Microbiomes of Aquatic Organisms: Functional Ecology, Health, and Environmental Change

Aquatic microbiology increasingly recognizes microbial communities associated with aquatic organisms as important determinants of host physiology and ecosystem function. Microbiomes associated with tissues, surfaces, cavities, and other internal or external niches of fish, cnidarians, sponges, molluscs, crustaceans, seaweed and other aquatic organisms can influence nutrition, metabolism, development, immunity, stress tolerance, disease susceptibility, and recovery. Their composition and activity are shaped by host biology, life history, environmental conditions, and human activities. Although advances in sequencing and multi-omics have expanded research on aquatic organism microbiomes, many studies remain primarily descriptive. Important challenges include distinguishing persistent microbial members from transient environmental taxa, identifying functional mechanisms, understanding microbiome stability and recovery, and linking microbial patterns to measurable host and ecological outcomes.Recent research has demonstrated that microbiome composition and activity vary across aquatic species, tissues, habitats, developmental stages, seasons, and production systems. Microbiome changes have been associated with infectious and non-infectious diseases, environmental stress, climate related change, altered nutrition, pollution, and aquaculture practices. Metagenomics, metatranscriptomics, metabolomics, culturomics, single-cell approaches, and experimental methods are increasingly being used to investigate microbial functions, metabolic pathways, and responses to environmental disturbance. In parallel, artificial intelligence and machine learning approaches, including predictive modelling and network analysis, offer new opportunities to identify microbiome organism associations, predict health and disease outcomes, and prioritize relationships for experimental validation. However, variation in sampling designs, analytical workflows, and reporting standards continues to limit comparisons across studies. Further research is needed to integrate microbial community data with functional, physiological, pathological, and environmental measurements.This Research Topic aims to advance the mechanistic and functional understanding of microbiomes associated with aquatic organisms, with a particular focus on aquatic consumers and other heterotrophic hosts in marine, freshwater, and transitional environments. It will consider how environmental conditions, life history, nutrition, disease, and human activities shape microbial communities and how these communities influence organismal health, immunity, physiology, disease resistance, stress responses, and recovery. Studies should, where possible, connect microbiome composition or activity with measurable organismal or ecological outcomes and contribute to functional interpretation or validation. Methodological innovation is encouraged, including multi-omics, culturomics, AI/ML based predictive modelling, network analysis, systems biology, and experimental approaches, although submissions will not be required to use advanced technologies.To gather further insights into the functional ecology, health relevance, and environmental dynamics of microbiomes associated with aquatic organisms, we welcome articles addressing, but not limited to, the following themes:• Diversity, composition, activity, and function of microbiomes associated with fish, cnidarians, sponges, molluscs, crustaceans, seaweed and other aquatic species, tissues, habitats, geographical regions, life stages, and seasons• Microbiome contributions to nutrition, metabolism, growth, development, immunity, stress physiology, disease resistance, and organismal recovery• Microbiome changes associated with pathogens, parasites, disease, environmental stress, pollution, climate change, habitat alteration, and other anthropogenic pressures• Effects of diet, antibiotics, probiotics, stocking density, and other aquaculture practices on microbiome structure and function• Metagenomic, metatranscriptomic, metabolomic, culturomic, single-cell, and other multi-omics approaches linked to functional or experimental validation• AI/ML-based prediction of microbiome organism interactions, health and disease outcomes, microbial functions, community stability, and recovery, including network-based and systems-biology approaches• Microbiome-informed biomarkers, interventions, and applications in aquatic organism health monitoring, aquaculture, fisheries, conservation, restoration, and species management• Data integration, analytical workflows, benchmarking, standardization, reproducibility, and reporting in aquatic microbiome research Topic editors: Jorge García-Márquez, Isabel M. Cerezo, Patricia Diaz-Rosales Source: https://www.frontiersin.org/research-topics/84629/microbiomes-of-aquatic-organisms-functional-ecology-health-and-environmental-change