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High taxonomic variability despite stable functional structure across microbial communities

Nature Ecology & Evolution volume 1, Article number: 0015 (2017) Cite this article

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Abstract

Understanding the processes that are driving variation of natural microbial communities across space or time is a major challenge for ecologists. Environmental conditions strongly shape the metabolic function of microbial communities; however, other processes such as biotic interactions, random demographic drift or dispersal limitation may also influence community dynamics. The relative importance of these processes and their effects on community function remain largely unknown. To address this uncertainty, here we examined bacterial and archaeal communities in replicate ‘miniature’ aquatic ecosystems contained within the foliage of wild bromeliads. We used marker gene sequencing to infer the taxonomic composition within nine metabolic functional groups, and shotgun environmental DNA sequencing to estimate the relative abundances of these groups. We found that all of the bromeliads exhibited remarkably similar functional community structures, but that the taxonomic composition within individual functional groups was highly variable. Furthermore, using statistical analyses, we found that non-neutral processes, including environmental filtering and potentially biotic interactions, at least partly shaped the composition within functional groups and were more important than spatial dispersal limitation and demographic drift. Hence both the functional structure and taxonomic composition within functional groups of natural microbial communities may be shaped by non-neutral and roughly separate processes.

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Figure 1: Bromeliad species used in this study.
Figure 2: Taxonomic and functional community structure.
Figure 3: Functional redundancy in the regional OTU pool.
Figure 4: Relating OTU proportions to environmental variables.
Figure 5: Variation partitioning of OTU composition.

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Acknowledgements

We thank M. Chen for help with the molecular work. We thank A. L. Gonzalez and A. MacDonald for discussions and comments on our paper. We thank T. Benevides for helping with the absorption measurements. S.L. acknowledges the financial support of the Department of Mathematics, University of British Columbia. S.L. and M.D. acknowledge the support of Natural Sciences and Engineering Research Council (NSERC). V.F.F. is grateful to the Brazilian Council for Research, Development and Innovation (CNPq) for research funds (Pesquisador Visitante Especial, PVE, Research Grant 400454/2014-9) and productivity grants. S.M.S.J. acknowledges the post-graduate scholarship provided by Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ). J.S.L. acknowledges the financial support of Coordenacao de Aperfeicoamento de Pessoal de Ensino Superior (CAPES). We thank M. P. F. Barros, A. R. Soares, J. L. Nepomuceno and their research groups of the Nucleus of Ecology and Socio-Environmental Development of Macae (NUPEM/UFRJ) for proving field and laboratory assistance during the samplings.

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Authors and Affiliations

  1. Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada

    Stilianos Louca, Diane S. Srivastava, Laura Wegener Parfrey & Michael Doebeli

  2. Institute of Applied Mathematics, University of British Columbia, Vancouver, V6T 1Z2, Canada

    Stilianos Louca

  3. Department of Ecology, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-590, Brazil

    Saulo M. S. Jacques, Aliny P. F. Pires, Juliana S. Leal & Vinicius F. Farjalla

  4. Programa de Pós-Graduação em Ecologia e Evolugão, Universidade Estadual do Rio de Janeiro, Rio de Janeiro, 20550-013, Brazil

    Saulo M. S. Jacques

  5. Programa de Pós-Graduação em Ecologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-971, Brazil

    Juliana S. Leal

  6. Department of Zoology, University of British Columbia, Vancouver, V6T 1Z4, Canada

    Diane S. Srivastava, Laura Wegener Parfrey & Michael Doebeli

  7. Department of Botany, University of British Columbia, Vancouver, V6T 1Z4, Canada

    Laura Wegener Parfrey

  8. Department of Mathematics, University of British Columbia, Vancouver, V6T 1Z2, Canada.

    Michael Doebeli

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Contributions

V.F.F., S.L., S.M.S.J., A.P.F.P. and J.S.L. performed the field work. V.F.F. and S.M.S.J. performed the chemical measurements in the laboratory. S.L. performed the molecular work in the laboratory, the DNA sequence analysis and the statistical analyses. S.L., M.D., V.F.F., D.S.S. and L.W.P. interpreted the statistical findings. S.L. wrote a first draft of the manuscript, and all authors contributed to the final preparation of the manuscript. M.D. and V.F.F. supervised the project.

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Correspondence to Stilianos Louca.

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Functional annotations of prokaryotic taxa (TXT 18 kb)

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Louca, S., Jacques, S., Pires, A. et al. High taxonomic variability despite stable functional structure across microbial communities. Nat Ecol Evol 1, 0015 (2017). https://doi.org/10.1038/s41559-016-0015

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