Impacts of chlorine disinfection of municipal sewage effluent on receiving rivers: Changes in organic matter and microbial communities

Effluents from wastewater treatment plants (WWTPs) can impact various aspects of receiving aquatic ecosystems, yet the specific effects of chlorine disinfection of effluents on these ecosystems remain poorly understood. In this study, a simulated flow-through channel system was employed to evaluate the changes in water quality and microbial community in receiving rivers resulting from the discharge of WWTP effluent, with or without chlorination. Results showed that dissolved organic matter (DOM) in secondary effluent from WWTPs exhibited higher fluorescence intensity and elevated levels of biopolymers, humic acids, and low molecular weight compounds compared to river water. Microbial analysis revealed that the input of secondary effluent promoted the proliferation of diverse microbial communities in periphyton of the receiving water, while the chlorinated effluents selectively inhibited chlorine-sensitive taxa in periphyton and favored chlorine-tolerant ones. Chlorine disinfection effectively reduced most pathogens in effluents; however, certain genera, such as Neisseriaceae and Escherichia-Shigella, persisted. Moreover, exposure to chlorinated effluent significantly elevated the relative abundance of Pseudomonas in periphyton compared to other conditions, raising concerns about the persistence of chlorine-tolerant pathogens in aquatic environments. These findings highlight the critical need to further evaluate the impact of the disinfection process in WWTPs on the long-term health and stability of riverine ecosystems.

Microbiota Dysbiosis in Mytilus chilensis Is Induced by Hypoxia, Leading to Molecular and Functional Consequences

Bivalve microbiota play a vital role in host health, supporting nutrient processing, immunity, and disease resistance. However, the increasing hypoxia in Chilean coastal waters, caused by climate change and eutrophication, threatens to disrupt this microbial balance, potentially promoting pathogens and impairing essential functions. Mytilus chilensis is vulnerable to hypoxia-reoxygenation cycles, yet the effects on its microbiota remain poorly understood. This study investigates the impact of hypoxia on the structure and functional potential of the microbial communities residing in the gills and digestive glands of M. chilensis. Employing full-length 16S rRNA gene sequencing, we explored hypoxia's effects on microbial diversity and functional capacity. Our results revealed significant alterations in the microbial composition, with a shift towards facultative anaerobes thriving in low oxygen environments. Notably, there was a decrease in dominant bacterial taxa such as Rhodobacterales, while opportunistic pathogens such as Vibrio and Aeromonas exhibited increased abundance. Functional analysis indicated a decline in critical microbial functions associated with nutrient metabolism and immune support, potentially jeopardizing the health and survival of the host. This study sheds light on the intricate interactions between host-associated microbiota and environmental stressors, underlining the importance of managing the microbiota in the face of climate change and aquaculture practices.

Holistic assessment of chemical and biological pollutants in a Mediterranean wastewater effluent-dominated stream: Interactions and ecological impacts

The discharge of treated wastewater from wastewater treatment plants (WWTPs) into river systems is a significant source of pollution, introducing a range of chemical and biological pollutants that impact the chemical and ecological quality status of rivers. This study evaluates the effect of a secondary treated wastewater effluent on the Onyar River, in the northeast of Spain. Water and biofilm samples were collected at one upstream and four downstream sampling points (up to 2.8 km from the discharge point) across four seasons. A wide array of pollutants, including metals, pharmaceuticals, microplastics (MPs), per- and polyfluoroalkyl substances (PFAS), antibiotic resistance genes (ARGs), among other emerging pollutants, were detected downstream, with significant differences between upstream and downstream concentrations. Our results show that WWTP discharge also altered biofilm microbiome composition and ARGs presence, being these changes distinguishable from seasonal variations. Nevertheless, a partial recovery further downstream (525 m) was observed for biofilm microbiome and ARGs composition. These findings highlight the value of microbiome analysis in assessing wastewater impacts on river ecosystems and emphasize the need for further research to improve pollutant attenuation and biofilm recovery strategies in river streams.

Biofilms as potential reservoirs of antimicrobial resistance in vulnerable settings

Antimicrobial resistance is a major global health threat, characterized by the ability of microorganisms to withstand the effects of antimicrobial agents. Biofilms, as unique microbial communities, significantly contribute to this threat. They provide a protective environment for pathogens, facilitate horizontal gene transfer, and create an ideal setting for the persistence and evolution of resistant bacteria. This issue can be particularly important in low-income settings and vulnerable communities, such as formal and informal refugee and migrant camps. These settings usually have limited access to healthcare resources and appropriate treatments, contributing to the selective pressure that promotes the survival and proliferation of resistant bacteria. Thus, biofilms formed in wastewater in these areas can play a critical role in spreading antimicrobial resistance or acting as hidden reservoirs for future outbreaks. While emerging efforts focus on detecting antibiotic resistance genes and planktonic bacteria in wastewater, biofilms may be a source of under-appreciated antimicrobial resistance, creating a significant gap in our understanding of resistance dynamics in wastewater systems. Incorporating biofilm surveillance into wastewater monitoring strategies in vulnerable settings can help develop a more comprehensive understanding of resistance transmission and more effective intervention measures in these settings.

Defective boron nitride aerogels by salt template synthesis: A green adsorbent for tetracycline removal

Hexagonal boron nitride (h-BN) exhibits unique application potential in water purification due to its large specific surface area, high porosity, and chemical inertness. Designing adsorbents with highly active adsorption sites is one effective method to improve their adsorption capacities. In this study, porous h-BN aerogels containing multiple defect types (DP-BN) were synthesized by using salt templates. The experimental results showed that DP-BN had an extremely low density. With outstanding adsorption capacity for tetracycline (TC), its maximum adsorption capacity was 1620.37 mg/g, which was 2.6 times higher than that reported in the known literature (623.018 mg/g). DP-BN adsorbed TC quickly, and its rate was influenced by liquid film diffusion, pore diffusion, and diffusion to the active adsorption site. The adsorption process was dominated by chemisorption and could take place spontaneously. The adsorption of TC by DP-BN was exothermic. As the environmental temperature increased, the adsorption capacity of DP-BN increased significantly. DP-BN exhibited excellent reusability. After five cycles, the adsorption removal rate remained up to 99.93%. Overall, the high adsorption capacity of DP-BN for TC was attributed to its abundant active adsorption sites, Π-Π interactions, and intermolecular interactions. This study provided a new idea to modulate the microstructure and improve the adsorption performance of h-BN, hoping to accelerate the application of h-BN in wastewater treatment.

Green solutions for treating groundwater polluted with nitrates, pesticides, antibiotics, and antibiotic resistance genes for drinking water production

The present study evaluates for the first time the seasonal performance of an innovative green groundwater treatment. The pilot plant combines microalgae-bacteria treatment and a cork-wood biofilter to reduce nitrates, pesticides, antibiotics (ABs), and antibiotic resistance genes (ARGs) from groundwater. Groundwater had nitrate concentrations ranging from 220 to 410 mg/L, while ABs (sulfonamides and fluoroquinolones) and pesticides (triazines) were detected at concentrations ranging from a few ng/L to 150 ng/L. Only the gene targets sul1, tetM and the class 1 integron-integrase gene (intl1) were detected in the groundwater. The microalgae-biofilter treatment system effectively removed 15%-98% of nitrates, depending on the season, and consistently eliminated over 90% of ABs and pesticides year-round. Among the components of the treatment system, the microalgal system was the most effective at removing ABs and pesticides. However, the cork-wood biofilter showed superior performance in reducing the bacterial load in groundwater, achieving more than a 1-log reduction in the absolute abundance of genes such as sul1 and intl1. The accumulation of ABs and pesticides in microalgae biomass was minimal or undetectable (<20 ng/g of fresh weight). Overall, our results indicate that the microalgae-biofilter treatment plant is an effective solution for significantly reducing nitrates, antibiotics, and pesticides from groundwaters, while also producing a valuable biomass, and meeting drinking water standards during warmer months.

Nature-based bioreactors: Tackling antibiotic resistance in urban wastewater treatment

The overuse and misuse of antibiotics have accelerated the selection of antibiotic-resistant bacteria, significantly impacting human, animal, and environmental health. As aquatic environments are vulnerable to antibiotic resistance, suitable management practices should be adopted to tackle this phenomenon. Here we show an effective, nature-based solution for reducing antibiotic resistance from actual wastewater. We utilize a bioreactor that relies on benthic (biofilms) and planktonic microbial communities to treat secondary effluent from a small urban wastewater treatment plant (<10,000 population equivalent). This treated effluent is eventually released into the local aquatic ecosystem. We observe high removal efficiency for genes that provide resistance to commonly used antibiotic families, as well as for mobile genetic elements that could potentially aid in their spread. Importantly, we notice a buildup of sulfonamide (sul1 and sul2) and tetracycline (tet(C), tet(G), and tetR) resistance genes specifically in biofilms. This advancement marks the initial step in considering this bioreactor as a nature-based, cost-effective tertiary treatment option for small UWWTPs facing antibiotic resistance challenges.

