Supplemental Lecture (97/04/28 update) by Stephen T. Abedon (abedon.1@osu.edu)

  1. Chapter title: Domains and Kingdoms
    1. A list of vocabulary words is found toward the end of this document
    2. "One of the most fascinating and attractive aspects of the microbial world is its extraordinary diversity. It seems that almost every possible experiment in shape, size, physiology, and life style has been tried." (p. 391, Prescott et al., 1996) Macroscopic organisms, in turn, are organized outgrowths of lineages of microscopic organisms, particularly gaining the ability to gather sunlight with greater efficiency or versatility, or gaining the ability to engulf and process ever larger chunks of food (as well as gather that food following ever more complex evolutionary algorithms and cultural contrivances).
    3. In this lecture we will delve into universal phylogonies of cellular organisms considering the grossest of features. We will then discuss cladograms representing these phylogonies considering especially the problems associated with traditional multi-kingdom reconstructions and how a new form of representation, the universal tree, eliminates many of these problems. In addition, I will remind you that science almost always displays greater uncertainty at higher resolutions and that phylogenetic reconstructions are no exception.

  2. Domains

    1. The basic known cellular morphologies and biochemistries may be divided into three distinct types (i.e., domains)

    2. Eukarya (eucaryotes)

    3. Bacteria (Eubacteria)

    4. Archaea (Archaeobacteria/Archaeabacteria)

  3. Eucaryotes [Eukarya]

    1. The eucaryotes, of course, may be distinguished from the two other domains by their distinctly nucleated cells, membrane-bound organelles, etc.

    2. The eucaryotes may be subdivided, often with some difficulty/ambiguity, into four taxa:

      1. metazoans (animals)

      2. protozoans/algae

      3. fungi

      4. plants/algae

  4. Protista [protozoa]

    1. The protozoans. These are all the:

      1. single celled

      2. non-algae

      3. non-fungal

      4. eucaryotes.

    2. Often, however, protozoa and some algae are lumped together.

    3. Genetic variation:

      1. The majority of the genetic variation among eucaryotes is found among the protists.

      2. In fact, looking beyond eucaryotes, the vast majority of genetic variation among organisms is found among single celled organisms including protists, bacteria, and archaeobacteria.

      3. For a graphical representation of these statements, see the universal tree presented below.

  5. Fungi [molds, yeasts, macrofungi]

    1. Extraorganismal nutrient absorbers:

      1. The fungi include the:

        1. molds

        2. yeasts

        3. macrofungi

    2. Fungi are eucaryotes which:

      1. employ exoenzymes (extracellular enzymes)

      2. form spores

      3. have cell walls

      4. lack flagella

      5. when existing as single celled organisms are called yeasts

  6. Plantae [plants]

    1. Plants are:

      1. chloroplast endosymbiont-containing

      2. multicelled

      3. developing from embryos

      4. eucaryotes

    2. Depending upon classification system, plantae can include various algae.

  7. Algae

    1. The algae are:

      1. aquatic

      2. photosynthetic (i.e., chloroplast-containing)

      3. eucaryotes

    2. Algae are classified by their photosynthetic absorption spectra.

    3. Algae can be multicellular or unicellular.

  8. Animalia [animals]

    1. Multicellular ingesters:

      1. Animals are motile metazoans (i.e., multicelled eucaryotes) whose cells lack walls.

      2. Animals, in contrast to fungi, are intraorganismal nutrient absorbers (i.e., they are ingesters and extracellular but internal digesters).

  9. Eubacteria [bacteria]

    1. Most common bacteria:

      1. Eubacteria are the common procaryotes including:

        1. all human bacterial pathogens

        2. most bacteria not living in extreme environments

        3. cyanobacteria (i.e., blue-green algae)

      2. Eubacteria are the typical, every day bacteria you work with in microbiology or biology lab, and otherwise have been getting to know while or when learning microbiology, or learning about procaryotes in general biology.

  10. Archaeobacteria [archaea]

    1. Biochemically/genetically distinct:

      1. Archaeobacteria are procaryotes but which differ from eubacteria in many aspects.

      2. Particularly, other than that both lack nuclei, archaeobacteria are approximately as different from eubacteria (and eucarya) as eubacteria are different from eucarya.

    2. Archaeobacteria are:

      1. less common than eubacteria

      2. tend to inhabit hostile environments

      3. include:

        1. extreme halophiles

        2. methanogens

        3. thermoacidophiles

    3. A new kingdom of life may have been discovered. Three newly discovered, hot spring-living archaeobacterium have been shown to not only be sufficiently different from all other life, including other archaeobacterium , to considered a third kingdom of archaeobacterium , but also to have diverged less from the inferred most recent common ancestor than any other organism. The discoverers of this "new form of life" have proposed that it be called Korarchaeota which is derived from the Greek word for youth. (Milstein, M., 1995) In other words, just as Eukarya may be subdivided into separate kingdoms based on evolutionary divergence, so too may Archaea.

