DESCRIPTION OF THE PHYLUM DEINOCOCCOBACTERIA (MARGULIS AND SCHWARTZ 1998)
| EUBACTERIA> FIRMICUTAE> DEINOCOCCOBACTERIA |
PHYLUM DEINOCOCCOBACTERIA LINKS
| Deinococcobacteria (pronounced di-no-KA-ko-bak-TE-re-uh) is formed from three Greek roots that mean “terrible” (deinos -δεινός) “berry or kernel” (kokkos -κόκκος) and “little stick” (bakterion -βακτήριον). The reference is to spherical cells that are awe-inspiring because they are thermophiles and one can withstand larges doses of radiation. Deinococcobacteria is a formal name derived from the genus, Deinococcus. |
| INTRODUCTION TO THE DEINOCOCCOBACTERIA This phylum is made up of two genera Deinococcus and Thermus, which are among the most resistant living things. Not only are they both thermophiles (text with tooltip) Thermophiles are organisms (usually bacteria) that have thermal optima of 45C or higher. , but they also seem to be able to tolerate conditions that wreak havoc on DNA. Makarova et al. (2001) and Cox and Battista (2005) indicate that Deinococcus radiodurans can survive in continuous exposure to radiation at 6,000 rads or to bursts of radiation at 1,500,000 rads! That they can continuously repair chromosomal damage from such repair has made them among the most interesting and sought-after organisms. Deinococcus, the organism dubbed Conan the Bacterium by Patrick Huyghe (1998), was isolated in from canned meat that had received gamma radiation at 250X the lethal dose for E. coli (Anderson et al. 1956). At first, it was considered to be a radiation-resistant Micrococcus. However, its unique nature was recognized by Brooks and Murray (1981), when it was moved to its own genus. Mattimore and Battista (1996) make the case that the same mechanisms that allow cells to survive ionizing radiation also allow them to survive prolonged dessication. Not surprisingly, Deinococcus species have been isolated from hot springs, as well as desert soils, and radioactively contaminated sites. The DNA repair mechanisms of Deinococcus have been under intense study (Cox et al. 2010) because they must have the ability to reassemble the DNA strand with great efficiency and almost no mistakes. The other line of organisms in this phylum is represented by Thermus, but does include at least four other taxa. Thermus aquaticus, an extreme thermophile, was isolated and defined by Brock and Freeze (1969) from a hot spring in Yellowstone National Park. It is an obligate aerobe and grows between 40 and 79C, with a growth optimum at 70C. Chien et al. (1976) purified a DNA polymerase that was stable at 80C. This became known as Taq polymerase, which now is the foundation of the PCR method and so valuable that Hoffman-LaRoche, the Swiss pharmaceutical company, paid $300,000,000.00 for the patent. Both Deinococcus and Thermus illustrate the value to society of pure or basic research rather than industrial research. The discoveries of these organisms and their subsequent outcomes (or potential outcomes) came about because of serendipitous discovery and then recognition of some aspect of the discovery that was useful. The benefits of Thermus, so far, are obvious. The benefits of Deinococcus likely are forthcoming. The mechanism of efficient and nearly mistake-free DNA reassembly cannot be ignored. Perhaps, Deinococcus one day may provide the basis for DNA computer information storage that is more stable and durable than any of the current systems. Certainly, the words of Louis Pasteur are appropriate here: Where observation is concerned, chance favors only the prepared mind. Margulis and Schwartz (1998) place these taxa together in a phylum that they designate B-13 (Deinococci). Garrity et al. (2001 and 2003) also place them together in a phylum that they designate “Deinococcus-Thermus”. Omelchenko et al. (2005) confirm that the two groups are related but Thermus lost many genes and acquired, through lateral gene transfer, many genes from thermophiles. The All Species Living Tree Project (Yarza et al. 2008 and 2010; Munoz et al. 2011) suggests that the Deinococci are not within the clade that includes the rest of the Firmicutes (see Figure 3). |
 |  |
| FIGURE 1. Deinococcus TEM micrograph in gfalse color that illustrates the tetrad appearance of the cells. Image from the Oak Ridge National Laboratories, Public Domain | FIGURE 2. SEM micrograph of Thermus. Image from Agricultural Board of the Canadian Gov., Public Domain |
FIGURE 3. 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). Note the sister relationship between the Cyanobacteria and the Firmicutes. Also, note that Actinobacteria and Deinococci are far removed from the Firmicutes.
