Microbial Interactions in Aquaculture Systems

Microbial communities in aquaculture environments underpin nutrient cycling, disease resistance and water quality. In pond and recirculating systems, bacteria, archaea and microalgae form dynamic consortia that process organic matter, transform nitrogen and phosphorus compounds and suppress pathogens. These consortia colonise biofilms on surfaces and constitute the gut microbiota of cultured animals, directly influencing host digestion, immune responses and growth performance. Interactions between heterotrophic and autotrophic microbes, as well as between beneficial and opportunistic species, shape system stability. Balanced microbial networks enhance feed utilisation, reduce pollutant load and mitigate disease outbreaks, thereby supporting sustainable, high-yield aquaculture. Advances in high-throughput sequencing and metagenomics now reveal spatial and temporal patterns of diversity across water, sediment and host tissues. Insights from recirculating aquaculture systems demonstrate how step-wise purification enriches nitrifying and denitrifying bacteria for efficient ammonia and nitrite removal. Integrated multitrophic aquaculture leverages complementary microbe–host interactions across trophic levels to optimise nutrient reuse. Probiotic development focuses on taxa such as Bacillus and Purple Nonsulfur Bacteria to stabilise gut communities and bolster stress resilience. Emerging work explores microbial biofilms as bioreactors for wastewater treatment and studies microbial metabolites in host–pathogen dynamics. A systems-level understanding of community structure and functional capacity is essential for designing robust, eco-efficient aquaculture at commercial scale.

Research from Nature Portfolio

No recent Nature Portfolio content available.

Microbial Interactions in Aquaculture Systems publication trend

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

Technical terms

Microbiota: The community of microorganisms, including bacteria, archaea and fungi, in a defined environment.

Recirculating aquaculture system (RAS): A culture method in which water is continuously treated and reused to maintain optimal quality.

Integrated multitrophic aquaculture (IMTA): The co-culture of species from different trophic levels to recycle nutrients and improve system sustainability.

Probiotic: Live microorganisms administered to confer health benefits by modulating host or environmental microbial communities.

Nitrification/Denitrification: Microbial processes converting ammonia to nitrate (nitrification) and nitrate to nitrogen gas (denitrification), essential for nitrogen removal.

References

1. Effects of Different Sources of Culture Substrate on the Growth and Immune Performance of the Red Swamp Crayfish (Procambarus clarkii). International Journal of Molecular Sciences (2023).
2. Water Treatment Effect, Microbial Community Structure, and Metabolic Characteristics in a Field-Scale Aquaculture Wastewater Treatment System. Frontiers in Microbiology (2020).
3. Feed Types Driven Differentiation of Microbial Community and Functionality in Marine Integrated Multitrophic Aquaculture System. Water (2019).
4. Effect of a Bacillus Probiotic Compound on Penaeus vannamei Survival, Water Quality, and Microbial Communities. Fishes (2023).
5. Genomic Characterization of Probiotic Purple Nonsulfur Bacteria Cereibacter sphaeroides Strains S3W10 and SS15: Implications for Enhanced Shrimp Aquaculture. Life (2024).
6. Microbiota composition and correlations with environmental factors in grass carp (Ctenopharyngodon idella) culture ponds in South China. PeerJ (2023).