The motile cells are covered with up to four layers of submicroscopic scales made of polysaccharides. Differences in scale structure separate Halosphaera species from each other and from species of Pyramimonas.

The flagellate cell cytoskeleton is based on an asymmetrical array of four flagellar bases and four microtubular roots. One of these roots is expanded into a layer ("spline") of ca. 20 microtubules.

At the anterior end of this root, next to the flagellar base from which it emerges, a complexproteinaceous structure ("multilayered structure") is present.

The overall cytoskeleton suggests the symmetrical arrangement present in "chlorophyte" green algae such as Chlamydomonas. However, the "spline-MLS" system suggests the cytoskeleton present in "charophyte" green algae and the land plants.

Also associated with the spline is the aperture of a duct system that extends from the flagellar pit to the posterior end of the cell. It has been suggested that this duct functions to capture food for the cell ("phagotrophy") - making Halosphaera one of the two green plants known that is phagotrophic at the cellular level (the other is the closely related Cymbomonas).

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