Article | February 14, 2018

Why We Should Use Naturally Occurring Microbes To Save Our Waterways

By Ralph Elliott

Hurricane River

How Do We Get Rid Of Bottom Sediment?

The most common technologies utilized in the treatment of natural bodies of water that become polluted,  or  begin  to  undergo  eutrophication, involve primarily some form of physical or chemical treatment such as chemical oxidizers, flocculants, activated carbon and zeolites, and/or mechanical treatments such as dredging.  The primary drawback to chemical treatments is that the treatments are based on stoichiometry or molecule to molecule interactions. As a result, they get very expensive when treating large volumes of water.

Likewise, dredging is expensive because it is labor and capital equipment intensive. There are other issues such as final disposition of dredge spoil, noise, disturbing of the site, total disruption of the marine habitat and surrounding areas, and the risk associated with operating large equipment that totally disrupts populated areas.

Is There A Better Way?

In recent years bio-remediation has proved to be, not only effective, but, in most cases, very economical in treating natural bodies of water. Bio-remediation takes advantage of nature's own processes for recycling of basic elements of most organic pollutants and organic bottom sediments back into the biosphere through what are known as biogeochemical cycles. To accelerate these natural processes bio-augmentation may be utilized. Bio-augmentation is the purposeful inoculation of a system with microorganisms that have been selected for their particular metabolic characteristic.

The technology has been successfully applied in a large number of natural and man-made bodies of water to improve water quality and break down bottom solids. A review of several project reports including retentions ponds in Jacksonville, FL, lakes in Naples, FL, as well as entire sections of a river in China, Malaysia, and a lake at Dartmouth College has proven the effectiveness of bio-augmentation. In these applications, substantial reductions in aqueous phase pollutants were observed including biochemical oxygen (BOD), total suspended solids (TSS), total nitrogen (TN), total phosphorous (TP), and the near total elimination of fecal coliform and specifically E. coli, F. coli, and salmonella. In addition, there was a reduction of 80 percent and more of the organic bottom solids without the need for dredging and associated spoil problems.

The above lifecycle of microbes used in bio-augmentation, indicates they can remain in a "lag phase" for a long time and then once applied to an organic, pollution rich environment, the microbes immediately begin to consume organic pollutants. With the right consortium of microbes, the product can consume all or most organic pollutants in a "Log or exponential phase". When there is no more "food" they enter a "Stationary phase" and then begin to die. During the "Death or logarithmic decline phase", the dead microbes become organic pollution and the remaining microbes consume the dead microbes cleaning up their own mess.

In a perfect world the same, naturally existing microbes found in our waterways  would  complete  this  same  cycle  over and  over  again,  but  when  excessive  pollutants enter a water way the natural microbes cannot keep up with  the pollution and they need to be augmented.

Studying, Planning, And Permitting An Ecosystem Restoration Project

Most Ecosystem Restoration Projects are done by the U.S. Army Corps of Engineers (COE) as a dredging or a combination of mechanical and chemical process under Section 206 of the Continuing Authorities Program (CAP). CAP is an annual “pot of money” in the federal budget that allows projects to be done that have not yet been identified and are expected to cost the federal government less than $5M as their share of a project sponsored by a public entity. There is a 65 percent/35 percent cost share, with the federal share at 65 percent but not to exceed $5M. There are other specific rules such as the complexity necessary to complete a Feasibility Study and the Environmental Assessment and they must be studied and full plans and specifications must be developed. All permits must be issued for the project which cannot be accomplished until a study, the Environmental Impact Assessment, has been completed and the plans and specifications have been formulated.

This process generally takes the COE from 8 to 12 years and sometimes longer.

Permitting For The Use Of 100% Natural Microbial Compounds

The EPA has agreed that as long as a microbe or consortium of microbes has not been chemically or genetically altered that they do not require permitting. The Army Corps of Engineers has agreed that their permitting authority does not extend into the use of naturally occurring microbes and therefore no permit is required. The Florida Department of Environmental Protection has determined that an Environmental Resource Permit may be required and that warning signs should be posted at a site where treatment is being conducted because there may be a reaction in "immunocompromised" humans similar to the reaction caused by high levels of fecal coliform. There is no evidence to indicate this will happen but is merely a precaution.

