(And Kingdoms go—Musings  on the Literature of Higher Classification and the New Phylogeny of Microorganisms)

By David B. Richman, USA


 Not many years ago higher classification in biology was much simpler than it is now.   Any living thing that was not an animal, was a plant by definition. On TV game shows there was the standard “Animal, Vegetable or Mineral” classification and this seemed to be sufficient for most uses, even though  “mineral kingdom” was not a biological concept.  However, the surface calm was only a façade  (The situation was similar to that in particle physics, where the equally simple scheme of proton, neutron and electron would soon be dramatically expanded and complicated.).  In biological circles scientists disputed where certain organisms fit—was Euglena, an animal (it moved), or a plant (it had chlorophyll and photosynthesized).  So both zoologists and botanists claimed it.  Similarly, many other flagellates with chlorophyll (that looked pretty much like flagellates without chlorophyll), as well as such odd creatures as slime molds, got pitched back and forth between animal and plant. In fact, one could only be sure of the higher classification of more complex life forms such as mosses and coelenterates and “above.”  Even sponges were a bit suspect, and anything below them seemed up for grabs.  So things stood until several people pointed out that it made no sense to consider bacteria and blue-green algae as plants because they completely lacked one characteristic of plants—cellular nuclei.   Ernst Haeckel had recognized these as a kingdom in their own right, the Monera, in the late 19th Century, but he vacillated between including all microbes and only the non-nucleated forms. In 1958 R. H. Whittaker, at Cornell University, proposed five kingdoms for living things.   These kingdoms were Animalia, Plantae, Protista (mostly nucleated “one-celled” organisms), Fungi and Monera (bacteria).  Viruses were, and are, left out of such classifications because they are not considered to be living.  Other scientists proposed four kingdom plans or modified the composition of current plans. However, the acceptance of the idea of more than two kingdoms was slow, as in many scientific revolutions, although it was obvious that bacteria, protists and fungi were fundamentally distinct from other living things and from each other.  Eventually support arose for the five-kingdom concept, and one of the most important proponents of this idea was and is Lynn Margulis, of the University of Massachusetts at Amherst. In her classification she and her associates pointed out that the term “Protista” had with time became associated only with what we had called Protozoa.  Thus, the kingdom of eukaryote, or nucleated, organisms that included diatoms, desmids, slime molds and green, brown and red algae, as well as protozoa, had to take on the rather ungainly name of Protoctista.

 Margulis is also well known as an early proponent (along with originator James Lovelock) of the Gaia Hypothesis.  The jury is still out on this idea, but her theories on the origin of cellular organisms and the relationships of living things have been much more successful.   It was she who popularized the notion that mitochondria were the remains of symbiotic bacteria (originally proposed in 1918 by French biologist Paul Portier) and that chloroplasts were similarly derived from symbiotic cyanobacteria (or blue-green algae) in plant cells.  In fact it soon became evident that both “unicellular” and multicellular organisms were built of bacterial cells somewhat like a complex construction of tinker toys (See Margulis and Sagan 1986, Microcosmos).

 What does all this have to do with amateur microscopy?   Well, it is certainly intriguing to think of our protoctist subjects (as well as our selves, the oak tree in the yard and the dog at our feet) as composite forms (much like lichens were known to be).  Also, while any classification system is a construct of the human mind and higher classifications are especially fuzzy, it is still worthwhile to engage in the exercise because it allows us to understand, at least at a rudimentary level, the scope and diversity of living things.  It is also important I think to understand, as much as we possibly can, how organisms are related to each other and the old animal and plant concepts just do not show us the true picture of relatedness. The most recent research based on RNA and DNA comparisons now give us some insight into how protoctistans and multicellular life evolved from bacteria.

 Both Margulis and her associate John O. Corliss noted in Illustrated Glossary of Protoctista (1993), that the five-kingdom concept was at least a step in the right direction, although still a conservative one.  The Glossary is a shortened version of Handbook of Protoctista (1990), a heavy volume which is almost impossible to find, and quite expensive.  More expansive material is covered in Five Kingdoms (3rd ed., 1998) and Diversity of Life (2nd ed. 1999), both of which involve the entire living world, not just protoctists.  More recent schemes have split the Protoctista into around 18 separate kingdoms and the “Monera” into about the same number, including several within the new domain Archaea (more about this later), with Fungi, Animalia and Plantae making up the last three of about 39 total kingdoms!  Most of this rearrangement of the bacterial groupings is based on the DNA and RNA studies of Carl Woese.  A more conservative approach would still give us at least six kingdoms because of the necessity of raising the Archaea out of the Bacteria. This ferment is well described by Tudge  (2000, The Variety of Life). Certainly this last book provides a remarkable (if somewhat incomplete in spots) vision of the panorama of living things.  Unfortunately Tudge does not spend as much time on the Protoctistan Kingdoms as I would like, but in most cases he does define the various groups so that at least the reader is able to place the organisms in the scheme of things.  Also, he mentions a lot of other microscopic or nearly microscopic organisms not belonging to the protoctistan kingdoms, such as many fungal groups, tardigrades,  gastrotrichs, rotifers, and some crustaceans.

