The abuse of antibiotics has caused the propagation of antibiotic resistance genes (ARGs) in aquaculture systems. Although the recirculating systems have been considered as a promising approach for preventing the coastal water pollution of antibiotics and ARG, rare information is available on the distribution and proliferation of ARGs in the recirculating mariculture system. This study firstly investigated the proliferation of ARGs in coastal recirculating mariculture systems. Ten subtypes of ARGs including tet (tetB, tetG, tetX), sul (sul1, sul2), qnr (qnrA, qnrB, qnrS), and erm (ermF, ermT) were detected. The absolute abundances of the ARGs detected in the mariculture farm were more than 1 × 10⁴ copies/mL. The sulfonamide resistance genes (sul1 and sul2) were the most abundant ARGs with the abundance of 3.5 × 10⁷–6.5 × 10¹⁰ copies/mL. No obvious correlation existed between the antibiotics and ARGs. Some bacteria were positively correlated with two or more ARGs to indicate the occurrence of multidrug resistance. The fluidized-bed biofilter for wastewater treatment in the recirculating system was the main breeding ground for ARGs while the UV sterilization process could reduce the ARGs. The highest flux of ARGs (6.5 × 10²¹ copies/d) indicated that the discharge of feces and residual baits was the main gateway for ARGs in the recirculating mariculture system to enter the environments.

Integrated systems with appropriate bio-filters can be used to treat aquaculture effluents. However, the information on bio-filters that alters the ecological functions of the bacterioplankton community (BC) in biodegradation of the aquaculture effluents remains controversial. In this study, we implemented a comprehensive restoration technology combined with bio-filters [biofilm, clam (Tegillarca granosa), and macrophytes (Spartina anglica)] to investigate their influence on the stability of the BC and nutrient removal. We found that the diversity of BC was linked with biogeochemical factors in processing and upcycling nitrogen-rich effluents into high-value biomass. The BC exhibited significant distinct patterns in the bio-filter areas. Potential biomarkers for constrained harmfully algae-bacteria (Nitriliruptoraceae, Bacillales, and Rhodobacteraceae) and nutrient removal were significantly higher in the bio-filters areas. The bio-filters significantly promoted the restoration effects of N and P balance by reducing 82.34% of total nitrogen (TN) and 81.64% of total phosphorus (TP) loads at the water interface. The main mechanisms for TN and TP removal and nutrient transformation were achieved by assimilation and absorption by the emergent macrophytes (Spartina anglica). The bio-filters significantly influenced the biodegradability and resolvability of particulate organic matter through ammonification, nitrification, and denitrification of microbes, which meliorated the nutrient removal. Beside bio-filter effects, the BC was significantly controlled by abiotic factors [nitrate (NO₃⁻-N), dissolved oxygen (DO), total nitrogen (TN), and water temperature (WT)], and biotic factors (chlorophyll ɑ and green algae). Our study revealed that the co-existence system with bio-filters may greatly improve our understanding on the ecological functions of the BC in aquaculture systems. Overall, combined bio-filters provide an opportunity for the development of efficient and optimized aquaculture wastewater treatment technology.

Periphyton have been widely applied in aquaculture systems, however, little information is available on how periphyton respond to such high nutrient levels in water. Thus, changes in the morphological characteristics, community structure, and metabolic function of periphyton under high eutrophic waters were evaluated. The results indicated that the morphology of periphyton was affected by increasing the nutrient concentration of water, which shifted the micromorphology of periphyton from spheriform to filamentous. The periphyton under higher water nutrient levels were able to utilize more carbon source types. Additionally, higher water nutrient levels increased the bacterial and protozoal proportions in periphyton. This study fills the gap in knowledge about the responses of periphytic communities to extremely eutrophic waters. It provides valuable information on the full understanding of the periphyton-nutrient relationship in aquaculture systems, which is beneficial for regulating the microbial species or communities in periphyton by manipulating the nutrient levels in water.

Widespread conversion of coastal wetlands into aquaculture ponds in coastal region often results in degradation of the wetland ecosystems, but its effects on sediment's potential to produce greenhouse gases remain unclear. Using field sampling, incubation experiments and molecular analysis, we studied the sediment CH₄ production potential and the relevant microbial communities in a brackish marsh and the nearby aquaculture ponds in the Min River Estuary in southeastern China. Sediment CH₄ production potential was higher in the summer and autumn months than in spring and winter months, and it was significantly correlated with sediment carbon content among all environmental variables. The mean sediment CH₄ production potential in the aquaculture ponds (20.1 ng g⁻¹ d⁻¹) was significantly lower than that in the marsh (45.2 ng g⁻¹ d⁻¹). While Methanobacterium dominated in both habitats (41–59%), the overall composition of sediment methanogenic archaea communities differed significantly between the two habitats (p < 0.05) and methanogenic archaea alpha diversity was lower in the aquaculture ponds (p < 0.01). Network analysis revealed that interactions between sediment methanogenic archaea were much weaker in the ponds than in the marsh. Overall, these findings suggest that conversion of marsh land to aquaculture ponds significantly altered the sediment methanogenic archaea community structure and diversity and lowered the sediment's capacity to produce CH₄.

The impact of typical pollutants upon the fish-farming was assessed by use of a battery of biomarkers in two typical marine aquaculture regions in South China. Biotransformation parameters including 7-ethoxyresorufin-O-deethylase (EROD), aminopyrine N-demethylase (APND), erythromycin N-demethylase (ERND), glutathione-S-transferase (GST) and Malondialdehyde (MDA) were measured in five cultured fish species. Pollutants such as polycyclic aromatic hydrocarbon (PAHs), organochlorinated compounds (OCs), heavy metals and antibiotics (quinolones and sulfonamides) in sediments were characterized. Higher pollutant residue levels were observed in Dapeng Cove. EROD, APND and ERND activities were lower in fish from Dapeng Cove compared with fish from Hailing Island, while it is just on the contrary for GST and MDA. ERND, APND and GST showed sensitivity corresponding to different pollutants. Small fish species seemed to exhibit more sensitive to pollutants. The study further supports usefulness of multi-biomarker approach considering multiple species to define the effects of anthropogenic inputs in marine aquaculture systems.

Tropical shrimp aquaculture systems in New Caledonia regularly face major crises resulting from outbreaks of Vibrio infections. Ponds are highly dynamic and challenging environments and display a wide range of trophic conditions. In farms affected by vibriosis, phytoplankton biomass and composition are highly variable. These conditions may promote the development of harmful algae increasing shrimp susceptibility to bacterial infections. Phytoplankton compartment before and during mortality outbreaks was monitored at a shrimp farm that has been regularly and highly impacted by these diseases. Combining information from flow cytometry, microscopy, pigment and phylogenetic analysis, the presence of Picocyanobacteria, Prasinophyceae and Diatomophyceae were detected as dominant phytoplankton groups and Cryptophyceae, Prymnesiophyceae and Dinophyceae as minor components. At the onset of the first shrimp mortalities, Bacillariophyceae increased while Cyanobacteria, Prymnesiophyceae and Dinophyceae decreased in the water column, followed by proliferation of Prasinophyceae. Several taxa were identified as potential harmful algae (Cyanobacteria, dinoflagellates and Phaeocystis).

The accumulation of ammonia and nitrite in natural water and aquaculture systems would suppresses the immune system of aquatic animal and reduces the fish growth. Nitrifying bacteria have been widely used to reduce the accumulation of ammonia and nitrite in aquaculture systems, but are still ineffective in many cases. An aquaculture model system consisting of red crucian carp, algae, nitrifying bacteria, and pond water from a natural fish culture was established to explore the limitation of algae and light to nitrifying bacteria content and bacterial nitrification in the presence of a predator. The concentrations of nitrifying bacteria and bacterial nitrification in the group containing algae and light were significantly limited, and addition of nitrifying bacteria in algae groups had little effect. In algae-free groups, the concentrations of ammonia and nitrite were decreased by nitrifying bacteria, and the potential ammonia oxidization rate was also increased. Our findings reveal that the combined effects of algae growth and light exposure are responsible for the observed ineffectiveness of nitrifying bacteria in natural aquaculture environments.

Bioaugmented zero water exchange aquaculture production systems (ZWEAPS) maintained with minimal or no water exchange prevent the ammonia accumulation in the system, leading to environmental sustainability and biosecurity. The microbes in the bioaugmented ZWEAPS plays a major role in maintaining low levels of ammonia through ammonia oxidation and nitrite oxidation. The comprehensive understanding on anammox population in the systems will provide an insight on the environmental factors controlling the functional anammox bacterial communities for potential biostimulation and augmented ammonia removal in ZWEAPS. The sediment metagenome of such three tropical bioaugmented ZWE shrimp culture ponds were analysed to determine the diversity, distribution and abundance of anaerobic ammonia-oxidizing (anammox) bacteria based on hydrazine oxidoreductase (hzo) gene as a phylogenetic marker. The restriction fragment length polymorphism (RFLP) phylotypes from the clone libraries were identified with maximum distribution to Candidatus Kuenenia, as the dominant population in the study sites with high ammonia load followed by Candidatus Scalindua. The environmental factors associated with the abundance and diversity of the anammox population were analysed using RDA and Pearson correlation. The samples of final culturing period (75th day) of TCR-S ZWE pond was observed with the highest operational taxonomic unit (OTU)–based diversity, where comparatively higher ammonia (water 0.71 mg L⁻¹ and sediment 1.21 mg L⁻¹) was recorded among the study sites. The gene abundance of the anammox population ranged from 10⁶ to 10⁷ copies per gram of sediment, in spite of less diversity. The physiochemical factors such as ammonia, nitrite, redox potential and the total organic carbon indicated a strong and positive correlation to the abundance and distribution of the anammox population, which highlights the importance of anammox communities and the potential of biostimulation for ammonia removal in the aquaculture systems.

The nutritional value and developmental variations of cultured fish were assessed for European seabass and gilthead seabream specimens reared in semi-intensive aquaculture systems in two Portuguese estuaries. Quantification of total protein and of carbohydrate and fatty acid profiles was carried out to determine differences between the composition of the same species in two development stages reared in four distinct farms. A significant influence of the rearing site on the nutritional composition of the same species was found for adult European seabass regarding saturated, monounsaturated and highly unsaturated fatty acids contents, both between estuaries and within each estuary. In gilthead seabream, saturated, monounsaturated, polyunsaturated and highly unsaturated fatty acids content were also influenced by the rearing site. Carbohydrate analysis showed a significant influence of the rearing site on free sugar and polysaccharide content in fish of both species, and there was no influence on the species’ protein content. Differences in fatty acid and carbohydrate content among juvenile and adult stages were found for all the groups studied. The present study supported the existing evidence that semi-intensive rearing systems are subjected to the variability of extrinsic factors in the rearing sites, influencing the nutritional value of the same species, namely regarding lipid and carbohydrate profiles, depending on the production site. From a consumer’s perspective, such differences may come as a disadvantage of the rearing method, as it is expected for a product to provide equal nutritional properties and benefits regardless its origin, especially within the same country.