Biology & Philosophy

, Volume 22, Issue 2, pp 155–191

Size doesn’t matter: towards a more inclusive philosophy of biology

Review

Abstract

Philosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy of biology’s standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology – including biofilm formation, chemotaxis, quorum sensing and gene transfer – that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations.

Keywords

Biodiversity Evolution Macrobes Microbes Microbiology Multicellularity Ontology Prokaryotes Taxonomy 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Adl S.M., Simpson G.B., Farmer M.A. et al. (2005) The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J. Eukaryot. Microbiol. 52: 399–451Google Scholar
  2. Adler J. (1969) Chemoreceptors in bacteria. Science 166: 1588–1597Google Scholar
  3. Allers T., Mevarech M. (2005) Archaeal genetics – the third way. Nat. Rev. Genet.6: 58–73Google Scholar
  4. Amann R.I., Ludwig W., Scleifer K.-H. (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microb. Rev. 59: 143–169Google Scholar
  5. Ameison J.C. (2002) On the origin, evolution, and nature of programmed cell death: a timeline of four billion years. Cell Death Differ. 9: 367–393Google Scholar
  6. Amend J.P., Shock E.L. (2001) Energetics of overall metabolic reactions of thermophilic and hyperthemophilic Archaea and Bacteria. FEMS Microbiol. Rev. 25: 175–243Google Scholar
  7. Andersson J.O. (2000) Is Buchnera a bacterium or an organelle? Curr. Biol. 10: R866–R868Google Scholar
  8. Andrews J.H. (1998) Bacteria as modular organisms. Annu. Rev. Microbiol. 52: 105–126Google Scholar
  9. Aravind L., Anantharaman V., Iyer L.M. (2003) Evolutionary connections between bacterial and eukaryotic signaling systems: a genomic perspective. Curr. Opin. Microbiol. 6: 490–497Google Scholar
  10. Atlas R.M., Bartha R. (1998) Microbial Ecology: Fundamentals and Applications (4th edn.). Benjamin/Cummings, Menlo Park, CAGoogle Scholar
  11. Avery O.T., MacLeod C.M., McCarty M. (1944) Studies on the chemical nature of the substance inducing transformation of pneumococcal types. Induction of transformation by a desoxyribonucleic acid fraction isolated from Pneumococcus Type III. J. Exp. Med. 79: 137–158Google Scholar
  12. Bäckhed F., Ley R.E., Sonnenburg J.L. et al. (2005) Host-bacterial mutualism in the human intestine. Science 307: 1915–1920Google Scholar
  13. Baker M.D., Wolanin P.M., Stock J.B. (2005) Signal transduction in bacterial chemotaxis. BioEssays 28: 9–22Google Scholar
  14. Bassler B.L. (2002) Small talk: cell-to-cell communication in bacteria. Cell 109: 421–424Google Scholar
  15. Beadle G., Tatum E. (1941) Genetic control of biochemical reactions in Neurospora. PNAS 27: 499–506Google Scholar
  16. Beiko R.G., Harlow T.J., Ragan M.A. (2005) Highways of gene sharing in prokaryotes. PNAS 102: 14332–14337Google Scholar
  17. Béjà O., Aravind L., Koonin E.V. et al. (2000) Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289: 1902–1906Google Scholar
  18. Bell S.D., Jackson S.P. (1998) Transcription and translation in archaea: a mosaic of eukaryal and bacterial features. Trends Microbiol. 6: 222–228Google Scholar
  19. Ben-Jacob E., Cohen I., Golding I. et al. (2000) Bacterial cooperative organization under antibiotic stress. Physica A 282: 247–282Google Scholar
  20. Berg R.D. (1996) The indigenous gastrointestinal microflora. Trends Microbiol. 4: 430–435Google Scholar
  21. Biagini G.A., Bernard C. (2000) Primitive anaerobic protozoa: a false concept? Microbiology 146: 1019–1020Google Scholar
  22. Bonner J.T. (1998) The origins of multicellularity. Integr. Biol. 1: 27–36Google Scholar
  23. Boucher Y., Nesbø C.L., Doolittle W.F. (2001) Microbial genomes: dealing with diversity. Curr. Opin. Microbiol. 4: 285–289Google Scholar
  24. Brandon R.N. (1999) The units of selection revisited: the modules of selection. Biol. Philos. 14: 167–180Google Scholar
  25. Brandon R.N., Burian R.M. (eds.) (1984) Genes, Organisms, Populations: Controversies over the Unit of Selection. MIT Press, Cambridge, MAGoogle Scholar
  26. Brehm-Stecher B.F., Johnson E.A. (2004) Single-cell microbiology: tools, technologies and applications. Microbiol. Mol. Biol. Rev. 68: 538–559Google Scholar
  27. Breitbart M., Felts B., Kelley S. et al. (2004) Diversity and population structure of a near-shore marine-sediment viral community. Proc. Roy. Soc. London B 271: 565–574Google Scholar
  28. Breitbart M., Hewson I., Felts B. et al. (2003) Metagenomic analyses of an uncultured viral community from human feces. J. Bacteriol. 185: 6220–6223Google Scholar
  29. Brock T.D. (1966) Principles of microbial ecology. Prentice-Hall, Englewood Cliffs, NJGoogle Scholar
  30. Brock T.D. (1987) The study of microorganisms in situ: progress and problems. Sym. Soc. General Microbiol. 41: 1–17Google Scholar
  31. Brock T.D. (1990) The Emergence of Bacterial Genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NYGoogle Scholar
  32. Bromham L. (2002) The human zoo: endogenous retroviruses in the human genome. Trends Ecol. Evol. 17: 91–97Google Scholar
  33. Brown J.H. (1932) The biological approach to bacteriology. J. Bacteriol. XXIII: 1–10Google Scholar
  34. Brown J.R. (2001) Genomic and phylogenetic perspectives on the evolution of prokaryotes. Syst. Biol. 50: 497–512Google Scholar
  35. Brown S.P., Johnstone R.A. (2001) Cooperation in the dark: signalling and collective action in quorum-sensing bacteria. Proc. Roy. Soc. London B 268: 961–965Google Scholar
