How to teach the new understanding of higher-level By Laura K. Baumgartner and Norman R. Pace What's in a name? Even the nomenclature for different he ability to sequence genes has vastly altered our un- kinds of organisms can be complicated derstanding of higher-level relationships among or- by the current change in understand- ganisms such as those found at the kingdom level. It is ing. When science textbooks rely on monera and , or even the important for biology teachers to incorporate these new more dated protozoans, what other Tviews and not retain outdated concepts still present in some text- terms can be used? To describe micro- books. This article provides an overview of our new understand- scopic organisms, we suggest microbe, ing of higher-level taxonomy, and suggestions for the utilization which includes microscopic eukaryotes of current taxonomy in classroom instruction. (e.g., amoebae) as well as bacteria and The advent of gene sequencing and other discoveries in biol- . What should be used to de- note anything that is not a eukaryote? ogy over the past three decades has fundamentally changed our We suggest actually using bacteria view of the course of evolution and how organisms are related. and archaea, which allows students Evolutionary distances as measured by DNA sequencing can to adjust to the often-unfamiliar terms be used to create phylogenetic trees or maps of relatedness and before they may encounter them at evolution. Although our understanding of these trees is new and the college level. occasionally contentious, general agreement has emerged from an evaluation of them. These new views dramatically alter our understanding of early evolution and of organismic relationships at the level of the kingdom.

46 The Science Teacher F i g u r e 1 A The three- molecular tree of life. Homo (human) represents all animals, Zea (maize) represents all plants, and Coprinus represents all fungi.

mitochondrion

tomyces

Rhodocyclu

Planc Esch p

Flavobacterium em erichia Methanobacterium t chloro cter

SynechococcusDesulfovibrio Archaea s

us Thermococcu p Flexiba las

t Agrobacterium ChlamydiaGloeobacte marine low Haloferax Me Archaeoglobus Chlorobium t r hanothermu Thermoplasma

s Methanococc Leptonema Methanopyru s marine Gp. 1 low temp Clostridium Gp. 1 s Gp. 2 lowl owtemp temp pSL 12 pSL 22 Gp. 3 low temp Heliobacterium Arthrobacter PyrodictiumSulfolobu pOPS19 s ThermofilumThermoproteus Root pSL 50 Thermus pOPS66 pJP 78 Chloroflexus Thermotoga pJP 27

Bacteria Aquifex EM17

Coprinus Ho m o

Zea Cryptomonas Eukarya Achlya

Costaria ium Porphyra Giardia

Babesia Paramec

Phys Trichomonas

Dictyostelium arum

Euglen Trypanosoma Encephalitozoon

Entamoeba Naegleria Vairimorpha a

October 2007 47 Darwin recommended that biological taxonomy F i g u r e 1 B be based on evolutionary relationships. Taxonomy in many textbooks is based on the “five kingdoms of life,” The three-domain molecular tree of life. typically including Animalia, Plantae, Fungi, Protista, and Monera as proposed by Whittaker in 1969. The Cartoons of the two models of evolution. The triangles indicate five kingdoms are often combined with the concept divergences of genetic lines (e.g., ) within the groups of (cells with no nucleus) versus eukaryote represented by each triangle. (cells with a nucleus). Both of these systems for organiz- ing life have largely been replaced in current scientific Previous model: Eukaryotes evolve from understanding with the concept of the three domains, prokaryotes which divides life into Bacteria, Eukarya, and Archaea. Bacteria In some textbooks, the third domain of Archaea has Prokaryotes Eukaryotes been grafted on to the five kingdom tree to create a six kingdom tree, but neither a five- or six-kingdom system properly portrays the evolutionary relationships. Origin Origin Eukarya What has replaced the familiar five kingdoms? Be- ginning in the 1970s, genetic studies have given us an en- tirely new, experimentally grounded perspective on the Current model: Three domains with a common Archaea interrelationships of organisms, culminating in the tree origin of life based on molecular evidence (Figure 1A, p. 47). We present here a short historyProkaryotes of how theEukaryotes five- Bacteria kingdom model came into popular use, how it has been replaced with the three-domain model (Figure 1B), and how this reappraisal can be used in the classroom. Origin Origin Eukarya A brief history of terms Until the mid–20th century there was little understand- ing of microbes and their relationships, and taxonomies Archaea were based on conjecture (Sapp 2005, 2006; Woese 1994).

