Distribution and relationship between antimicrobial resistance genes and heavy metals in surface sediments of Taihu Lake, China

Study on the biodegradation characteristics and mechanism of tetracycline by Serratia entomophila TC-1

Microbial degradation is an important solution for antibiotic pollution in livestock and poultry farming wastes. This study reports the isolation and identification of the novel bacterial strain Serratia entomophila TC-1, which can degrade 87.8 % of 200 mg/L tetracycline (TC) at 35 °C, pH 6.0, and an inoculation amount of 1 % (v/v). Based on the intermediate products, a possible biological transformation pathway was proposed, including dehydration, oxidation ring opening, decarbonylation, and deamination. Using Escherichia coli and Bacillus subtilis as biological indicators, TC degraded metabolites have shown low toxicity. Whole-genome sequencing showed that the TC-1 strain contained tet (d) and tet (34), which resist TC through multiple mechanisms. In addition, upon TC exposure, TC-1 participated in catalytic and energy supply activities by regulating gene expression, thereby playing a role in TC detoxification. We found that TC-1 showed less interference with changes in the bacterial community in swine wastewater. Thus, TC-1 provided new insights into the mechanisms responsible for TC biodegradation and can be used for TC pollution treatment.

Vertical variation of antibiotic resistance genes and their interaction with environmental nutrients in sediments of Taihu lake

Antibiotic resistance is a growing environmental issue. As a sink for antibiotic resistance genes (ARGs), lake surface sediments are well known for the spread of ARGs. However, the distribution pattern of ARGs and their relationship with environmental factors in vertical sediment layers are unclear. In this study, we investigated the resistome distribution in sediment cores from Taihu Lake using metagenomic analysis. The results showed that the abundance of total ARGs increased by 153% as the sediment depth rose from 0 to 50 cm, and the ARG Shannon index significantly increased. Among all the ARG types, efflux pump genes (e.g., mexT and mexW) were dominant, especially in 40-50 cm sediment. The variation in ARG with depth described above was related to the changes in bacterial adaptation to environmental gradients. Specifically, sulfate and nitrate concentrations decreased with depth, and random forest analysis showed that they were the main factors affecting the changes in ARG abundance. Environmental factors were also found to indirectly impact the distribution of ARGs by affecting the bacterial community. Potential sulfate-reducing gene/nitrate-reducing gene-ARG co-hosts were annotated through metagenomic assembly. The dominant co-hosts, Curvibacter, and Comamonas, which were enriched in deeper sediments, may have contributed to the enrichment of ARGs in deep sediments. Overall, our findings demonstrated that bacterial-mediated sulfate and nitrate reduction was closely related to sediment resistance, which provided new insights into the control of antibiotic resistance.

Assessment of antibiotic resistance genes in soils polluted by chemical and technogenic ways with poly-aromatic hydrocarbons and heavy metals

Anthropogenic activities are leaving lots of chemical footprints on the soil. It alters the physiochemical characteristics of the soil thereby modifying the natural soil microbiome. The prevalence of antimicrobial-resistance microbes in polluted soil has gained attention due to its obvious public health risks. This study focused on assessing the prevalence and distribution of antibiotic-resistance genes in polluted soil ecosystems impacted by industrial enterprises in southern Russia. Metagenomic analysis was conducted on soil samples collected from polluted sites using various approaches, and the prevalence of antibiotic-resistance genes was investigated. The results revealed that efflux-encoding pump sequences were the most widely represented group of genes, while genes whose products replaced antibiotic targets were less represented. The level of soil contamination increased, and there was an increase in the total number of antibiotic-resistance genes in proteobacteria, but a decrease in actinobacteria. The study proposed an optimal mechanism for processing metagenomic data in polluted soil ecosystems, which involves mapping raw reads by the KMA method, followed by a detailed study of specific genes. The study's conclusions provide valuable insights into the prevalence and distribution of antibiotic-resistance genes in polluted soils and have been illustrated in heat maps.

Assessing antibiotic residues in sediments from mangrove ecosystems: A review

Antibiotics' widespread and abusive use in aquaculture and livestock leads to extensive environmental dissemination and dispersion, consequently increasing antibiotic-resistant bacteria in marine ecosystems. Hence, there is an increased need for efficient methods for identifying and quantifying antibiotic residues in soils and sediments. From a review of the last 20 years, we propose and compare different chromatographic techniques for detecting and quantifying antibiotics in sediment samples from marine ecosystems, particularly in mangrove forest sediments. The methods typically include three stages: extraction of antibiotics from the solid matrix, cleaning, and concentration of samples before quantification. We address the leading causes of the occurrence of antibiotics in marine ecosystem sediments and analyze the most appropriate methods for each analytical stage. Ultimately, selecting a method for identifying antibiotic residues depends on multiple factors, ranging from the nature and physicochemical properties of the analytes to the availability of the necessary equipment and the available resources.

Migration and transformation behaviors of antibiotics in water-sediment system under simulated light and wind waves

Antibiotics can generally be detected in the water-sediment systems of lakes. However, research on the migration and transformation of antibiotics in water-sediment systems based on the influences of light and wind waves is minimal. To address this research gap, we investigated the specific impacts of light and wind waves on the migration and transformation of three antibiotics, norfloxacin (NOR), trimethoprim (TMP), and sulfamethoxazole (SMX), under simulated light and wind waves disturbance conditions in a water-sediment system from Taihu Lake, China. In the overlying water, NOR was removed the fastest, followed by TMP and SMX. Compared to the no wind waves groups, the disturbance of big wind waves reduced the proportion of antibiotics in the overlying water. The contributions of light and wind waves to TMP and SMX degradation were greater than those of microbial degradation. However, the non-biological and biological contributions of NOR to degradation were almost equal. Wind waves had a significant impact on the microbial community changes in the sediment, especially in Methylophylaceae. These results verified the influence of light and wind waves on the migration and transformation of antibiotics, and provide assistance for the risk of antibiotic occurrence in water and sediments.

Expanding the focus of the One Health concept: links between the Earth-system processes of the planetary boundaries framework and antibiotic resistance

The scientific community warns that our impact on planet Earth is so acute that we are crossing several of the planetary boundaries that demarcate the safe operating space for humankind. Besides, there is mounting evidence of serious effects on people's health derived from the ongoing environmental degradation. Regarding human health, the spread of antibiotic resistant bacteria is one of the most critical public health issues worldwide. Relevantly, antibiotic resistance has been claimed to be the quintessential One Health issue. The One Health concept links human, animal, and environmental health, but it is frequently only focused on the risk of zoonotic pathogens to public health or, to a lesser extent, the impact of contaminants on human health, i.e., adverse effects on human health coming from the other two One Health "compartments". It is recurrently claimed that antibiotic resistance must be approached from a One Health perspective, but such statement often only refers to the connection between the use of antibiotics in veterinary practice and the antibiotic resistance crisis, or the impact of contaminants (antibiotics, heavy metals, disinfectants, etc.) on antibiotic resistance. Nonetheless, the nine Earth-system processes considered in the planetary boundaries framework can be directly or indirectly linked to antibiotic resistance. Here, some of the main links between those processes and the dissemination of antibiotic resistance are described. The ultimate goal is to expand the focus of the One Health concept by pointing out the links between critical Earth-system processes and the One Health quintessential issue, i.e., antibiotic resistance.

Antibiotic resistance genes profile in the surface sediments of typical aquaculture areas across 15 major lakes in China

Aquatic farming is considered as a major source of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) for the natural environment of the lakes. ARB and ARGs in the natural environment have increased quickly because of the human activities. Here, we have profiled the diversity and abundance of ARGs in sediments from the typical aquaculture areas around 15 major lakes in China using PCR and qPCR, and further assessed the risk factor shaping the occurrence and distribution of ARGs. And class 1, 2 and 3 integrons were initially detected by PCR with specific primers. ARGs were widely distributed in the lakes: Weishan Lake and Poyang Lake showed high diversity of ARGs, followed by Dongting Lake, Chao Lake and Tai Lake. Generally, the ARGs in the Middle-Lower Yangtze Plain were more abundant than those in the Qinghai-Tibet Plateau. Tetracycline resistance genes (tet(C), tet(A) & tet(M)) were prominent in sediments, and the next was AmpC β-lactamase gene group BIL/LAT/CMY, and the last was the genes resistance to aminoglycoside (strA-strB). Partial least squares path modeling analysis (PLS-PMA) revealed that livestock had a significant direct effect on the distribution of ARGs in lakes, and population might indirectly influence the profiles of ARGs by affecting the scale of livestock and aquaculture. The detectable rate of class 1, 2 and 3 integrons were 80%, 100% and 46.67%, respectively. The prevalence of integrons might play a key role in promoting more frequent horizontal gene transfer (HGT) events, resulting in the environmental mobilization and dissemination of ARGs between bacteria.

