Is rice-crayfish co-culture a better aquaculture model: From the perspective of antibiotic resistome profiles

Distribution and ecological risk assessment of antibiotics in different freshwater aquaculture ponds in a typical agricultural plain, China

Freshwater aquaculture serves as a significant focal point for antibiotic contamination, yet understanding antibiotic distribution across different aquaculture models and stages remains limited. This study evaluated antibiotic pollution in three distinct freshwater aquaculture models: rice-crayfish coculture, fish aquaculture, and crab-crayfish aquaculture, during various aquaculture stages. Of the 33 target antibiotics, 16 antibiotics were detected, with the total concentrations ranging from 111.81 ng/L to 15,949.05 ng/L in water and 10.11 ng/g to 8986.30 ng/g in sediment. Among these antibiotics, erythromycin and lomefloxacin are prohibited for use in Chinese aquaculture. Dominant antibiotics in water included lincomycin, enrofloxacin, and enoxacin, whereas in sediment, oxytetracycline and erythromycin were predominant. Notably, lincomycin emerged as a dominant antibiotic in aquaculture for the first time. The concentrations of these dominant antibiotics were high compared to other aquaculture settings and exhibited elevated ecological risk. Critical periods for antibiotic contamination in water and sediment were found to be incongruent, occurring during the rainy season in July for water and the dry season in October for sediment. Notably, the rice-crayfish coculture model exerts a good effect in reducing antibiotic pollution. Overall, these findings offer valuable evidence for the healthful and sustainable advancement of aquaculture.

Variations in antibiotic resistomes associated with archaeal, bacterial, and viral communities affected by integrated rice-fish farming in the paddy field ecosystem

Antibiotic resistance genes (ARGs) serving as a newly recognized pollutant that poses potential risks to global human health, which in the paddy soil can be potentially altered by different agricultural production patterns. To elucidate the impacts and mechanisms of the widely used and sustainable agricultural production pattern, namely integrated rice-fish farming, on the antibiotic resistomes, we applied metagenomic sequencing to assess ARGs, mobile genetic elements (MGEs), bacteria, archaea, and viruses in paddy soil. There were 20 types and 359 subtypes of ARGs identified in paddy soil. The integrated rice-fish farming reduced the ARG and MGE diversities and the abundances of dominant ARGs and MGEs. Significantly decreased ARGs were mainly antibiotic deactivation and regulator types and primarily ranked level IV based on their potential threat to human health. The integrated rice-fish farming decreased the alpha diversities and altered microbial community compositions. MGEs, bacteria, archaea, and virus exhibited significant correlations with ARGs, while integrated rice-fish farming effectively changed their interrelationships. Viruses, bacteria, and MGEs played crucial roles in affecting the ARGs by the integrated rice-fish farming. The most crucial pathway by which integrated rice-fish farming affected ARGs was through the modulation of viral communities, thereby directly or indirectly influencing ARG abundance. Our research contributed to the control and restoration of ARGs pollution from a new perspective and providing theoretical support for the development of clean and sustainable agricultural production.

Characteristics and driving factors of antibiotic resistance genes in aquaculture products from freshwater ponds in China Yangtze River Delta

Antibiotic resistance genes (ARGs) are widespread in aquaculture and pose a huge threat to aquaculture organisms and human health. In this study, occurrences and relative abundances of ARGs were analysed in the guts of products cultured in freshwater ponds in the Yangtze River Delta region in China. A total of 29 ARGs were found in the gut samples, with detection frequencies ranging from 4.8% to 81%, and the relative abundances (ARGs/16S rRNA) ranging from 10-7 to 1. In addition, the human dietary intake of ARGs via aquaculture products was assessed, where the daily intake of most ARGs via aquaculture products was higher than those via PM2.5 and drinking water, but lower than that via vegetables. The relative abundances of MGE (IS613, Tp614, tnpA and int1) were significantly correlated with those of multiple ARGs, indicating the horizontal gene transfer (HGT) of ARGs among gut microorganisms. Proteobacteria, Firmicutes and Actinobacteria were the dominated microbial communities found in the guts of aquaculture products. In addition, significant correlations were found between Cyanobacteria and int1, between Nitrospira and tetE, and between sul2 and aadA2, indicating potential same hosts of these genes. In addition, results from co-correlation indicated both HGT (dominated by MGEs) of ARGs and the enrichment of ARGs in bacteria. MGEs, mostly int1, were more effective than bacteria in increasing the ARG abundance. This study could provide a better understanding of the transmission of ARGs in the aquaculture environment and improve the quality of aquaculture products and the ecology.

