Insights into the microbiome of aquatic environments: a step towards sustainable fish production

Abstract

Aquatic ecosystems and aquaculture systems are dynamic environments that host diverse microbial communities, playing critical roles in fish health, water quality, and environmental stability. This dissertation explores the microbiomes of fish and their environments across various contexts, providing insights into microbial diversity, structure, and function, with implications for aquaculture management and environmental health.Chapter 1 provides an overview of fish microbiome research, focusing on the salmonid microbiome and aquaculture systems. In Chapter 2, a scoping review and meta-analysis of 16S rRNA-based studies revealed significant variability in the composition of microbiomes associated with gill, skin, and gastrointestinal (GI) samples of salmonid species. Analysis of 3,554 samples from a total of 36 studies, showed that technical factors, such as study methodology and hypervariable region selection, often outweighed biological variables in determining microbiome patterns. Key microbial phyla differed across mucosal sites, underscoring the complexity of microbiome in salmonids. Chapter 3 examines the impact of aquaculture system design on microbial communities by comparing flow-through (FT) and recirculating aquaculture systems (RAS) in U.S. salmonid farming. Using 16S rRNA sequencing, significant differences were observed in microbial diversity and composition between system types. RAS fostered more stable microbiomes and enriched nitrifying bacteria, highlighting its influence on microbial ecology and its potential for sustainable aquaculture practices. Chapter 4 advances this analysis by reconstructing metagenome-assembled genomes (MAGs) from metagenomic data in FT and RAS systems. A total of 282 high-quality MAGs were revealed. Several MAGs identified at the species level were phylogenetically related across sample types in both RAS and FT systems. This research provides a foundation for the description of related genomes and associated metabolic functions in different sample types and facilities.Chapter 5 shifts focus to wild fish and natural environments, examining the gut microbiome and resistome of yellow perch in Minnesota lakes under varying anthropogenic pressures. This study underscores the influence of anthropogenic inputs on antimicrobial resistance genes and opportunistic pathogens found within the gut of wild fish in natural lakes. Collectively, these investigations enhance our understanding of fish-associated microbiomes in both aquaculture and natural ecosystems, providing insights that may inform sustainable aquaculture practices, improve fish health, and control human impacts on aquatic environments.