  36. Brune A., Friedrich M. (2000) Microecology of the termite gut: structure and function on a microscale. Curr. Opin. Microbiol. 3: 263–269Google Scholar
  37. Bryant C. (eds) (1991) Metazoan Life without Oxygen. Chapman & Hall, LondonGoogle Scholar
  38. Bryant D., Moulton V. (2004) Neighbor-Net: an agglomerative method for the construction of phylogenetic networks. Mol. Biol. Evol 21: 255–265Google Scholar
  39. Buckley M.R. (2004) The Global Genome Question: Microbes as the Key to Evolution and Ecology. American Academy of Microbiology, Washington, DCGoogle Scholar
  40. Bull A.T., Slater J.H. (1982a) Historical perspectives on mixed cultures and microbial communities. In: Bull A.T., Slater J.H. (eds) Microbial Interactions and Communities. Academic Press, London, UK, pp. 1–12Google Scholar
  41. Bull A.T., Slater J.H. (1982b) Microbial interactions and community structure. In: Bull A.T., Slater J.H. (eds) Microbial Interactions and Communities. Academic Press, London, UK, pp. 13–44Google Scholar
  42. Bult C.J., White O., Olsen G.J. et al. (1996) Complete genome sequence of the methanogenic archaeon. Methanococcus jannaschii, Science 273: 1058–1072Google Scholar
  43. Bushman F. (2001) Lateral DNA Transfer: Mechanisms and Consequences. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NYGoogle Scholar
  44. Buss L.W. (1987) The Evolution of Individuality. Princeton University Press, PrincetonGoogle Scholar
  45. Caldwell D.E., Atuku E., Wilkie D.C. et al. (1997) Germ theory vs. community theory in understanding and controlling the proliferation of biofilms. Adv. Dent. Res. 11: 4–13CrossRefGoogle Scholar
  46. Caldwell D.E., Costerton J.W. (1996) Are bacterial biofilms constrained to Darwin’s concept of evolution through natural selection? Microbiología SEM 12: 347–358Google Scholar
  47. Carlile M.J. (1980) From prokaryote to eukaryote: gains and losses. In: Gooday G.W., Lloyd D., Trinci A.P.J. (eds) The Eukaryotic Microbial Cell. Cambridge University Press, Cambridge, pp. 1–40Google Scholar
  48. Carroll S.B. (2001) Chance and necessity: the evolution of morphological complexity and diversity. Nature 409: 1102–1109Google Scholar
  49. Casadesús J., D’Ari R. (2002) Memory in bacteria and phage. BioEssays 24: 512–518Google Scholar
  50. Charlebois R.L., Beiko R.G., Ragan M.A. (2003) Microbial phylogenomics: branching out. Nature 421: 217Google Scholar
  51. Cho J.-C., Tiedje J.M. (2000) Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil. Appl. Environ. Microbiol. 66: 5448–5456Google Scholar
  52. Cleland, C.E. and Copley, S.D.:2005, The possibility of alternative microbial life on earth, Int. J. Astrobiol 4: 165--173Google Scholar
  53. Coenye T., Gevers D., de Peer Y.V. et al. (2005) Towards a prokaryotic genomic taxonomy. FEMS Microbiol. Rev. 29: 147–167Google Scholar
  54. Cohan F.M. (2002) What are bacterial species? Annu. Rev. Microbiol. 56: 457–487Google Scholar
  55. Collins J.P. (2003) What can we learn from community genetics? Ecology 84: 574–577Google Scholar
  56. Colwell R.R. (1997) Microbial diversity: the importance of exploration and conservation. J. Indust. Microb. Technol. 18: 302–307Google Scholar
  57. Conway Morris S. (1998) The evolution of diversity in ancient ecosystems: a review. Philos. Trans. Roy. Soc. London B 353: 327–345Google Scholar
  58. Conway-Morris S. (2003) The Cambrian ‘explosion’ of metazoans and molecular biology: would Darwin be satisfied? Int. J. Dev. Biol. 47: 505–515Google Scholar
  59. Corliss J.O. (1999) Biodiversity, classification, and numbers of species of protists. In: Raven P.H. (eds) Nature and Human Society: The Quest for a Sustainable World. National Academy Press, Washington, DC, pp. 130–155Google Scholar
  60. Costerton B. (2004) Microbial ecology comes of age and joins the general ecology community. PNAS 101: 16983–16984Google Scholar
  61. Costerton J.W., Lewandowski Z., Caldwell D.E., Korber D.R., Lappin-Scott H.M. (1995) Microbial biofilms. Annu. Rev. Microbiol. 49: 711–745Google Scholar
  62. Croal L.R., Gralnick J.A., Malasarn D., Newman D.K. (2004) The genetics of geochemistry. Annu. Rev. Genet. 38: 175–202Google Scholar
  63. Crespi B.J. (2001) The evolution of social behaviour in microorganisms. TREE 16: 178–183Google Scholar
  64. Cutler D.W., Crump L.M. (1935) Problems in Soil Microbiology. Longmans, Green & Co., LondonGoogle Scholar
  65. Daims H., Lücker S., Wagner M. (2006) daime, a novel image analysis program for microbial ecology and biofilm research.Environ. Microbiol. 8: 200–213Google Scholar
  66. Daniel R. (2004) The soil metagenome – a rich resource for the discovery of novel natural products. Curr. Opin. Biotechnol. 15: 199–204Google Scholar
  67. Davey M.E., O’Toole G.A. (2000) Microbial biofilms: from ecology to molecular genetics. Microbiol. Mol. Biol. Rev. 64: 847–867Google Scholar
  68. Davies D.G. (2000) Physiological events in biofilm formation. In: Allison D.G., Gilbert P., Lappin-Scott H.M., Wilson M. (eds) Community Structure and Cooperation in Biofilms. CUP, Cambridge, pp. 37–52Google Scholar
  69. DeLong E.F. (2002) Towards microbial systems science: integrating microbial perspective from genomes to biomes. Environ. Microbiol. 4: 9–10Google Scholar
  70. DeLong E.F. (2004) Reconstructing the wild types. Nature 428: 25–26Google Scholar
  71. DeLong E.F. (2005) Microbial community genomics in the ocean. Nat. Rev. Microbiol. 3: 459–469Google Scholar