Molecular mechanisms of tigecycline-resistance among Enterobacterales

The global emergence of antimicrobial resistance to multiple antibiotics has recently become a significant concern. Gram-negative bacteria, known for their ability to acquire mobile genetic elements such as plasmids, represent one of the most hazardous microorganisms. This phenomenon poses a serious threat to public health. Notably, the significance of tigecycline, a member of the antibiotic group glycylcyclines and derivative of tetracyclines has increased. Tigecycline is one of the last-resort antimicrobial drugs used to treat complicated infections caused by multidrug-resistant (MDR) bacteria, extensively drug-resistant (XDR) bacteria or even pan-drug-resistant (PDR) bacteria. The primary mechanisms of tigecycline resistance include efflux pumps' overexpression, tet genes and outer membrane porins. Efflux pumps are crucial in conferring multi-drug resistance by expelling antibiotics (such as tigecycline by direct expelling) and decreasing their concentration to sub-toxic levels. This review discusses the problem of tigecycline resistance, and provides important information for understanding the existing molecular mechanisms of tigecycline resistance in Enterobacterales. The emergence and spread of pathogens resistant to last-resort therapeutic options stands as a major global healthcare concern, especially when microorganisms are already resistant to carbapenems and/or colistin.

An evaluation of conventional and nature-based technologies for controlling antibiotic-resistant bacteria and antibiotic-resistant genes in wastewater treatment plants

Antibiotic resistance is a globally recognized health concern which leads to longer hospital stays, increased morbidity, increased mortality, and higher medical costs. Understanding how antibiotic resistance persists and exchanges in environmental systems like soil, water, and wastewater are critically important for understanding the emergence of pathogens with new resistance profiles and the subsequent exposure of people who indirectly/directly come in contact with these pathogens. There are concerns about the widespread application of prophylactic antibiotics in the clinical and agriculture sectors, as well as chemicals/detergents used in food and manufacturing industries, especially the quaternary ammonium compounds which have been found responsible for the generation of resistant genes in water and soil. The rates of horizontal gene transfer increase where there is a lack of proper water/wastewater infrastructure, high antibiotic manufacturing industries, or endpoint users - such as hospitals and intensive agriculture. Conventional wastewater treatment technologies are often inefficient in the reduction of ARB/ARGs and provide the perfect combination of conditions for the development of antibiotic resistance. The wastewater discharged from municipal facilities may therefore be enriched with bacterial communities/pathogens and provide a suitable environment (due to the presence of nutrients and other pollutants) to enhance the transfer of antibiotic resistance. However, facilities with tertiary treatment (either traditional/emerging technologies) provide higher rates of reduction. This review provides a synthesis of the current understanding of wastewater treatment and antibiotic resistance, examining the drivers that may accelerate their possible transmission to a different environment, and highlighting the need for tertiary technologies used in treatment plants for the reduction of resistant bacteria/genes.

The HpSGNi system: A compact approach for genetic suppression without sequence limitation in Escherichia coli

Targeted gene regulation is indispensable for exploring gene functions in microbes and the development of microbial cell factories. While most loci can be regulated by CRISPRi, it cannot be used for targets lacking protospacer adjacent motifs (PAM) or protospacer flanking sequences (PFS). Here, we characterized a genetic suppression approach named the hpDNA-assisted structure-guided nuclease mediating interference system (HpSGNi). It was composed of a flap endonuclease 1 (FEN1) and mis-hairpin DNA probes (mis-hpDNA) to suppress the expression of target genes simply and efficiently in microbe without sequence restrictions. By inhibiting the initiation and elongation of the transcription, HpSGNi successfully silenced the transcription of exogenous fluorescent protein genes, ampicillin resistance gene and endogenous folP/sulA genes in Escherichia coli BL21(DE3) and K-12 MG1655. Meanwhile, aiming at optimizing the mis-hpDNA, we displayed the characteristics by detecting the tolerance to the single base mismatch and length of the guide sequence. This DNA-guided recognition platform provides a simple approach for selectively inhibiting gene expression.

Fate of high-risk antibiotic resistance genes in large-scale aquaculture sediments: Geographical differentiation and corresponding drivers

Antibiotic resistance genes (ARGs), emerging environmental contaminants, have become challenges of public health security. However, the distribution and drivers of ARGs, especially high-risk ARGs, in large-scale aquaculture sediments remain unknown. Here, we collected sediment samples from 40 crayfish ponds in seven main crayfish culture provinces in China and then investigated the distribution and risk of ARGs based on high-throughput sequencing and quantitative PCR techniques. Our results suggested that aquaculture sediment was potential reservoir of ARGs and the abundance of aadA-02 was the highest. High-risk ARG (floR) was also prevalent in the sediment and was the most abundant in Jiangsu Province, where opportunistic pathogens were also enriched. The abundance of floR was positively correlated with different environmental factors, such as total phosphorus in water and total carbon in sediment. In addition, Mycobacterium sp., opportunistic pathogenic bacteria, might be potential host for floR. Furthermore, the potential propagation pathway of ARGs was from sediment to crayfish gut, and Bacteroidetes and Proteobacteria might be the main bacterial groups responsible for the proliferation of ARGs. Generally, our results illustrate that pond sediment may be an ARG reservoir of aquatic animals. Meanwhile, our study helps develop valuable strategies for accessing risks and managing ARGs.

Comparative resistome analysis of Aeromonas species in aquaculture reveals antibiotic resistance patterns and phylogeographic distribution

The overuse of antibiotics in aquaculture drives the emergence of multi-drug-resistant bacteria, and antibiotic-resistant genes (ARGs) can be disseminated to other bacteria through vertical- and horizontal gene transfer (VGT and HGT) under selective pressure. Profiling the antibiotic resistome and understanding the global distribution of ARGs constitutes the first step in developing a control strategy. Hence, this study utilized extensive genomic data from hundreds of Aeromonas strains in aquaculture to profile resistome patterns and explores their association with isolation year, country, and species characteristics. Overall, ∼400 Aeromonas genomes were used to predict the ARGs from A. salmonicida, A. hydrophila, A. veronii, A. media, and A. sobria. ARGs such as sul1, tet(A), and tet(D), which display a similar proportion of positive strains among species, were subjected to phylodynamic and phylogeographic analyses. More than a hundred ARGs were identified, some of which exhibited either species-specific or non-species-specific patterns. A. salmonicida and A. media were found to have a higher proportion of species-specific ARGs than other strains, which might lead to more distinct patterns of ARG acquisition. Overall, ∼25% of strains have either sul1, tet(A), or tet(D) gene(s), but no significant difference was observed in the proportion of positive strains by species. Phylogeographic analysis revealed that the abundant numbers of sul1, tet(A), and/or tet(D) introduced in a few East Asian and North American countries could spread to both adjacent and faraway countries. In recent years, the proportions of these ARGs have dramatically increased, particularly in strains sourced from aquatic environments, suggesting control is required of the overuse of antibiotics in aquaculture. The findings of this research offer significant insights into the global dissemination of ARGs.

Spatial distribution of antibiotics and antibiotic resistance genes in tidal flat reclamation areas in China

Tidal flat areas are important resources for land development and are becoming antibiotic resistance receivers that trigger major health concerns. The spatial distributions of forty-nine antibiotics, nine antibiotic resistance genes (ARGs), one mobile gene element (MGE) gene, and nine available metals in the soils and sediments along the coastlines of the Yellow Sea in China were quantified. Hierarchical linear model analysis was used to explore relationships between the antibiotics and ARGs across multiple effects resulting from human activities and environmental factors. Fish farm sediments and farmland soils showed high levels of quinolones (QNs) (maximum 637 ng·g-1), sulfonamides (SAs) (maximum 221 ng·g-1), and corresponding ARGs. Significant positive correlations (P from 5.47 × 10-14 to 0.0487) were observed between the antibiotics (QNs, SAs, and chlortetracycline) and their corresponding ARGs (qnrA, qnrD, aac(6')-Ib-cr, dfrA, sul2, and tetA), indicating the selective pressure from antibiotics in soils and sediments. Nine available metals had positive correlations with at least one ARG, indicating heavy metal pollution could enhance the ARGs. Sheep and poultry husbandry and marine aquaculture contribute the most to the antibiotic resistance in the coastlines. In conclusion, antibiotic pollutions have promoting effects at sub-inhibitory concentrations and more attention should be given to inhibit the enrichment of ARGs during tidal flat reclamation processes. The study also suggests the induction effects from metal pollutions, MGE spread, and the antibiotic pollutions from the usage in livestock and aquaculture.

