Antibiotic concentration and antibiotic-resistant bacteria in two shallow urban lakes after stormwater event

Longitudinal Analysis of Urban Stormwater Microbiome and Resistome from Watersheds with and without Green Infrastructure using Long-Read Sequencing

Since stormwater conveys a variety of contaminants into water bodies, green infrastructure (GI) is increasingly being adopted as an on-site treatment solution in addition to controlling peak flows. The purpose of this study was to identify differences in microbial water quality of stormwater in watersheds retrofitted with GI vs. those without GI. Considering stormwater is recently recognized as a contributor to the antibiotic resistance (AR) threat, another goal of this study was to characterize changes in the microbiome and collection of AR genes (resistome) of urban stormwater with season, rainfall characteristics, and fecal contamination. MinION long-read sequencing was used to analyze stormwater microbiome and resistome from watersheds with and without GI in Columbus, Ohio, United States, over 18 months. We characterized fecal contamination in stormwater via culturing Escherichia coli and with molecular microbial source tracking (MST) to identify sources of fecal contamination. Overall, season and storm event (rainfall) characteristics had the strongest relationships with changes in the stormwater microbiome and resistome. We found no significant differences in microbial water quality or the microbiome of stormwater in watersheds with and without GI implemented. However, there were differences between the communities of microorganisms hosting antibiotic resistance genes (ARGs) in stormwater from watersheds with and without GI, indicating the potential sensitivity of AR bacteria to treatment. Stormwater was contaminated with high concentrations of human-associated fecal bacterial genes, and the ARG host bacterial community had considerable similarities to human feces/wastewater. We also identified 15 potential pathogens hosting ARGs in these stormwater resistome, including vancomycin-resistant Enterococcus faecium (VRE) and multidrug-resistant Pseudomonas aeruginosa. In summary, urban stormwater is highly contaminated and has a great potential to spread AR and microbial hazards to nearby environments. This study presents the most comprehensive analysis of stormwater microbiome and resistome to date, which is crucial to understanding the potential microbial risk from this matrix. This information can be used to guide future public health policy, stormwater reuse programs, and urban runoff treatment initiatives.

Urbanization and land use regulate soil vulnerability to antibiotic contamination in urban green spaces

The presence of antibiotics in environment is an emerging concern because of their ubiquitous occurrence, adverse eco-toxicological effects, and promotion of widespread antibiotic resistance. Urban soil, which plays a noticeable role in human health, may be a reservoir of antibiotics because of intensive human disturbance. However, little is understood about the vulnerability of soil to antibiotic contamination in urban areas and the spatial-temporal characteristics of anthropogenic and environmental pressures. In this study, we developed a framework for the dynamic assessment of soil vulnerability to antibiotic contamination in urban green spaces, combining antibiotic release, exposure, and consequence layers. According to the results, soil vulnerability risks shown obvious spatial-temporal variation in urban areas. Areas at a high risk of antibiotic contamination were usually found in urban centers with high population densities and in seasons with low temperature and vegetation coverage. Quinolones (e.g., ofloxacin and norfloxacin) were priority antibiotics that posed the highest vulnerability risks, followed by tetracyclines. We also confirmed the effectiveness of the vulnerability assessment by correlating soil vulnerability indexes and antibiotic residues in urban soils. Furthermore, urbanization- and land use-related parameters were shown to be critical in regulating soil vulnerability to antibiotic contamination based on sensitivity analysis. These findings have important implications for the prediction and mitigation of urban soil contamination with antibiotics and strategies to improve human health.

The role of water matrix on antibiotic resistance genes transmission in substrate layer from stormwater bioretention cells

Recently, extensive attention has been paid to antibiotic resistance genes (ARGs) transmission. However, little available literature could be found about ARGs transmission in stormwater bioretention cells, especially the role of water matrix on ARGs transmission. Batch experiments were conducted to investigate target ARGs (blaTEM, tetR and aphA) transmission behaviors in substrate layer from stormwater bioretention cells under different water matrices, including nutrient elements (e.g., carbon, nitrogen and phosphorus), water environmental conditions (dissolved oxygen (DO), pH and salinity, etc.) and pollution factors (like heavy metals, antibiotics and disinfectants), showing that ARGs conjugation frequency increased sharply with the enhancement of water matrices (expect DO and pH), while there were obvious increasing tendencies for all ARGs transformation frequencies under only the pollution factor. The correlation between dominant bacteria and ARGs transmission implied that conjugation and transformation of ARGs were mainly determined by Firmicutes, Bacteroidota, Latescibacterota, Chloroflexi and Cyanobacteria at the phylum level, and by Sphingomonas, Ensifer, IMCC26256, Rubellimicrobium, Saccharimonadales, Vicinamibacteraceae, Nocardioides, JG30-KF-CM66 at the genus level. The mentioned dominant bacteria were responsible for intracellular reactive oxygen species (ROS) and cell membrane permeability (CMP) in the substrate layer, where the amplification of intracellular ROS variation were the largest with 144 and 147 % under the condition of TP and salinity, respectively, and the one of CMP variation were the highest more than 165 % under various pollution factors. Furthermore, both increasing DO and reducing salinity could be potential approaches for the inhibition of ARGs transmission in bioretention cells taking into account the simultaneous removal of conventional pollutants.

Resistomes in freshwater bioaerosols and their impact on drinking and recreational water safety: A perspective

Antibiotic resistance genes (ARGs) are widespread environmental pollutants of biological origin that pose a significant threat to human, animal, and plant health, as well as to ecosystems. ARGs are found in soil, water, air, and waste, and several pathways for global dissemination in the environment have been described. However, studies on airborne ARG transport through atmospheric particles are limited. The ARGs in microorganisms inhabiting an environment are referred to as the "resistome". A global search was conducted of air-resistome studies by retrieving bioaerosol ARG-related papers published in the last 30 years from PubMed. We found that there is no dedicated methodology for isolating ARGs in bioaerosols; instead, conventional methods for microbial culture and metagenomic analysis are used in combination with standard aerosol sampling techniques. There is a dearth of information on the bioaerosol resistomes of freshwater environments and their impact on freshwater sources used for drinking and recreational activities. More studies of aerobiome freshwater environments are needed to ensure the safe use of water and sanitation. In this review we outline and synthesize the few studies that address the freshwater air microbiome (from tap water, bathroom showers, rivers, lakes, and swimming pools) and their resistomes, as well as the likely impacts on drinking and recreational waters. We also discuss current knowledge gaps for the freshwater airborne resistome. This review will stimulate new investigations of the atmospheric microbiome, particularly in areas where both air and water quality are of public health concern.

Review of emerging contaminants in green stormwater infrastructure: Antibiotic resistance genes, microplastics, tire wear particles, PFAS, and temperature

Green stormwater infrastructure is a growing management approach to capturing, infiltrating, and treating runoff at the source. However, there are several emerging contaminants for which green stormwater infrastructure has not been explicitly designed to mitigate and for which removal mechanisms are not yet well defined. This is an issue, as there is a growing understanding of the impact of emerging contaminants on human and environmental health. This paper presents a review of five emerging contaminants - antibiotic resistance genes, microplastics, tire wear particles, PFAS, and temperature - and seeks to improve our understanding of how green stormwater infrastructure is impacted by and can be designed to mitigate these emerging contaminants. To do so, we present a review of the source and transport of these contaminants to green stormwater infrastructure, specific treatment mechanisms within green infrastructure, and design considerations of green stormwater infrastructure that could lead to their removal. In addition, common removal mechanisms across these contaminants and limitations of green infrastructure for contaminant mitigation are discussed. Finally, we present future research directions that can help to advance the use of green infrastructure as a first line of defense for downstream water bodies against emerging contaminants of concern.

A decennial study of the trend of antibiotic studies in China

Antibiotics are one of the greatest inventions in human history and are used worldwide on an enormous scale. Besides its extensive usage in medical and veterinary arenas to treat and prevent the infection, its application is very prominent in other fields, including agriculture, aquaculture, and horticulture. In recent decades, the increased consumption of antibiotics in China saw a vast increase in its production and disposal in various environments. However, in this post-antibiotic era, the abuse and misuse of these valuable compounds could lead to the unreversible consequence of drug resistance. In China, antibiotics are given a broad discussion in various fields to reveal their impact on both human/animals health and the environment. To our knowledge, we are the first paper to look back at the development trend of antibiotic-related studies in China with qualitative and quantitative bibliometric analysis from the past decades. Our study identified and analyzed 5559 papers from its inception (1991) to December 6, 2021, from the Web of Science Core Collection database. However, with few authors and institutions focusing on long-term studies, we found the quality of contributions was uneven. Studies mainly focused on areas such as food science, clinical research, and environmental studies, including molecular biology, genetics and environmental, ecotoxicology, and nutrition, which indicate possible primary future trends. Our study reports on including potentially new keywords, studies' milestones, and their contribution to antibiotic research. We offer potential topics that may be important in upcoming years that could help guide future research.

