How to identify wastewater treatment microorganisms under the microscope

Wastewater treatment plants are home to a wide variety of microorganisms, but not all of them are welcome guests.

The presence of particular microorganisms, or even irregular ratios of normally desirable microorganisms, are good indicators of the health of your facility’s biomass.

If you want to detect bulking, shocks and food-microorganism ratio changes before they get out of hand, you will greatly benefit from a Phase Contrast Microscope.

With a good quality microscope you can recognise the important indicator organisms and some of the main culprits of undesirable plant conditions  – bacteria, protozoa and metazoa – quickly and easily, 

Here’s a short identification guide to some of the microorganisms you might encounter. Available for purchase is our Microbes Identification Chart

Most aquatic microorganisms are naturally translucent, so it can be difficult to make out details or internal structure without taking the time and trouble to stain them. It is therefore recommended when viewing microorganisms in wastewater monitoring to choose wastewater treatment microscope with phase contrast.


Bacteria are most populous organism in your wastewater plant – small (often between 0.5 and 10 µm in diameter) and difficult to see individually without high magnifications. When they form flocs or larger colony structures, they are easier to see.

Cocci Bacteria


This species of bacteria presents as finger-shaped or amorphous growths. They can have a slimy or gelatinous appearance due to the production of extracellular polysaccharides. This substance acts like ‘glue’ and can be clearly seen when using an India ink stain.

The presence of Zoogloea can indicate nutrient deficiencies (often nitrogen) and high levels of soluble organics.

Size: 0.5–1.3 µm

Sphaerotilus natans

This filamentous bacteria is characterised by long, rod-shaped cells with a thick tubular sheath. They can also exhibit what’s known as ‘false branching’ where a second line of cell growth emerges from the side of a filament, resembling a new tree branch. The species is both Gram and Neisser negative.

The presence of Sphaerotilus natans can indicate low oxygen levels or high oxygen demand, and the filaments themselves can cause bulking in your system.

Size: 1.4–1.6 µm


Another filamentous bacteria, Thiothrix has rectangular cells with a sheath that usually extends from the floc structures. They are quite unusual in that they can store sulfur inside themselves. Thiothrix is typically Gram negative but can occasionally possess Gram-positive granules. If growth is particularly rapid, Thiothrix can form asterisk-shaped rosettes when the filaments curl around themselves.

The presence of Thiothrix can indicate low oxygen levels or the presence of sulfurous compounds. They are a common cause of bulking problems if growth gets out of hand.

Size: 0.8–2.5 µm


Protozoans are larger, single-celled organisms that improve effluent quality by grazing voraciously on dispersed bacteria. They can be important indicators of biomass health and effluent quality.

Protozoa are responsive to changes in toxicity, dissolved oxygen levels and food-microorganism ratios.


They often have quite distinct characteristics and are easy to identify under a microscope.


This is a diverse group of protozoa that are named for the thin, tail-like flagella they use to propel themselves around. This ‘tail’ is longer than their main body and lets them zip around quite fast. They may have more than one flagellum.


Flagellates grow faster than other organisms so they’re often present in higher numbers when the plant is recovering from a shock, when there are excess nutrients or when the sludge is young.

Size: 5–20 µm


The classic protozoa, amoeba can grow quite large and slowly move around using their arm-like pseudopodia to engulf organic particles and bacteria.

Amoeba appearance can vary – while some have the stereotypical look of a melting starfish, they can also appear ovaloid or circular in shape.


‘Normal’ amoeba tend to be present in younger sludge, while the more circular ‘testate’ variety tends to be more common in older sludge.

Testate Amoeba

The presence of amoeba can indicate high levels of biological oxygen demand or high levels of free bacteria.

Size: 5–200 µm


This branch of protozoa is named for the many hair-like cilia that propel them through the water. They can be stalked or free-swimming.


Stalked ciliates are known as an excellent indicator organism because they’re only present in environments with low soluble organics, ideal levels of dissolved oxygen, and good conditions for floc formation. They can also be very sensitive to shocks.

Stalked ciliates

Stalked ciliates use their stalks to attach themselves to floc. They can have single stalks, or they can form larger colonies – their heads will resemble bells in both forms.

Free-swimming ciliates tend to be elliptical or ovaloid in appearance with a variety of cilia around their body.

The presence of free-swimming ciliates can indicate a surplus of active bacteria or that nutrients haven’t yet depleted.

Size: 30 – 200 µm


Metazoa are multicellular organisms that feed on bacteria and protozoa, and sometimes other metazoa. They are large and live at the top of the food chain.


Also known as water bears, these hardy organisms are quite large and have 8 small, clawed legs on a chubby body.


The presence of tardigrades usually indicates that the sludge is very old, or that there are low nutrient or ammonia levels. Their absence suggests low oxygen or high toxicity.

Size: 200–1200 µm


This species can vary in appearances and size, but can be distinguished by a forked foot on one end and a small ‘mouth’ in the mid region. They can grow very large and can resemble a thin vase or sometimes a stingray.


The presence of this species indicates a healthy or middle-aged sludge. Dead or damaged rotifers can sometimes indicate toxicity as they are usually among the first to be affected.

Size: 40–2000 µm

A final word

A wastewater treatment plant is a complex ecosystem, and you’ll need to identify a wide range of microorganisms if you’re going to keep your biomass healthy.

You’ll need to use all the tools at your disposal to stay on top of things, from advanced stains to genomic analysis. But your best day-to-day option is your humble microscope.

It’s fast, easy to use and a good indicator of general conditions.

Ideally, your Wastewater Treatment Microscope will have phase contrast. For example our BM2000-PH Phase Contrast Microscope (Infinity PLAN Objectives) is our recommended choice of microscope for waste water management. 

BM2000-PH Phase Contrast Waste water Treatment Microscope

This is a technique that allows you to see transparent organisms with much greater clarity and contrast – it’s very useful when performing wastewater examinations.

With a good microscope, you’ll be able to monitor the health of your biomass in real-time and head off any major problems before they escalate.

Good luck in getting to know your microscopic co-workers!

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