Nature-based solutions for antibiotics and antimicrobial resistance removal in tertiary wastewater treatment: Microbiological composition and risk assessment

This field-scale study evaluates the seasonal effectiveness of employing nature-based solutions (NBSs), particularly surface flow and horizontal subsurface flow constructed wetland configurations, as tertiary treatment technologies for the removal of antibiotics (ABs) and antibiotic resistance genes (ARGs) compared to a conventional treatment involving UV and chlorination. Out of the 21 monitored ABs, 13 were detected in the influent of three tertiary wastewater treatments, with concentrations ranging from 2 to 1218 ng·L-1. The ARGs sul1 and dfrA1 exhibited concentrations ranging from 1 × 105 to 9 × 106 copies/100 mL. NBSs were better at reducing ABs (average 69 to 88 %) and ARGs (2-3 log units) compared to the conventional tertiary system (average 36 to 39 % and no removal to 2 log units) in both seasons. Taxonomic compositions in influent water samples shifted from wastewater-impacted communities (Actinomycetota and Firmicutes) to a combination of plant rhizosphere-associated and river communities in NBS effluents (Alphaproteobacteria). In contrast, the conventional technology showed no substantial differences in community composition. Moreover, NBSs substantially reduced the ecotoxicological risk assessment (cumulative RQs). Furthermore, NBSs reduced the ecotoxicological risk (cumulative RQs) by an average of over 70 % across seasons, whereas the benchmark technology only achieved a 6 % reduction. In conclusion, NBSs present a robust alternative for minimizing the discharge of ABs and ARGs into surface water bodies.

Accumulation of polyethylene microplastics in river biofilms and effect on the uptake, biotransformation and toxicity of the antimicrobial triclosan

The interaction of multiple stressors in freshwater ecosystems may lead to adverse effects on aquatic communities and their ecological functions. Microplastics (MPs) are a class of contaminants of emerging concern that can exert both direct and indirect ecotoxicological effects. A growing number of studies have investigated MPs-attached microbial communities, but the interaction between MPs and substrate-associated biofilm (i.e., on natural river substrates, such as stones and sediments) remains poorly studied. In this work, the combined effects of polyethylene MPs (PE-MPs) with a particle size of 10-45 μm (2 mg/L) and the antimicrobial triclosan (TCS) (20 μg/L) were investigated on river biofilms through a short-term exposure experiment (72 h). To the best of authors' knowledge, this is the first time that the combined effects of MPs and chemical contaminants in substrate-associated river biofilms were assessed. Different response parameters were evaluated, including (i) exposure assessment and ii) contaminants effects at different levels: bacterial community composition, antibiotic resistance, extracellular polymeric substances (EPS), photosynthetic efficiency (Yeff), and leucine aminopeptidase activity (LAPA). Triclosan was accumulated in river biofilms (1189-1513 ng/g dw) alongside its biotransformation product methyl-triclosan (20-29 ng/g dw). Also, PE-MPs were detected on biofilms (168-292 MP/cm2), but they had no significant influence on the bioaccumulation and biotransformation of TCS. A moderate shift in bacterial community composition was driven by TCS, regardless of PE-MPs co-exposure (e.g., increased relative abundance of Sphingomonadaceae family). Additionally, Yeff and EPS content were significantly disrupted in TCS-exposed biofilms. Therefore, the most remarkable effects on river biofilms were related to the antimicrobial TCS, whereas single PE-MPs exposure did not alter any of the evaluated parameters. These results demonstrate that biofilms might act as environmental sink of MPs. Although no interaction between PE-MPs and TCS was observed, the possible indirect impact of other MPs-adsorbed contaminants on biofilms should be further assessed.

Differential effects of wastewater treatment plant effluents on the antibiotic resistomes of diverse river habitats

Wastewater treatment plants (WWTPs) are key sources of antimicrobial resistance genes (ARGs) that could influence the resistomes of microbial communities in various habitats of the receiving river ecosystem. However, it is currently unknown which habitats are most impacted and whether ARGs, like certain chemical contaminants, could be accumulated or enriched in the river ecosystem. We conducted a systematic metagenomic survey on the antibiotic resistomes of WWTP effluent, four riverine habitats (water, suspended particles, sediment, epilithic biofilm), and freshwater amphipod gut microbiomes. The impact of WWTP effluent on the downstream habitats was assessed in nine Swiss rivers. While there were significant differences in resistomes across habitats, the wastewater resistome was more similar to the resistome of receiving river water than to the resistomes of other habitats, and river water was the habitat most strongly impacted by the WWTPs effluent. The sulfonamide, beta-lactam, and aminoglycoside resistance genes were among the most abundant ARGs in the WWTP effluents, and especially aadA, sul1, and class A beta-lactamase genes showed significantly increased abundance in the river water of downstream compared to upstream locations (p < 0.05). However, this was not the case for the sediment, biofilm, and amphipod gut habitats. Accordingly, evidence for accumulation or enrichment of ARGs through the riverine food web was not identified. Our study suggests that monitoring riverine antimicrobial resistance determinants could be conducted using "co-occurrence" of aadA, sul1, and class A beta-lactamase genes as an indicator of wastewater-related pollution and should focus on the water as the most affected habitat.

Occurrence and risk assessment of pharmaceuticals in hospital wastewater in Costa Rica

This work aims to determine the occurrence, hazard and prioritization of pharmaceuticals from hospital wastewater in Costa Rica through the monitoring of 70 compounds and assessing their environmental risk through a hazard quotient approach (HQ). Moreover, the quantification of selected antibiotic resistance genes (ARGs) was conducted for the first time in this matrix in this geographical location. Thirty-four pharmaceuticals were detected, being caffeine, 1,7-dimethylxanthine, acetaminophen, ibuprofen, naproxen, ciprofloxacin and ketoprofen the most frequent (>50% of the samples). Eighteen pharmaceuticals exhibited high hazard (HQ ≥ 1), while five more showed medium hazard (1 > HQ ≥ 0.1). Prioritization, which also included frequency parameters, revealed caffeine, lovastatin, diphenhydramine, acetaminophen, ibuprofen, ciprofloxacin, and sildenafil as the compounds of major concern. Similarly, cumulative hazard per sample (ΣHQ) estimated high hazard towards aquatic organisms in every sample. All selected ARGs, except mcr-1 (polymyxin resistance), were detected. Among genes conferring resistance to beta-lactams, blaCTX-M and blaKPC were the most abundant, related to resistance to cephalosporins and carbapenems. Ecotoxicological evaluation showed mostly low toxicity towards Daphnia magna and Vibrio fischeri, contrary to the marked effect observed towards Lactuca sativa. These findings provide relevant and novel information on the risk posed by hospital wastewater and their pharmaceutical content in the Latin American environmental context.

Wastewater treatment plants, an "escape gate" for ESCAPE pathogens

Antibiotics are an essential tool of modern medicine, contributing to significantly decreasing mortality and morbidity rates from infectious diseases. However, persistent misuse of these drugs has accelerated the evolution of antibiotic resistance, negatively impacting clinical practice. The environment contributes to both the evolution and transmission of resistance. From all anthropically polluted aquatic environments, wastewater treatment plants (WWTPs) are probably the main reservoirs of resistant pathogens. They should be regarded as critical control points for preventing or reducing the release of antibiotics, antibiotic-resistant bacteria (ARB), and antibiotic-resistance genes (ARGs) into the natural environment. This review focuses on the fate of the pathogens Enterococcus faecium, Staphylococcus aureus, Clostridium difficile, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacteriaceae spp. (ESCAPE) in WWTPs. All ESCAPE pathogen species, including high-risk clones and resistance determinants to last-resort antibiotics such as carbapenems, colistin, and multi-drug resistance platforms, were detected in wastewater. The whole genome sequencing studies demonstrate the clonal relationships and dissemination of Gram-negative ESCAPE species into the wastewater via hospital effluents and the enrichment of virulence and resistance determinants of S. aureus and enterococci in WWTPs. Therefore, the efficiency of different wastewater treatment processes regarding the removal of clinically relevant ARB species and ARGs, as well as the influence of water quality factors on their performance, should be explored and monitored, along with the development of more effective treatments and appropriate indicators (ESCAPE bacteria and/or ARGs). This knowledge will allow the development of quality standards for point sources and effluents to consolidate the WWTP barrier role against the environmental and public health AR threats.

