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 microbes in ecosystem function. This is particularly relevant in ocean environments, where microbes constitute the majority of biomass and control most of the major biogeochemical cycles, including those that regulate the Earth's climate. Coastal marine environments provide goods and services that are imperative to human survival and well-being (e.g. fisheries, water purification), and emerging evidence indicates that these ecosystem services often depend on complex relationships between communities of microorganisms (the 'microbiome') and their hosts or environment -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 evaluated the current state of knowledge on coastal marine microbiome research and identified 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.

The Seagrass Holobiont: What We Know and What We Still Need to Disclose for Its Possible Use as an Ecological Indicator

“…Host-microbes interactions play crucial roles in biological and ecological functions, thus, organisms are better considered as a network of interactions between the host and all the associated microorganisms (bacteria, fungi and viruses), with which the host establishes transient or lasting complex relationships [40][41][42]. The host and the entirety of microorganisms living in/on its tissues represent a complex functional unit, the holobiont [33].…”

Distinct fungal communities associated with different organs of the mangrove Sonneratia alba in the Malay Peninsula

“…These discoveries are occurring during a time of growing interest and appreciation of the marine microbiome and how this is influenced by, or influences the microbiome of species found in coastal areas (Glasl et al 2019a , b ; Trevathan-Tackett et al 2019 ). Yet, there remains a lack of research into the coastal microbiome and this is especially apparent in comparison to most other microbiome types (e.g., the human microbiome) (Trevathan-Tackett et al 2019 ; Wilkins et al 2019 ).…”

“…These discoveries are occurring during a time of growing interest and appreciation of the marine microbiome and how this is influenced by, or influences the microbiome of species found in coastal areas (Glasl et al 2019a , b ; Trevathan-Tackett et al 2019 ). Yet, there remains a lack of research into the coastal microbiome and this is especially apparent in comparison to most other microbiome types (e.g., the human microbiome) (Trevathan-Tackett et al 2019 ; Wilkins et al 2019 ). Specifically, despite the recognised necessity of mangroves and the critical ecosystem services they provide, work on the mangrove microbiome is embryonic at best, especially in contrast to the more charismatic coral reefs (Buddemeier and Smith 1999 ) where studies are relatively numerous and advanced in comparison (Ainsworth and Gates 2016 ; Hernandez-Agreda et al 2017 ; Gardner et al 2019 ; Wainwright et al 2019a ).…”

The Role of Biofilms Developed under Different Anthropogenic Pressure on Recruitment of Macro-Invertebrates

“…These cascading effects would represent a new scale of impacts beyond the reported consequences on the recruitment of macroinvertebrates. In addition, it evidences the important role that biofilm (or microbiome) could be playing here as an ecological control of the functioning fluxes (i.e., "holobiont"; [68]). Conservation of biofilms developed in pristine habitats, e.g., MPAs, can be therefore of direct relevance for the conservation of coastal ecosystem function, especially considering the unstopped urbanization of marine coastal habitats.…”