Filamentous Identification


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Lab Services:



Filamentous Identification Lab Service. One reason to identify filaments is to determine the filaments characteristics and then determine the type present.  If the type is found out, a root cause can usually be associated with a particular filament.  If the cause is known, then a correction can be made to alleviate problems. Chlorination is only a quick fix.  Without process changes, filaments will grow back after chlorination.

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Training is an integral part of any job. Not everyone is at the same level of training. Many people want beginning concepts and basics. Some need technical information or troubleshooting. Some want equipment, technology or process information.

We have developed a full set of Basic training, Advanced training, Filamentous Identification the Easy Way as well as custom training CD's Manuals. We also provide hands-on training classes and soon will have an Online "E-University".


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An onsite audit is conducted to examine system parameters, process controls, and current monitor and control procedures. A physical walk-through is conducted, process flow diagrams are examined, previous design criteria are examined and current standard operating procedures are evaluated along with data logs.




Filamentous Identification

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I don't have filaments at my plant.......You might want to check again.

Stalked ciliates

A common misnomer in many wastewater treatment plants is that unless they have filaments that are bridging and they can see them between the floc structures, they do not have filaments.  In reality, internal bulking can cause more problems than slight bridging.

Many plants think there is only a problem when they have external filaments that are causing bulking problems.   In reality there are three ways to cause bulking at a plant, internal filaments, external filaments or non-filamentous bulking- which can be caused by zooglea, fungi and in many municipalities or paper mills, fiber or tissue.  


Wastewater Biomass Analyses document with Filamentous Identification.


What is the difference and how do they impact the plant?  Let's take a closer look at all of these scenarios.


Filaments can be internal, external or free floating.  Internal filaments are like a sponge.  They can be hard to settle and dewater.  External filaments keep the floc structures from coming together and compacting.  Free-floating filaments can cause TSS problems. Zooglea and fungi can cause foaming, sliming or bulking.


Let's first look at some samples from a few plants that have external bulking and what most operators think is the only case for filamentous problems.  External filaments are those filaments that extend into the bulk solution and cause difficulty in settling. They form a bridge between the floc structures and make compaction difficult. They can take up large amounts of space in a clarifier or digestor or even aeration basin.


BRanching filamentsFilamentous identification

It is easy to pick out the filaments extending from the floc structure.

The first photo shows the start of bridging, the second photo from a plant has abundant levels of filaments and the last one has excessive levels of filaments. This will make it hard to settle in the clarifier, hard to dewater and increase polymer consumption and increase solids hauling costs. This is typically what people think of when they talk about filamentous bulking. While you may think you have a large amount of bacteria when doing a Settleometer, in reality, the filaments are just taking up more space.

Bulking settleometer                      after chlorination

Typical SSV30 with Filamentous Bulking  before and after Chlorination

How do you know if you have filamentous bulking or if you just have too much MLSS in your settleometer? 


Obviously, looking under the microscope is the first thing you should do, but you also can use your settleometer to tell what issettleometer going on. Run a normal settleometer. Say for example your settling only drops down to 800.  Then run a 50/50 dilute sample. 50% water and 50% normal MLSS. In reality, it should settle down to 400 in the same amount of time if it was just too much MLSS. If in fact it is due to filamentous bulking, it will probably not settle down to 400 or even close to that number. That will be a quick indicator to look closer under the microscope and see just how many filaments there are and what types are present so you can find a cause and make a process change to make them go away. Remember, chlorine and peroxide can kill filaments, but if you do not make a process change, they will always come back. Change the system, and you select for the right type of bacteria

Normal vs. 50/50 dilute before and after

There are other ways to have bulking.  Internal filaments are just as bad if not worse than external filaments in the long run.

What is the difference and why is it so important and often overlooked?  Internal filaments are found mostly within the floc structure.

internal filaments invertinverted internal filaments

Look closer, what appears to be nice floc, in reality is full of holes and spaces. Think of internal filaments as more like forming a sponge. Imagine trying to dewater a sponge. It would not only take quite a bit of pressure, but also polymer. It would hold water and not want to compact either. Internal filaments are just as much of a problem if not more. External filaments can at least be compressed with polymer. It takes more for internal filaments. Do not overlook them. Use your microscope and blow up the sample to 400x or 1000x and take a closer look.


