Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Uncovering the rules of microbial community invasions


Understanding the ecological and evolutionary processes determining the outcome of biological invasions has been the subject of decades of research with most work focusing on macro-organisms. In the context of microbes, invasions remain poorly understood despite being increasingly recognized as important. To shed light on the factors affecting the success of microbial community invasions, we perform simulations using an individual-based nearly neutral model that combines ecological and evolutionary processes. Our simulations qualitatively recreate many empirical patterns and lead to a description of five general rules of invasion: (1) larger communities evolve better invaders and better defenders; (2) where invader and resident fitness difference is large, invasion success is essentially deterministic; (3) propagule pressure contributes to invasion success, if and only if, invaders and residents are competitively similar; (4) increasing the diversity of invaders has a similar effect to increasing the number of invaders; and (5) more diverse communities more successfully resist invasion.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Diagrammatic representation of the model and simulation experiments.
Fig. 2: One hundred independent invasion experiments for each of three unique invader community sizes.
Fig. 3: Adaptive divergence of resident and invader community determines invasion success.
Fig. 4: Propagule pressure and invader genotype richness can increase invasion success.
Fig. 5: Larger and/or more diverse communities better resist invasions.
Fig. 6: Model simulations are consistent with published experimental results.

Data availability

All data presented in this paper has been deposited in a public repository and can be accessed at

Code availability

All code presented in this paper has been deposited in a public repository and can be accessed at


  1. 1.

    Ehrenfeld, J. G. Ecosystem consequences of biological invasions. Annu. Rev. Ecol. Evol. Syst. 41, 59–80 (2010).

    Google Scholar 

  2. 2.

    Lowry, E. et al. Biological invasions: a field synopsis, systematic review, and database of the literature. Ecol. Evol. 3, 182–196 (2012).

    PubMed  Google Scholar 

  3. 3.

    Chapman, D., Purse, B. V., Roy, H. E. & Bullock, J. M. Global trade networks determine the distribution of invasive non-native species. Glob. Ecol. Biogeogr. 26, 907–917 (2017).

    Google Scholar 

  4. 4.

    Gorby, G. L., Robinson, E. N. Jr, Barley, L. R., Clemens, C. M. & McGee, Z. A. Microbial invasion: a covert activity? Can. J. Microbiol. 34, 507–512 (1988).

    CAS  PubMed  Google Scholar 

  5. 5.

    Cossart, P. & Sansonetti, P. J. Bacterial invasion: the paradigms of enteroinvasive pathogens. Science 304, 242–248 (2004).

    CAS  PubMed  Google Scholar 

  6. 6.

    Mallon, C. A., van Elsas, J. D. & Salles, J. F. Microbial invasions: the process, patterns, and mechanisms. Trends Microbiol. 23, 719–729 (2015).

    CAS  PubMed  Google Scholar 

  7. 7.

    Baas Becking, L. G. M. Geobiologie of Inleiding tot de Milieukunde (Van Stockum & Zoon, 1934)

  8. 8.

    Martiny, J. B. H. et al. Microbial biogeography: putting microorganisms on the map. Nat. Rev. Microbiol. 4, 102–112 (2006).

    CAS  Google Scholar 

  9. 9.

    O’Malley, M. A. The nineteenth century roots of ‘everything is everywhere’. Nat. Rev. Microbiol. 5, 647–651 (2007).

    PubMed  Google Scholar 

  10. 10.

    Barberán, A., Casamayor, E. O. & Fierer, N. The microbial contribution to macroecology. Front. Microbiol. 5, 203 (2014).

    PubMed  PubMed Central  Google Scholar 

  11. 11.

    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  PubMed  Google Scholar 

  12. 12.

    Fierer, N. in Accessing Uncultivated Microorganisms: From the Environment to Organisms and Genomes and Back (ed. Zengler, K.) Ch. 6 (ASM Press, 2008).

  13. 13.

