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Beyond biogeographic patterns: processes shaping the microbial landscape

Nature Reviews Microbiology volume 10, pages 497–506 (2012)Cite this article

Subjects

Key Points

  • Biogeography is the study of the distribution of organisms and the ecological and evolutionary processes that shape those distributions. Over the past decade, microbiologists have established the existence of biogeographic patterns among a wide variety of microorganisms, and interest is now shifting towards identifying the mechanisms that shape these patterns.

  • Traditionally, mechanisms that shape the composition and diversity within species are considered to be evolutionary processes, and those that shape the composition and diversity among species are considered to be ecological processes. However, microbial biogeography studies often characterize diversity along a continuous scale of taxonomic resolution using the nucleotide sequences of a single marker gene. In this case, the boundary between ecological and evolutionary processes is particularly blurry. Hence, we merge concepts from both fields to describe the processes that shape microbial biogeographic patterns.

  • Here, we propose a theoretical framework that describes just four processes — selection, drift, dispersal and mutation — which interact to create and maintain microbial biogeographic patterns at all taxonomic scales. As an illustrative example, we show how these processes shape the most commonly studied biogeographic pattern: the distance–decay relationship.

  • We carried out a literature review to assess the evidence for the relative importance of these processes in shaping microbial biogeographic patterns. Although selection imposed by current environmental factors had the strongest influence on microbial spatial distributions, historical processes driven by dispersal limitation also influenced the distribution of at least some microorganisms from all domains of life and from various habitat types, spatial scales and taxonomic resolutions.

  • As different combinations of the same four processes can interact to create the same pattern, we conclude that it remains difficult to disentangle the relative importance of selection, drift, dispersal and mutation by analysing distance–decay patterns alone. We suggest that the field might advance by emphasizing process over pattern: tailoring studies to detect and evaluate specific processes through manipulative experiments, temporal data sets and the incorporation of theoretical models.

Abstract

Recently, microbiologists have established the existence of biogeographic patterns among a wide range of microorganisms. The focus of the field is now shifting to identifying the mechanisms that shape these patterns. Here, we propose that four processes — selection, drift, dispersal and mutation — create and maintain microbial biogeographic patterns on inseparable ecological and evolutionary scales. We consider how the interplay of these processes affects one biogeographic pattern, the distance–decay relationship, and review evidence from the published literature for the processes driving this pattern in microorganisms. Given the limitations of inferring processes from biogeographic patterns, we suggest that studies should focus on directly testing the underlying processes.

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Figure 1: The sliding scale of microbial taxonomic definitions and its influence on microbial biogeographic patterns.
Figure 2: The effect of the four processes on the relationship between compositional similarity and spatial distance.
Figure 3: Studies reporting a significant correlation between microbial composition and spatial distance or an environmental variable.
Figure 4: Explained variance in microbial composition.

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References

  1. Lomolino, M. V., Riddle, B. R., Whittaker, R. & Brown, J. H. Biogeography (Sinauer Associates, 2010).

    Google Scholar 

  2. Green, J. & Bohannan, B. J. M. Spatial scaling of microbial biodiversity. Trends Ecol. Evol. 21, 501–507 (2006).

    Article  PubMed  Google Scholar 

  3. Lindström, E. S. & Langenheder, S. Local and regional factors influencing bacterial community assembly. Environ. Microbiol. Rep. 4, 1–9 (2012).

    Article  PubMed  Google Scholar 

  4. Ramette, A. & Tiedje, J. M. Biogeography: an emerging cornerstone for understanding prokaryotic diversity, ecology, and evolution. Microb. Ecol. 53, 197–207 (2007).

    Article  PubMed  Google Scholar 

  5. Foissner, W. Biogeography and dispersal of micro-organisms: a review emphasizing protists. Acta Protozool. 45, 111–136 (2006).

    Google Scholar 

  6. Martiny, J. B. H. et al. Microbial biogeography: putting microorganisms on the map. Nature Rev. Microbiol. 4, 102–112 (2006). This article outlines the environment versus the history approach to assessing the processes underlying microbial biogeographic patterns; this Review serves as a conceptual update to this framework.

