Nutrient pollution alters the gut microbiome of a territorial reef fish

Highlights: • Nutrient enrichment triggers diversification of Stegastes nigricans gut microbiome. • Differential abundance analyses reveal region-specific microbiome changes. • Downregulation of predicted pathways suggests a loss of function. • Algal microbiome analysis confirms gut microbiome changes are autochthonous. Human-induced nutrient pollution threatens coral reefs worldwide. Although eutrophication disrupts coral microbiomes, often leading to coral mortality, it is unknown whether eutrophication impacts the microbiomes of other coral reef organisms. Of particular interest are herbivorous fishes, whose algae consumption is critical in maintaining healthy corals. To examine the effects of eutrophication on fish gut microbiomes, we experimentally enriched territories of Stegastes nigricans, a predominantly herbivorous damselfish that farms turf algae. Using 16S RNA sequencing, we demonstrate that hindgut and foregut microbiomes have significantly higher alpha diversity in nutrient-enriched territories as compared to unenriched controls. S. nigricans gut microbiomes also exhibited significantly different compositions across treatments. In contrast, these changes were not observed in the microbiomes of the turf algae consumed by S. nigricans, indicating that the gut microbiome changes were autochthonous. Combined, our results provide a novel example of endogenous microbial shifts in wild vertebrates caused by simulated anthropogenic stress.