Insights into the Coral Microbiome: Underpinning the Health and Resilience of Reef Ecosystems

Abstract

Corals are fundamental ecosystem engineers, creating large, intricate reefs that support diverse and abundant marine life. At the core of a healthy coral animal is a dynamic relationship with microorganisms, including a mutually beneficial symbiosis with photosynthetic dinoflagellates (Symbiodinium spp.) and enduring partnerships with an array of bacterial, archaeal, fungal, protistan, and viral associates, collectively termed the coral holobiont. The combined genomes of this coral holobiont form a coral hologenome, and genomic interactions within the hologenome ultimately define the coral phenotype. Here we integrate contemporary scientific knowledge regarding the ecological, host-specific, and environmental forces shaping the diversity, specificity, and distribution of microbial symbionts within the coral holobiont, explore physiological pathways that contribute to holobiont fitness, and describe potential mechanisms for holobiont homeostasis. Understanding the role of the microbiome in coral resilience, acclimation, and environmental adaptation is a new frontier in reef science that will require large-scale collaborative research efforts.

Rapid adaptive responses to climate change in corals

“…The coral holobiont 67 is an inter-domain community of complex and dynamic associations involving the photosynthetic alveolate Symbiodinium and a range of bacteria, fungi and viruses, some of which have been central to the success of the Scleractinia as the dominant contemporary tropical reef-builder 68 (Fig. 3).…”

“…3). Although components of the holobiont have separate evolutionary trajectories 69 , the intimate nature of some coral-microbial associations implies that their interactions may contribute to the overall fitness of the holobiont 68 . In comparison with the coral host, the orders of magnitude greater diversity, shorter generation times, and remarkable metabolic range of the coral microbiome suggest that some microbes could make contributions to adaptive responses of the holobiont.…”

“…Host-associated bacterial communities could also contribute to the adaptive capacity of their coral hosts, given the enormous breadth of their metabolic capabilities and of mechanisms that contribute to their rapid evolution 84 . Roles in immunity, nitrogen fixation, nutrient cycling, osmoregulation and oxidative stress responses have been suggested for bacteria associated with different microhabitats within the coral host 68 . The potential significance of specific bacterial groups is suggested by their vertical transmission 80 and common presence within the tissues of a wide range of corals 85,86 .…”

Establishing microbial baselines to identify indicators of coral reef health

“…Microorganisms play an essential role in coral reef ecosystem processes and form diverse symbiotic relationships with benthos-dominating macro-organisms such as corals, sponges and algae [10][11][12] (Figure 2). The functional role of microbes in coral reefs include biochemical cycling of nutrients, degradation and remineralisation, host nutrition, vitamin synthesis, production of secondary metabolites and host defence via the production of antimicrobial peptides 10,11 .…”

“…The functional role of microbes in coral reefs include biochemical cycling of nutrients, degradation and remineralisation, host nutrition, vitamin synthesis, production of secondary metabolites and host defence via the production of antimicrobial peptides 10,11 . Microbes often form specific and stable associations with their host species 13 and can assist them to acclimate to the prevailing environmental conditions 14,15 .…”