    Hejda, M., Pyšek, P. & Jarošík, V. Impact of invasive plants on the species richness, diversity and composition of invaded communities. J. Ecol. 97, 393–403 (2009).

    Google Scholar 

  14. 14.

    Litchman, E. Invisible invaders: non-pathogenic invasive microbes in aquatic and terrestrial ecosystems. Ecol. Lett. 13, 1560–1572 (2010).

    PubMed  Google Scholar 

  15. 15.

    Acosta, F., Zamor, R. M., Najar, F. Z., Roe, B. A. & Hambright, K. D. Dynamics of an experimental microbial invasion. Proc. Natl Acad. Sci. USA 112, 11594–11599 (2015).

    CAS  PubMed  Google Scholar 

  16. 16.

    Rivett, D. W. et al. Elevated success of multispecies bacterial invasions impacts community composition during ecological succession. Ecol. Lett. 21, 516–524 (2018).

    PubMed  Google Scholar 

  17. 17.

    Jani, A. J. & Briggs, C. J. The pathogen Batrachochytrium dendrobatidis disturbs the frog skin microbiome during a natural epidemic and experimental infection. Proc. Natl Acad. Sci. USA 111, E5049–E5058 (2014).

    CAS  PubMed  Google Scholar 

  18. 18.

    Wei, Z. et al. Trophic network architecture of root-associated bacterial communities determines pathogen invasion and plant health. Nat. Commun. 6, 8413 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. 19.

    Koch, H. & Schmid-Hempel, P. Socially transmitted gut microbiota protect bumble bees against an intestinal parasite. Proc. Natl Acad. Sci. USA 108, 19288–19292 (2011).

    CAS  Google Scholar 

  20. 20.

    Elton, C. S. The Ecology of Invasions by Animals and Plants (Springer, 1958).

  21. 21.

    Schulze, E.-D. & Mooney, H. A. in Biodiversity and Ecosystem Function (eds Schulze, E.-D. & Mooney, H. A.) 497–510 (Springer, 1994).

  22. 22.

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

    Google Scholar 

  23. 23.

    Prosser, J. I. et al. The role of ecological theory in microbial ecology. Nat. Rev. Microbiol. 5, 384–392 (2007).

    CAS  Google Scholar 

  24. 24.

    Lenski, R. E., Rose, M. R., Simpson, S. C. & Tadler, S. C. Long-term experimental evolution in Escherichia coli. I. adaptation and divergence during 2,000 generations. Am. Nat. 138, 1315–1341 (1991).

    Google Scholar 

  25. 25.

    Wright, E. S. & Vetsigian, K. H. Inhibitory interactions promote frequent bistability among competing bacteria. Nat. Commun. 7, 11274 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. 26.

    Higgins, L. M., Friedman, J., Shen, H. & Gore, J. Co-occurring soil bacteria exhibit a robust competitive hierarchy and lack of non-transitive interactions. Preprint at (2017).

  27. 27.

    Foster, K. R. & Bell, T. Competition, not cooperation, dominates interactions among culturable microbial species. Curr. Biol. 22, 1845–1850 (2012).

    CAS  Google Scholar 

  28. 28.

    Coyte, K. Z., Schluter, J. & Foster, K. R. The ecology of the microbiome: networks, competition, and stability. Science 350, 663–666 (2015).

    CAS  Google Scholar 

  29. 29.

    Momeni, B., Xie, L. & Shou, W. Lotka–Volterra pairwise modeling fails to capture diverse pairwise microbial interactions. eLife 6, e25051 (2017).

  30. 30.

    Goldford, J. E. et al. Emergent simplicity in microbial community assembly. Science 361, 469–474 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. 31.

    Jousset, A., Schulz, W., Scheu, S. & Eisenhauer, N. Intraspecific genotypic richness and relatedness predict the invasibility of microbial communities. ISME J. 5, 1108–1114 (2011).

    PubMed  PubMed Central  Google Scholar 

  32. 32.