Life in an unsuspected antibiotics world: River biofilms

Waterborne bacteria that naturally live in biofilms are continuously exposed to pharmaceutical residues, regularly released into the freshwater environment. At the source level, the discharge of antibiotics into rivers has already been repeatedly linked to the development of antimicrobial resistance. But what about biofilms away from the discharge point? Two rivers, with sites subject to dispersed contamination of medium intensity, were studied as typical representatives of high- and middle-income countries. The biofilms developed on rocks indigenous to rivers are perfectly representative of environmental exposure. Our results show that away from the hotspots, the amount of antibiotics in the biofilms studied favours the maintenance and enrichment of existing resistant strains as well as the selection of new resistant mutants, and these favourable conditions remain over a period of time. Thus, in this type of river, the environmental risk of selection pressure is not only present downstream of urbanized areas but is also possible upstream and far downstream of wastewater treatment plant discharges. Despite this, correlation analysis found no strong positive correlation between antibiotic concentrations and the abundance of measured integrons and their corresponding resistance genes. Nevertheless, this work highlights the need to consider the risks of antibiotics beyond hotspots as well.

Residual enrofloxacin in cattle manure increased persistence and dissemination risk of antibiotic resistance genes during anaerobic digestion

Anaerobic digestion is a common approach to dispose and recycle livestock manures, and the agricultural application of anaerobic digestives represents an important pathway of spreading antibiotic resistance genes (ARGs) from livestock manures to soils. Enrofloxacin is a clinically important fluoroquinolone antibiotic with high residual concentrations in livestock manure, and propagation of fluoroquinolone resistance genes poses a huge risk to public health. Compared with other antibiotics, enrofloxacin is relatively durable in anaerobic digestion system. However, its effect on the persistence of ARGs during anaerobic digestion and its mechanism are not clear. In this study, we investigated effects of 0, 4, and 8 mg/L enrofloxacin on the abundance, persistence, and transferring risk of five plasmid-mediated fluroquinolone ARGs and five typic clinically important non-fluoroquinolone ARGs during cattle manure digestion. The responses of integrons and microbial communities to enrofloxacin were assessed to uncover the underlying mechanisms. All the ten detected ARGs were highly persistent in anaerobic digestion, among them seven ARGs increased over 8.2 times after digestion. Network analysis revealed that the potential hosts of ARGs were critical functional taxa during anaerobic digestion, which can explain the high persistence of ARGs. Residual enrofloxacin significantly increased the abundance of aac(6')-ib-cr, sul1, intI1, and intI2 throughout the digestion, but had no impact on the other ARGs, demonstrating its role in facilitating horizontal gene transfer of the plasmid-mediated aac(6')-ib-cr. The influence of enrofloxacin on microbial communities disappeared at the end of digestion, but the ARG profiles remained distinctive between the enrofloxacin treatments and the control, suggesting the high persistence of enrofloxacin induced ARGs. Our results suggested the high persistence of ARGs in anaerobic digestion system, and highlighted the role of residual enrofloxacin in livestock manure in increasing dissemination risk of fluroquinolone resistance genes.

Aquatic Environments as Hotspots of Transferable Low-Level Quinolone Resistance and Their Potential Contribution to High-Level Quinolone Resistance

The disposal of antibiotics in the aquatic environment favors the selection of bacteria exhibiting antibiotic resistance mechanisms. Quinolones are bactericidal antimicrobials extensively used in both human and animal medicine. Some of the quinolone-resistance mechanisms are encoded by different bacterial genes, whereas others are the result of mutations in the enzymes on which those antibiotics act. The worldwide occurrence of quinolone resistance genes in aquatic environments has been widely reported, particularly in areas impacted by urban discharges. The most commonly reported quinolone resistance gene, qnr, encodes for the Qnr proteins that protect DNA gyrase and topoisomerase IV from quinolone activity. It is important to note that low-level resistance usually constitutes the first step in the development of high-level resistance, because bacteria carrying these genes have an adaptive advantage compared to the highly susceptible bacterial population in environments with low concentrations of this antimicrobial group. In addition, these genes can act additively with chromosomal mutations in the sequences of the target proteins of quinolones leading to high-level quinolone resistance. The occurrence of qnr genes in aquatic environments is most probably caused by the release of bacteria carrying these genes through anthropogenic pollution and maintained by the selective activity of antimicrobial residues discharged into these environments. This increase in the levels of quinolone resistance has consequences both in clinical settings and the wider aquatic environment, where there is an increased exposure risk to the general population, representing a significant threat to the efficacy of quinolone-based human and animal therapies. In this review the potential role of aquatic environments as reservoirs of the qnr genes, their activity in reducing the susceptibility to various quinolones, and the possible ways these genes contribute to the acquisition and spread of high-level resistance to quinolones will be discussed.

Abundance and diversity of antibiotic resistance genes and bacterial communities in the western Pacific and Southern Oceans

This study investigated the abundance and diversity of antibiotic resistance genes (ARGs) and the composition of bacterial communities along a transect covering the western Pacific Ocean (36°N) to the Southern Ocean (74°S) using the Korean icebreaker R/V Araon (total cruise distance: 14,942 km). The relative abundances of ARGs and bacteria were assessed with quantitative PCR and next generation sequencing, respectively. The absolute abundance of ARGs was 3.0 × 10⁶ ± 1.6 × 10⁶ copies/mL in the western Pacific Ocean, with the highest value (7.8 × 10⁶ copies/mL) recorded at a station in the Tasman Sea (37°S). The absolute abundance of ARGs in the Southern Ocean was 1.8-fold lower than that in the western Pacific Ocean, and slightly increased (0.7-fold) toward Terra Nova Bay in Antarctica, possibly resulting from natural terrestrial sources or human activity. β-Lactam and tetracycline resistance genes were dominant in all samples (88-99%), indicating that they are likely the key ARGs in the ocean. Correlation and network analysis showed that Bdellovibrionota, Bacteroidetes, Cyanobacteria, Margulisbacteria, and Proteobacteria were positively correlated with ARGs, suggesting that these bacteria are the most likely ARG carriers. This study highlights the latitudinal profile of ARG distribution in the open ocean system and provides insights that will help in monitoring emerging pollutants on a global scale.

Occurrence and distribution of Carbapenem-resistant Enterobacterales and carbapenemase genes along a highly polluted hydrographic basin

We determined the distribution and temporal variation of Carbapenem Resistant Enterobacterales (CRE), carbapenemase-encoding genes and other antibiotic resistance genes (ARGs) in a highly polluted river (Lis River; Portugal), also assessing the potential influence of water quality to this distribution. Water samples were collected in two sampling campaigns performed one year apart (2018/2019) from fifteen sites and water quality was analyzed. CRE were isolated and characterized. The abundance of four ARGs (bla_NDM, bla_KPC, tetA, bla_CTX-M), two Microbial Source Tracking (MST) indicators (HF183 and Pig-2-Bac) and the class 1 integrase gene (IntI1) was measured by qPCR. RESULTS: confirmed the poor quality of the Lis River water, particularly in sites near pig farms. A collection of 23 CRE was obtained: Klebsiella (n = 19), Enterobacter (n = 2) and Raoultella (n = 2). PFGE analysis revealed a clonal relationship between isolates obtained in different sampling years and sites. All CRE isolates exhibited multidrug resistance profiles. Klebsiella and Raoultella isolates carried bla_KPC while Enterobacter harbored bla_NDM. Conjugation experiments were successful for only four Klebsiella isolates. All ARGs were detected by qPCR on both sampling campaigns. An increase in ARGs and IntI1 abundances was detected in sites located downstream of wastewater treatment plants. Strong correlations were observed between bla_CTX-M, IntI1 and the human-pollution marker HF183, and also between tetA and the pig-pollution marker Pig-2-bac, suggesting that both human- and animal-derived pollution in the Lis River are a potential source of ARGs. Plus, water quality parameters related to eutrophication and land use were significantly correlated with ARGs abundances. Our findings demonstrated that the Lis River encloses high levels of antibiotic resistant bacteria and ARGs, including CRE and carbapenemase-encoding genes. Overall, this study provides a better understanding on the impacts of water pollution resulting from human and animal activities on the resistome of natural aquatic systems.

Assessing the occurrence of pharmaceuticals and antibiotic resistance genes during the anaerobic treatment of slaughterhouse wastewater at different temperatures

This study investigates the effect of psychrophilic, mesophilic and thermophilic temperatures on the anaerobic treatment of slaughterhouse wastewater, in terms of biogas production, occurrence of 30 pharmaceutical compounds of veterinary use, 4 antibiotic resistance genes (ARGs) which provide resistance to tetracyclines (tetW), fluoroquinolones (qnrS), macrolide-lincosamide-streptogramin (ermB) and sulfonamides (sul1) antibiotics, as well as class I integron-integrase gene (intI1), related to horizontal gene transfer. The highest methane yield was obtained at a mesophilic temperature (35 °C) (323 mL CH₄/g TCOD) followed by the yield obtained at thermophilic temperature (53 °C) (242 mL CH₄/g TCOD). Regarding pharmaceuticals, chlortetracycline, oxytetracycline, tilmicosin, and lincomycin were the most abundant in the slaughterhouse wastewater, being detected predominantly in the solid phase (with median concentrations >200 μg/kg dry weight). On the other hand, ciprofloxacin, ofloxacin, norfloxacin, lincomycin and ibuprofen were the most predominant in the anaerobic digestate regardless of the treatment temperature. Psychrophilic temperatures (21 °C) exhibited moderate to low pharmaceuticals removal, while a large fraction of them were removed at a thermophilic temperature reaching 70-90% removals for tetracycline, macrolides and one sulfonamide (sulfapyridine). The highest relative abundance of the quantified ARGs was found at 53 °C, suggesting that thermophilic temperatures normally associated with better removals of pathogens do not necessarily show better removals of antibiotic resistance genes.

