Cryptic Interactions in a Marine Microcosm: Sponges Shape the Microbiome of a Resident Goby

Microbial symbionts influence ecological and evolutionary processes in their multicellular hosts; yet they remain poorly characterised in marine systems. Sponges host exceptionally diverse microbiomes, potentially providing rich microbial reservoirs for their residents. The tusked goby (Risor ruber), an obligate sponge-dweller, and its sponge hosts provide an ideal model to investigate the causes and consequences of shared microbial taxa in host-resident systems. Using 16S rRNA sequencing, we characterised the microbiomes of R. ruber skin and gut, their sponge hosts, a non-obligate, sponge-associated goby (Elacatinus prochilos) and seawater. We quantified microbial overlap among hosts, examined ontogenetic patterns of shared microbiomes across goby body size and assessed the putative ecological benefits of shared microbial taxa for R. ruber. We reveal more than 500 microbial ASVs shared between R. ruber and their sponge hosts. The unique microbial overlap between R. ruber and their sponge hosts far exceeded overlap with E. prochilos and seawater. Shared taxa are putatively linked to nutrient acquisition, vitamin biosynthesis and pathogen defence, suggesting potential benefits for R. ruber from inhabiting microbially rich sponges. The proportion of the shared microbiome between R. ruber gut and sponges declines with goby body size, which suggests that the goby may undergo ontogenetic changes in diet or gut development. Thus, sponges provide more than shelter: they may function as microbial reservoirs and nutritional sources for residents. These findings underscore the need to protect microbially rich habitats and further study host-resident microbial interactions in marine systems and beyond.