  72. DeLong E.F., Pace N.R. (2001) Environmental diversity of Bacteria and Archaea. Syst. Biol. 50: 470–478Google Scholar
  73. Diaz-Torres M.L., McNab R., Spratt D.A. et al. (2003) Novel tetracycline resistance determinant from the oral metagenome. Antimicrob. Agents chemother. 47: 1430–1432Google Scholar
  74. Dijkshoorn L., Ursing B.M., Ursing J.B. (2000) Strain, clone and species: comments on three basic concepts of bacteriology. J. Med. Microbiol. 49: 397–401Google Scholar
  75. Doney S.C., Abbott M.R., Cullen J.J. et al. (2004) From genes to ecosystems: the ocean’s new frontier. Front. Ecol. Environ. 2: 457–466Google Scholar
  76. Dixon B. (1994) Power Unseen: How Microbes Rule the World. Freeman, OxfordGoogle Scholar
  77. Doolittle W.F. (1999) Phylogenetic classification and the universal tree. Science 284: 2124–2128Google Scholar
  78. Doolittle W.F. (2002) Diversity squared. Environ. Microbiol. 4: 10–12Google Scholar
  79. Doolittle W.F. (2005) If the tree of life fell, would we recognize the sound. In: Sapp J. (eds) Microbial Phylogeny and Evolution: Concepts and Controversies. OUP, Oxford, pp. 119–133Google Scholar
  80. Doolittle W.F., Boucher Y., Nesbø C.L. et al. (2003) How big is the iceberg of which organellar genes are but the tip? Philos. Trans. Roy. Soc. London B358: 39–58Google Scholar
  81. Douglas A.E., Raven J.A. (2002) Genomes at the interface between bacteria and organelles. Philos. Trans. Roy. Soc. London B 358: 5–18Google Scholar
  82. Drews G. (2000) The roots of microbiology and the influence of Ferdinand Cohn on microbiology of the 19th century. FEMS Microbiol. Rev. 24: 225–249Google Scholar
  83. Dunny G.M., Leonard B.A.B. (1997) Cell-cell communication in gram-positive bacteria. Annu. Rev. Microbiol. 51: 527–564Google Scholar
  84. Dunny, G.M. and Winans, S.C. 1999. Bacterial life: Neither lonely nor boring. In: G.M. Dunny and S.C. Winans (eds), Cell-Cell Signalling in Bacteria, ASM, Washington, DC, pp. 1–5Google Scholar
  85. Dupré J. (2002) Humans and Other Animals. OUP, OxfordGoogle Scholar
  86. Dworkin M. (1985) Developmental Biology of the Bacteria. Benjamin/Cummings, Reading, MAGoogle Scholar
  87. Dworkin M. (1996) Recent advances in the social and developmental biology of the Myxobacteria. Microbiol. Rev. 60: 70–102Google Scholar
  88. Dworkin M. (1997) Multiculturism versus the single microbe. In: Shapiro J.A., Dworkin M. (eds) Bacteria as Multicellular Organisms. OUP, NY, pp. 3–13Google Scholar
  89. Dykhuizen D.E. (1998) Santa Rosalia revisited: why are there so many species of bacteria? Antonie van Leeuwenhoek 73: 25–33Google Scholar
  90. Ehlers L.J. (2000) Gene transfers in biofilms. In: Allison D.G., Gilbert P., Lappin-Scott H.M., Wilson M. (eds) Community Structure and Co-operation in Biofilms. CUP, Cambridge, pp. 215–256Google Scholar
  91. Ehrlich P.R., Wilson E.O. (1991) Biodiversity studies: science and policy. Science 253: 758–762Google Scholar
  92. Eisenbach, M.:2005, Bacterial chemotaxis, Encylopedia of Life Sciences, doi: 10.1038/npg.els. 0003952Google Scholar
  93. Engelberg H., Hazan R. (2003) Cannibals defy starvation and avoid sporulation. Science 301:467–468Google Scholar
  94. Faguy D.M., Jarrell K.F. (1999) A twisted tale: the origin and evolution of motility and chemotaxis in prokaryotes. Microbiology 145: 279–281CrossRefGoogle Scholar
  95. Falke J.J., Bass R.B., Butler S.L. et al. (1997) The two-component signaling pathway of bacterial chemotaxis: a molecular view of signal transduction by receptors, kinases and adaptation enzymes. Annu. Rev. Cell Develop. Biol. 13: 457–512Google Scholar
  96. Falkowski P.G., de Vargas C. (2004) Shotgun sequencing in the sea: a blast from the past? Science 304: 58–60Google Scholar
  97. Federle M.J., Bassler B.L. (2003) Interspecies communication in bacteria. J. Clin. Invest. 112: 1291–1299Google Scholar
  98. Feil E.J., Spratt B.G. (2001) Recombination and the population structures of bacterial pathogens. Annu. Rev. Microbiol. 55:561–590Google Scholar
  99. Fenchel T. (1996) Eukaryotic life: anaerobic physiology. In: Roberts D.M., Sharp P., Alderson G., Collins M.A. (eds) Evolution of Microbial Life. CUP, Cambridge, pp. 185–203Google Scholar
  100. Figge R.M., Gober J.W. (2003) Cell shape, division and development: the 2002 American Society for Microbiology (ASM) conference on prokaryotic development. Mol. Microbiol. 47: 1475–1483Google Scholar
  101. Finlay B.J., Clarke K.J. (1999) Ubiquitous dispersal of microbial species. Nature 400: 828Google Scholar
  102. Finlay B.J., Maberly S.C., Cooper J.I. (1997) Microbial diversity and ecosystem function. Oikos 80: 209–213Google Scholar
  103. Fleischmann R.D., Adams M.D., White O. et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496–512Google Scholar
  104. Fox G.E., Stackebrandt E., Hespell R.B. et al. (1980) The phylogeny of prokaryotes. Science 209: 457–463Google Scholar
  105. Fraser C.M., Gocayne J.D., White O. et al. (1995) The minimal gene complement of Mycoplasma genitalium. Science 270: 397–403Google Scholar
  106. Gans J., Wolinsky M., Dunbar J. (2005) Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309: 1387–1390Google Scholar
  107. Genereux D.P., Logsdon Jr. J.M. (2003) Much ado about bacteria-to-vertebrate lateral gene transfer. Trends Genet. 19: 191–195Google Scholar
  108. Gevers D., Cohan F.M., Lawrence J.G. et al. (2005) Re-evaluating prokaryote species. Nat. Rev. Microbiol. 3: 733–739Google Scholar