 What we are left with, whatever classification system we agree to, is a collection of quite strange and fascinating organisms, many of which are microscopic or nearly so.  Perhaps the best popular treatment of these microscopic members of the living world (exclusive of Animalia, Plantae and Fungi) is that of Sagan and Margulis in Garden of Microbial Delights (1988).  I would highly recommend this book for beginners in microscopy.   The text is charming and will lead the amateur microscopist, at whom it is aimed, through the mind-boggling complexities of the microbial world. How one can resist the “ray beings,” “crypters,” “chalk makers,”  “sea whirlers,” “slime nets,” “chytrids” and other such seeming alien life forms, described therein is beyond me.

 Tudge’s book would be my second recommendation, along with the various permutations of Five Kingdoms.  The latter  have more detailed descriptions of the various protoctist groups, but Tudge is more up to date on the current thinking on the kingdoms. These will get a more advanced amateur into the realm of the phylogeny ferment and they can then judge themselves which schema is preferable.  Diversity of Life is more ecologically oriented than Five Kingdoms, and may appeal to those who like to examine whole ecosystems rather than arranging everything totally by taxon.

 Finally, even more advanced amateurs may find much to occupy themselves in the Handbook of Protoctista and the shortened Glossary of Protoctista, while keeping in mind that several of the higher (and even lesser) subdivisions of Protoctista, such as Giardia, slime molds, mastigotes, amoebas, cilliates, malarial parasites and their relatives, are considered separate Kingdoms in Tudge’s book.  These two books are primarily intended for professional biologists and graduate students, and so can be a bit rough going unless you know the jargon.   At the same time both have huge glossaries and the second book is essentially composed of two glossaries; one for terms and one for classification.  Numerous illustrations clarify the terms and taxa. The author-editors of the Glossary also throw in a gallery of photos of famous “Protoctistologists”, starting with van Leeuwenhoek, the man who discovered many of the major microscopic organisms with his single lens microscopes.

 It should be noted that one great discovery that helped lead to the new kingdom concepts, not much noticed by the general public, was that of the aforementioned group, the Archaea, in the 1980s.   These “bacteria” differed from other prokaryotes (true bacteria or Eubacteria) more than plants differ from animals and are apparently more closely related to eukaryotes  (all organisms with nucleated cells).  As noted earlier, Tudge, following the work of Carl Woese, would subdivide the bacteria even more than into two kingdoms. Another recent source is the web site “The Microbial World” at the University of Edinburgh, which has a simplified 18 “Kingdom” tree with many of the protoctistan and bacterial kingdoms not included. Also I would recommend the “Tree of Life” for an overall view of the living world on earth.  The kingdoms of life as defined by these sources fit under three “Domains” (collections of related kingdoms) – Bacteria (or Eubacteria), Archaea, and Eucarya (Eukaryotes).   As Corliss observes in his contribution to the Illustrated Glossary of the Protoctista, there is still a lot of controversy in the concept of kingdoms just for the  “Protoctista” and it may be a while before we sort it all out.  In any case, it is obvious that the microbial world has not gotten its due from us in the past, probably because we are prejudiced toward visible multicellular organisms like ourselves.   Indeed, the seemingly alien insects are more like us than most of the microscopic creatures we observe in our professional or home laboratories.  Paradoxically some of these creatures, or more precisely their ancestors, were the building blocks that produced multicellular life forms, such as ourselves. These are exciting times in which to be either a professional biologist or an amateur microscopist!

All comments to the author David Richman are welcomed.

Books Mentioned in this Review:

Margulis, L., J. O. Corliss, M. Melkonian and D. J. Chapman.  1990. Handbook of Protoctista. Jones and artlett, Boston.  914 pp.

Margulis, L., H. I. McKhann, and L. Olendzenski. 1993. Illustrated Glossary of Protoctista. Jones and Bartlett, Boston. 288 pp.

Margulis, L., and D. Sagan. 1986. Microcosmos: Four Billion Years of Microbial Evolution.  University of California Press, Berkley. 300 pp.

Margulis, L., and K. V. Schwartz.  1998. Five Kingdoms: An Illustrated Guide to the Phyla of Life on Earth, 3rd. Ed. W. H. Freeman, New York. 520 pp.

Margulis, L., K. V. Schwartz, and M. Dolan.  1999.   Diversity of Life: The Illustrated Guide to the Five Kingdoms, 2nd ed. Jones and Bartlett, Boston. 248 pp.

Sagan, D., and L. Margulis. 1988. Garden of Microbial Delights: A Practical Guide to the Subvisible World.  Harcourt Brace Jovanovich, Boston, 229 pp.

Tudge, T.  2000. The Variety of Life : A Survey and a Celebration of All the Creatures That Have Ever Lived. Oxford University Press. 528 pp.


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