Microorganisms can be isolated as strains or clones. The primary classification unit is a species, which is defined as a collection of similar strains. The higher taxonomic units are genus, family, order, and kingdom. The reference strains are stored in the culture collections. Microorganisms are classified (grouped) by their functional properties (phenotypic classification) or their genetic properties (phylogenetic classification). The major object for phylogenetic classification of prokaryotes is at present the 16S rRNA gene. All eukaryotes are aerobic organisms. Only a few unicellular fungi (yeasts) can grow under anaerobic conditions. Fungi are used in the composting, soil bioremediation, and biodegradation of xenobiotics in the soil. Protozoa are unicellular animals obtaining nutrients by ingesting other microbes, or by ingesting macromolecules. The cells form cysts under adverse environmental conditions. The cysts are resistant to desiccation, starvation, high temperature, and, a condition that is important from a public health point of view, disinfection in wastewater treatment plants. Changes in the protozoan community reflect the operating conditions of an aeration tank. A quiz bank is added to this chapter.