Eukaryotes

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Eukarya tree
Redrawn from Ciccarelli et al Science 2006:1283

Obviously it is not possible to cover this huge phylogenetic group at an acceptable level of detail in a single section of a course on microbial diversity. And so we’ll be only hitting the tips of the icebergs. However, the question might be asked, “why cover the eukaryotes at all in a class on microbial diversity?” The answer to this question is, of course, that most eukaryotes are microbial. By far the greatest diversity of eukaryotes is unicellular; these are usually lumped together as “protists”. But like “prokaryotes” or “invertebrates”, the term “protist” does not tell you what and organism is, only what it is not, and so is not a meaningful scientific term. Interestingly, the term “protist” is not usually applied to most phototrophic unicellular eukaryotes, which are typically called “algae”, nor to unicellular fungi, which are called “yeast”.

Nevertheless, most eukaryotes are unicellular microbes, and even most green plants, most fungi, and even most animals are microscopic. The microscopic green plants we call green algae, and these are often at least colonial, if not clearly multicellular. Fungi are generally microscopic, although the hyphae of an individual “colony” (actually a single organism by most criteria) may span many acres of soil and producing macroscopic fruiting bodies (e.g. mushrooms). Even most animals are microscopic; the world abounds with microscopic nematodes, arthropods, rotifers, tardigrades, sponges, &c. Many of the cryptic animal phyla you never hear about are microscopic, and even familiar groups are riddled with microscopic members. Our perception of even the plant and animal world is skewed by the fact that we largely ignore creatures that exist in a different size range.

Taxonomy

Rather than list an unsatisfying taxonomy of eukaryotes, another way to look at the eukaryotic taxonomy is an unrooted tree:

eukatyotic groups
From Keeling, et al. 2005 Trends Ecol Evol. 20:676

Note that this is not a quantitative tree, rather just a graph showing relationships.

General properties of the Eukaryotes

Diversity

The eukaryotes are comprized of about 5 major "super Kingdoms": Excavates, Chromalveolates, Plantae, Rhizaria, and Unikonts. How these are related to each other is unclear, and is the subject of heated debate. Within each of these super-Kingdoms” are groups that are sometimes considered Kingdoms, but there is little consistency about how these labels are applied.

As far as the current analysis can tell, early eukaryotic diversification might represent a more-or-less single radiation. However, traditional ribosomal RNA analysis (and other good molecular clocks) suggest that the root of this tree is probably amongst the Excavates, as shown it the tree at the beginning of the page.

Metabolism

The eukaryotes are generally heterotrophic or phototrophic; however, in most cases these are supported by organelles derived from endosymbiosis. Phototrophic lifestyles are based on plastids/chloroplasts, with are either derived directly from cyanobacteria or secondarily by endosymbiosis of other eukaryotic phototrophs that, in turn, contain cyanobacterial endosymbionts. Most of the rest of the eukaryotes are aerobic heterotrophs, whose metabolism is based on aerobic respiration in the mitochondria, which are derived from α-proteobacterial endosymbionts. Anaerobic (fermentative) heterotrophs may lack mitochondria (or not use them for oxidative phosphorylation), or contain hydrogenosomes, hydrogen-generating organelles that in some cases are probably derivatives of mitochondria, and in others probably represent independent endosymbionts.

Morphology

Typical eukaryotic cell structure is familiar; the universal aspects are the presence of a nuclear envelope, at least some endoplasmic reticulum, vesicles of various types, and a tubulin/actin cytoskeleton. Most also contain a Golgi apparatus, distinct smooth and rough endoplasmic reticulum, cilia or flagella, and mitochondria. The structure of these features, and others that are more sporadic, are surprisingly variable to those used to seeing a typical plant and animal cell as representative eukaryotes. Most eukaryotes have various cellular morphotypes at different stages of their sometimes complex life cycles, or specialized cells with distinct morphotypes in multicellular individuals, or both.