Microbial Ecology

, Volume 53, Issue 2, pp 197–207 | Cite as

Biogeography: An Emerging Cornerstone for Understanding Prokaryotic Diversity, Ecology, and Evolution

  • Alban RametteEmail author
  • James M. Tiedje


New questions about microbial ecology and diversity combined with significant improvement in the resolving power of molecular tools have helped the reemergence of the field of prokaryotic biogeography. Here, we show that biogeography may constitute a cornerstone approach to study diversity patterns at different taxonomic levels in the prokaryotic world. Fundamental processes leading to the formation of biogeographic patterns are examined in an evolutionary and ecological context. Based on different evolutionary scenarios, biogeographic patterns are thus posited to consist of dramatic range expansion or regression events that would be the results of evolutionary and ecological forces at play at the genotype level. The deterministic or random nature of those underlying processes is, however, questioned in light of recent surveys. Such scenarios led us to predict the existence of particular genes whose presence or polymorphism would be associated with cosmopolitan taxa. Furthermore, several conceptual and methodological pitfalls that could hamper future developments of the field are identified, and future approaches and new lines of investigation are suggested.


Lateral Gene Transfer Adaptive Mutant Biogeographic Pattern Cosmopolitan Distribution Biogeographic Study 
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.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.



We thank J. Fredrickson and Y. Cohen for the invitation to write this article and two anonymous reviewers for helpful comments.

We acknowledge support from NSF grant no. DEB-00755564, DOE Office of Science (BER) DE-FG02-98ER62535, and a postdoctoral fellowship from the Swiss NSF to A.R.


