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Amoebae range in size from 100 to 300 micrometers. They are unique in that they have no distinct shape. They continually range from round to oval to irregular shapes with protrusions periodically extending from the main cell mass and then withdrawing. They move by the use of foot-like protrusions called pseudopodia (false feet). A pseudopodia is pushed out and the main cell mass moves by flowing into the extended portion. They are sometimes harder to detect because they usually move extremely slowly.

Bare, or naked, amoebae are commonly found during startups or in heavily loaded plants. Testate, or shelled, amoebae will usually indicate a stable, lightly loaded wastewater system.