Three Fields of Science That Can Influence the Life Cycle of a Water Well

Part III: Microbiology

 Spreading colony growth on a heterotrophic plate.

By Eric Duderstadt

This article serves as the third and final installment of a series of articles which have covered the three primary fields of science which impact the life cycles of water wells.

The first two articles, addressing geology and chemistry, discussed the science of water and rock relationships and the many roles they can play within wells regarding aquifer conditions, corresponding water characteristics, and a number of subsequent influences on the well itself.

The third scientific discipline within the water well is that of microbiology. As compared to other sciences, microbiology is a relatively young science and a field dramatically evolving, especially within the last half-century.

Aided by advancements in laboratory technology, we now can analyze and measure biological entities which were once not even known to exist or were only speculated in theory.

Microbiology is defined as the study of microorganisms and their activities. Bacteria represent an extremely diverse group of organisms that can play several beneficial roles in the environment and within some industries.

Within the well setting, however, bacteria can potentially be problematic, posing risks to production, corrosion, health risks, and overall decline in water quality.

Bacteria Are Everywhere

On a fundamental level, one must understand that bacteria naturally exist everywhere on earth, including in our aquifers.

Varied colony growth is shown on a heterotrophic plate.

In the well setting, bacteria typically exist within one of three areas.

The upper zone of a well is most susceptible to surface water influences. This includes the upper casing, column pipe, and area of interaction between static and pumping water levels.

As such, larger microbes or shallow surface-dwelling bacteria can be found in this area. These organisms can be introduced into the well environment through flooding events, grout failures and compromised sanitary seals, or cascading water conditions through breached casing.

A second zone within the well is the middle or active well zone. This is the area of greatest production where water is sourced by one or more screened intervals by the placement of a pump. The movement of water in this area not only carries minerals from the surrounding geology which can develop into scale formations, but also delivers essential nutrients which are utilized by the available bacteria.

The more consistent turnover of freshwater within this zone also delivers oxygen. Consequently, the bacteria which inhabit this area are aerobic, meaning they rely on oxygen for their metabolism.

Iron-oxidizing bacteria (Gallionella) are identifiable by their distinct twisted “double helix” stalked structure.

The lower portion of the well represents a third zone of a well. This area includes the lower screen and gravel pack and may contain a sump. Because flow is often reduced, or stagnant in some cases in this area, water conditions can become deprived of oxygen, or anaerobic. Thus, anaerobic bacteria, which do not require oxygen for their metabolism, reside within this zone.

Anaerobic bacteria include groups of bacteria which are known for their ability to impair water quality through taste and odor issues and are often most difficult to reach during cleaning and disinfection efforts.

Biofilms Impact Wells

Perhaps one of the biggest influences that bacteria can have on a well regarding operation is through the loss of production due to the formation of biofilm. Biofilm is a natural expression of bacteria resulting from the excretion of slimy polysaccharide exopolymer material. Bacteria exude this slime as a means of surface attachment for propagation, nutrient capture, protection, and growth.

Within this matrix, the concentration of bacteria can be many magnitudes greater than free-swimming, or planktonic, bacteria located outside the biofilm complex. While this slimy, sticky material is a great aid to bacteria, it is equally detrimental to the operation of the well.

Biofilms promote scale buildup by providing an excellent surface for adhesion of mineral-forming ions, fine-grained sediments and debris, mobilized towards a well during operation. In addition to the slime and bacteria themselves, these additional materials often become entrapped in biofilm, and increasing the fouling potential.

Thiothrix is a filamentous bacterium associated with sulfur oxidation.

Another noteworthy aspect of biofilm growth relates to its level of maturity and establishment. As the development of biofilm reaches more advanced levels, a trait which is commonly observed is the stratification of layers in which the upper exposed aerobic stratum overlays lower anaerobic layers.

This is of particular importance as it relates to an increase in the relative density and fouling potential of the biofilm, as well as offering suitable conditions and additional protection for the harboring of more problematic bacteria.

