The response of sediment microbial communities to temporal and site-specific variations of pollution in interconnected aquaculture pond and ditch systems

Exploring seasonal variations, assembly dynamics, and relationships of bacterial communities in different habitats of marine ranching

Offshore coastal marine ranching ecosystems provide habitat for diverse and active bacterial communities. In this study, 16S rRNA gene sequencing and multiple bioinformatics methods were applied to investigate assembly dynamics and relationships in different habitats. The higher number of edges in the water network, more balanced ratio of positive and negative links, and more keystone species included in the co-occurrence network of water. Stochastic processes dominated in shaping gut and sediment community assembly (R2 < 0.5), while water bacterial community assembly were dominated by deterministic processes (R2 > 0.5). Dissimilarity-overlap curve model indicated that the communities in different habitats have general dynamics and interspecific interaction (P < 0.001). Bacterial source-tracking analysis revealed that the gut was more similar to the sediment than the water bacterial communities. In summary, this study provides basic data for the ecological study of marine ranching through the study of bacterial community dynamics.

Enhanced bioremediation of cyclohexaneacetic acid in offshore sediments with green synthetic iron oxide and Pseudoalteromonas sp

Naphthenic acids (NAs) have been found to exert serious threats on offshore sediment ecosystems and human health in recent years, which entails us the urgent need for NAs remediation. Bioremediation is considered an ideal method for sediment remediation due to ecological sustainability and economic feasibility. However, current bioremediation efficiency of offshore sediments suffers from relatively slow and there has never any attempts to bioremediate offshore sediment NAs contamination hitherto. In this study, the green synthetic iron oxides (gFeOx) based on Laminaria extracts was employed to enhance the biodegradation of NAs (Cyclohexylacetic acid, CHAA) in offshore sediments by Pseudoalteromonas sp. JSTW (an indigenous microorganism). The results showed that CHAA (20 mg·kg-1) in offshore sediments was removed almost 100% within 7 days at 30 mg·kg-1 gFeOx and 0.6 mg·kg-1 Strain JSTW. High-throughput sequencing results revealed that the structure and function of sediment microbial community were essentially restored to uncontaminated levels after bioremediation, highlighting the joint remediation approach is an efficient and eco-friendly method. Overall, this work has firstly provided insights into the application for NAs in situ bioremediation in offshore sediments.

Differences in environmental microbial community responses under rice-crab co-culture and crab monoculture models under cyanobacterial bloom

Cyanobacterial blooms (CBs) present significant challenges to Chinese mitten crab (CMC) culture, posing hazards to the aquatic microbial ecology. However, the current focus on the microbial ecological changes within the CMC culture system under the influence of CBs is somewhat insufficient. There's an urgent need to analyze the microbial ecosystem of the CMC culture system under CBs. This study employed 16S rRNA gene amplicon sequencing to investigate the dynamics of the environmental microbial community in both the rice-crab co-culture (RC) and crab monoculture (CM) models. The results revealed that cyanobacteria reached high levels in the CM water in July, while they began to increase in the RC water in August. Notably, OTU147 (uncultured bacterium g_Planktothrix NIVA-CYA 15), identified as the dominant taxon associated with CBs, showed a significant linear relationship with TP, NO2 --N, and the N:P ratio. TP, TN, NO2 --N, and CODMn had a more pronounced impact on the structure of bacterial communities and cyanobacterial taxa in the water. The bacterial community structure involved in carbon metabolism displayed temporal succession in the water. The co-occurrence network of the bacterial community primarily consisted of Chloroflexi, Proteobacteria, and Firnicutes in the sediment, and Actinobacteria, Proteobacteria, Chloroflexi, and Bacteroidota in the water. In contrast, the co-occurrence network included different peripheral species in the sediment and water. Keystone species were predominantly represented by OTU22 (uncultured actinobacterium g_ hgcI clade) and OTU12 (uncultured Opitutae bacterium g_ norank) in the RC water, and by OTU25 (uncultured bacterium g_ Limnohabitans) in the CM water. TP, TN, NO2 --N, and CODMn were identified as the primary environmental factors influencing these keystone taxa within the culture water. In conclusion, this study on the microbial ecology of the CMC culture system under the influence of CBs provides valuable insights that can be instrumental in subsequent management efforts.