| LITERATURE CITED Anderson, A. W., H. C. Nordon, R. F. Cain, G. Parrish, and D. Duggan. 1956. Studies on a radio-resistant micrococcus. I. Isolation, morphology, cultural characteristics, and resistance to gamma radiation. Food Technol. 10: 575-578. Barnes, R. S. K. 1984b. Kingdom Monera. IN: Barnes, R.S.K., ed. A synoptic classification of living organisms. Sinauer Associates. Sunderland, Mass. Black, J. G. 2002. Microbiology, Principles and Explorations. 5th ed. John Wiley and Sons, Inc. New York. Brim, H., S. C. McFarlan, J. K. Fredrickson, K. W. Minton, M. Zhai, L. P. Wackett, and M. J. Daly. 2000. Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments. Nature Biotechnology 18: 85-90. H. Brim, A. Venkateswaran, H. M. Kostandarithes, J. K. Fredrickson, and M. J. Daly. 2003. Genetic Development of Deinococcus geothermalis for bioremediation of high temperature radioactive waste environments. Appl. Environ. Microbiol., 69, 4575-4582. Brock, T. D. and H. Freeze. 1969. Thermus aquaticus gen. n. and sp. n., a non-sporulating extreme thermophile. Journal of Bacteriology. 98(1): 289-297. Brock, T. D., M. T. Madigan, J. M. Martinko, and J. Parker. 1994. Biology of Microorganisms. 7th ed. Prentice Hall. Englewood Cliffs, NJ. Brooks, B. W. and R. G. E. Murray. 1981. Nomenclature for “Micrococcus radiodurans” and other radiation-resistant cocci: Deinococcaceae fam. nov., and Deinococcus gen. nov., including five species. Int. J. Syst. Bacteriol. 31: 353-360. Chien, A., D. B. Edgar, and J. M. Trela. 1976. Deoxyribonucleic acid polymerase from the extreme thermophile Thermus aquaticus. Journal of Bacteriology. 127(3): 1550-1557. Daly, M. J. 2000. Engineering radiation-resistant bacteria for environmental biotechnology. Curr. Opin. Biotechnol.11:280-285. Ferreira, A. C., M. F. Nobre, F. A. Rainey, M. T. Silva, R. Wait, J. Burghardt, A. P. Chung, and M. S. da Costa. 1997. Deinococcus geothermalis sp. nov. and Deinococcus murrayi sp. nov., two extremely radiation-resistant and slightly thermophilic species from hot springs. Int. J. Syst. Bacteriol. 47: 939-947. 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. Huyghe, P. 1998. Conan the bacterium. The Sciences. July/August: 16-19. Krieg, N. R. 1984. Gram-negative aerobic rods and cocci. In: Krieg, N. R. and J. G. Holt, eds. Bergey´s Manual of Systematic Bacteriology, Vol. 1: 140-408. Makarova, K. S., L., Aravind, Y. L. Wolf, R. L. Tatusov, K.W. Minton, E.V. Koonin, and M. J. Daly. 2001. Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol. Mol. Biol. Rev. 65:44-79. 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. Mattimore, V. and J. R. Battista. 1996. Radioresistance of Deinococcus radiodurans: Functions necessary to survive ionizing radiation are also necessary to survive prolonged dessication. Journal of Bacteriology. 178(3): 633-637. Omelchenko, M. V., Y. I. Wolf, E. K. Gaidamakova, V. Y. Matrosova, A. Vasilenko, M. Zhai, M. J. Daly, E. V. Koonin, and K. S. Marakova.2005. Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance. BMC Evolutionary Biology. 5:57 http://www.biomedcentral.com/1471-2148/5/57 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. |
| By Jack R. Holt. Last revised: 02/11/2013 |