Enhanced Escherichia coli removal from stormwater with bermudagrass-derived activated biochar filtration systems

Stormwater treatment and reuse can alleviate water pollution and scarcity while current sand filtration systems showed low treatment performance for stormwater. For enhancing E. coli removal in stormwater, this study applied the bermudagrass-derived activated biochars (BCs) in the BC-sand filtration systems for E. coli removal. Compared with the pristine BC (without activation), the FeCl3 and NaOH activations increased the BC carbon content from 68.02% to 71.60% and 81.22% while E. coli removal efficiency increased from 77.60% to 81.16% and 98.68%, respectively. In all BCs, the BC carbon content showed a highly positive correlation with E. coli removal efficiency. The FeCl3 and NaOH activations also led to the enhancement of roughness of BC surface for enhancing E. coli removal by straining (physical entrapment). The main mechanisms for E. coli removal by BC-amended sand column were found to be hydrophobic attraction and straining. Additionally, under 105-107 CFU/mL of E. coli, final E. coli concentration in NaOH activated BC (NaOH-BC) column was one order of magnitude lower than those in pristine BC and FeCl3 activated BC (Fe-BC) columns. The presence of humic acid remarkably lowered the E. coli removal efficiency from 77.60% to 45.38% in pristine BC-amended sand column while slightly lowering the E. coli removal efficiencies from 81.16% and 98.68% to 68.65% and 92.57% in Fe-BC and NaOH-BC-amended sand columns, respectively. Moreover, compared to pristine BC, the activated BCs (Fe-BC and NaOH-BC) also resulted in the lower antibiotics (tetracycline and sulfamethoxazole) concentrations in the effluents from the BC-amended sand columns. Therefore, for the first time, this study indicated NaOH-BC showed high potential for effective treatment of E. coli from stormwater by the BC-amended sand filtration system compared with pristine BC and Fe-BC.

Characteristics of antibiotic resistance gene distribution in rainfall runoff and combined sewer overflow

Rainfall runoff and combined sewer overflow (CSO) converge with organic waste, nutrients, and microbes from the ground and wastewater. These pollutants promote the spread and transformation of antibiotic resistance genes (ARGs). In this study, four rainfall runoff and one CSO outfall were chosen, and samples were collected to explore the occurrence and distribution of ARGs. The ARGs were extracted from suspended solids and analyzed using metagenomic sequencing. A total of 888 ARG subtypes, belonging to 17 ARG types, were detected in all samples. Eleven ARG types were shared by all the samples. Multidrug resistance genes had the highest relative abundance. Their total relative abundance reached 1.07 ratio (ARG copy number/16S rRNA gene copy number) and comprised 46.6% of all the ARGs. In all samples, the CSO outfall had the highest total relative abundance (8.25 × 10^-1 ratio) of ARGs, with a ratio ranging ND (not detected)-3.78 × 10^-1 ratio. Furthermore, the relationship between ARG types and environmental factors was determined using redundancy analysis. The results showed that chemical organic demand (COD) and bacterial abundance were positively correlated with most ARG types, including multidrug, bacitracin, aminoglycoside, β-lactam, tetracycline, and sulfonamide. NH₃-N, TN, and TP were positively correlated with rifamycin, fosmidomycin, and vancomycin resistance genes. The relationship among the ARG subtypes was investigated using network analyses. The multidrug resistance gene subtypes had the highest frequency of co-occurrence. This study provides insights into the occurrence and distribution of ARGs under non-point source pollution and may contribute to the control of ARGs.

Inactivation of antibiotic resistant bacteria from stormwater runoff using UVA/LED and its potential risks

Recently, increasing attention has been paid to antibiotic resistance in stormwater runoff. However, there is no available literature about the control of antibiotic resistant bacteria (ARB) through 365 nm ultraviolet light-emitting diode (UVA/LED). In this study, batch experiments were conducted to investigate ARB inactivation kinetics, effects of light intensity and water matrix (including suspended solid (SS) concentration, initial pH and bacteria concentration), and potential transmission risks after UVA/LED irradiation. Results showed that ARB inactivation efficiencies reached 6.31 log reduction at 8 mW/cm² (86 J/cm²) of UVA/LED for 180 min. ARB inactivation efficiencies increased with the increase of light intensity, and showed a linear relationship. ARB inactivation decreased with increasing SS levels, and the largest inactivation efficiencies was 3.56 log reduction at 50 mg/L of SS. Initial pH had slight effect on ARB inactivation through UVA/LED irradiation. A low initial bacteria concentration (10⁵ CFU/mL) was not necessarily associated with good ARB inactivation (3.59 log reduction). After UVA/LED irradiation, ARB was hardly detected during 12 hr of dark repair, and the transfer frequency of kanamycin resistance gene was increased to 5.43 × 10^-4. These suggested that the application of UVA/LED to inactivate ARB in stormwater runoff was feasible and desirable in this study.

Seasonal Dynamics in Bacteriological and Physicochemical Water Quality of the Southern Gulf of Lake Tana

Freshwater lakes are important sources of water for domestic, agricultural, and industrial uses. Lake Tana offers a range of ecosystem services to the surrounding communities. However, this lake is facing deterioration in water quality due to pollution caused by anthropogenic influences. Therefore, regular monitoring of key water quality parameters is critical to understanding the water quality status of the lake. This study aimed to assess the seasonal fluctuation of water quality of the Southern Gulf of Lake Tana using indicator bacteria and some physicochemical parameters. A total of 48 water samples were collected in dry and wet seasons from eight sites in the study area. Total coliforms (TC), faecal coliforms (FC), and some physicochemical parameters (pH, temperature, turbidity, electrical conductivity, total dissolved solids, dissolved oxygen, biochemical oxygen demand, ammonium, nitrate, and phosphate) were determined following standard methods. The results revealed that coliform counts were above the permissible level set by Ethiopian Standards and varied significantly among sites (P < 0.05). FC counts ranged from 1 to 1600 MPN/100 ml (with the lowest and highest mean value of 1 at site 8 to 1076.5 ± 3.1 at site 4) and again TC counts ranged from 1 to 1600 MPN/100 ml (with a mean value of 4.8 ± 1.81 at site 6 to 1600 at site 4 and site 8). The findings also confirmed that the highest counts of coliforms were observed during the wet season. The high counts are attributed to the discharge of human excreta and animal wastes during the rainy season from the different anthropogenic activities near the Gulf. Significant variations in most of the physicochemical parameters were also observed between sites and seasons. FC and biochemical oxygen demand (BOD₅₎ in most sites did not meet the EPA standard for surface water. Corrective measures are highly recommended for anthropogenic activities driving high pollution loads in the lake.

Impact of biochar on persistence and diffusion of antibiotic resistance genes in sediment from an aquaculture pond

Aquaculture sediments are a purported sizable pool of antibiotic resistance genes (ARGs). However, the pathways for transmission of ARGs from sediments to animals and humans remain unclear. We conducted an ARG survey in sediments from a bullfrog production facility located in Guangdong, China, and simulated zebrafish breeding systems were constructed, with or without biochar addition in sediments, to explore the effects of biochar on ARGs and their precursors of the sediment and zebrafish gut. After 60 days, 6 subtypes of ARGs and intI1 were detected, with sediments harboring more ARGs than zebrafish gut. The addition of biochar reduced the abundance of ARGs in the sediment and zebrafish gut, as well as suppressed the horizontal transmission of ARGs from sediment to zebrafish gut. Network analysis and partial least squares path modeling revealed that ARG enrichment was mainly affected by bacterial groups dominated by Nitrospirae, Gemmatimonades, Chloroflexi, and Cyanobacteria and intI1. Our findings provide insights into the transmission of ARGs from sediment to animals and highlight the efficacy of biochar amendments to aquaculture sediments to reduce the transmission of ARGs.

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.