Responses of Phragmites communis and its rhizosphere bacteria to different exposure sequences of molybdenum disulfide and levofloxacin

The effect of the molybdenum disulfide (MoS2)/levofloxacin (LVF) co-exposure was explored on Phragmites communis and rhizosphere soil bacterial communities. The sequence of MoS2/LVF exposure and the different MoS2 dosages (10 mg/kg and 100 mg/kg) contributed to different degrees of effect on the plant after 42 days of exposure. The treatment with priority addition of low dosage MoS2 significantly ameliorated P. communis growth, with root length growing up to 532.22 ± 46.29 cm compared to the sole LVF stress (200.04 ± 29.13 cm). Besides, MoS2 served as an alleviator and reduced the accumulation of reactive oxygen species (ROS) and malondialdehyde (MDA) in P. communis under LVF stress, and activated bacteria in rhizosphere soil. These rhizosphere soil microbes assisted in mitigating toxic pollution in the soil and inducing plant resistance to external stress, such as bacteria genera Bacillus, Microbacterium, Flavihumibacter and altererythrobacter. Potential functional profiling of bacterial community indicated the addition of MoS2 contributed to relieve the reduction in functional genes associated with amino acid metabolism and the debilitation of gram_negative and aerobic phenotypic traits caused by LVF stress. This finding reveals the effect of different exposure sequences of MoS2 nanoparticles and antibiotic for plant-soil systems.

Occurrence, distribution and their correlation with different parameters of antibiotics and antibiotic resistance genes in lakes of China: A review

The exposure of antibiotics and antibiotic resistance genes (ARGs) as potential threats to the environment has raised global concern. This study provides discussion on the emergence and distribution of antibiotics and ARGs in lakes. The correlation of critical water quality parameters with antibiotics and ARGs are evaluated along with their integrative potential ecological risk. Sulfonamides (∼67.18 ng/L) and quinolones (∼77.62 ng/L) were the dominant antibiotics distributed in the aqueous phase, while the quinolones and tetracyclines were the primary contamination factors in the sediment phase. The temporal and spatial distribution revealed that the antibiotic concentrations were significantly lower in summer than other seasons and the lakes in Hebei and Jiangsu provinces exhibited the highest antibiotic pollution. The detection frequency and relative abundance of sul1 gene have been the highest among all detected ARGs. Moreover, ARGs in lakes were driven by several factors, with bacterial communities and mobile genetic elements that prevailed the positive distribution of ARGs. Antibiotics have been identified as critical factors in inducing the propagation of ARGs, which could be further enhanced by chemical contaminants (e.g., heavy metals and nutrients). Involving the risk assessment strategies, research attention should be paid on three antibiotics (ofloxacin, sulfamethoxazole and erythromycin) to strengthen the policy and management of Baiyangdian Lake and East Dongting Lake. This review analysis will provide in-depth understanding to the researchers and policy-makers in formulation of strategies for remediation of antibiotic contamination in the lakes.

Risk assessment and binding mechanisms of potentially toxic metals in sediments from different water levels in a coastal wetland

The excessive accumulation of potentially toxic metals (Pb and Cd) in coastal wetlands is among the main factors threatening wetland ecosystems. However, the effects of water table depth (WTD) on the risk and binding mechanisms of potentially toxic metals in sediments remain unclear. Here, sediments from different WTD obtained from a typical coastal wetland were evaluated using a newly developed strategy based on chemical extraction methods coupled with high-resolution spectroscopy. Our findings indicated that the WTD of the coastal wetland fluctuates frequently and the average enrichment factor for Pb was categorized as minor, whereas Cd enrichment was categorized as moderate. High-resolution spectroscopy techniques also demonstrated that organic functional groups and partly inorganic compounds (e.g., Fe-O/Si-O) played a vital role in the binding of Pb and Cd to surface sediments. Additionally, mineral components rather than organic groups were mainly bound to these metals in the bottom sediments. Collectively, our findings provide key insights into the potential health effects and binding characteristics of potentially toxic metals in sediments, as well as their dynamic behavior under varying sediment depths at a microscale.

Impact of different organic matters on the occurrence of antibiotic resistance genes in activated sludge

The occurrence of antibiotic resistance genes (ARGs) in various environments has drawn worldwide attention due to their potential risks. Previous studies have reported that a variety of substances can enhance the occurrence and dissemination of ARGs. However, few studies have compared the response of ARGs under the stress of different organic matters in biological wastewater treatment systems. In this study, seven organic pollutants were added into wastewater treatment bioreactors to investigate their impacts on the ARG occurrence in activated sludge. Based on high-throughput sequencing, it was found that the microbial communities and ARG patterns were significantly changed in the activated sludge exposed to these organic pollutants. Compared with the non-antibiotic refractory organic matters, antibiotics not only increased the abundance of ARGs but also significantly changed the ARG compositions. The increase of Gram-negative bacteria (e.g., Archangium, Prosthecobacter and Dokdonella) carrying ARGs could be the main cause of ARG proliferation. In addition, significant co-occurrence relationships between ARGs and mobile genetic elements were also observed in the sludge samples, which may also affect the ARG diversity and abundance during the organic matter treatment in the bioreactors. Overall, these findings provide new information for better understanding the ARG occurrence and dissemination caused by organic pollutants in wastewater treatment systems.

Induced development of oxytetracycline tolerance in bacterial communities from soil amended with well-aged cow manure

The use of animal manure as organic fertilizer is a common agricultural practice that can improve soil health and crop yield. However, antibiotics and their metabolites are often present in animal manure and, hence, in manure-amended soil. The aim of this study was to assess the induced development of oxytetracycline (OTC) tolerance in soil bacterial communities as a result of the addition of OTC to soil amended with well-aged cow manure. To this purpose, soil amended with well-aged cow manure was repeatedly - three times - spiked with different OTC concentrations (0, 2, 20, 60, 150, and 500 mg OTC kg^-1 dry weight soil, each time) according to a pollution-induced community tolerance (PICT) assay. The PICT detection phase was conducted in Biolog EcoPlates^TM in the presence of the following OTC concentration gradient in the wells: 0, 5, 20, 40, 60, and 100 mg L^-1. For all treatments, the application of OTC in the PICT selection phase resulted in lower values of bacterial metabolic activity (i.e., lower values of average well color development) in the PICT detection phase. A significant increase in OTC tolerance was observed in soil bacterial communities that had been exposed three times to ≥ 20 mg OTC kg^-1 DW soil during the PICT selection phase. In general, higher levels of OTC exposure during the PICT selection phase resulted in bacterial tolerance to higher OTC concentrations during the PICT detection phase, pointing to a dose-dependent induced tolerance. It is important to (i) rationalize the amount of antibiotics administered to livestock, and (ii) treat properly the antibiotic-containing manure before its application to agricultural soil as fertilizer.

Metal- and antibiotic-resistant heterotrophic plate count bacteria from a gold mine impacted river: the Mooi River system, South Africa

The Wonderfonteinspruit, South Africa, is highly impacted by a century of gold mining activities. The aim of this study was to investigate the physico-chemical properties of the Wonderfonteinspruit and the receiving Mooi River system, the levels of antimicrobial (metals and antibiotics) resistance characteristics and heterotrophic bacteria levels in these water systems. Various physico-chemical parameters were determined. R2A agar and R2A agar supplemented with antimicrobials were used to enumerate heterotrophic bacteria. Morphologically distinct antimicrobial-resistant isolates were purified and screened for antibiotic susceptibility by a disc diffusion method. Selected isolates were identified, and minimum inhibitory concentration ranges determined. Among the antimicrobial resistant isolates, 87% were resistant to at least one antibiotic. Of these, almost 50% were resistant to more than 3 antibiotic classes. A large proportion was resistant to all 7 antibiotics tested. Phyla detected were Proteobacteria, Firmicutes and Bacteriodetes. High MIC levels for metals and antibiotics were detected among all the genera. Results demonstrate potential impacts of physico-chemical properties on levels of antimicrobial-resistant bacteria. Metal-resistant bacteria were also resistant to multiple antibiotics, suggesting that metal pollution from mining may be responsible for co-selection and maintenance of antibiotic-resistant bacteria in this aquatic system.

