Fate and transport of antibiotics and antibiotic resistance genes in runoff and soil as affected by the timing of swine manure slurry application

The influence of urbanization and water reclamation plants on fecal indicator bacteria and antibiotic resistance in the Los Angeles River watershed: A case study with complementary monitoring methods

Urban land use and water reclamation plants (WRPs) can impact fecal indicator bacteria (FIB) and antimicrobial resistance (AMR) in coastal watersheds. However, there is a lack of studies exploring these effects on the US West Coast. Additionally, there is limited research using a complementary approach across culture-, qPCR-, and metagenomics-based techniques for characterizing environmental AMR. In this study, sixteen locations were sampled in the Los Angeles River, encompassing both upstream and downstream of three WRPs discharging into the river. Culture-dependent methods quantified Enterococcus, total coliforms, E. coli, and extended spectrum beta-lactamase-producing E. coli as a low-cost screening tool for AMR, while qPCR measured selected antibiotic resistance genes (ARGs): sul1, ermF, tetW, blaSHV, along with intI1 and 16S rRNA genes. Bacteroides HF183 and crAssphage markers were quantified via ddPCR. All samples underwent shotgun sequencing to investigate gene abundance and mobility and an overall risk score for AMR. Results reveal downstream sites contain ARGs at least two orders of magnitude greater than upstream locations. Developed areas had the highest ARG sequence abundances and the most ARG classes as indicated by metagenomic analysis. WRP effluent exhibited elevated ARGs and co-location of ARGs, mobile genetic elements, and pathogens. A culture-based assessment of AR in E. coli and Pseudomonas aeruginosa revealed increased resistance ratios for most antibiotics from upstream to downstream a WRP discharge point. This study highlights the impacts of land use and WRPs on ARGs and FIB, offering a multi-pronged analysis of AMR.

Combined Treatment Methods for Removal of Antibiotics from Beef Wastewater

Use of antibiotics is common practice in agriculture; however, they can be released into the environment, potentially causing antimicrobial resistance. Naturally mined diatomaceous earth with bentonite was tested as a remediation material for tylosin, chlortetracycline, and ceftiofur in wastewater from a beef cattle feedlot. Langmuir binding affinity in 10 mM sodium phosphate buffer at pH 6.7 was established prior to testing wastewater to determine binding potential. Chlortetracycline was found to have a binding affinity of 15.2 mM-1 and a binding capacity of 123 mg per g of diatomaceous earth while ceftiofur showed a much lower binding affinity and loading at 7.8 mM-1 and 3 mg per g of diatomaceous earth, respectively. From spiked wastewater, tylosin (50 μg mL-1, pH 8) and chlortetracycline (300 μg mL-1, pH 6) were removed (100 and 80%, respectively) when treated with 20 mg of diatomaceous earth while ceftiofur (300 μg mL-1, pH 8) remained in solution. When the spiked wastewater was flocculated with aluminum sulfate, a change in pH from 8 to 4 was observed, and chlortetracycline was removed from the wastewater; tylosin and ceftiofur remained in solution. When subsequently treated with diatomaceous earth, ceftiofur and tylosin were completely removed by diatomaceous earth from the flocculated wastewater.

Vertical migration and leaching behavior of antibiotic resistance genes in soil during rainfall: Impact by long-term fertilization

The vertical migration and leaching behavior of antibiotic resistance genes (ARGs) during rainfall in soils subjected to long-term fertilization remain largely unclear. In this study, ARGs in vertical profiles (0-60 cm) and leachates from three soils (acidic, neutral, and calcareous) in a long-term (13 years) field fertilization experiment were monitored by high-throughput quantitative PCR after each rainfall event throughout an entire year. The results showed that, compared with unfertilized soils, long-term manure fertilization mainly promoted the vertical migration and leaching of aminoglycoside, beta-lactam, and multidrug resistance genes in the soil profiles. As a result, the annual cumulative loads of ARGs in leachates from the three soils with long-term manure fertilization were significantly increased compared to the controls and were in the order of acidic soil > neutral soil > calcareous soil. SourceTracker analyses revealed that manured soil was the predominant source of the ARGs in the soil leachate samples. Pseudomonas, Anaeromyxobacter, IMCC26256, and MND1 were identified as the dominant potential hosts responsible for the vertical migration and leaching of ARGs in the three soils. PiecewiseSEM analysis further showed that long-term manure fertilization affected the vertical migration of ARGs during rainfall mainly by altering soil properties (i.e., pH, soil organic carbon, and sand). Our results suggest that the ARGs in soils with long-term manure fertilization are a significant potential source of ARG pollution in groundwater, and the measures should be taken to mitigate the vertical migration and leaching of ARGs during rainfall.

