Larger Microorganisms in Well Systems

It’s important to understand and monitor the millions of microorganisms in water wells.

By Michael Schnieders, PG, PH-GW

The distinct green from the chlorophyll presence in algae is evident under the microscope at 400 times magnification. The presence of green algae serves as confirmation of surface influence on a well.

Biofouling or biologically related fouling is a common problem in wells, storage tanks, and various means of water conveyance and management.

Differentiating between naturally occurring bacteria and organisms generally associated with surface water is an important tool in the management of wells.

“Groundwater under the direct influence of surface water” means a groundwater source is located close enough to nearby surface water such as a river, lake, or marshland to receive direct surface water recharge.

As wells constructed in the proximity of surface water bodies can potentially receive a portion of their recharge from the surface, it’s important to understand the risks of contamination from larger microorganisms.

The Types

Microorganisms or microbes are microscopic organisms invisible to the unaided eye. Microorganisms exist as unicellular, multicellular, or clusters of cells. Widely distributed in nature, microorganisms are beneficial to life but some can cause serious harm. They can be divided into six major types: bacteria, archaea, fungi, protozoa, algae, and viruses.


Bacteria are a single-celled form of biological life which are widely dispersed on our planet and found in every environment. Bacteria vary in size and shape, and can exist as single cells, in pairs, chains, or clusters. Bacteria make up a large portion of prokaryotic microorganisms, akin to protozoa, algae, and fungi.

Arthropoda appendage identified in a large diameter, high capacity irrigation well in California. Magnification is at 40 times. All images courtesy Water Systems Engineering Inc.

All bacteria exude a polysaccharide exopolymer as a means of nutrient capture and shelter from changes within their respective environments. This exopolymer is referred to as biofilm and is considered to be the primary mode of existence for bacteria in aqueous environments. Biofilm production varies among species and environmental stimuli and has been estimated to be as high as 1500 times the mass of the producing cell.

In a 2002 study, the National Institutes of Health noted that biofilms accounted “for over 80% of microbial infections in the body.” Similarly, an American Water Works Association Research Foundation study in 2002 concluded that bacteria were responsible for 80% of the fouling in well systems.


Archaea (formerly called archaebacteria) are a subgroup of bacteria. Archaea are considered to be some of the oldest known life forms on the planet, emerging approximately 3.5 billion years ago. Archaea differ from the more common bacteria in the composition of their plasma membranes and cell walls, as well as their ribosomal RNA.

Archaea are commonly found in harsh environments such as hydrothermal vents, highly concentrated saltwater, and anaerobic-rich locations such as bogs and sewage treatment plants. These environments reflect the major groups of archaea: methanogens, halophiles, and thermophiles.


Fungi are part of a large group of eukaryotic organisms that includes microorganisms such as yeast and mold. These organisms are classified as a kingdom (Fungi) which is separate from bacteria and plants, based on the development of fungal cell walls (chitin).

A nematode, often referred to as a “microscopic worm,” present in an older, shallow completion, public water supply well. Magnification is at 200 times.

Abundant worldwide, most fungi are inconspicuous because of the small size of their structures, and their somewhat hidden existence in soil, dead and decaying matter, and as symbionts of plants, animals, and other fungi. Within waterborne deposits, fungal groups are distinct from the similar myxomycetes (slime mold) and oomycetes (water mold).

Yeast are eukaryotic microorganisms classified in the kingdom Fungi. Yeasts are generally unicellular, although some species with yeast forms may become multicellular through the formation of strings of connected budding cells known as pseudo-hyphae as found in mold.

Yeast size can vary greatly depending on the species, typically measuring 3-4 micrometers in diameter. Reproduction occurs asexually by mitosis, and many do so by an asymmetric division process called budding. Some species of yeast are opportunistic pathogens and can cause infections in humans.


Protozoa are single-celled eukaryotic organisms present in water, ranging in size from 1 micrometer to several millimeters. Protozoa are most often associated with surface water bodies, indicating large, diverse, and mature microbiological communities.

The occurrence of protozoa in a sample is a concern as some are parasitic and others, like Giardia and Cryptosporidium, are pathogenic. The identification of protozoa within a water sample is dependent on microscopic evaluation, as neither heterotrophic plate tests nor total coliform tests indicate their presence.

A larger protozoa and algae present in a flooded public water supply well in the central United States. Magnification is at 400 times.

Some small protozoa (such as ciliates or flagellates) are occasionally found in aquifer systems, but even then, they are suspected of some type of surface water or near-surface infiltration.

There have been attempts to indicate protozoa may indeed live full time in aquifers or that an infestation has become permanent, but it has never been accepted or proven. Our lab occasionally sees small ciliates in groundwater samples, but only in well systems that display excessively large microbial communities and severe biofouling.

Some of the more common protozoa which raise concerns of the integrity of a well system or the impaction of a recharge zone include amoeba, nematodes, paramecium, and rotifers.

Amoeba is a genus of protozoa consisting of shapeless, unicellular organisms. Amoebas often live in biofilm and other water-soil, water-air, and water-plant interfaces. Among protozoa, amoeba specifically are associated with surface water bodies, generally a reflection of a direct conduit between the groundwater source and surface water, or a breach of the well. When confronted with harsh environmental conditions that threaten them, they convert to a form known as a cyst. Amoeba cysts are resistant to chlorination, adverse pH changes, osmotic pressure, and temperature.

