Microbial biogeography: putting microorganisms on the map

Key Points

  • Since the eighteenth century, biologists have investigated plant and animal biogeography, but only recently have the distributions of microorganisms been examined.

  • We consider microbial biogeography in light of habitats types (the contemporary environment) and provinces (legacies of historical events such as dispersal limitation). This framework is useful for addressing whether the distributions of microbial taxa, like those of macroorganisms, reflect the influences of both contemporary environmental conditions and past events.

  • We review a growing body of literature that suggests that microbial assemblages are not only influenced by their current environment, but that some display a degree of provincialism — evidence that these microbial assemblages have diverged and are maintained by genetic isolation. We also find that the relative influence of historical versus environmental factors appears to be related to the scale of sampling.

  • As a first hypothesis, we suggest that the same processes that influence macroorganism biogeography (colonization, diversification and extinction) also apply to microbial life, but that their rates scale with body size, or for single-celled organisms, cell size. Therefore, we use the idea of allometry as a structure for discussing the rates of biogeographic processes in microorganisms.

  • We conclude that the rates of biogeographic processes probably vary more widely for microorganisms of a given size than for macroorganisms of a given size.

  • To tackle the mechanisms generating microbial biogeographic patterns, we recommend that new microbial biogeography studies should systematically sample and record data from various distances, habitats and environmental conditions.

Abstract

We review the biogeography of microorganisms in light of the biogeography of macroorganisms. A large body of research supports the idea that free-living microbial taxa exhibit biogeographic patterns. Current evidence confirms that, as proposed by the Baas-Becking hypothesis, 'the environment selects' and is, in part, responsible for spatial variation in microbial diversity. However, recent studies also dispute the idea that 'everything is everywhere'. We also consider how the processes that generate and maintain biogeographic patterns in macroorganisms could operate in the microbial world.

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Figure 1: Assessing the contributions of environmental and historical effects on microbial biogeography.
Figure 2: Hypothetical relationship between body mass (at an organism's largest life stage) and lifetime dispersal capability.
Figure 3: Hypothetical dispersal distribution of a typical passively dispersed macroorganism.
Figure 4: Hypothesized constraints on a taxon's population density in a given body-size class.
Figure 5: Hypothesized constraints on an organism's geographic-range size for a given body mass.
Figure 6: Hypothesized relationships between number of species and body mass.

References

  1. 1

    Brown, J. H. & Lomolino, M. V. Biogeography (Sinauer, Sunderland, 1998). A definitive textbook on the biogeography of macroorganisms; has just been updated in a 2005 edition.

    Google Scholar 

  2. 2

    Ward, D. M., Weller, R. & Bateson, M. M. 16S ribosomal-RNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345, 63–65 (1990).

    CAS  PubMed  Google Scholar 

  3. 3

    Øvreås, L. Population and community level approaches for analysing microbial diversity in natural environments. Ecol. Lett. 3, 236–251 (2000).

    Google Scholar 

  4. 4

    Floyd, M. M., Tang, J., Kane, M. & Emerson, D. Captured diversity in a culture collection: case study of the geographic and habitat distributions of environmental isolates held at the American type culture collection. Appl. Environ. Microbiol. 71, 2813–2823 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. 5

    Schloss, P. D. & Handelsman, J. Status of the microbial census. Microbiol. Mol. Biol. Rev. 68, 686–691 (2004).

    PubMed  PubMed Central  Google Scholar 

  6. 6

    Venter, J. C. et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66–74 (2004).

    CAS  Article  Google Scholar 

  7. 7

    Fenchel, T., Esteban, G. F. & Finlay, B. J. Local versus global diversity of microorganisms: cryptic diversity of ciliated protozoa. Oikos 80, 220–225 (1997).

    Google Scholar 

  8. 8

    Staley, J. T. Biodiversity: are microbial species threatened? Curr. Opin. Biotechnol. 8, 340–345 (1997).

    CAS  PubMed  Google Scholar 

  9. 9

    Finlay, B. J. Global dispersal of free-living microbial eukaryote species. Science 296, 1061–1063 (2002). A summary of the arguments for why microbial eukaryotes might not be restricted by geographic barriers.

