A horizon scan of priorities for coastal marine microbiome research.

Stacey M Trevathan-Tackett,Torsten Thomas,Valentina Hurtado-Mccormick,Peter D Steinberg,Leo Hardtke,Marco Fusi,Peter I Macreadie,Laura Vann,Alana Firl,Lauren F Messer,Han Ming Gan,Daniele Daffonchio,Ezequiel M Marzinelli,Megan J Huggett,Bonnie Laverock,Justin R Seymour,Suhelen Egan,Tracy D Ainsworth,Alexandra H Campbell,Aschwin H Engelen,Craig D H Sherman ,Alejandra Hernández‐Agreda ,Karita Negandhi

doi:10.1038/s41559-019-0999-7

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.

Highlights

Coastal marine ecosystems provide a range of ecologically and economically important ecosystem services, including habitat provisions, nutrient cycling, coastal protection and fisheries enhancement[1]
We have provided a diversity of references to support the presented themes throughout, with the aim to create a comprehensive vision that may unify the strategy of research on coastal marine microbiomes
We identify several questions that we hope will move the field forward and lead into innovative approaches that determine the functional roles of coastal marine microbiomes, and thereby resolve the relationship between microbiome diversity and their functions:

Summary

Background

Coastal marine ecosystems provide a range of ecologically and economically important ecosystem services, including habitat provisions, nutrient cycling, coastal protection and fisheries enhancement[1]. The large national and international collaborations or consortium efforts that have produced the descriptive data on environmental microbiomes todate, may be useful in progressing hypothesis-driven questions through concerted manipulative experimental approaches[107], e.g. temperature effects on holobiont resilience at the biogeographic limits of the host (Themes, 5, 4 and 2, respectively) or how holobionts can act as sources or sinks of pathogenic microbiota under various point source or diffuse pollution scenarios (Theme 7). The list of research themes we present here is broad and ambitious, the ongoing collaborative networks along with well-executed hypothesis-driven manipulative experiments are significantly progressing the definition and functional relationship between the core microbiome and host, illuminating global microbiome biogeography, and identifying key regional- and global-scale environmental influences on coastal marine microbiomes and holobionts. Code availability: The code used the extract literature from databases is available in the supplementary materials

Literature Cited

Limitations

Molecular Approaches

Manipulative Experiments

Findings

Coastal Marine Microbiome Management