How We Do, Don’t, and Should Look at Bacteria and Bacteriology

Reference work entry


Microbiology today has a new-found wealth far greater than any it possessed before. The source of that wealth is the universal phylogenetic tree—the framework essential for understanding organismal relationships. The power that flows from phylogenetic ordering permeates the field. Microbiologists now accomplish with ease things that were previously impossible and approach bacteria in ways that 20 years ago were unthinkable. Microbial ecology is no longer the faux ecology it had been—when defining a niche in organismal terms was not an option. Today, the field rests on a par with plant and animal ecology and exceeds them in importance, for it is in the microbial realm that the base and fount of the global ecosystem lie. Studying microbial diversity used to be the equivalent of hunting through antique shops for curios—which resulted in a collection of species no more connected to one another than the items in a bower bird’s nest. Now all organisms sit on the well-ordered tips of branches on the universal phylogenetic tree (Woese 1987; Olsen et al. 1994), and the study of one, far from being an isolated adventure, can contribute to the study of all. An interest in bacterial evolution used to be perceived as metaphysical and worthless. Today, evolutionary relationships are the foundation and motive force behind a new and resurgent microbiology and hence biology as a whole.


Horizontal Gene Transfer Universal Tree Bacterial Evolution Microbial World Extreme Halophile 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. Ambler RP, Daniel M, Hermoso J, Meyer TE, Bartsch RG, Kamen MD (1979a) Cytochrome c2 sequence variation among the recognised species of purple nonsulphur photosynthetic bacteria. Nature 278:659–660PubMedCrossRefGoogle Scholar
  2. Ambler RP, Meyer TE, Kamen MD (1979b) Anomalies in amino acid sequence of small cytochromes c and cytochromes c’ from two species of purple photosynthetic bacteria. Nature 278:661–662PubMedCrossRefGoogle Scholar
  3. Barns SM, Fundyga RE, Jeffries MW, Pace NR (1994) Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc Natl Acad Sci USA 91:1609–1613PubMedCrossRefGoogle Scholar
  4. Barns SM, Delwiche CF, Palmer JD, Pace NR (1996) Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc Natl Acad Sci USA 93:9188–9193PubMedCrossRefGoogle Scholar
  5. Beifuss U, Tietze M, Baumer S, Deppenmeier U (2000) Methanophenazine: structure, total synthesis, and function of a new cofactor from methanogenic Archaea. Angew Chem Int Ed Engl 39:2470–2472PubMedCrossRefGoogle Scholar
  6. Beijerinck MW (1905) Versl K Akad Wet Amsterdam 14:168–169Google Scholar
  7. Bell SD, Jackson SP (2001) Mechanism and regulation of transcription in archaea. Curr Opin Microbiol 4:208–213PubMedCrossRefGoogle Scholar
  8. Breed RS (1939) Bergey’s manual of systematic bacteriology, 2nd edn. Williams & Wilkins, BaltimoreGoogle Scholar
  9. Burggraf S, Ching A, Stetter KO, Woese CR (1991) The sequence of Methanospirillum hungatei 23S rRNA confirms the specific relationship between the extreme halophiles and the Methanomicrobiales. Curr Opin Microbiol 14:358–363Google Scholar
  10. Burkhardt F, Smith S (1990) The correspondence of Charles Darwin, vol 6. Cambridge University Press, Cambridge, UK, pp 1856–1857Google Scholar
  11. Crick FHC (1958) The biological replication of macromolecules. Symp Soc Exp Biol 12:138–163PubMedGoogle Scholar
  12. Darwin C (1859) The origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. John Murray, London, p 69Google Scholar