  11. The universal tree

    1. Universal cladogram:

      1. Shown below is a sketch of a phylogeny based on a cladogram presented by Woese, 1994.

      2. (Anybody with any interest in pursuing microbiology or evolutionary biology owes it to themselves to read this article.)

    2. Considerations:

      1. Note how little of the evolutionary diversity of life is made up by plants and animals, and how much diversity there is within protists and among procaryotes .

      2. Note how cellular life forms are also divided up into eucaryotes and the two procaryotic forms, eubacteria and archaeobacteria .

      3. Note that, by at least some criteria, archaeobacteria are more closely related to eucaryotes (and therefore to us) than are eubacteria .

      4. Note how a large fraction of the earth's genetic diversity is found among single celled organisms (protists, eubacteria, and archaeobacteria).

  12. Illustration, universal tree

  13. Five-kingdom system

    1. The five-kingdom system is an older, alternative method of classification to that of Woese in which organisms are divided somewhat haphazardly into five kingdoms:

      1. eucaryotic food absorbers (fungi )

      2. eucaryotic photosynthesizers (plants)

      3. eucaryotic ingesters (animals)

      4. all other mostly unicellular, certainly paraphyletic, eucaryotes (protists )

      5. the also paraphyletic bacteria

    2. Macrobiological, phenotypic classification:

      1. Note that because it consists of numerous paraphyletic groupings, the five-kingdom system is clearly obsolete.

      2. More basically, the five-kingdom system is a flawed attempt at imposing a phylogenetic classification system upon a phenotypic classification system.

      3. The five-kingdom system also displays intractable phenotypic biases particularly against the diversity of organisms which cannot be studied by the naked eye.

  14. Six-kingdom system

    1. Division of bacteria into eubacteria and archaeobacteria converts the five-kingdom system into a six-kingdom system.

    2. Macrobiological, phenotypic classification:

      1. Although closer to reality, the six-kingdom system still retains the glaringly paraphyletic protists.

      2. In addition, though giving a nod to Woese's universal tree by splitting up the bacteria into two kingdoms, the six-kingdom system nevertheless retains the macrobiological biases of the five-kingdom system in describing the Bacteria, the Archaea, and the various Eukarya kingdoms as all displaying similar taxonomic rank.

      3. Similar taxonomic rank should, ideally, imply similar evolutionary divergence. While ideal may be to some extent approximated in terms of macroscopic morphology, focusing on morphological diversity to the exclusion of other aspects of evolutionary divergence is clearly a biased approach to systematics.

  15. Greater than six-kingdom system

    1. Further splitting:

      1. Division of Protista into two kingdoms and Plantae also into two kingdoms (Plantae and some algae) converts the six-kingdom system into an eight kingdom system.

      2. It is probable, given the high degree of genetic variation found among the protists (see universal tree) that not even eight-kingdoms sufficiently splits the three domain system.

      3. Adding on the various Archaea kingdoms results in at least a ten kingdom system.

      4. Clearly a greater than six kingdom system is anything but a definitive, final word. Why bother

    2. The "who cares how many kingdoms there are" system:

      1. As you can see, greater than six kingdom systems are a splitters delight and no doubt many will argue for long periods over just how inclusive or exclusive any particular kingdom ought to be.

      2. Better, I think, to stick with a three domain system (universal tree) and let the specialists argue over how many monophyletic kingdoms are associated with each domain.

  16. Don't trust the details

    1. Details generally less robust:

      1. Remember, that the methods by which phylogonies are constructed are not fool proof. Consequently, uncertainty always exists in any such reconstructions.

      2. Nevertheless, when reconstructions of the evolutionary history of organisms are based on two or more independent and robust lines of evidence (e.g., sequence comparison plus physiological, morphological, or historical consideration), they too may be considered to be reasonably robust.

      3. Thus, when viewing a graphical representation of organismal lineages and relationships, it is often reasonable to accept the general picture but to simultaneously be increasingly skeptical as you attempt to resolve ever greater details.

      4. Bottom line: Phylogenetic reconstructions are great fun and can be highly useful, but always trust the broad, obvious strokes much more than the subtleties.

    2. How science is done:

      1. Mistrusting the details but not carrying that mistrust to the overall picture, of course, is as all good science should be done (and is analogous to the proper usage of significant figures as you learned in inorganic chemistry).

      2. Arguing about details found at the limits of the resolution of current scientific techniques essentially defines the nature of the scientific process in taxonomy or any field of investigation.

    3. The question of whether the gorillas or chimpanzees are the apes most closely related to the hominids may be reasonably argued. However, the idea that of extant organisms it is either the gorillas or the chimpanzees which are most closely related to hominids is considered to be settled. Particularly, there is robust evidence that orangutans and other apes are more distantly related from hominids than are either gorillas or chimpanzees. In this case, we are considering the nodes linking three extant lineages which we know are closely linked in space and time, but are arguing over the ever finer defining of their spatio-temperal locations (especially relative to one another).