    Article  CAS  Google Scholar 

  7. Fuhrman, J. A. et al. Annually reoccurring bacterial communities are predictable from ocean conditions. Proc. Natl Acad. Sci. USA 103, 13104–13109 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Gilbert, J. A. et al. Defining seasonal marine microbial community dynamics. ISME J. 6, 298–308 (2012).

    Article  CAS  PubMed  Google Scholar 

  9. Caporaso, J. G., Paszkiewicz, K., Field, D., Knight, R. & Gilbert, J. A. The Western English Channel contains a persistent microbial seed bank. ISME J. 10 Nov 2011 (doi:10.1038/ismej.2011.162). A recent example of temporal variation in microbial distributions, highlighting the issue of rarity and dormancy in defining microbial community composition.

  10. Cho, J. C. & Tiedje, J. M. Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil. Appl. Environ. Microbiol. 66, 5448–5456 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Oakley, B. B., Carbonero, F., van der Gast, C. J., Hawkins, R. J. & Purdy, K. J. Evolutionary divergence and biogeography of sympatric niche-differentiated bacterial populations. ISME J. 4, 488–497 (2010).

    Article  PubMed  Google Scholar 

  12. Takacs-Vesbach, C., Mitchell, K., Jackson-Weaver, O. & Reysenbach, A. L. Volcanic calderas delineate biogeographic provinces among Yellowstone thermophiles. Environ. Microbiol. 10, 1681–1689 (2008).

    Article  CAS  PubMed  Google Scholar 

  13. Whitaker, R. J., Grogan, D. W. & Taylor, J. W. Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301, 976–978 (2003). This classic study in microbial biogeography finds evidence for both endemism and distance–decay and uses a population genetics approach to interpret those patterns.

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  15. Nemergut, D. R. et al. Global patterns in the biogeography of bacterial taxa. Environ. Microbiol. 13, 135–144 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  16. Lozupone, C. A. & Knight, R. Global patterns in bacterial diversity. Proc. Natl Acad. Sci. USA 104, 11436–11440 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Vos, M. & Velicer, G. J. Isolation by distance in the spore-forming soil bacterium Myxococcus xanthus. Curr. Biol. 18, 386–391 (2008).

    Article  CAS  PubMed  Google Scholar 

  18. Slatkin, M. Isolation by distance in equilibrium and non-equilibrium populations. Evolution 47, 264–279 (1993).

    Article  PubMed  Google Scholar 

  19. Wright, S. The genetical structure of populations. Ann. Eugenic. 15, 323–354 (1951).

    Article  CAS  Google Scholar 

  20. Martin, A. P. Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl. Environ. Microbiol. 68, 3673–3682 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Hu, X.-S., He, F. & Hubbell, S. P. Community differentiation on landscapes: drift, migration and speciation. Oikos 118, 1515–1523 (2009).

    Article  Google Scholar 

  22. Bahl, J. et al. Ancient origins determine global biogeography of hot and cold desert cyanobacteria. Nature Commun. 2, 163 (2011).

    Article  CAS  Google Scholar 

  23. O'Mullan, G. D. & Ward, B. B. Relationship of temporal and spatial variabilities of ammonia-oxidizing bacteria to nitrification rates in Monterey Bay, California. Appl. Environ. Microbiol. 71, 697–705 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Soininen, J., McDonald, R. & Hillebrand, H. The distance decay of similarity in ecological communities. Ecography 30, 3–12 (2007).

    Article  Google Scholar 

  25. Green, J. L. et al. Spatial scaling of microbial eukaryote diversity. Nature 432, 747–750 (2004).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  27. Nekola, J. C. & White, P. S. The distance decay of similarity in biogeography and ecology. J. Biogeogr. 26, 867–878 (1999).

