Abstract / Summary:
Coral reef fishes represent one of the most diverse vertebrate groups in marine ecosystems. Fish gills are multifunctional organs responsible for respiration, osmoregulation, immunity, and waste exchange, while also serving as the primary interface between the fish and the surrounding seawater. This constant exposure creates opportunities for colonization by diverse microorganisms and viruses, making gills a potentially important site of host–microbe interactions. While advances in sequencing technologies have greatly improved our understanding of fish-associated microbiomes, research has focused predominantly on the gut, leaving the gill microbiome and virome comparatively unexplored. As a result, the diversity, metabolic capabilities, and ecological interactions of microorganisms inhabiting fish gills remain poorly understood.
This thesis aims to characterize microbial and viral communities associated with the gills of Caribbean hamlet fishes (Hypoplectrus spp.) using genome-resolved metagenomics. By reconstructing microbial and viral genomes from shotgun metagenomic data, I examine the diversity, metabolic functions, and virus–host associations of microorganisms inhabiting this understudied vertebrate habitat.
The analyses revealed that a previously undescribed lineage within the Burkholderiaceae family was consistently detected across host species, sampling locations, and years. Genome reconstruction identified genes for sulfur oxidation and carbon fixation, providing the first metagenomic evidence that fishes may host sulfur-oxidizing chemosynthetic bacteria in their gills and extending a type of association previously documented primarily in marine invertebrates. I then characterized the viral component of the gill microbiome. Viral sequences occurred at relatively low abundance and were dominated by bacteriophages belonging to the class Caudoviricetes. Among viruses with predicted hosts, most were associated with Endozoicomonas despite the greater prevalence of the Burkholderiaceae lineage in the gill microbiome, suggesting that viral and bacterial communities may be shaped by different ecological processes. Taken together, the results presented in this thesis reveal previously unrecognized microbial and viral diversity in reef fish gills, including evidence for a potentially chemosynthetic bacterial association in a vertebrate host. More broadly, they highlight how little is known about the ecological and evolutionary interactions between bacteria, viruses, and their fish hosts in the gill environment. These findings provide a foundation for future studies investigating the functional roles of gill microbiomes and viromes in marine fishes and may ultimately inform strategies to promote fish health and welfare in aquaculture.