Highly variable removal of pathogens, antibiotic resistance genes, conventional fecal indicators and human-associated fecal source markers in a pilot-scale stormwater biofilter operated under realistic stormflow conditions

Green stormwater infrastructure systems, such as biofilters, provide many water quality and other environmental benefits, but their ability to remove human pathogens and antibiotic resistance genes (ARGs) from stormwater runoff is not well documented. In this study, a field scale biofilter in Southern California (USA) was simultaneously evaluated for the breakthrough of a conservative tracer (bromide), conventional fecal indicators, bacterial and viral human-associated fecal source markers (HF183, crAssphage, and PMMoV), ARGs, and bacterial and viral pathogens. When challenged with a 50:50 mixture of untreated sewage and stormwater (to mimic highly contaminated storm flow) the biofilter significantly removed (p < 0.05) 14 of 17 microbial markers and ARGsin descending order of concentration reduction: ermB (2.5 log(base 10) reduction) > Salmonella (2.3) > adenovirus (1.9) > coliphage (1.5) > crAssphage (1.2) > E. coli (1.0) ∼ 16S rRNA genes (1.0) ∼ fecal coliform (1.0) ∼ intl1 (1.0) > Enterococcus (0.9) ∼ MRSA (0.9) ∼ sul1 (0.9) > PMMoV (0.7) > Entero1A (0.5). No significant removal was observed for GenBac3, Campylobacter, and HF183. From the bromide data, we infer that 0.5 log-units of attenuation can be attributed to the dilution of incoming stormwater with water stored in the biofilter; removal above this threshold is presumably associated with non-conservative processes, such as physicochemical filtration, die-off, and predation. Our study documents high variability (>100-fold) in the removal of different microbial contaminants and ARGs by a field-scale stormwater biofilter operated under transient flow and raises further questions about the utility of human-associated fecal source markers as surrogates for pathogen removal.

Antimicrobial Resistance Development Pathways in Surface Waters and Public Health Implications

Human health is threatened by antibiotic-resistant bacteria and their related infections, which cause thousands of human deaths every year worldwide. Surface waters are vulnerable to human activities and natural processes that facilitate the emergence and spread of antibiotic-resistant bacteria in the environment. This study evaluated the pathways and drivers of antimicrobial resistance (AR) in surface waters. We analyzed antibiotic resistance healthcare-associated infection (HAI) data reported to the CDC's National Healthcare Safety Network to determine the number of antimicrobial-resistant pathogens and their isolates detected in healthcare facilities. Ten pathogens and their isolates associated with HAIs tested resistant to the selected antibiotics, indicating the role of healthcare facilities in antimicrobial resistance in the environment. The analyzed data and literature research revealed that healthcare facilities, wastewater, agricultural settings, food, and wildlife populations serve as the major vehicles for AR in surface waters. Antibiotic residues, heavy metals, natural processes, and climate change were identified as the drivers of antimicrobial resistance in the aquatic environment. Food and animal handlers have a higher risk of exposure to resistant pathogens through ingestion and direct contact compared with the general population. The AR threat to public health may grow as pathogens in aquatic systems adjust to antibiotic residues, contaminants, and climate change effects. The unnecessary use of antibiotics increases the risk of AR, and the public should be encouraged to practice antibiotic stewardship to decrease the risk.

Conurbation size drives antibiotic resistance along the river

With growing concerns about antibiotic resistance, the tracking of antibiotic resistance genes (ARGs) in urban waterways will facilitate our increased understanding of the impact of urbanization on ARGs dissemination. In the current study, we assessed the ARGs profiles and antibiotic resistome in water samples along the Jiulong River basin, a distance of 250 km, to better understand the impact of anthropogenic activities. A total of 244 ARGs and 12 MGEs were detected from 21 sampling sites. Both relative and absolute abundance of the observed resistome decreased with increasing distance from urban areas. Ordinary least-squares (OLS) regression revealed that both the relative and absolute resistome abundance were positively correlated with city size. The resistome had several inputs and outputs and Fast Expectation Maximization Microbial Source Tracking (FEAST), suggested that the majority of the antibiotic resistome originated from anthropogenic activities. A total of 8 ARGs and 20 microbial OTUs were considered as biomarkers that differentiated the location of sampling sites. Bacterial communities were significantly correlated with ARGs according to Procrustes analysis and Mantel test, which was also supported by a co-occurrence network. Variation partitioning analysis revealed that ARG profiles were driven by multiple factors. Although antibiotic resistome abundance significantly increased near urban conurbations, overall resistome abundance decreased as the river flowed downstream. Our study highlights the effect of conurbation size on antibiotic resistance profiles within the river basin and the potential resilience of rivers to recover from ARGs contamination.

Antibiotic resistance genes in an urban stream before and after a state fair

The global spread of antibiotic resistance genes (ARGs) concomitant with a decrease in antibiotic effectiveness is a major public health issue. While research has demonstrated the impact of various urban sources, such as wastewater treatment plant (WWTP) effluent, stormwater runoff, and industrial discharge on ARG abundance in receiving waters, the impact of short-term gatherings such as state fairs is not comprehensively understood. The objective of this research was to explore the impact of a 2-week Wisconsin State Fair gathering - over 1.1 million visitors and 7,100 farm animals - on the abundance of the ARG bla_TEM, the integrase of the class 1 integron (intI1), a marker for horizontal gene transfer, and the 16S rRNA gene, a marker for total biomass, in an urban stream receiving runoff from the state fair. Stream samples downstream of the state fair were taken before and after the event and quantified via a droplet digital polymerase chain reaction. The absolute abundance of all genes was significantly higher (p<0.05) following the event. This research showcases the prevalence and persistence of ARG contamination in an urban stream before and after a state fair gathering, suggesting that short-term events can be a significant source of ARGs into the environment.

Tracing Antibiotic Resistance Genes along the Irrigation Water Chain to Chive: Does Tap or Surface Water Make a Difference?

Irrigation water is well known as potential source of pathogens in fresh produce. However, its role in transferring antibiotic resistance determinants is less well investigated. Therefore, we analyzed the contribution of surface and tap water to the resistome of overhead-irrigated chive plants. Field-grown chive was irrigated with either surface water (R-system) or tap water (D-system), from planting to harvest. Water along the two irrigation chains as well as the respective plants were repeatedly sampled and screened for 264 antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), using high-capacity qPCR. Differentially abundant (DA) ARGs were determined by comparing the two systems. On R-chive, β-lactam ARGs, multidrug-resistance (MDR) determinants, and MGEs were most abundant, while D-chive featured DA ARGs from the vancomycin class. Diversity and number of DA ARGs was the highest on young chives, strongly diminished at harvest, and increased again at the end of shelf life. Most ARGs highly enriched on R- compared to D-chive were also enriched in R- compared to D-sprinkler water, indicating that water played a major role in ARG enrichment. Of note, blaKPC was detected at high levels in surface water and chive. We conclude that water quality significantly affects the resistome of the irrigated produce.

Biological nitrogen removal from stormwater in bioretention cells: a critical review

Excess nitrogen in stormwater degrades surface water quality via eutrophication and related processes. Bioretention has been recognized as a highly effective low-impact development (LID) technology for the management of high runoff volumes and reduction of nitrogen (N) pollutants through various mechanisms. This paper provides a comprehensive and critical review of recent developments on the biological N removal processes occurring in bioretention systems. The key plant- and microbe-mediated N transformation processes include assimilation (N uptake by plants and microbes), nitrification, denitrification, and anammox (anaerobic ammonia oxidation), but denitrification is the major pathway of permanent N removal. Overall, both laboratory- and field-scale bioretention systems have demonstrated promising N removal performance (TN: >70%). The phyla Bacteroidetes and Proteobacteria are the most abundant microbial communities found to be enriched in biofilter media. Furthermore, the denitrifying communities contain several functional genes (e.g., nirK/nirS, and nosZ), and their concentrations increase near the surface of media depth. The N removal effectiveness of bioretention systems is largely impacted by the hydraulics and environmental factors. When a bioretention system operates at: low hydraulic/N loading rate, containing a saturation zone, vegetated with native plants, having deeper and multilayer biofilter media with warm climate temperature and wet storm events periods, the N removal efficiency can be high. This review highlights shortcomings and current knowledge gaps in the area of total nitrogen removal using bioretention systems, as well as identifies future research directions on this topic.

Loading, transport, and treatment of emerging chemical and biological contaminants of concern in stormwater

Stormwater is a largely uncontrolled source of pollution in rural and urban environments across the United States. Concern regarding the growing diversity and abundance of pollutants in stormwater, as well as their impacts on water quality, has grown significantly over the past several decades. In addition to conventional contaminants like nutrients and heavy metals, stormwater is a well-documented source of many contaminants of emerging concern, which can be toxic to both aquatic and terrestrial organisms and remain a barrier to maintaining high quality water resources. Chemical pollutants like pharmaceuticals and personal care products, industrial pollutants such as per- and polyfluoroalkyl substances, and tire wear particles in stormwater are of great concern due to their toxic, genotoxic, mutagenic and carcinogenic properties. Emerging microbial contaminants such as pathogens and antibiotic resistance genes also represent significant threats to environmental water quality and human health. Knowledge regarding the transport, behavior, and the remediation capacity of these pollutants in runoff is key for addressing these pollutants in situ and minimizing ecosystem perturbations. To this end, this review paper will analyze current understanding of these contaminants in stormwater runoff in terms of their transport, behavior, and bioremediation potential.