Impact of wastewater on the microbial diversity of periphyton and its tolerance to micropollutants in an engineered flow-through channel system

Wastewater treatment plants (WWTPs) play an important role in retaining organic matter and nutrients but to a lesser extent micropollutants. Therefore, treated wastewater is recognized as a major source of multiple stressors, including complex mixtures of micropollutants. These can potentially affect microbial communities in the receiving water bodies and the ecological functions they provide. In this study, we evaluated in flow-through channels the consequences of an exposure to a mixture of stream water and different percentages of urban WWTP effluent, ranging from 0% to 80%, on the microbial diversity and function of periphyton communities. Assuming that micropollutants exert a selective pressure for tolerant microorganisms within communities, we further examined the periphyton sensitivity to a micropollutant mixture extracted from passive samplers that were immersed in the wastewater effluent. As well, micropollutants in water and in periphyton were comprehensively quantified. Our results show that micropollutants detected in periphyton differed from those found in water, both in term of concentration and composition. Especially photosystem II inhibitors accumulated in periphyton more than other pesticides. Although effects of other substances cannot be excluded, this accumulation may have contributed to the observed higher tolerance of phototrophic communities to micropollutants upon exposure to 30% and 80% of wastewater. On the contrary, no difference in tolerance was observed for heterotrophic communities. Exposure to the gradient of wastewater led to structural differences in both prokaryotic and eukaryotic communities. For instance, the relative abundance of cyanobacteria was higher with increasing percentage of wastewater effluent, whereas the opposite was observed for diatoms. Such results could indicate that differences in community structure do not necessarily lead to higher tolerance. This highlights the need to consider other wastewater constituents such as nutrients and wastewater-derived microorganisms that can modulate community structure and tolerance. By using engineered flow-through channels that mimic to some extent the required field conditions for the development of tolerance in periphyton, our study constitutes a base to investigate the mechanisms underlying the increased tolerance, such as the potential role of microorganisms originating from wastewater effluents, and different treatment options to reduce the micropollutant load in effluents.

Manure derived nutrients alter microbial community composition and increase the presence of potential pathogens in freshwater sediment

AIM

To determine the impact of an acute, pulse disturbance of nutrients from manure on freshwater sediment microbiomes in an experimental system.

METHODS AND RESULTS

A controlled freshwater mesocosm experiment was designed to compare the effect of disturbance from nutrients derived from sterile manure (SM), disturbance from equivalent concentrations of laboratory-derived nutrients, and a nondisturbed control on freshwater sediment microbial community composition and function using 16S rRNA amplicon sequencing. Sediment microbiomes impacted by nutrients from SM showed no sign of compositional recovery after 28 days but those impacted by laboratory-derived chemicals lead to a new steady-state (p < 0.05). Carbon and nitrate sources within disturbed mesocosms were the primary drivers of altered microbial community composition. Additionally, multiple potential pathogens (based on exact sequence matching at the species level) were enriched in mesocosms treated with SM.

CONCLUSIONS

Nutrient disturbance from SM, in the absence of the manure microbial community, alters the microbiome of sediments without recovery after 28 days and enriches potential pathogens.

SIGNIFICANCE AND IMPACT OF THE STUDY

These results suggest manure land application practices should be re-evaluated to account for impact of nutrient disturbance on environmental microbiomes in addition to the impact of the manure microbial community.

Determination of antibiotic resistance genes in a WWTP-impacted river in surface water, sediment, and biofilm: Influence of seasonality and water quality

Many pathogenic bacteria are adapted to live in aquatic habitats, which makes rivers possible sources and spread pathways of antibiotic resistance, since they usually receive effluents from wastewater treatment plants (WWTP), possibly containing antibiotic residues and also antibiotic-resistant bacteria. This study investigates different monitoring strategies to identify the occurrence of antibiotic-resistant bacteria in rivers. We analyzed the presence of 13 antibiotic resistance genes (ARGs) and seven gene markers for facultative pathogenic bacteria (FPB) with qPCR in sampling sites upstream and downstream of a small WWTP in Southern Germany. Five sampling campaigns were conducted from February to June 2019. Surface water, sediment, and biofilm samples were analyzed. The biofilm was collected from an artificial sampler placed in the river. bla_TEM, ermB, tetM, and sul1 genes were detected in all samples analyzed. The results showed there was a previous background in the river, but the WWTP and the water quality of the river influenced the concentration and occurrence of ARGs and FPB. Genes representing resistance against strong or last-resort antibiotics, such as mecA, bla_CMY-2, bla_KPC-3, and mcr-1, and multidrug resistance were also detected, mainly in samples collected downstream of the WWTP. Downstream of the WWTP, the occurrence of ARG and FPB correlated with ammoniacal nitrogen, while upstream of the WWTP correlated with turbidity, suspended solids, and seasonal factors such as UVA radiation and the presence of macrophytes. Biofilm samples presented higher abundances of ARGs and FPB. The biofilm sampler was efficient and allowed to collect biofilms from specific periods, which helped to identify seasonal patterns.

Micropollutant biotransformation and bioaccumulation in natural stream biofilms

Micropollutants are ubiquitously found in natural surface waters and pose a potential risk to aquatic organisms. Stream biofilms, consisting of bacteria, algae and other microorganisms potentially contribute to bioremediating aquatic environments by biotransforming xenobiotic substances. When investigating the potential of stream biofilms to remove micropollutants from the water column, it is important to distinguish between different fate processes, such as biotransformation, passive sorption and active bioaccumulation. However, due to the complex nature of the biofilm community and its extracellular matrix, this task is often difficult. In this study, we combined biotransformation experiments involving natural stream biofilms collected up- and downstream of wastewater treatment plant outfalls with the QuEChERS extraction method to distinguish between the different fate processes. The QuEChERS extraction proved to be a suitable method for a broad range of micropollutants (> 80% of the investigated compounds). We found that 31 out of 63 compounds were biotransformed by the biofilms, with the majority being substitution-type biotransformations, and that downstream biofilms have an increased biotransformation potential towards specific wastewater-relevant micropollutants. Overall, using the experimental and analytical strategy developed, stream biofilms were demonstrated to have a broad inherent micropollutant biotransformation potential, and to thus contribute to bioremediation and improving ecosystem health.

Structure of Bacterial Community with Resistance to Antibiotics in Aquatic Environments. A Systematic Review

Aquatic environments have been affected by the increase in bacterial resistant to antibiotics. The aim of this review is to describe the studies carried out in relation to the bacterial population structure and antibiotic resistance genes in natural and artificial water systems. We performed a systematic review based on the PRISMA guideline (preferred reporting items for systematic reviews and meta-analyzes). Articles were collected from scientific databases between January 2010 and December 2020. Sixty-eight papers meeting the inclusion criteria, i.e., "reporting the water bacterial community composition", "resistance to antibiotics", and "antibiotic resistance genes (ARG)", were evaluated according to pre-defined validity criteria. The results indicate that the predominant phyla were Firmicutes and Bacteroidetes in natural and artificial water systems. Gram-negative bacteria of the family Enterobacteraceae with resistance to antibiotics are commonly reported in drinking water and in natural water systems. The ARGs mainly reported were those that confer resistance to β-lactam antibiotics, aminoglycosides, fluoroquinolones, macrolides and tetracycline. The high influence of anthropogenic activity in the environment is evidenced. The antibiotic resistance genes that are mainly reported in the urban areas of the world are those that confer resistance to the antibiotics that are most used in clinical practice, which constitutes a problem for human and animal health.

New insights on the combined removal of antibiotics and ARGs in urban wastewater through the use of two configurations of vertical subsurface flow constructed wetlands

The occurrence and removal of 49 antibiotics and 11 selected antibiotic resistance genes (ARGs) were investigated in 2 vertical subsurface flow (VF) constructed wetlands (1.5 m² each): an unsaturated (UVF) unit and a partially saturated (SVF) unit (0.35 m saturated out of 0.8 m) operating in parallel and treating urban wastewater. Thirteen antibiotics were detected in influent wastewater, 6 of which were present in all samples. The SVF showed statistical significance on the removal of 4 compounds (namely ciprofloxacin, ofloxacin, pipemidic acid and azithromycin), suggesting that the wider range of pH and/or redox conditions of this configuration might promote the microbial degradation of some antibiotics. In contrast, the concentration of the latter (except pipemidic acid) and also clindamycin was higher in the effluent than in the influent of the UVF. Five ARGs were detected in influent wastewater, sul1 and sul2, bla_TEM, ermB and qnrS. All of them were detected also in the biofilm of both wetlands, except qnrS. Average removal rates of ARGs showed no statistical differences between both wetland units, and ranged between 46 and 97% for sul1, 33 and 97% for sul2, 9 and 99% for ermB, 18 and 97% for qnrS and 11 and 98% for bla_TEM.