To illustrate this point, laboratory testing has shown that as the percentage of anaerobic bacteria within the overall bacterial population increases, so too does the occurrence rate of coliforms. As a point of reference, when anaerobic bacteria represent less than 10% of the total bacterial population, coliform occurrence is below 2%. However, when anaerobic growth climbs to approximately 15% or greater, coliform occurrence rates grow to roughly 25%, with coliform rates doubling to approximately 50% with anaerobic growth of 30% or greater.

Colony growth of Bacillus polymyxa, a slime-forming bacterium, is visible.

Assessment of the biological activity within wells is a valuable necessity in determining the overall cleanliness of water and general operation. For centuries quality water was defined by smell, appearance, taste, and later, chemical analysis.

However, as mentioned earlier, modern technology has made possible the study and understanding of microorganisms on a much more timely and affordable level.

Testing for Bacteria

While bacteria can pose a significant threat to the life cycle of a well, the regulation of bacteria within the water industry is largely reliant on a single group of bacteria referred to as coliforms, which are identified by a single test often referred to as a Bac-T.

This is in larger part due to the sheer volume of microorganisms found within soils and water and the need within the industry to establish the use of indicator organisms—a strategy that assumes certain conditions to be true through the identification of a single or a few organisms. This group of indicator organisms is a group of closely related bacteria which behave similarly to a variety of other bacteria known to be harmful if consumed in drinking water.

Yet, it should be understood that the presence of coliforms and the practice of targeting indicator organisms to judge the likelihood of another microbe’s presence only suggests the potential presence of more problematic organisms; it does not truly confirm it.

In fact, coliforms are widely dispersed throughout a wide range of environments and only a small group of them are representative of contamination. Additionally, it should be noted that the absence of coliforms does not confirm a water sample is completely free of other harmful microorganisms.

While the presence of coliforms does present health risks and should be monitored, they represent only a small fraction of the potentially dangerous microbes found in water. Furthermore, current regulations fail to account for nuisance organisms which can cause degraded water quality and costly maintenance.

Data generated from testing conducted on more than 2000 samples from problematic potable water wells across the United States within the last 10 years found that the occurrence of these so-called nuisance organisms or problematic levels of bacteria capable of causing changes in production or water quality occur far more often than coliforms.

Further, the detection of other bacterial markers often occurs prior to more drastic changes in well performance, making them useful tools as preventative monitoring and maintenance before conditions become more problematic.

One noteworthy group of nuisance bacteria are sulfatereducing bacteria (SRBs), a group of anaerobic bacteria known to produce hydrogen sulfide gas. SRBs obtain energy by oxidizing organic compounds and reducing sulfate to hydrogen sulfide. The presence of even small quantities of this gas is unpleasant to the consumer and produces a foul, rotten egg–like odor. Additionally, as the hydrogen sulfide is released, the environment often turns acidic and corrosion can develop as the unpleasant gas is mobilized up the well column.

Another significant group of nuisance bacteria is that of the iron oxidizers. Iron-oxidizing bacteria utilize iron as an energy source and secrete gelatinous stalks or sheaths of iron-oxyhydroxide, often far larger than the bacterium itself. These larger structures are often responsible for accumulations of iron oxide in wells and can rapidly clog screens and pump intakes, effectively reducing flow into and out of wells.

In addition to fouling concerns, iron-oxidizing bacteria are also a chief form of microbial-induced corrosion (MIC). In its attachment to iron-bearing surfaces, many of these bacteria will actually pit 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. Laboratory data suggests iron-oxidizing bacteria are present in a large portion of problematic wells, with testing showing occurrence rates near 50%. Gallionella are one of the most common groups of iron-oxidizing bacteria, accounting for more than 75% of all samples where iron-oxidizing bacteria are identified.

Read the Entire Series on the Fields of Science
Read parts one and two of the series, Three Fields of Science That Can Influence the Life Cycle of a Water Well. Part I was authored by Michael Schnieders, PG, PH-GW, focused on geology, and was published in the April 2020 issue. Part II by Roger Miller detailed chemistry and was published in the May 2020 issue.

Knowing the Numbers

Beyond identifying which bacteria are present in a well, quantifying the population is also important. Although an exact count is not always needed, some estimate of the total bacterial population is useful in determining how established the community is and the need for cleaning or disinfection.