    Eisenhauer, N., Scheu, S. & Jousset, A. Bacterial diversity stabilizes community productivity. PLoS ONE 7, e34517 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. 33.

    Mallon, C. A. et al. Resource pulses can alleviate the biodiversity–invasion relationship in soil microbial communities. Ecology 96, 915–926 (2015).

    PubMed  Google Scholar 

  34. 34.

    Yang, T. et al. Resource availability modulates biodiversity–invasion relationships by altering competitive interactions. Environ. Microbiol. 19, 2984–2991 (2017).

    PubMed  Google Scholar 

  35. 35.

    Jones, M. L., Ramoneda, J., Rivett, D. W. & Bell, T. Biotic resistance shapes the influence of propagule pressure on invasion success in bacterial communities. Ecology 98, 1743–1749 (2017).

    PubMed  Google Scholar 

  36. 36.

    Rillig, M. C. et al. Interchange of entire communities: microbial community coalescence. Trends Ecol. Evol. 30, 470–476 (2015).

    PubMed  Google Scholar 

  37. 37.

    Lu, N., Sanchez-Gorostiaga, A., Tikhonov, M. & Sanchez, A. Cohesiveness in microbial community coalescence. Preprint at (2018).

  38. 38.

    Hellweger, F. L., Clegg, R. J., Clark, J. R., Plugge, C. M. & Kreft, J.-U. Advancing microbial sciences by individual-based modelling. Nat. Rev. Microbiol. 14, 461–471 (2016).

    CAS  PubMed  Google Scholar 

  39. 39.

    Volterra, V. Variations and fluctuations of the number of individuals in animal species living together. ICES J. Mar. Sci. 3, 3–51 (1928).

    Google Scholar 

  40. 40.

    Mounier, J. et al. Microbial interactions within a cheese microbial community. Appl. Environ. Microbiol. 74, 172–181 (2008).

    CAS  Google Scholar 

  41. 41.

    MacArthur, R. Species packing and competitive equilibrium for many species. Theor. Popul. Biol. 1, 1–11 (1970).

    CAS  PubMed  Google Scholar 

  42. 42.

    Chesson, P. MacArthur’s consumer-resource model. Theor. Popul. Biol. 37, 26–38 (1990).

    Google Scholar 

  43. 43.

    Bashan, A. et al. Universality of human microbial dynamics. Nature 534, 259–262 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. 44.

    Wade, M. J. et al. Perspectives in mathematical modelling for microbial ecology. Ecol. Model. 321, 64–74 (2016).

    Google Scholar 

  45. 45.

    Zuñiga, C., Zaramela, L. & Zengler, K. Elucidation of complexity and prediction of interactions in microbial communities. Microb. Biotechnol. 10, 1500–1522 (2017).

    PubMed  PubMed Central  Google Scholar 

  46. 46.

    Kinnunen, M. et al. A conceptual framework for invasion in microbial communities. ISME J. 10, 2773–2775 (2016).

    PubMed  PubMed Central  Google Scholar 

  47. 47.

    Kinnunen, M., Dechesne, A., Albrechtsen, H.-J. & Smets, B. F. Stochastic processes govern invasion success in microbial communities when the invader is phylogenetically close to resident bacteria. ISME J. 12, 2748–2756 (2018).

  48. 48.

    Phillips, B. L., Brown, G. P., Webb, J. K. & Shine, R. Invasion and the evolution of speed in toads. Nature 439, 803 (2006).

    CAS  PubMed  Google Scholar 

  49. 49.

    Sanchez, A. & Gore, J. Feedback between population and evolutionary dynamics determines the fate of social microbial populations. PLoS Biol. 11, e1001547 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. 50.

    Faillace, C. A. & Morin, P. J. Evolution alters the consequences of invasions in experimental communities. Nat. Ecol. Evol. 1, 13 (2016).

    PubMed  Google Scholar 

  51. 51.