Since there is basically no permit required for this process, it could be completed long before the actual Section 206 project begins, meaning that if half of the material to be removed was organic sediment then only half would be dredged and or chemically treated.

Project Summaries

In January 2009, the facility manager of the Jacksonville Zoo approached EWQR about a problem in their "Swan Pond". The pond had a distinct odor, was very cloudy, and the swans were developing what could be described as sores on their bodies. EWQR agreed to do a test/demonstration to prove we could fix their problem and water samples were taken and analyzed for pollutants. The results were the following: BOD - 16 mg/L; COD - 240 mg/L; Nitrate - 0.60 mg/L; Nitrite - 0.32 mg/L; TSS - 62 mg/L and Fecal Coliform - 36,000 CFU/ 100 mL. The pond was approximately 60 feet in diameter. It was treated twice, once in January and again in March, and tested between treatments. The final results were: BOD - 16 mg/L (no change); COD - 120 mg/L (50 percent reduction); Nitrate - Below Detectable Limits (BDL) (100 percent reduction); Nitrate - BDL (100 percent reduction); TSS - 106 (increased due to "death phase" of microbes); and Fecal Coliform - 4,600 (87 percent decrease). The swans began to recover and the water clarity improved after the first treatment. The odor was gone. This demonstration was done for free with the microbial consortium provided by the laboratory.

In August 2014, the FDEP accepted the product and process into their "Accepted Technology library" and in September the City of Jacksonville agreed to a meeting and presentation that focused on Hogan's Creek. The creek had been in the news as being very much polluted.

As the briefing progressed it became obvious that the City was more interested in their retention ponds and the reduction of pollutants in them, but was reluctant to accept more than 30 years of project data and results. We had stated that we could reduce most, if not all, organic pollutants within six months by 50 percent. The Vice President of Ecological Laboratories Inc., the company that produces the microbial consortium we use, was present in the presentation and stated that they would provide the products if we would agree to provide the labor to do a six-month demonstration project for the City of Jacksonville. The City asked for three ponds instead of one and stated that if it did what we said they would find funding for a second phase. They also stated that they were only interested in reducing total nitrogen and fecal coliform. We all agreed as long as each of the three ponds was 1 acre or less.

Six months later, the nitrogen was reduced in all three ponds by an average of 76 percent with all reduced by more than 50 percent. The fecal coliform was reduced an average of 84 percent with all reduced by more than 50 percent.

The project concluded in June of 2015 with no phase 2 funding as of January 2018.

This product and process have been used for over 30 years all over the world with amazing results. It has been used in stagnate ponds, lakes, and flowing rivers with fresh, brackish, and saltwater conditions with great success.

Many project reports are available upon request from EWQR at 904-545-0377, or email at

There are many microbial products out there but none formulated into a consortium with the success of this one.

Why Do Something Different Than We Have Done In The Past?

The answer to that question is simple.  It saves money, time, and energy.

The following cost comparisons are based on two different projects. The first is a completed project done in Clearwater Florida. The second is a pending project in Jacksonville, FL. Both are CAP Section 206 projects.

Stevenson Creek – Clearwater, FL

This project was requested by the City of Clearwater, through their congressman, first in 1999. A contract was awarded to do the work in 2009 for $4.67 million. The original CEO estimate presented to Clearwater was a total project cost of $3.2M, which included COE fees of $800,000. It was completed in 2012, three years later, at a cost of approximately $12M. The original construction contract completion time was 270 days to complete.

If we use the original contract amount for a cost comparison, the following shows what could have been saved by using a bio-augmentation pre-dredge treatment during the two years prior to award.

What caused these large savings?

