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Flagellates belong to the class Mastigophora and range in size from 5-20 micrometers in diameter. They are commonly ovoid or pear-shaped with one to four flagella, hair-like projections used for locomotion, attached to one or both ends of the cell. The flagella can usually be observed at 1000X magnification. Some flagellates may form colonies in which the cell bodies are clumped together with their flagella projecting outward. Some flagellates contain chlorophyll and are capable of photosynthesis. Due to the particular characteristic of resembling plants, they are often classified as flagellated algae rather than protozoa.

The locomotion of flagellates is usually fast and they seem to flip and twist as the flagella are “whipped” around to propel them. Some flagellates have multiple flagella. This makes them appear “bouncy” and unorganized due to their locomotion mechanism while other higher life forms such as free-swimming ciliates present a more organized locomotion mechanism. This is sometimes helpful in identifying flagellates under the microscope. When counting flagellates under the microscope, a 400X magnification should be used in order to identify them better due to their small size.

Flagellates feed on soluble organic matter and dispersed bacteria. Flagellates are more common in heavily loaded plants or during startups. They predominate when there is a high dispersed (single-celled) bacteria population density. They are sometimes associated with turbid effluents produced during toxic upsets. They also bloom when septic sludge or inadequate aeration causes anaerobic conditions in the aeration basin. Their presence in a wastewater treatment system indicates high soluble biochemical demand levels, low dissolved oxygen, and high organic load. Typically higher life forms disappear when a chemical upset goes through a wastewater system. Flagellates are the first higher life form to come back after a chemical upset in the wastewater system. Flagellates can indicate when the wastewater system is getting healthier or if it is still overcoming a chemical upset.