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A horizon scan of priorities for coastal marine microbiome research

Nature Ecology & Evolution volume 3, pages 1509–1520 (2019)Cite this article

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Abstract

Research into the microbiomes of natural environments is changing the way ecologists and evolutionary biologists view the importance of microorganisms in ecosystem function. This is particularly relevant in ocean environments, where microorganisms constitute the majority of biomass and control most of the major biogeochemical cycles, including those that regulate Earth’s climate. Coastal marine environments provide goods and services that are imperative to human survival and well-being (for example, fisheries and water purification), and emerging evidence indicates that these ecosystem services often depend on complex relationships between communities of microorganisms (the ‘microbiome’) and the environment or their hosts — termed the ‘holobiont’. Understanding of coastal ecosystem function must therefore be framed under the holobiont concept, whereby macroorganisms and their associated microbiomes are considered as a synergistic ecological unit. Here, we evaluate the current state of knowledge on coastal marine microbiome research and identify key questions within this growing research area. Although the list of questions is broad and ambitious, progress in the field is increasing exponentially, and the emergence of large, international collaborative networks and well-executed manipulative experiments are rapidly advancing the field of coastal marine microbiome research.

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Fig. 1: Determining microbiome contribution to coastal ecosystem health.

Coral reef, Alexander J. Fordyce; mangrove, Michael Bradley.

Fig. 2: Conceptual design of the potential relationships between coastal marine microbiomes and humans.
Fig. 3: A conceptual diagram depicting several of the major research themes in coastal marine microbiome research.

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Article 30 June 2022

Tara Ocean Foundation, Tara Oceans, … European Marine Biological Resource Centre - European Research Infrastructure Consortium (EMBRC-ERIC)

Data availability

The original questions for the horizon scan are available in the Supplementary Information.

Code availability

The code used to extract literature from databases is available in the Supplementary Information.

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Acknowledgements

We thank Deakin University’s School of Life and Environmental Sciences and the Centre for Integrative Ecology for funding the workshop (New Activities Scheme 2017). B.L.’s attendance at the workshop was funded by the New Zealand Ministry of Business, Innovation and Employment Smart Ideas project UOWX1602. L.M.’s attendance was supported by an Australian Research Council Discovery Project (DP160103811). A.H.C.’s attendance was funded by the Centre for Marine Bio-Innovation at UNSW Australia. A.H.E. was supported by CCMAR/ID/16/2018, within CEECINST/00114/2018 and UID/Multi/04326/2019 financed by Fundação para a Ciência e a Tecnologia (FCT). D.D. was supported by King Abdullah University of Science and Technology through the baseline research fund and the Competetive Research Grant CRG-7-3739, Microlanding. S.M.T.-T. was supported by Deakin University’s SEBE Postdoctoral Industry Fellowship, the Mary Collins Trust and the Alfred Deakin Postdoctoral Research Fellowship. We thank J. Martiny, S. Robbins, G. Tyson, C. Weihe and K. Whiteson for their input in the horizon scanning exercise. We thank L. Koop for producing the conceptual designs.

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Authors and Affiliations

  1. Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia

    Stacey M. Trevathan-Tackett, Craig D.H. Sherman, Han Ming Gan & Peter I. Macreadie

  2. Centre for Marine Ecosystems Research and Centre for Ecosystem Management, School of Science, Edith Cowan University, Joondalup, Western Australia, Australia

    Megan J. Huggett

  3. School of Environmental and Life Sciences, The University of Newcastle, Ourimbah, New South Wales, Australia

    Megan J. Huggett

  4. Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia

    Alexandra H. Campbell, Tracy D. Ainsworth, Suhelen Egan, Torsten Thomas, Ezequiel M. Marzinelli & Peter D. Steinberg

  5. University of the Sunshine Coast, Sippy Downs, Queensland, Australia

    Alexandra H. Campbell

  6. School of Science, Auckland University of Technology, Auckland, New Zealand

    Bonnie Laverock

  7. Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia

    Valentina Hurtado-McCormick, Justin R. Seymour & Leo Hardtke

  8. Genome Center, University of California, Davis, Davis, CA, USA

    Alana Firl & Laura Vann

  9. Australian Centre for Ecogenomics, University of Queensland, St Lucia, Queensland, Australia

    Lauren F. Messer

  10. Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia

    Tracy D. Ainsworth & Alejandra Hernandez-Agreda

  11. Department of Earth and Planetary Sciences, Macquarie University, North Ryde, New South Wales, Australia

    Karita L. Negandhi

  12. Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia

    Daniele Daffonchio & Marco Fusi

  13. Centre for Marine Sciences, Universidade do Algarve, Faro, Portugal

    Aschwin H. Engelen

  14. School of Applied Sciences, Edinburgh Napier University, Edinburgh, UK

    Marco Fusi

  15. The College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia

    Alejandra Hernandez-Agreda

  16. Sydney Institute of Marine Science, Mosman, New South Wales, Australia

    Ezequiel M. Marzinelli & Peter D. Steinberg

  17. Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore

    Ezequiel M. Marzinelli & Peter D. Steinberg

  18. School of Life and Environmental Sciences, Coastal and Marine Ecosystems, The University of Sydney, Sydney, New South Wales, Australia

    Ezequiel M. Marzinelli

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  1. Stacey M. Trevathan-Tackett
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Contributions

S.M.T.-T. conceived the idea; S.M.T.-T., C.D.H.S. and P.I.M. developed and led the workshop; S.M.T.-T., C.D.H.S., P.I.M., M.J.H., A.H.C., B.L., V.H.-M., J.R.S., L.F.M., T.D.A. and K.L.H. attended the workshop that structured the themes of the manuscript; S.M.T.-T., C.D.H.S., P.I.M., M.J.H., A.H.C., B.L., V.H.-M., J.R.S., L.F.M., T.D.A., K.L.H., A.F., D.D., S.E., A.H.E., M.F., T.T., L.V., A.H.-A., H.M.G., E.M.M. and P.D.S. contributed to the questions and wrote the manuscript; A.F., V.H.-M., S.M.T.-T. and L.H. contributed to the literature search.

Corresponding author

Correspondence to Stacey M. Trevathan-Tackett.

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Supplementary Figs. 1 and 2, methods and Data 1.

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Trevathan-Tackett, S.M., Sherman, C.D., Huggett, M.J. et al. A horizon scan of priorities for coastal marine microbiome research. Nat Ecol Evol 3, 1509–1520 (2019). https://doi.org/10.1038/s41559-019-0999-7

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