Unraveling the roles of host genetics, microbial interactions, and environmental factors in shaping aquatic animal microbiomes

Abstract

Aquatic animals experience a unique and increased pressure from their surrounding environment as they are in constant contact with billions of microorganisms, many of which may cause adverse health outcomes. Microorganisms that live within and/or on aquatic animals (microbiomes) can protect their host from potential pathogens along with aiding in nutrient metabolism and host immunity. These relationships are well documented in human and terrestrial systems, and in some model aquatic organisms; however, the majority of aquatic microbiomes are under characterized. 16S rRNA gene and metagenomic sequencing was used to study these microbial communities. 16S rRNA gene sequencing targets a conserved bacterial gene with variable regions that allow for the taxonomic identification of bacterial taxa, the quantification of their relative abundance, and the comparison of microbial diversity between samples. Metagenomic sequencing includes the whole genetic content within a sample, allowing for further taxonomic classification of bacteria within a complex community, while also identifying potential functions of those microorganisms. With these approaches, the impact of host hybridization on catfish digesta microbiome community structure and predictive function were analyzed. This study found that hybrid catfish harbor a unique microbiome from both parental microbiomes, with increased taxa and metabolic pathways associated with host immunity and growth. Additionally, catfish embryo microbiomes in aquaculture were characterized and how the potential impact those communities have on embryo protection during development was investigated. Catfish embryo microbiomes were distinct from water microbiomes, and many of the enriched taxa were associated with nutrient cycling and antioxidant production. Functional groups associated with antimicrobial production and resistance were identified and may contribute to host defense. Lastly, 16S rRNA gene sequencing was used to study the dominant and hypothesized coral symbiont, Endozoicomonas, and how its relative abundance varies by coral type, ocean depth, and marine protection status. Endozoicomonas was more abundant in soft coral microbiomes compared to hard corals, with higher abundances in unprotected marine areas for soft corals and in shallower depths in hard corals. Together, these studies demonstrate how host genetics, microbial interactions, environmental factors, and the complexity of these relationships, contribute to microbiome community structure and potential metabolic function.