Mar 10, 2022

Microbes: An Important Piece to the Water Quality Puzzle

Bioaugmentation and bioremediation harness and enhance natural biodegradation processes, helping prepare wastewater for release

Microbes, water quality

Everyone prefers clean lakes, rivers, and drinking water. Part of making that preference a reality is to clean up the soil and wastewater feeding into waterways. While there are many pieces to the cleanup puzzle, one important factor is the role microbes play in keeping environmental contaminants in check. Biotechnology has harnessed these natural biodegradation processes to make biological treatment of soil and wastewater a powerful tool in improving water quality.

Key Targets of Wastewater Treatment

The state of water released from industrial facilities or wastewater treatment plants has a direct impact on the environment. Therefore, one of the priorities of wastewater treatment is to purify the water to a condition reasonably acceptable for release into waterways. BOD, or biological oxygen demand, is one of the measurements used to evaluate water quality.

BOD is an indicator of how much biodegradable organic waste is in the wastewater. During an aerobic digestion process, free oxygen is used up as organics decay.  A higher BOD reflects a higher level of organic waste content in the water (i.e., more oxygen is needed to keep up with the degradation process). High levels of organic waste chemicals can themselves be toxic to the environment. Furthermore, since water quality depends heavily on the amount of dissolved oxygen in the water and affects the health of fish and other aquatic species, it is important for wastewater treatment to bring BOD levels down sufficiently before the wastewater is released to the environment. Otherwise, the organic overload (high oxygen demand) will transfer to the ponds or streams, depleting the oxygen to a level that cannot sustain aquatic life and could lead to putrid odors or septic conditions.

Another common wastewater pollutant is nitrogen, which includes organic-, ammonia-, nitrite-, and nitrate-nitrogen. High levels of nitrogen can cause nutrient pollution in lakes. Nutrient pollution fosters the problem of algae growth. Excess ammonia is hazardous to fish and also uses up oxygen during its conversion to nitrites and further to nitrates, which encourage algae growth.2 These are key reasons for monitoring and targeting nitrogen removal during wastewater treatment.


Wastewater Bioaugmentation

Standard wastewater treatment systems already rely on natural microbial activity to degrade waste substances. Naturally occurring heterotrophic microorganisms use waste materials for food, breaking large contaminants into smaller portions that they digest as part of their metabolic growth and reproduction processes, giving off carbon dioxide and water as final byproducts.3 Sometimes, though, the original microbial population is not able to keep up with the high level of organic waste. In such cases, the wastewater treatment plant is a good candidate for bioaugmentation.

Bioaugmentation augments, or adds to, the existing microbial population by introducing non-pathogenic bacteria to the wastewater. In effect, it is calling in reinforcements to tackle a job that is too big for the current biological “workforce” to handle. By encouraging the growth of a larger microbial population that consumes organic waste and nitrogen (among other macro and micro elements such as phosphorus, sulfur, iron, etc.), the waste treatment process can be done more efficiently and with fewer odor problems. Sometimes “biostimulants” (e.g., micro or macro nutrients for microbes) are added to further promote the health of the microbial population and their efficiency.

Bioaugmentation can be done at the municipal treatment plant (typically during secondary treatment) or at industrial and commercial facilities, which sometimes face fines for exceeding BOD requirements for discharge either to the wastewater plant or, in some cases, directly to the environment. Several cases illustrate how this can work.

Starch Factory Discharge Compliance4

Without a local wastewater treatment facility, a starch factory in Russia was left with the challenge of discharging 1100 m³ (290,589 gallons) of wastewater per day in compliance with local regulations. However, they far exceeded the acceptable limits of TSS (total suspended solids—another key indicator of wastewater treatment quality) and BOD5 allowed. To remedy the problem, they added two biological based products with a high count of “good” bacteria to the production area drain. In just two weeks, the municipal authority lab analyzed the results and found a TSS reduction of 65.5% and a BOD5 reduction of over 88%.

Ammonia reduction chart, microbes, water quality
Ammonia reduction from April to June 2020. Bionetix Case History #39.

Pig Farm Lagoon Effluent Treatment5

A pig farm in Europe was investigating treatment options for high ammonia wastewater lagoons. They also wanted to reduce COD (another indicator of wastewater contaminant levels). Lagoon effluent samples were subjected to lab shake flask testing. The results showed classic nitrification action in the sample to which nitrifying bacteria were added, with overall ammonia dropping by 93.8%. Nitrate concentration was high since ammonia is converted to nitrites and then nitrates during nitrification. The other sample was treated with another, non-nitrifying, high-count bacteria blend and experienced a 41% COD reduction trending downward at the end of six days. Ammonia reduction was less drastic (18.8% overall) but did not result in a high level of nitrates, unlike the nitrifying bacteria sample. This demonstrates that different bacteria are sometimes better suited for different treatment routes (processes).

Inorganic nitrogen reduction, microbes, water quality
Total inorganic nitrogen reduction from April to June 2020. Bionetix Case History #39.

