Skin microbiome mirrors habitat divergence in amphibious combtooth blenny fish (Teleostei, Blenniidae)

Abstract Host–associated microbiomes play vital roles in species’ ecology and evolution, yet little is known about their shift during the transition from aquatic to terrestrial habitats. We characterize the skin microbiomes of three combtooth blenny species (Blenniella paula, Praealticus labrovittatus, Alticus arnoldorum) that occupy distinct positions along the intertidal gradient—from fully subtidal to intertidal and supratidal environments. Using 16S rRNA sequencing, we compared skin-associated bacterial communities with those in seawater and substrate biofilms. The divergence between skin and substrate microbiomes parallels fishes’ distribution along progressively higher intertidal zones. The supratidal A. arnoldorum had the most divergent microbiome, characterized by higher Gammaproteobacteria abundance and enrichment of epiphytic and mucus-associated taxa. Fish skins were enriched in 27 microbial orders that included genera commonly associated with fish (e.g., Vibrio, Alteromonas, Cetobacterium) but others rarely reported (e.g., Rubritalea, Granulosicoccus). Together, our findings suggest that variation in fish skin microbiomes parallels the ecological transition from subtidal (aquatic) to supratidal (terrestrial) habitats, although host and habitat effects could not be disentangled. We hypothesize that microbial symbionts may contribute to adaptations enabling amphibious lifestyles. This is the first study on fish microbiome variation across the intertidal gradient and offers a framework for predicting microbiome responses to environmental change.