bacteria still to be identified in our aquifers.”

Part of our new understanding is we have improved technology allowing us to identify smaller bacteria of varying types and in different ecosystems, surpassing our understanding of these microorganisms.

Bacteria live essentially in communities. Biofilm is a naturally occurring expression of bacteria resulting from the extrusion of a slimy polysaccharide exopolymer. Bacteria exude this slime to attach themselves to a smooth surface for propagation, nutrient capture, and growth.

Biofilm acts as a suburban community within a well system, developing in numerous locations, sustaining life and rapidly expanding throughout the well environment. Biofilms are not exclusive to one type of bacteria but are a mixture of aerobic (oxygen present) and anaerobic (oxygen absent) bacteria, and can exist throughout the well system.

Focusing on Quality

Generally, we are concerned with water quality. In the current U.S. Environmental Protection Agency drinking water regulations, only 7 of the 85 parameters are biological. The biological testing parameters focus on the occurrence of coliform organisms, which would then trigger additional testing to rule out surface water contamination. Within the regulations, there is no quantitative evaluation of the bacterial community or assessments of biofilm.

Typically, most well owners test for and are concerned with coliform occurrence. Aside from fecal or E.coli related coliforms, most coliform occurrences are a reflection of insufficient activity or fouling.

Maintenance and even disinfection efforts are commonly postponed until action is required due to a coliform occurrence. Unfortunately, coliform occurrence is a reactionary evaluation—once an “environmental” coliform has been found in a well, typically the resident microbial population is elevated and heavier biofilm production has occurred.

Present throughout nature, biofilms are an excellent source for the development of mineral scale within a well system. Biofilms promote scale buildup by providing a surface for adhesion of mineral forming ions, further complicating well operation.

Similarly, fine grained sediments and debris, mobilized towards a well during operation, often become entrapped in biofilm, increasing the fouling potential. Each of these issues can exist without impacting a coliform test, so in monitoring a well’s condition, it is advisable to not rely on the presence/absence of coliform as an indication of biofouling.

Asking the Right Questions

When periodically evaluating a well, we strongly encourage microbiological testing in addition to the general water chemistry and the presence of local contaminants of concern. Check with your local lab regarding their capabilities.

Several questions you might ask of the microbial community:

  • What is the total number of organisms present?
  • Is the population viable (active)?
  • Is the microbial community predominantly aerobic or anaerobic?
  • And, if you have concerns with iron bacteria, ask to evaluate the presence of iron oxidizing organisms.

In addition, the sampling of an idle well may not accurately reflect downhole conditions. We recommend collecting both an idle and an active pumping sample for comparison purposes to better evaluate conditions downhole. If you suspect the aquifer may have a problem or is influencing the well, multiple samples timed with a pump test may aid in understanding and classifying the problem.

Biological testing is a valuable tool in evaluating a well’s condition and should occur alongside chemical testing, physical evaluation, pump inspection, and an evaluation of the well’s efficiency. Unfortunately, it can be a misunderstood part of water quality and the role it plays in well fouling.

A better understanding of the conditions downhole is key to managing a well more effectively.


Michael J. Schnieders, PG, PH-GW
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Michael Schnieders, PG, PH-GW, is a professional geologist currently serving as the principal hydrogeologist and president of Water Systems Engineering Inc. in Ottawa, Kansas. Schnieders’ primary work involves water resource investigation and management, specializing in the diagnosis and treatment of fouled well systems. Schnieders was the 2017 McEllhiney Distinguished Lecturer in Water Well Technology. He can be reached at mschnieders@h2osystems.com.