Integrating novel tools to elucidate the metabolic basis of microbial symbiosis in reef holobionts

Microorganisms form symbiotic relationships with the majority of animals and plants on earth and are integral to their health and functioning in the ecosystem. Coral reefs in particular, one of the most productive ecosystems in the world, depend upon a plethora of organisms (e.g., corals, sponges, and macroalgae) and their microbial symbionts to exist. Yet, little is known about the metabolic basis of microbial symbiosis in these reef holobionts. A wide array of molecular techniques to characterise symbiotic microbial communities and map their metabolic interactions can now be exploited to reveal the extent to which microorganisms underpin both holobiont and ecosystem functioning. However, despite their utility in revealing and validating the functional role of specific microbes, ‘omic’ tools, stable isotope probing, and advanced imaging approaches such as NanoSIMS and Raman spectroscopy are rarely utilised in complex environmental settings like coral reefs. In this review, we describe molecular techniques and experimental approaches that can be employed to provide insight into microbial interactions and symbiotic function in coral reef holobionts. We further describe the inherent challenges involved in their application and suggest methods to solve these challenges to unravel the metabolic interactions underpinning these complex reef symbioses.