.png){kind=icon}
.png){kind=icon}
Return
Unexpected enrichment of antibiotic resistance genes in recirculating aquaculture effluents of rainbow trout (Oncorhynchus mykiss): microbial community assembly and mobile genetic elements as key drivers
.png){kind=icon}
OA
AI
X
L
J
J
S
DOI：10.3389/fmicb.2026.1913067.png)
.png){kind=icon}
Original request for help.png){kind=icon}
Share.png){kind=icon}
Save
Abstract
En 中文
IntroductionRecirculating aquaculture systems (RAS) are increasingly used in intensive aquaculture because of their capacity to reduce nitrogen; phosphorus; and organic matter discharges. However; whether improved conventional effluent quality is accompanied by a reduced antibiotic resistance gene (ARG) burden remains unclear.MethodsDuring the mid-cultivation stage; effluents were collected from four RAS farms and four paved flow-through raceway systems (PFRS). Water quality parameters; including total nitrogen (TN); total phosphorus (TP); chemical oxygen demand (COD); chlorophyll-a (Chl-a); and dissolved oxygen (DO); were measured. Microbial community composition was characterized using 16S rRNA gene sequencing; while ARGs and mobile genetic elements (MGEs) were quantified using GeoChip 5.0. Multivariate statistics and co-occurrence network analyses were used to evaluate associations among environmental conditions; microbial communities; ARG profiles; and MGE profiles.ResultsRAS effluents showed substantially lower nutrient and organic loads than PFRS; confirming improved conventional water quality. However; total ARG abundance was significantly higher in RAS than in PFRS; increasing from 35.39 ± 11.43 × 106 to 63.99 ± 15.33 × 106; corresponding to a 1.81-fold increase. In contrast; total MGE abundance was numerically higher in RAS but did not differ significantly between systems. Microbial alpha diversity was lower in RAS; and beta diversity analysis showed distinct community structuring between cultivation modes; with both compositional differences and dispersion effects contributing to group separation. ARG class- and subtype-level profiles showed heterogeneous abundance patterns; with several major ARG categories remaining highly abundant in RAS; although most feature-level differences were not significant after FDR correction. Co-occurrence network analysis further revealed structured associations among microbial species; ARGs; and MGEs; with modular organization and highly connected resistance-associated nodes.ConclusionThis study demonstrates a “low-pollution but non-reduced ARG burden” pattern in RAS effluents. Improved removal of conventional pollutants did not correspond to a proportional reduction in ARG or MGE profiles. These findings indicate that conventional water-quality indicators alone are insufficient to evaluate resistance-associated genetic pollution in engineered aquaculture systems; and that ARGs; MGEs; microbial community structure; and species–ARG/MGE association patterns should be integrated into future RAS monitoring and management.
Keywords:
microbial community
mobile genetic elements (MGEs)
antibiotic resistance genes (ARGs)
recirculating aquaculture system
aquaculture effluent
rainbow trout (oncorhynchus mykiss)
Journal
IF:
4.5
Papers:
4.0W
Citations:
16.6W
Organization
Cited Papers