Nematodes are a multicellular organism often referred to as a microscopic worm. Nematodes inhabit a broad range of ecosystems, including freshwater and saltwater environments, but are mainly found in shallow soil settings. Nematodes have a distinctive alimentary canal which aids in their identification. Many nematodes are considered pathogenic. Several intestinal diseases affecting human beings are attributed to nematodes including ascariasis, trichuriasis, and hookworm disease.

A planktonic crustacean identified as Daphnia or “water flea” identified in a damaged well in the southeastern United States. Magnification is at 40 times.

Paramecium are a genus of microscopic, single-celled protozoans. Paramecium are larger microorganisms, varying in length from about 0.05 to 0.32 millimeters. Their basic shape is an elongated oval with rounded ends, covered in fine hair like organelles called cilia which aid in movement.

Rotifers are a group of larger multicellular microbes usually around 0.1-0.5 millimeters long (although their size can grow to more than 2 mm). They get their name from a Latin word meaning “wheel-bearer” due to the corona around the mouth that moves in concerted sequential motion resembling a wheel. They are common in freshwater environments throughout the world, with some being free swimming and truly planktonic, others moving by inch worming along a substrate, and still other being sessile or immobile.

Rotifers are an important part of the freshwater zooplankton, with many species contributing to the decomposition of soil organic matter and the digestion of particulate organic detritus, dead bacteria, algae, and protozoans.

Water crustaceans, which identification depends on the life stage and size, are occasionally found in severely impacted well systems. Crustaceans (phylum Anthropoda) generally fall under the classification of an invertebrate animal. Complexity and size vary dramatically, and identification can be difficult beyond presence.

Microbial cysts are a resting or dormant stage of a microorganism, usually a bacterium or a protist, that helps the organism to survive in unfavorable environmental conditions. It can be thought of as a state of suspended animation in which the metabolic processes of the cell are slowed down and the cell ceases all activities like feeding and locomotion.

Encystment also helps the microbe to disperse easily, from one host to another or to a more favorable environment. When the encysted microbe reaches an environment favorable to its growth and survival, the cyst wall breaks down by a process known as excystation.


Algae are a large and diverse group of simple, typically autotrophic organisms, ranging from unicellular to multicellular forms that occur naturally in saltwater and freshwater. Algae are photosynthetic eukaryotes and conduct photosynthesis within membrane-bound organelles called chloroplasts.

Algae have cell walls composed of cellulose, pectin, or silica and may live singly or in colonies. There are six groups of algae recognized: green algae, euglenoids, diatoms, dinoflagellates, brown algae, and red algae.

The presence of algae within a water sample is generally a reflection of a more advanced biological community, with sufficient nutrients present for expanded biomass development. While larger accumulations of algae are often visible to the naked eye, the identification of algae within a water sample is typically dependent on microscopic evaluation, with neither heterotrophic plate tests nor total coliform tests indicating its presence.

Significant accumulations of algae, including algal blooms, can overtake water bodies and be detrimental to the aquatic ecosystem.

Algae occurrence in groundwater wells is generally a reflection of contamination through flooding, grout/seal compromise, or rapid recharge of surface water-influenced shallow groundwater systems.


Viruses are the smallest of all microorganisms, ranging in size from 20 nanometers to 350 nm. A virus is comprised of genetic material such as DNA or RNA and is surrounded by a protective outer layer called a capsid. A true form of parasite, viruses are only able to live and reproduce inside the cells of other living things. Understanding the occurrences of viruses in water is important as they can cause various diseases in humans, animals, and plants.

The identification of viruses in groundwater is difficult and generally conducted in a forensic manner after an outbreak of illness has occurred. As they require the host, tracking and evaluating for larger microorganisms is generally a more effective means of monitoring virus movement.

The Management

Most of the regulated microbial testing in groundwater falls on the total coliform test as a means of water quality evaluation. As an indication of the potential for problematic bacteria, the test is not the single indicator of a vast array of possibilities that it is so often assumed to be.

Truth be told, like the evaluation of water chemistry, there is no single test which can account for the millions of microbial species potentially present in a water sample. As such, multiple testing methods are necessary to effectively assess the biological component of a water sample. Even then, as with chemical analysis, the usage of the well, the maintenance record, and the integrity of the structure can dictate results between sampling events.

It’s important to remember these microorganisms have a broad and almost universal occurrence on our planet. Many aspects of microbiology continue to be unveiled and more and more is understood each year. With such a wide expanse and adaptability, it’s important to understand that we as an industry will not be one to “sterilize” a well or water pipeline, but we can manage and mitigate the potential for problematic microorganisms to occur.

That’s why I advise routine monitoring of general conditions as well as specific problems or challenges known to the aquifer and well. A good assessment of microbial conditions includes the quantification of the total population, evaluation of the differences in aerobic and anaerobic growth, as well as testing for specific nuisance species and known pathogens.

Lastly, microscopic evaluation remains one of the best methods for the detection of larger microorganisms as well as the levels of microbial activity and biomass development.

Michael J. Schnieders, PG, PH-GWMichael Schnieders, PG, PH-GW, is the president and principal hydrogeologist at Water Systems Engineering Inc. in Ottawa, Kansas. Schnieders was the 2017 NGWA McEllhiney Lecturer in Water Well Technology. He has an extensive background in groundwater geochemistry, geomicrobiology, and water resource investigation and management. He can be reached at