F i g u r e 2

Author(s) Linnaeus Haeckel Chatton Whittaker Woese, Fox Woese et al. Year 1735 1866 1938 1969 1977 1990 System 2 Kingdoms 3 Kingdoms 2 Empires 5 Kingdoms 3 Urkingdoms 3 Domains Major taxonomic Eubacteria Bacteria unit of Bacteria Classified Not Included within Kingdom Prokaryotes Monera Major Protista taxonomic Archaebacteria Archaea unit of Archaea Major taxonomic unit of Vegetabilia Plantae Plantae Eukaryota Eukaryotes Eukaryotae Eukarya Protista Protista Animalia Fungi Animalia Animalia

48 The Science Teacher Current Taxonomy in Classroom Instruction

For example, Linnaeus (1735) organized all living things ally came into common usage. (More details about this into merely two kingdoms: Vegetabilia and Animalia. interesting chapter in the history of science are found in In the 19th century, a widely embraced concept was em- Sapp [2005], available online at www.pubmedcentral.nih. bodied in Haeckel’s (1866) three-kingdom scheme, which gov/articlerender.fcgi?artid=1197417.) encompassed animals, plants, protists, and at the origin of it all, the little-understood monera, which he included in The next step: Three domains of life the protist kingdom (Figure 2). In the late 1960s, Whit- Microbiologists were never comfortable with the ill- taker (1969) included fungi in the collection and codified defined concept of monera, but also had not developed the five kingdoms that are widely taught today. a clear definition of bacteria. By the mid–20th century, The term prokaryote was coined by Chatton (1938), many leading microbiologists had lost hope for devel- who first proposed organizing life into two great “em- oping a taxonomy for bacteria based on evolutionary pires,” prokaryotes and eukaryotes (Figure 1B). His plan relationships. Instead, they had turned to shape (mor- noted differences among cell structures rather than any phology) and physiology as the basis for classification of proposed evolutionary or taxonomic differences among these organisms. But in 1977, Woese and Fox provided a the groups. Chatton’s prescient plan was rediscovered molecular means for understanding microbial relation- and made more widely known decades later by Stanier ships and evolution through comparison of ribosomal and van Neil. They defined the prokaryote as an organ- RNA sequences. Woese and Fox determined the re- ism with no nucleus or mitosis, no membrane-bound lationships of 13 representative organisms and found internal structures, and the presence of a cell wall with a that four of the supposed bacteria were, in fact, no more specific mucopeptide (1962). Many scientists questioned related to the bacteria (prokaryotes) than they were to this definition of prokaryote, which relies on negative the eukaryotes. They proposed a new taxonomic level definition (based on the absence of traits). For example, above kingdom, the “urkingdom” or primary kingdom, the simple presence or absence of traits is not sufficient in a system containing three urkingdoms: eubacteria, reason to lump flying animals such as birds, bats, and in- archaebacteria, and eukaryotae (Woese and Fox 1977). sects together; the trait of flight arose several times and Later, the urkingdoms became domains and the domain does not create an evolutionary taxonomy. Nonetheless, Archaea would be born on the sequences of these four absence became a trait, and the term prokaryote eventu- “bacteria.” Today we know that there are thousands

F i g u r e 3 Biochemical characteristics of the three domains. Characteristic Domain Archaea Bacteria Eukarya Ribosome type (by sequence) Archaeal Bacterial Eukaryal Histone packing of DNA Yes No Yes Membrane-enclosed nucleus No No * Yes Membrane lipids Ether-linked Ester-linked Ester-linked Initiator tRNA Methionine Formylmethionine Methionine Operons Common Common Rare Ribosome sensitive to Yes No Yes diptheria toxin Sensitive to chloramphenicol, No Yes No streptomycin, and kanamycin Transcription promoter TATA box -10, -35 boxes TATA box Transcription initiation TATA binding protein Sigma factor TATA binding protein RNA polymerase type Pol II Pol II homolog Pol I, II, III Muramic acid in cell wall? No Yes No *Membrane enclosed nuclei have been observed in members of the planctomycetes, but these probably are not homologous to the eukaryal nuclear membrane.