Designing a marine outfall to reduce microbial risk on a recreational beach: Field experiment and modeling

A marine outfall can be a wastewater management system that discharges sewage and stormwater into the sea; hence, it is a source of microbial pollution on recreational beaches, including antibiotic resistant genes (ARGs), which lead to an increase in untreatable diseases. In this regard, a marine outfall must be efficiently located to mitigate these risks. This study aimed to 1) investigate the spatiotemporal variability of Escherichia coli (E. coli) and ARGs on a recreational beach and 2) design marine outfalls to reduce microbial risks. For this purpose, E. coli and ARGs with influential environmental variables were intensively monitored on Gwangalli beach, South Korea in this study. Environmental fluid dynamic code (EFDC) was used and calibrated using the monitoring data, and 12 outfall extension scenarios were explored (6 locations at 2 depths). The results revealed that repositioning the marine outfall can significantly reduce the concentrations of E. coli and ARGs on the beach by 46-99%. Offshore extended outfalls at the bottom of the sea reduced concentrations of E. coli and ARGs on the beach more effectively than onshore outfalls at the sea surface. These findings could be helpful in establishing microbial pollution management plans at recreational beaches in the future.

Horizontal and vertical gene transfer drive sediment antibiotic resistome in an urban lagoon system

Rapid urbanization has resulted in pervasive occurrence of antibiotic resistance genes (ARGs) in urban aquatic ecosystems. However, limited information is available concerning the ARG profiles and the forces responsible for their assembly in urban landscape lagoon systems. Here, we employed high-throughput quantitative PCR (HT-qPCR) to characterize the spatial variations of ARGs in surface and core sediments of Yundang Lagoon, China. The results indicated that the average richness and absolute abundance of ARGs were 11 and 53 times higher in the lagoon sediments as compared to pristine reference Tibetan lake sediments, highlighting the role of anthropogenic activities in ARG pollution. Co-occurrence network analysis indicated that various anaerobic prokaryotic genera belonging to Alpha-, Deltaproteobacteria, Bacteroidetes, Euryarchaeota, Firmicutes and Synergistetes were the potential hosts of ARGs. The partial least squares-path modeling (PLS-PM) analysis revealed positive and negative indirect effects of physicochemical factors and heavy metals on the lagoon ARG profiles, via biotic factors, respectively. The horizontal (mediated by mobile genetic elements) and vertical (mediated by prokaryotic communities) gene transfer may directly contribute the most to drive the abundance and composition of ARGs, respectively. Furthermore, the neutral community model demonstrated that the assembly of sediment ARG communities was jointly governed by deterministic and stochastic processes. Overall, this study provides novel insights into the diversity and distribution of ARGs in the benthic habitat of urban lagoon systems and underlying mechanisms for the spread and proliferation of ARGs.

High throughput sequencing reveals the abundance and diversity of antibiotic-resistant bacteria in aquaculture wastewaters, Shandong, China

An innovative investigation was undertaken into the abundance and diversity of high antibiotic-resistant bacteria in aquaculture waters in Shandong Province, China, through cumulation incubation, PCR amplification of 16S rDNA, and high-throughput sequencing. The results showed that Vibrio, Bacillus, Vagococcus, Acinetobacter, Shewanella, Psychrobacter, Lactococcus, Enterococcus, Marinimonus and Myroids were abundant in the aquaculture waters, whereas other phylum including Actinobacteria, Deinococcus-Thermus, Omnitrophica and Nitrospirae had relatively lower abundance. Our studies revealed the presence of different bacteria in different locations in the aquaculture waters, most of which were resistant to multiple antibiotics. That is, the same microbial species from the same aquaculture wastewater can resist different antibiotics. Altogether, a considerable portion of the microbial community were found to be multi-drug resistant. It is essential that the spread of the antibiotic-resistant bacteria is controlled so that the distribution of antibiotic resistance genes to other environments is avoided.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02656-4.

Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond

BACKGROUND

Ponds are important freshwater habitats that support both human and environmental activities. However, relative to their larger counterparts (e.g. rivers, lakes), ponds are understudied, especially with regard to their microbial communities. Our study aimed to fill this knowledge gap by using culture-independent, high-throughput sequencing to assess the dynamics, taxonomy, and functionality of bacterial and viral communities in a freshwater agricultural pond.

RESULTS

Water samples (n = 14) were collected from a Mid-Atlantic agricultural pond between June 2017 and May 2018 and filtered sequentially through 1 and 0.2 μm filter membranes. Total DNA was then extracted from each filter, pooled, and subjected to 16S rRNA gene and shotgun sequencing on the Illumina HiSeq 2500 platform. Additionally, on eight occasions water filtrates were processed for viral metagenomes (viromes) using chemical concentration and then shotgun sequenced. A ubiquitous freshwater phylum, Proteobacteria was abundant at all sampling dates throughout the year. However, environmental characteristics appeared to drive the structure of the community. For instance, the abundance of Cyanobacteria (e.g. Nostoc) increased with rising water temperatures, while a storm event appeared to trigger an increase in overall bacterial diversity, as well as the relative abundance of Bacteroidetes. This event was also associated with an increase in the number of antibiotic resistance genes. The viral fractions were dominated by dsDNA of the order Caudovirales, namely Siphoviridae and Myovirdae.

CONCLUSIONS

Overall, this study provides one of the largest datasets on pond water microbial ecology to date, revealing seasonal trends in the microbial taxonomic composition and functional potential.

Prevalence of antibiotic resistance and virulence genes in the biofilms from an aquifer recharged with stormwater

An improved understanding of the diversity and composition of microbial communities carrying antibiotic resistance genes (ARGs) and virulence genes (VGs) in aquifers recharged with stormwater is essential to comprehend potential human health risks from water reuse. A high-throughput functional gene array was used to study the prevalence of ARGs and VGs in aquifer biofilms (n = 27) taken from three boreholes over three months. Bacterial genera annotated as opportunistic pathogens such as Aeromonas, Burkholderia, Pseudomonas, Shewanella, and Vibrio were ubiquitous and abundant in all biofilms. Bacteria from clinically relevant genera, Campylobacter, Enterobacter, Klebsiella, Mycobacterium, Mycoplasma, and Salmonella were detected in biofilms. The mean travel time of stormwater from the injection well to P1 and P3 boreholes was 260 and 360 days respectively. The presence of ARGs and VGs in the biofilms from these boreholes suggest a high spatial movement of ARGs and VGs in the aquifer. The ARGs with the highest abundance were small multidrug resistance efflux pumps (SMR) and multidrug efflux (Mex) followed by β-lactamase C genes. β- lactamase C encoding genes were primarily detected in Enterobacteriaceae, Pseudomonadaceae, Bacillaceae, and Rhodobacteraceae families. The VGs encoding siderophores, including aerobactin (iro and iuc genes), followed by pilin, hemolysin, and type III secretion were ubiquitous. Canonical correspondence analysis suggested that Total Organic Carbon (TOC), Dissolved Organic Carbon (DOC), turbidity, and Fe concentration has a significant impact on the microbial community structure of bacteria carrying ARGs and VGs. Post abstraction treatment of groundwater may be prudent to improve water security and reduce potential health risks.

Impact of wave action and rainfall on incidence and antibiotic resistance of total coliforms in Southern California beaches

Coliforms are important bacterial contamination indicators in recreational waters. Little is known about the antibiotic resistance of coliforms from Southern California beaches. This study examined the numbers of coliforms as well as the incidence of antibiotic-resistant coliforms in beaches with restricted and non-restricted wave action by sampling from the shores of both types of beaches following dry and wet weather. Total coliforms were selected by membrane filtration onto mEndo agar and then enumerated. Randomly selected isolates from each location were screened for resistance to nine classes of antibiotics by disk diffusion, and the multiple antibiotic resistance (MAR) index was calculated. Numbers of total coliforms were significantly higher following rain compared to dry weather. Total coliform numbers were not significantly elevated at non-restricted wave action sites. Restricted wave action sites had a 78.5% increase in MAR index following wet weather compared to dry weather. Resistance to ampicillin was observed in almost 50% of isolates and was not significantly impacted by wave action or weather. Minimum inhibitory concentration testing revealed that many isolates were highly resistant to ampicillin. This study is the first to report on the antibiotic resistance of coliforms found in Southern California beaches and highlights the prevalence of ampicillin resistance.