  17. Vocabulary

    1. Animals

    2. Archaea

    3. Archaeobacteria

    4. Bacteria

    5. Domains

    6. Greater than six-kingdom systems

    7. Eubacteria

    8. Eucaryotes

    9. Eukarya

    10. Five-kingdom system

    11. Fungi

    12. Molds

    13. Phenotypic classification

    14. Phylogenetic classification

    15. Phylogeny

    16. Plantae

    17. Plants

    18. Protista

    19. Protozoa

    20. Scepticism

    21. Six-kingdom system

    22. Universal tree

    23. Universal tree, illustration

    24. Yeasts

  18. Practice questions

    1. Sketch a rooted universal tree being sure to specifically label it sufficiently that I know that there are at least three fundamental forms of cellular kinds of life that are all related evolutionarily. Place E. coli and humans on the tree. [PEEK]

    2. Which of the following is the best evidence for the three kingdom system (circle only one correct answer) [PEEK]

      1. there are three distinctly different cell structures

      2. there are three distinctly different cellular chemical compositions

      3. there are three distinctly different gram reactions

      4. some bacteria live in extreme environments

      5. all of the above

      6. none of the above

    3. In the five kingdom system, in what paraphyletic eucaryotic kingdom is the majority of the genetic variation found? (one word answer) [PEEK]

    4. Ecologically (i.e., in terms of what they do for a living), how do archaeobacteria differ from eubacteria?[PEEK]

    5. True or false, the procaryotes are a monophyletic taxon. [PEEK]

    6. Name a characteristic which is common to those organisms which exhibit the overwhelmingly greatest portion of genetic diversity found among all extant (living) eucaryotic organisms? (one word answer) [PEEK]

    7. Archaeobacteria are to eubacteria as (circle only one correct answer) [PEEK]

      1. plants are to animals

      2. protists are to eucaryotes

      3. eubacteria are to eucaryotes

      4. Escherichia coli is to bacteria

      5. all of the above

      6. none of the above

    8. Sketch a universal tree being sure to indicate where humans, plants, fungi, and protists lie on it. [PEEK]

    9. Of what significance is Korarchaeota? [PEEK]

  19. Practice question answers

    1. See universal tree . Note that E. coli is a eubacteria and humans are eucaryotes .

    2. ii, there are three distinctly different cellular chemical compositions. Note that the 16S rRNA , upon which the universal tree is based, is a cellular chemical. (a) is wrong because there are two distinct cellular structures: procaryote and eucaryote . (c) is wrong because gram staining does not apply to eucaryotes . (d) is nearly meaningless but was included because archaeobacteria often live in extreme environments.

    3. Protista

    4. the former (archaeobacteria) tend to live in much more extreme environments; pathogens of humans are far more likely to be counted among the latter (eubacteria).

    5. False, the procaryotes are a polyphyletic taxon consisting of both eubacteria and archaeobacteria, each no more greatly related to the other than either is related to eucaryotes.

    6. Unicellularity

    7. iii, eubacteria are to eucaryotes; all are intra-domain comparisons.

    8. below:


    9. They may represent a newly recognized additional kingdom of life, one belonging to domain archaea.

  20. References

    1. Campbell, N.A. (1996). Biology. Fourth Edition. Benjamin/Cummings Pub. Co. Menlo Park, CA. p. 542.

    2. Li, W-.H., Graur, D. (1991). Fundamentals of Molecular Evolution. Sinauer Ass., Inc., Pub. Sunderland, Massachusetts. pp. 118-119.

    3. Milstein, M. (1995) A glimpse of early life forms. Science 270:226.

    4. Postlethwait, J.H. and Hopson, J.L. (1995). The Nature of Life. Third Edition. McGraw-Hill, Inc. New York. pp. 433-441.

    5. Prescott, L.M., Harley, J.P., Klein, D.A. (1996). Microbiology. Third Edition. Wm. C. Brown Pub. Dubuque, Iowa. pp. 390-414.

    6. Raven, P.H., Johnson, G.B. (1995). Biology (updated version). Third Edition. Wm. C. Brown publishers, Dubuque, Iowa. pp. 560-572.

    7. Raven, P. H., Johnson, G. B. (1996). Biology. Fourth Edition. Wm. C. Brown publishers, Dubuque, Iowa. pp. 634-648.

    8. Tortora, G.J., Funke, B.R., Case, C.L. (1995). Microbiology. An Introduction. Fifth Edition. The Benjamin/Cummings Publishing, Co., Inc., Redwood City, CA, pp. 250-255.

    9. Woese, C. R. (1994). There must be a prokaryote somewhere: Microbiology's search for itself. Microbiological Reviews 58:1-9.