A comprehensive review on the application of semiconducting materials in the degradation of effluents and water splitting

In this comprehensive review article, we delve into the critical intersection of environmental science and materials science. The introduction sets the stage by emphasizing the global water shortage crisis and the dire consequences of untreated effluents on ecosystems and human health. As we progress into the second section, we embark on an intricate exploration of piezoelectric and photocatalytic principles, illuminating their significance in wastewater treatment and sustainable energy production. The heart of our review is dedicated to a detailed analysis of the detrimental impacts of effluents on human health, underscoring the urgency of effective treatment methods. We dissected three key materials in the realm of piezo-photocatalysis: ZnO-based materials, BaTiO3-based materials, and bismuth-doped materials. Each material is scrutinized for its unique properties and applications in the removal of pollutants from wastewater, offering a comprehensive understanding of their potential to address this critical issue. Furthermore, our exploration extends to the realm of hydrogen production, where we discuss various types of hydrogen and the role of piezo-photocatalysis in generating clean and sustainable hydrogen. By illuminating the synergistic potential of these advanced materials and technologies, we pave the way for innovative solutions to the pressing challenges of water pollution and renewable energy production. This review article not only serves as a valuable resource for researchers and scholars in the fields of material science and environmental engineering but also underscores the pivotal role of interdisciplinary approaches in addressing complex global issues.

Exposure and Health Risk Assessment of Heavy Metal in Crayfish from the Middle and Lower Reaches of the Yangtze River

Red swamp crayfish (Procambarus clarkia) is an exposed species to heavy metals due to their lifestyle of direct contact with sediments. Based on the complete crayfish industry, we focus on the presence of heavy metals in crayfish from different circulation links, which provides a new idea for the investigation of heavy metals in food. To analyze the exposure levels of heavy metals in crayfish during aquaculture and circulation, the five elements (Cd, Pb, Hg, Cr, Cu) in crayfish from 126 sampling sites were investigated. Cultured environmental samples were collected for Spearman correlation analysis. Monte Carlo simulation was used to analyze the uncertain health risks of heavy metals in crayfish. The results indicated that the average heavy metal concentrations in crayfish were all below the limit threshold values. The hepatopancreas was the main target organ for heavy metal accumulation (Cd: 0.3132 mg/kg; Pb: 0.0258 mg/kg; Hg: 0.0072 mg/kg; Cr: 0.1720 mg/kg; Cu: 10.6816 mg/kg). The positive correlation of heavy metal content between crayfish and sediments was not significant under the crayfish-rice coculture model. The 95th HI values for adults and children ranged from 0.022 to 0.042 and 0.071 to 0.137, well below 1, indicating that heavy metals do not pose a noncarcinogenic risk to humans. The potential carcinogenic risk of Cd and Cr in crayfish should be taken seriously, as the 95th CR values for children have reached 4.299 × 10-5 and 6.509 × 10-5, respectively.

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.

Alizarin enhancement of the abundance of ARGs and impacts on the microbial community in water

Alizarin, a dyestuff from herbs, showed effective inhibition effects on pathogenic bacteria, and thus has been frequently used in the world as the main alternative to antibiotics in the treatment of inflammations and pathogen infections. However, it was unclear whether alizarin played key a role in antibiotic-induced antibiotic-resistant gene (ARG) alterations and impacted microbial community shifts in aquatic environments. In this study, the effects of alizarin or co-exposure of alizarin with antibiotics on the fate of ARGs, class 1 integron-integrase gene (intI1), and microbial populations in lake water were investigated, and the potential hosts for ARGs were analyzed. The results showed that the absolute abundance of 16s rRNA gene, ARGs (tetA, tetC, and qnrS), and intI1 were increased during the treatment of alizarin. The combination of alizarin and antibiotics was superior to alizarin in its ability to promote population growth of bacteria and induce ARGs. Additionally, alizarin more significantly altered the community composition of microorganisms in water, which resulted in differences in bacterial communities and functions.

