Knowing Well Microbiology

Published On: January 1, 2017By Categories: Features, Groundwater Quality, Well Rehabilitation

Knowledge of biofouling mechanisms can help drive maintenance of well systems.

By Eric Duderstadt

Despite the long held view aquifers are pristine water sources, a diverse and large group of bacteria inhabiting groundwater are now being analyzed to better understand the many varied influences they have on wells and the quality of water being produced.

Efforts to monitor bacteria in groundwater wells have primarily been in regard to water quality. But a deeper knowledge of these bacterial communities is more available than ever—and can serve as a valuable resource in assessing maintenance requirements that protect the increasingly important asset that is a groundwater well.

Breaking with Tradition

In large part, our view of bacteria in water wells continues to be in the context of water quality, the origins of which go back to the human need for clean, safe drinking water.

Rightfully so, our first priority has been to manage the health risks posed by bacteria in our water supplies. The industry standard for determining drinking water’s sanitary quality comes from regulatory actions put in place by the U.S. Environmental Protection Agency, which rely on a small group of bacteria called coliforms. A group of closely related bacteria, coliforms have become the poster child for bacterial water quality, earning the role of indicator organisms due to their similarities to a variety of other pathogenic microbes.

While the primary goal may be safety, production of clean and aesthetically pleasing water also remains a chief goal of any water producer. A number of bacteria within water supplies are known for their undesirable effects on water quality—negatively impacting taste, odor, and visual appearances.

A well-known member of this group of nuisance organisms are sulfate-reducing bacteria. SRBs are a form of anaerobic bacteria often identified in fouled or stagnant well systems. They are identified through a presence-absence test— but their presence is readily identifiable by the distinctive hydrogen sulfide gas produced by the bacteria and the rottenegg odor the gas is known for.

While removing bacteria responsible for impacting water quality from both a safety and aesthetic viewpoint is certainly valid, it does not ensure a well will be a good producer. Nor does it give any indication of a well’s need of maintenance. To this end, the examination of bacterial communities within wells from a performance perspective should also be used to help guide routine maintenance and extend the operational life spans of wells.

The Roles of Biofilm

Within the industry, “biofouling” has come to encompass a number of known tactics bacteria use to adversely affect water systems. Perhaps the most influential fouling mechanism is the formation of biofilm. Biofilm is a naturally occurring expression of bacteria resulting from the extrusion of a slimy extracellular polymeric substance (EPS).

The EPS matrix covers the cells and consists of polysaccharides, proteins, and nucleic acids used by the bacteria. Bacteria discharge this slime as a means of attaching themselves to a smooth surface for propagation, nutrient capture, growth, and can even facilitate communication between the encompassed microbes.

Biofilms are not as rare as one might think and can actually be beneficial in some applications. They are used and can be specifically engineered for water and wastewater filtration and remediation of contaminated soils and water— they even make up dental plaque.

Unfortunately, the aspects of biofilm that make it advantageous for bacteria are also extremely detrimental to well systems. As the biofilm matrix grows, it can physically restrict flow paths— specifically within the producing zones of a well where screened, perforated, or slotted openings are found often in conjunction with surrounding gravel pack. Filling in the spaces in between these areas can rapidly decrease production and result in increased drawdowns.

More advanced biofilm growth can also result in the stratification of different layers within the biofilm matrix, which not only increases the relative density and fouling potential of the biofilm, but also reduces oxygen levels in the deeper layers where anaerobic bacteria can thrive. This layering effect not only impedes disinfection efforts, but has also been shown to harbor more harmful organisms, such as coliforms thriving in anoxic environments.

Additionally, as biofilms mature, cells from the colony are known to leave the matrix to spread and colonize new surfaces. Dispersion of these cells enables fouling to migrate into different zones throughout the well environment and beyond—including the pump, distribution system, and treatment facilities where new biofilms can be established.

Fortunately, a number of tools are available to help monitor biofilm growth before it reaches problematic levels. A common approach is to generally quantify the total bacterial load within the well, with the notion greater population sizes reflect a greater potential for biofilm formation. Periodic monitoring of population sizes in conjunction with well performance can also allow for correlations to be made and acceptable operational limits to be set.

Various quantification techniques are available which fluctuate greatly in cost and accuracy. Of those methods, adenosine triphosphate (ATP) analysis is a simple test which can quickly and accurately quantify a biological load in a water sample—it measures the amount of ATP, a molecule found universally within living cells, within a sample. The ATP test is relatively inexpensive and is even available in field applications.

An additional step in assessing the potential severity of biofilm growth can be taken through identifying specific anaerobic bacteria whose presence often signifies the layering effect observed in more mature biofilm growth that was described earlier.

Anaerobic growth can be determined via nutrient characterization assays. Tests such as these monitor the growth of anaerobic species as a function of the total bacterial population through the response to specific macro-nutrients, and can even be adapted to more specific anaerobes such as SRBs.

Scale Potential

Bacteria and subsequent biofilm formations also play a pivotal role in forming mineral incrustation within wells. As water containing mineral ions, crystals, clays, and other inorganic debris flows toward and enters the well, these compounds may become entrapped by any biofilm formation present on the surfaces over which it is flowing. The accumulation of inorganic debris to the surface is made possible by the excellent surface adhesion capabilities of biofilm—making biofilm a catalyst for the conglomeration of mineral scales.

In most cases, well blockage is often a combination of biological material and minerals formed either as deposits of water constituents or from the adhesion of particulate matter or sand. As the content of inorganic debris increases within these matrixes, the result is a denser, more hardened mass representing a more formidable barrier to water flow.