    Hubbell, S. The Unified Neutral Theory of Biodiversity and Biogeography (MPB-32) (Princeton Univ. Press, 2001).

  52. 52.

    Fisher, C. K. & Mehta, P. The transition between the niche and neutral regimes in ecology. Proc. Natl Acad. Sci. USA 111, 13111–13116 (2014).

    CAS  PubMed  Google Scholar 

  53. 53.

    O’Dwyer, J. P. & Chisholm, R. A mean field model for competition: from neutral ecology to the Red Queen. Ecol. Lett. 17, 961–969 (2014).

    PubMed  Google Scholar 

  54. 54.

    Rosindell, J., Harmon, L. J. & Etienne, R. S. Unifying ecology and macroevolution with individual-based theory. Ecol. Lett. 18, 472–482 (2015).

    PubMed  PubMed Central  Google Scholar 

  55. 55.

    Gilpin, M. Community-level competition: asymmetrical dominance. Proc. Natl Acad. Sci. USA 91, 3252–3254 (1994).

    CAS  PubMed  Google Scholar 

  56. 56.

    Rillig, M. C., Tsang, A. & Roy, J. Microbial community coalescence for microbiome engineering. Front. Microbiol. 7, 1967 (2016).

    PubMed  PubMed Central  Google Scholar 

  57. 57.

    Sierocinski, P. et al. A single community dominates structure and function of a mixture of multiple methanogenic communities. Curr. Biol. 27, 3390–3395 (2017).

    CAS  PubMed  Google Scholar 

  58. 58.

    Fisher, R. A. The Genetical Theory of Natural Selection (Clarendon Press, 1930).

  59. 59.

    Ohta, T. Slightly deleterious mutant substitutions in evolution. Nature 246, 96–98 (1973).

    CAS  Google Scholar 

  60. 60.

    Desai, M. M., Fisher, D. S. & Murray, A. W. The speed of evolution and maintenance of variation in asexual populations. Curr. Biol. 17, 385–394 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. 61.

    Doolittle, W. F. & Papke, R. T. Genomics and the bacterial species problem. Genome Biol. 7, 116 (2006).

    PubMed  PubMed Central  Google Scholar 

  62. 62.

    van Elsas, J. D. et al. Microbial diversity determines the invasion of soil by a bacterial pathogen. Proc. Natl Acad. Sci. USA 109, 1159–1164 (2012).

    PubMed  Google Scholar 

  63. 63.

    Rouzine, I. M., Brunet, E. & Wilke, C. O. The traveling-wave approach to asexual evolution: Muller’s ratchet and speed of adaptation. Theor. Popul. Biol. 73, 24–46 (2008).

    PubMed  Google Scholar 

  64. 64.

    Wiser, M. J., Ribeck, N. & Lenski, R. E. Long-term dynamics of adaptation in asexual populations. Science 342, 1364–1367 (2013).

    CAS  PubMed  Google Scholar 

  65. 65.

    Lenski, R. E. et al. Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment with Escherichia coli. Proc. Biol. Sci. 282, 20152292 (2015).

    PubMed  PubMed Central  Google Scholar 

  66. 66.

    MacArthur, R. H. & Wilson, E. O. The Theory of Island Biogeography (Princeton Univ. Press, 1967).

  67. 67.

    Muller, H. J. Some genetic aspects of sex. Am. Nat. 66, 118–138 (1932).

    Google Scholar 

  68. 68.

    Gerrish, P. J. & Lenski, R. E. in Mutation and Evolution (eds. Woodruff, R. C. & Thompson, J. N.) 127–144 (Springer, 1998).

  69. 69.

    Park, S.-C. & Krug, J. Clonal interference in large populations. Proc. Natl Acad. Sci. USA 104, 18135–18140 (2007).

    CAS  PubMed  Google Scholar 

  70. 70.

    Rosindell, J., Hubbell, S. P., He, F., Harmon, L. J. & Etienne, R. S. The case for ecological neutral theory. Trends Ecol. Evol. 27, 203–208 (2012).