  1. 1.
    GCJ Abell and JP Bowman, Ecological and biogeographic relationships of class Flavobacteria in the Southern Ocean. FEMS Microbiol Ecol 51 (2005) 265-277PubMedCrossRefGoogle Scholar
  2. 2.
    RI Amann, W Ludwig, KH Schleifer, VL Torsvik and J Goksoyr, Phylogenetic identification and in situ detection of individual microbial-cells without cultivation. Microbiol Rev 59 (1995) 143-169PubMedGoogle Scholar
  3. 3.
    LGM Baas-Becking, Geobiologie of Inleiding Tot de Milieukunde. The Hague, The Netherlands: Van Stockkum & Zoon (1934).Google Scholar
  4. 4.
    N Bano, S Ruffin, B Ransom and JT Hollibaugh, Phylogenetic composition of Arctic Ocean archaeal assemblages and comparison with Antarctic assemblages. Appl Environ Microbiol 70 (2004) 781-789PubMedCrossRefGoogle Scholar
  5. 5.
    MW Beijerinck, De infusies en de ontdekking der backteriën, Jaarboek van de Koninklijke Akademie v. Wetenschoppen. Amsterdam, The Netherlands: Muller (1913).Google Scholar
  6. 6.
    BR Boles, M Thoendel and PK Singh, Self-generated diversity produces ‘insurance effects’ in biofilm communities. Proc Natl Acad Sci USA 101 (2004) 16630-16635PubMedCrossRefGoogle Scholar
  7. 7.
    JP Bowman, Psychrophilic prokaryote structural–functional relationships, biogeography and evolution within marine sediment. Cell Mol Biol 50 (2004) 503-515PubMedGoogle Scholar
  8. 8.
    JP Bowman and RD McCuaig, Biodiversity, community structural shifts, and biogeography of prokaryotes within Antarctic continental shelf sediment. Appl Environ Microbiol 69 (2003) 2463-2483PubMedCrossRefGoogle Scholar
  9. 9.
    JH Brown, VK Gupta, BL Li, BT Milne, C Restrepo and GB West, The fractal nature of nature: power laws, ecological complexity and biodiversity. Philos Trans R Soc Lond, B 357 (2002) 619-626CrossRefGoogle Scholar
  10. 10.
    RW Castenholz, The biogeography of hot spring algae through enrichment cultures. Mitt Int Ver Limnol 21 (1978) 296-315Google Scholar
  11. 11.
    JC Cho and JM Tiedje, Biogeography and degree of endemism of fluorescent Pseudomonas strains in soil. Appl Environ Microbiol 66 (2000) 5448-5456PubMedCrossRefGoogle Scholar
  12. 12.
    T Coenye, D Gevers, YV dePeer, P Vandamme and J Swings, Towards a prokaryotic genomic taxonomy. FEMS Microbiol Rev 29 (2005) 147-167PubMedCrossRefGoogle Scholar
  13. 13.
    FM Cohan, Concepts of bacterial biodiversity for the age of genomics. In: CM Fraser, TD Read and KE Nelson (eds.) Microbial Genomes. Totowa, NJ: Humana Press (2004) pp. 175-194Google Scholar
  14. 14.
    FM Cohan, What are bacterial species?. Annu Rev Microbiol 56 (2002) 457-487PubMedCrossRefGoogle Scholar
  15. 15.
    EE DeLong and NR Pace, Environmental diversity of Bacteria and Archaea. Syst Biol 50 (2001) 470-478PubMedCrossRefGoogle Scholar
  16. 16.
    JA Eastgate, Erwinia amylovora: the molecular basis of fireblight disease. Mol Plant Pathol 1 (2000) 325-329CrossRefGoogle Scholar
  17. 17.
    D Falush, T Wirth, B Linz, JK Pritchard, M Stephens, M Kidd, MJ Blaser, DY Graham, S Vacher, GI Perez-Perez, Y Yamaoka, F Megraud, K Otto, U Reichard, E Katzowitsch, XY Wang, M Achtman and S Suerbaum, Traces of human migrations in Helicobacter pylori populations. Science 299 (2003) 1582-1585PubMedCrossRefGoogle Scholar
  18. 18.
    EJ Feil and BG Spratt, Recombination and the population structures of bacterial pathogens. Annu Rev Microbiol 55 (2001) 561-590PubMedCrossRefGoogle Scholar
  19. 19.
    FO Glöckner, E Zaichikov, N Belkova, L Denissova, J Pernthaler, A Pernthaler and R Amann, Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria. Appl Environ Microbiol 66 (2000) 5053-5065PubMedCrossRefGoogle Scholar
  20. 20.
    JP Gogarten, WF Doolittle and JG Lawrence, Prokaryotic evolution in light of gene transfer. Mol Biol Evol 19 (2002) 2226-2238PubMedGoogle Scholar
  21. 21.
    DM Gordon, Geographical structure and host specificity in bacteria and implications for tracing the source of coliform contamination. Microbiology 147 (2001) 1079-1085PubMedGoogle Scholar