Composting of chicken litter from commercial broiler farms reduces the abundance of viable enteric bacteria, Firmicutes, and selected antibiotic resistance genes

We examined the ability of composting to remove ARGs and enteric bacteria in litter obtained from broiler chickens fed with a diet supplemented with Bacitracin methylene disalicylate (BDM) (conventional chicken litter), or an antibiotic-free diet (raised without antibiotic (RWA) chicken litter). This was done by evaluating the litter before and after composting for the abundance of ten gene targets associated with antibiotic resistance or horizontal gene transfer, the composition of the bacterial communities, and the abundance of viable enteric bacteria. The abundance of gene targets was determined by qPCR and the microbial community composition of chicken litter determined by 16S rRNA gene amplicon sequencing. Enteric bacteria were enumerated by viable plate count. A majority of the gene targets were more abundant in conventional than in RWA litter. In both litter types, the absolute abundance of all of the target genes decreased after composting except sul1, intI1, incW and erm(F) that remained stable. Composting significantly reduced the abundance of enteric bacteria, including those carrying antibiotic resistance. The major difference in bacterial community composition between conventional and RWA litter was due to members affiliated to the genus Pseudomonas, which were 28% more abundant in conventional than in RWA litter. Composting favoured the presence of thermophilic bacteria, such as those affiliated with the genus Truepera, but decreased the abundance of those bacterial genera associated with cold-adapted species, such as Carnobacterium, Psychrobacter and Oceanisphaera. The present study shows that chicken litter from broilers fed with a diet supplemented with antibiotic has an increased abundance of some ARGs, even after composting. However, we can conclude that fertilization with composted litter represents a reduced risk of transmission of antibiotic resistance genes and enteric bacteria of poultry origin to soil and crops than will fertilization with raw litter.

Localized effect of treated wastewater effluent on the resistome of an urban watershed

BACKGROUND

Wastewater treatment is an essential tool for maintaining water quality in urban environments. While the treatment of wastewater can remove most bacterial cells, some will inevitably survive treatment to be released into natural environments. Previous studies have investigated antibiotic resistance within wastewater treatment plants, but few studies have explored how a river's complete set of antibiotic resistance genes (the "resistome") is affected by the release of treated effluent into surface waters.

RESULTS

Here we used high-throughput, deep metagenomic sequencing to investigate the effect of treated wastewater effluent on the resistome of an urban river and the downstream distribution of effluent-associated antibiotic resistance genes and mobile genetic elements. Treated effluent release was found to be associated with increased abundance and diversity of antibiotic resistance genes and mobile genetic elements. The impact of wastewater discharge on the river's resistome diminished with increasing distance from effluent discharge points. The resistome at river locations that were not immediately downstream from any wastewater discharge points was dominated by a single integron carrying genes associated with resistance to sulfonamides and quaternary ammonium compounds.

CONCLUSIONS

Our study documents variations in the resistome of an urban watershed from headwaters to a major confluence in an urban center. Greater abundances and diversity of antibiotic resistance genes are associated with human fecal contamination in river surface water, but the fecal contamination effect seems to be localized, with little measurable effect in downstream waters. The diverse composition of antibiotic resistance genes throughout the watershed suggests the influence of multiple environmental and biological factors.

Contrasting distribution of antibiotic resistance genes and microbial communities in suspended activated sludge versus attached biofilms in an integrated fixed film activated sludge (IFAS) system

Suspended activated sludge (AS) and carrier-attached biofilms simultaneously exist in an integrated fixed film activated sludge (IFAS) system. However, the differentiation of antibiotic resistance genes (ARGs) and microbial communities in different types of biofilms is rarely reported. In this study, successions of ARGs and microbial communities of AS and two types of suspended carrier-attached biofilms over seasons were investigated in the IFAS system of one municipal wastewater treatment plant. Results showed that substantial differences were found in the distribution pattern of ARGs, bacterial communities, and predicted microbial function between AS and attached biofilms. The relative abundances of all detected ARGs in AS were significantly higher than those in attached biofilms. ARGs with higher relative abundances generally existed in K3 carrier (surface area ≥ 800 m²/m³) attached biofilms than those in K1 carrier (surface area ≥ 450 m²/m³) biofilms. The relative abundances of ARGs were negatively correlated with temperature and biochemical oxygen demand (BOD₅) and positively correlated with ammonium nitrogen contents for AS but not for attached biofilms. No significant relationship was found between the extracellular polymeric substance (EPS) content and ARG abundance for all samples. Temperature, BOD₅, and ammonium nitrogen contents were closely connected to microbial communities. The Bray-Curtis distance of bacterial communities between two adjacent sampling seasons for AS was larger than those of two attached biofilms. Network analysis indicated that the AS network had more positive links and intense connections than the attached biofilm networks, potentially facilitating the dissemination of ARGs. The differential distribution of ARGs among the three types of samples was significantly correlated with the microbial co-occurrence network topological properties. Bray-Curtis distance and network analysis suggest that microbial community is more robust in attached biofilms than in suspended AS. This work provides a more in-depth understanding of ARGs and microbial community distributions in wastewater biofilms.

Survivor microbial populations in post-chlorinated wastewater are strongly associated with untreated hospital sewage and include ceftazidime and meropenem resistant populations

Wastewater treatment plant (WWTP) effluent has been implicated in the spread of antibiotic resistant bacteria (ARB), including pathogens, as the WWTP environment contains multiple selective pressures that may increase mutation rates, pathogen survivability, and induce gene transfer between bacteria. In WWTPs receiving hospital sewage, this selective effect may be more pronounced due to increased concentrations of antibiotics, ARB, and clinical pathogens from hospital sewage. To determine the extent to which hospital sewage contributes to the microbial community of disinfected wastewater which is released into the environment, we used 16S rRNA sequencing of hospital sewage, WWTP influent, primary effluent, Post-Chlorinated Effluent, and receiving sediments in a combined sewage system to track changes in microbial community composition. We also sequenced the culturable survivor community resistant to β-lactam antibiotics within disinfected effluent. Using molecular source tracking, we found that the hospital sewage microbiome contributes an average of 11.49% of the microbial community in Post-Chlorinated Effluents, suggesting microorganisms identified within hospital sewage can survive or are enriched by the chlorination disinfection process. Additionally, we identified 28 potential pathogens to the species level, seven of which remained detectable in Post-Chlorinated Effluent and environmental sediments. When Post-Chlorinated Effluents were cultured on media containing β-lactam antibiotics ceftazidime and meropenem, a diverse antibiotic resistant survivor community was identified including potential human pathogens Bacillus cereus, Bacillus pumilus, and Chryseobacterium indologenes. Together, these results indicate that although wastewater treatment does significantly reduce pathogenic loads and ARBs, their continual presence in disinfected wastewater and receiving sediments suggests additional treatment and microbial tracking systems are needed to reduce human and animal health risks.

Freshwater Sediment Microbial Communities Are Not Resilient to Disturbance From Agricultural Land Runoff

Microorganisms are critically important for the function of surface water ecosystems but are frequently subjected to anthropogenic disturbances at either acute (pulse) or long-term (press) scales. Response and recovery of microbial community composition and function following pulse disturbance is well-studied in controlled, laboratory scale experiments but is less well-understood in natural environments undergoing continual press disturbance. The objectives of this study were to determine the drivers of sediment microbial compositional and functional changes in freshwaters receiving continual press disturbance from agricultural land runoff and to evaluate the ability of the native microbial community to resist disturbance related changes as a proxy for freshwater ecosystem health. Freshwater sediments were collected seasonally over 1 year in Kewaunee County, Wisconsin, a region impacted by concentrated dairy cattle farming, manure fertilization, and associated agricultural runoff which together serve as a press disturbance. Using 16S rRNA gene amplicon sequencing, we found that sediments in locations strongly impacted by intensive agriculture contain significantly higher abundances (p < 0.01) of the genera Thiobacillus, Methylotenera, Crenotrhix, Nitrospira, and Rhodoferax compared to reference sediments, and functions including nitrate reduction, nitrite reduction, and nitrogen respiration are significantly higher (p < 0.05) at locations in close proximity to large farms. Nine species-level potential human pathogens were identified in riverine sediments including Acinetobacer lwoffi and Arcobacter skirrowii, two pathogens associated with the cattle microbiome. Microbial community composition at locations in close proximity to intensive agriculture was not resistant nor resilient to agricultural runoff disturbance within 5 months post-disturbance but did reach a new, stable microbial composition. From this data, we conclude that sediment microbial community composition is sensitive and shifts in response to chemical and microbial pollution from intensive agriculture, has a low capacity to resist infiltration by non-native, harmful bacteria and, overall, the natural buffering capacity of freshwater ecosystems is unable to fully resist the impacts from agricultural press disturbance.