    Article  Google Scholar 

  28. Casteleyn, G. et al. Limits to gene flow in a cosmopolitan marine planktonic diatom. Proc. Natl Acad. Sci. USA 107, 12952–12957 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  29. Soininen, J., Korhonen, J. J., Karhu, J. & Vetterli, A. Disentangling the spatial patterns in community composition of prokaryotic and eukaryotic lake plankton. Limnol. Oceanogr. 56, 508–520 (2011).

    Article  Google Scholar 

  30. Hewson, I., Steele, J. A., Capone, D. G. & Fuhrman, J. A. Temporal and spatial scales of variation in bacterioplankton assemblages of oligotrophic surface waters. Mar. Ecol. Prog. Ser. 311, 67–77 (2006).

    Article  Google Scholar 

  31. Queloz, V., Sieber, T. N., Holdenrieder, O., McDonald, B. A. & Grünig, C. R. No biogeographical pattern for a root-associated fungal species complex. Global Ecol. Biogeogr. 20, 160–169 (2011).

    Article  Google Scholar 

  32. Finlay, B. J. Global dispersal of free-living microbial eukaryote species. Science 296, 1061–1063 (2002).

    Article  CAS  PubMed  Google Scholar 

  33. Pommier, T. et al. Global patterns of diversity and community structure in marine bacterioplankton. Mol. Ecol. 16, 867–880 (2007).

    Article  CAS  PubMed  Google Scholar 

  34. Sogin, M. L. et al. Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc. Natl Acad. Sci. USA 103, 12115–12120 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Curtis, T. P., Sloan, W. T. & Scannell, J. W. Estimating prokaryotic diversity and its limits. Proc. Natl Acad. Sci. USA 99, 10494–10499 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Fulthorpe, R. R., Roesch, L. F. W., Riva, A. & Triplett, E. W. Distantly sampled soils carry few species in common. ISME J. 2, 901–910 (2008).

    Article  CAS  PubMed  Google Scholar 

  37. Hedlund, B. P. & Staley, J. T. in Microbial Diversity and Bioprospecting (ed. Bull, A. T.) 225–231 (ASM Press, 2003).

    Google Scholar 

  38. Logue, J. B. & Lindstrom, E. S. Biogeography of bacterioplankton in inland waters. Freshwater Rev. 1, 99–114 (2008).

    Article  Google Scholar 

  39. Holyoak, M., Leibold, M. A. & Holt, R. D. (eds) Metacommunities: Spatial Dynamics and Ecological Communities (Univ. of Chicago Press, 2005).

    Google Scholar 

  40. Leibold, M. A. et al. The metacommunity concept: a framework for multi-scale community ecology. Ecol. Lett. 7, 601–613 (2004). A concise, conceptual summary of metacommunity theory.

    Article  Google Scholar 

  41. Hubbell, S. P. The Unified Neutral Theory of Biodiversity and Biogeography (Princeton Univ. Press, 2001). The theoretical derivation of neutral theory as applied to multispecies communities.

    Google Scholar 

  42. Bell, G. Ecology — neutral macroecology. Science 293, 2413–2418 (2001).

    Article  CAS  PubMed  Google Scholar 

  43. Drakare, S. & Liess, A. Local factors control the community composition of cyanobacteria in lakes while heterotrophic bacteria follow a neutral model. Freshwater Biol. 55, 2447–2457 (2010).

    Article  Google Scholar 

  44. Barberán, A. & Casamayor, E. O. Global phylogenetic community structure and β-diversity patterns in surface bacterioplankton metacommunities. Aquat. Microb. Ecol. 59, 1–10 (2010).

    Article  Google Scholar 

  45. Keymer, D. P., Lam, L. H. & Boehm, A. B. Biogeographic patterns in genomic diversity among a large collection of Vibrio cholerae isolates. Appl. Environ. Microbiol. 75, 1658–1666 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Sloan, W. T. et al. Neutral assembly of bacterial communities. FEMS Microbiol. Ecol. 62, 171–180 (2007).

    Article  CAS  PubMed  Google Scholar 

  47. Van der Gucht, K. et al. The power of species sorting: local factors drive bacterial community composition over a wide range of spatial scales. Proc. Natl Acad. Sci. USA 104, 20404–20409 (2007).

    Article  PubMed  PubMed Central  Google Scholar 

  48. Vellend, M. Conceptual synthesis in community ecology. Q. Rev. Biol. 85, 183–206 (2010). An introduction to the many theoretical frameworks in community ecology that could be used to explain species distributions and arguments for how all of these frameworks can be merged by focusing on just four fundamental processes.

    Article  PubMed  Google Scholar 

  49. Slatkin, M. Gene flow and the geographic structure of natural-populations. Science 236, 787–792 (1987). A general, conceptual description of the effects of mutation, drift, gene flow and selection on spatial variation in within-species diversity.

    Article  CAS  PubMed  Google Scholar 

  50. Wright, S. Evolution in Mendelian populations. Genetics 16, 97–159 (1931).

    CAS  PubMed  PubMed Central  Google Scholar 

  51. Dobzhansky, T. G. Genetics and the Origin of Species (Columbia Univ. Press, 1937).

    Google Scholar 

  52. Hartl, D. L. & Clark, A. G. Principles of Population Genetics (Sinauer Associates, 2007). A general textbook reference for the evolutionary processes that generate diversity within species.

    Google Scholar 

  53. Kimura, M. The Neutral Theory of Molecular Evolution (Cambridge Univ. Press, 1983).

    Book  Google Scholar 

  54. Antonovics, J. The input from population genetics: “the new ecological genetics”. Syst. Bot. 1, 233–245 (1976).

    Article  Google Scholar 

  55. Lenski, R. E. in Ecology: Achievement and Challenge (eds Press, M. C., Huntly, N. J. & Levin, S.) 25–45 (Blackwell Science, 2001).

    Google Scholar 

  56. Kerr, B., Riley, M. A., Feldman, M. W. & Bohannan, B. J. M. Local dispersal promotes biodiversity in a real-life game of rock–paper–scissors. Nature 418, 171–174 (2002).

    Article  CAS  PubMed  Google Scholar 

  57. Lenski, R. E. et al. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461, 1243–1247 (2009).

    Article  CAS  PubMed  Google Scholar 

  58. Travisano, M., Mongold, J. A., Bennett, A. F. & Lenski, R. E. Experimental tests of the roles of adaptation, chance, and history in evolution. Science 267, 87–90 (1995).

    Article  CAS  PubMed  Google Scholar 

  59. Lewontin, R. C. The units of selection. Annu. Rev. Ecol. Syst. 1, 1–18 (1970).

    Article  Google Scholar 

  60. Futuyma, D. J. Evolution (Sinauer Associates, 2005).

    Google Scholar 

  61. Ramette, A. & Tiedje, J. M. Multiscale responses of microbial life to spatial distance and environmental heterogeneity in a patchy ecosystem. Proc. Natl Acad. Sci. USA 104, 2761–2766 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Daubin, V., Moran, N. A. & Ochman, H. Phylogenetics and the cohesion of bacterial genomes. Science 301, 829–832 (2003).

    Article  CAS  PubMed  Google Scholar 

  63. Fraser, C., Alm, E. J., Polz, M. F., Spratt, B. G. & Hanage, W. P. The bacterial species challenge: making sense of genetic and ecological diversity. Science 323, 741–746 (2009).

    Article  CAS  PubMed  Google Scholar 

  64. Konstantinidis, K. T. & Tiedje, J. M. Genomic insights that advance the species definition for prokaryotes. Proc. Natl Acad. Sci. USA 102, 2567–2572 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Caro-Quintero, A. & Konstantinidis, K. T. Bacterial species may exist, metagenomics reveal. Environ. Microbiol. 14, 347–355 (2011).

    Article  CAS  PubMed  Google Scholar 

  66. Achtman, M. & Wagner, M. Microbial diversity and the genetic nature of microbial species. Nature Rev. Microbiol. 6, 431–440 (2008).