October 2007 49 of archaea and that they are significant contributors to a primordial beginning, at about the same time as the ge- the biosphere. This fascinating group includes the ex- netic line that led to the archaea. tremeophiles, archaea that live in the most inhospitable There are other problems with the five- or six-king- habitats on Earth. Because habitats on other planets are dom concept. First, as with the term prokaryote, monera generally extreme by Earth’s definitions, scientists expect implies a similarity between the archaea and bacteria that that extraterrestrial life will have similar characteristics is true only with respect to their approximate size, not in to these extremeophiles. their fundamental relationships to other organisms. Sec- Initially, Woese named these four “bacteria” Archae- ond, five kingdoms (or six, as they appear in some text- bacteria to denote their seemingly ancient qualities and books) imply equivalence in taxonomic level among the simple metabolism, and added them as a sixth kingdom animals, plants, and fungi, and the combined archaea and (Figure 2, p. 48). With further study, however, it turned bacteria. The diversity of either the archaea or the bacte- out that archaea are vastly different from bacteria. In fact, ria is on par with that of all of the eukarya, never mind in some ways the archaea more closely resemble eukarya the kingdoms within the eukarya (plant, animal, and fun- than they do traditional bacteria. These relationships are gi) (Dawson and Pace 2002). The original kingdoms were reflected in the biochemistry of the proposed when the only well-stud- three groups (Figure 3, p. 49) and A presentation of both ied bacteria were those that could in the current shape of the phy- be easily cultured. Now we realize logenetic tree (Figure 1A, p. 47). views of taxonomy and that less than 1% of all bacteria can The current names for the three the history of their be cultured, and molecular tools domains of life—Archaea, Bac- are required to understand the rest teria, and Eukarya (Figure 1B, p. development will allow of this uncultivated diversity (Pace 48)—were proposed only relatively students to appreciate the 1997). Third, the concept of a king- recently, in 1990 (Woese, Kandler, dom of “protists” is fatally flawed. and Wheelis 1990) (Figure 2). larger state of the science The protists, microbial eukaryotes, This evolution-based taxonomy of classification that now are comprised of several kingdom- was resisted by many, who clung level groups that (by molecular to both the five-kingdom model includes the molecular criteria) are at least as diverse as and the prokaryote-eukaryote animals or plants (Dawson and dichotomy (Figure 1B). Later basis for heredity. At the Pace 2002). For example, one need discussion between the two sides same time, students can only consider the diversity between is played out in literature, and the euglena (plant-like photosyn- provides intriguing insight into experience science as an thetic autotrophs) and amoeba scientific discussion (e.g., Martin ongoing discussion rather (animal-like heterotrophs). Finally, and Koonin 2006; Mayr 1998; Pace the five-kingdom model reasons, 2006; Woese 1998). Carl Woese’s than a stale set of facts. as does the prokaryote-eukaryote 1994 reflection on the 15 years of model, that eukaryotes arose from work that followed his seminal paper portrays his toil monera. Indeed, some texts equate monera and prokary- and frustration (Woese 1994). Now, nearly 30 years after otes, which is a misleading conclusion. it was introduced, the three-domain model is commonly accepted and taught. Applying this discussion in the classroom The National Science Education Standards (NSES) Five (or six) kingdoms and the place of include evolution as the basis of biological classification prokaryotes (NRC 1996), making it imperative that classification The name prokaryote is doubly misleading: First, it im- systems correctly represent fundamental evolutionary plies that the archaea and bacteria are similar and evolved relationships. Additionally, the NSES include systems separately from the eukarya. In fact, the archaea are more and organization, the structure of the cell, change in sci- similar to the eukarya, both in their evolutionary history ence, historical perspectives of science, and the nature of (Iwabe et al. 1989) and much of their physiology (Figure science knowledge (NRC 1996). Finally, the NSES call 3). Second, the term prokaryote is also misleading be- for an emphasis on science as argument (NRC 1996). A cause it implies that prokaryotes gave rise to eukaryotes. presentation of both views of taxonomy and the history It is true that mitochondria and chloroplasts had their of their development will allow students to appreciate origins among bacteria and joined the eukaryotic cell by the larger state of the science of classification that now endosymbiosis, however the nucleus itself is derived from includes the molecular basis for heredity. At the same neither bacteria nor archaea. Rather, as depicted in Figure time, students can experience science as an ongoing dis- 1B, the genetic line that led to nucleated cells arose from cussion rather than a stale set of facts.