Effect of Urban Wastewater Discharge on the Abundance of Antibiotic Resistance Genes and Antibiotic-Resistant Escherichia coli in Two Italian Rivers

Background: Wastewater treatment plants (WWTPs) are microbial factories aimed to reduce the amount of nutrients and pathogenic microorganisms in the treated wastewater before its discharge into the environment. We studied the impact of urban WWTP effluents on the abundance of antibiotic resistance genes (ARGs) and antibiotic-resistant Escherichia coli (AR-E. coli) in the last stretch of two rivers (Arrone and Tiber) in Central Italy that differ in size and flow volume. Methods: Water samples were collected in three seasons upstream and downstream of the WWTP, at the WWTP outlet, and at sea sites near the river mouth, and analyzed for the abundance of ARGs by qPCR and AR-E. coli using cultivation followed by disk diffusion assays. Results: For all studied genes (16S rRNA, intI1, sul1, ermB, blaTEM, tetW and qnrS), absolute concentrations were significantly higher in the Tiber than in the Arrone at all sampling sites, despite their collection date, but the prevalence of target ARGs within bacterial communities in both rivers was similar. The absolute concentrations of most ARGs were also generally higher in the WWTP effluent with median levels between log 4 and log 6 copies per ml but did not show differences along the studied stretches of rivers. Statistically significant site effect was found for E. coli phenotypic resistance to tetracycline and ciprofloxacin in the Arrone but not in the Tiber. Conclusions: In both rivers, diffuse or point pollution sources other than the studied WWTP effluents may account for the observed resistance pattern, although the Arrone appears as more sensitive to the wastewater impact considering its lower flow volume.

Characterization of the Nairobi River catchment impact zone and occurrence of pharmaceuticals: Implications for an impact zone inclusive environmental risk assessment

The largely uncontrolled release of active pharmaceuticals ingredients (APIs) within untreated wastewater discharged to waterbodies, associated with many rapidly urbanising centres is of growing concern owing to potential antimicrobial resistance, endocrine disruption and potential toxicity. A sampling campaign has been undertaken to assess the source, occurrence, magnitude and risk associated with APIs and other chemicals within the Nairobi/Athi river basin, in Kenya, East Africa. The catchment showed an extensive downstream impact zone estimated to extend 75 km, mostly, but not exclusively, derived from the direct discharge of untreated wastewater from the urban centre of Nairobi city. The exact extent of the downstream boundary of the Nairobi city impact zone was unclear owing to the inputs of untreated wastewater sources from the continuous urbanized areas along the river, which counteracted the natural attenuation caused by dilution and degradation. The most frequently detected APIs and chemicals were caffeine, carbamazepine, trimethoprim, nicotine, and sulfamethoxazole. Paracetamol, caffeine, sulfamethoxazole, and trimethoprim alone contributed 86% of the total amount of APIs determined along the Nairobi/Athi catchment. In addition to direct discharge of untreated domestic wastewater attributed to the informal settlements within the conurbation, other sources were linked to the industrial area in Nairobi City where drug formulation is known to occur, the Dandora landfill and veterinary medicines from upstream agriculture. It was shown that there was a possible environmental risk of API ecotoxicological effects beyond the end of the traditional impact zone defined by elevated biochemical oxygen demand concentrations; with metronidazole and sulfamethoxazole exhibiting the highest risk.

Small-scale wastewater treatment plants as a source of the dissemination of antibiotic resistance genes in the aquatic environment

Wastewater treatment plants (WWTPs) are significant source of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs), which can spread further in the environment by reaching rivers together with effluents discharged from WWTPs. In this study untreated and treated wastewater (UWW, TWW), upstream and downstream river water (URW, DRW) were collected from 4 WWTPs, in the winter and autumn seasons. The occurrence of ARB resistant to beta-lactams and tetracyclines as well as the presence of antibiotics from these classes were analysed in water and wastewater samples. Additionally, the amounts of 12 ARGs, 2 genes of mobile genetic elements (MGEs), gene uidA identifying E. coli and 16S rRNA were also determined. Resistance to beta-lactams prevailed among ARB in water and wastewater samples (constituting 82-88% of total counts of bacteria). The dominant genes in water and wastewater samples were bla_TEM, tetA, sul1. The gene bla_OXA demonstrated high variability of its concentration in samples collected in both seasons. Despite the high per cent reduction of ARB and ARGs concentration observed during the wastewater treatment processes, their large quantities are still transmitted into the environment. The research focuses on WWTPs' role in the dissemination of ARGs and MGEs in the aquatic environment.

High-quality treated wastewater causes remarkable changes in natural microbial communities and intI1 gene abundance

We carry out a mesocosms experiment to assess the impact of high-quality treated wastewater intended for agricultural reuse (HQWR) on freshwater bacteria seldom exposed to anthropogenic pollution. Effects were assessed by comparing the abundance and composition of bacterial communities as well as their resistance profile under control (source water from an unpolluted lake) and treatment conditions (source water mixed 1:1 with HQWR, with and without 5 μg L^-1 of cefotaxime). We investigated the effect of the different conditions on the abundance of genes encoding resistance to β-lactams and carbapenems (bla_TEM, bla_CTX-M, bla_OXA, and bla_KPC), fluoroquinolones (qnrS), tetracyclines (tetA), sulfonamides (sul2), macrolides (ermB), arsenic and cadmium (arsB and czcA, respectively), and on the gene encoding the Class 1 integron integrase (intI1). Bacterial communities exposed to HQWR showed a significant higher abundance of tetA, arsB, czcA, and intI1 genes, whereas those exposed to Cefotaxime-amended HQWR did not. Genes conferring resistance to carbapenems, β-lactams, fluoroquinolones, and macrolides were below detection limit in all treatments. Besides, the higher availability of nutrients under treatment conditions favored bacterial growth in comparison to those exposed to control conditions. Particularly, Acinetobacter spp. and Pseudomonas spp. were significantly enriched after 22 days of treatment exposure. The presence of cefotaxime (a third generation cephalosporine) in the feeding medium caused an enrichment of bacterial communities in sequences affiliated to Acinetobacter thus suggesting that these resistant forms may possess resistance genes other than those studied here (bla_CTX-M, bla_OXA, and bla_KPC). Although derived from a mesocosm experiment in continuous cultures, our results call attention to the need of refined regulations regarding the use of reclaimed water in agriculture since even high-quality treated wastewater may lead to undesired effects on receiving bacterial communities in terms of composition and dissemination of antibiotic resistance genes.

Mapping Micro-Pollutants and Their Impacts on the Size Structure of Streambed Communities

Recently there has been increasing concern over the vast array of emerging organic contaminants (EOCs) detected in streams and rivers worldwide. Understanding of the ecological implications of these compounds is limited to local scale case studies, partly as a result of technical limitations and a lack of integrative analyses. Here, we apply state-of-the-art instrumentation to analyze a complex suite of EOCs in the streambed of 30 UK streams and their effect on streambed communities. We apply the abundance–body mass (N–M) relationship approach as an integrative metric of the deviation of natural communities from reference status as a result of EOC pollution. Our analysis includes information regarding the N and M for individual prokaryotes, unicellular flagellates and ciliates, meiofauna, and macroinvertebrates. We detect a strong significant dependence of the N–M relationship coefficients with the presence of EOCs in the system, to the point of shielding the effect of other important environmental factors such as temperature, pH, and productivity. However, contrary to other stressors, EOC pollution showed a positive effect on the N–M coefficient in our work. This phenomenon can be largely explained by the increase in large-size tolerant taxa under polluted conditions. We discuss the potential implications of these results in relation to bioaccumulation and biomagnification processes. Our findings shed light on the impact of EOCs on the organization and ecology of the whole streambed community for the first time.

Prolonged exposure of Stenotrophomonas maltophilia biofilms to trace levels of clofibric acid alters antimicrobial tolerance and virulence

The presence of pharmaceuticals in water sources, including in drinking water (DW), is increasingly being recognized as an emerging and global concern for the environment and public health. Based on the principles of the "One Health" initiative, the present work aims to understand the effects of clofibric acid (CA), a lipid regulator, on the behavior of a selected bacterium isolated from drinking water (DW). Biofilms of the opportunistic pathogen Stenotrophomonas maltophilia were exposed to CA for 12 weeks at 170 and 17000 ng/L. The effects of CA were evaluated on planktonic S. maltophilia susceptibility to chlorine and antibiotics (amoxicillin, ciprofloxacin, erythromycin, kanamycin, levofloxacin, oxacillin, spectinomycin, tetracycline and trimethoprim-sulfamethoxazole), biofilm formation, motility, siderophores production and on the adhesion and internalization of the human colon adenocarcinoma cell line (HT-29). It was found that CA did not affect planktonic S. maltophilia tolerance to chlorine exposure. Additionally, no effects were observed on biofilm formation, motility and siderophores production. However, biofilms formed after CA exposure were more tolerant to chlorine disinfection and lower CFU reductions were obtained. Of additional concern was the effect of CA exposure on S. maltophilia increased tolerance to erythromycin. CA exposure also slightly reduced S. maltophilia ability to invade HT-29 cells. In conclusion, this work reinforces the importance of studying the effects of non-antibiotic contaminants on the behavior of environmental microorganisms, particularly their role as drivers affecting resistance evolution and selection.