Spatio-seasonal patterns of the impact of wastewater treatment plant effluents on antibiotic resistance in river sediments

There is a growing concern about the risk of antibiotic resistance emergence and dissemination in the environment. Here, we evaluated the spatio-seasonal patterns of the impact of wastewater treatment plant (WWTP) effluents on antibiotic resistance in river sediments. To this purpose, sediment samples were collected in three river basins affected by WWTP effluents in wet (high-water period) and dry (low-water period) hydrological conditions at three locations: (i) upstream the WWTPs; (ii) WWTP effluent discharge points (effluent outfall); and (iii) downstream the WWTPs (500 m downriver from the effluent outfall). The absolute and relative abundances of 9 antibiotic resistance genes (ARGs), 3 mobile genetic element (MGE) genes, and 4 metal resistance genes (MRGs) were quantified in sediment samples, as well as a variety of physicochemical parameters, metal contents, and antibiotic concentrations in both sediment and water samples. In sediments, significantly higher relative abundances of most genes were observed in downstream vs. upstream sampling points. Seasonal changes (higher values in low-water vs. high-water period) were observed for both ARG absolute and relative abundances in sediment samples. Chemical data revealed the contribution of effluents from WWTPs as a source of antibiotic and metal contamination in river ecosystems. The observed positive correlations between ARG and MGE genes relative abundances point out to the role of horizontal gene transfer in antibiotic resistance dissemination. Monitoring plans that take into consideration spatio-temporal patterns must be implemented to properly assess the environmental fate of WWTP-related emerging contaminants in river ecosystems.

Source-oriented ecological risk assessment of heavy metals in sediments of West Taihu Lake, China

The geographical location of West Taihu Lake determines that it is the entrance of the whole Taihu Lake, and the intensive industries around it pose a great threat to the ecology of Taihu Lake. We innovatively combined Pb isotope ratio analysis with ecological risk assessment index to quantify the source-oriented ecological risk of heavy metals (HMs) in the sediments of West Taihu Lake. In this study, the representative HMs Zn, Pb, Cr, and Cd in the surface (0-2 cm) sediments of West Tai Lake were determined, and the ecological risk assessment of HM sources was carried out based on the Pb isotope ratio and ecological risk index. The results showed that HMs were significantly enriched in the south and the west of the study area. The average geo-accumulation index (I_geo) of Pb was unpolluted, Cr and Zn were between unpolluted and moderately polluted, and Cd was moderately polluted. The average ecological risk index (E_i) of Pb, Cr, and Zn was low, and only Cd reached a considerable risk (E_Cd = 120.7), which accounted for 89.8% of the comprehensive ecological risk index (RI). However, the RI in the whole study area (RI = 134.4) still indicated low risk. There was a significant correlation between Pb and other HMs (P < 0.05). The IsoSource analysis showed that the order of contribution rate was fossil fuels (48.0%) > industrial sources (35.8%) > natural sources (14.9%) > agricultural sources (1.3%). The HM pollution caused by fossil fuel combustion and industrial activities reaches a moderate ecological risk, whereas natural sources and agricultural sources pose a low risk. Overall, the main sources of HM pollution are anthropogenic, which pose moderate ecological risk to the study area and should be paid more attention to.

Ecological mechanisms of sedimental microbial biodiversity shift and the role of antimicrobial resistance genes in modulating microbial turnover

The mechanisms of phylogenetic turnover of microbial communities to environmental perturbations in sediments remain unclear. In this study, the molecular mechanisms of phylogenetic turnover, and impact of antibiotics and antibiotic resistance genes (ARGs) on the modification of microbial assemblages were unravelled. We investigated 306 ARGs, 8 transposases, and 4 integron integrases, bacteria, and eukaryotic diversity through high-throughput quantitative PCR and illumina sequencing, 21 antibiotics and 3 tetracycline byproducts. The freshwater and estuary ecosystems were mainly dominated by genus Sulfurovum and colonised by closely related species compared with the estuary (closeness centrality = 0.42 vs. 0.46), which was dominated by genus Mycobacterium. Eighty-six percent of the ecological process in the bacterial community was driven by stochastic processes, while the rest was driven by deterministic processes. Environmental-related concentrations of antibiotics (0.15-32.53 ng/g) stimulated the proliferation of ARGs which potentially modulated the microbial community assembly. ARG acquisition significantly (P < 0.001) increased eukaryotic diversity through protection mechanisms. ARGs showed complex interrelationships with the microbial communities, and phylum arthropods and Nematea demonstrated the strongest ARG acquisition potential. This study provides key insights for environmental policymakers into understanding the ecological impact of antibiotics and the role of ARGs in modulating the phylogenetic turnover of microbial communities and trophic transfer mechanisms.

Pollution status of heavy metals and metalloids in Chinese lakes: Distribution, bioaccumulation and risk assessment

Due to intensive human activities, most of Chinese lakes are suffering from the pollution of heavy metals and metalloids. Previous studies on heavy metals and metalloids in Chinese lakes were limited to a few lakes and mainly focused on sediments, to date the knowledge on heavy metals and metalloids in multiple media of Chinese lakes from a national perspective is scarce. We collected the data of nine heavy metals and metalloids including Copper (Cu), Cadmium (Cd), Lead (Pb), Mercury (Hg), Arsenic (As), Chromium (Cr), Nickel (Ni), Zinc (Zn), and Manganese (Mn) in water, surface sediments, and fish of 87 Chinese lakes sampled in the period from 2009 to 2019 from the literature, summarized the distribution of heavy metals and metalloids, evaluated their pollution, and apportioned their sources from a national perspective. Concentration of individual heavy metal and metalloid in water, surface sediments, and fish in Chinese lakes was in the ranges of 0.0080-282 μg/L, 0.020-33858 μg/g, and 0.00030-207 μg/g, respectively. 5.6 % and 33.3 % of lake water were polluted by Cd and As. 88.2 %, 78.6 %, and 66 % of lake sediments were polluted by Cd, Hg, and As. 35.3 %, 11.3 %, 52.4 %, and 12.8 % of Cd, Pb, As, and Cr concentrations in lake fish exceeded the food limits. Concentrations of heavy metals and metalloids in fish viscera were higher than those in other organs. Higher partition coefficient and bioaccumulation factors were found for Pb and Cd, Hg and Zn, respectively. Concentrations of heavy metals and metalloids in both water and sediments of lakes in eastern China were higher than those in western China. Concentrations of heavy metals and metalloids in both lake water and sediments of urban lakes were higher than those of rural lakes. Lakes with extremely high ecological risk of heavy metals and metalloids were mainly located in central China and eastern China. Pollution of heavy metals and metalloids in Chinese lakes was closely correlated with regional economic development. Heavy metals and metalloids in Chinese lakes were mainly derived from industrial, domestic, and mixed discharges. Cd and Hg were selected as the heavy metals for priority control in Chinese lakes.

Non-corresponding contaminants in marine surface sediments as a factor of ARGs spread in the Sea of Azov

The present study aims to analyze the level and total toxicity of the most common pollutants in surface sediments and assess their impact on the occurrence of antibiotic resistance genes (ARGs) in the Sea of Azov. Biotesting using the whole-cell bacterial lux-biosensors showed high integral toxicity of surface sediments and the presence of genotoxicants and substances that cause oxidative stress and protein damage. Using cluster analysis, it was shown that the distribution of pollutants in the Sea of Azov depends on the type of surface sediments. The relative abundance and distribution of 14 ARGs in surface sediments were shown. Principle component analyses results suggest that non-corresponding contaminants do not exert direct influence on the ARGs abundance in the surface sediments of the Sea of Azov. Thus, the need to investigate the significance of non-corresponding pollutants in the selection and distribution of ARGs in the aquatic environment remains a pressing problem.

Diversity and abundance of antibiotic resistance genes and their relationship with nutrients and land use of the inflow rivers of Taihu Lake

Taihu Lake is the third largest freshwater lake in China and an important source for drinking water, flood protection, aquaculture, agriculture, and other activities. This lake is connected to many principal and small rivers with inflow from west and outflow on the eastern side of the lake and these inflow rivers are believed to significantly contribute to the water pollution of the lake. This study was aimed at assessing the diversity and abundance of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), and their relationship with water quality parameters and land use patterns. Water samples were collected from 10 major inflow rivers and the source water protection area of the Taihu Lake in spring and summer 2019. High-throughput profiling was used to detect and quantify 384 ARGs and MGEs and in addition, 11 water quality parameters were analyzed. The results showed that the number of ARGs/MGEs detected in each inflow river ranged from 105 to 185 in spring and 107 to 180 in summer. The aminoglycoside resistance genes were the most dominant types ARGs detected followed by beta-lactam resistance, multidrug resistance, macrolide-lincosamide-streptogramin B (MLSB) resistance genes, which contributed to 65% of the ARGs. The water quality parameters showed significant correlation with absolute abundance of ARGs. Furthermore, significant correlation between ARGs and MGEs were also observed which demonstrates potential gene transfer among organisms through horizontal gene transfer via MGEs. ARGs showed strong positive correlation with cultivated and industrial lands whereas, negative correlation was observed with river, lake, forest, land for green buffer, and land for port and harbor. The overall results indicate that the inflow rivers of Taihu Lake are polluted by various sources including multiple nutrients and high abundance of ARGs, which needs attention for better management of the inflow rivers of this lake.

