Host genotype and environmental factors differentially shape the black piranha’s gill microbiota

ABSTRACT Gills play a crucial role in teleost fish, contributing to respiration, osmoregulation, and immunity. The mucus they secrete, and their associated microbiota, support these physiological functions and serve as a first line of defense against pathogens. However, the relative influence of host genotype and environment on gill microbiota remains poorly understood, particularly under field conditions. The black piranha ( Serrasalmus rhombeus ) is a widespread Amazonian predator that harbors multiple genetic groups found in sympatry across different water types: black (acidic, tannin-rich, nutrient-poor), clear (neutral, nutrient-poor), and white (neutral, nutrient-rich, turbid). This makes it an excellent model to explore these interactions. Therefore, to assess the relative contributions of host genotype and environmental factors to gill microbiota composition, we analyzed 252 individuals sampled from 14 sites using Genotyping-by-sequencing to determine host genetic structure, and 16S rRNA gene metabarcoding to characterize the active bacterial communities in gill mucus and surrounding bacterioplankton. Our findings show that host genotype significantly affects gill microbiota composition, with distinct beta diversity and exclusive microbial taxa associated with different genetic groups, even when exposed to the same water type. Nonetheless, variation in microbiota composition was more strongly associated with site-specific environmental factors, particularly bacterioplankton communities. These results reveal a complex interplay between genetic and environmental drivers of fish-associated microbiota under natural conditions. They suggest a potentially important ecological relationship between bacterioplankton and host-associated microbiota and suggest that gill microbial communities may serve as sensitive biomarkers for detecting environmental disturbances in tropical freshwater ecosystems. IMPORTANCE Fish gills are protected by a layer of mucus that hosts a community of beneficial bacteria essential for many vital functions. Understanding the factors that shape this gill microbiota is crucial not only for fish health but also for developing reliable microbial biomarkers to support habitat monitoring and conservation. In this study, we examined black piranhas from different genetic groups sampled across sites with contrasting water physicochemical parameters. This model provided a unique opportunity to disentangle the effects of host genetics and environmental conditions on gill microbiota composition under field conditions. Our findings show that although individuals from different genetic groups hosted distinct microbial communities, local environmental factors, especially the bacteria in the surrounding water, had a stronger influence. These results highlight the complex interplay between host and environment in shaping microbial communities and offer new insights into how fish and their microbiota respond to ecological variability in tropical freshwater ecosystems.