Pulp and Paper Wastewater Lagoon Treatment6

Facultative anaerobic heterotrophs act as denitrifiers in the absence of free or low dissolved oxygen.  In still another case, these bacteria were used to treat wastewater lagoons fed mainly with pulp and paper waste. These bacteria use organic nitrogen for growth and at low dissolved oxygen levels can make use of oxygen that is bonded to nitrates, converting nitrates to nitrogen in the process.  Aeration of the lagoons began in the spring, and the denitrifier was added to the lagoons and accumulation basin feeding the lagoons for one month. Over the summer months, ammonia was almost completely removed, and total inorganic nitrogen dropped by 89%. A slight increase in nitrate concentration stayed below the ammonia reduction level, suggesting that a different process than nitrification was at work.

Soil Bioremediation

Water quality is affected by soil quality. Oil spills contaminate the soil with hydrocarbons and can take years to resolve on their own. Even worse, these contaminants could gradually leach into nearby lakes and groundwater. Bioremediation speeds the cleanup process by introducing microorganisms (and often supporting nutrients) specially suited to degrade hydrocarbons. Bioremediation can be done on location (in situ) or offsite (ex-situ) and is a welcome substitute for other options such as physical or chemical remediation (e.g., burning or solvent extraction, respectively).7


Phenanthrene and Naphthalene Reduction8

In a Bulgarian trial, an oil and gas extraction company decided to test the results of bioremediation on a pile of soil containing 39,574 mg/kg of petroleum products. The goal was to reduce this to 5,000 mg/kg. Microorganisms were added to the soil along with various nutrients to support their health and growth. Aeration was periodically performed. By the end of the first month, the two most common contaminants (phenanthrene and naphthalene) were nearly absent (Polycyclic Aromatic Hydrocarbon [PAH] compounds are very resistant to biodegradation; phenanthrene and naphthalene are typical compounds belonging to PAH). Total petroleum hydrocarbons (TPH) had dropped by approximately 49%. Unfortunately, testing was interrupted first by COVID and later by freezing winter temperatures. However, by the 16-month mark, the reduction had decreased by approximately 85%, nearing the trial’s goal of reaching 5,000 mg/kg of TPH. A temporary spike in TPH at 17 weeks may have been due to either an unnecessary third treatment, a false positive, or an increase in smaller chain hydrocarbons detectable in the C10-C40 range as a result of longer chain hydrocarbon breakdown.

TPH reduction, microbes, water quality
TPH (total petroleum hydrocarbon) reduction over time. Bionetix Case History #38.

Natural and Manmade Pond Treatment

Natural and manmade ponds also experience contamination by means of nutrient pollution (e.g., rainwater runoff containing fertilizers) or waste products from fish and other aquatic species. Again, adding the right microorganisms designated for these applications can promote cleaner ponds and healthier aquaculture environments.

One great example comes from a pond at a golf course in Chile. The pond was dark, with bad odors and algae. A special microbial blend apt to reduce organic waste, nitrogen (including ammonia-nitrogen),  and phosphorus was added to the pond twice, 15 days apart. A month after the first treatment, the bad odor was gone, there was less algae, and the pond was clearer. The results were attributed to reduction of nutrient pollution.9 The same treatment can be used to improve the quality of manmade ponds for pisciculture (fish farming).

Time to Add the Bioaugmentation Piece to the Puzzle

Protecting and improving water quality has many facets, including proper treatment of wastewater and polluted soil that could feed into the ecosystem. Bioaugmentation and bioremediation harness and enhance natural biodegradation processes to help prepare wastewater for release and clean up soil contaminants. Given the encouraging results of the bioaugmentation and bioremediation trials mentioned above, perhaps it is time for more industries to deliberately add microorganisms to the water quality puzzle.


1 Britannica. “Sources of water pollution.” Accessed 2.14.22

2 Ibid. “Oxidation pond.” Accessed 2.14.22

3 Ibid. “Primary treatment.” Accessed 2.14.22

4 Bionetix International. “Improving Sewage Quality to Avoid Municipal Fees.” Case History #32. November 2019. Accessed 2.14.22

5 Ibid. “Reducing COD and Ammonium in Agricultural Wastewater.” Case History #28. May 2019. Accessed 2.14.22 from

6 Ibid. “Lowering Ammonia Concentration in Lagoons.” Case History #39. October 2021. Accessed 2.14.22 

7 Decterov, Tonya, Ph.D. “Soil bioremediation and how Bionetix products fit in.” PowerPoint presentation. 5 August 2016.

8 Bionetix. “Soil Bioremediation Experiment in Bulgaria.” Case History #38. August 2021. Accessed 2.15.22

9 Ibid. “Pond Treatment at Santo Domingo Golf Course.” Case History #24. January 2019. Accessed 2.14.22 


About the author

Tonya Decterov ( is a technical sales representative at Bionetix International, a supplier of biological cleanup solutions ( She holds a Ph.D. in Biology (Soil Science). 

Julie Holmquist ( is content writer at Cortec Corporation, a global leader in corrosion solutions for industries involving metal ( Bionetix is a subsidiary of Cortec.