Microbial Dynamics in Aquaculture Systems

Aquaculture is expanding globally to meet rising demands for protein, and microbial communities lie at the heart of system performance, animal health and environmental sustainability. From eggs and larvae to juveniles and adults, bacterial, archaeal, fungal and viral populations colonise hosts and rearing water in distinct successional phases linked to developmental stage, diet and system design. Recirculating aquaculture systems (RAS) and flow-through systems exert contrasting selection pressures on microbial assemblages, influencing community stability, nutrient cycling and pathogen loads. Management approaches range from disinfection and K-selection to probiotic addition, each aiming to steer microbiota towards mutualistic relationships that enhance growth, disease resistance and welfare. Advances in molecular tools—including short- and long-amplicon sequencing and shotgun metagenomics—now permit integrated profiling of taxonomic and functional diversity across domains. A comprehensive understanding of spatio-temporal dynamics, host-microbe interactions and environmental drivers is indispensable for optimising system architecture, feed regimes and water treatment, thereby underpinning the sustainable intensification of aquaculture worldwide.

Research from Nature Portfolio

High-resolution analysis of the salmon mycobiome has revealed pronounced temporal and spatial shifts in fungal communities from eggs through to adult fish. ITS-based sequencing showed low fungal diversity compared with bacteria, but clear stage-specific phylotypes emerged, with taxa such as Candida tropicalis and Saccharomyces cerevisiae dominating at key developmental milestones and following seawater transfer. These insights underscore the importance of monitoring fungal as well as bacterial communities in health management strategies. In tilapia larvae, early exposure to a single probiotic strain led to persistent alterations in gut microbiota composition long after probiotic removal. Probiotic-treated groups exhibited reduced inter-individual variability and a more stable community assembly trajectory, demonstrating that targeted microbial interventions during critical windows can establish beneficial host-microbiota relationships and improve uniformity in larval performance.

Microbial Dynamics in Aquaculture Systems publication trend

The graph below shows the total number of articles in microbial dynamics in aquaculture systems across all publications each year (not limited to Nature Index journals).

Technical terms

Microbiome: The community of microorganisms inhabiting a particular environment or host.

Metagenomics: Sequencing and analysis of mixed DNA from environmental samples to profile community composition and functional potential.

Amplicon sequencing: Targeted sequencing of specific genetic markers (for example, the 16S rRNA gene) to identify and quantify microbial taxa.

Recirculating aquaculture system (RAS): A closed-loop water management approach that filters and reuses water in aquaculture facilities.

Probiotic: Live microorganism introduced to a host to confer a health benefit by modulating its microbiota.

Mycobiome: The assemblage of fungal species within a microbial community.

Alpha diversity: A measure of species richness and evenness within a single sample or community.

Beta diversity: A measure of compositional differences between microbial communities across samples.

References

1. Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems. Environmental Microbiome (2023).
2. K-Selection as Microbial Community Management Strategy: A Method for Improved Viability of Larvae in Aquaculture. Frontiers in Microbiology (2018).
3. Microbiomes in the context of developing sustainable intensified aquaculture. Frontiers in Microbiology (2023).
4. Unravelling the temporal and spatial variation of fungal phylotypes from embryo to adult stages in Atlantic salmon. Scientific Reports (2024).
5. Probiotic legacy effects on gut microbial assembly in tilapia larvae. Scientific Reports (2016).
6. Characterization of Host-Associated Microbiota and Isolation of Antagonistic Bacteria from Greater Amberjack (Seriola dumerili, Risso, 1810) Larvae. Microorganisms (2023).