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

Key findings

• ▸Bacterial richness and diversity increased across compartments in the RAS, but remained stable in the aquaponic system.
• ▸Significant differences in bacterial community structure and composition were found between the two systems and across different habitat types.
• ▸Fish gut bacteria in the RAS were typical teleost commensals associated with positive gut health and disease resistance.

Keywords

Identifiers

DOI

10.3389/fmicb.2026.1706522

Journal

Frontiers in Microbiology

Year

2026