Metagenomic analysis to determine the characteristics of antibiotic resistance genes in typical antibiotic-contaminated sediments

Exploring the distribution and transmission mechanism of ARGs in crab aquaculture ponds and ditches using metagenomics

Aquaculture provides notable economic benefits; however, the excessive use of antibiotics has resulted in the production and spread of antibiotic resistance genes (ARGs). The intricate pollution dynamics in aquaculture areas complicate the comprehension of the distribution and transmission of ARGs in aquaculture systems. Using metagenomic sequencing technology, this study used eight ponds and four ditches in a large crab aquaculture area in Taizhou City, where Proteobacteria (61.58 %) and Acidobacteria (6.04 %) were identified as the dominant phyla and Thiobacillus (1.84 %) and Lysobacter (0.99 %) were the dominant genera. Network and linear discriminant analysis effect size (LEfse) analyses showed that Proteobacteria and Lysobacter were the main host phyla of ARGs, and Lysobacter, which are key host bacteria in ponds, played an important role in determining the abundance of ARGs in ponds. Co-occurrence network analysis (spearman r > 0.7, p < 0.01) revealed that prophages can dominate the spread of ARGs by carrying several ARG subtypes (rsmA, OXA-21, THIN-B and lnuF). Analysis of variance demonstrated that functions related to the horizontal gene transfer (HGT) of ARGs, such as EPS synthesis (lptF), oxidative stress (gor and ompR), ATP synthesis (lapB and vcaM), and cell membrane permeability (yajC and gspJ), were significantly expressed in the pond (p < 0.05), confirming that ARGs had stronger transmission potential in the pond. The Mantel test and partial least squares path modeling (PLS-PM) analysis showed that ARGs exist in bacteria and spread among them through mobile genetic elements and HGT. This study revealed the distribution and transmission mechanism of ARGs in the ponds and ditches of a crab aquaculture system and provided a theoretical basis for controlling the spread of ARGs in crab aquaculture in this area.

Antibiotic resistome dynamics in agricultural river systems: Elucidating transmission mechanisms and associated risk to water security

Usage of antibiotics in agriculture has increased dramatically recently, significantly raising the influx of antibiotic resistance genes (ARGs) into river systems through organic manure runoff, seriously threatening water security. However, the dynamics, transmission mechanisms, and potential water security risk of ARGs, as well as their response to land use spatial scale and seasonal variations in agricultural river systems remain unclear. To address these challenges, this work employed metagenomic technique to systematically evaluate the pollution and dissemination of ARGs in overlying water and sediment within a typical agricultural catchment in China. The results demonstrated significant differences between overlying water and sediment ARGs. Overlying water dominated by multidrug ARGs exhibited higher diversity, whereas sediment predominantly containing sulfonamide ARGs had higher abundance. The dynamics of ARGs in overlying water were more responsive to seasonal variations compared to sediment due to greater changes in hydrodynamics and nutrient conditions. The profiles of ARGs in overlying water were largely regulated by microbiota, whereas mobile genetic elements (MGEs) were the main forces driving the dissemination of ARGs in sediment. The variation in dissemination mechanisms led to different resistance risks, with sediment presenting a higher resistance risk than overlying water. Furthermore, Mantel test was applied to discover the impact of land use spatial scale and composition on the transmission of ARGs in river systems. The findings showed that cultivated land within 5 km of the riverbank was the key influencing factor. Cultivated land exacerbated ARGs spread by increasing MGEs abundance and nutrient concentrations, resulting in the abundance of ARGs in high-cultivated sites being twice that in low-cultivated sites, and raising the regional water security risk, with a more pronounced effect in sediment. These findings contribute to a better understanding of ARGs dissemination in agricultural watersheds, providing a basis for implementing effective resistance control measures and ensuring water security.

Oxidation of antibiotic micropollutants in various water resources through integration of Bi2WO6 and g-C3N4

Recently, the hazardous effects of antibiotic micropollutants on the environment and human health have become a major concern. To address this challenge, semiconductor-based photocatalysis has emerged as a promising solution for environmental remediation. Our study has developed Bi2WO6/g-C3N4 (BWCN) photocatalyst with unique characteristics such as reactive surface sites, enhanced charge transfer efficiency, and accelerated separation of photogenerated electron-hole pairs. BWCN was utilized for the oxidation of tetracycline antibiotic (TCA) in different water sources. It displayed remarkable TCA removal efficiencies in the following order: surface water (99.8%) > sewage water (88.2%) > hospital water (80.7%). Further, reusability tests demonstrated sustained performance of BWCN after three cycles with removal efficiencies of 87.3, 71.2 and 65.9% in surface water, sewage, and hospital water, respectively. A proposed photocatalytic mechanism was delineated, focusing on the interaction between reactive radicals and TCA molecules. Besides, the transformation products generated during the photodegradation of TCA were determined, along with the discussion on the potential risk assessment of antibiotic pollutants. This study introduces an approach for utilizing BWCN photocatalyst, with promising applications in the treatment of TCA from various wastewater sources.