    CAS  PubMed  PubMed Central  Google Scholar 

  10. 10

    Hedlund, B. P. & Staley, J. T. Microbial endemism and biogeography. In Microbial Diversity and Bioprospecting (ed. Bull, A. T.) (ASM, Washington DC, 2003).

    Google Scholar 

  11. 11

    Anagnostakis, S. Chestnut blight: the classical problem of an introduced pathogen. Mycologia 79, 23–27 (1987).

  12. 12

    Falush, D. et al. Traces of human migrations in Helicobacter pylori populations. Science 299, 1582–1585 (2003).

  13. 13

    Breitbart, M. & Rohwer, F. Here a virus, there a virus, everywhere the same virus? Trends Microbiol. 13, 278–284 (2005).

    CAS  Google Scholar 

  14. 14

    de Candolle, A. P. Essai Elementaire de Geographie Botanique (F. G. Levrault, Paris, 1820).

    Google Scholar 

  15. 15

    Beijerinck, M. W. De infusies en de ontdekking der backteriën. In Jaarboek van de Koninklijke Akademie van Wetenschappen (Müller, Amsterdam, 1913).

    Google Scholar 

  16. 16

    Baas-Becking, L. G. M. Geobiologie of Inleiding Tot de Milieukunde (Van Stockkum & Zoon, The Hague, 1934).

    Google Scholar 

  17. 17

    Zhang, N. & Blackwell, M. Population structure of dogwood anthracnose fungus. Phytopathology 92, 1276–1283 (2002).

    CAS  PubMed  Google Scholar 

  18. 18

    Bala, A., Murphy, P. & Giller, K. E. Distribution and diversity of rhizobia nodulating agroforestry legumes in soils from three continents in the tropics. Mol. Ecol. 12, 917–929 (2003).

    CAS  PubMed  Google Scholar 

  19. 19

    Papke, R. T. & Ward, D M. The importance of physical isolation to microbial diversification. FEMS Microbiol. Ecol. 48, 293–303 (2004). A recent review discussing how physical isolation might affect prokaryote evolution.

    CAS  PubMed  Google Scholar 

  20. 20

    Cho, J. C. & Tiedje, J. M. Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil. Appl. Environ. Microbiol. 66, 5448–5456 (2000). One of the first examples of relating the genetic similarity of a free-living bacterial assemblage with geographic distance, using fluorescent Pseudomonas isolates.

    CAS  PubMed  PubMed Central  Google Scholar 

  21. 21

    Oda, Y., Star, B., Huisman, L. A., Gottschal, J. C. & Forney, L. J. Biogeography of the purple nonsulfur bacterium Rhodopseudomonas palustris. Appl. Environ. Microbiol. 69, 5186–5191 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. 22

    Crump, B. C., Hopkinson, C. S., Sogin, M. L. & Hobbie, J. E. Microbial biogeography along an estuarine salinity gradient: combined influences of bacterial growth and residence time. Appl. Environ. Microbiol. 70, 1494–1505 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. 23

    Øvreås, L., Forney, L., Daae, R. L. & Torsvik, V. Distribution of bacterioplankton in meromictic Lake Sælenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl. Environ. Microbiol. 63, 3367–3373 (1997).

    PubMed  PubMed Central  Google Scholar 

  24. 24

    Schwalbach, M. S., Hewson, I. & Fuhrman, J. A. Viral effects on bacterial community composition in marine plankton microcosms. Aquat. Microb. Ecol. 34, 117–127 (2004).

    Google Scholar 

  25. 25

    Rosenzweig, M. L. Species Diversity in Space and Time. (Cambridge University Press, Cambridge, 1995).

    Google Scholar 

  26. 26

    Green, J. L. et al. Spatial scaling of microbial eukaryote diversity. Nature 432, 747–750 (2004). Along with reference 27, this study uses distance–decay curves to demonstrate non-random bacterial-assemblage distributions; the studies then test whether the non-random distributions are due to isolation by distance and/or local environmental conditions.

    CAS  Google Scholar 

  27. 27

    Horner-Devine, M. C., Lage, M., Hughes, J. B. & Bohannan, B. J. M. A taxa–area relationship for bacteria. Nature 432, 750–753 (2004).

    CAS  Google Scholar 

  28. 28

    Noguez, A. M. et al. Microbial macroecology: highly structured prokaryotic soil assemblages in a tropical deciduous forest. Glob. Ecol. Biogeogr. 14, 241–248 (2005).

    Google Scholar 

  29. 29

    Bell, T. et al. Larger islands house more bacterial taxa. Science 308, 1884 (2005).

  30. 30

    Smith, V. H. et al. Phytoplankton species richness scales consistently from laboratory microcosms to the world's oceans. Proc. Natl Acad. Sci. USA 102, 4393–4396 (2005).

    CAS  PubMed  Google Scholar 

  31. 31

    Cam, E. et al. Disentangling sampling and ecological explanations underlying species–area relationships. Ecology 84, 1118–1130 (2002).

    Google Scholar 

  32. 32

    Colwell, R. K., Mao, C. X. & Chang, J. Interpolating, extrapolating, and comparing incidence-based species accumulation curves. Ecology 85, 2717–2727 (2004).

    Google Scholar 

  33. 33

    Kuske, C. R. et al. Comparison of soil bacterial communities in rhizospheres of three plant species and the interspaces in an arid grassland. Appl. Environ. Microbiol. 68, 1854–1863 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. 34

    Yannarell, A. C. & Triplett, E. W. Within- and between-lake variability in the composition of bacterioplankton communities: investigations using multiple spatial scales. Appl. Environ. Microbiol. 70, 214–223 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. 35

    Legendre, P. & Legendre, L. Numerical Ecology 2nd edn (Elsevier, Amsterdam, 1998).

    Google Scholar 

  36. 36

    Papke, R. T., Ramsing, N. B., Bateson, M. M. & Ward, D. M. Geographical isolation in hot spring cyanobacteria. Environ. Microbiol. 5, 650–659 (2003).

    CAS  Google Scholar 

  37. 37

    Whitaker, R. J., Grogan, D. W. & Taylor, J. W. Geographic barriers isolate endemic populations of hyperthermophilic Archaea. Science 301, 976–978 (2003). Already a classic microbial biogeography study, it considers both the effects of spatial isolation and contemporary environmental parameters on hotspring Sulfolobus assemblages within and across continents.

    CAS  PubMed  PubMed Central  Google Scholar 

  38. 38

    Reche, I., Pulido-Villena, E., Morales-Baquero, R. & Casamayor, E. O. Does ecosystem size determine aquatic bacterial richness? Ecology 86, 1715–1722 (2005).

    Google Scholar 

  39. 39

    Brown, J. H., West, G. B. & Enquist, B. J. Scaling in biology: patterns and processes, causes and consequences. In Scaling in Biology (eds Brown, J. H. & West, G. B.) 1–24 (Oxford University Press, Oxford, 2000). A comprehensive introduction to allometric patterns in biology.

    Google Scholar 

  40. 40

    Bell, G. The distribution of abundance in neutral communities. Am. Nat. 155, 606–617 (2000).

    Google Scholar 

  41. 41

    Hubbell, S. P. The Unified Neutral Theory of Biodiversity and Biogeography (Princeton University Press, Princeton, 2001).

    Google Scholar 

  42. 42

    Clark, J. S., Silman, M., Kern, R., Macklin, E. & HilleRisLambers, J. Seed dispersal near and far: patterns across temperate and tropical forests. Ecology 80, 1475–1494 (1999).

    Google Scholar 

  43. 43

    Brown, J. H. & Maurer, B. A. Evolution of species assemblages: effects of energetic constraints and species dynamics on the diversification of the North American avifauna. Am. Nat. 130, 1–17 (1987).

    Google Scholar 

  44. 44

    Morse, D. R., Stork, N. E. & Lawton, J. H. Species number, species abundance and body length relationships of arboreal beetles in Bornean lowland rain forest trees. Ecol. Entomol. 13, 25–37 (1988).

    Google Scholar 

  45. 45

    Lawton, J. H. Species richness and population dynamics of animal assemblages. Patterns in body size: abundance space. Philos. Trans. R. Soc. Lond. B Biol. Sci. 330, 283–291 (1990).

    Google Scholar 

  46. 46

    Siemann, E., Tilman, D. & Haarstad, J. Insect species diversity, abundance and body size relationships. Nature 380, 704–706 (1996).

    CAS  Google Scholar 

  47. 47

    Brown, J. H. Macroecology (Chicago University Press, Chicago, 1995).

    Google Scholar 

  48. 48

    Li, W. K. W. Macroecological patterns of phytoplankton in the northwestern North Atlantic Ocean. Nature 419, 154–157 (2002).

    CAS  PubMed  Google Scholar 

  49. 49

    Roberts, M. S. & Cohan, F. M. Recombination and migration rates in natural populations of Bacillus subtilis and Bacillus mojavensis. Evolution 49, 1081–1094 (1995).

    PubMed  Google Scholar 

  50. 50

    Stanley, S. M. Macroevolution: Pattern and Process (W. H. Freeman, San Francisco, 1979).

    Google Scholar 

  51. 51

    Paradis, E. Statistical analysis of diversification with species traits. Evolution 59, 1–12 (2005).

    PubMed  Google Scholar 

  52. 52

    Lenski, R. E. & Travisano, M. Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial-populations. Proc. Natl Acad. Sci. USA 91, 6808–6814 (1994).

    CAS  Google Scholar 

  53. 53

    Rainey, P. B. & Travisano, M. Adaptive radiation in a heterogeneous environment. Nature 394, 69–72 (1998).

    CAS  Google Scholar 

  54. 54

    Manne, L. L., Brooks, T. M. & Pimm, S. L. Relative risk of extinction of passerine birds on continents and islands. Nature 399, 258–261 (1999).

    CAS  Google Scholar 

  55. 55

    Purvis, A., Gittleman, J. L., Cowlishaw, G. & Mace, G. M. Predicting extinction risk in declining species. Proc. R. Soc. Lond. B Biol. Sci. 267, 1947–1952 (2000).

    CAS  Google Scholar 

  56. 56

    Lawton, J. H. Range, Population abundance and conservation. Trends Ecol. Evol. 8, 409–413 (1993).

    CAS  PubMed  Google Scholar 

  57. 57

    Silva, M. & Downing, J. A. Allometric scaling of minimal mammal densities. Conserv. Biol. 8, 732–743 (1994).

    Google Scholar 

  58. 58

    Meretsky, V. J., Snyder, N. F. R., Beissinger, S. R., Clendenen, D. A. & Wiley, J. W. Demography of the California condor: implications for reestablishment. Conserv. Biol. 14, 957–967 (2000).

    Google Scholar 

  59. 59

    Finlay, B. J. & Clarke, K. J. Apparent global ubiquity of species in the protist genus Paraphysomonas. Protist 150, 419–430 (1999).

    CAS  PubMed  Google Scholar 

  60. 60

    Massana, R., DeLong, E. F. & Pedrós-Alió, C. A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces. Appl. Environ. Microbiol. 66, 1777–1787 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. 61

    Lindström, E. S. & Leskinen, E. Do neighboring lakes share common taxa of bacterioplankton? Comparison of 16S rDNA fingerprints and sequences from three geographic regions. Microb. Ecol. 44, 1–9 (2002).

    PubMed  Google Scholar 

  62. 62

    Brown, J. H., Stevens, G. C. & Kaufman, D. M. The geographic range: size, shape, boundaries, and internal structure. Annu. Rev. Ecol. Syst. 27, 597–623 (1996).

    Google Scholar 

  63. 63

    May, R. M. How many species are there on Earth? Science 241, 1441–1449 (1988).

    CAS  PubMed  PubMed Central  Google Scholar 

  64. 64

    Gaston, K. J., Chown, S. L. & Mercer, R. D. The animal species-body size distribution of Marion Island. Proc. Natl Acad. Sci. USA 98, 14493–14496 (2001).

    CAS  PubMed  Google Scholar 

  65. 65

    Dykhuizen, D. E. Santa Rosalia revisited: why are there so many species of bacteria? Antonie Van Leeuwenhoek 73, 25–33 (1998).

    CAS  PubMed  Google Scholar 

  66. 66

    Avise, J. C. & Aquadro, C. F. A comparative summary of genetic distances in the vertebrates. Evol. Biol. 15, 151–185 (1982).

    Google Scholar 

  67. 67

    de Vargas, C., Norris, R., Zaninetti, L., Gibb, S. W. & Pawlowski, J. Molecular evidence of cryptic speciation in planktonic foraminifers and their relation to oceanic provinces. Proc. Natl Acad. Sci. USA 96, 2864–2868 (1999).

    CAS  PubMed  Google Scholar 

  68. 68

    Cohan, F. M. What are bacterial species? Annu. Rev. Microbiol. 56, 457–487 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  69. 69

    Coyne, J. A., Orr, H. A. & Futuyma, D. J. Do we need a new species concept? Syst. Zool. 37, 190–200 (1988).

    Google Scholar 

  70. 70

    Green, J. L. & Bohannan, B. J. M. Spatial scaling of microbial biodiversity in Scaling Biodiversity (eds Storch, D. & Marquet, P. A. & Brown, J. H.) (Cambridge University Press, Cambridge, 2006).

    Google Scholar 

  71. 71

    Martiny, J. B. H. & Field, D. Ecological perspectives on the sequenced genome collection. Ecol. Lett. (in the press).

  72. 72

    Naeem, S., Thompson, L. J., Lawler, S. P., Lawton, J. H. & Woodfin, R. M. Declining biodiversity can alter the performance of ecosystems. Nature 368, 734–737 (1994).

    Google Scholar 

  73. 73

    Hooper, D. U. &. Vitousek, P. M. The effects of plant composition and diversity on ecosystem processes. Science 277, 1302–1305 (1997).

    CAS  Google Scholar 

  74. 74

    Dukes, J. S. Biodiversity and invasibility in grassland microcosms. Oecologia 126, 563–568 (2001).

    PubMed  Google Scholar 

  75. 75

    Treseder, K. K. & Vitousek, P. M. Potential ecosystem-level effects of genetic variation among populations of Metrosideros polymorpha from a soil fertility gradient in Hawaii. Oecologia 126, 266–275 (2001).

    PubMed  Google Scholar 

  76. 76

    McGrady-Steed, J., Harris, P. M. & Morin, P. J. Biodiversity regulates ecosystem predictability. Nature 390, 162–165 (1997).

    CAS  Google Scholar 

  77. 77

    Bell, T., Newman, J. A., Silverman, B. W., Turner, S. L. & Lilley, A. K. The contribution of species richness and composition to bacterial services. Nature 436, 1157–1160 (2005).

    CAS  PubMed  Google Scholar 

  78. 78

    Naeem, S. & Li, S. B. Biodiversity enhances ecosystem reliability. Nature 390, 507–509 (1997).

    CAS  Google Scholar 

  79. 79

    van der Heijden, M. G. A. et al. Mycorrhizal fungal diversity determines plant biodiversity, ecosystem variability and productivity. Nature 396, 69–72 (1998).

    CAS  Google Scholar 

  80. 80

    Cavigelli, M. A. & Robertson, G. P. The functional significance of denitrifier community composition in a terrestrial ecosystem. Ecology 81, 1402–1414 (2000).

    Google Scholar 

  81. 81

    Horz, H. -P., Barbrook, A., Field, C. B. & Bohannan, B. J. M. Ammonia-oxidizing bacteria respond to multifactorial global change. Proc. Natl Acad. Sci. USA 101, 15136–15141 (2004).

    CAS  PubMed  Google Scholar 

  82. 82

    Bull, A. T., ed. Microbial Diversity and Bioprospecting. (ASM Press, Washington DC, 2003).

    Google Scholar 

  83. 83

    Finlay, B. J., Esteban, G. F., Olmo, J. L. & Tyler, P. A. Global distribution of free-living microbial species. Ecography 22, 138–144 (1999).

    Google Scholar 

  84. 84

    Magurran, A. E. Ecological Diversity and Its Measurement (Princeton University Press, Princeton, 1988).

    Google Scholar 

  85. 85

    Chao, A., Chazdon, R. L., Colwell, R. K. & Shen, T. J. A new statistical approach for assessing similarity of species composition with incidence and abundance data. Ecol. Lett. 8, 148–159 (2005).

    Google Scholar 

  86. 86

    Ricketts, T. H. The matrix matters: effective isolation in fragmented landscapes. Am. Nat. 158, 87–99 (2001).

    CAS  PubMed  Google Scholar 

  87. 87

    Mantel, N. The detection of disease clustering and a generalized regression approach. Cancer Res. 27, 209–220 (1967).

    CAS  PubMed  PubMed Central  Google Scholar 

  88. 88

    Borcard, D., Legendre, P. & Drapeau, P. Partialling out the spatial component of ecological variation. Ecology 73, 1045–1055 (1992).

    Google Scholar 

  89. 89

    Smouse, P. E., Long, J. C. & Sokal, R. R. Multiple regression and correlation extensions of the Mantel test of matrix correspondence. Syst. Zool. 35, 627–632 (1986).

    Google Scholar 

  90. 90

    Fulthorpe, R. R., Rhodes, A. N. & Tiedje, J. M. High levels of endemicity of 3-chlorobenzoate-degrading soil bacteria. Appl. Environ. Microbiol. 64, 1620–1627 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  91. 91

    Schwalbach, M. S. & Fuhrman, J. A. Wide-ranging abundances of aerobic anoxygenic phototrophic bacteria in the world ocean revealed by epifluorescence microscopy and quantitative PCR. Limnol. Oceanogr. 50, 620–628 (2005).

    CAS  Google Scholar 

  92. 92

    Garcia-Martinez, J. & Rodriguez-Valera, F. Microdiversity of uncultured marine prokaryotes: the SAR11 cluster and the marine Archaea of Group I. Mol. Ecol. 9, 935–948 (2000).

    CAS  PubMed  Google Scholar 

  93. 93

    Glaeser, J. & Overmann, J. Biogeography, evolution, and diversity of epibionts in phototrophic consortia. Appl. Environ. Microbiol. 70, 4821–4830 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  94. 94

    Yeager, C. M. et al. Diazotrophic community structure and function in two successional stages of biological soil crusts from the Colorado plateau and Chihuahuan desert. Appl. Environ. Microbiol. 70, 973–983 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  95. 95

    Sliwinski, M. K. & Goodman, R. M. Spatial heterogeneity of Crenarchaeal assemblages within mesophilic soil ecosystems as revealed by PCR-single-stranded conformation polymorphism profiling. Appl. Environ. Microbiol. 70, 1811–1820 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  96. 96

    Sliwinski, M. K. & Goodman, R. M. Comparison of Crenarchaeal consortia inhabiting the rhizosphere of diverse terrestrial plants with those in bulk soil in native environments. Appl. Environ. Microbiol. 70, 1821–1826 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  97. 97

    Riemann, L. & Middelboe, M. Stability of bacterial and viral community compositions in Danish coastal waters as depicted by DNA fingerprinting techniques. Aquat. Microb. Ecol. 27, 219–232 (2002).

    Google Scholar 

  98. 98

    Pinhassi, J. et al. Spatial variability in bacterioplankton community composition at the Skagerrak–Kattegat Front. Mar. Ecol. Prog. Ser. 255, 1–13 (2003).

    CAS  Google Scholar 

  99. 99

    Troussellier, M. et al. Bacterial activity and genetic richness along an estuarine gradient (Rhone River plume, France). Aquat. Microb. Ecol. 28, 13–24 (2002).

    Google Scholar 

  100. 100

    Casamayor, E. O. et al. Changes in archaeal, bacterial and eukaryal assemblages along a salinity gradient by comparison of genetic fingerprinting methods in a multipond solar saltern. Environ. Microbiol. 4, 338–348 (2002).

    PubMed  Google Scholar 

  101. 101

    McArthur, J. V., Kovacic, D. A. & Smith, M. H. Genetic diversity in natural populations of a soil bacterium across a landscape gradient. Proc. Natl Acad. Sci. USA 85, 9621–9624 (1988).