    Article  CAS  Google Scholar 

  67. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Condit, R. et al. Beta-diversity in tropical forest trees. Science 295, 666–669 (2002).

    Article  CAS  PubMed  Google Scholar 

  69. Hutchison, D. W. & Templeton, A. R. Correlation of pairwise genetic and geographic distance measures: inferring the relative influences of gene flow and drift on the distribution of genetic variability. Evolution 53, 1898–1914 (1999).

    Article  PubMed  Google Scholar 

  70. Hedrick, P. W. Perspective: highly variable loci and their interpretation in evolution and conservation. Evolution 53, 313–318 (1999).

    Article  PubMed  Google Scholar 

  71. Ricklefs, R. E. A comprehensive framework for global patterns in biodiversity. Ecol. Lett. 7, 1–15 (2004).

    Article  Google Scholar 

  72. Svenning, J. C. & Skov, F. The relative roles of environment and history as controls of tree species composition and richness in Europe. J. Biogeogr. 32, 1019–1033 (2005).

    Article  Google Scholar 

  73. Yergeau, E., Newsham, K. K., Pearce, D. A. & Kowalchuk, G. A. Patterns of bacterial diversity across a range of Antarctic terrestrial habitats. Environ. Microbiol. 9, 2670–2682 (2007).

    Article  CAS  PubMed  Google Scholar 

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

    Article  Google Scholar 

  75. Baker, K. L. et al. Environmental and spatial characterisation of bacterial community composition in soil to inform sampling strategies. Soil Biol. Biochem. 41, 2292–2298 (2009).

    Article  CAS  Google Scholar 

  76. Cottenie, K. Integrating environmental and spatial processes in ecological community dynamics. Ecol. Lett. 8, 1175–1182 (2005). A literature review that uses a metacommunity perspective to evaluate the relative importance of selection versus dispersal-driven processes for driving variation in the spatial distribution of primarily non-microbial organisms.

    Article  PubMed  Google Scholar 

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

    Article  Google Scholar 

  78. St-Arnaud, M. et al. Patterns of Fusarium community structure and abundance in relation to spatial, abiotic and biotic factors in soil. FEMS Microbiol. Ecol. 71, 34–42 (2010).

    Article  CAS  PubMed  Google Scholar 

  79. Yergeau, E. et al. Influences of space, soil, nematodes and plants on microbial community composition of chalk grassland soils. Environ. Microbiol. 12, 2096–2106 (2010).

    CAS  PubMed  Google Scholar 

  80. Zinger, L. et al. Contrasting diversity patterns of crenarchaeal, bacterial and fungal soil communities in an alpine landscape. PLoS ONE 6, e19950 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Fenchel, T. There are more small than large species. Oikos 68, 375–378 (1993).

    Article  Google Scholar 

  82. Bissett, A., Richardson, A. E., Baker, G., Wakelin, S. & Thrall, P. H. Life history determines biogeographical patterns of soil bacterial communities over multiple spatial scales. Mol. Ecol. 19, 4315–4327 (2010).

    Article  CAS  PubMed  Google Scholar 

  83. Cermeño, P. & Falkowski, P. G. Controls on diatom biogeography in the ocean. Science 325, 1539–1541 (2009).

    Article  CAS  PubMed  Google Scholar 

  84. Chase, J. N. & Forbes, A. E. The role of habitat connectivity and landscape geometry in experimental zooplankton metacommunities. Oikos 96, 433–440 (2002).

    Article  Google Scholar 

  85. Verleyen, E. et al. The importance of dispersal related and local factors in shaping the taxonomic structure of diatom metacommunities. Oikos 118, 1239–1249 (2009).

    Article  Google Scholar 

  86. Martiny, J. B. H., Eisen, J. A., Penn, K., Allison, S. D. & Horner-Devine, M. C. Drivers of bacterial β-diversity depend on spatial scale. Proc. Natl Acad. Sci. USA 108, 7850–7854 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  87. Morlon, H. et al. A general framework for the distance–decay of similarity in ecological communities. Ecol. Lett. 11, 904–917 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  88. Petrosino, J. F., Highlander, S., Luna, R. A., Gibbs, R. A. & Versalovic, J. Metagenomic pyrosequencing and microbial identification. Clin. Chem. 55, 856–866 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Harder, J., Schauer, R., Bienhold, C. & Ramette, A. Bacterial diversity and biogeography in deep-sea surface sediments of the South Atlantic Ocean. ISME J. 4, 159–170 (2010).