Mass variations and transfer process of shrimp farming pollutants in aquaculture drainage systems: Effects of DOM features and physicochemical properties

The expansion of aquaculture produces increasing pollutant loads, necessitating the use of drainage systems to discharge wastewater into surface water. To assess the mass variations and transfer process of aquaculture wastewater, an entire aquaculture drainage investigation lasting for 48 h was conducted, focusing on the nutrients, heavy metals, dissolved organic matter (DOM), and physicochemical properties of drainage in a commercial shrimp farm. The findings revealed that early drainage produced more heavy metals, total nitrogen (TN), dissolved organic nitrogen (DON), and feed-like proteins from aquaculture floating feed and additives, whereas late drainage produced more PO43--P and total dissolved phosphorus (TP). A few pollutants, including DON, Cu, and feed-like proteins, were effectively removed, whereas the contents of TN, dissolved inorganic nitrogen, and Zn increased in the multi-level aquaculture drainage system. Limited dilution indicated that in-stream transfer was the main process shaping pollutant concentrations within the drainage system. In the lower ditches, NO3--N, heavy metals, and feed-like proteins exhibited evident in-stream attenuation, while TN and NH4+-N underwent significant in-stream enrichment processes, especially in ditch C, with the transfer coefficient values (vf) of -1.74E-5 and -2.04E-5. This indicates that traditional aquaculture drainage systems serve as nitrogen sinks, rather than efficient nutrient purge facilitators. Notably, DOM was identified as a more influential factor in shaping the in-stream transfer process in aquaculture drainage systems, with an interpretation rate 40.79% higher than that of the physiochemical properties. Consequently, it is necessary to eliminate the obstacles posed by DOM to pollutant absorption and net zero emissions in aquaculture drainage systems in the future. ENVIRONMENTAL IMPLICATIONS: Nutrients, heavy metals, and dissolved organic matter are hazardous pollutants originating from high-density aquaculture. As the sole conduit to natural waters, aquaculture drainage systems have pivotal functions in receiving and purifying wastewater, in which the in-stream transfer process is affected by ambient conditions. This field study investigated the spatial variations, stage distinctions, effects of physicochemical properties, and dissolved organic matter (DOM) features. This finding suggests that the aquaculture drainage system as a nitrogen sink and DOM source. While the DOM is the key factor in shaping the in-stream transfer process, and obstacles for pollutant elimination. This study helps in understanding the fate of aquaculture pollutants and reveals the drawbacks of traditional aquaculture drainage systems.

Distribution characteristics of microorganisms in sediments of Dagu River and their biological indicator function for evaluating eco-environmental quality of rural river

The microorganisms in sediments play a crucial role in biogeochemical cycle processes, and numerous studies have shown that microbial community is closely related to environmental factors. However, the usability of sediment microorganisms to evaluate the eco-environment quality of rural rivers has not been adequately explored. This study investigated the distribution characteristics and response of sediment microorganisms to environmental parameters and benthic organisms. Based on the environmental parameters and benthic community indices, the 12 stations were divided into high-polluted group A, moderate-polluted group B and low-polluted group C. Station DG01 and DG02 in group A had the highest level of As and Ni pollution and nutrient concentration, and DG09 in group A had the lowest benthic diversity. Correspondingly, group A had the lowest abundance of Proteobacteria, which has a higher requirement for the environment than Planctomycetes. Group B had the highest sulfide level (97.45 mg/kg), and bacteria (Thiobacillus, Sulfurisoma and Sulfuritalea) with genes involved in sulfur cycling were more enriched in this group. Group C had the lowest level of total nitrogen (243.36 mg/kg), and Rhodanobacteraceae in Xanthomonadales might be a key bioindicator for low nitrogen. In addition, Chlorophyta was found to be more susceptible to heavy metals, and moreover co-occurrence networks showed that microeukaryotes were more sensitive to heavy metal pollution compared to benthic animals and prokaryotes. Therefore, this study suggested that benthic microorganisms especially microeukaryotes could be used as good indicators for evaluating the eco-environmental quality of rural rivers.