  109. Gogarten J.P., Doolittle W.F., Lawrence J.G. (2002) Prokaryotic evolution in the light of gene transfer. Mol. Biol. Evol. 19: 2226–2238Google Scholar
  110. Gogarten J.P., Townsend J.P. (2005) Horizontal gene transfer, genome innovation and evolution. Nat. Rev. Microbiol. 3: 679–687Google Scholar
  111. Goodnight C.J., Stevens L. (1997) Experimental studies of group selection: what do they tell us about group selection in nature? Am. Nat. 150(Supplement): S59–S79Google Scholar
  112. Gould S.J. (1994) The evolution of life on earth. Sci. Am. 271: 84–91Google Scholar
  113. Gray K.M. (1997) Intercellular communication and group behaviour in bacteria. Trends Microbiol. 5: 184–188Google Scholar
  114. Grebe T.W., Stock J. (1998) Bacterial chemotaxis: the five sensors of a bacterium. Curr. Biol. 8: R154–R157Google Scholar
  115. Gregory T.R. (2001) Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma. Biol. Rev. 76: 65–101Google Scholar
  116. Griffiths D.J. (2001) Endogenous retroviruses in the human genome sequence. Genome Biol. 2: 1017.1–1017.5Google Scholar
  117. Griffin A.S., West S.A., Buckling A. (2004) Cooperation and competition in pathogenic bacteria. Nature 430: 1024–1027Google Scholar
  118. Handelsman J. (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 68: 669–685Google Scholar
  119. Handelsman J., Rondon M.R., Brady S.F. et al. (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem. Biol. 5: R245–249Google Scholar
  120. Hausner M., Wuertz S. (1999) High rates of conjugation in bacterial biofilms as determined by quantitative in situ analysis. Appl. Environ. Microbiol. 65: 3710–3713Google Scholar
  121. Henke J.M., Bassler B.L. (2004) Bacterial social engagements. Trends Cell Biol. 14: 648–656Google Scholar
  122. Hooper L.V., Bry L., Falk P.G., Gordon J.I. (1998) Host-microbial symbiosis in the mammalian intestine: exploring an internal ecosystem. BioEssays 20: 336–343Google Scholar
  123. Hooper L.V., Gordon J.I. (2001) Commensal host-bacterial relationships in the gut. Science 292: 1115–1118Google Scholar
  124. Hooper L.V., Wong M.H., Thelin A. et al. (2001) Molecular analysis of commensal host-microbial relationships in the intestine. Science 291: 881–884Google Scholar
  125. Horikoshi K., Grant W.D. (eds) (1998) Extremophiles: Microbial Life in Extreme Environments. Wiley-Liss, NYGoogle Scholar
  126. Hugenholtz, Goebels B.M., Pace N.R. (1998) The impact of culture-independent studies on the emerging phylogenetic view of biodiversity. J. Bacteriol. 180: 4765–4774Google Scholar
  127. Hull D.L. (1987a) The ideal species concept – and why we can’t get it. In: Claridge M.F., Dawah H.A., Wilson M.R. (eds) Species: The Units of Biodiversity. Chapman and Hall, London, pp. 357–380Google Scholar
  128. Hull D.L. (1987b) Genealogical actors in ecological roles. Biol. Philos. 2: 168–183Google Scholar
  129. Huson D.H. (1998) SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 14: 68–73Google Scholar
  130. Iyer L.M., Aravind L., Coon S.L. et al. (2004) Evolution of cell-cell signaling in animals: did late horizontal gene transfer from bacteria have a role? Trends Genet. 20: 292–299Google Scholar
  131. Jannasch H.W., Jones G.E. (1959) Bacterial populations in sea water as determined by different methods of enumeration. Limnol. Oceanogr. 4: 128–139Google Scholar
  132. Koshland Jr. D.E. (1979) A model regulatory system: bacterial chemotaxis. Physiol. Rev. 59: 811–862Google Scholar
  133. Jefferson K.K. (2004) What drives bacteria to produce a biofilm? FEMS Microbiol. Lett. 236: 163–173Google Scholar
  134. Joseph S.J., Hugenholtz P., Sangwan P. et al. (2003) Laboratory cultivation of widespread and previously uncultured bacteria. Appl. Environ. Microbiol. 69: 7210–7215Google Scholar
  135. Kaeberlein T., Lewis K., Epstein S.S. (2002) Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. Science 296: 1127–1129Google Scholar
  136. Kaiser D. (2001) Building a multicellular organism. Annu. Rev. Genet. 35: 103–123Google Scholar
  137. Kämpfer P., Rosselló-Mora R. (2004) The species concept for prokaryotic microorganisms – an obstacle for describing diversity? Poiesis Prax 3: 62–72Google Scholar
  138. Kasting J.F., Siefert J.L. (2002) Life and the evolution of earth’s atmosphere. Science 296: 1066–1068Google Scholar
  139. Keim C.N., Abreu F., Lins U. et al. (2004) Cell organization and ultrastructure of a magnetotactic multicellular organism. J. Struct. Biol 145: 254–262Google Scholar
  140. Kerr R.A. (2005) The story of O2. Science 308: 1730–1732Google Scholar
  141. Kitano, H. and Oda, K.: 2006, Robustness trade-offs and host-microbial symbiosis in the immune system, Molecular Systems Biology 2: 2006.0022Google Scholar
  142. Kohler Jr. R.E. (1973) The enzyme theory and the origin of biochemistry. Isis 64: 181–196Google Scholar
  143. Kolenbrander P.E. (2000) Oral microbial communities: biofilms, interactions, and genetic systems. Annu. Rev. Microbiol. 54: 413–437Google Scholar
  144. Konstantinidis K.T., Tiedje J.M. (2005) Genomic insights that advance the species definition for prokaryotes. PNAS 102: 2567–2572Google Scholar
  145. Koonin E.V., Makarova K.S., Aravind L. (2001) Horizontal gene transfer in prokaryotes: quantification and classification. Annu. Rev. Microbiol. 55: 709–742Google Scholar
  146. Kreft J.-U. (2004) Conflict of interest in biofilms. Biofilms 1: 265–276Google Scholar
