Coral reefs are fundamental in providing ecological, social and economical benefits to local communities, governments and nations. In Australia, the Great Barrier Reef is an iconic symbol in our national psyche, representing approximately 17% of the global tropical coral reef area with an estimated economic value at greater than AUD$5 billion per year. Coral reefs are constructed through the close association between reef building corals and their symbiotic dinoflagellate microalgae (Symbiodinium). However just as in other animal systems, corals are now thought of as a holobiont, forming additional close and intricate associations with a range of other microbial organisms such as bacteria, archaeae, fungi and viruses. Over the last decade a greater understanding has been obtained in how corals shape and structure their microbial partners, providing important functional roles in maintaining overall coral fitness. The cycling of nitrogen and sulfur compounds within the holobiont are increasingly being recognised as driving many of these coral microbial associations and have important consequences for coral health and the subsequent resilience of coral reefs. For example, nitrogen fixing bacteria (diazotrophs) within the Rhizobia group, which accomplish nitrogen fixation after establishing symbiosis in the roots of host plants, also appear common and specific to corals. These associations are established at the earliest larval life stages and maintained as the coral grows in mature colonies. Using fluorescence in situ hybridization (FISH) and nanoscale secondary ion mass spectrometry (NanoSIMS) the uptake of diazotrophic bacteria and passage of nitrogen into coral larvae can be observed, providing evidence that diazotrophs can provide an additional nitrogen source to the animal. Reef-building corals are the most prolific producers of dimethylsulphoniopropionate (DMSP), a molecule central in the marine sulphur cycle and precursor of the climate-active gas dimethylsulphide (DMS). Recent work has shown that the coral animal itself can produce DMSP, hence overturning the paradigm that photosynthetic organisms are the sole biological source of this compound. DMSP represents a rich nutrient source for bacteria with diversity surveys highlighting an extensive overlap between bacterial species associated with corals and species implicated in the degradation of dimethylsulfoniopropionate (DMSP). Again using FISH and NanoSIMS approaches, this close interaction between corals, their Symbiodinium partners and associated bacteria can be visualised. Interestingly, through the metabolism of DMSP, a Pseudovibrio sp. commonly associated with corals produced tropodithietic acid (TDA), a sulfur-containing antimicrobial which is suspected to act in protecting corals from invasive microbial species. Anthropogenic stresses such as increased sea surface temperatures, nutrient input and sedimentation can shift these coral-microbiota associations, thereby contributing to reduced coral fitness. For example, production of TDA by the coral associated Pseudovibrio sp.was significantly reduced at higher temperatures potentially reducing the protective effect the compound can provide the coral holobiont. Temperature stress also causes shifts in coral associated microbial communities, with a metagenomic approach demonstrating a shift in the microbial community away from autotrophy and an increase in virulence associated genes. Coral diseases are on the rise with disease outbreaks contributing to significant loss of both key reef organisms and coral cover. Recent assessments have documented sharp declines in coral reefs globally, therefore an understanding of the microbial factors that underlie coral health and fitness are paramount.