Composition, diversity and response dynamics of fish skin microbiomes under environmental stress, including antibiotic exposure

Abstract

Fish are one of the most important vertebrates globally, representing over 34,000 species with immense economic and cultural importance. They are keystone species playing fundamental roles in ecosystem function, also for fisheries and aquaculture industries. Fish population declines are often linked to overfishing, but also environmental stressors including poor water quality and/or pollution, which in turn can lead to disease and increased fish mortality. Microbiomes of the fish mucosal surfaces play key roles in health, including immune priming, nutrient degradation, and pathogenic exclusion. While much research has focused on the gut microbiomes of finfish, the skin and gill microbiomes, which form a key interface between pathogens and the environment, including the burdens of water pollution, remain comparatively understudied. Little is known about how the skin microbial community reacts to stressors, with microbiome disruptions predicted to result in reduced host resilience to stressors and, in turn, reduced fitness. This thesis investigates the composition, diversity, and dynamics of fish skin microbiomes under environmental stress and antibiotic exposure. By analysing the existing literature, it identifies key knowledge gaps regarding the nature and magnitude of microbiome shifts caused by stressors. The thesis explores how documented perturbations of the fish skin microbiome affect fish health and subsequent disease resilience. It emphasises that alterations in fish health due to taxonomic changes in the microbiome are highly dependent on disruptions that affect overall microbiome functionality. A major challenge in studying fish mucosal surface microbiomes is obtaining a sufficient enrichment of the skin microbial fraction, which is typically dominated by host DNA. This hinders the assessment of the functional capacity of the skin microbiome, crucial for understanding the relationship between microbiome dysbiosis and fish health. Various commercial host depletion methods were evaluated to provide a meaningful proportional increase in skin microbial relative to host DNA, but none proved highly successful. In this work, however, suggestions are provided on how to assess and better ensure the non-biased recovery of microbiota. Assessment of fish skin microbiomes using a meta-analysis highlights the impact of physiochemical factors and cultivation environment on bacterial community composition. Correlations between fish skin microbiome compositions in laboratory, wild, or aquaculture systems suggest that the effects of stressors on microbial composition assessed in one system may not be directly transferable to others. While general trends and common bacterial genera were identified across 98 fish species, responses to stressors were host species-specific. This is evidenced by the limited shared changes in bacterial genera, despite studying the same stressor and fish species in different studies. A study of antimicrobial resistance genes and functional pathways in pondwater microbiomes from Bangladeshi aquaculture ponds exposed to antibiotics revealed resistance to a wide range of antibiotics, encompassing eighteen different classes. Aminoglycosides and sulphonamides were the most commonly identified resistance types. Similarities in pondwater antimicrobial resistance gene and functional gene compositions were observed within the same farms, but not across different geographical districts or between farms cultivating different fish species. This suggests that shared farming practices, such as the type and duration of antibiotic exposure, are likely a key driver for the composition of these resistance genes. A major laboratory study in this thesis investigated the effects of exposure to environmentally relevant mixtures of antibiotics affect the skin microbiome in Eurasian/common carp (Cyprinus carpio). The study tracked individual carp microbiomes over multiple time points during antibiotic exposure and depuration to assess how individual microbiomes reacted and recovered from antibiotic stress. The study shows significant microbiome perturbations captured through changes in beta diversity under antibiotic exposure that did not return to pre-treatment levels even after two weeks of depuration. It links bacteria such as the genus Arcicella as potential biomarkers of antibiotic-mediated stress in carp skin microbiomes. Together the data and studies reported upon show that many different environmental stressors can perturb fish skin, leading to detrimental effects on fish health, but with implications also for exposures to antibiotics to the wider environment through the proliferation of antimicrobial resistance genes. Efforts towards their conservation are critical to maintaining fish as a globally abundant species important culturally and socially, by also as a sustainable food source for a growing global population.