Also, increases to the overall bacterial load often correlate with the occurrence of anaerobic conditions and other indicators for more mature biofilm growth. The size of microbial populations can be measured either directly or indirectly using direct counts, measurements of the population’s mass, or through measurement of cellular components and can vary greatly in cost.

More conventional quantification tests include the Heterotrophic Plate Counts (HPC), while one of the most reliable rapid screening methods available is Adenosine Triphosphate (ATP) analysis. However, while both methods are quantitative in nature, they differ fundamentally in how they provide data.

HPC methods are based on culturing any bacteria present in a sample on non-selective nutrient-based agar with the aim of counting the colonies that form. HPCs are useful in that they eliminate dead organisms from being counted. However, one colony may develop from a single cell or tens of thousands of cells and clumping of cells in colonies is random, thus making accurate bacterial counts difficult.

Perhaps the biggest downfall of the HPC methods is that research has shown that only a small percentage of the bacteria found in water wells are culturable using common laboratory media.

Like HPCs, the ATP analysis is also a quantitative method. However, ATP analysis is a culture-independent method. The basis of the test exposes microorganisms to enzymes that catalyze a reaction, converting the ATP molecule within the cell into light energy.

Each molecule of ATP consumed in the reaction produces one photon of light. However, diversity among microorganisms found in water supplies is immensely vast and differences in metabolic processes, shapes, sizes, food sources, and physiological states can influence ATP concentrations.

Nonetheless, using average ATP levels can then allow for estimated bacterial counts in samples. ATP analysis is a valuable test in that it accounts for all living organisms present, is not influenced by inorganic particulate, can offer accurate bacterial counts, and detects those bacteria which are considered un-culturable.

While both HPCs and ATP are quantitative tests, comparison of the two methods illustrates the importance of understanding the advantages and disadvantages when selecting the proper tests to meet your needs.

Numerous methods are also available to identify individual bacteria, including both nuisance and pathogenic organisms. While identifying all bacteria present within the well is neither practical nor necessary, having an idea of who the major players are and the threats they pose is important.

Tests used to identify specific microbes include PCR (Polymerase Chain Reaction), DNA sequencing, phenotype microarrays, and nutrient characterization assays. Some nuisance organisms, such as iron-oxidizing and sulfate-reducing bacteria, can also be identified using microscopy. Identifying these specific organisms is not always necessary but can be helpful in locating problem areas in a system and setting priorities for maintenance operations.

Wrapping Up

Biofouling of well systems is the result of both bacterial presence and adequate conditions for sustainable growth, with sufficient maturation of the bacterial community resulting in the constricting of flow paths and impedance of the well structure.

The groundwater well is a relatively basic entity in theory but a much more complicated machine in practice. This is because of the many variables which are in play once a well is drilled—which are primarily based on the three sciences covered in this series of articles.

Some of these variables were touched on in previous articles in this series and include surrounding geographical features, nearby land uses, and available nutrients within the water. The method in which a well is constructed, materials used, and the way a well is operated are additional variables that can greatly influence the life cycle of the well.

The makeup of a bacterial population within a well and surrounding formation at a given location is yet another variable that impacts wells, and at the same time, can be itself influenced by any one of the before-mentioned variables.

These layers of complexity can make the observance and understanding of fouling in a well difficult. However, a supportive and constructive coexistence between a scientist, water well contractor, engineer, and system operator allow everyone involved to approach issues from a more informed and educated perspective.

Effective monitoring of well conditions can provide for changes in operation, proper maintenance, and treatment to maximize the life cycle of the well—ensuring it remains the effective and healthy asset it was designed to be.

Find Books on Water Treatment in the NGWA Bookstore
There are several books available in the NGWA Bookstore that focus on matters relating to water treatment, water well technology, and more. Included is Operational Stage of the Well, whose coauthor is Michael Schnieders, PG, PH-GW, the author of the first installment of this series. The book goes over various factors of well deterioration and how they impact well operation and maintenance. Visit the NGWA Bookstore section on water treatment.

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