50 The Science Teacher Current Taxonomy in Classroom Instruction

Often, we teach the concept of changing understand- Haeckel, E. 1866. Generalle morphologie der Oganismen. Berun, Ger- ing in science in terms of ancient concepts that have little many: George Kelmer. relevance to students, such as phlogiston, Lamarckism, Iwabe, N., K.I. Kuma, M. Hasegawa, S. Osawa, and T. Miyata. or spontaneous generation. Presentation of this current 1989. Evolutionary relationship of archaebacteria, eubacteria, and change in the way we perceive evolutionary processes al- eukaryotes inferred from phylogenetic trees of duplicated genes. lows students to examine a change in science occurring Proceedings of the National Academy of Sciences of the United States within their lifetimes. It allows them to see the flexible, of America 86(23): 9355–9359. tentative nature of scientific understanding and knowl- Linnaeus, C. 1735. Systema naturae. edge. Additionally, as the three domains are more heav- Martin, W., and E.V. Koonin. 2006. A positive definition of prokary- ily taught at the college level, early exposure will prepare otes. Nature 442(24): 868. students and help them understand variations in different Mayr, E. 1998. Two empires or three? Proceedings of the National textbooks they might encounter. Finally, discussion of the Academy of Sciences of the United States of America 93: 9720– issue alerts students to a world of microbial life that they 9723. probably never thought much about, except as “germs.” National Research Council (NRC). 1996. National science education For less-advanced students, it may be sufficient to standards. Washington, DC: National Academy Press. present the two taxonomic systems and show the similari- Pace, N.R. 1997. A molecular view of microbial diversity and the ties and differences among the three domains of life. Stu- biosphere. Science 276(5313): 734–740. dents could then discuss which system provides a better Pace, N.R. 2006. Time for a change. Nature 441: 289. understanding of biological organization as we know it. Sapp, J. 2005. The prokaryote-eukaryote dichotomy: Meanings Another exercise might present the chart of physiologic and mythology. Microbiology and Molecular Biology Reviews differences among the three domains, and discuss with 69(2): 292–305. www.pubmedcentral.nih.gov/articlerender. students the characteristics that make archaea more simi- fcgi?artid=1197417. lar to bacteria, and which characteristics make them more Sapp, J. 2006. Two faces of the prokaryote concept. International Mi- similar to eukarya. This would allow students to learn crobiology 9: 163–172. about and apply understanding of cellular organization. Stanier, R.Y., and C.B. van Neil. 1962. The concept of a bacterium. Advanced students who understand the basic concepts Archives of Microbiology 42: 427–466. (taxonomy, five/six kingdoms, three domains, and- pro Whittaker, R.H. 1969. New concepts of the kingdoms of organisms. karyote/eukaryote) could be given some of the articles Science 163: 150–163. mentioned in this article, either the historical reviews Woese, C.R. 1994. There must be a prokaryote somewhere: Microbi- (e.g., Sapp 2005) or a pair of the discussion articles (e.g., ology’s search for itself. Microbiological Reviews 94: 1–9. Woese 1998; Mayr 1998). Although they may require as- Woese, C.R. 1998. Default taxonomy: Ernst Mayr’s view of the mi- sistance with the more technical portions of the articles, crobial world. Proceedings of the National Academy of Sciences of such a strategy would expose students to primary scientif- the United States of America 95: 11043–11046. ic literature, allow them to see how a scientific discussion Woese, C.R., and G.E. Fox. 1977. Phylogenetic structure of the is conducted, and encourage them to apply their knowl- prokaryotic domain: The primary kingdoms. Proceedings of the edge as they interpret the articles. Students might discuss National Academy of Sciences of the United States of America 74 or even debate which system provides more understand- (11): 5088–5090. ing of the natural world. n Woese, C.R., O. Kandler, and M.L. Wheelis. 1990. Towards a natu- ral system of organisms: Proposal for the domains archaea, bacte- Laura K. Baumgartner ([email protected]) is a ria, and eucarya. Proceedings of the National Academy of Sciences of postdoctoral researcher and Norman R. Pace (nrpace@colorado. the United States of America 87: 4576–4579. edu) is a professor, both at the University of Colorado in Boulder. Resources Acknowledgments Campbell N.A., and J.B. Reece. 2004. Biology. New York: Pearson We would like to thank the teachers who graciously provided text- Education. book information: Jackie Bilan, Cindy Gsy, Sue Kamal, Jeff Keidel, Byker, C. 1999. Intimate strangers: Unseen life on Earth, Part 1: The Jacob Miller, and Ann Stanford. tree of life. ASM Press. http://microbeworld.org Microbe Library. http://microbelibrary.org References Colorado Department of Wildlife. 2006. The species question: Apply- Chatton, E. 1938. Titre et travaux scientifique (1906–1937) de Edouard ing taxonomy to wildlife research and management. http://wildlife. Chatton. Sottano, Italy: Sette. state.co.us/Education/TeacherResources/Workshops Dawson S.C., and N.R. Pace. 2002. Novel kingdom-level eukary- Woese, C.R. 2000. Interpreting the universal phylogenetic tree. Pro- otic diversity in anoxic environments. Proceedings of the Na- ceedings of the National Academy of the Sciences 97(15): 8392–8396. tional Academy of Sciences of the United States of America 99(12): Woese, C.R. 2004. A new biology for a new century. Microbiology 6324–6329. and Molecular Biology Reviews 68(2): 173–186.

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