    PubMed  Google Scholar 

  71. 71.

    Guisan, A. & Zimmermann, N. E. Predictive habitat distribution models in ecology. Ecol. Model. 135, 147–186 (2000).

    Google Scholar 

  72. 72.

    Uden, D. R., Allen, C. R., Angeler, D. G., Corral, L. & Fricke, K. A. Adaptive invasive species distribution models: a framework for modeling incipient invasions. Biol. Invasions 17, 2831–2850 (2015).

    Google Scholar 

  73. 73.

    Barbet-Massin, M., Rome, Q., Villemant, C. & Courchamp, F. Can species distribution models really predict the expansion of invasive species? PLoS ONE 13, e0193085 (2018).

    PubMed  PubMed Central  Google Scholar 

  74. 74.

    Miralles, R., Gerrish, P. J., Moya, A. & Elena, S. F. Clonal interference and the evolution of RNA viruses. Science 285, 1745–1747 (1999).

    CAS  PubMed  Google Scholar 

  75. 75.

    Tilman, D., Wedin, D. & Knops, J. Productivity and sustainability influenced by biodiversity in grassland ecosystems. Nature 379, 718 (1996).

    CAS  Google Scholar 

  76. 76.

    Tilman, D. Resource competition and community structure. Monogr. Popul. Biol. 17, 1–296 (1982).

    CAS  PubMed  Google Scholar 

  77. 77.

    Tilman, D. Niche tradeoffs, neutrality, and community structure: a stochastic theory of resource competition, invasion, and community assembly. Proc. Natl Acad. Sci. USA 101, 10854–10861 (2004).

    CAS  PubMed  Google Scholar 

  78. 78.

    Loreau, M. & Hector, A. Partitioning selection and complementarity in biodiversity experiments. Nature 412, 72–76 (2001).

    CAS  PubMed  Google Scholar 

  79. 79.

    De Roy, K. et al. Environmental conditions and community evenness determine the outcome of biological invasion. Nat. Commun. 4, 1383 (2013).

    PubMed  Google Scholar 

  80. 80.

    Houseman, G. R., Foster, B. L. & Brassil, C. E. Propagule pressure–invasibility relationships: testing the influence of soil fertility and disturbance with Lespedeza cuneata. Oecologia 174, 511–520 (2014).

    PubMed  Google Scholar 

  81. 81.

    Ketola, T., Saarinen, K. & Lindström, L. Propagule pressure increase and phylogenetic diversity decrease community’s susceptibility to invasion. BMC Ecol. 17, 15 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  82. 82.

    Barney, J. N., Ho, M. W. & Atwater, D. Z. Propagule pressure cannot always overcome biotic resistance: the role of density-dependent establishment in four invasive species. Weed Res. 56, 208–218 (2016).

    Google Scholar 

  83. 83.

    Dillon, R. J., Vennard, C. T., Buckling, A. & Charnley, A. K. Diversity of locust gut bacteria protects against pathogen invasion. Ecol. Lett. 8, 1291–1298 (2005).

    Google Scholar 

  84. 84.

    Fargione, J. E. & Tilman, D. Diversity decreases invasion via both sampling and complementarity effects: diversity causes invader underyielding. Ecol. Lett. 8, 604–611 (2005).

    Google Scholar 

  85. 85.

    Jiang, L. & Morin, P. J. Productivity gradients cause positive diversity–invasibility relationships in microbial communities. Ecol. Lett. 7, 1047–1057 (2004).

    Google Scholar 

  86. 86.

    Ratzke, C. & Gore, J. Modifying and reacting to the environmental pH can drive bacterial interactions. PLoS Biol. 16, e2004248 (2018).

    PubMed  PubMed Central  Google Scholar 

  87. 87.

    Simberloff, D. The role of propagule pressure in biological invasions. Annu. Rev. Ecol. Evol. Syst. 40, 81–102 (2009).

