DESCRIPTION OF THE DOMAIN EUBACTERIA (EHRENBERG 1828)
| EUBACTERIA |
DOMAIN EUBACTERIA LINKS
| EUBACTERIA Eubacteria (pronounced: u-bak-TE-ree-a) is a combination of two Greek root that mean “well or true” (eu -εὖ) and “little stick” (bakterion -βακτήριον). These organisms have many names and synonyms that are in common and technical usage. Some of the names are: Monera, Prokaryota, Bacteria, and Eubacteria. All are used interchangeably in reference to taxa of this domain. Monera and Prokaryota refer to cellular organisms without nuclei, and thus include the Archaea. Bacteria has become the preferred technical term, though it too can refer to any prokaryote in an ecological sense. We prefer the term, Eubacteria, because it is the least ambiguous formal name to apply to these organisms. Ehrenberg (1828) first used the term, Bacterium in reference to prokaryotic microbes. |
| INTRODUCTION The Eubacteria is a prokaryotic domain of life with a set of characters that unite its extraordinarily diverse taxa. Unlike the Archaea, the Eubacteria have been known and studied for more than 150 years. This is because all known bacterial pathogens are Eubacteria (We reserve the use of the term bacteria as a descriptive term that is a synonym of prokaryote). Also, some of them like Lactobacillus are otherwise economically important. Perhaps more importantly, many of them inhabit environments that are easily studied and sampled. The Eubacteria differ from the Archaea in the form and structure of their ribosomes, the type and linkage of their lipids, the structure of their cell covering, and the type of RNA polymerase (Margulis and Schwartz 1998). Traditionally, the Eubacteria have been separated into the Gram positive (text with tooltip) A Gram + cell retains the blue-black crystal-violet color following destaining with alcohol during the Gram Stain procedure. and Gram negative (text with tooltip) A Gram - cell loses the blue-black crystal-violet color following destaining with alcohol during the Gram Stain procedure. Then, it takes on the color of the counterstain, typically iodine. groups, based upon a standard stain technique. As it turns out, the way a cell stains is related to the type and structure of the cell wall. Gram positive cells have a single membrane with a murien (text with tooltip) Murein is a class of peptidoglycans found in the walls of Eubacteria. or peptidoglycan wall to the outside of the single membrane. Gram negative cells have an inner membrane and an outer membrane with a murein layer sandwiched between them. The system of Margulis and Schwartz (1998) is based on the fundamental separation of gram positive and gram negative cells (called Firmicutes and Gracilicutes, respectively). Phylogenies based on small subunit r RNA, however, show that the eubacteria are marked by 10 or 11 deep clades that we interpret as kingdoms (see Figure 1). This could just be the tip of the iceberg with respect to their true diversity. Garrity et al. (2001) separate the Eubacteria (a group that they call “Bacteria”) into 23 groups. Also, the problems of lateral gene transfer further blur the distinctions of the groups. We present a tentative system for the Eubacteria with 9 kingdoms (see below). This system is based largely on Margulis and Schwartz (1998), with modifications from Garrity et al. (2001, 2003, and 2005), Tudge (2000), and Black (2002). The All-Species Living Tree Project (Figure 2; Yarza et al. 2008 & 2010; Munoz et al. 2011) release 104 is based on a matrix of 8545 sequences of complete 16S rRNA. The resulting cladogram shows a much more complex set of relationships between the higher taxa of Eubacteria. Notable are the removal of the Actinobacteria from the Firmicutes and the association of the Spirochaetes with Proteobacteria (alpha through gamma) and the clade containing Delta- and Epsilon-Proteobacteria. |
FIGURE 1. Relationships between the kingdoms of Eubacteria that we use in this system. This tree uses Margulis and Schwartz (1998), with modifications from Garrity et al. (2001, 2003, and 2005), Tudge (2000), and Black (2002) in its structure. Note that the topology is very different from that of the All Species Living Tree Project (Yarza et al. 2008 and 2010; Munoz et al. 2011; see Figure 2).