Accumulation of heavy metals in meat and their relationship with water and food intake of aquatic animals in Kermanshah, western Iran

Accumulation of heavy metals in aquatic meat can have a destructive role in food safety and is also closely related to the water and feed consumed by animals. Thus, the aim of this study is to evaluate the heavy metals in three aquatic species and their relationship with water and food. Fresh samples included 65 trout, 40 carp, and 45 shrimp, and their water and food were collected from Kermanshah aquaculture. After the preparation phase, the concentration of heavy metals was determined by using inductively-coupled plasma-mass-spectrometry. Lead in carp, arsenic in shrimp, cadmium, and mercury in trout had the highest concentrations of toxic metals. The lead, arsenic, and mercury concentrations in all three farmed aquatic species were higher than the maximum permissible limits. A significant correlation coefficient was observed between the concentration of these metals in the meat and their consumed water and food (p≤0.001). Of the essential metals, except for selenium in trout, and zinc in all three aquatic species, the concentration of other metals was higher than that of the permissible consumption limit. There was also a significant correlation between the concentration of essential metals and their consumed feed (p<0.001). The target hazard quotient of toxic metals was less than 1, but the target cancer risk for arsenic and mercury was in the range of carcinogenicity. Thereby, it is vital to monitor the quality of aquatic meat and pay special attention to their water and feed sources in this region of Iran, which will consequently guarantee human health.

Microplastics shape microbial interactions and affect the dissemination of antibiotic resistance genes in different full-scale wastewater treatment plants

Wastewater treatment plants (WWTPs) pose a potential threat to the environment because of the accumulation of antibiotic resistance genes (ARGs) and microplastics (MPs). However, the interactions between ARGs and MPs, which have both indirect and direct effects on ARG dissemination in WWTPs, remain unclear. In this study, spatiotemporal variations in different types of MPs, ten ARGs (sul1, sul2, tetA, tetO, tetM, tetX, tetW, qnrS, ermB, and ermC), class 1 integron integrase (intI1) and transposon Tn916/1545 in three typical WWTPs were characterized. Sul1, tetO, and sul2 were the predominant ARGs in the targeted WWTPs, whereas the intI1 and transposon Tn916/1545 were positively correlated with most of the targeted ARGs. Saccharimonadales (4.15 %), Trichococcus (2.60 %), Nitrospira (1.96 %), Candidatus amarolinea (1.79 %), and SC-I-84 (belonging to phylum Proteobacteria) (1.78 %) were the dominant genera. Network and redundancy analyses showed that Trichococcus, Faecalibacterium, Arcobacter, and Prevotella copri were potential hosts of ARGs, whereas Candidatus campbellbacteria and Candidatus kaiserbacteria were negatively correlated with ARGs. The potential hosts of ARGs had a strong positive correlation with polyethylene terephthalate, silicone resin, and fluor rubber and a negative correlation with polyurethane. Candidatus campbellbacteria and Candidatus kaiserbacteria were positively correlated with polyurethane, whereas potential hosts of ARGs were positively correlated with polypropylene and fluor rubber. Structural equation modeling highlighted that intI1, transposon Tn916/1545 and microbial communities, particularly microbial diversity, dominated the dissemination of ARGs, whereas MPs had a significant positive correlation with microbial abundance. Our study deepens the understanding of the relationships between ARGs and MPs in WWTPs, which will be helpful in designing strategies for inhibiting ARG hosts in WWTPs.

Community assembly patterns and processes of bacteria in a field-scale aquaculture wastewater treatment system

Microbial communities are responsible for the biological treatment of wastewater, however, our comprehension of their diversity, assembly patterns, and functions remains limited. In this study, we analyzed bacterial communities in both water and sediment samples. These samples were gathered from a novel field-scale aquaculture wastewater treatment system (FAWTS), which employs a multi-stage purification process to eliminate nutrients from pond culture wastewater. Significant variations were observed in bacterial diversity and composition across various ponds within the system and at different stages of the culture. Notably, the bacterial community in the FAWTS displayed a distinct species abundance distribution. The influence of dispersal-driven processes on shaping FAWTS communities was found to be relatively weak. The utilization of neutral and null models unveiled that the assembly of microbial communities was primarily governed by stochastic processes. Moreover, environmental factors variables such as total nitrogen (TN), dissolved oxygen (DO), and temperature were found to be associated with both the composition and assembly of bacterial communities, influencing the relative significance of stochastic processes. Furthermore, we discovered a close relationship between that bacterial community composition and system functionality. These findings hold significant implications for microbial ecologists and environmental engineers, as they can collaboratively refine operational strategies while preserving biodiversity. This, in turn, promotes the stability and efficiency of the FAWTS. In summary, our study contributes to an enhanced mechanistic understanding of microbial community diversity, assembly patterns, and functionality within the FAWTS, offering valuable insights into both microbial ecology and wastewater treatment processes.