  13. Deckert G, Warren PV, Gaasterland T, Young WG, Lenox AL, Graham DE, Overbeek R, Snead MA, Keller M, Aujay M, Huber R, Feldman RA, Short JM, Olsen GJ, Swanson RV (1998) The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature 392:353–358PubMedCrossRefGoogle Scholar
  14. DeLong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci USA 89:5685–5689PubMedCrossRefGoogle Scholar
  15. DeLong EF (1997) Marine microbial diversity: the tip of the iceberg. Trends Biotechnol 15:203–207PubMedCrossRefGoogle Scholar
  16. DeLong EF, Wickham GS, Pace NR (1989) Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243:1360–1363PubMedCrossRefGoogle Scholar
  17. Deppenmeier U, Johann A, Hartsch T, Merkl R, Schmitz RA, Martinez-Arias R, Henne A, Wiezer A, Baumer S, Jacobi C, Bruggemann H, Lienard T, Christmann A, Bomeke M, Steckel S, Bhattacharyya A, Lykidis A, Overbeek R, Klenk HP, Gunsalus RP, Fritz HJ, Gottschalk G (2002) The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea. J Mol Microbiol Biotechnol 4:453–461PubMedGoogle Scholar
  18. Dobzhansky T (1963) Evolution, genetics and man. Wiley, New YorkGoogle Scholar
  19. Eisen JA, Nelson KE, Paulsen IT, Heidelberg JF, Wu M, Dodson RJ, Deboy R, Gwinn ML, Nelson WC, Haft DH, Hickey EK, Peterson JD, Durkin AS, Kolonay JL, Yang F, Holt I, Umayam LA, Mason T, Brenner M, Shea TP, Parksey D, Nierman WC, Feldblyum TV, Hansen CL, Craven MB, Radune D, Vamathevan J, Khouri H, White O, Gruber TM, Ketchum KA, Venter JC, Tettelin H, Bryant DA, Fraser CM (2002) The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proc Natl Acad Sci USA 99:9509–9514PubMedCrossRefGoogle Scholar
  20. Fitch WM, Margoliash E (1967) Construction of phylogenetic trees. Science 155:279–284PubMedCrossRefGoogle Scholar
  21. Fox GE, Magrum LJ, Balch WE, Wolfe RS, Woese CR (1977a) Classification of methanogenic bacteria by 16S ribosomal RNA characterization. Proc Natl Acad Sci USA 74:4537–4541PubMedCrossRefGoogle Scholar
  22. Fox GE, Pechman KR, Woese CR (1977b) Comparative cataloging of 16S ribosomal ribonucleic acid: molecular approach to procaryotic systematics. Int J Syst Bacteriol 27:44–57CrossRefGoogle Scholar
  23. Fox G, Stackebrandt E, Hespell RB, Gibson J, Maniloff J, Dyer TA, Wolfe RS, Balch WE, Tanner RS, Magrum LJ, Zablen LB, Blakemore R, Gupta R, Bonen L, Lewis BJ, Stahl DA, Luehrsen KR, Chen KN, Woese CR (1980) The phylogeny of prokaryotes. Science 209:457–463PubMedCrossRefGoogle Scholar
  24. Galagan JE, Nusbaum C, Roy A, Endrizzi MG, Macdonald P, FitzHugh W, Calvo S, Engels R, Smirnov S, Atnoor D, Brown A, Allen N, Naylor J, Stange-Thomann N, DeArellano K, Johnson R, Linton L, McEwan P, McKernan K, Talamas J, Tirrell A, Ye W, Zimmer A, Barber RD, Cann I, Graham DE, Grahame DA, Guss AM, Hedderich R, Ingram-Smith C, Kuettner HC, Krzycki JA, Leigh JA, Li W, Liu J, Mukhopadhyay B, Reeve JN, Smith K, Springer TA, Umayam LA, White O, White RH, Conway de Macario E, Ferry JG, Jarrell KF, Jing H, Macario AJ, Paulsen I, Pritchett M, Sowers KR, Swanson RV, Zinder SH, Lander E, Metcalf WW, Birren B (2002) The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res 12:532–542PubMedCrossRefGoogle Scholar
  25. Gillespie D, Spiegelman S (1965) A quantitative assay for DNA-RNA hybrids with DNA immobilized on a membrane. J Mol Biol 12:829–842PubMedCrossRefGoogle Scholar
  26. Golyshina OV, Pivovarova TA, Karavaiko GI, Kondrateva TF, Moore ER, Abraham WR, Lunsdorf H, Timmis KN, Yakimov MM, Golyshin PN (2000) Ferroplasma acidiphilum gen. nov., sp. nov., an acidophilic, autotrophic, ferrous-iron-oxidizing, cell-wall-lacking, mesophilic member of the Ferroplasmaceae fam. nov., comprising a distinct lineage of the Archaea. Int J Syst Evol Microbiol 50:997–1006PubMedCrossRefGoogle Scholar
  27. Graham DE, White RH (2002) Elucidation of methanogenic coenzyme biosyntheses: from spectroscopy to genomics. Nat Prod Rep 19:133–147PubMedCrossRefGoogle Scholar
  28. Graham DE, Overbeek R, Olsen GJ, Woese CR (2000) An archaeal genomic signature. Proc Natl Acad Sci USA 97:3304–3308PubMedCrossRefGoogle Scholar
  29. Gray MW, Burger G, Lang BF (2001) The origin and early evolution of mitochondria (Reviews). Genome Biol 2:1018CrossRefGoogle Scholar
  30. Hafenbradl D, Keller M, Dirmeier R, Rachel R, Rossnagel P, Burggraf S, Huber H, Stetter KO (1996) Ferroglobus placidus gen. nov., sp. nov., a novel hyperthermophilic archaeum that oxidizes Fe2+ at neutral pH under anoxic conditions. Arch Microbiol 166:308–314PubMedCrossRefGoogle Scholar
  31. Hartman H (1984) The origin of the eukaryotic cell. Speculations Sci Technol 7:77–81PubMedGoogle Scholar
  32. Hartman H, Fedorov A (2002) The origin of the eukaryotic cell: a genomic investigation. Proc Natl Acad Sci USA 99:1420–1425PubMedCrossRefGoogle Scholar
  33. Hartmann E, König H (1990) Comparison of the biosynthesis of the methanobacterial pseudomurein and the eubacterial murein. Naturwissenschaften 77:472–475PubMedCrossRefGoogle Scholar
  34. Heberlein GT, De Ley J, Tijtgat R (1967) Deoxyribonucleic acid homology and taxonomy of Agrobacterium, Rhizobium, and Chromobacterium. J Bacteriol 94:116–124PubMedGoogle Scholar
  35. Huber R, Langworthy TA, Konig H, Thomm M, Woese CR, Sleytr UB, Stetter KO (1986) Thermotoga maritima sp. nov. represents a new genus of unique extremely thermophilic eubacteria growing up to 90 °C. Arch Microbiol 144:324–333CrossRefGoogle Scholar
  36. Huber R, Wilharm T, Huber D, Trincone A, Burggraf S, Konig H, Rachel R, Rockinger I, Fricke H, Stetter KO (1992) Aquifex pyrophilus gen. nov., sp. nov., represents a novel group of marine hyperthermophilic hydrogen-oxidizing bacteria. Syst Appl Microbiol 15:340–351CrossRefGoogle Scholar
  37. Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO (2002) A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417:63–67PubMedCrossRefGoogle Scholar
  38. Jenkins C, Samudrala R, Anderson I, Hedlund BP, Petroni G, Michailova N, Pinel N, Overbeek R, Rosati G, Staley JT (2002) Genes for the cytoskeletal protein tubulin in the bacterial genus Prosthecobacter. Proc Natl Acad Sci USA 99:17049–17054PubMedCrossRefGoogle Scholar
  39. Kamp AF, La Riviere JWM, Verhoeven W (eds) (1959) Albert Jan Kluyver: his life and works. North Holland, AmsterdamGoogle Scholar
  40. Kandler O, Hippe H (1977) Lack of peptidoglycan in the cell walls of Methanosarcina barkeri. Arch Microbiol 113:57–60PubMedCrossRefGoogle Scholar
  41. Kandler O, König H (1985) Cell envelopes of archaebacteria. In: Woese CR, Wolfe RS (eds) The bacteria, vol 8, Archaebacteria. Academic, New York, pp 413–458Google Scholar
  42. Kates M (1964) Bacterial lipids. Adv Lipid Res 2:17–90PubMedGoogle Scholar
  43. Kates M, Wassef MK, Kushner DJ (1968) Radioisotopic studies on the biosynthesis of the glyceryl diether lipids of Halobacterium cutirubrum. Can J Biochem 46:971–977PubMedCrossRefGoogle Scholar
  44. Kelman Z (2000) DNA replication in the third domain (of life). Curr Protein Pept Sci 1:139–154PubMedCrossRefGoogle Scholar
  45. Kluyver AJ (1931) The chemical activities of microorganisms. University Press, LondonGoogle Scholar
  46. Kluyver AJ, Donker HJL (1926) Die Einheit in der Biochemie. Chem Zell Gewiss 13:134–190Google Scholar
  47. Kluyver AJ, van Niel CB (1936) Prospects for a natural system of classification of bacteria. Zentralbl Bakteriol Parasitenkd Infektionskrankh 94:369–403Google Scholar
