16S amplicon sequencing of Red Sea coral reef fish to assess the application of coral probiotics

The ongoing fourth mass global coral bleaching event evidences the threats posed by increasing seawater temperatures and reinforces the need for active solutions to support coral reefs through this major crisis. The use of beneficial microorganisms for corals (BMCs), the so-called coral probiotics, has emerged as a promising nature-based solution to enhance coral resistance through restoring and rehabilitating dysbiotic microbiomes. While the benefits to corals are increasingly recognized, the impacts on associated reef organisms, such as fish, remain unexplored. This study investigated the effects of BMCs on the tissue-associated microbiomes of Dascyllus abudafur (Pomacentridae), a damselfish with high fidelity to Pocillopora verrucosa coral colonies, providing a suitable model for studying BMCs secondary effects in situ. Over three months, we applied BMCs three times per week to healthy P. verrucosa colonies in the central Red Sea and analyzed the resultant changes in the fish's microbiomes. Our findings reveal significant, tissue-specific shifts in bacterial communities, particularly in the skin and the gut, with moderate changes observed in the gills. Notably, putative beneficial bacteria such as Mitsuokella spp. were enriched in the skin, while various Firmicutes, including Prevotella spp. and Ruminococcus torques group spp. increased in abundance in the gut. Furthermore, there was a marked decrease in potential fish pathogens, such as Serratia spp., Photobacterium spp., Lactococcus spp., and some Vibrio within the skin microbiome. This study not only highlights the potential extended benefits of BMCs on coral reef fish but also sets a foundation for understanding the broader ecological interactions between BMCs and reef-associated organisms.