The effect of novel aquaculture mode on phosphorus sorption-release in pond sediment

The emergence of aquaculture modes has brought considerable changes to the aquaculture landscape and profoundly influenced environmental processes. However, there is limited research on nutrient cycling in emerging aquaculture modes. This study investigated the characteristics and mechanisms of sediment phosphorus (P) sorption-release in traditional earthen pond culture (TEP) and pond-tank culture mode (PTC), which represents novel aquaculture modes. The results showed that under higher nutrient load, the PTC did not show significant differences in nutrient concentration in water and sediments compared to TEP. Although there are no significant differences in overlying water P concentration between the modes throughout the entire aquaculture period, the trends of its variation over time are different, which significantly affected the P sorption-release characteristics of sediment. Additionally, correlation analysis suggested that calcium-bound P and hot NaOH-extractable organic P may affect the sorption-release characteristics of sediment as active P fractions. The change in redox condition caused by enzyme-mediated organic matter decomposition (such as protein and lipids) is also an important reason for sediment P release. However, the P fractions and organic matter content showed no significant differences between the two modes. Sediment microbial analysis showed that TEP exhibited a significant dominance of inorganic P-solubilizing bacteria, especially Actinobacteria and Bacilli classes. PTC had a higher proportion of organic P-solubilizing bacteria, primarily in the Bacteroidia class. The quantitative results of the key functional gene phoD in organic P decomposition also showed that the abundance in PTC was significantly higher than that in TEP. This suggested that microbial differences may be another reason for differences in P sorption-release behavior. This study revealed the differences in P sorption-release characteristics and mechanisms between the TEP and PTC, which holds positive implications for water quality and pollution management in novel aquaculture modes.

Gross yield driving the mass fluxes of fishery drugs: Evidence of occurrence from full aquaculture cycle in lower Yangtze River Basin

Expanding aquaculture has generated pollutants like fishery drugs in wastewater, which affects the aquatic environments and hinders sustainable development of aquaculture. To evaluate the occurrence, mass fluxes and production factors of fishery drugs in aquaculture, full-aquaculture-cycle monitoring in finfish and crustacean wastewater was conducted in the lower Yangtze River Basin, and 28 pesticides and 15 antibiotics were detected. The results showed that individual fishery drugs varied from ppt to ppb levels. Among them, sulfonamides were dominant with a mean concentration of 105.95 ± 4.13 ng·L-1 in finfish aquacultural wastewater, and insecticides were prevailing in crustacean aquacultural wastewater with a content of 146.56 ± 0.66 ng·L-1. Since the susceptibility to finfish disease determined the aquaculture practice, there were significant differences between two types of aquacultural wastewater. Finfish aquacultural wastewater contained more drugs and reached peak earlier in rapid-growth period, yet crustacean aquacultural wastewater peaked at the harvest period, to prevent against disease. Meanwhile, higher ecological risk, especially for florfenicol, were found in finfish wastewater. With 6 production factors from Good Aquaculture Practice, the gross yield was the most influential factor of drug mass flux, explaining 98 % variance by stepwise regression. Apart from increasing concentrations of fishery drugs in wastewater, regional high-yield aquaculture also significantly impacted the corresponding mass flux. As estimated by linear regression, 1.63 tons of target drugs would be discharged by 1 Mt. aquatic products, and 7.77 tons were discharged from aquaculture in the lower Yangtze River Basin in 2021. This is the first report to quantify mass fluxes of fishery drugs and to highlight gross yield as the most influential factor, which provides guidance for the supervision and regulation of sustainable aquaculture.