  147. Kroos L., Maddock J.R. (2003) Prokaryotic development: emerging insights. J. Bacteriol. 185: 1128–1146Google Scholar
  148. Lan R., Reeves P.R. (2000) Intraspecies variation in bacterial genomes: the need for a species genome concept. Trends Microbiol. 8: 396–401Google Scholar
  149. Lan R., Reeves P.R. (2001) When does a clone deserve a name? A perspective on bacterial species based on population genetics. Trends Microbiol. 9: 419–424Google Scholar
  150. Lawrence J.G. (2002) Gene transfer in bacteria: speciation without species? Theoret. Popul. Biol. 61: 449–460Google Scholar
  151. Lawrence J.G., Hendrickson H. (2003) Lateral gene transfer: when will adolescence end? Mol. Microbiol. 50: 739–749Google Scholar
  152. Lawrence J.G., Hendrickson H. (2005) Genome evolution in bacteria: order beneath chaos. Curr. Opin. Microbiol. 8: 1–7Google Scholar
  153. Leadbetter J.R. (2003) Cultivation of recalcitrant microbes: cells are alive, well and revealing their secrets in the 21st century laboratory. Curr. Opin. Microbiol. 6: 274–281Google Scholar
  154. Lederberg J., Tatum E.L. (1946) Novel genotypes in mixed cultures of biochemical mutants of bacteria. Cold Spring Harbor Symp. Quant. Biol. 11: 113–114Google Scholar
  155. Lee K. (2004) There is biodiversity and biodiversity: implications for environmental philosophers. In: Oksanen M., Pietarinen J. (eds) Philosophy and Biodiversity. CUP, NY, pp. 152–171Google Scholar
  156. Lee M.S., Morrison D.A. (1999) Identification of a new regulator in Streptococcus pneumoniae linking quorum sensing to competence for genetic transformation. J. Bacteriol. 181: 5004–5016Google Scholar
  157. Levin B.R., Bergstrom C.T. (2000) Bacteria are different: observations, interpretations, speculations, and opinions about the mechanisms of adaptive evolution in prokaryotes. PNAS 97: 6951–6985Google Scholar
  158. Lewis C.S. (1945) That Hideous Strength. Scribner, NYGoogle Scholar
  159. Lewis K. (2000) Programmed death in bacteria. Microbiol. Mol. Biol. Rev. 64: 503–514Google Scholar
  160. Lloyd D. (2004) ‘Anaerobic protists’: some misconceptions and confusions. Microbiology 150: 1115–1116Google Scholar
  161. Lloyd E.A. (1989) A structural approach to defining units of selection. Philos. Sci. 56: 395–418Google Scholar
  162. Lloyd E.A. (2000) Groups on groups: some dynamics and possible resolution of the units of selection debates in evolutionary biology. Biol. Philos. 15: 389–401Google Scholar
  163. Looijen R.C. (2000) Holism and Reductionism in Biology and Ecology: The Mutual Dependence of Higher and Lower Level Research Programmes. Kluwer, DordrechtGoogle Scholar
  164. Loreau M., Naeem S., Inchausti P. et al. (2001) Biodiversity and ecosystem functioning: current knowledge and future challenges. Science 294: 804–808Google Scholar
  165. Luria S.E. (1947) Recent advances in bacterial genetics. J. Bacteriol. 11: 1–40Google Scholar
  166. Luria S.E., Darnell J.E., Baltimore D., Campbell A. (eds) (1978) General Virology (3rd edn.). John Wiley & Sons, NYGoogle Scholar
  167. Luria S.E., Delbrück M. (1943) Mutations of bacteria from virus sensitivity to virus resistance. Genetics 28: 491–511Google Scholar
  168. Magasanik B. (1999) A midcentury watershed: the transition from microbial biochemistry to molecular biology. J. Bacteriol. 181: 357–358Google Scholar
  169. Maier R.M., Pepper I.L., Gerba C.P. (2000) Environmental Microbiology. Academic Press, San DiegoGoogle Scholar
  170. Manchester K.L. (2000) Biochemistry comes of age: a century of endeavour. Endeavour 24: 22–27Google Scholar
  171. Margulis L. (1970) Origin of Eukaryotic Cells. Yale University Press, New HavenGoogle Scholar
  172. Martin W., Russell M.J. (2003) On the origin of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Philos. Trans. Roy. Soc. London B. 358: 59–85Google Scholar
  173. Martiny J.B.H., Bohannan B.J.M., Brown J.H. et al. (2006) Microbial biogeography: putting microorganisms on the map. Nat. Rev. Microbiol. 4: 102–112Google Scholar
  174. Maynard Smith J. (1995) Do bacteria have population genetics? In: Baumberg S., Young J.P.W., Saunders J.R., Wellington E.M.H. (eds) Population Genetics of Bacteria, Society for General Microbiology Symposium 52. CUP, Cambridge, pp. 1–12Google Scholar
  175. Maynard Smith J., Feil E.J., Smith N.H. (2000) Population structure and evolutionary dynamics of pathogenic bacteria. BioEssays 22: 1115–1122Google Scholar
  176. Maynard Smith J., Smith N.H., O’Rourke M., Spratt B.G. (1993) How clonal are bacteria? Proc. Nat. Acad. Sci. 90: 4384–4388Google Scholar
  177. Maynard Smith J. and Szathmáry, E. 1995. The Major Transitions in Evolution. W. H. Freeman, NYGoogle Scholar
  178. Mayr E. (1998) Two empires or three? PNAS 95: 9720–9723Google Scholar
  179. McFall-Ngai M.J. (2001) Identifying ‘prime suspects’: symbioses and the evolution of multicellularity. Compar. Biochem.Physiol. Part B 129: 711–723Google Scholar
  180. McFall-Ngai M.J. (2002) Unseen forces: the influence of bacteria on animal development. Develop. Biol. 242: 1–14Google Scholar
  181. McShea D.W. (2004) A revised Darwinism. Biol. Philos. 19: 45–53Google Scholar
  182. Medini D., Donati C., Tettelin H. et al. (2005) The microbial pan-genome. Curr. Opin. Genet. Develop. 15: 589–594Google Scholar
  183. Michod R.E. (1997a) Cooperation and conflict in the evolution of individuality. I. Multilevel selection of the organism. Am. Nat. 149: 607–645Google Scholar
  184. Michod R.E. (1997b) Evolution of the individual. Am. Nat. 150: S5–S21Google Scholar
