Microbial communities often exhibit incredible taxonomic diversity, raising questions regarding the mechanisms enabling species coexistence and the role of this diversity in community functioning. On the one hand, many coexisting but taxonomically distinct microorganisms can encode the same energy-yielding metabolic functions, and this functional redundancy contrasts with the expectation that species should occupy distinct metabolic niches. On the other hand, the identity of taxa encoding each function can vary substantially across space or time with little effect on the function, and this taxonomic variability is frequently thought to result from ecological drift between equivalent organisms. Here, we synthesize the powerful paradigm emerging from these two patterns, connecting the roles of function, functional redundancy and taxonomy in microbial systems. We conclude that both patterns are unlikely to be the result of ecological drift, but are inevitable emergent properties of open microbial systems resulting mainly from biotic interactions and environmental and spatial processes.

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We thank M. Pennell, F. Doolittle, A. C. Martiny and I. Rubin for discussions and for participation at a workshop from which this Perspective emerged. We thank the Canadian Institute for Ecology and Evolution (CIEE) for financial support of all authors, by means of a Thematic Working Group grant on the ‘evolution of microbial metabolic and genomic diversity at multiple scales’. We thank the Biodiversity Research Centre and the Adapting Biosystems programme, University of British Columbia, for financial support, and K. Beall for logistical support. S.L. was supported by an NSERC grant and a postdoctoral fellowship from the Biodiversity Research Centre, UBC. J.A.H. was supported by the NSF Center for Dark Energy Biosphere Investigations (OCE-0939564).

Author information


  1. Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada

    • Stilianos Louca
    • , Florent Mazel
    • , Mary I. O’Connor
    • , Diane S. Srivastava
    • , Michael Doebeli
    •  & Laura Wegener Parfrey
  2. Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada

    • Stilianos Louca
    • , Mary I. O’Connor
    • , Diane S. Srivastava
    • , Michael Doebeli
    •  & Laura Wegener Parfrey
  3. Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA

    • Martin F. Polz
  4. Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada

    • Florent Mazel
    •  & Laura Wegener Parfrey
  5. Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada

    • Florent Mazel
  6. Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA

    • Michaeline B. N. Albright
  7. Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA

    • Julie A. Huber
  8. Department of Environmental Systems Science, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland

    • Martin Ackermann
  9. Department of Environmental Microbiology, Eawag, Dübendorf, Switzerland

    • Martin Ackermann
  10. Ecosystem Services, Commercialization Platforms, and Entrepreneurship (ECOSCOPE) Training Program, University of British Columbia, Vancouver, British Columbia, Canada

    • Aria S. Hahn
    •  & Sean A. Crowe
  11. Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada

    • Sean A. Crowe
  12. Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada

    • Sean A. Crowe
  13. Department of Mathematics, University of British Columbia, Vancouver, British Columbia, Canada

    • Michael Doebeli


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S.L., L.W.P. and M.D. organized the workshop from which this Perspective emerged. S.L. performed the data analyses. All authors contributed to the writing of the manuscript.

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The authors declare no competing interests.

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Correspondence to Stilianos Louca.

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