Resident damselfish influence the coral holobiont: species-specific responses in Acropora millepora and Acropora digitifera

Abstract Symbiotic interactions are central to coral ecology, spanning the coral holobiont’s internal microbial partnerships to broader associations with reef fishes and other motile species. Coral-dwelling damselfish live in close association with coral colonies, using their branches as shelter. These associations can influence the coral’s immediate environment through various mechanisms including nutrient inputs, oxygen dynamics, and sediment removal, while fish may also serve as vectors for microorganisms. Despite their ecological prevalence, our understanding of how these damselfish-coral associations influence holobiont composition and ultimately coral health remains limited. Here, we investigated how resident damselfish influence the holobiont composition of two coral species, Acropora millepora and Acropora digitifera, along Ningaloo Reef in Western Australia. Tissue samples were collected from coral colonies hosting varying numbers of resident damselfish and characterised for Symbiodiniaceae density, pigmentation, and community composition, alongside bacterial community composition using ITS2 and 16S rRNA amplicon sequencing. Our findings reveal distinct holobiont signatures between coral species, with A. millepora exhibiting higher symbiont cell density and bacterial alpha diversity. While both species were dominated by symbionts of the genus Cladocopium and bacteria of the family Endozoicomonadaceae, they predominantly hosted sequence variants unique to each species. At the colony level, those with damselfish showed reduced bacterial diversity and subtle shifts in community structure in A. millepora but not A. digitifera , while symbiont density, pigmentation and community composition remained largely unaffected in both species. Our results offer an initial snapshot of coral–damselfish–microbe interactions and a framework for understanding how ecological associations can influence holobiont dynamics.