Linking the removal of enrofloxacin to the extracellular polymers of microalgae in water bodies: A case study focusing on the shifts in microbial communities

Microalgae can promote antibiotic removal, which has attracted growing attention. However, its synergistic removal performance with bacteria in antibiotic pollutants is still poorly understood. In this study, firstly, we selected two green algae (Dictyosphaerium sp. and Chlorella sp.) and exposed them to Enrofloxacin (ENR) to observe their extracellular polysaccharides (EPS) concentration dynamic and the removal of antibiotics. Secondly, EPS was extracted and added to in situ lake water (no algae) to investigate its combined effect with bacteria. The results indicate that both Dictyosphaerium sp. and Chlorella sp. exhibited high tolerance to ENR stress. When the biomass of microalgae was low, ENR could significantly stimulate algae to produce EPS. The removal rates of Dictyosphaerium sp. and Chlorella sp. were 15.8% and 10.5%, respectively. The addition of EPS can both alter the microbial community structure in the lake water and promote the removal of ENR. The LEfSe analysis showed that there were significant differences in the microbial marker taxa, which promoted the increase of special functional bacteria for decomposing ENR, between the EPS-added group and the control group. The EPS of Dictyosphaerium sp. increased the abundance of Moraxellaceae and Spirosomaceae, while the EPS of Chlorella sp. increased the abundance of Sphingomonadaceae and Microbacteriaceae. Under the synergistic effect, Chlorella sp. achieved a maximum removal rate of 24.2%, while Dictyosphaerium sp. achieved a maximum removal rate of 28.9%. Our study provides new insights into the removal performance and mechanism of antibiotics by freshwater microalgae in water bodies and contribute to the development of more effective water treatment strategies.

Comparative analysis of characteristics of antibiotic resistomes between Arctic soils and representative contaminated samples using metagenomic approaches

Antibiotic resistance is one of the most concerned global health issues. However, comprehensive profiles of antibiotic resistance genes (ARGs) in various environmental settings are still needed to address modern antibiotic resistome. Here, Arctic soils and representative contaminated samples from ARG pollution sources were analyzed using metagenomic approaches. The diversity and abundance of ARGs in Arctic soils were significantly lower than those in contaminated samples (p < 0.01). ARG profiles in Arctic soils were featured with the dominance of vanF, ceoB, and bacA related to multidrug and bacitracin, whereas those from ARG pollution sources were characterized by prevalent resistance to anthropogenic antibiotics such as sulfonamides, tetracyclines, and beta-lactams. Mobile genetic elements (MGEs) were found in all samples, and their abundance and relatedness to ARGs were both lower in Arctic soils than in polluted samples. Significant relationships between bacterial communities and ARGs were observed (p < 0.01). Cultural bacteria in Arctic soils had clinically-concerned resistance to erythromycin, vancomycin, ampicillin, etc., but ARGs relevant to those antibiotics were undetectable in their genomes. Our results suggested that Arctic environment could be an important reservoir of novel ARGs, and antibiotic stresses could cause ARG pollution via horizontal gene transfer and enrichment of resistant bacteria.

Occurrence and distribution of antibiotics and antibiotic resistance genes from the land to ocean in Daliao River-Liaodong Bay, China

In this study, the pollution status of antibiotics and ARGs in sediments from the land-sea intersection of Liaodong Bay was analyzed. The results showed that the level of antibiotic pollution ranged from ND to 433.27 ng/kg, with quinolones and tetracycline as the dominant antibiotics. The relative abundance of ARGs ranged from 3.62 × 10-3 to 1.32 × 10-1 copies/16SrRNA copies, with aminoglycoside and MLSB resistance genes being dominant. Regarding spatial distribution, the land and estuary areas showed higher antibiotic pollution levels than the offshore areas. Similarly, the land and estuary areas exhibited higher antibiotic diversity than the offshore areas. The ARGs were widely distributed on land, and their abundance gradually decreased to the downstream estuary area. Land and coastal areas exhibited higher ARG diversity than estuary areas. Analysis of environmental factors revealed a significant correlation between ARGs and non-corresponding antibiotics, and some ARGs were affected by heavy metals Cu and Pb.

A simulation-optimization approach based on the compound eutrophication index to identify multi-nutrient allocated load

Eutrophication with nutrient enrichment is a global marine ecosystem concern that threatens human health, economic activities, and ecosystem functions. Therefore, a nutrient load optimization method is required to help control marine eutrophication. However, eutrophication-based nutrient allocated load optimization is a multi-objective project due to a series of eutrophication pressures, such as cross-regional land-based nutrient loads and multi-nutrient regimes and ratios. In this study, a synergistic multi-nutrient control method was developed for the Bohai Sea (BS), China, which links multi-nutrient pressures with eutrophication states. Based on the eutrophication control standard, which is the second level of compound eutrophication index (CEI), the total maximum allocated loads (CEI-based TMALs) of total dissolved nitrogen (TDN), total dissolved phosphorus (TDP), and the chemical oxygen demand (COD) were calculated by a simulation-optimization approach. Using the end year of China's 13th Five-Year Plan (2020) as the reference year, 154 high load pressure jurisdictions (HLPJs) that contribute to eutrophication response segments in the BS were identified. Accordingly, practiced the optimized annual reduction rates of TDN, TDP, and COD in the HLPJs at 15 %, 11 %, and 2 % according to CEIII, respectively, the proportion of eutrophicated areas gradually decreased from 32 % in 2020 to 15 % in 2025 and might be 0 % in 2035 with ecosystem resilience in 2035. In particular, under the annual reduction rates of TDN and TDP optimized based on CEIII, the DIN/DIP molar ratio in the BS decreased to 16:1 by 2035. The simulation-optimization approach associated with the CEI-based TMALs for multi-nutrient control in this study might make implementing land-sea coordination more efficiency and marine nutrient regime stably. This can provide scientific and technological support for improving the health of coastal ecosystems.