  22. 22.
    DW Griffin, CA Kellogg, VH Garrison and EA Shinn, The global transport of dust—an intercontinental river of dust, microorganisms and toxic chemicals flows through the Earth's atmosphere. Am Sci 90 (2002) 228-235CrossRefGoogle Scholar
  23. 23.
    GL Grundmann, Spatial scales of soil bacterial diversity—the size of a clone. FEMS Microbiol Ecol 48 (2004) 119-127CrossRefPubMedGoogle Scholar
  24. 24.
    GL Grundmann and D Debouzie, Geostatistical analysis of the distribution of NH4 + and NO2 − oxidizing bacteria and serotypes at the millimeter scale along a soil transect. FEMS Microbiol Ecol 34 (2000) 57-62PubMedGoogle Scholar
  25. 25.
    MW Hahn, Isolation of strains belonging to the cosmopolitan Polynucleobacter necessarius cluster from freshwater habitats located in three climatic zones. Appl Environ Microbiol 69 (2003) 5248-5254PubMedCrossRefGoogle Scholar
  26. 26.
    JM Halley, S Hartley, AS Kallimanis, WE Kunin, JJ Lennon and SP Sgardelis, Uses and abuses of fractal methodology in ecology. Ecol Lett 7 (2004) 254-271CrossRefGoogle Scholar
  27. 27.
    BP Hedlund and JT Staley, Microbial endemism and biogeography. In: AT Bull (ed.) Microbial Diversity and Bioprospecting. Washington, DC: ASM Press (2003) pp. 225-231Google Scholar
  28. 28.
    MC Horner-Devine, M Lage, JB Hughes and BJM Bohannan, A taxa–area relationship for bacteria. Nature 432 (2004) 750-753PubMedCrossRefGoogle Scholar
  29. 29.
    MC Horner-Devine, KM Carney and BJM Bohannan, An ecological perspective on bacterial biodiversity. Proc R Soc Lond, B 271 (2003) 113-122CrossRefGoogle Scholar
  30. 30.
    SP Hubbell, The Unified Neutral Theory of Biodiversity and Biogeography. Princeton Monographs in Population Biology. Princeton, NJ,: Princeton University Press (2001).Google Scholar
  31. 31.
    R Huber, P Stoffers, JL Cheminee, HH Richnow and KO Stetter, Hyperthermophilic archaebacteria within the crater and open-sea plume of erupting Macdonald Seamount. Nature 345 (1990) 179-181CrossRefGoogle Scholar
  32. 32.
    E Jaspers and J Overmann, Ecological significance of microdiversity: identical 16 S rRNA gene sequences can be found in bacteria with highly divergent genomes and ecophysiologies. Appl Environ Microbiol 70 (2004) 4831-4839PubMedCrossRefGoogle Scholar
  33. 33.
    CM Jessup, R Kassen, SE Forde, B Kerr, A Buckling, PB Rainey and BJM Bohannan, Big questions, small worlds: microbial model systems in ecology. Trends Ecol Evol 19 (2004) 189-197PubMedCrossRefGoogle Scholar
  34. 34.
    A Johansson, J Farlow, P Larsson, M Dukerich, E Chambers, M Bystrom, J Fox, M Chu, M Forsman, A Sjostedt and P Keim, Worldwide genetic relationships among Francisella tularensis isolates determined by Multiple-Locus Variable-Number Tandem Repeat analysis. J Bacteriol 186 (2004) 5808-5818PubMedCrossRefGoogle Scholar
  35. 35.
    KT Konstantinidis and JM Tiedje, Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 102 (2005) 2567-2572PubMedCrossRefGoogle Scholar
  36. 36.
    R Lan and PR Reeves, When does a clone deserve a name? A perspective on bacterial species based on population genetics. Trends Microbiol 9 (2001) 419-424PubMedCrossRefGoogle Scholar
  37. 37.
    JG Lawrence, Gene transfer in bacteria: speciation without species?. Theor Popul Biol 61 (2002) 449-460PubMedCrossRefGoogle Scholar
  38. 38.
    P Legendre and L Legendre, Numerical Ecology. Amsterdam: Elsevier (1998).Google Scholar
  39. 39.
    MA Leibold, M Holyoak, N Mouquet, P Amarasekare, MF Chase, MF Hoopes, RD Holt, JB Shurin, R Law, D Tilman, M Loreau and A Gonzalez, The metacommunity concept: a framework for multi-scale community ecology. Ecol Lett 7 (2004) 601-613CrossRefGoogle Scholar
  40. 40.
    AM Liebhold and J Gurevitch, Integrating the statistical analysis of spatial data in ecology. Ecography 25 (2002) 553-557CrossRefGoogle Scholar