  185. Miller M.B., Bassler B.L. (2001) Quorum sensing in bacteria. Annu. Rev. Microbiol. 55: 165–199Google Scholar
  186. Molin S., Tolker-Nielsen T. (2003) Gene transfer occurs with enhanced efficiency in biofilms and induces stabilisation of the biofilm structure. Curr.Opin. Biotechnol. 14: 255–261Google Scholar
  187. Myers G., Paulsen I., Fraser C. (2006) The role of mobile DNA in the evolution of prokaryotic genomes. In: Caporale L.H. (eds) The Implicit Genome. OUP, Oxford, pp. 121–137Google Scholar
  188. Nanney D. (1999) When is a rose?: the kinds of Tetrahymena. In: Wilson R.A. (eds) Species: New Unterdisciplinary Essays. MIT Press, Cambridge, MA, pp. 97–118Google Scholar
  189. Nee S. (2004) More than meets the eye. Nature 429: 804–805Google Scholar
  190. Nee S. (2005) The great chain of being. Nature 435: 429Google Scholar
  191. Newman D.K., Banfield J.F. (2002) Geomicrobiology: how molecular scale interactions underpin biogeochemical systems. Science 296: 1071–1077Google Scholar
  192. Nisbet E.G., Sleep N.H. (2001) The habitat and nature of early life. Nature 409: 1083–1091Google Scholar
  193. Ochman H., Lawrence J.G., Groisman E.A. (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299–304Google Scholar
  194. O’Donnell A.G., Goodfellow M., Hawksworth D.L. (1994) Theoretical and practical aspects of the quantification of biodiversity among microorganisms. Philos.Trans. Roy. Soc. London B 345: 65–73Google Scholar
  195. Okasha S. (2003) Recent work on the levels of selection problem. Human Nat. Rev. 3: 349–356Google Scholar
  196. Okasha, S. 2004. Multi-level selection and the major transitions in evolution. Proceedings PSA 19th Biennial Meeting – PSA 2004: PSA Contributed Papers, Austin, Texas, PSAGoogle Scholar
  197. Oksanen M., Pietarinen J. (2004) Philosophy and Biodiversity. CUP, NYGoogle Scholar
  198. Olsen G.J., Lane D.J., Giovannoni S.J., Pace N.R. (1986) Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40: 337–365Google Scholar
  199. Olsen G.J., Woese C.R., Overbeek R. (1994) The winds of (evolutionary) change: breathing new life into microbiology. J. Bacteriol. 176: 1–6Google Scholar
  200. O’Malley M.A., Boucher Y. (2005) Paradigm change in evolutionary microbiology. Stud. Hist. Philos. Biol. Biomed. Sci. 36: 183–208Google Scholar
  201. O’Toole G., Kaplan H.B., Kolter R. (2000) Biofilm formation as microbial development. Annu. Rev. Microbiol. 54: 49–79Google Scholar
  202. Pääbo S. (2001) The human genome and our view of ourselves. Science 291: 1219–1220Google Scholar
  203. Pace N.R. (1997) A molecular view of microbial diversity and the biosphere. Science 276: 734–740Google Scholar
  204. Palys T., Nakamura L.K., Cohan F.M. (1997) Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data. Int. J. Syst. Bacteriol. 47: 1145–1156CrossRefGoogle Scholar
  205. Papke R.T., Ward D.M. (2004) The importance of physical isolation to microbial diversification. FEMS Microbiol. Ecol. 48: 293–303Google Scholar
  206. Park S., Wolanin P.M., Yuzbashyan E.A., Silberzan P., Stock J.B., Austin R.H. (2003) Motion to form a quorum. Science 301: 188Google Scholar
  207. Parker V.T. (2004) The community of an individual: implications for the community concept. Oikos 104: 27–34Google Scholar
  208. Parsek M.R., Fuqua C. (2004) Biofilms 2003: emerging themes and challenges in studies of surface-associated microbial life. J. Bacteriol. 186: 4427–4440Google Scholar
  209. Pauling L., Zuckerkandl E. (1963) Chemical paleogenetics: molecular “restoration studies” of extinct forms of life. Acta Chem. Scand. 17: S9–S16CrossRefGoogle Scholar
  210. Penn M., Dworkin M. (1976) Robert Koch and two visions of microbiology. Bacteriol. Rev. 40: 276–283Google Scholar
  211. Peterson S.N., Sung C.K., Kline R. et al. (2004) Identification of competence pheromone responsive genes in Streptococcus pneumoniae by use of DNA microarrays. Mol. Microbiol. 51: 1051–1070Google Scholar
  212. Postgate J.R. (1976) Death in macrobes and microbes. In: Gray T.R.G., Postgate J.R. (eds) The Survival of Vegetative Microbes. Cambridge University Press, Cambridge, pp. 1–18Google Scholar
  213. Price P.B. (2000) A habitat for psychrophiles in deep Antarctic ice. PNAS 97: 1247–1251Google Scholar
  214. Queller D.C. (2004) Kinship is relative. Nature 430: 975–976Google Scholar
  215. Raoult D., Audic S., Robert C. et al. (2004) The 1.2-megabase genome sequence of Mimivirus. Science 306: 1344–1350Google Scholar
  216. Reanney D.C., Roberts W.P., Kelly W.J. (1982) Genetic interactions among microbial communities. In: Bull A.T., Slater J.H. (eds) Microbial Interactions and Communities. Academic Press, London, UK, pp. 287–322Google Scholar
  217. Redfield R.J. (2002) Is quorum sensing a side effect of diffusion sensing? Trends Microbiol. 10: 365–370Google Scholar
  218. Relman D.A., Falkow S. (2001) The meaning and impact of the human genome sequence for microbiology. Trends Microbiol. 9: 206–208Google Scholar
  219. Rice K.C., Bayles K.W. (2003) Death’s toolbox, examining the molecular components of bacterial programmed cell death. Mol. Microbiol. 50: 729–738Google Scholar
  220. Riesenfeld C.S., Schloss P.D., Handelsman J. (2004) Metagenomics: genomic analysis of microbial communities. Annu. Rev. Genet. 38: 525–552Google Scholar
  221. Robert J.S. (2004) Embryology, Epigenesis, and Evolution: Taking Development Seriously. CUP, CambridgeGoogle Scholar