  48. König H, Kandler O (1979) The amino acid sequence of the peptide moiety of the pseudomurein from Methanobacterium thermoautotrophicum. Arch Microbiol 121:271–275PubMedCrossRefGoogle Scholar
  49. Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci USA 82:6955–6959PubMedCrossRefGoogle Scholar
  50. Langer D, Hain J, Thuriaux P, Zillig W (1995) Transcription in archaea: similarity to that in eucarya. Proc Natl Acad Sci USA 92:5768–5772PubMedCrossRefGoogle Scholar
  51. Lederberg J, Tatum EL (1946) Gene recombination in E. coli. Nature 158:558PubMedCrossRefGoogle Scholar
  52. Lewin RA (1984) Prochloron—a status report. Phycologia 23:203–208PubMedCrossRefGoogle Scholar
  53. Maidak BL, Cole JR, Lilburn TG, Parker CY Jr, Saxman PR, Farris RJ, Garrity GM, Olsen GJ, Schmidt TM, Tiedje JM (2001) The RDP-II (ribosomal database project). Nucleic Acids Res 29:173–174PubMedCrossRefGoogle Scholar
  54. Martin W, Mueller M (1998) The hydrogen hypothesis for the first eukaryote. Nature 392:37–41PubMedCrossRefGoogle Scholar
  55. Meyer TE, Cusanovich MA, Kamen MD (1986) Evidence against use of bacterial amino acid sequence data for construction of all-inclusive phylogenetic trees. Proc Natl Acad Sci USA 83:217–220PubMedCrossRefGoogle Scholar
  56. Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA, McDonald L, Utterback TR, Malek JA, Linher KD, Garrett MM, Stewart AM, Cotton MD, Pratt MS, Phillips CA, Richardson D, Heidelberg J, Sutton GG, Fleischmann RD, Eisen JA, Fraser CM et al (1999) Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399:323–329PubMedCrossRefGoogle Scholar
  57. Olsen GJ, Woese CR (1996) Lessons from an archaeal genome: what are we learning from Methanococcus jannaschii. Trends Genet 12:377–379PubMedCrossRefGoogle Scholar
  58. Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR, Stahl DA (1986) Microbial ecology and evolution: a ribosomal RNA approach. Annu Rev Microbiol 40:337–365PubMedCrossRefGoogle Scholar
  59. Olsen GJ, Woese CR, Overbeek R (1994) The winds of (evolutionary) change: breathing new life into microbiology. J Bacteriol 176:1–6PubMedGoogle Scholar
  60. Pace NR (1997) A molecular view of microbial diversity and the biosphere. Science 276:734–740PubMedCrossRefGoogle Scholar
  61. Paster BJ, Dewhirst FE, Olsen GJ, Fraser I (1994) Phylogeny of Bacteroides, Prevotella, and Porphyromonas spp. and related bacteria. J Bacteriol 176:725–732PubMedGoogle Scholar
  62. Reeve JN, Sandman K, Daniels CJ (1997) Archaeal histones, nucleosomes, and transcription initiation. Cell 89:999–1002PubMedCrossRefGoogle Scholar
  63. Sanger F, Thompson EOP (1953) The amino-acid sequence in the glycyl chain of insulin. Soc Gen Microbiol Symp 53:353–374Google Scholar
  64. Sanger F, Tuppy H (1951) The amino-acid sequence in the phenylalanyl chain of insulin. Biochem J 49:481–490PubMedGoogle Scholar
  65. Sanger F, Brownlee GG, Barrell BG (1965) A two-dimensional fractionation procedure for radioactive nucleotides. J Mol Biol 13:373–398PubMedCrossRefGoogle Scholar
  66. Schleifer K-H, Kandler O (1972) Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36:407–477PubMedGoogle Scholar
  67. Sogin SJ, Sogin ML, Woese CR (1971) Phylogenetic measurement in procaryotes by primary structural characterization. J Mol Evol 1:173–184PubMedCrossRefGoogle Scholar
  68. Stahl DA, Lane DJ, Olsen GJ, Pace NR (1985) Characterization of a Yellowstone hot spring microbial community by 5S rRNA sequences. Appl Environ Microbiol 49:1379–1384PubMedGoogle Scholar
  69. Stanier RY (1970) Organization and control in prokaryotic and eukaryotic cells. In: Charles HP, Knight BCJG (eds) Society for general microbiology symposium 20. Cambridge University Press, Cambridge, UK, pp 1–38Google Scholar