Residential urban stormwater runoff: A comprehensive profile of microbiome and antibiotic resistance

Non-point stormwater runoff is a major contamination source of receiving waterbodies. Heightened incidence of waterborne disease outbreaks related to recreational use and source water contamination is associated with extreme rainfall events. Such extreme events are predicted to increase in some regions due to climate change. Consequently, municipal separate storm sewer systems (MS4s) conveying pathogens to receiving waters are a growing public health concern. In addition, the spread of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria in various environmental matrices, including urban runoff, is an emerging threat. The resistome and microbiota profile of MS4 discharges has yet to be fully characterized. To address this knowledge gap, we first analyzed the relationship between rainfall depth and intensity and E. coli densities (fecal indicator) in stormwater from four MS4 outflows in Columbus, Ohio, USA during the spring and summer of 2017. Microbial source tracking (MST) was conducted to examine major fecal contamination sources in the study sewersheds. A subset of samples was analyzed for microbial and resistome profiles using a metagenomic approach. The results showed a significant positive relationship between outflow E. coli density and rainfall intensity. MST results indicate prevalent fecal contamination from ruminant populations in the study sites (91% positive among the samples tested). Protobacteria and Actinobacteria were two dominant bacteria at a phylum level. A diverse array of ARGs and potentially pathogenic bacteria (e.g. Salmonella enterica Typhimurium), fungi (e.g. Scedosporium apiospermum), and protists (e.g. Acanthamoeba palestinensis) were found in urban stormwater outflows that discharge into adjacent streams. The most prevalent ARGs among samples were β-lactam resistance genes and the most predominant virulence genes within bacterial community were related with Staphylococcus aureus. A comprehensive contamination profile indicates a need for sustainable strategies to manage urban stormwater runoff amid increasingly intense rainfall events to protect public and environmental health.

Influence of hydrologic and anthropogenic drivers on emerging organic contaminants in drinking water sources in the Susquehanna River Basin

Occurrence of emerging organic contaminants (EOCs) in surface water bodies can cause adverse effects on non-target organisms. When surface waters are used as drinking water sources, temporal variability in EOC concentrations can potentially impact drinking water quality and human health. To better understand spatiotemporal variability of EOCs in drinking water sources in Central Pennsylvania, EOCs were evaluated in six drinking water sources during a two-year study period (April 2016-June 2018) in the Susquehanna River Basin (SRB). The study was conducted in two phases: Phase I was a spatially distributed sampling approach within the SRB focusing on seven human pharmaceuticals and Phase II was a temporally intensive sampling regime at a single site focusing on a broader range of EOCs. Concentration-discharge relationships were utilized to classify EOC transport dynamics and understand the extent to which hydrologic and anthropogenic factors, such as surface runoff and wastewater effluent, may contribute to EOC occurrence. Overall, EOCs were present at higher concentrations in colder seasons than warmer seasons. Thiamethoxam, a neonicotinoid insecticide, and caffeine exhibited accretion dynamics during high-flow periods, suggesting higher transport during surface runoff events. Human pharmaceuticals known to persist in wastewater effluent were inversely correlated with discharge, indicating dilution characteristics consistent with diminished wastewater signals during high-flow periods. Acetaminophen exhibited near-chemostatic transport dynamics, indicating nonpoint source inputs during high-flow periods. Risk calculations revealed that although EOCs posed medium-to-high risk to aquatic organisms, human health risk through fish consumption was low.

Response of prokaryotic communities to extreme precipitation events in an urban coastal lagoon: A case study of Yundang lagoon, China

Increasing extreme precipitation events (EPEs) can induce biogeochemical disturbances in the coastal lagoon ecosystems. Very little is known about the response of prokaryotic communities to such influences, which are the key components mediating the biogeochemical cycling in lagoons. Here 16S rRNA gene amplicon sequencing and high-through quantitative PCR (HT-qPCR) were employed to investigate the distribution of prokaryotic communities and fecal indicator genes in the surface waters of Yundang lagoon, Xiamen, China during EPEs, respectively. Prokaryotic communities from rainwaters, influents (IFs) and effluents (EFs) from a nearby wastewater treatment plant were also characterised. The results indicated a significant variation in the composition of lagoon prokaryotic communities compared with rainwaters, IFs and EFs. Multivariate and phylogenetic signal analyses revealed that environmental filtering, mainly controlled by salinity, was the major ecological process responsible for the temporal succession of lagoon prokaryotic communities during EPEs. Moreover, the pollution indicator taxa (based on amplicon sequencing) and fecal indicator genes (based on HT-qPCR) demonstrated that EPEs may induce sewage overflows and fecal pollution (mainly from humans and dogs), resulting in an increase in the relative abundance of pollution indicator taxa and genes in Yundang lagoon. Network analysis illustrated that the number of network edges and keystone species decreased along the sampling times, implying that EPEs-induced disturbances may affect prokaryotic species associations. Taken together, this study provides an enhanced understanding of the responses of lagoon prokaryotic communities to EPEs-induced disturbances.

Analysis of interdomain taxonomic patterns in urban street mats

Streets are constantly crossed by billions of vehicles and pedestrians. Their gutters, which convey stormwater and contribute to waste management, and are important for human health and well-being, probably play a number of ecological roles. Street surfaces may also represent an important part of city surface areas. To better characterize the ecology of this yet poorly explored compartment, we used filtration and DNA metabarcoding to address microbial community composition and assembly across the city of Paris, France. Diverse bacterial and eukaryotic taxonomic groups were identified, including members involved in key biogeochemical processes, along with a number of parasites and putative pathogens of human, animals and plants. We showed that the beta diversity patterns between bacterial and eukaryotic communities were correlated, suggesting interdomain associations. Beta diversity analyses revealed the significance of biotic factors (cohesion metrics) in shaping gutter microbial community assembly and, to a lesser extent, the contribution of abiotic factors (pH and conductivity). Co-occurrences analysis confirmed contrasting non-random patterns both within and between domains of life, specifically when comparing diatoms and fungi. Our results highlight microbial coexistence patterns in streets and reinforce the need to further explore biodiversity in urban ground transportation infrastructures.

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.

Tracking sources and transfer of contamination according to pollutants variety at the sediment-biota interface using a clam as bioindicator in peri-alpine lakes

Point pollution sources may differently impact lakes littoral, possibly leading to local ecological risks. The concomitant chemical analysis of littoral-benthic organisms and sediment can provide insights into the bioavailability and thus the ecological risk of contaminants. In this study, the autochthonous Corbicula fluminea was used to assess the sources and transfer of six trace metals (TMs) and fourteen Polycyclic Aromatic Hydrocarbons (PAHs) to the littoral-benthic biota of a large lake. The contaminant concentrations spatially varied with a value scale from 1 to 280 000 times along the lake littoral in both the sediment and clams. Multiple linear regressions were performed to explain the spatial variability of Corbicula fluminea contamination by considering both watershed and in-lake sources. The concentration of the sum of PAHs in clams was significantly correlated with sediment contamination, suggesting that PAHs contamination of the benthic biota mainly occur from the sediment. Most of the internal TM concentrations of clams were significantly correlated with stormwater drainage areas in the lake watershed, highlighting the importance of stormwater runoffs in the littoral biota contamination. The transfer of TMs and PAHs was assessed through the bioconcentration factor defined as the ratio of internal and sediment concentrations. As, Cd, Cu, Zn and light molecular weight PAHs were more bioconcentrated in C. fluminea than Pb, Sn and heavy molecular weight PAHs, suggesting differences in their bioavailability. This study underlines the relevance of using autochthonous organisms as bioindicators of lake littoral biota contamination concomitantly with sediment matrices, and illustrates the challenge of tracking pollution sources in lakes.