Constructed wetlands as hotspots of antibiotic resistance genes and pathogens: Evidence from metagenomic analysis in Chinese rural areas

In rural China, many constructed wetlands (CWs) have been developed to treat rural wastewater sustainably. However, due to the scarce information on those rural CWs, it is difficult to analyze the biological contaminants within those systems, such as antibiotic resistance genes (ARGs) and pathogens. Based on the data collected from two pilot-scale, one-year-observed CWs, for the first time, this study explored the accumulation of ARGs and pathogens using the metagenomic sequencing approach and SourceTracker analysis under different hydraulic loading rates. The Shannon index of ARGs in the effluent surpassed the level found in the influent. The DESeq2 analysis showed that up to 21.49% of the total pathogen species had increased relative abundance in the effluent compared with the influent. By combining the contribution of substrate and rhizosphere, the CW became a more influencing factor for ARGs and pathogens contamination than the influent. The network analysis revealed a critical but latent fact that the development of antibiotic-resistant pathogens is highly likely to be triggered by the co-occurrence of ARGs and pathogens. Collectively, from the aspect of biological risk, our study showed that CWs alone might not be an ideal solution for improving wastewater treatment in rural China.

Tracking soil resistance and virulence genes in rice-crayfish co-culture systems across China

Rice-crayfish co-culture (RC) has been widely and rapidly promoted as a sustainable agricultural system in many countries. The accumulation of crayfish residues could enhance soil organic matters; however, impacts of this integrated farming model on the dissemination and pathogenicity of resistance and virulence genes remain poorly understood. Here, we characterized antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), metal resistance genes (MRGs) and virulence factor genes (VFGs) using metagenomic methods in paired RC and rice monoculture (RM) systems across China. The RC model did not increase the abundance of soil ARGs, BRGs, MRGs, or VFGs in comparison to the RM model, but selectively enriched 35 subtypes of these potential resistance and virulence genes. Network analysis revealed that resistance and virulence genes had a higher number of connections with mobile genetic elements (MGEs) in the RC system than that in the RM system, suggesting a higher horizontal transfer potential of these genes. Moreover, the RC model had a higher abundance of human opportunistic pathogens such as Salmonella enterica, Vibrio cholerae, and Shigella dysenteriae which were potential hosts of VFGs such as phoP, fleS, and gspE, suggesting a potential threat to human health. We further unraveled that stochastic process was the main driver of the assembly of resistance and virulence genes in the RC system. The abundance of ARGs and VFGs were primarily associated with microbial community compositions, while the abundance of BRGs and MRGs were mainly associated with that of MGEs. Taken together, our results suggest that the RC model has potential to cause the dissemination and pathogenicity of resistance and virulence genes, which has important implications for the control of soil-borne biological risks and the strategic management of sustainable agriculture.

Distribution and influencing factors of antibiotic resistance genes of crayfish (Procambarus clarkii) intestine in main crayfish breeding provinces in China

The propagation of antibiotic resistance genes (ARGs) has become a global public health concern. However, the distribution and influencing factors of ARGs, especially high-risk ARGs, in the gut of aquaculture animals remain unclear. Here, we employed 16S rRNA gene sequencing and high-throughput quantitative PCR techniques to determine crayfish gut microbiota and ARGs collected from 40 culture ponds in major crayfish farming provinces of China. We detected 74 ARGs in crayfish gut. Among them, the beta-lactamase and tetracycline resistance genes were dominant. The total ARG abundance was the highest in Hubei Province. High-risk ARGs were also found in crayfish gut, and ermB had the highest abundance and distributed in Anhui, Hubei, Henan and Jiangxi Province. In addition, opportunistic pathogens (Streptococcus, Aeromonas and Acinetobacter) might be potential hosts for ARGs, including high-risk ARGs. Finally, habitat, environmental factors (NO₃-N, pH and temperature), microbial alpha diversity and mobile genetic elements (MGEs) showed significant influence on ARGs profiles. Generally, our results illustrate that ARGs are prevalent in crayfish gut and may pose potential risk to human health, which will help develop targeted strategies for the risk management and assessment of ARGs in the aquaculture.