  70. Stanier RY, van Niel CB (1941) The main outlines of bacterial classification. J Bacteriol 42:437–466PubMedGoogle Scholar
  71. Stanier RY, van Niel CB (1962) The concept of a bacterium. Arch Mikrobiol 42:17–35PubMedCrossRefGoogle Scholar
  72. Stanier RY, Doudoroff M, Adelberg EA (1957) The microbial world, 1st edn. Prentice-Hall, Engelwood CliffsGoogle Scholar
  73. Stanier RY, Doudoroff M, Adelberg EA (1963) The microbial world, 2nd edn. Prentice-Hall, Engelwood CliffsGoogle Scholar
  74. Stanier RY, Doudoroff M, Adelberg EA (1970) The microbial world, 3rd edn. Prentice-Hall, Engelwood CliffsGoogle Scholar
  75. Stanier RY, Adelberg EA, Ingraham JL (1976) The microbial world, 4th edn. Prentice-Hall, Engelwood CliffsGoogle Scholar
  76. Tjian R (1996) The biochemistry of transcription in eukaryotes: a paradigm for multisubunit regulatory complexes. Philos Trans R Soc Lond B 51:491–499CrossRefGoogle Scholar
  77. Tornabene TG, Langworthy TA (1979) Diphytanyl and dibiphytanyl glycerol ether lipids of methanogenic archaebacteria. Science 203:51–53PubMedCrossRefGoogle Scholar
  78. van Iterson Jr G, den Dooren de Jong LE, Kluyver AJ (1940) Martinus Willem Beijerinck: his life and his work. Delftsch Hoogeschoolfonds, DelftCrossRefGoogle Scholar
  79. van Niel CB (1946) The classification and natural relationships of bacteria. Cold Spring Harb Symp Quant Biol 11:285–301CrossRefGoogle Scholar
  80. van Niel CB (1949) The “Delft School” and the rise of general microbiology. Bacteriol Rev 13:161–174PubMedGoogle Scholar
  81. van Niel CB (1955) Classification and taxonomy of the bacteria and blue green algae. A century of progress in the natural sciences 1853–1953. California Academy of Sciences, San Francisco, pp 89–114Google Scholar
  82. Weisberg WG, Giovannoni SJ, Woese CR (1989) The Deinococcus-Thermus phylum and the effect of mRNA composition on phylogenetic tree construction. Syst Appl Microbiol 11:128–134CrossRefGoogle Scholar
  83. Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271PubMedGoogle Scholar
  84. Woese CR (2000) Interpreting the universal phylogenetic tree. Proc Natl Acad Sci USA 97:8392–8396PubMedCrossRefGoogle Scholar
  85. Woese CR (2002) On the evolution of cells. Proc Natl Acad Sci USA 99:8742–8747PubMedCrossRefGoogle Scholar
  86. Woese CR, Fox GE (1977a) The concept of cellular evolution. J Mol Evol 10:1–6PubMedCrossRefGoogle Scholar
  87. Woese CR, Fox GE (1977b) The phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74:5088–5090PubMedCrossRefGoogle Scholar
  88. Woese CR, Sogin ML, Sutton LA (1974) Procaryote phylogeny. I: concerning the relatedness of Aerobacter aerogenes to Escherichia coli. J Mol Evol 3:293–299PubMedCrossRefGoogle Scholar
  89. Woese CR, Fox GE, Zablen L, Uchida T, Bonen L, Pechman K, Lewis BJ, Stahl D (1975) Conservation of primary structure in 16S ribosomal RNA. Nature 254:83–96PubMedCrossRefGoogle Scholar
  90. Woese CR, Debrunner-Vossbrinck BA, Oyaizu H, Stackebrandt E, Ludwig W (1985a) Gram-positive bacteria: possible photosynthetic ancestry. Science 229:762–765PubMedCrossRefGoogle Scholar
  91. Woese CR, Stackebrandt E, Macke TJ, Fox GE (1985b) A phylogenetic definition of the major eubacterial taxa. Syst Appl Microbiol 6:143–151PubMedCrossRefGoogle Scholar
  92. Woese CR, Olsen GJ, Ibba M, Söll D (2000) Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol Mol Biol Rev 64:202–236PubMedCrossRefGoogle Scholar
  93. Wolfe RS (1992) Biochemistry of methanogenesis. Biochem Soc Symp 58:41–49PubMedGoogle Scholar
  94. Zuckerkandl E, Pauling L (1965) Molecules as documents of evolutionary history. J Theor Biol 8:357–366PubMedCrossRefGoogle Scholar

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