Distribution and co-occurrence of antibiotic and metal resistance genes in biofilms of an anthropogenically impacted stream

Urban stream biofilms are potential hotspots for resistomes and antibiotic resistance genes (ARGs). Biofilm communities that harbor resistance genes may be influenced by contaminant input (e.g., metals and antibiotics) from urban drainage (i.e., Wastewater Treatment Plant effluent and stormwater runoff); understanding the ecology of these communities and their resistome is needed. Given the potential importance of the co-occurrence of ARGs and metal resistance genes (MRGs), we investigated the spatial and temporal distribution of three ARGs (tetracycline [tetW] and sulfonamides [sulI and sulII]), four MRGs (lead [pbrT], copper [copA], and cadmium/cobalt/zinc [czcA and czcC]) via quantitative PCR and biofilm bacterial community composition via MiSeq 16S sequencing at four time points along an urbanization gradient (i.e., developed, agriculture, and forested sites) in a stream's watershed. Our results revealed that ARG and MRG abundances were significantly affected by land use-time interaction, with greater resistance abundances occurring in more urban locations during particular times of the year. It was also observed that changes in ARG and MRG profiles were influenced by differences in community composition among land use types, and that these differences were in response to changes in stream physicochemical parameters (pH, redox, temperature, nutrient availability, and metal concentration) that were driven by sub-watershed land use. Moreover, the dynamics between ARGs and MRGs within these communities correlated strongly and positively with one another. Taken altogether, our results demonstrate that changes in environmental properties due to human activity may drive the ARG-MRG profiles of biofilm communities by modulating community structure over time and space.

Effects of UV disinfection on phenotypes and genotypes of antibiotic-resistant bacteria in secondary effluent from a municipal wastewater treatment plant

To elucidate the effects of UV disinfection on antibiotic resistance in biologically-treated wastewater, we investigated the antibiotic resistance profiles, species of cultivable heterotrophic bacteria, and antibiotic-resistance genes (ARGs) in antibiotic-resistant bacteria before and after treatment. UV disinfection greatly changed the bacterial community structure and the antibiotic resistance in wastewater. The antibiotic resistance in wastewater samples was strongly associated with the bacterial community. The proportions of Gram-positive bacteria gradually increased with increasing UV fluence. The proportions of bacteria resistant to cephalexin, penicillin, and vancomycin all greatly decreased after UV treatment in both sampling events (July 2018 and January 2019), and those for bacteria resistant to ofloxacin, ciprofloxacin, and sulfadiazine increased, resulting from the alternative antibiotic resistance profiles among different genera. UV disinfection induced the selection of multi-antibiotic resistant (MAR) bacteria. For example, the MAR indices of Aeromonas, the dominant genus during the treatments, were significantly increased after UV irradiation (P < 0.05). The MAR index was also markedly increased (P < 0.05) at a fluence of 5 mJ/cm² in both events. In UV10 treatment, the bacterial community structure was greatly changed. The genera with relatively low MAR indices replaced that with high MAR indices, and became the dominant genera. As a result, the MAR indices of treated samples showed a decreased trend after 10 mJ/cm² UV irradiation. The detection frequencies of ARGs located on the chromosome varied mainly due to the evolution of the microbial community. The occurrence of ARGs (tetA, tetC, tetM, tetW, tetX, and sul1) located on plasmid DNA decreased after UV disinfection, and the average detection frequencies of tet and sul genes decreased by 15% and 6%, respectively (P < 0.05). Generally speaking, the effect of UV disinfection on the enrichment of antibiotic resistance is limited in this study, and horizontal gene transfer via the plasmids in surviving bacteria might be impaired due to the decreased abundance of ARGs on the plasmids.

Antibiotic resistance in urban runoff

Aquatic ecosystems subjected to anthropogenic pressures are places of rapid evolution of microbial communities and likely hotspots for selection and emergence of antibiotic resistant bacteria. In urban settings, water quality and the risk of infection are generally assessed in sewers and in effluents of wastewater treatment plants. Physical and chemical parameters as well as the presence of antibiotics, antibiotic-resistant bacteria and genes of resistance are driven by urban activities, with adverse effects on aquatic ecosystems. In this paper we review the environmental pressures exerted on bacterial communities in urban runoff waters and discuss the impact of these settings on antibiotic resistance. Considering the worrisome epidemiology of infectious diseases and estimated mortality due to antimicrobial resistance in the coming decades, there is an urgent need to identify all environmental reservoirs of resistant bacteria and resistance genes to complete our knowledge of the epidemiological cycle and of the dynamics of urban antibiotic resistance.

Biochar combined with polyvalent phage therapy to mitigate antibiotic resistance pathogenic bacteria vertical transfer risk in an undisturbed soil column system

The vertical migration of antibiotic resistance pathogenic bacteria (ARPB) and antibiotic resistance genes (ARGs) in the surface soil-vadose soil system has become a new threat to ecological safety and public health; there is an imperative need to develop an efficient technique for targeted control and inactivation of ARPB in these systems. In this work, undisturbed soil columns (0 ∼ -5 m) were constructed to investigate the impact of biochar amendment or/and polyvalent bacteriophage (ΦYSZ-KK) therapy on the vertical control and inactivation of tetracycline-resistant Escherichia coli K-12 and chloramphenicol-resistant Klebsiella pneumonia K-6. The simultaneous application of polyvalent phage and biochar impeded the vertical migration of ARPB from the top soil to lower soil layers and stimulated the ARPB dissipation in the soil column. After 60-day incubation, levels of ARPB and ARGs decreased significantly in the soil column by magnitudes of 2-6. Additionally, high throughput sequencing indicated that the simultaneous application of biochar and phage clearly maintained the structure and diversity of the soil microbial communities (p <  0.05). This work therefore demonstrates that the application of a biochar/phage combination is an environmentally friendly, efficacious measure for the control and inactivation of ARPB/ARGs in vertical soil column systems.

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

Heavy metals, pharmaceuticals, and other wastes released into the environment can significantly influence environmental antibiotic resistance. We investigated the occurrence of 22 antimicrobial resistance genes (ARGs) and 10 heavy metal concentrations, and the relationship between ARGs and heavy metals in surface sediment from seven sites of Lake Taihu. The results showed significant correlations (p < 0.05) between sediment ARG levels, especially for tetracycline and sulfonamides (e.g., tet(A), tet(D), tet(E), tet(O), sul1, sul2 and int-1) and specific heavy metals (Fe, Mn, Cr, Cu, Zn, among others) in the Lake. In the surface sediments, heavy metals showed an interaction with resistance genes, but the strength of interaction was diminished with increasing depth. For most of the heavy metals, the concentration of elements in the top sediments was higher than that in other depths. Tetracycline resistance genes (tet(A), tet(B), tet(D), tet(E) and tet(O), β-lactam resistance genes (SHV, TEM, CTX, OXA and OXY) and sulfonamide resistance genes (sulA, sul1, sul2, sul3 and int-1) were detected. They showed a trend which inferred a statistically significant increase followed by decreases in the relative abundance of these ARGs (normalized to 16S rRNA genes) with increasing depth. This study revealed that tet(A), tet(O), TEM, OXY, int-1, sul1 and sul3 were widespread in surface sediments with high abundance, indicating that these genes deserve more attention in future work.

Diversity of potential antibiotic-resistant bacterial pathogens and the effect of suspended particles on the spread of antibiotic resistance in urban recreational water

Evidence of the increasing incidence of antibiotic resistance in watersheds has attracted worldwide attention. Limited in formation is available on the occurrences of health-related antibiotic-resistant bacterial pathogens (ARBPs) in recreational waters. The effects of certain environmental factors (e.g., suspended particles) on the spread of resistance also has not been characterized to date. In this study, a combination of culture and molecular methods was employed to comprehensively investigate the patterns of microbial resistance to representative antibiotics in samples from three recreational lakes in Beijing. The antibiotic resistance index (ARI) based on the gradient concentration assay revealed that samples showed high resistance to penicillin-G, moderate resistance to ampicillin, vancomycin and erythromycin and low resistance to ceftriaxone, gentamycin, tetracycline and chloramphenicol. Antibiotic-resistant bacteria (ARB) were cultured and collected, and the diversity of potential ARBP species was further explored using next-generation sequencing (NGS). The results showed that most of the identified ARBPs were environmental opportunistic pathogens with emerging clinical concerns, e.g., the multidrug-resistant Acinetobacter junii. Furthermore, particle-attached (PA) fractions presented higher ARI values than free-floating (FL) fractions did, indicating that the PA fractions were more resistant to selected antibiotics. And the NGS results revealed that the PA fractions showed higher similarity in the screened ARB community compositions in comparison with the FL fractions, primarily due to a protective effect provided by the particles. Accordingly, ARBPs could persist for a longer time in protective particle matrices. However, quantification of antibiotic-resistant genes (ARGs) by qPCR showed no significant abundance differences between the two fractions. Overall, these findings suggest a potential health risk from the prevalence of ARBPs in recreational waters and provides a better understanding of the contribution of particles in the spread of antibiotic resistance in aquatic systems, with implications for the control of excessive suspended particles by water management.