  222. Rodríguez-Valera F. (2002) Approaches to prokaryotic diversity: a population genetics approach. Environ. Microbiol. 4: 628–633Google Scholar
  223. Rodríguez-Valera F. (2004) Environmental genomics: the big picture. FEMS Microbiol. Lett. 231: 153–158Google Scholar
  224. Rohwer F. (2003) Global phage diversity. Cell 113: 141Google Scholar
  225. Roselló-Mora R., Amann R. (2001) The species concept for prokaryotes. FEMS Microbiol. Rev. 25: 39–67Google Scholar
  226. Sapp J. (1987) Beyond the Gene: Cytoplasmic Inheritance and the Struggle for Authority in Genetics. OUP, NYGoogle Scholar
  227. Sapp J. (2003) Genesis: The Evolution of Biology. OUP, OxfordGoogle Scholar
  228. Sapp J. (2005) The prokaryote-eukaryote dichotomy: meanings and mythology. Microbiol. Mol. Biol. Rev. 69: 292–305Google Scholar
  229. Sarkar S. (2002) Defining “biodiversity”: assessing biodiversity. Monist 85: 131–155Google Scholar
  230. Saunders N.J., Boonmee P., Peden J.F., Jarvis S.A. (2005) Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori. BMC Genomics 6(1): 9Google Scholar
  231. Savage D.C. (1977) Microbial ecology of the gastrointestinal tract. Annu. Rev. Microbiol. 31: 107–133Google Scholar
  232. Schloss P.D., Handelsman J. (2004) Status of the microbial census. Microbiol. Mol. Biol. Rev. 68: 686–691Google Scholar
  233. Schmeisser C., Stöckigt C., Raasch C. et al. (2003) Metagenome survery of biofilms in drinking-water networks. Appl. Environ. Microbiol. 69: 7298–7309Google Scholar
  234. Schoolnik G.K. (2001) The accelerating convergence of genomics and microbiology. Genome Biol. 2: 4009.1–4009.2Google Scholar
  235. Schulz H.N., Jørgensen B.B. (2001) Big bacteria. Annu. Rev. Microbiol. 55: 105–137Google Scholar
  236. Shapiro J.A. (1997) Multicellularity: the rule, not the exception. In: Shapiro J.A., Dworkin M. (eds) Bacteria as Multicellular Organisms. OUP, NY, pp. 14–49Google Scholar
  237. Shapiro J.A. (1998) Thinking about bacterial populations as multicellular organisms. Annu. Rev. Microbiol. 52: 81–104Google Scholar
  238. Shapiro J.A., Dworkin M. (eds) (1997) Bacteria as Multicellular Organisms. OUP, NYGoogle Scholar
  239. Shimkets L.J. (1999) Intercellular signalling during fruiting-body development of Myxococcus xanthus. Annu. Rev. Microbiol. 53: 525–549Google Scholar
  240. Shimkets L.J., Brun Y.V. (2000) Prokaryotic development: strategies to enhance survival. In: Brun Y.V., Shimkets L.J. (eds) Prokaryotic Development. ASM Press, Washington, DCGoogle Scholar
  241. Shiner E.K., Rumbaugh K.P., Williams S.C. (2005) Interkingdom signaling: deciphering the language of acyl homoserine lactones. FEMS Microbiol. Rev. 29: 935–947Google Scholar
  242. Simpson A.G.B., Roger A.J. (2004) The real ‘kingdoms’ of eukaryotes. Curr. Biol. 14: R693–R696Google Scholar
  243. Slater J.H., Bull A.T. (1978) Interactions between microbial populations. In: Bull A.T., Meadow P.M. (eds) Companion to Microbiology: Selected Topics for Further Study. Longman, London, pp. 181–206Google Scholar
  244. Sober E., Wilson D.S. (1994) A critical review of philosophical work on the units of selection problem. Philos. Sci. 61: 534–555Google Scholar
  245. Solomon J.M., Grossman A.D. (1996) Who’s competent and when: regulation of natural competence in bacteria. Trends Genet. 12: 150–155Google Scholar
  246. Sonea S., Mathieu L.G. (2001) Evolution of the genomic systems of prokaryotes and its momentous consequences. Int. Microbiol. 4: 67–71Google Scholar
  247. Stackebrandt E., Frederisksen W., Garrity G.M. et al. (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int. J. Syst. Evol. Microbiol. 52: 1043–1047Google Scholar
  248. Staley J.T. (1997) Biodiversity: are microbial species threatened? Curr. Opin. Biotechnol. 8: 340–345Google Scholar
  249. Stahl D.A., Lane D.J., Olsen G.J., Pace N.R. (1985) Characterization of a Yellowstone hot spring microbial community by 5S rRNA sequences. Appl. Environ. Microbiol. 49: 1379–1384Google Scholar
  250. Stahl D.A., Tiedje J.M. (2002) Microbial Ecology and Genomics: A Crossroads of Opportunity. American Academy of Microbiology, Washington, DCGoogle Scholar
  251. Staley J.T., Gosink J.J. (1999) Poles apart: biodiversity and biogeography of sea ice bacteria. Annu. Rev. Microbiol. 53: 189–215Google Scholar
  252. Staley J.T., Konopka A. (1985) Measurements of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu. Rev. Microbiol. 39: 321–346Google Scholar
  253. Stanier R.Y., Doudoroff M., Adelberg E.A. (1957) The Microbial World. Prentice-Hall, Englewood Cliffs, NJGoogle Scholar
  254. Stanier R.Y., Van Niel C.B. (1941) The main outlines of bacterial classification. J. Bacteriol. 42: 437–466Google Scholar
  255. Stanier R.Y., van Niel C.B. (1962) The concept of a bacterium. Archiv für Mikrobiol. 42: 17–35Google Scholar
  256. Sterelny K. (1999) Species as ecological mosaics. In: Wilson R.A. (eds) Species: New Interdisciplinary Essays. MIT Press, Cambridge, MA, pp. 119–138Google Scholar
  257. Sterelny K. (2004) Symbiosis, evolvability and modularity. In: Schlosser G., Wagner G.P. (eds) Modularity in Evolution and Development. University of Chicago Press, Chicago, pp. 490–518Google Scholar
  258. Sterelny K., Griffiths P.E. (1999) Sex and Death: An Introduction to the Philosophy of Biology. University of Chicago Press, ChicagoGoogle Scholar
  259. Stewart P.S., Costerton J.W. (2001) Antibiotic resistance of bacteria in biofilms. The Lancet 358: 135–138Google Scholar