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.

Understanding drivers of antibiotic resistance genes in High Arctic soil ecosystems

Soils in tropical and temperate locations are known to be a sink for the genetic potential of anthropogenic-driven acquired antibiotic resistance (AR). In contrast, accumulation of acquired AR is less probable in most Polar soils, providing a platform for characterizing background resistance and establishing a benchmark for assessing AR spread. Here, high-throughput qPCR and geochemistry were used to quantify the abundance and diversity of both antibiotic resistance genes (ARGs) and selected mobile genetic elements (MGEs) across eight soil clusters in the Kongsfjorden region of Svalbard in the High Arctic. Relative ARG levels ranged by over two orders of magnitude (10^-6 to 10^-4 copies/16S rRNA gene copy), and showed a gradient of potential human and wildlife impacts across clusters as evidenced by altered geochemical conditions and increased "foreign" ARG abundances (i.e., allochthonous), including bla_NDM-1. Impacted clusters exhibited 100× higher total ARGs and MGEs in tandem with elevated secondary nutrients, especially available P that is typically low and limiting in Arctic soils. In contrast, ARGs in less-impacted clusters correlated strongly to local soil lithology. The most plausible source of exogenous P and allochthonous ARGs in this region is bird and other wildlife guano, disseminated either by local human wastes or via direct carriage and deposition. Regardless of pathway, accumulation of apparent allochthonous ARGs and MGEs in High Arctic soils is concerning, highlighting the importance of characterizing Arctic sites now to establish benchmarks for tracking AR spread around the world.

Impact of industrial wastewater on the dynamics of antibiotic resistance genes in a full-scale urban wastewater treatment plant

Urban Wastewater Treatment Plants (UWTPs) treating mixed urban sewage and industrial wastewater are among the major hotspots for the spread of Antibiotic Resistance Genes (ARGs) into the environment. This study addresses the impact of the wastewater origin on ARG dynamics in a full-scale UWTP (15,000 Population Equivalent, PE) by operating the plant with and without industrial wastewater. Composite samples (4 L) from different treatment points were characterized for their chemical composition, bacterial abundance and for the abundance of four resistance genes against tetracycline, sulfonamides, erythromycin, and quinolones (tetA, sul2, ermB, and qnrS), and of the class 1 integrons (intI1). Although the chemical composition of the outflow significantly differed when the plant operated with or without industrial wastewater, the system efficiency in the removal of bacterial cells, ARGs, and intI1 was constant. The final disinfection by peracetic acid (PAA) did not affect the removal of ARGs, independently of the wastewater origin and the chemical characteristics of the inflows. Our results demonstrated that a well-functioning small size UWTP could treat a significant amount of industrial wastewater mixed in the urban sewage without affecting the overall ARGs and class 1 integrons released into the environment.

Analysis of Bacterial Community Characteristics, Abundance of Antibiotics and Antibiotic Resistance Genes Along a Pollution Gradient of Ba River in Xi'an, China

The microbial communities in freshwater have raised concerns about the ecosystem and human health. Many ecological environmental problems have been found in urban river because of the unreasonable use and long-term wastewater discharge. In this study, we explored the bacterial community composition, abundance of 14 antibiotics and 21 antibiotic resistance genes (ARGs), and water environment features in seven water samples and seven sediment samples from Ba River in Xi'an, China. Results showed Proteobacteria and Bacteroidetes were the dominant phyla in all samples, and sediment samples had a higher bacterial diversity and richness than it in water. Bacterial communities of site 5 and 6 were clustered in discrepant patterns compared to those at remaining sites from other samples. It might be influenced by nutrients, heavy metals and antibiotics. Antibiotics concentrations ranged from 1.26 to 1.61 × 10³ ng L^-1 in water samples and 1.55 to 4.05 × 10² μg kg^-1 in sediment samples. Sulfamerazine (SM1) and erythromycin (ERY) were the chief antibiotics in water samples, while the level of oxytetracycline (OTC) and cefazolin (CFZ) were higher in sediment samples. Canonical correspondence analysis showed that trimethoprim (TMP) was significantly related to Acinetobacter in W6, and that SM1 and OTC had positive correlation with Arcobacter in W5. The tetC, bla_{TEM ,} ermF and sul1 had higher pollution abundance ranging from 10^-4 to 10⁰ copies/16S rRNA gene copies in all samples. Significant correlations were observed between ARGs and matching antibiotics, suggesting that antibiotics can pose the selective pressure on ARGs in this river. In summary, these finding might provide some new data to the limited information available on the bacterial community characteristics, abundance of antibiotics and ARGs in urban river of China.

The effects of emerging environmental contaminants on Stenotrophomonas maltophilia isolated from drinking water in planktonic and sessile states

Concerns on the presence of emerging contaminants (ECs) in water sources have increased in recent years. The lack of efficient technologies to remove ECs from residual waters contributes for their appearance in drinking water distribution systems (DWDS). Therefore, sessile microorganisms on DWDS pipes are continuously exposed to trace concentrations of ECs. However, no data exists on the role of ECs on the resident microbiota. The present work aims to understand the effects of prolonged exposure of a bacterial strain of Stenotrophomonas maltophilia, isolated from a DWDS, in both planktonic and biofilm states, to trace concentrations of selected ECs (antipyrine-ANTP; diclofenac sodium salt-DCF; ibuprofen-IBP; galaxolide-GAL; tonalide-TON; carbamazepine-CBZ; clofibric acid-CA; tylosin-TY) on its tolerance to sodium hypochlorite (NaOCl) and resistance to antibiotics. Pre-established S. maltophilia biofilms were exposed to ECs for 26 d. Subsequently, the planktonic behaviour of the biofilm cells grown in the presence of ECS was characterized in terms of susceptibility to NaOCl and to selected antibiotics (levofloxacin and trimethoprim-sulfamethoxazole). Moreover, S.maltophilia was tested on its biofilm productivity in the presence of ECs (alone and mixed). These biofilms were challenged by NaOCl in order to assess the role of ECs on biofilm susceptibility. The results did not evidence remarkable effects of ECs on planktonic S. maltophilia susceptibility to NaOCl and antibiotics. However, S. maltophilia biofilm production and susceptibility to NaOCl was affected from ECs pre-exposure, particularly by the combination of different ECs (CA + CBZ, CA + IBP, CA + CBZ + IBP). S. maltophilia biofilms became more resistant to removal by NaOCl when developed in the presence of mixtures of CA + CBZ and CA + CBZ + IBP. Also, biofilm production was significantly affected. CA was present in all the combinations that altered biofilm behaviour. The overall results propose that exposure to ECs for 26 days had not a huge impact on S. maltophilia planktonic antimicrobial susceptibility. Nevertheless, the prolonged exposure to some ECs altered biofilm production and tolerance to NaOCl, with a potential practical outcome of hindering DWDS disinfection. The simultaneous presence of different ECs in the environment may amplify biofilm resilience.

Occurrence and distribution of antibiotics and antibiotic resistance genes in Ba River, China

The riverine system is usually considered as a natural reservoir of antibiotic resistance genes (ARGs) and more susceptible to anthropogenic activities. In this study, the occurrence and distribution of 14 antibiotics belonging to 7 categories together with 23 corresponding ARGs in Ba River of Xi'an China were investigated in March and July 2017. Sulfonamides, quinolones, macrolides and tetracyclines were detected in high frequencies ranged from 85.7% to 100%. Tetracyclines were detected with high concentrations in water samples (up to 8.54 × 10² ng L^-1) and sediment samples (up to 2.08 × 10³ μg kg^-1), respectively. The total concentrations of antibiotics were much higher in July in comparison with March. The sul1, tetA, tetC, tetZ, gyrA, ermF, cmlA and bla_TEM were the predominant ARGs in terms of absolute abundance. For both water and sediment samples in March compared with July, the relative abundance of ARGs had no significant difference except for sul3. The tetracyclines had positive correlation with tet genes, whereas the remaining antibiotics had no significant correlations with their corresponding ARGs, suggesting that environmental factors and cross-selection may significantly influenced the distribution of ARGs. Redundancy analysis was performed to further predict the influences of environmental factors on antibiotics and ARG abundance. The findings suggest that anthropogenic activities contribute significantly to the persistence of antibiotics pollution.