Occurrence, Bioaccumulation, Metabolism and Ecotoxicity of Fluoroquinolones in the Aquatic Environment: A Review

In recent years, there has been growing concern about antibiotic contamination in water bodies, particularly the widespread presence of fluoroquinolones (FQs), which pose a serious threat to ecosystems due to their extensive use and the phenomenon of "pseudo-persistence". This article provides a comprehensive review of the literature on FQs in water bodies, summarizing and analyzing contamination levels of FQs in global surface water over the past three years, as well as the bioaccumulation and metabolism patterns of FQs in aquatic organisms, their ecological toxicity, and the influencing factors. The results show that FQs contamination is widespread in surface water across the surveyed 32 countries, with ciprofloxacin and norfloxacin being the most heavy contaminants. Furthermore, contamination levels are generally higher in developing and developed countries. It has been observed that compound types, species, and environmental factors influence the bioaccumulation, metabolism, and toxicity of FQs in aquatic organisms. FQs tend to accumulate more in organisms with higher lipid content, and toxicity experiments have shown that FQs exhibit the highest toxicity to bacteria and the weakest toxicity to mollusk. This article summarizes and analyzes the current research status and shortcomings of FQs, providing guidance and theoretical support for future research directions.

Differences in Physiological Performance and Gut Microbiota between Deep-Sea and Coastal Aquaculture of Thachinotus Ovatus: A Metagenomic Approach

Aquaculture has become the fastest growing sector in global agriculture. The environmental degradation, diseases, and high density of mariculture has made for an inevitable shift in mariculture production from coastal to deep-sea areas. The influence that traditional coastal and emerging deep-sea farming environments exert on aquatic growth, immunity and gut microbial flora is unclear. To address this question, we compared the growth performance, physiological indicators and intestinal microbiological differences of deep-sea and coastal aquaculture in the Guangxi Beibu Gulf of China. The results showed that the growth performance and the complement of C3 and C4 (C3, C4), superoxide dismutase (SOD), and lysozyme (LYS), these physiological and biochemical indicators in the liver, kidney, and muscle of Trachinotus ovatus (T. ovatus), showed significant differences under different rearing conditions. Metagenome sequencing analysis showed Ascomycota, Pseudomonadota, and Bacillota were the three dominant phyla, accounting for 52.98/53.32 (coastal/deep sea), 24.30/22.13, and 10.39/11.82%, respectively. Aligned against the CARD database, a total of 23/2 (coastal/deep-sea) antibiotic resistance genes were screened and grouped into 4/2 genotypes. It indicated that compared with deep-sea fish, higher biological oxygen levels (3.10 times), inorganic nitrogen (110.00 times) and labile phosphate levels (29.00 times) in coastal waters might contributed to the existence of eutrophication with antibiotic resistance. The results of the study can provide complementary data on the study of the difference between deep-sea farming and traditional coastal farming, serving as a reference to future in-depth work on the transformation of fisheries development and scientific standardization of deep-sea farming.

A Review of Antibiotics, Antibiotic Resistant Bacteria, and Resistance Genes in Aquaculture: Occurrence, Contamination, and Transmission

Antibiotics are commonly used to prevent and control diseases in aquaculture. However, long-term/overuse of antibiotics not only leaves residues but results in the development of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Antibiotics, ARB, and ARGs are widespread in aquaculture ecosystems. However, their impacts and interaction mechanisms in biotic and abiotic media remain to be clarified. In this paper, we summarized the detection methods, present status, and transfer mechanisms of antibiotics, ARB, and ARGs in water, sediment, and aquaculture organisms. Currently, the dominant methods of detecting antibiotics, ARB, and ARGs are UPLC-MS/MS, 16S rRNA sequencing, and metagenomics, respectively. Tetracyclines, macrolides, fluoroquinolones, and sulfonamides are most frequently detected in aquaculture. Generally, antibiotic concentrations and ARG abundance in sediment are much higher than those in water. Yet, no obvious patterns in the category of antibiotics or ARB are present in organisms or the environment. The key mechanisms of resistance to antibiotics in bacteria include reducing the cell membrane permeability, enhancing antibiotic efflux, and structural changes in antibiotic target proteins. Moreover, horizontal transfer is a major pathway for ARGs transfer, including conjugation, transformation, transduction, and vesiculation. Identifying, quantifying, and summarizing the interactions and transmission mechanisms of antibiotics, ARGs, and ARB would provide useful information for future disease diagnosis and scientific management in aquaculture.