Trimastix trophic cells are "naked"; that is, no conspicuous cell covering is found on cell body or flagella.

The single nucleus in a Trimastix cell contains a conspicuous central nucleolus. This is the standard condition for most protists, however many protozoa that look like, and may be confused with, Trimastix species do not have this feature. Rough endoplasmic reticulum surrounds the nucleus and forms an organized array extending towards the posterior end of the cell. Compare the epifluorescence image

The Golgi apparatus consists of a single membrane stack ("dictyosome"). The dictyosome is located adjacent to the basal bodies of the kinetid. The cis face of the dictyosome is oriented towards the cell membrane, the trans face towards the nuclear envelope. This orientation is somewhat unusual, but it is also found in the jakobid flagellates.

Retortamonad protists look like, and may be confused with, Trimastix, but in retortamonads, endoplasmic reticulum and Golgi stacks cannot be shown by "routine" transmission electron microscopy or fluorescent lipid labelling. Compare the epifluorescence image

Mitochondria are absent. Cells have a few small double-membrane-bound structures scattered throughout the cytoplasm. These structures have been identified, tentatively, as hydrogenosomes, but the biochemical makeup and the function of these bodies is unknown.

The posterior flagellum in trophic cells possesses two conspicuous and characteristic flagellar vanes, arising on opposite sides of the flagellum near its insertion into the cell. Each vane has a striated substructure, especially near the margin of the vane. The position and structure of the vanes is similar to jakobids, where only one vane is present, and in retortamonads where two are found. The function of the vanes is not known, but the best guess is that it is involved in establishing water currents through the ventral groove, through which the bacteria upon which Trimastix feeds are passed.

The cytoskeleton is an asymmetrical system of four flagellar bases, a dorsal (anterior) and three ventral microtubular roots, and secondary cytoskeletal microtubules arising from the anterior root and forming a "fan" along the dorsal surface of the cell. The ventral roots extend to the posterior cell, where they terminate at a common point. These roots define the margins and the floor of the ventral groove. The kinetid of Trimastix marina is slightly more complex than are the kinetids in the other Trimastix species that have been studied.

The Trimastix kinetid is similar to those of jakobids and retortamonads. The motif of left, intermediate and right ventral roots extending in parallel from the basal bodies to the posterior end of the cell and defining a ventral groove, is not found in other protists. Trimastix shares with Malawimonas the presence of an anterior root with associated microtubules, the addition of microtubules to the inside of the left root, and the absence of a laminate structure below the left root. In other jakobids (Jakoba, Histiona and Reclinomonas), and in the retortamonads, the anterior root is absent, microtubules are added to the outside of the left root, and a laminate structure (MLS) is present below the left root.

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