Taxonomy and structure

In the past the eukaryotic photosynthetic and nonphotosynthetic microorganisms were divided into form groups, the algae and the protozoa, based on the presence or absence of chloroplasts.The algae were further subdivided into groups based on pigmentation, the number and type of flagella, and other structural characteristics. Protozoa were divided on similar structural characteristics into four polyphyletic form groups, the ciliates, flagellates, sporozoans and amebas.

Advances in molecular biology now allow us to begin to create a monophyletic taxonomy of the eukaryotic microorganisms and such a scheme includes many former members of the algae, fungi, and protista. Monophyletic groups are also called clades and are considered to be the only ‘natural’ kind of group.

Only those organisms included in the microbial world will be discussed here. Three supergroups, the Archaeplastida, Excavata, and Chromalveolata, have been proposed, which include most of the previous chlorophytan and protistan organisms. The Amoe- bozoa contain the amebae, and current work indicates that this branch of the eukaryotic tree is a sister group of the fungi within the opisthokonts. The organisms once considered as basal branches to the eukaryotic tree have now been shown not to be primitive, amitochondrial species (i.e. lacking mitochondria), but to have affinities with flagellate species in the Excavates.