MICROBIAL COMMUNITIES IN RECIRCULATING AQUACULTURE SYSTEMS: EXPLORING THE ROLE OF DIET AND NUTRIENT DYNAMICS ON ASSEMBLY MECHANISMS

Background and approach

Recirculating aquaculture systems (RAS) are increasingly adopted in marine aquaculture due to their sustainability and efficiency. Central to their performance are microbial communities, which play vital roles in nutrient cycling, water quality maintenance, and ultimately, fish health and welfare. While nutrient dynamics are well-recognized drivers of microbial community structure, the influence of diet—particularly via fish-derived nutrient excretion—remains underexplored, especially in the context of novel aquafeed ingredients (Syropoulou et al., 2025). As the aquaculture industry transitions toward sustainable feed alternatives, it becomes essential to understand their impacts on microbial ecology within RAS. Microbial assembly processes indicate how how a community of microorganisms comes together and forms a certain composition, and it is governed by a dynamic interplay between deterministic (predictable, niche-based) and stochastic (random, neutral) processes (Li et al. 2022). These forces determine which microorganisms colonize, survive, and interact within a specific environment, and can be largely affected by nutrient presence.

In this study, we investigated how diet, through fish excretion and water nutrient dynamics, influences microbial community structure and assembly processes across key RAS compartments: water, biomedia, and fish skin. For this purpose, we collected samples from two experimental trials with juvenile European seabass, reared under controlled conditions in marine RAS, and fed either a plant-based or chitin-based diet over two six-week trials. We performed biweekly samplings across the three niches and analysed nutrients in the water (Chemical and biological oxygen demand, total nitrogen, bacterial activity) along with 16S rRNA gene sequencing to characterize the microbial communities.

Results and Discussion

Our findings revealed significant effects of both diet and time on the alpha diversity of water-associated microbial communities, whereas fish skin communities were primarily shaped by temporal dynamics. In terms of beta diversity, diet significantly influenced the phylogenetic similarity (measured as Weighted Unifrac distance) in water and skin microbiota (Figure 1B), but not in biomedia. Levels of dissolved carbon and nitrogen in the water explained up to 50% of the variation (Figure 1A), showing the nutrients are essential shaping the microbial communities. Notably, fish skin and water shared the greatest number of taxa and exhibited similar taxonomic profiles. Nutrient gradient analysis indicated that carbon was the primary driver of microbial turnover, followed by nitrogen. Community assembly processes varied by niche: stochastic processes (drift) predominantly shaped water and skin microbiota, while deterministic processes (selection) played a larger role in biomedia. The type of diet modulated these dynamics; drift dominated in fish fed chitin-based diets, whereas homogeneous dispersal was more prevalent under plant-based diets in water and skin. In biomedia, dispersal remained a key factor regardless of diet, with selection contributing significantly.

A

B

Figure 1. A. Distance-based (Bray Curtis) redundancy analysis (dbRDA) on water microbial communities over the six week experimental period. Vectors indicate the weight and direction of the different water nutrient parameters; COD: Chemical Oxygen Demand; BOD; Biological Oxygen Demand. The dbRDA axes describe the percentage of the fitted or total variation explained by each axis while being constrained to account for group differences. B. Weighted Unifrac distance showing within group variation in the plant-based (DDGS) and the chitin-based (SSM) diets. Stars indicate significance P<0.001.

In summary, our results demonstrate that dietary inputs, via fish excreta, can substantially influence microbial communities in water and on fish skin, with carbon gradients acting as major ecological drivers. Although diet had a measurable impact on community structure, its influence on microbial assembly mechanisms was more niche-dependent and less pronounced. These findings highlight the importance of considering feed formulation not only for fish nutrition but also for optimizing microbial dynamics in RAS ecosystems.

Acknowledgment

This work was supported by the Marie Skłodowska-Curie Innovative Training Network (ITN) fellowship under grant agreement No. 956697 (EATFISH).

References

Li, W., Kuzyakov, Y., Zheng, Y., Li, P., Li, G., Liu, M., …. & Li, Z. (2022). Depth effects on bacterial community assembly processes in paddy soils. Soil Biology and Biochemistry, 165, 108517.

Syropoulou, E., Prakash, S., Smeenge, D., Sipkema, D., Schrama, J. W., & Kokou, F. (2025). Carbohydrates in dietary ingredients for European seabass: Impact on nutrient digestibility and waste production when reared in recirculating aquaculture systems. Aquaculture, 599, 742182.