 Filamentous identificationFilamentous phase contrast

When there are excessive levels of filaments, chlorination or peroxide will take forever to burn off these filaments.  It is actually better to find out the cause, make a process change, slowly waste alongside chlorination and reseed with a commercial product if necessary. Otherwise, it could take 3-6 months to a year to make these filaments go away. A process change is always necessary, even if heavy chlorination is used. If the condition that caused the filaments to grow does not change, the filaments will always come back.  They are very good BOD degraders, they just cause too many solids, dewatering problems and bulking in the clarifier.


bridging filaments 021nexcessive filaments

Free-floating filaments are another way you can have problems in your plant.

Free-floating means the filaments can be found floating in the bulk solution and can cause serious TSS problems.

Zooglea and Nocardia

All of these plants needed to make process changes in order to get rid of the filaments and reduce chances of violating on TSS due to filaments that were free floating.


Zooglea and fungi can cause problems at a plant but are caused by very different situations in a plant and many times are overlooked.

Fingered zoogleaFungi and filaments

1000x Fungi and zooglea low pH and low nutrients at a pig farm lagoon.  This sample on the right is a digestor at a municipal plant. Tons of fiber and fungi. They were turning off the air to try to get more settling during decant and left the air off too long. This can cause serious growth of filaments and fungi.

Below is a perfect example of a plant that had problems and foaming. This is a municipal plant but they do have some industry that discharges to the plant. They were hit with a high loading and had tons of foaming on the plant. They assumed it was filamentous problems. Most operators do not look past 100 or 400x under their microscope.

At 100x bright field it does not look too bad.  Zoom in to 1000x and use some stains. Here is 1000 x with Gram and Neisser stain. It appears there is quite a bit of amorphous zooglea.

1000x gram stainzooglea neisser stain

As you can see, very few filaments, but the main issue here is zooglea.  Be careful-Chlorination would only make the zooglea problems worse and increase the amount of zooglea. If you think you have filaments and instead have zooglea, you can make your plants worse. This plant needed to add some nitrogen and phosphorus and immediately the foaming and zooglea will disappear.  Most municipalities would never assume they need to add nutrients, since the majority of them have excess nutrients.  If you have industry that discharges, you may get upsets that can cause this issue.  Cheat and use decant from your digestor that is usually high in nutrients if this is only an occasional upset. If this is a normal problem at your plant, you may need to keep nutrients on hand for upset conditions. Use the microscope and let the microbiology tell you what the problem is and which solution to use.

foaming from septicitysepticity foaming

Filamentous bulking from septicity

foamingm parvicella foamingfoaming

Here are plants with foaming from Nocardia or M. parvicella- they needed to focus on grease control

You cannot tell by looking at the foam what is really wrong with the plant. Pull a sample, get out your microscope and then look at what is present. The bugs will tell you what is going on and then you can fix it and change the process!


Still not convinced?

Here is why it is so important to worry about solids and how they impact your plant… money, when it comes right down to everything, here are some of the critical cost factors involved with running a wastewater treatment plant


Electricity is usually the number one cost at a plant. Then solids handling and last polymers used for dewatering.  The drier cake solids you can get, the less volume your sludge takes up, the lighter it weighs. If you are paying for solids handling costs based upon volume or weight, it is very critical. 

How are your bugs doing?
Click this Link to start Learning the Filaments of Wastewater: Wastewater Training Materials

Contact us today to set up a Filamentous Identification of your MLSS and start saving money at your plant~

Phone 630-906-9791 or Email us at - Click on the links below for additional information and training.


1 - Wastewater Biomass Analyses with Filamentous Identification

2 - A full set of Stained Filaments-Microscope Slide Set

microscope slides

3 - © Filamentous ID The Easy Way™ - Wastewater Training CD

4 - Click Here for All of our Wastewater Training Materials in PDF form to Print

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Wastewater basics   How to use the microscopeVisual troubleshooting a wastewater lagoonNitrification and denitrification


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Lab Poster


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Environmental Leverage Lab Poster for Wastewater Training. This Microbiology Poster has photos as well as descriptions and troubleshooting recommendations of common micro organisms
found in most wastewater treatment plants.


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