Tracking the influence of antibiotics, antibiotic resistomes, and salinity gradient in modulating microbial community assemblage of surface water and the ecological consequences

The ecological impacts of antibiotics and antibiotic resistance genes (ARGs) on water ecology remain elusive in natural environments. We investigated the influence of antibiotics, ARGs and salinity gradient on the surface water ecosystem. Cefquinome (104.2 ± 43.6 ng/L) and cefminox (16.2 ± 7.50 ng/L) cephalosporins were predominant in all sites. Antibiotic contamination was increased in the estuary ecosystems compared to the freshwater ecosystems by 6%. Bacterial diversity could resist changes in salinity, but the relative abundance of some bacterial genera; Pseudoalteromonas, Glaciecola, norank_f__Arcobacteraceae, and Pseudohongiella was increased in the estuary zone (salinity>0.2%). The eukaryotic composition was increased in the subsaline environments (<0.2%), but the higher salinity in the saline zone inhibited the eukaryotic diversity. The relative abundance of ARGs was significantly higher in the estuary than in freshwater ecosystems, and ARGs interactions and mobile elements (aac(6')-Ib(aka_aacA4)-01, tetR-02, aacC, intI1, intI-1(clinic), qacEdelta1-01, and strB) were the predominant factors responsible for the ARGs propagation. Antibiotics associated with corresponding and non-corresponding ARGs and potentially created an adverse environment that increased the predation and pathogenicity of the aquatic food web and inhibited the metabolic functions. Surface water are first-line-ecosystems receiving antibiotics and ARGs hence our findings provided vital insights into understanding their ecological consequences on surface water ecosystems.

Monitoring the exposure and emissions of antibiotic resistance: Co-occurrence of antibiotics and resistance genes in wastewater treatment plants

The COVID-19 pandemic has brought new momentum to 'wastewater-based epidemiology' (WBE). This approach can be applied to monitor the levels of antibiotic-resistant genes (ARGs), which in terms are used to make inferences about the burden of antimicrobial resistance (AMR) in human settlements. However, there is still little information about temporal variability in ARG levels measured in wastewater streams and how these influence the inferences made about the occurrence of AMR in communities. The goal of this study was hence to gain insights into the variability in ARG levels measured in the influent and effluent of two wastewater treatment plants in The Netherlands and link these to levels of antibiotic residues measured in the same samples. Eleven antibiotics were detected, together with all selected ARGs, except for VanB. Among the measured antibiotics, significant positive correlations (p > 0.70) with the corresponding resistance genes and some non-corresponding ARGs were found. Mass loads varied up to a factor of 35 between days and in concomitance with rainfall. Adequate sampling schemes need to be designed to ensure that conclusions are drawn from valid and representative data. Additionally, we advocate for the use of mass loads to interpret levels of AMR measured in wastewater.

Hospital effluents as sources of antibiotics residues, resistant bacteria and heavy metals in Benin

This study aims to evaluate the bacteriological, chemical, and toxicological quality of hospital effluents in Benin. Eighteen (18) samples were collected from the south and north of Benin, and poles were set up. Bacteriological analysis was carried out according to the French National Organization for Standardization (AFNOR) standard. Identification of the bacterial species isolated was performed using the API 20E gallery and specific biochemical tests. Antibiotic residues were searched by following ELISA kit instructions. 109 bacterial isolates were obtained, with a predominance of non-enterobacteria (37.7%) and Acinetobacter spp. (24.6%), followed by Klebsiella spp. (11.48%); S. aureus and Coagulase-negative staphylococci (CoNS) were isolated at the same frequency (6.5%). Physico-chemical and toxicological parameter analyses showed that they were in conformity with the standards of discharge into the environment. The pH, temperature, electrical conductivity, total solids below, P-redox and suspended solids measured were, on average, 6.83, 27.21 °C, 693.68 µS/cm, 693.68 mg/l, 1.68 mV and 0.15 mg/l, respectively. For heavy metals, cadmium was most prevalent (0.22 mg/l), followed by nickel (0.18 mg/l) and lead (0.03 mg/l). The average antibiotic residue concentrations ranged from 0.043 to 7.65 µg/l. Ciprofloxacin, metronidazole and sulfamethoxazole had the highest residue concentrations of 7.65 ± 2.272 µg/l, 6.61 ± 0.051 µg/l and 3.88 ± 3.088 µg/l, respectively. The heavy metal concentrations obtained were below those required by Benin standards. These effluents therefore present health and environmental risks. It is then more than necessary to develop treatment methods for them before their rejection into the natural environment.

A review on synergistic coexisting pollutants for efficient photocatalytic reaction in wastewater remediation

With the tremendous development of the economy and industry, the pollution of water is becoming more serious due to the excessive chemical wastes that need to remove thru reduction or oxidation reactions. Simultaneous removal of dual pollutants via photocatalytic redox reaction has been tremendously explored in the last five years due to effective decontamination of pollutants compared to a single pollutants system. In a photocatalysis mechanism, the holes in the valence band can remarkably promote the oxidation of a pollutant. At the same time, photoexcited electrons are also consumed for the reduction reaction. The synergistic between the reduction and oxidation inhibits the recombination of electron-hole pairs extending their lifetime. In this review, the binary pollutants that selectively removed via photocatalysis reduction or oxidation are classified according to heavy metal-organic pollutant (HM/OP), heavy metal-heavy metal (HM/HM) and organic-organic pollutants (OP/OP). The intrinsic between the pollutants was explained in three different mechanisms including inhibition of electron-hole recombination, ligand to metal charge transfer and electrostatic attraction. Several strategies for the enhancement of this treatment method which are designation of catalysts, pH of mixed pollutants and addition of additive were discussed. This review offers a recent perspective on the development of photocatalysis system for industrial applications.

Antimicrobial Resistance and Transconjugants Characteristics of sul3 Positive Escherichia coli Isolated from Animals in Nanning, Guangxi Province

Sulfonamides are the second most popular antibiotic in many countries, which leads to the widespread emergence of sulfonamides resistance. sul3 is a more recent version of the gene associated with sulfonamide resistance, whose research is relatively little. In order to comprehend the prevalence of sul3 positive E. coli from animals in Nanning, a total of 146 strains of E. coli were identified from some farms and pet hospitals from 2015 to 2017. The drug resistance and prevalence of sul3 E. coli were analyzed by polymerase chain reaction (PCR) identification, multi-site sequence typing (MLST), drug sensitivity test, and drug resistance gene detection, and then the plasmid containing sul3 was conjugated with the recipient strain (C600). The effect of sul3 plasmid on the recipient was analyzed by stability, drug resistance, and competitive test. In this study, forty-six sul3 positive E. coli strains were separated. A total of 12 ST types were observed, and 1 of those was a previously unknown type. The ST350 is the most numerous type. All isolates were multidrug-resistant E. coli, with high resistant rates to penicillin, ceftriaxone sodium, streptomycin, tetracycline, ciprofloxacin, gatifloxacin, and chloramphenicol (100%, 73.9%, 82.6%, 100%, 80.4%, 71.7%, and 97.8%, respectively). They had at least three antibiotic resistance genes (ARGs) in addition to sul3. The plasmids transferred from three sul3-positive isolates to C600, most of which brought seven antimicrobial resistance (AMR) and increased ARGs to C600. The transferred sul3 gene and the plasmid carrying sul3 could be stably inherited in the recipient bacteria for at least 20 days. These plasmids had no effect on the growth of the recipient bacteria but greatly reduced the competitiveness of the strain at least 60 times in vitro. In Nanning, these sul3-positive E. coli had such strong AMR, and the plasmid carrying sul3 had the ability to transfer multiple resistance genes that long-term monitoring was necessary. Since the transferred plasmid would greatly reduce the competitiveness of the strain in vitro, we could consider limiting the spread of drug-resistant isolates in this respect.

Relationship between water quality, heavy metals and antibiotic resistance genes among three freshwater lakes

Urban recreational lakes are impacted by consistent anthropogenic activities and are significant sources of heavy metals and antibiotic resistance genes (ARGs). In this study, three urban lakes of varying size and anthropogenic impact in Nanjing, China, were investigated for the abundance of ten ARGs, six physicochemical factors and four heavy metals. Correlations between heavy metals and physicochemical parameters against ARGs were performed to investigate the presence of ARGs in the lakes. The water quality data indicated that the lakes were on par with levels 3 and 4 of the Chinese surface water environmental standards, signifying disturbing pollution levels in the lakes. The lakes were dominant with high amounts of sul1, sul2 and strA genes, and the sum of these three genes appropriated over 38.9-84.4% in all three lakes, while the sum of tetM, tetQ and ermB genes occupied a minor proportion (0.1-1.4%). High levels of vancomycin resistance genes were found in the three lakes. Spearman analysis indicated that Chlα, cadmium, lead and copper had a significant positive correlation with sul2 and strB. The results of redundancy analysis displayed that Chlα and co-selection with certain heavy metals were the major factors driving the propagation of specific genes in three lakes. We believe our study contributes by adding further knowledge to existing antibiotic resistance gene abundance studies in recreational urban lakes with significant anthropogenic impacts.

