The ecology and plasticity of fish skin and gill microbiomes: Seeking what matters in health and disease

Abstract The microbiomes of skin and gill mucosal surfaces are critical components in fish health and homeostasis by competitively excluding pathogens, secreting beneficial compounds, and priming the immune system. Disruption of these microbiomes can compromise their capacity for disease resilience and maintaining host homeostasis. However, the extent and nature of microbiome disruption required to impact fish health negatively remains poorly understood. This review examines how various stressors influence the community composition and functionality of fish skin and gill microbiomes, and the subsequent effects on fish health. Our findings highlight that the impact of stressors on skin and gill microbiomes may differ for different body sites and are highly context-dependent, influenced by a complex interplay of host-specific factors, stressor characteristics, and environmental conditions. By evaluating current knowledge on the genesis and homeostasis of these microbiomes, we highlight a strong influence of environmental factors especially on skin and gill microbiomes compared with fish gut microbiomes, which appear to be more closely regulated by the host's homeostatic and immunological systems. This review emphasises the importance of understanding the ecology and plasticity of fish skin and gill microbiomes to identify critical thresholds for microbiome shifts that impact fish health and disease resilience.