The mesopelagic zone, between 100 and 1000 m depth, contains up to 90% of marine vertebrate biomass. Mesopelagic fishes are key components of these ecosystems through their feeding interactions and play a critical role in the ocean's biological carbon pump through their diel vertical migrations, yet the bacterial communities associated with these fishes remain poorly characterized. Because bioluminescence and light-related interactions are widespread ecological traits in mesopelagic ecosystems, we investigated the bacterial communities associated with the gut, liver, and skin of mesopelagic fishes from the Northeast Atlantic. Particular attention was given to genera known to include bioluminescent species. 16S rRNA gene sequencing revealed marked tissue-specific differences. Skin microbiomes were the most diverse and appeared more influenced by the surrounding environment, whereas gut and liver communities were less diverse and compositionally similar. Internal tissues were dominated by Vibrionaceae (especially Vibrio and Photobacterium) and Moraxellaceae (Acinetobacter). Microbiome composition was significantly associated with host family, trophic position, and migratory behavior. Fishes at lower trophic levels, particularly migratory species, harbored higher proportions of Vibrionaceae, including genera that include bioluminescent lineages, whereas non-migratory deep-sea species showed more variable communities. Moreover, targeted qPCR detected bioluminescence-related lux genes in gut samples. Mesopelagic fish microbiomes are influenced by tissue type and host ecological traits. The recurrent detection of Vibrio and Photobacterium, together with lux genes in selected gut samples, suggests that some mesopelagic fish-associated microbiomes may include bacteria with bioluminescence-related genetic potential. These findings provide an input for future studies on the ecological role of these bacteria in mesopelagic ecosystems.
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