Immobilization of phosphorus in water-sediment system by iron-modified attapulgite, calcite, bentonite and dolomite under feed input condition: Efficiency, mechanism, application mode effect and response of microbial communities and iron mobilization

Four kinds of iron-based materials, i.e., iron-modified attapulgite, calcite, bentonite and dolomite (abbreviated as Fe-ATP, Fe-CA, Fe-BT and Fe-DOL, respectively) were prepared and used to immobilize the phosphorus in the system of overlying water (O-water) and sediment under the feed input condition, and their immobilization efficiencies and mechanisms were investigated. The influence of application mode on the immobilization of phosphorus in the water-sediment system by Fe-ATP, Fe-CA, Fe-BT and Fe-DOL was researched. The effects of Fe-ATP, Fe-CA, Fe-BT and Fe-DOL on the concentration of labile iron in the water-sediment system and the microbial communities in sediment were also studied. The results showed that the Fe-ATP, Fe-CA, Fe-BT and Fe-DOL addition all can effectively immobilize the soluble reactive phosphorus (SRP), dissolved total phosphorus (DTP) and diffusive gradients in thin-films (DGT)-labile phosphorus in O-water under the feed input condition, and also had the ability to inactivate the DGT-labile phosphorus in the top sediment. Although the change in the application mode from the one-time addition to the multiple addition reduced the inactivation efficiencies of SRP and DTP in O-water in the early period of application, it increased the immobilization efficiencies in the later period of application. Although Fe-ATP, Fe-CA, Fe-BT and Fe-DOL had a certain releasing risk of iron into the pore water, they had negligible risk of iron release into O-water. The addition of Fe-ATP, Fe-CA, Fe-BT or Fe-DOL reshaped the sediment bacterial community structure and can affect the microorganism-driven phosphorus cycle in the sediment. Results of this work suggest that Fe-ATP, Fe-CA, Fe-BT and Fe-DOL are promising phosphorus-inactivation materials to immobilize the phosphorus in the water-sediment system under the feed input condition.

Community assembly of comammox Nitrospira in coastal wetlands across southeastern China

Complete ammonia oxidizers (comammox Nitrospira) are ubiquitous in coastal wetland sediments and play an important role in nitrification. Our study examined the impact of habitat modifications on comammox Nitrospira communities in coastal wetland sediments across tropical and subtropical regions of southeastern China. Samples were collected from 21 coastal wetlands in five provinces where native mudflats were invaded by Spartina alterniflora and subsequently converted to aquaculture ponds. The results showed that comammox Nitrospira abundances were mainly influenced by sediment grain size rather than by habitat modifications. Compared to S. alterniflora marshes and native mudflats, aquaculture pond sediments had lower comammox Nitrospira diversity, lower clade A.1 abundance, and higher clade A.2 abundance. Sulfate concentration was the most important factor controlling the diversity of comammox Nitrospira. The response of comammox Nitrospira community to habitat change varied significantly by location, and environmental variables accounted for only 11.2% of the variations in community structure across all sites. In all three habitat types, dispersal limitation largely controlled the comammox Nitrospira community assembly process, indicating the stochastic nature of these sediment communities in coastal wetlands. IMPORTANCE Comammox Nitrospira have recently gained attention for their potential role in nitrification and nitrous oxide (N2O) emissions in soil and sediment. However, their distribution and assembly in impacted coastal wetland are poorly understood, particularly on a large spatial scale. Our study provides novel evidence that the effects of habitat modification on comammox Nitrospira communities are dependent on the location of the wetland. We also found that the assembly of comammox Nitrospira communities in coastal wetlands was mainly governed by stochastic processes. Nevertheless, sediment grain size and sulfate concentration were identified as key variables affecting comammox Nitrospira abundance and diversity in coastal sediments. These findings are significant as they advance our understanding of the environmental adaptation of comammox Nitrospira and how future landscape modifications may impact their abundance and diversity in coastal wetlands.

The Gill-Associated Bacterial Community Is More Affected by Exogenous Chlorella pyrenoidosa Addition than the Bacterial Communities of Water and Fish Gut in GIFT Tilapia (Oreochromis niloticus) Aquaculture System

Microalgae has been widely used in aquaculture to improve both the water environment and fish growth; however, the current understanding of the effects of microalgae addition on the key players involved in regulating the water environment and fish health, such as microorganisms, remains limited. Here, a 50-day mesocosm experiment was set up to simulate the culture of Genetic Improvement of Farmed Tilapia (GIFT, Oreochromis niloticus) with an average weight of 14.18 ± 0.93 g and an average length of 82.77 ± 2.80 mm. Different amounts of Chlorella pyrenoidosa were added into these artificial systems to investigate dynamics of bacterial communities in aquaculture water, fish gill, and gut using amplicon-based high-throughput sequencing technology. Our results showed that Chlorella pyrenoidosa addition increased diversity and network complexity of gill-associated bacterial communities rather than those of the water and gut. Furthermore, more biomarkers in the gill-associated bacterial communities were detected in response to Chlorella pyrenoidosa addition than the water and fish gut samples. These findings highlighted the high sensitivity of gill-associated bacterial communities in response to the Chlorella pyrenoidosa addition, implying Chlorella pyrenoidosa addition could play important roles in regulating the fish mucosal immunity by altering the gill-associated microbiota.

Insight into the spatiotemporal distribution of antibiotic resistance genes in estuarine sediments during long-term ecological restoration

In this study, we aimed to investigate the long-term spatiotemporal changes in hydrodynamics, antibiotics, nine typical subtypes of antibiotic resistance genes (ARGs), class 1 integron gene (intI1), and microbial communities in the sediments of a semi-enclosed estuary during ecological restoration with four treatment stages (influent (#1), effluent of the biological treatment area (#2), oxic area (#3), and plant treatment area (#4)). Ecological restoration of the estuary reduced common pollutants (nitrogen and phosphorus) in the water, whereas variations in ARGs showed noticeable seasonal and spatial features. The absolute abundance of ARGs at sampling site #2 considerably increased in autumn and winter, while it significantly increased at sampling site #3 in spring and summer. The strong intervention of biological treatment (from #1 to #2) and aerators (from #2 to #3) in the estuary substantially affected the distribution of ARGs and dominant antibiotic-resistant bacteria (ARB). The dominant ARB (Thiobacillus) in estuarine sediments may have low abundance but important dissemination roles. Meanwhile, redundancy and network analysis revealed that the microbial communities and intl1 were key factors related to ARG dissemination, which was affected by spatial and seasonal ecological restoration. A positive correlation between low flow velocity and certain ARGs (tetM, tetW, tetA, sul2, and ermC) was observed, implying that flow optimization should also be considered in future ecological restoration to remediate ARGs. Furthermore, the absolute abundance of ARGs can be utilized as an index to evaluate the removal capacity of ARGs by estuarine restoration.

Microbial biogeochemical cycling reveals the sustainability of the rice-crayfish co-culture model

Aquaculture has great potential in nourishing the global growing population, while such staggering yields are coupled with environmental pollution. Rice-crayfish co-culture models (RCFP) have been widely adopted in China due to their eco-friendliness. However, little is known about RCFP's microbiome pattern, which hinders our understanding of its sustainability. This study has conducted metagenomic analysis across aquaculture models and habitats, which revealed aquaculture model-specific biogeochemical cycling pattern (e.g., nitrogen (N), sulfur (S), and carbon (C)): RCFP is advantageous in N-assimilation, N-contamination, and S-pollutants removal, while non-RCFP features N denitrification process and higher S metabolism ability, producing several hazardous pollutants in non-RCFP (e.g., nitric oxide, nitrogen monoxide, and sulfide). Moreover, RCFP has greater capacity for carbohydrate enzyme metabolism compared with non-RCFP in environmental habitats, but not in crayfish gut. Collectively, RCFP plays an indispensable role in balancing aquaculture productivity and environmental protection, which might be applied to the blue transformation of aquaculture.

Nutrient enrichment drives the sediment microbial communities in Chinese mitten crab Eriocheir sinensis culture

Microbial communities play a critical role in aquaculture ecosystems. To identify the influence of sediment nutrient levels on microbial communities, sediment and water samples were collected from Chinese mitten crab Eriocheir sinensis culture ponds with different nutrient enrichment levels. Relevant physicochemical properties were measured, and 16 S rRNA gene sequencing was applied to identify relevant bacterial communities in the sediments. The results showed that the diversity and composition of microbial communities in sediments with different levels of nutrient enrichment varied considerably. Proteobacteria was the most abundant phylum in all samples, followed by Bacteroidetes, and Desulfobacterota with relative abundances of 23.5-40.9%, 9.8-21.5%, and 9.6-18.1%, respectively. Notably, total nitrogen (TN), organic matter (OM), and pH were important factors driving sediment bacterial community aggregation, the TN concentration explaining 61.5% of the microbial community variation. This study highlights that long-term culture activities alter the degree of sediment nutrient enrichment, which in turn affects microbial community composition and may ultimately have an impact on culture efficiency.

Exploring the interactions between the gut microbiome and the shifting surrounding aquatic environment in fisheries and aquaculture: A review

The rise of "new" sequencing technologies and the development of sophisticated bioinformatics tools have dramatically increased the study of the aquaculture microbiome. Microbial communities exist in complex and dynamic communities that play a vital role in the stability of healthy ecosystems. The gut microbiome contributes to multiple aspects of the host's physiological health status, ranging from nutritional regulation to immune modulation. Although studies of the gut microbiome in aquaculture are growing rapidly, the interrelationships between the aquaculture microbiome and its aquatic environment have not been discussed and summarized. In particular, few reviews have focused on the potential mechanisms driving the alteration of the gut microbiome by surrounding aquatic environmental factors. Here, we review current knowledge on the host gut microbiome and its interrelationship with the microbiome of the surrounding environment, mainly including the main methods for characterizing the gut microbiome, the composition and function of microbial communities, the dynamics of microbial interactions, and the relationship between the gut microbiome and the surrounding water/sediment microbiome. Our review highlights two potential mechanisms for how surrounding aquatic environmental factors drive the gut microbiome. This may deepen the understanding of the interactions between the microbiome and environmental factors. Lastly, we also briefly describe the research gaps in current knowledge and prospects for the future orientation of research. This review provides a framework for studying the complex relationship between the host gut microbiome and environmental stresses to better facilitate the widespread application of microbiome technologies in fisheries and aquaculture.

Metagenomic insights into the spatiotemporal responses of antibiotic resistance genes and microbial communities in aquaculture sediments

The dissemination of antibiotic resistance genes (ARGs) in aquaculture systems is a potential threat to environmental safety and human health. However, the spatiotemporal distribution pattern of ARGs and key factors associated with their dissemination in aquaculture sediments remain unclear. In this study, ARGs, mobile genetic elements, microbial community composition, heavy metal contents, and nutrient contents of samples collected from a whole culture cycle of fish in a representative aquaculture farm were characterized. The distribution patterns of nine subtypes of ARGs (tetW, tetM, tetA, ermC, ermB, sul1, sul2, floR, and qnrS) showed clear spatiotemporal differences. The absolute abundance of ARGs in aquaculture sediments was higher in winter and in rivers of the aquaculture farm. Proteobacteria was the dominant phylum in all sediment samples. The results of network and redundancy analyses confirmed that the Dechloromonas, Candidatus Accumulibacter, Smithella, Geobacter, and Anaeromyxobacter belonging to Proteobacteria were positively correlated with ARGs, suggesting that these microbial species are potential hosts of corresponding ARGs. Our study highlights that the microbial community is the determining factor for ARG dissemination. Strategies for inhibiting these potential hosts of ARGs should be developed based on controllable factors.

Anoxic/oxic treatment without biomass recycle

The Anoxic/Oxic (A/O) process involves recirculating mixed liquor between its A and O tanks so that nitrate produced in the O tank can be used to for denitrification with influent COD in the A tank. Because biomass is recirculated along with nitrate, A/O operation leads to similar microbial communities in the A and O tanks, which may decrease the rates of denitrification and nitrification in each tank. Here, bench-scale experiments simulated this aspect of the A/O process by exchanging biomass between an anoxic flask and an oxic cylinder at exchange ratios of 0%, 20%, 30%, and 50%. Nitrification and denitrification rates were only 40% and 19% for 50% biomass exchange of that for no biomass exchange. Phylogenetic analysis documented that the microbial communities became much more similar with biomass exchange, and the finding was consistent with community composition in a full-scale A/O process in a municipal wastewater treatment plant. A two-stage vertical baffled bioreactor (VBBR) realized efficient total‑nitrogen removal in recirculation without biomass exchange. Average removals of COD and TN were respectively 6% and 22% higher for the two-stage VBBR than the conventional A/O process, but its hydraulic retention time (HRT) was 55% to 70% of the volume of a conventional A/O process treating the same influent wastewater. The VBBR was more efficient because its anoxic biofilm was enriched in denitrifying bacteria, while its oxic biofilm was enriched in nitrifying bacteria. For example, the phylum Chloroflexi was greater in the An-VBBR, while the phylum Proteobacteria was greater in the Ox-VBBR.