Ecological impact of antibiotics on bioremediation performance of constructed wetlands: Microbial and plant dynamics, and potential antibiotic resistance genes hotspots

Constructed wetlands (CWs) are nature-based solutions for treating domestic and livestock wastewater which may contain residual antibiotics concentration. Antibiotics may exert selection pressure on wetland's microbes, thereby increasing the global antibiotics resistance problems. This review critically examined the chemodynamics of antibiotics and antibiotics resistance genes (ARGs) in CWs. Antibiotics affected the biogeochemical cycling function of microbial communities in CWs and directly disrupted the removal efficiency of total nitrogen, total phosphorus, and chemical oxygen demand by 22%, 9.3%, and 24%, respectively. Since changes in microbial function and structure are linked to the emergence and propagation of antibiotic resistance, antibiotics could adversely affect microbial diversity in CWs. The cyanobacteria community seemed to be particularly vulnerable, while Proteobacteria could resist and persist in antibiotics contaminated wetlands. Antibiotics triggered excitation responses in plants and increased the root activities and exudates. Microbes, plants, and substrates play crucial roles in antibiotic removal. High removal efficiency was exhibited for triclosan (100%) > enrofloxacin (99.8%) > metronidazole (99%) > tetracycline (98.8%) > chlortetracycline (98.4%) > levofloxacin (96.69%) > sulfamethoxazole (91.9%) by the CWs. This review showed that CWs exhibited high antibiotics removal capacity, but the absolute abundance of ARGs increased, suggesting CWs are potential hotspots for ARGs. Future research should focus on specific bacterial response and impact on microbial interactions.

Tracking antibiotic resistance genes (ARGs) during earthworm conversion of cow dung in northern China

Using cow dung to breed earthworms poses a risk of environmental transmission of antibiotic resistance genes (ARGs). The purpose of this study was to address the occurrence, persistence and environmental fate of ARGs during earthworm conversion of cow dung. The results showed that ARGs persisted through the whole process. Notably, earthworm conversion effectively reduced some ARGs in cow dung, but a definite concentration of ARGs still remained in earthworms and vermicompost (up to 10^-1 and 10^-2 copies/16S copies, respectively). We found that tet-ARGs were the most abundant in 15 earthworm farms (10^-6~10^-1 copies/16S copies) and some high-risk ARGs (i.e., bla_ampC, bla_OXA-1 and bla_TEM-1) were even prevalent in these farms. Interestingly, although ARGs differ widely in cow dung (10^-10~10^-1 copies/16S copies), the ARGs levels were comparable in vermicompost samples from different farms (10^-8~10^-2 copies/16S copies). Notably, earthworm conversion effectively reduced some ARGs in cow dung, but significant level of ARGs still remained in earthworms and vermicompost (up to 10^-1 and 10^-2 copies/16S copies, respectively). Nevertheless, the concentrations of some heavy metals (Cu, Zn and Ni), the abundance of mobile genetic elements (MGEs) and total nitrogen content were confirmed to be correlated to the enrichment of some ARGs. Overall, this study demonstrated the high prevalence of ARGs contamination in earthworm farms, and also highlighted the dissemination risk of ARGs during the earthworm conversion of cow dung.

The fate of tetracycline in vegetated mesocosmic wetlands and its impact on the water quality and epiphytic microbes

The fate of antibiotics and their impact on antibiotic resistance genes (ARGs) and microbial communities are far from clear in wetlands. The fate and impact of tetracycline (TC) on the nutrient degradation of wetlands and epiphytic microbes were investigated. This study showed that after TC spiking, 99.7% of TC were removed from the surface water of wetlands containing Vallisneria spiralis within 4 days post-treatment. TC spiking impaired the nutrient removal capacity and disrupted epiphytic microbial community structure while enhancing the abundance of 11 ARGs subtypes, including tetracycline resistance genes, tetX, tetM, tetO, tetQ, tetS, and tet36. TC decreased bacterial biodiversity but amplified the relative abundance of Proteobacteria and Firmicutes by 4% and 61%, respectively, and increased eukaryotic diversity. 16 metabolic pathways including Carbohydrate, Energy, Amino acid, 'cofactor and vitamins' metabolisms were significantly (p < 0.01) increased in TC treatment. Phylogenetic, functional prediction analysis indicated that Flavobacterium was positively related with xenobiotics, cell motility, 'terpenoids and polyketides' metabolism but negatively related to nucleotide metabolism, while Rhodobacter showed a reverse trend but positively related with nucleotide and 'glycan biosynthesis' and metabolism. These data highlighted that TC has negative impacts on epiphytic microbial community and nutrients removal in wetlands.

Adsorption behaviours and transfer simulation of levofloxacin in silty clay

Fluoroquinolone antibiotics in soil can cause serious antibiotic pollution. Adsorption is the main factor that influences their destination and transport of antibiotics. Therefore, research on the behaviour of antibiotics once they reach the soil environment is meaningful to design appropriate measures to reduce their potential risks. This research took levofloxacin (LVFX) as the research object and used a static adsorption experiment to study the adsorption behaviour of the vadose zone of silty clay on the North China Plain. The results showed that LVFX had high retention in silty clay, with an average adsorption ratio of more than 90%. Adsorption of LVFX on silty clay reached equilibrium in 24 h with an adsorption amount of 93.5 mg/kg at an initial LVFX concentration of 10 mg/L. Acidity, cations and soil organic matter could affect the adsorption of LVFX, with adsorption variation ratio of 3.3%, 3.4% and 0.6%, respectively. In addition, numerical simulation with Hydrus-1D was utilized, and the results show that LVFX may infiltrate into underground water through silty clay after 28 days and completely penetrate in 100 days.

Heavy metal contamination in surface sediments from lakes and their surrounding topsoils of China

Due to rapid urbanization, industrialization, agricultural development, and mining activities, soil heavy metal pollution has become a severe issue in China. To explore the regional heavy metal ecological risk of lake sediment and surrounding topsoil, we analyzed 237 lakes, with 1797 lake sediment sampling points and 1164 surrounding topsoil sampling points. Lower mean concentrations were detected for most heavy metals in soils than sediment (except for Hg). Cd and Hg in sediments and soils showed a more significant variation, with the coefficient of variation exceeding 110%. Linear regressions and Pearson's correlation analyses demonstrated that sediments and soils exhibited significant positive correlations. The principal heavy metals exceeding the Agricultural Soil Control Standard (ASCS) in sediments and soils were As and Cd, respectively. The Yunnan-Guizhou Plateau Lake Region (YGPLR) was the most seriously affected, exceeding the ASCS for Cd. The lakes with the most severe pollution were located in YGPLR impacted by the high background concentration of heavy metals in soil and mineral development activities. The Eastern Plain Lake Region, the Southeast Lake Region, and the Northeast Plain and Mountain Lake Region showed a clear anthropogenic impact. Lakes in the Inner Mongolia-Xinjiang Lake Region and the Tibetan Plateau Lake Region were estimated to have relatively low ecological risks due to their sparse population and slight environmental disturbance. The impact of geochemical factors on the ecological risk of heavy metals in lake sediments is more substantial than that of human activities at the regional scale.

Agricultural land-use change and rotation system exert considerable influences on the soil antibiotic resistome in Lake Tai Basin

In this study, we use high-throughput quantitative polymerase chain reaction approaches to comprehensively assess the effects of agricultural land-use change on the antibiotic resistome of agricultural runoffs after rainfalls in Lake Tai Basin. For the first time in this region, our findings show that orchard runoffs harbored more diverse and abundant antibiotic resistance genes (ARGs) than traditional cropland runoffs. Network analysis demonstrated that orchard runoffs possessed a strong ability for ARG dissemination via horizontal gene transfer. These results suggest that residents might be exposed to a higher public health threat than before. Moreover, the present study confirmed that the rice-wheat rotation system plays a key role in regulating the soil antibiotic resistome profile. Using 16S rRNA high-throughput sequencing technology, this study clarified the relationships between the antibiotic resistome and soil microbiome composition. Finally, we discuss the key environmental factors driving changes in the soil antibiotic resistome. In summary, this study gives insight into the dissemination of environmental ARGs to the people living in the Lake Tai Basin.