    CAS  PubMed  Google Scholar 

  102. 102

    Buckley, D. H. & Schmidt, T. M. Diversity and dynamics of microbial communities in soils from agro-ecosystems. Environ. Microbiol. 5, 441–452 (2003).

    PubMed  Google Scholar 

  103. 103

    Staddon, W. J., Trevors, J. T., Duchesne, L. C. & Colombo, C. A. Soil microbial diversity and community structure across a climatic gradient in western Canada. Biodivers. Conserv. 7, 1081–1092 (1998).

    Google Scholar 

  104. 104

    Franklin, R. B., Taylor, D. R. & Mills, A. L. The distribution of microbial communities in anaerobic and aerobic zones of a shallow coastal plain aquifer. Microb. Ecol. 38, 377–386 (1999).

    CAS  PubMed  Google Scholar 

  105. 105

    Franklin, R. B. & Mills, A. L. Multi-scale variation in spatial heterogeneity for microbial community structure in an eastern Virginia agricultural field. FEMS Microbiol. Ecol. 44, 335–346 (2003).

    CAS  PubMed  Google Scholar 

  106. 106

    Martiny, A. C., Jorgensen, T. M., Albrechtsen, H. J., Arvin, E. & Molin, S. Long-term succession of structure and diversity of a biofilm formed in a model drinking water distribution system. Appl. Environ. Microbiol. 69, 6899–6907 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  107. 107

    Franklin, R. B., Blum, L. K., McComb, A. C. & Mills, A. L. A geostatistical analysis of small-scale spatial variability in bacterial abundance and community structure in salt marsh creek bank sediments. FEMS Microbiol. Ecol. 42, 71–80 (2002).

    CAS  PubMed  Google Scholar 

  108. 108

    Rohwer, F., Seguritan, V., Azam, F. & Knowlton, N. Diversity and distribution of coral-associated bacteria. Mar. Ecol. Prog. Ser. 243, 1–10 (2002).

    Google Scholar 

  109. 109

    Yannarell, A. C. & Triplett, E. W. Geographic and environmental sources of variation in lake bacterial community composition. Appl. Environ. Microbiol. 71, 227–239 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  110. 110

    Hewson, I. & Fuhrman, J. A. Richness and diversity of bacterioplankton species along an estuarine gradient in Moreton Bay, Australia. Appl. Environ. Microbiol. 70, 3425–3433 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

This work was conducted as part of the Patterns in Microbial Biodiversity Working Group supported by the National Center for Ecological Analysis and Synthesis, a centre funded by the National Science Foundation, the University of California at Santa Barbara and the State of California. We thank M. Liebold, G. Muyzer, O. Petchey and D. Ward for useful and lively discussions, and C. van der Gast for comments on the manuscript. Any opinions, findings and conclusions or recommendations expressed in this study are those of the authors and do not necessarily reflect the views of the National Science Foundation.

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NCEAS

Glossary

Province

A region the biotic composition of which reflects the legacies of historical events.

Habitat type

An environment defined by the suite of its abiotic and biotic characteristics.

Beta diversity

Taxonomic diversity due to turnover in composition between assemblages.

Distance effect

The influence of isolation on biotic composition after controlling for the influence of the contemporary environment.

Genetic drift

Changes in gene frequencies in a population caused solely by chance.

Allometry

The relationship between organismal attributes and body size of the form Y = Y0 Mb, in which Y is a variable such as metabolic rate, lifespan or population density, Y0 is a normalization constant (the y-intercept on a logarithmic graph), M is body mass (or other measure of body size) and b is the scaling exponent (the slope on the graph).

Ecological drift

The influence of random demographic variability (such as birth, death and migration rates) on biotic composition.

Propagule

The smallest unit of dispersal that is necessary to colonize a new population.

Geographic range

The area encompassing the extent of a taxon's distribution.

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Martiny, J., Bohannan, B., Brown, J. et al. Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 4, 102–112 (2006). https://doi.org/10.1038/nrmicro1341

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