Symbiotic microbial communities support the survival and success of their hosts and help shape host responses to environmental change. Corals engage in a nutritional symbiosis with populations of single-celled dinoflagellate algae in the family Symbiodiniaceae; they also harbor diverse assemblages of other microbiota (eg, bacteria, fungi) that support coral health in diverse ways. Different members of this menagerie are infected by viruses, resulting in a complex “multipartite” symbiosis. In this dissertation, I addressed several drivers of microbiota assembly with the goal of clarifying how they affect coral reef persistence under future climate change conditions. Chapter 1 addresses the dynamics of a lineage of Symbiodiniaceae-infecting RNA viruses (“dinoRNAVs”) under thermal stress in fragments of a common reef-building coral. Diverse and heterogeneous assemblages of these viruses were detected in coral fragments, suggesting that these viruses are prevalent and persistent within Symbiodiniaceae cells in hospite. Furthermore, dinoRNAVs in coral fragments exposed to thermal stress were more diverse and variable than those associated with fragments of the same coral genets maintained in control conditions. These results suggest that dinoRNAVs become more productive under thermal stress conditions and may sometimes impact the coral-Symbiodiniaceae relationship by infecting, and perhaps lysing, Symbiodiniaceae cells. Chapters 2 and 3 address the role of coral reef fishes in dispersing coral-associated microbiota that can impact colony health. Chapter 2 demonstrates that corallivorous fish (coral predators) disperse large quantities of live Symbiodiniaceae across the reefscape, potentially making them available for uptake by juvenile corals or stressed adult corals. Chapter 3 indicates that coral-eating fish disperse diverse bacterial taxa, including some beneficial bacterial symbionts of corals. Corallivore feces contained higher relative abundances of bacteria that are putatively beneficial to coral health, and lower relative abundances of coral pathogens, than grazer/detritivore feces. Experimental addition of feces to coral fragments showed that feces from grazer/detritivores containing live microbiota caused corals to develop lesions (partial mortality) at double the frequency and four times the size compared to sterilized feces controls, while live microbiota in corallivore feces did not increase lesions sizes or frequencies compared to sterile feces controls. Altogether, the findings of this dissertation demonstrate several ways in which abiotic and biotic drivers can impact coral health. More broadly, studying how biotic entities such as viruses and consumers (herbivores, predators etc.) affect microbiota assembly in host organisms can help advance conservation, agriculture, and medicine.