Effects on microbiomes and resistomes and the source-specific ecological risks of heavy metals in the sediments of an urban river

This study aims to better understand the effects of heavy metal enrichment on microbiomes and resistomes and the source-specific ecological risks of metals in the sediments of an urban river. Geo-accumulation index and enrichment factor suggested the river sediments were contaminated by Cd, Cu, Pb, and Zn in varying degrees. High-throughput sequencing-based metagenomics analysis identified 430 types of antibiotic resistance genes (ARGs), dominated by the multidrug, MLS, bacitracin, quinolone, and aminoglycoside ARGs, and 52 metal resistance genes (MRGs) mainly conferring resistance to zinc, copper, cadmium, lead, mercury and multiple metals. Spearman correlation analysis and Mantel test showed the heavy metal enrichment exerted significant effects on the microbial community, ARGs and MRGs. Source apportionment using positive matrix factorization revealed that natural source (42.8%) was the largest contributor of metals in the river sediments, followed by urban activities (35.4%) and a mixed source (21.7%). However, when incorporating the apportionment results into a modified risk model to evaluate the source-specific ecological risks, results showed human activities dominated the risks of metals. Comparatively, the urban activities majorly caused moderate- and considerable- ecological risks, while the mixed source with respect to agricultural and industrial activities contributed higher percentages on high- and extremely high- ecological risks.

Impact factors of the accumulation, migration and spread of antibiotic resistance in the environment

Antibiotic resistance is a great concern, which leads to global public health risks and ecological and environmental risks. The presence of antibiotic-resistant genes and antibiotic-resistant bacteria in the environment exacerbates the risk of spreading antibiotic resistance. Among them, horizontal gene transfer is an important mode in the spread of antibiotic resistance genes, and it is one of the reasons that the antibiotic resistance pollution has become increasingly serious. At the same time, free antibiotic resistance genes and resistance gene host bacterial also exist in the natural environment. They can not only affect horizontal gene transfer, but can also migrate and aggregate among environmental media in many ways and then continue to affect the proliferate and transfer of antibiotic resistance genes. All this shows the seriousness of antibiotic resistance pollution. Therefore, in this review, we reveal the sensitive factors affecting the distribution and spread of antibiotic resistance through three aspects: the influencing factors of horizontal gene transfer, the host bacteria of resistance genes and the migration of antibiotic resistance between environmental media. This review reveals the huge role of environmental migration in the spread of antibiotic resistance, and the environmental behavior of antibiotic resistance deserves wider attention. Meanwhile, extracellular antibiotic resistance genes and intracellular antibiotic resistance genes play different roles, so they should be studied separately.

Ciprofloxacin increased abundance of antibiotic resistance genes and shaped microbial community in epiphytic biofilm on Vallisneria spiralis in mesocosmic wetland

This study investigated the fate of ciprofloxacin (CIP) in wetlands dominated by Vallisneria spiralis. About 99% of CIP was degraded from overlaying water within 4 days of treatment but significantly inhibited the nutrient removal capacity (TN, TP, and COD) by causing a drastic reduction in microbial aggregation in epiphytic biofilm and bacterial biodiversity. CIP triggered resistance mechanisms among dominant bacteria phyla such as Proteobacteria, Actinobacteria, and Planctomycetes causing their increased relative abundance. Additionally, the relative abundances of eukaryotic microorganisms (including; Chloroplastida, Metazoa, and Rhizaria) and 13 ARGs subtypes (including; Efflux pump, Tetracycline, Multi-drug, Rifampin, Beta-lactam, Peptide, Trimethoprim) were significantly increased. While dominant metabolic pathways such as Carbohydrate, amino acid, energy and nucleotide metabolism were inhibited. This study revealed that V. spiralis has great sorption capacity for CIP than sediment and though CIP was effectively removed from the overlying water, it caused a prolonged effect on the epiphytic biofilm microbial communities.

Azole antifungal resistance in fungal isolates from wastewater treatment plant effluents

Wastewater treatment plants (WWTPs) can be significant sources of antifungal resistant fungi, which can disseminate further in the environment by getting into rivers together with effluents discharged from WWTPs and pose a risk for human health. In this study, the presence of azole resistance was determined in fungal isolates from treated effluents of two WWTPs using the standard microdilution method from Clinical and Laboratory Standards Institute (CLSI). A total of 41 fungal isolates representing 23 fungal species and 16 fungal genera were obtained. Fungal genera related to the known human and/or plant pathogens such as Aspergillus, Fusarium, and Candida were detected. Among the observed species, the susceptibility of Aspergillus fumigatus and Fusarium oxysporum was tested against fluconazole (FCZ), ketoconazole (KTZ), itraconazole (ITZ), and voriconazole (VCZ). The isolate A. fumigatus was susceptible to KTZ, ITZ, and VCZ, while it showed resistance against FCZ. On the contrast, the isolate F. oxysporum showed resistance to KTZ, ITZ, and VCZ. Comparatively, VCZ showed highest activity against both A. fumigatus and F. oxysporum. Analysis of the gene Cyp51A for the A. fumigatus isolate showed no evidence of drug resistance that could be related to point mutations and/or tandem repeats in the gene. To the best of our knowledge, this is the first susceptibility test study on A. fumigatus and F. oxysporum isolates from the WWTPs of South Africa. In conclusion, this study indicated an urgent need for thorough investigation with larger group of fungal isolates from different regions of South Africa to broadly understand the role of WWTPs in the dissemination of azole antifungal drug resistance.

Source apportionment and source-oriented risk assessment of heavy metals in the sediments of an urban river-lake system

Heavy metal pollution in lakes has attracted concerns worldwide since long retention times in lakes allow metals to accumulate and may pose significant threat to ecosystem health. For designing targeted risk mitigation strategies, it is necessary to identify the source-specific risks of heavy metals in the environment. Although previous studies have addressed either risk assessment or source identification of heavy metals in the environment, few have attempted to establish a link between them. In the study, we perform a combination of source apportionment and risk assessment for characterizing the pollution sources and source-specific risks of heavy metals in the sediments of an urban river-lake system. To this end, positive matrix factorization (PMF) was employed to apportion the potential sources of heavy metals, combined with a support vector machine classifier and the referential source fingerprints of metals in the study area. Then, the apportionment results were incorporated into the environmental risk models to evaluate the ecological and human health risks posed by heavy metals from the identified pollution sources. Results showed the river-lake system was contaminated by Cd, Cu, Zn and other metals in varying degree. Particularly, the element of Cd presented moderate to heavy pollution level. In relative, the industrial activities were identified as the largest contributor (48.0%) of heavy metals in the river-lake sediments, mainly associating with electroplating and paper making, followed by the agricultural activities (27.3%) and mix source (24.7%). Overall, the non-carcinogenic and carcinogenic risks posed by the heavy metals were acceptable, however, the element of Cd showed moderate ecological effect. Further, source-oriented risk evaluation suggested industrial processes made higher contributions to the ecological risk of heavy metals in the river-lake system. The study will provide regulators help to update the information by adding apportionment analysis in the context of risk assessment to facilitate subsequent mitigation strategies.

Distribution of antibiotic resistance genes in an agriculturally disturbed lake in China: Their links with microbial communities, antibiotics, and water quality

In this study, six antibiotic resistance genes (ARGs), one mobile genetic element (int1), and their relation with microbial communities, antibiotics, and water quality were investigated in and around of an agriculturally disturbed lake, namely, Lake Honghu. The ARGs and int1 in the research area had a 100 % detection frequency in each sample during two sampling times. The ARGs were higher in the rivers and inlets than in Lake Honghu. Sul1 was the main ARG in this area. Antibiotics, nutrients, and dissolved oxygen were significantly, positively, and negatively correlated with nearly all of the ARGs, respectively. This finding suggests that reducing antibiotics and the eutrophication level could reduce the risk of ARGs. Microbial community shift had the most direct contribution to ARG variation. However, when the indirect effect was considered, environmental factors contributed 34 % to the ARGs' variance, the microbial community contributed 28 %, and their joint effect contributed 27 % to the ARG profiles. The abundance of Firmicutes, Gemmatimonadetes, Proteobacteria, etc. and their positive correlation with ARGs were significant, suggesting that these phyla probably carry ARGs. The study provides a systematic profile of ARG distribution and dissemination in a typical Chinese lake and new ideas to control this emerging contaminant in lakes.