Hot spots of antibiotic tolerant and resistant bacterial subpopulations in natural freshwater biofilm communities due to inevitable urban drainage system overflows

Antibiotic resistant bacteria are a threat to human life. Recently, sewers have been identified as potential reservoirs. The intermittent injection of sewage into adjacent surface waters is inevitable, due to capacity limitations of the urban drainage system. Information regarding the effect to natural freshwater biofilms (NFB) due to the intermittent contaminations are scarce. Therefore, a fundamental screening is necessary. In April, we placed NFB-attachment constructions in a brook upstream and downstream from urban drainage overflow constructions. In meanwhile two sampling campaigns were conducted. The sewage and the brook water were collected to gather information about antibiotic background exposure of ciprofloxacin (CIP), clarithromycin (CLA) and doxycycline (DOX). Six months later we experimentally determined the oxygen uptake rate (OUR) of the NFB-communities after a 24 h lasting exposure with additionally dosed antibiotics. Concentrations of 0.1, 1.0 and 10.0 mg L^-1 were selected. CIP, CLA and DOX were individually dosed, and also in mixtures. The mean antibiotic background concentration in sewage was in a range of 575.5-1289.1 ng L^-1, which mainly exceeded the concentrations published in literature. The determined mean concentration in the brook was in a range of 4.6-539.0 ng L^-1. The first significant inhibition of the OUR with individually dosed antibiotics started mainly at a concentration of 1.0 mg L^-1. Antibiotics in a mixture with concentrations of 0.1 and 1.0 mg L^-1 were as effective as single dosed antibiotics with a concentration of 10.0 mg L^-1. The increased antibiotic tolerance and resistance of NFB-communities downstream of the combined sewer overflow (CSO) structure was a consequence of a severe impact due to urban drainage overflows. Hence, NFB-communities downstream of CSO-constructions are hot spots of antibiotic tolerant and resistant subpopulations and access restrictions should be announced, if an infection risk is present.

Characterization of sub-watershed-scale stream chemistry regimes in an Appalachian mixed-land-use watershed

An exploratory study was conducted in an urbanizing, mixed-land-use Appalachian watershed. Six study sites, characterized by contrasting land use/land cover, were instrumented to continuously monitor stream stage. Weekly grab samples were collected from each site and analyzed for elemental composition via spectrometric and spectrophotometric methods. Additional physico-chemical parameters were measured in situ. Data were analyzed using a suite of statistical methods, including hypothesis testing, correlation analysis, and principal components analysis (PCA). Significant differences (p < 0.05) between study sites were identified for every measured parameter except Co, Cu, Pb, and Ti concentrations. However, different parameters showed significant differences (p < 0.05) between site pairings. PCA results highlight consistent spatial differences between elemental composition and physico-chemical characteristics of streamwater samples. Results from correlation analyses indicated varying significant (p < 0.05) relationships between chemical parameters and hydroclimate metrics, with certain elements (e.g., Ca and Sr) and physico-chemical parameters (e.g., specific conductance) displaying greater sensitivity to hydroclimate at mixed-land-use sites, as compared to predominately urban, agricultural, or forest sites. Given the geological, topographical, and climatological similarities between the sites, and their close proximity, it was concluded that land use characteristics and associated hydrologic regime contrasts were the primary factors contributing to the observed results. Results comprise valuable information for land and water managers seeking to mitigate the impacts of land use practices on water resources and aquatic ecosystem health. The applied methodology can be used to more effectively target sub-watershed-scale remediation/restoration efforts within mixed-use watersheds, thereby improving the ultimate efficacy of management practices.

Antibiotic resistance in urban and hospital wastewaters and their impact on a receiving freshwater ecosystem

The main objective of this study was to investigate the antibiotic resistance (AR) levels in wastewater (WW) and the impact on the receiving river. Samples were collected once per season over one year in the WW of a hospital, in the raw and treated WW of two wastewater treatment plants (WWTPs), as well as upstream and downstream from the release of WWTPs effluents into the Zenne River (Belgium). Culture-dependent methods were used to quantify Escherichia coli and heterotrophic bacteria resistant to amoxicillin, sulfamethoxazole, nalidixic acid and tetracycline. Six antibiotic resistance genes (ARGs) were quantified in both particle-attached (PAB) and free-living (FLB) bacteria. Our results showed that WWTPs efficiently removed antibiotic resistant bacteria (ARB) regardless of its AR profile. The ARGs levels were the highest in the hospital WW and were significantly reduced in both WWTPs. However, ARB and ARGs abundances significantly increased into the Zenne River downstream from the WWTPs outfalls. The variation in the relative abundance of ARGs through WW treatment differed depending on the WWTP, fraction, and gene considered. The sul1 and sul2 genes in PAB fraction showed significantly higher relative abundances in the effluent compared to the influent of both WWTPs. This study demonstrated that WWTPs could be hotspots for AR spread with significant impacts on receiving freshwater ecosystems. This was the first comprehensive study investigating at the same time antibiotics occurrence, fecal bacteria indicators, heterotrophic bacterial communities, and ARGs (distinguishing PAB and FLB) to assess AR levels in WW and impacts on the receiving river.

Emerging contaminants and nutrients synergistically affect the spread of class 1 integron-integrase (intI1) and sul1 genes within stable streambed bacterial communities

Wastewater effluents increase the nutrient load of receiving streams while introducing a myriad of anthropogenic chemical pollutants that challenge the resident aquatic (micro)biota. Disentangling the effects of both kind of stressors and their potential interaction on the dissemination of antibiotic resistance genes in bacterial communities requires highly controlled manipulative experiments. In this work, we investigated the effects of a combined regime of nutrients (at low, medium and high concentrations) and a mixture of emerging contaminants (ciprofloxacin, erythromycin, sulfamethoxazole, diclofenac, and methylparaben) on the bacterial composition, abundance and antibiotic resistance profile of biofilms grown in artificial streams. In particular, we investigated the effect of this combined stress on genes encoding resistance to ciprofloxacin (qnrS), erythromycin (ermB), sulfamethoxazole (sul1 and sul2) as well as the class 1 integron-integrase gene (intI1). Only genes conferring resistance to sulfonamides (sul1 and sul2) and intI1 gene were detected in all treatments during the study period. Besides, bacterial communities exposed to emerging contaminants showed higher copy numbers of sul1 and intI1 genes than those not exposed, whereas nutrient amendments did not affect their abundance. However, bacterial communities exposed to both emerging contaminants and a high nutrient concentration (1, 25 and 1 mg L^-1 of phosphate, nitrate and ammonium, respectively) showed the highest increase on the abundance of sul1 and intI1 genes thus suggesting a factors synergistic effect of both stressors. Since none of the treatments caused a significant change on the composition of bacterial communities, the enrichment of sul1 and intI1 genes within the community was caused by their dissemination under the combined pressure exerted by nutrients and emerging contaminants. To the best of our knowledge, this is the first study demonstrating the contribution of nutrients on the maintenance and spread of antibiotic resistance genes in streambed biofilms under controlled conditions. Our results also highlight that nutrients could enhance the effect of emerging contaminants on the dissemination of antibiotic resistance.

Distribution of Escherichia coli, coliphages and enteric viruses in water, epilithic biofilms and sediments of an urban river in Germany

Fecal contamination of surface water is commonly evaluated by quantification of bacterial or viral indicators such as Escherichia coli and coliphages, or by direct testing for pathogens such as enteric viruses. Retention of fecally derived organisms in biofilms and sediments is less frequently considered. In this study, we assessed the distribution of E. coli, somatic coliphages, and enteric viruses including human adenovirus (HAdV), enterovirus (EV), norovirus genogroup GII (NoV GII) and group A rotavirus (RoV) in an urban river environment in Germany. 24 samples each of water, epilithic biofilms and sediments were examined. E. coli and somatic coliphages were prevalent not only in the flowing water, but also in epilithic biofilms and sediments, where they were accumulated compared to the overlying water. During enhanced rainfall, E. coli and coliphage concentrations increased by approximately 2.5 and 1 log unit, respectively, in the flowing water, whereas concentrations did not change significantly in epilithic biofilms and sediments. The occurrence of human enteric viruses detected by qPCR was higher in water than in biofilms and sediments. 87.5% of all water samples were positive for HAdV. Enteric viruses found less frequently were EV, RoV and NoV GII in 20.8%, 16.7% and 8.3% of the water samples, respectively. In epilithic biofilms and sediments, HAdV was found in 54.2% and 50.0% of the samples, respectively, and EV was found in 4.2% of both biofilm and sediment samples. RoV and NoV GII were not detected in any of the biofilms and sediments. Overall, the prevalence of enteric viruses was in the order of HAdV > EV > RoV ≥ NoV GII. In conclusion, epilithic biofilms and sediments can be reservoirs for fecal indicators and enteric viruses and thus should be taken into consideration when assessing microbial pollution of surface water environments.