  41. 41.
    MV Lomolino, A call for a new paradigm of island biogeography. Glob Ecol Biogeogr 9 (2000) 1-6CrossRefGoogle Scholar
  42. 42.
    RH MacArthur and EO Wilson, The Theory of Island Biogeography. Princeton, NJ: Princeton University Press (1967).Google Scholar
  43. 43.
    MCJ Maiden, JA Bygraves, E Feil, G Morelli, JE Russell, R Urwin, Q Zhang, JJ Zhou, K Zurth, DA Caugant, IM Feavers, M Achtman and BG Spratt, Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci USA 95 (1998) 3140-3145PubMedCrossRefGoogle Scholar
  44. 44.
    R Massana, EF DeLong and C Pedros-Alio, A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces. Appl Environ Microbiol 66 (2000) 1777-1787PubMedCrossRefGoogle Scholar
  45. 45.
    J Maynard Smith, CG Dowson and BG Spratt, Localized sex in bacteria. Nature 349 (1991) 29-31CrossRefGoogle Scholar
  46. 46.
    S Molin and M Givskov, Application of molecular tools for insitu monitoring of bacterial activity. Environ Microbiol 1 (1999) 383-391PubMedCrossRefGoogle Scholar
  47. 47.
    JM Musser, Molecular population genetic analysis of emerged bacterial pathogens: selected insights. Emerg Infect Dis 2 (1996) 1-17PubMedCrossRefGoogle Scholar
  48. 48.
    G Muyzer, Structure, function and dynamics of microbial communities: the molecular biological approach. In: GR Carvalho (ed.) Advances in Molecular Ecology. Amsterdam: IOS Press (1998) pp. 87-117Google Scholar
  49. 49.
    S Nee, EC Holmes, RM May and PH Harvey, Extinction rates can be estimated from molecular phylogenies. Philos Trans R Soc Lond, B 344 (1994) 77-82CrossRefGoogle Scholar
  50. 50.
    GW Nicol, LA Glover and JI Prosser, Spatial analysis of archaeal community structure in grassland soil. Appl Environ Microbiol 69 (2003) 7420-7429PubMedCrossRefGoogle Scholar
  51. 51.
    H Ochman and SR Santos, Exploring microbial microevolution with microarrays. Infect Genet Evol 5 (2005) 103-108PubMedCrossRefGoogle Scholar
  52. 52.
    H Ochman, JG Lawrence and EA Groisman, Lateral gene transfer and the nature of bacterial innovation. Nature 405 (2000) 299-304PubMedCrossRefGoogle Scholar
  53. 53.
    RT Papke and DM Ward, The importance of physical isolation to microbial diversification. FEMS Microbiol Ecol 48 (2004) 293-303CrossRefPubMedGoogle Scholar
  54. 54.
    RT Papke, NB Ramsing, MM Bateson and DM Ward, Geographical isolation in hot spring cyanobacteria. Environ Microbiol 5 (2003) 650-659PubMedCrossRefGoogle Scholar
  55. 55.
    JLW Rademaker, FJ Louws and FJ Bruijn De, Characterization of the diversity of ecologically important microbes by rep-PCR genomic fingerprinting. Mol Microb Ecol Man. 3.4.3 (1998) 1-27Google Scholar
  56. 56.
    A Ramette, JJ LiPuma and JM Tiedje, Species abundance and diversity of Burkholderia cepacia complex in the environment. Appl Environ Microbiol 71 (2005) 1193-1201PubMedCrossRefGoogle Scholar
  57. 57.
    EM Rauch and Y Bar-Yam, Theory predicts the uneven distribution of genetic diversity within species. Nature 431 (2004) 449-452PubMedCrossRefGoogle Scholar
  58. 58.
    E Rejmánková, J Komárek and J Komárková, Cyanobacteria—a neglected component of biodiversity: patterns of species diversity ininland marshes of northern Belize (Central America). Divers Distrib 10 (2004) 189-199CrossRefGoogle Scholar
  59. 59.
    MS Roberts and FM Cohan, Recombination and migration rates in natural populations of Bacillus subtilis and Bacillus mojavensis. Evolution 49 (1995) 1081-1094CrossRefGoogle Scholar
  60. 60.
    R Rosselló-Mora and R Amann, The species concept for prokaryotes. FEMS Microbiol Rev 25 (2001) 39-67PubMedCrossRefGoogle Scholar
  61. 61.
    SR Santos and H Ochman, Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins. Environ Microbiol 6 (2004) 754-759PubMedCrossRefGoogle Scholar
  62. 62.