Genomic Characterisation of a Multiple Drug Resistant IncHI2 ST4 Plasmid in Escherichia coli ST744 in Australia

Antibiotic resistance genes (ARGs) including those from the bla_CTX-M family and mcr-1 that encode resistance to extended spectrum β–lactams and colistin, respectively, have been linked with IncHI2 plasmids isolated from swine production facilities globally but not in IncHI2 plasmids from Australia. Here we describe the first complete sequence of a multiple drug resistance Australian IncHI2-ST4 plasmid, pTZ41_1P, from a commensal E. coli from a healthy piglet. pTZ41_1P carries genes conferring resistance to heavy-metals (copper, silver, tellurium and arsenic), β-lactams, aminoglycosides and sulphonamides. The ARGs reside within a complex resistance locus (CRL) that shows considerable sequence identity to a CRL in pSDE_SvHI2, an IncHI2:ST3 plasmid from an enterotoxigenic E. coli with serotype O157:H19 of porcine origin that caused substantial losses to swine production operations in Australia in 2007. pTZ41_1P is closely related to IncHI2 plasmids found in E. coli and Salmonella enterica from porcine, avian and human sources in Europe and China but it does not carry genes encoding resistance to clinically-important antibiotics. We identified regions of IncHI2 plasmids that contribute to the genetic plasticity of this group of plasmids and highlight how they may readily acquire new resistance gene cargo. Genomic surveillance should be improved to monitor IncHI2 plasmids.

Health risk assessment of groundwater nitrate contamination: a case study of a typical karst hydrogeological unit in East China

Nitrate pollution in rivers, lakes, shallow groundwater, and even deep groundwater occurs in many parts of the world. And, it's essential to assessing the relationship between nitrate pollution and human health, which is called human health risk assessment (HHRA). In this paper, groundwater samples were collected for their nitrate content in a typical karst hydrogeological unit in East China during the wet and dry seasons. Then, a human health risk assessment was conducted using the four-step risk assessment process developed by the US Environmental Protection Agency (USEPA), which aimed to determine the potential risk posed to human health by nitrate in the groundwater. To make the assessment more authentic and objective, the drinking water and dermal contact exposure pathways were considered, and the people were divided into four groups, including infants (0~6 months), children (7 months~17 years old), females (18 years and older), and males (18 years and older), in the wet and dry seasons to determine the impacts of the exposure pathway, age, sex, and precipitation period. The results indicated that more than half of the groundwater samples exceeded 10 mg/L (measured as nitrogen), which is the drinking water standard of China. The children and infants had greater health risks than the adults at the same groundwater nitrate concentration, and those two groups need to be paid more attention; the adult females had a greater health risk than the adult males in the two precipitation periods, which shows that the order of the health risk was infants ˃ children ˃ adult females ˃ adult males. In addition, the value of the hazard quotient (HQ) and the area of the adverse effects were both higher in the wet season than in the dry season, which explains that precipitation can affect the human health risk as well. The HQ caused by the drinking water exposure pathway was much higher than that caused by the dermal contact exposure pathway. This study can provide information for more effective and reasonable decisions to city managers for groundwater nitrate pollution prevention.

Prevalence of fluoroquinolone, macrolide and sulfonamide-related resistance genes in landfills from East China, mainly driven by MGEs

Landfills are one of the most important reservoirs of antibiotic resistance genes (ARGs), and ARG pollution in landfills has been well investigated. However, the various factors contributing to the widespread prevalence of ARGs in landfills have rarely been explored. Here, we quantified three classes of antibiotics, six kinds of heavy metals, eight types of ARGs, and five varieties of mobile genetic elements (MGEs) in refuse samples from 10 landfills in Zhejiang Province, China. Compared with sulfonamides and macrolides, fluoroquinolones were present at much higher concentrations in all refuse samples, reaching a concentration of 1406.85 μg/kg in the Jiaxing region. The relative abundances of qnrD, qnrS, mexF, ermA, ermB, mefA, sul1, and sul2 in most landfills were >10^-4 copies per 16S rRNA, suggesting the presence of highly contaminated ARGs. No significant correlations between most target antibiotics and their corresponding ARGs were found. Variation partitioning analysis indicated that MGEs could be the determining factor in the spread of ARGs in landfills. This research not only reveals high levels of ARGs and the ubiquitous presence of antibiotics in refuse, but also provides guidance for controlling the spread of ARGs in landfills.

Profiles of ARGs and their relationships with antibiotics, metals and environmental parameters in vertical sediment layers of three lakes in China

Antibiotic resistance is a global health problem, and the role of antibiotics and metal pollution in antibiotic resistance in sediment biocenosis is limited. The occurrence and relationship between antibiotic resistance genes (ARGs), antibiotics, metals and environmental parameters were investigated in vertical layers of sediments in rural and urban lakes. Generally, the total concentrations of seven antibiotics were significantly higher in the rural lake (Lake Taihu = 96%) than in the urban lakes (Xuanwu = 0.3%, Wulongtan = 3%), while similar concentrations were observed for metals (Taihu (34%), Xuanwu (33%) and Wulongtan (33%)). The concentration of metals and antibiotics were mostly higher in the surface sediment layers than the deeper ones (for antibiotics; surface layers = 89%, deeper layer = 11%, for metals; surface = 65%, deep = 35%). The ARGs showed no significant difference between surface and deeper sediments (surface = 48%, deep = 52%, p < 0.05). The potential ecological risk index of Ni, Cu, Zn, Cr, Mn, As, Cd, and Pb contamination showed that Lake Taihu and Wulongtan had moderate ecological risks while Lake Xuanwu had a low ecological risk. Pearson coefficient and network analysis showed that direct and indirect relationship existed among antibiotics, metals, environmental parameters, and ARGs, and the relationship was linked by key environmental components. tetA, bla_TEM, SDZ, TOC, OFL, Cd, OTC, NOR, Ni, sulA, AUR, TC, DOX and TN were the major factors that influence the distribution of resistance genes, forming a complex network mechanism of antibiotic resistance. Our study revealed that antibiotics and heavy metals are widely distributed in the surficial sediments and the proliferation of ARGs are influenced by some key environmental components.

Does soil CuO nanoparticles pollution alter the gut microbiota and resistome of Enchytraeus crypticus?

Growing evidence suggests that metallic oxide nanoparticles can pose a severe risk to the health of invertebrates. Previous attention has been mostly paid to the effects of metallic oxide nanoparticles on the survival, growth and physiology of animals. In comparison, the effects on gut microbiota and incidence of antibiotic resistance genes (ARGs) in soil fauna remain poorly understood. We conducted a microcosm study to explore the responses of the non-target soil invertebrate Enchytraeus crypticus gut microbiota and resistomes to copper oxide nanoparticles (CuO NPs) and copper nitrate by using bacterial 16S rRNA gene amplicons sequencing and high throughput quantitative PCR. The results showed that exposure to Cu²⁺ resulted in higher bioaccumulation (P < 0.05) and lower body weight and reproduction (P < 0.05) of Enchytraeus crypticus than exposure to CuO NPs. Nevertheless, exposure to CuO NPs for 21 days markedly increased the alpha-diversity of the gut microbiota of Enchytraeus crypticus (P < 0.05) and shifted the gut microbial communities, with a significant decline in the relative abundance of the phylum Planctomycetes (from 37.26% to 19.80%, P < 0.05) and a significant elevation in the relative abundance of the phyla Bacteroidetes, Firmicutes and Acidobacteria (P < 0.05). The number of detected ARGs in the Enchytraeus crypticus gut significantly decreased from 45 in the Control treatment to 16 in the Cu(NO₃)₂ treatment and 20 in the CuO NPs treatment. The abundance of ARGs in the Enchytraeus crypticus gut were also significantly decreased to 38.48% when exposure to Cu(NO₃)₂ and 44.90% when exposure to CuO NPs (P < 0.05) compared with the controls. These results extend our understanding of the effects of metallic oxide nanoparticles on the gut microbiota and resistome of soil invertebrates.

Advances in characterizing microbial community change and resistance upon exposure to lead contamination: Implications for ecological risk assessment

Recent advancement in molecular techniques has spurred waves of studies on responses of microorganisms to lead contamination exposure, leveraging detailed phylogenetic analyses and functional gene identification to discern the effects of lead toxicity on microbial communities. This work provides a comprehensive review of recent research on (1) microbial community changes in contaminated aquatic sediments and terrestrial soils; (2) lead resistance mechanisms; and (3) using lead resistance genes for lead biosensor development. Sufficient evidence in the literature, including both in vitro and in situ studies, indicates that exposure to lead contamination inhibits microbial activity resulting in reduced respiration, suppressed metabolism, and reduced biomass as well as altered microbial community structure. Even at sites where microbial communities do not vary compositionally with contamination levels due to extremely long periods of exposure, functional differences between microbial communities are evident, indicating that some microorganisms are susceptible to lead toxicity as others develop resistance mechanisms to survive in lead contaminated environments. The main mechanisms of lead resistance involve extracellular and intracellular biosorption, precipitation, complexation, and/or efflux pumps. These lead resistance mechanisms are associated with suites of genes responsible for specific lead resistance mechanisms and may serving as indicators of lead contamination in association with dominance of certain phyla. This allows for development of several lead biosensors in environmental biotechnology. To promote applications of these advanced understandings, molecular techniques, and lead biosensor technology, perspectives of future work on using microbial indicators for site ecological assessment is presented.