  260. Stoodley P., Sauer K., Davies D.G., Costerton J.W. (2002) Biofilms as complex differentiated communities. Annu. Rev. Microbiol. 56: 187–209Google Scholar
  261. Summers W.C. (1991) From culture as organism to organism as cell: historical origins of bacterial genetics. J. Hist. Biol. 24: 171–190Google Scholar
  262. Suttle C.A. (2005) Viruses in the sea. Nature 437: 356–644Google Scholar
  263. Thomas C.M., Nielsen K.M. (2005) Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat. Rev. Microbiol. 3: 711–721Google Scholar
  264. Travisano M., Velicer G.J. (2004) Strategies of microbial cheater control. Trends Microbiol. 12: 72–78Google Scholar
  265. Tyson G.W., Chapman J., Hugenholz P. et al. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37–43Google Scholar
  266. Underwood A.J. (1996) What is a community? In: Raup D.M., Jablonski D. (eds) Patterns and Processes in the History of Life. Springer-Verlag, Berlin, pp. 351–367Google Scholar
  267. van Haastert P.J.M., Devreotes P.N. (2004) Chemotaxis: signalling the way forward. Nat. Rev. Mol. Cell Biol. 5: 626–634Google Scholar
  268. Vandamme P., Pot B., Gillis M. et al. (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol. Rev. 60: 407–438Google Scholar
  269. Velicer G.J. (2003) Social strife in the microbial world. Trends Microbiol. 11: 330–337Google Scholar
  270. Venter J.C., Remington K., Heidelberg J.F. et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66–74Google Scholar
  271. Villarreal L.P. (2004a) Are viruses alive? Sci. Am. 291: 100–105CrossRefGoogle Scholar
  272. Villarreal L.P. (2004b) Can viruses make us human? Proc. Am. Philos. Soc. 148: 296–323Google Scholar
  273. Visick K.L., Fuqua C. (2005) Decoding microbial chatter: cell-cell communication in bacteria. J. Bacteriol. 187: 5507–5519Google Scholar
  274. Wadhams G.H., Armitage J.P. (2004) Making sense of it all: bacterial chemotaxis. Nat. Rev. Mol. Cell Biol. 5: 1024–1037Google Scholar
  275. Waggoner B. (2001) Eukaryotes and multicells: origins, Encyclopedia of Life Sciences, http://www.els.net
  276. Wainwright M. (2003) An alternative view of the early history of microbiology. Adv. Appl. Microbiol. 52: 333–355Google Scholar
  277. Walsh D.A., Doolittle W.F. (2005) The real ‘domains’ of life. Curr. Biol. 15: R237–R240Google Scholar
  278. Ward B.B. (2002) How many species of prokaryotes are there? PNAS 99: 10234–10236Google Scholar
  279. Ward D.M. (1998) A natural species concept for prokaryotes. Curr. Opin. Microbiol. 1: 271–277Google Scholar
  280. Ward N., Fraser C.M. (2005) How genomics has affected the concept of microbiology. Curr. Opin. Microbiol. 8: 564–571Google Scholar
  281. Watnick P., Kolter R. (2000) Biofilm, city of microbes. J. Bacteriol. 182: 2675–2679Google Scholar
  282. Webb J.S., Givskov M., Kjelleberg S. (2003) Bacterial biofilms: prokaryotic adventures in multicellularity. Curr. Opin. Microbiol. 6: 578–585Google Scholar
  283. Webre D.J., Wolanin P.M., Stock J.B. (2003) Bacterial chemotaxis. Curr. Biol. 13: R47–R49Google Scholar
  284. Weinbauer M.G., Rassoulzadegan F. (2004) Are viruses driving microbial diversification and diversity? Environ. Microbiol. 6: 1–11Google Scholar
  285. Wertz J.E., Goldstone C., Gordon D.M., Riley M.A. (2003) A molecular phylogeny of enteric bacteria and implications for a bacterial species concept. J. Evol. Biol. 16: 1236–1248Google Scholar
  286. Whitaker R.J., Grogan D.W., Taylor J.W. (2003) Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301: 976–978Google Scholar
  287. Whitham T.G., Young W.P., Martinsen G.D. et al. (2003) Community and ecosystem genetics: a consequence of the extended phenotype. Ecology 84: 559–573Google Scholar
  288. Whitman W.B., Coleman D.C., Wiebe W.J. (1998) Prokaryotes: the unseen majority. PNAS 95: 6578–6583Google Scholar
  289. Wilkins J.S. (2003) How to be a chaste species pluralist-realist: the origin of species modes and the synapomorphic species concept. Biol. Philos.18: 621–638Google Scholar
  290. Wilson D.S. (1997) Altruism and organism: disentangling the themes of multilevel selection theory. Am. Nat. 150(Supplement): S122–S134Google Scholar
  291. Wimpenny J. (2000) An overview of biofilms as functional communities. In: Allison D.G., Gilbert P., Lappin-Scott H.M., Wilson M. (eds) Community Structure and Cooperation in Biofilms. CUP, Cambridge, pp. 1–24Google Scholar
  292. Woese C.R. (1987) Bacterial evolution. Microb. Rev. 51: 221–271Google Scholar
  293. Woese C.R. (2005) Evolving biological organization. In: Sapp J. (eds) Microbial Phylogeny and Evolution: Concepts and Controversies. OUP, Oxford, pp. 99–117Google Scholar
  294. Woese C.R., Fox G.G. (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. PNAS 11: 5088–5090Google Scholar
  295. Woese C.R., Kandler O., Wheelis M.L. (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. PNAS 87: 4576–4579Google Scholar
  296. Xu J., Gordon J.I. (2003) Honor thy symbionts. PNAS 100: 10452–10459Google Scholar
  297. Young J.M. (2001) Implications of alternative classifications and horizontal gene transfer for bacterial taxonomy. Int. J. Syst. Evol. Microbiol. 51: 945–953Google Scholar
  298. Zuckerkandl E., Pauling L. (1965) Molecules as documents of evolutionary history. J. Theoret. Biol. 8: 357–366Google Scholar

Copyright information

© Springer Science+Business Media, Inc. 2007

Authors and Affiliations

  1. 1.Egenis (ESRC Centre for Genomics in Society)University of ExeterExeterUK

Personalised recommendations