Tracking the Sources of Antibiotic Resistance Genes in an Urban Stream during Wet Weather using Shotgun Metagenomic Analyses

Stormwater runoff has been known to cause increases in bacterial loadings in urban streams. However, little is known about its impacts on antibiotic resistance genes (ARGs) in urban watersheds. This study was performed to characterize the ARG composition of various environmental compartments of an urban watershed and to quantify their contributions of microbes and ARGs to an urban stream under wet weather conditions. Shotgun metagenomic results showed that the ARG abundance in wet weather flow was significantly higher than in base flow. Multidrug resistance genes were the most common ARG type across environmental samples. Vancomycin resistance genes were abundant in embankment soil and street sweeping samples. Analyses using SourceTracker estimated storm drain outfall water to be the biggest contributor of microbes (54-57%) and ARGs (82-88%) in the urban stream during wet weather flows. Furthermore, results on street sweepings showed that wash-off from streets was the biggest known contributor of microbes (41-45%) and ARGs (92-96%) in storm drain outfall water. Pantoea and Pseudomonas were associated with the highest numbers of ARGs and were most abundant in stormwater-related samples. Results from this study can advance our knowledge about ARGs in urban streams, an important medium linking environmental ARGs to the general public.

Effects of wind-wave disturbances on adsorption and desorption of tetracycline and sulfadimidine in water-sediment systems

Wind-wave disturbances frequently disperse sediment particles into overlying water, which facilitates the adsorption and desorption of contaminants in aquatic ecosystems. Tetracycline (TC) and sulfadimidine (SM2) are common antibiotics that are frequently found in aquatic environments. This study utilized microcosms, comprising sediment and water from Lake Taihu, China, to examine the adsorption and desorption of TC and SM2 under different wind-wave disturbances in a shallow lake environment. The adsorption experiments were conducted with three different concentrations (1, 5, 10 mg/L) of TC and SM2 in the overlying water, and two different (background and strong) wind-wave conditions for 72 h. Subsequently, four microcosms were employed in a 12-h desorption study. Analysis of adsorption progress showed that TC concentration in the overlying water decreased quickly, while SM2 remained almost constant. In the desorption experiments, SM2 released to the overlying water was an order of magnitude greater than TC. These results indicate that sediment particles strongly adsorb TC but weakly adsorb SM2. Compared to background conditions, the strong wind-wave conditions resulted in higher concentrations of TC and SM2 in sediment and facilitated their migration to deeper sediment during adsorption, correspondingly promoting greater release of TC and SM2 from sediment particles into the overlying water during desorption.

Taxon-Driven Functional Shifts Associated with Storm Flow in an Urban Stream Microbial Community

Urban streams are susceptible to stormwater and sewage inputs that can impact their ecological health and water quality. Microbial communities in streams play important functional roles, and their composition and metabolic potential can help assess ecological state and water quality. Although these environments are highly heterogenous, little is known about the influence of isolated perturbations, such as those resulting from rain events on urban stream microbiota. Here, we examined the microbial community composition and diversity in an urban stream during dry and wet weather conditions with both 16S rRNA gene sequencing across multiple years and shotgun metagenomics to more deeply analyze a single storm flow event. Metagenomics was used to assess population-level dynamics as well as shifts in the microbial community taxonomic profile and functional potential before and after a substantial rainfall. The results demonstrated general trends present in the stream under storm flow versus base flow conditions and also highlighted the influence of increased effluent flow following rain in shifting the stream microbial community from abundant freshwater taxa to those more associated with urban/anthropogenic settings. Shifts in the taxonomic composition were also linked to changes in functional gene content, particularly for transmembrane transport and organic substance biosynthesis. We also observed an increase in relative abundance of genes encoding degradation of organic pollutants and antibiotic resistance after rain. Overall, this study highlighted some differences in the microbial community of an urban stream under storm flow conditions and showed the impact of a storm flow event on the microbiome from an environmental and public health perspective.IMPORTANCE Urban streams in various parts of the world are facing increased anthropogenic pressure on their water quality, and storm flow events represent one such source of complex physical, chemical, and biological perturbations. Microorganisms are important components of these streams from both ecological and public health perspectives. Analysis of the effect of perturbations on the stream microbial community can help improve current knowledge on the impact such chronic disturbances can have on these water resources. This study examines microbial community dynamics during rain-induced storm flow conditions in an urban stream of the Chicago Area Waterway System. Additionally, using shotgun metagenomics we identified significant shifts in the microbial community composition and functional gene content following a high-rainfall event, with potential environment and public health implications. Previous work in this area has focused on specific genes/organisms or has not assessed immediate storm flow impact.

Antibiotics and antibiotic resistance genes in global lakes: A review and meta-analysis

Lakes are an important source of freshwater, containing nearly 90% of the liquid surface fresh water worldwide. Long retention times in lakes mean pollutants from discharges slowly circulate around the lakes and may lead to high ecological risk for ecosystem and human health. In recent decades, antibiotics and antibiotic resistance genes (ARGs) have been regarded as emerging pollutants. The occurrence and distribution of antibiotics and ARGs in global freshwater lakes are summarized to show the pollution level of antibiotics and ARGs and to identify some of the potential risks to ecosystem and human health. Fifty-seven antibiotics were reported at least once in the studied lakes. Our meta-analysis shows that sulfamethoxazole, sulfamerazine, sulfameter, tetracycline, oxytetracycline, erythromycin, and roxithromycin were found at high concentrations in both lake water and lake sediment. There is no significant difference in the concentration of sulfonamides in lake water from China and that from other countries worldwide; however, there was a significant difference in quinolones. Erythromycin had the lowest predicted hazardous concentration for 5% of the species (HC₅) and the highest ecological risk in lakes. There was no significant difference in the concentration of sulfonamide resistance genes (sul1 and sul2) in lake water and river water. There is surprisingly limited research on the role of aquatic biota in propagation of ARGs in freshwater lakes. As an environment that is susceptible to cumulative build-up of pollutants, lakes provide an important environment to study the fate of antibiotics and transport of ARGs with a broad range of niches including bacterial community, aquatic plants and animals.

Phytotoxicity of amoxicillin to the duckweed Spirodela polyrhiza: Growth, oxidative stress, biochemical traits and antibiotic degradation

The increasing availability of antibiotics in wastewater has created a serious threat to non-target organisms in the environment. The aim of this study was to evaluate the potential toxicity of amoxicillin on duckweed Spirodela polyrhiza during a short-term exposure (7 d). The duckweed was exposed to a range of environmentally relevant (0.0001-0.01 mg L^-1) and high (0.1 and 1 mg L^-1) concentrations of amoxicillin. Subsequently, biomarkers of toxicity such as growth, pigments (Chl a, Chl b and carotenoids), antioxidative enzyme activity (catalase, CAT; superoxide dismutase, SOD; and ascorbate peroxidases, APX), and biochemical content (protein, lipid and starch) were analysed in their fronds. The high dose (1 mg L^-1) of amoxicillin caused a significant (p < 0.05) decrease in photopigments, protein, starch and lipid content and an increase in carotenoids/total Chl and Chl a/Chl b ratios in fronds of Spirodela polyrhiza. The results showed a shift in biomarkers: a decrease in frond growth and relative growth rate (RGR) (16.2-53.8%) and an increase in the activities (mmol mg protein^-1) of CAT (0.021-0.041), APX (0.84-2.49) and SOD (0.12-0.23) in fronds. The significantly (p < 0.05) greater reduction in amoxicillin content in duckweed setups (84.6-100%) than in the control (62.1-73%) suggested that phytodegradation is an important mechanism in removing antibiotics from water, apart from hydrolysis and photodegradation, which occur in control setups. Overall, the results suggested a toxic effect of amoxicillin on Spirodela polyrhiza, even at low concentrations, and nonetheless, the duckweed contributed directly to the degradation of antibiotics in the water and throughout the phytoremediation process.