Another way to monitor biofilm accumulations and their composition is the microscope. Biofilm can be observed under the microscope with as little as 100-times magnification. Centrifugation of samples can also be used to aid in collecting free-floating biofilm growths within a sample for further observation under the scope. One or two drops of centrifuged concentrate from a sample is usually sufficient.

Once collected, a microscopic view of the sample can show not only the degree of buildup present but also the makeup of the matrix itself. Iron oxides, one of the most common mineral constituents found in problematic wells, are easily identifiable under the scope, as are calcium carbonates and other mineral compounds. Formation materials such as silica sands and clays are also readily identifiable.

Similarly, plant particulate matter, indicative of surface water influences, are also visible if present. The microscope observing the presence and severity of these inorganic materials in combination with biofilm accumulations is another valuable and simple tool in assessing bacterial fouling and the potential need for maintenance.

Microbially Influenced Corrosion

Yet another prominent way bacteria can drive the need for maintenance in wells is their roles in influencing the basic principles of corrosion. Any mode of corrosion which incorporates microbes that react and cause corrosion or influence other corrosion processes is called “microbially influenced corrosion.” MIC often occurs in the form of pitting, but can also be seen in any number of other forms of corrosion.

A number of bacteria can introduce corrosion-assisting constituents, such as acids and sulfides, during growth phases and in carrying out their basic metabolic processes. A commonly recognized example of this is the reduction of sulfate (SO2−4) to hydrogen sulfide (H2S) by SRBs.

Uneven colonization of microorganisms over a surface can also contribute to corrosion by influencing oxygen concentration gradients. Aerobic bacteria located in biofilms near the water interface can create an oxygen gradient during oxygen consumption, leaving oxygen levels depleted in lower portions of the biofilm matrix near the substrate surface. This results in the surface area under the biofilm becoming anodic to the area exposed to the bulk aqueous phase.

Direct degradation of materials can also occur from the presence of specific bacteria, such as iron-oxidizing bacteria. One of the more recognized species of iron-oxidizing bacteria is Gallionella, a naturally occurring bacteria found in a variety of aquatic environments— including aquifers. Gallionella are a stalked bacterium that use iron as an energy source and secrete an iron-oxy-hydroxide byproduct. In its attachment to iron-bearing surfaces, Gallionella pits the metal in an effort to secure the iron necessary for energy. All iron-bearing structures, including stainless steel, are susceptible to this form of pitting.

Better Maintenance

Well biology goes beyond just its influences on water quality. A better understanding of its role in well performance can help establish better maintenance practices and more accurate chemical cleaning and disinfection for our wells.

Monitoring biofilm growth through quantifying bacterial populations with additional testing centered on determining the composition and maturity of biofilm accumulations gives us a much better indication of the overall fouling potential.

Simple quantification techniques can gauge the timeliness of maintenance efforts. This data is also useful in determining better operational practices that can help minimize biological fouling— as idle wells often allow bacterial populations to enter unregulated growth phases that result in a higher fouling potential. A rise in bacterial growth, especially in conjunction with decreased performance, can trigger the need for routine maintenance before fouling becomes even more problematic.

Identification of not just the organisms themselves, but also the inorganic and mineral debris trapped within the matrix, can guide the design of treatment efforts and the selection of mechanical and chemical techniques.

In cases where heavy amounts of mineral constituents are present in the deposit matrix, mineral acids or more stringent mechanical agitation methods may be needed to break apart the more hardened scales. Further, if chemical agents are selected, their required quantities can be more closely calculated, keeping costs down and minimizing the risks of damaging well components or aquifer contamination associated with overtreatment.

Similar information can also target specific problem areas during maintenance, resulting in more efficient use of time and effort with a greater chance of success and reduced risk of redoing costly work in the future. For example, a biofilm with a heavy anaerobic population may indicate the growth is advanced and likely most prevalent in oxygen-depleted areas within the well.

In many wells these areas are found in the deeper depths where flow is reduced or where sumps are present. More mechanical agitation may be needed there to physically disrupt the deposits, a higher chemical dosage may be used, or perhaps adjusting the pump depth or filling in the sump is needed to remove and prevent the problem from reoccurring. In addition, specialty chemicals to enhance traditional cleaning chemistries, such as biodispersants and surfactants, can be selected to supplement traditional chlorine treatments to aid in penetrating and disrupting biofilm formations that may have otherwise been undisturbed.

A profile of other dominant bacterial species, including those associated with MIC, can also be beneficial in determining ongoing maintenance strategies. Identifying such organisms can expedite maintenance to prevent material degradation but also allow for better material selection in those cases where well components are already in need of replacement.


Degraded water quality is a common result of bacterial fouling. But the knowledge of biological fouling mechanisms with regards to well operation gives us the ability to make much more informed decisions about maintenance.

Assessments of the biological communities inhabiting wells can allow for more effective treatment strategies, selection of the proper chemistries, and more accurate chemical volumes— ultimately extending the life of the well.

While even the best cleaning and disinfection efforts fail to sterilize a well, better control and operation gained from proactive monitoring and supportive data ultimately allows for improved produced water quality.


Duderstadt, Eric. 2016. “The Mysterious ‘Bac-T’ Test.” Water Well Journal 70, no. 7: 18-23.

Sterrett, Robert J. 2007. Groundwater & Wells: Third Edition. Bloomington, Minnesota: Litho Tech.ts.

Eric Duderstadt is an environmental biologist with Water Systems Engineering Inc. of Ottawa, Kansas, where he works as a consultant. He earned his bachelor’s degree in biology at Ottawa University in 2007 and has since become certified as a corrosion technician within the National Association of Corrosion Engineers. He also works within the firm’s research department and investigative laboratory centering on microbiology and chemistry. Duderstadt can be reached at eduderstadt

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