In the case of Clearwater, there were four major areas that contributed to the savings. The staging and dewatering area was required by contract to be paved or otherwise hydrological isolated because of the contamination in the creek. The dredge spoil had to be mechanically separated into clean sand, organic muck, and water. The sand was to be used to build three littoral shelves to be planted with wetland vegetation and the organic muck had to be trucked away to an area 18 miles away. All of that effort would have been eliminated if the organic muck was eliminated first.

There was a requirement to do Elutriate toxicity testing on a regular basis because of the organic contaminants in the creek that would have been eliminated during the bio-augmentation treatments; furthermore, 100,000 cubic yards would have been eliminated so only 32,000 cubic yards of clean sand would remain and could have been directly pumped from the dredge area to the littoral shelf areas, eliminating the need for 3,500 additional feet of dredge pipe.

Another huge savings was energy. Fuel costs for the dredge were originally estimated at $157,500 for the 7 months of the job and $83,000 for truck fuel needed to move all the organic muck 18 away. The truck fuel could have been eliminated completely and the dredge would only be needed for a month and a half, saving $112,500 of dredge fuel. The mechanical material separation equipment had to have a 480-volt power supply connected to the dewatering site and the power consumption cost about $4,300 per month for 6 months. The connection and power usage would not be necessary saving about $60,000.

The contamination in the creek caused two construction firms to be terminated and the final cost to complete the project was in excess of $12M. We used the original contract cost to calculate the savings, but if we used the actual final cost the savings would have been over 800 percent.

Remember this project was a Section 206 project and federal statutes only allowed the COE to pay up to $5M, so the sponsor, the City of Clearwater, had to pay the rest.

Fishweir Creek – Jacksonville, FL

This project was also requested in 1999 by the City of Jacksonville. In 2002, a study was completed by the COE and presented to the City that showed a total project cost of $1,661,002. It showed the anticipated cost to the City of $553,113.67. The most recent available costs estimated by the COE is a total project cost of $7,161,000 and the cost to the City of $2,384,613. This is four (4) times the amount that the City had anticipated when they agreed to let the COE do the work for them. The COE has not increased the total cubic yards of material since 2002 when the cost per cubic was estimated at $20.59 per cubic. In 2015, that cost jumped to $88.77 per cubic yard. If we use the most current available COE figures, the comparison with and without bio-augmentation follows.

What caused these large savings?

In the case of Fishweir Creek, the major savings would be cost reduction because of the reduced amount of dredge material and the reduction of mobilized equipment necessary due to the fact that all organics upstream of the Herschel Street Bridge would be eliminated. Additionally, the area is not navigable, so what sand is there can stay there. A dredge would only be needed for about a month and a half. Water quality would not need to be monitored because no organics would be present to cause turbidity. The cost per cubic yard would be greatly reduced. The littoral shelf could be directly pumped because the remaining bottom sediment would be clean sand instead of muck so it would not tend to sluff back into the creek. And the time necessary for a dredge to be in the creek would be drastically reduced since so much of the material would already be gone.


Microbes are Mother Nature's janitors for natural purification and the primary decomposer of all organic waste matter by a slow ongoing biological process. Bio-augmentation works. It is cost-saving. It is a safe way to clean our waterways of organic pollution and organic bottom sediment. Bio-augmentation is the process by which we provide more of the natural microbes to a water body to boost and speed up that process.

Through a fermentation process we can formulate a consortium of microbes to be effective in any water body and in aerobic, anaerobic, and anoxic environments. It removes dead organics from within the water column as well as the bottom sediment leaving clean sand or other inorganic material.

Using bio-augmentation to pretreat an ecosystem is a cost savings process that should be done in every project where the sediment samples show a presence of organic material greater than 20 percent.

One of the best parts of using a bio-augmentation procedure is that it can be accomplished while the COE is still trying to study, design, and permit a project, and the permit would be much easier to get because all the pollution would no longer be a hindrance to the permit.

With public funds getting shorter and shorter, we must find ways to accomplish projects at less cost.

Ralph Elliott is Managing Member of Enviro Water Quality Restoration, LLC (EWQR). Phone: 904-545-0377; web:

Image credit: "Hurricane River," KOMUnews © 2010, used under an Attribution 2.0 Generic license: