Spatial homogeneity and limited transmission of microbial species among coral reef fishes from the Great Barrier Reef, Australia

Reef fishes account for one-third of all extant marine fishes and exhibit enormous biodiversity in a highly interactive ecosystem. Yet relatively little is known about the diversity and evolution of microbial species (bacteria, viruses, and eukaryotes) associated with reef fish, even though this may provide valuable insights into the factors that shape microbial communities within vertebrates and the extent and patterns of cross-species transmission. Through metatranscriptomic sequencing we characterised the viruses, bacteria and single-celled eukaryotes from 128 reef fish species inhabiting Lizard Island and Orpheus Island in the Great Barrier Reef, Australia, examining whether these microbial communities differ between these islands that are separated by approximately 450 kilometres. Notably, the same families and subfamilies of viruses and bacteria were found on both islands, comprising the Picornaviridae, Astroviridae, Parvoviridae, Hantaviridae, Orthomyxoviridae, Coronaviridae, Hepeviridae and Iridoviridae as well as Proteobacteria of the Vibrionaceae, Enterobacteriaceae, and Endozoicomonadaceae. However, despite strong ecological interactions in the reef environment, there was minimal evidence for individual microorganisms being shared among fish species. An exception was the high prevalence of the bacterial pathogen Photobacterium damselae among apparently healthy cardinalfishes from both islands, indicating that these fish species are natural reservoirs within the reef system. Overall, these data suggest that reef fishes harbour core microbial families that have long-established host associations, and that there are strong host barriers to cross-species microbial transmission even within the highly interactive and species-rich reef environment.