    Google Scholar 

  88. 88.

    Huey, R. B., Gilchrist, G. W., Carlson, M. L., Berrigan, D. & Serra, L. Rapid evolution of a geographic cline in size in an introduced fly. Science 287, 308–309 (2000).

    CAS  PubMed  Google Scholar 

  89. 89.

    Ochocki, B. M. & Miller, T. E. X. Rapid evolution of dispersal ability makes biological invasions faster and more variable. Nat. Commun. 8, 14315 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  90. 90.

    Wilson, E. O. & Peter, F. M. Diversity and Biological Invasions of Oceanic Islands (National Academies Press, 1988).

  91. 91.

    Carlquist, S. J. Island Biology (Columbia Univ. Press, 1974).

  92. 92.

    Colautti, R. I., Bailey, S. A., van Overdijk, C. D. A., Amundsen, K. & MacIsaac, H. J. Characterised and projected costs of nonindigenous species in canada. Biol. Invasions 8, 45–59 (2006).

    Google Scholar 

  93. 93.

    Rosindell, J. & Harmon, L. J. A unified model of species immigration, extinction and abundance on islands. J. Biogeogr. 40, 1107–1118 (2013).

    Google Scholar 

  94. 94.

    Rosindell, J., Cornell, S. J., Hubbell, S. P. & Etienne, R. S. Protracted speciation revitalizes the neutral theory of biodiversity. Ecol. Lett. 13, 716–727 (2010).

    PubMed  Google Scholar 

  95. 95.

    Buckling, A. & Rainey, P. B. The role of parasites in sympatric and allopatric host diversification. Nature 420, 496–499 (2002).

    CAS  PubMed  Google Scholar 

  96. 96.

    Hansen, S. K., Rainey, P. B., Haagensen, J. A. J. & Molin, S. Evolution of species interactions in a biofilm community. Nature 445, 533–536 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  97. 97.

    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).

    CAS  PubMed  Google Scholar 

  98. 98.

    Mickalide, H. & Kuehn, S. Higher-order interaction inhibits bacterial invasion of a phototroph-predator microbial community. Preprint at (2019).

  99. 99.

    Li, M. et al. Facilitation promotes invasions in plant‐associated microbial communities. Ecol. Lett. 22, 149–158 (2019).

    PubMed  Google Scholar 

  100. 100.

    Niehaus, L. et al. Microbial coexistence through chemical-mediated interactions. Nat. Commun. 10, 2052 (2019).

    PubMed  PubMed Central  Google Scholar 

Download references


J.V. and M.P. were postgraduate students on the Computational Methods in Ecology and Evolution course at Imperial College, London. J.R. was funded by fellowships from the Natural Environment Research Council (NE/I021179, NE/L011611/1). T.B. was supported by a Royal Society University Research Fellowship. We thank members of the A. Sanchez and R. Chisholm Laboratories for useful discussions about the work. We thank N. Kristensen for comments on the manuscript. We thank A. Jousset and D. Hambright for providing us with access to data for re-plotting in Fig. 6. Our simulations were performed using the high-performance computing facility at Imperial College, London. This study is a contribution to Imperial College’s Grand Challenges in Ecosystems and the Environment initiative.

Author information




All authors contributed to designing the study. J.C.C.V. performed the analyses with input from J.R. and with reference to code written by M.P. J.C.CV. and J.R. wrote the paper. All authors revised the paper. J.C.C.V. and M.P. were postgraduate students in the research group of J.R. M.L.J. was a PhD student in the group of T.B.

Corresponding author

Correspondence to Jean C. C. Vila.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary methods, Table 1 and Figs. 1–7.

Reporting Summary

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Vila, J.C.C., Jones, M.L., Patel, M. et al. Uncovering the rules of microbial community invasions. Nat Ecol Evol 3, 1162–1171 (2019).

Download citation

Further reading


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing