A horizon scan of priorities for coastal marine microbiome research

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.

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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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.

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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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