Comparison of environmental microbiomes in an antibiotic resistance-polluted urban river highlights periphyton and fish gut communities as reservoirs of concern

Natural waterways near urban areas are heavily impacted by anthropogenic activities, including their microbial communities. A contaminant of growing public health concern in rivers is antibiotic resistant genes (ARGs), which can spread between neighboring bacteria and increase the potential for transmission of AR bacteria to animals and humans. To identify the matrices of most concern for AR, we compared ARG burdens and microbial community structures between sample types from the Scioto River Watershed, Ohio, the United States, from 2017 to 2018. Five environmental matrices (water, sediment, periphyton, detritus, and fish gut) were collected from 26 river sites. Due to our focus on clinically relevant ARGs, three carbapenem resistance genes (bla_KPC, bla_NDM, and bla_OXA-48) were quantified via DropletDigital™ PCR. At a subset of nine urbanized sites, we conducted16S rRNA gene sequencing and functional gene predictions. Carbapenem resistance genes were quantified from all matrices, with bla_KPC being the most detected (88 % of samples), followed by bla_NDM (64 %) and bla_OXA-48 (23 %). Fish gut samples showed higher concentrations of bla_KPC and bla_NDM than any other matrix, indicating potential ARG bioaccumulation, and risk of broader dissemination through aquatic and nearshore food webs. Periphyton had higher concentrations of bla_NDM than water, sediment, or detritus. Microbial community analysis identified differences by sample type in community diversity and structure. Sediment samples had the most diverse microbial communities, and detritus, the least. Spearman correlations did not reveal significant relationships between the concentrations of the monitored ARGs and microbial community diversity. However, several differentially abundant taxa and microbial functions were identified by sample type that is definitive of these matrices' roles in the river ecosystem and habitat type. In summary, the fish gut and periphyton are a concern as AR reservoirs due to their relatively high concentration of carbapenem resistance genes, diverse microbial communities, and natural functions that promote AR.

Heavy metal residues, releases and food health risks between the two main crayfish culturing models: Rice-crayfish coculture system versus crayfish intensive culture system

High-density culturing with excessive feeding of commercial feed has caused heavy metals pollution to agricultural production system. In this study, the dynamic changes and transfer of heavy metals in rice-crayfish coculture system (RCCS) and crayfish intensive culture system (CICS) within a completed culture cycle were systematically quantified. Our results showed that Cd in feed represented more than 50% of the total Cd input, and the inputs of As and Cr were mainly from irrigation. The residues of As and Pb in RCCS were slightly higher than those in CICS, while the residues of Cd and Cr in RCCS were far fewer than those in CICS. Moreover, the metal pollution index in CICS was 0.781, while it was 0.543 in the RCCS. Furthermore, a large proportion of the Cd and Pb in CICS was released into the external environment through drainage. Notably, the absorption and solidification of heavy metals by straw did not increase the residues of As and Pb in the major components of RCCS in the second year. Compared to CICS, RCCS did not produce many heavy metal residues or cause heavy metal discharge pressure on the external environment, and its food product had a low risk of heavy metal contamination.

Sustainability of the rice-crayfish co-culture aquaculture model: microbiome profiles based on multi-kingdom analyses

While the rice-crayfish culture (RCFP) model, an important aquaculture model in Asia, is generally considered a sustainable model, its sustainability in terms of microbial community profiles has not been evaluated. In this study, multi-kingdom analyses of microbiome profiles (i.e., bacteria, archaea, viruses, and eukaryotes) were performed using environmental (i.e., water and sediment) and animal gut (i.e., crayfish and crab gut) microbial samples from the RCFP and other aquaculture models, including the crab-crayfish co-culture, crayfish culture, and crab culture models, to evaluate the sustainability of the RCFP systematically. Results showed that RCFP samples are enriched with a distinct set of microbes, including Shewanella, Ferroplasma, Leishmania, and Siphoviridae, when compared with other aquaculture models. Additionally, most microbes in the RCFP samples, especially microbes from different kingdoms, were densely and positively connected, which indicates their robustness against environmental stress. Whereas microbes in different aquaculture models demonstrated moderate levels of horizontal gene transfer (HGT) across kingdoms, the RCFP showed relatively lower frequencies of HGT events, especially those involving antibiotic resistance genes. Finally, environmental factors, including pH, oxidation-reduction potential, temperature, and total nitrogen, contributed profoundly to shaping the microbial communities in these aquaculture models. Interestingly, compared with other models, the microbial communities of the RCFP model were less influenced by these environmental factors, which suggests that microbes in the latter have stronger ability to resist environmental stress. The findings collectively reflect the unique multi-kingdom microbial patterns of the RCFP model and suggest that this model is a sustainable model from the perspective of microbiome profiles.