    Article  CAS  PubMed  Google Scholar 

  90. Martiny, A. C., Tai, A. P. K., Veneziano, D., Primeau, F. & Chisholm, S. W. Taxonomic resolution, ecotypes and the biogeography of Prochlorococcus. Environ. Microbiol. 11, 823–832 (2009).

    Article  PubMed  Google Scholar 

  91. Cale, W. G., Henebry, G. M. & Yeakley, J. A. Inferring process from pattern in natural communities. Bioscience 39, 600–605 (1989).

    Article  Google Scholar 

  92. Hu, X. S., He, F. L. & Hubbell, S. P. Neutral theory in macroecology and population genetics. Oikos 113, 548–556 (2006). A concise, conceptual summary and comparison of neutral theory as it applies to population genetics and ecology.

    Article  Google Scholar 

  93. Lennon, J. T. & Jones, S. E. Dormancy contributes to the maintenance of microbial diversity. Proc. Natl Acad. Sci. USA 107, 5881–5886 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  94. Karl, S. A. & Avise, J. C. Balancing selection at allozyme loci in oysters — implications from nuclear RFLPs. Science 256, 100–102 (1992).

    Article  CAS  PubMed  Google Scholar 

  95. Ricklefs, R. E. History and diversity: explorations at the intersection of ecology and evolution. Am. Nat. 170, S56–S70 (2007).

    Article  PubMed  Google Scholar 

  96. Keiser, A. D., Strickland, M. S., Fierer, N. & Bradford, M. A. The effect of resource history on the functioning of soil microbial communities is maintained across time. Biogeosciences 8, 1477–1486 (2011).

    Article  Google Scholar 

  97. Langenheder, S. & Szekely, A. J. Species sorting and neutral processes are both important during the initial assembly of bacterial communities. ISME J. 5, 1086–1094 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  98. Ayarza, J. M. & Erijman, L. Balance of neutral and deterministic components in the dynamics of activated sludge floc assembly. Microb. Ecol. 61, 486–495 (2011).

    Article  PubMed  Google Scholar 

  99. Bell, T. Experimental tests of the bacterial distance–decay relationship. ISME J. 4, 1357–1365 (2010). An example of a manipulative experimental study to assess the mechanisms contributing to spatial variation in microbial community composition.

    Article  PubMed  Google Scholar 

  100. Sharma, N. K. & Singh, S. Differential aerosolization of algal and cyanobacterial particles in the atmosphere. Indian J. Microbiol. 50, 468–473 (2010).

    Article  CAS  PubMed  Google Scholar 

  101. Figuerola, J. & Green, A. J. Dispersal of aquatic organisms by waterbirds: a review of past research and priorities for future studies. Freshwater Biol. 47, 483–494 (2002).

    Article  Google Scholar 

  102. McMahon, K. D., Jones, S. E. & Newton, R. J. Potential for atmospheric deposition of bacteria to influence bacterioplankton communities. FEMS Microbiol. Ecol. 64, 388–394 (2008).

    Article  CAS  PubMed  Google Scholar 

  103. Banat, I. M. et al. Thermophilic bacteria in cool temperate soils: are they metabolically active or continually added by global atmospheric transport? Appl. Microbiol. Biot. 78, 841–852 (2008).

    Article  CAS  Google Scholar 

  104. Perfumo, A. & Marchant, R. Global transport of thermophilic bacteria in atmospheric dust. Environ. Microbiol. Rep. 2, 333–339 (2010).

