For nearly 30 years Ehrenberg examined samples of water, soil, sediment, blowing dust and rock and described thousands of new species, among them well-known flagellates such as Euglena, ciliates such as "Paramecium aurelia" and "Paramecium caudatum", and many fossils, in nearly 400 scientific publications. He was particularly interested in a unicellular group of protists called diatoms, but he also studied, and named, many species of radiolaria, foraminifera and dinoflagellates.