    LM Schouls, HGJ Heide van der, L Vauterin, P Vauterin and FR Mooi, Multiple-Locus Variable-Number Tandem Repeat analysis of Dutch Bordetella pertussis strains reveals rapid genetic changes with clonal expansion during the late 1990s. J Bacteriol 186 (2004) 5496-5505PubMedCrossRefGoogle Scholar
  63. 63.
    V Souza, TT Nguyen, RR Hudson, D Pinero and RE Lenski, Hierarchical analysis of linkage disequilibrium in rhizobium populations: evidence for sex. Proc Natl Acad Sci USA 89 (1992) 8389-8393PubMedCrossRefGoogle Scholar
  64. 64.
    E Stackebrandt, W Frederiksen, GM Garrity, PAD Grimont, P Kämpfer, MCJ Maiden, X Nesme, R Rosselló-Mora, J Swings, HG Trüper, L Vauterin, AC Ward and WB Whitman, Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52 (2002) 1043-1047PubMedCrossRefGoogle Scholar
  65. 65.
    JT Staley and JJ Gosink, Poles apart: biodiversity and biogeography of sea ice bacteria. Annu Rev Microbiol 53 (1999) 189-215PubMedCrossRefGoogle Scholar
  66. 66.
    V Torsvik, L Ovreas and TF Thingstad, Prokaryotic diversity: magnitude, dynamics, and controlling factors. Science 296 (2002) 1064-1066PubMedCrossRefGoogle Scholar
  67. 67.
    DS Treves, B Xia, J Zhou and JM Tiedje, A two-species test of the hypothesis that spatial isolation influences microbial diversity in soil. Microb Ecol 45 (2003) 20-28PubMedCrossRefGoogle Scholar
  68. 68.
    A Belkum van, M Struelens, A Visser de, H Verbrugh and M Tibayrenc, Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology. Clin Microbiol Rev 14 (2001) 547-560PubMedCrossRefGoogle Scholar
  69. 69.
    P Vandamme, B Pot, M Gillis, P Vos de, K Kersters and J Swings, Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60 (1996) 407-438PubMedGoogle Scholar
  70. 70.
    P Vinuesa, C Silva, D Werner and E Martínez-Romero, Population genetics and phylogenetic inference in bacterial molecular systematics: the roles of migration and recombination in Bradyrhizobium species cohesion and delineation. Mol Phylogenet Evol 34 (2005) 29-54PubMedCrossRefGoogle Scholar
  71. 71.
    DM Ward, A natural species concept for prokaryotes. Curr Opin Microbiol 1 (1998) 271-277PubMedCrossRefGoogle Scholar
  72. 72.
    DM Ward, R Weller and MM Bateson, 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345 (1990) 63-65PubMedCrossRefGoogle Scholar
  73. 73.
    LG Wayne, DJ Brenner, RR Colwell, PAD Grimont, O Kandler, L Krichevsky, LH Moore, C Moore, RGE Murray, MP Stackebrandt, MP Starr and HG Trüper, Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37 (1987) 463-464CrossRefGoogle Scholar
  74. 74.
    RJ Whitaker, DW Grogan and JT Taylor, Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301 (2003) 976-978PubMedCrossRefGoogle Scholar
  75. 75.
    D White, T Phelps and T Onstott, What's up down there?. Curr Opin Microbiol 1 (1998) 286-290PubMedCrossRefGoogle Scholar
  76. 76.
    M Wilson, HL Campbell, P Ji, JB Jones and DA Cuppels, Biological control of bacterial speck of tomato under field conditions at several locations in north America. Phytopathology 92 (2002) 1284-1292PubMedGoogle Scholar
  77. 77.
    L Wu, DK Thompson, X Liu, MW Fields, CE Bagwell, JM Tiedje and JM Zhou, Development and evaluation of microarray-based whole-genome hybridization for detection of microorganisms within the context of environmental applications. Environ Sci Technol 38 (2004) 6775-6782PubMedCrossRefGoogle Scholar
  78. 78.
    Q Yu, AM Alvarez, PH Moore, F Zee, MS Kim, A Silva de, PR Hepperly and R Ming, Molecular diversity of Ralstonia solanacearum isolated from ginger in Hawaii. Phytopathology 93 (2003) 1124-1130PubMedGoogle Scholar
  79. 79.
    JZ Zhou, BC Xia, DS Treves, LY Wu, TL Marsh, RV O'Neill, AV Palumbo and JM Tiedje, Spatial and resource factors influencing high microbial diversity in soil. Appl Environ Microbiol 68 (2002) 326-334PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  1. 1.Center for Microbial EcologyMichigan State UniversityEast LansingUSA
  2. 2.Max Planck Institute for Marine MicrobiologyBremenGermany

Personalised recommendations