    Article  CAS  PubMed  Google Scholar 

  105. Green, J. L., Womack, A. M. & Bohannan, B. J. M. Biodiversity and biogeography of the atmosphere. Phil. Trans. R. Soc. B. 365, 3645–3653 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  106. Fukami, T. in Community Ecology: Processes, Models and Applications (eds Verhoef, H. A. & Morin, P. J.) 45–54 (Oxford Univ. Press, 2010).

    Google Scholar 

  107. Jessup, C. M. et al. Big questions, small worlds: microbial model systems in ecology. Trends Ecol. Evol. 19, 189–197 (2004).

    Article  PubMed  Google Scholar 

  108. Hubert, C. et al. A constant flux of diverse thermophilic bacteria into the cold arctic seabed. Science 325, 1541–1544 (2009).

    Article  CAS  PubMed  Google Scholar 

  109. Willson, M. F. Dispersal mode, seed shadows, and colonization patterns. Vegetatio 108, 261–280 (1993).

    Google Scholar 

  110. Chase, J. M. Drought mediates the importance of stochastic community assembly. Proc. Natl Acad. Sci. USA 104, 17430–17434 (2007).

    Article  PubMed  PubMed Central  Google Scholar 

  111. Drake, J. A. Community-assembly mechanics and the structure of an experimental species ensemble. Am. Nat. 137, 1–26 (1991).

    Article  Google Scholar 

  112. Fukami, T. & Morin, P. J. Productivity-biodiversity relationships depend on the history of community assembly. Nature 424, 423–426 (2003).

    Article  CAS  PubMed  Google Scholar 

  113. Peay, K. G., Belisle, M. & Fukami, T. Phylogenetic relatedness predicts priority effects in nectar yeast communities. Proc. Biol. Sci. 279, 749–758 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  114. Legendre, P. & Legendre, L. Numerical Ecology (Developments in Environmental Modelling) (Elsevier, 1998).

    Google Scholar 

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Acknowledgements

The authors thank A. Martiny, S. Allison, A. Amend, L. Crummett, K. Whiteson, A. Durbin, K. Matulich, S. Kivlin, N. Hynson and J. Talbot for feedback and discussions. This work was supported by a US National Oceanic and Atmospheric Administration–National Estuarine Research Reserve System (NOAA–NERRS) Graduate Research Fellowship to C.A.H. and a US National Science Foundation Grant (OCE-1031783) to J.B.H.M.

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  1. Department of Ecology and Evolutionary Biology, University of California, Irvine, 92697, California, USA

    China A. Hanson & Jennifer B. H. Martiny

  2. Department of Biological Sciences, University of Southern California, MC0371, Los Angeles, 90089, California, USA

    Jed A. Fuhrman

  3. School of Aquatic and Fishery Sciences, University of Washington, Seattle, 98195, Washington, USA

    M. Claire Horner-Devine

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Correspondence to China A. Hanson or Jennifer B. H. Martiny.

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Glossary

Richness

The number of taxa in a sample, assemblage or community.

Composition

The identity and relative abundance of taxa in a sample, assemblage or community.

Taxonomic resolution

The level of genetic variation of the taxa considered.

Taxon

A group into which related organisms are classified. For microorganisms, taxa are usually defined by sequence similarity of one or more genomic regions. This includes the possibility that taxa are defined by entirely unique genomes (at the highest genetic resolution possible).

Community

All individuals of a defined set of many taxa within an area (for instance, all bacterial taxa).

Taxonomic breadth

The extent of taxa considered.

Cosmopolitan

Having a widespread distribution, present almost everywhere.

Horizontal gene transfer

Transfer of genetic material between independent organisms other than transfer by direct decent.

Environment effect

A correlation of biotic composition with measured environmental variables after controlling for the influence of geographic distance.

Distance effect

A correlation of biotic composition with geographic distance after controlling for the influence of the contemporary environment.

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Hanson, C., Fuhrman, J., Horner-Devine, M. et al. Beyond biogeographic patterns: processes shaping the microbial landscape. Nat Rev Microbiol 10, 497–506 (2012). https://doi.org/10.1038/nrmicro2795

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