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Tardigrades, also called water bears, are metazoan that overlap in size with protozoa, but are easy to distinguish when identifying organisms. They have a tubular pharynx, an eyespot, claws, and intestine. They resemble teddy bears with six legs. Tardigrades usually indicate low food to mass ratios and good BOD degradation.

Gastrotrichs are a group of poorly understood metazoan. Their size range overlaps that of ciliates, with which they are often confused because of the cilia and spines. They are distinguished by two adhesive structures, like a forked tail, at the posterior end of the cell and by the presence of a discrete pharynx. They usually glide rather than swim. Gastrotrichs are sensitive to hostile conditions and only appear when treatment conditions are stable.