Benzyldimethyldodecyl ammonium chloride shifts the proliferation of functional genes and microbial community in natural water from eutrophic lake

Benzylalkyldimethylethyl ammonium compounds are pervasive in natural environments and toxic at high concentrations. The changes in functional genes and microbial diversity in eutrophic lake samples exposed to benzyldimethyldodecyl ammonium chloride (BAC) were assessed. BAC exerted negative effects on bacteria abundance, particularly at concentrations of 100 μg L^-1 and higher. A significant increase in the number of the quaternary ammonium compound-resistant gene qacA/B was recorded within the 10 μg L^-1 treatment after the first day of exposure. Not all antibiotic resistance genes increased in abundance as the concentrations of BAC increased; rather, gene abundances were dependent on the gene type, concentrations of BAC, and contact time. The nitrogen fixation-related gene nifH and ammonia monooxygenase gene amoA were inhibited by high concentrations of BAC after the first day, whereas an increase of the nitrite reductase gene nirK was stimulated by exposure. Microbial communities within higher treatment levels (1000 and 10 000 μg L^-1) exhibited significantly different community composition compared to other treatment levels and the control. Selective enrichment of Rheinheimera, Pseudomonas, and Vogesella were found in the higher treatment levels, suggesting that these bacteria have some resistance or degradation capacity to BAC. Genes related with RNA processing and modification, transcription, lipid transport and metabolism, amino acid transport and metabolism, and cell motility of microbial community function were involved in the process exposed to the BAC stress.

Application of membrane bioreactor for sulfamethazine-contained wastewater treatment

The presence of antibiotics in wastewater has been widely confirmed. Membrane bioreactor (MBR), as an efficient wastewater treatment technology, has attracted increasing interest in its ability to remove antibiotics in recent years. However, its long-term operation stability and the underlying mechanisms for antibiotics removal are still poorly understood. In this study, a hollow fiber MBR was used to treat low concentration sulfamethazine (SMZ) contained wastewater. The long-term effects of various SMZ concentrations on nutrients removal, SMZ degradation, and sludge characteristics were investigated. During the 244 days operation, the overall SMZ removal efficiency could reach 95.4 ± 4.5% under various SMZ concentrations and hydraulic retention times. The reactor exhibited high chemical oxygen demand and NH₄⁺-N removal efficiencies, which reached 93.0% and 96.2%, respectively. A sludge concentration of 4.1 ± 0.3 g/L was maintained in the system without excess sludge discharge. The dosage of SMZ had obvious effect on sludge characteristics. The contents of extracellular polymeric substances (EPS) in MBR decreased after a long-term operation of the reactor under SMZ pressure. The low sludge concentration and the reduced EPS content were also beneficial for mitigating membrane fouling. Thus, this study provides a low-cost, efficient and simple approach to treat SMZ-contained wastewater.

Stormwater loadings of antibiotic resistance genes in an urban stream

Antibiotic resistance presents a critical public health challenge and the transmission of antibiotic resistance via environmental pathways continues to gain attention. Factors driving the spread of antibiotic resistance genes (ARGs) in surface water and sources of ARGs in urban stormwater have not been well-characterized. In this study, five ARGs (sul1, sul2, tet(O), tet(W), and erm(F)) were quantified throughout the duration of three storm runoff events in an urban inland stream. Storm loads of all five ARGs were significantly greater than during equivalent background periods. Neither fecal indicator bacteria measured (E. coli or enterococci) was significantly correlated with sul1, sul2, or erm(F), regardless of whether ARG concentration was absolute or normalized to 16S rRNA levels. Both E. coli and enterococci were correlated with the tetracycline resistance genes, tet(O) and tet(W). Next-generation shotgun metagenomic sequencing was conducted to more thoroughly characterize the resistome (i.e., full complement of ARGs) and profile the occurrence of all ARGs described in current databases in storm runoff in order to inform future watershed monitoring and management. Between 37 and 121 different ARGs were detected in each stream sample, though the ARG profiles differed among storms. This study establishes that storm-driven transport of ARGs comprises a considerable fraction of overall downstream loadings and broadly characterizes the urban stormwater resistome to identify potential marker ARGs indicative of impact.

Environmental analysis of typical antibiotic-resistant bacteria and ARGs in farmland soil chronically fertilized with chicken manure

Antibiotics and the corresponding resistant bacteria and resistance genes (ARGs) are generally considered emerging pollutants. To assess the impacts of tetracycline (TC) and sulfonamide (SA) antibiotics that are eliminated with fecaluria as drug prototypes, farmland soil used to research long-term fertilization with chicken manure was collected at four sites in Shandong Province. In this study, the rates of bacterial drug resistance to the same antibiotic decreased with an increase in the concentration of that antibiotic, and the resistance rates to TCs were lower than those to SAs. PCR of ARGs revealed that the ARGs detected at the highest frequency were the TC resistance genes tetW and tetO and the SA resistance genes sul1 and sul2. Real-time qPCR showed that the quantities of ARGs in farmland soil fertilized with chicken manure were significantly greater compared with the control soil. Moreover, significant correlations (R²=0.9525, p<0.05) between the number of sul ARGs and the total SA concentration were observed in all of the soil samples. In summary, this study showed that SAs can induce the appearance of ARGs and pollute the soil environment.

Rainfall increases the abundance of antibiotic resistance genes within a riverine microbial community

Infections with antibiotic resistant bacteria are among the major threats for human health. Studies elucidating the role of the environment in their spread are still in their infancy, it, however, seems that different environments might function as a long-term reservoir of antibiotic resistance genes (ARGs) that reside within their microbial communities. An increasing number of studies target the presence and the persistence of ARGs in waters and soils that are exposed to human activities; they, however, rarely consider the spatial/temporal variability that predominate in these environments. Here we evaluated the effect of a moderate rain event (4 mm rain h^-1) on the abundance and distribution of ARGs (tetA, ermB, bla_CTXM, sulII, and qnrS), by comparing measurements of gene abundances during the rainfall to the yearly average, in the waters of a large subalpine river. ARG abundances, which all increased during the rain event, were then correlated to several microbiological, physical and chemical variables, in order to establish their potential origin. Increments in ARG abundances during rainfall (total ARGs: 24 fold) was concomitant to an increase in total phosphorous, N-NH₄, and microbial aggregates. Our results show a strong influence of a moderate rainfall on the abundances of ARGs, and suggest the catchment as their source. The impact of moderate rainfalls in areas exposed to anthropic activities should then be considered in modelling and management of ARG dynamics.

Degradation of streptomycin in aquatic environment: kinetics, pathway, and antibacterial activity analysis

Streptomycin used in human and veterinary medicine is released into the environment mainly through excretions. As such, its elimination in water should be investigated to control pollution. In this study, the degradation of streptomycin in water was studied, and the influence of variables, including light exposure, solution pH, temperature, ionic strength, dissolved organic matter (DOM), and coexisting surfactants, on degradation was investigated. Streptomycin degradation was consistent with the first-order model in aquatic environments. Its degradation rate under light exposure was 2.6-fold faster than that in the dark. Streptomycin was stable under neutral conditions, but it was easily decomposed in acidic and basic environments. Streptomycin degradation was enhanced by high temperature, and its half-life decreased from 103.4 days at 15 °C to 30.9 days at 40 °C. This process was also accelerated by the presence of Ca²⁺ and slightly improved by the addition of HA. Streptomycin degradation was suppressed by high levels of the cationic surfactant cetyltri- methylammonium bromide (CTAB), but was promoted by the anionic surfactant sodium dodecyl benzene sulfonate (SDBS). The main degradation intermediates/products were identified through liquid chromatography-mass spectrometry, and the possible degradation pathway was proposed. The antibacterial activity of streptomycin solution was also determined during degradation. Results showed that STR degradation generated intermediates/products with weaker antibacterial activity than the parent compound.

Content of biogenic amines in Lemna minor (common duckweed) growing in medium contaminated with tetracycline

Aquatic plants are continuously exposed to a variety of stress factors. No data on the impact of antibiotics on the biogenic amines in duckweed (Lemna minor) have been available so far, and such data could be significant, considering the ecological role of this plant in animal food chains. In the tissues of control (non-stressed) nine-day-old duckweed, the following biogenic amines were identified: tyramine, putrescine, cadaverine, spermidine and spermine. Based on the tetracycline contents and the computed EC values, the predicted toxicity units have been calculated. The obtained results demonstrated phytoxicity caused by tetracycline in relation to duckweed growth rate, yield and the contents of chlorophylls a and b. The carotenoid content was not modified by tetracycline. It was found that tetracycline as a water pollutant was a stress factor triggering an increase in the synthesis of amines. Tetracycline at 19, 39 and 78μM concentrations increased biogenic amine synthesis by 3.5 times. Although the content of tyramine increased fourteen times with the highest concentration of the drug (and of spermidine - only three-fold) the increase of spermidine was numerically the highest. Among the biogenic amines the most responsive to tetracycline were spermine and tyramine, while the least affected were putrescine and spermidine. Despite putrescine and spermidine being the least sensitive, their sum of contents increased five-fold compared to the control. These studies suggest that tetracycline in water reservoirs is taken up by L. minor as the antibiotic clearly modifies the metabolism of this plant and it may likely pose a risk.