FIGURE 2. A simplified summary tree for the Eubacteria adapted from the All Species Living Tree Project (Yarza et al. 2008 and 2010; Munoz et al. 2011).
| KINGDOMS OF THE EUBACTERIA |
- PROTEOBACTERIAE (Stackebrandt et al. 1988)
SPIROCHAETAE (Cavalier-Smith 2002)
OXYPHOTOBACTERIAE (Gibbons and Murray 1978) Murray 1988
SAPROSPIRAE (Margulis and Schwartz 1998)
CHLOROFLEXAE (Garrity and Holt 2001)
CHLOROSULFATAE1
PIRELLAE (Margulis and Schwartz 1998)
FIRMICUTAE (Gibbons and Murray 1978)
THERMOTOGAE (Margulis and Schwartz 1998)
| PHYLA OF UNCERTAIN STATUS |
| 1. The name for this group has been Chlorobi or Chlorobia, both of which can be confused with Chlorobionta, a Kingdom of photosynthetic eukaryotes. The name also is similar to a genus in form as well as some of the other green bacteria. We chose Chlorosulfatae as a direct reference to their being green sulfur bacteria. |
| LITERATURE CITED Black, J. G. 2002. Microbiology, Principles and Explorations. 5th ed. John Wiley and Sons, Inc. New York. Brock, T. D., M.T. Madigan, J.M. Martinko, and J. Parker. 1994. Biology of Microorganisms. 7th ed. Prentice Hall. Englewood Cliffs, NJ. Ehrenberg, C. G. 1828. Symbolae Physioe. Animalia evertebrata. Decas prima. Berlin. Gao, B. and R. S. Gupta. 2007. Phylogenetic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis. BMC Genomics. 8:86. http://www.biomedcentral.com/1471-2164/8/86. Garrity, G. M., M. Winters, and D. Searles. 2001. Bergey’s manual of systematic bacteriology. 2nd ed. Springer-Verlag. New York. Garrity, G. M., J. A. Bell, and T. G. Lilburn. 2003. Taxonomic Outline of the Prokaryotes. Bergey’s Manual of Systematic Bacteriology. 2nd edition. Release 4.0. Springer-Verlag. New York. pp. 1-397. Margulis, L. and K. Schwartz. 1988. Five kingdoms, an illustrated guide to the phyla of life on earth. 2nd Edition. W. H. Freeman and Co. New York. Margulis, L. and K. Schwartz. 1998. Five kingdoms, an illustrated guide to the phyla of life on earth. 3rd Edition. W. H. Freeman and Co. New York. Munoz, R., P. Yarza, W. Ludwig, J. Euzeby, R. Amann, K-H. Schleifer, F. O. Glöckner, and R. Rosello-Mora. 2011. Release LTPs 104 of the All-Species Living Tree. Systematic and Applied Microbiology 34: 169-170. Tudge, C. 2000. The Variety of Life, A Survey and a Celebration of all the Creatures That Have Ever Lived. Oxford University Press. New York. Woese, C. R. and G. E. Fox. 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proceedings of the National Academy of Sciences USA. 74:5088-5090. Woese, C. R., O. Kandler, and M. L. Wheelis. 1990. Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA. 87: 4576-4579. Yarza, P., M. Richter, J. R. Peplies, J. Euzeby, R. Amann, H-H. Schleifer, W. Ludwig, F. O. Glöckner, and R. Rosello-Mora. 2008. The all-species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Systematic and Applied Microbiology. 31: 241-250. Yarza, P., W. Ludwig, J. Euzeby, R. Amann, H-H. Schleifer, F. O. Glöckner, and R. Rosello-Mora. 2010. Update of the all-species living tree project based on 16S and 23S rRNA sequence analyses. Systematic and Applied Microbiology. 33: 291-299. |
| By Jack R. Holt. Last revised: 02/07/2013 |
