# System design and habitat type drive microbial communities in recirculating aquaculture systems: comparison of conventional fish-only and sustainable aquaponic systems

## TL;DR

This study shows how system design and habitat type influence microbial communities in aquaculture systems, affecting fish and plant health and system efficiency.

## Contribution

The study reveals how microbial community structures differ between conventional and sustainable aquaculture systems, linking these differences to system design and functionality.

## Key findings

- Bacterial richness and diversity increased in RAS compartments but remained stable in aquaponic systems.
- Aquaponic systems showed higher abundances of plant growth-promoting and nutrient-cycling bacteria.
- Nitrifying and denitrifying bacteria in biofilters supported efficient nitrogen cycling in both systems.

## Abstract

This study compares how system design and experimental conditions shape bacterial communities across distinct habitats in a coupled seawater aquaponic system and a marine RAS, and explores their functional implications for system efficiency and productivity. Bacterial communities from fish guts, biofilters, biofilms and water were characterized after 4 months of rearing flathead grey mullet (Mugil cephalus) and glasswort (Salicornia patula) using 16S rRNA gene sequencing. In the RAS, bacterial richness (Chao1 and ACE) and diversity (Shannon and Simpson) progressively increased across compartments, while they remained stable in the aquaponic system, likely due to the differences in system design such as UV filtration in the RAS. Significant differences in bacterial community structure (weighted UniFrac) and composition were found in the four habitat types compared between systems, reflecting the different design and functionality of each system. In particular, fish gut bacteria were typical teleost commensals associated with positive gut health and disease resistance, dominated by the phylum Pseudomonadota and the genus Pseudomonas but showing differences in lower abundant taxa between systems. The biofilm and water of the aquaponic system showed genera with plant growth-promoting, disease-resistance and nutrient-cycling properties, at higher abundances than in the RAS (Mycobacterium, Sulfitobacter, Marivita, Fuerstiella, Blastopirellula, Hoeflea). Furthermore, the balance of nitrifying (i.e., Nitrosomonas) and denitrifying bacteria (Pseudomonas, Blastopirellula) in the biofilters of both systems supported efficient nitrogen cycling and water quality maintenance. Collectively, these results demonstrate that microbial assembly in aquaculture systems is governed by system design and habitat type, with potential functional consequences for fish gut health, plant growth, and overall system efficiency, highlighting the promise of integrated marine systems as sustainable food production strategies.