Tetracycline antibiotics in agricultural soil: Dissipation kinetics, transformation pathways, and structure-related toxicity

Tetracyclines (TCs) are the most common antibiotics in agricultural soil, due to their widespread usage and strong persistence. Biotic and abiotic degradation of TCs may generate toxic transformation products (TPs), further threatening soil ecological safety. Despite the increasing attention on the environmental behavior of TCs, a systematic review on the dissipation of TCs, evolution of TPs, and structure-toxicity relationship of TCs in agricultural soil remains lacking. This review aimed to provide a comprehensive overview of the environmental fate of TCs in agricultural soil. We first introduced the development history and structural features of different generations of TCs. Then, we comparatively evaluated the dissipation kinetics, transportation pathways, and ecological impacts of three representative TCs, namely tetracycline (TC), oxytetracycline (OTC), and chlortetracycline (CTC), in agricultural soil. The results showed that the dissipation kinetics of TCs generally followed the first-order kinetic model, with the median dissipation half-lives ranging from 20.0 to 38.8 days. Among the three TCs, OTC displayed the lowest dissipation rates due to its structural stability. The typical degradation pathways of TCs in soil included epimerization/isomerization, demethylation, and dehydration. Isomerization and dehydration reactions may lead to the formation of more toxic TPs, while demethylation was accompanied by the alteration of the minimal pharmacophore of TCs thus potentially reducing the toxicity. Toxicological experiments are urgently needed in future to comprehensively evaluate the ecological risks of TCs in agricultural soil.

Source apportionment and ecological risk assessment of antibiotics in Dafeng River Basin using PMF and Monte-Carlo simulation

Antibiotics, prevalent in aquatic ecosystems, pose a grave threat to human health and the ecological well-being. This paper performed a case study on Dafeng River Basin in southern China. Specifically, techniques including positive matrix factorization (PFM) and Monte-Carlo simulation were employed to comprehensively investigate the spatial variations, possible sources, and ecological risks of antibiotics in four groups: sulfonamides (SAs), macrolides (MLs), quinolones (QNs), and tetracyclines (TCs). The major findings were as follows: first, 43 and 39 antibiotics were detected in the surface water and sediments of the basin, respectively, where the respective total content were ND-490.08 ng/L and ND-144.34 μg/kg, and the QNs and TCs were the two dominating groups. Second, the highest antibiotic content in surface water (441.43 ng/L) was observed in the midstream area, whereas the highest concentration in sediments (68.41 μg/kg) was found in the upstream region. Third, the investigation identified five sources of antibiotics discharged to surface water: domestic sewage, agricultural drainage, livestock discharge, sewage treatment plants, and aquaculture; three sources were detected for antibiotics in sediments: aquaculture, sewage treatment plants, and livestock discharge. Fourth, QNs had a significantly higher ecological risk than the other three groups of antibiotics, and livestock discharge (31.4% contribution) and aquaculture (23.4% contribution) were the main sources of risks of antibiotic contamination in Dafeng River Basin. This study is expected to provide some reference for control and risk management of antibiotic pollution in Dafeng River Basin.

Challenges and effective tracking down strategies of antibiotic contamination in aquatic ecosystem

A growing environmental concern revolves around the widespread use of medicines, particularly antibiotics, which adversely impact water quality and various life forms. The unregulated production and utilization of antibiotics not only affect non-targeted organisms but also exert significant evolutionary pressures, leading to the rapid development of antimicrobial resistance (AMR) in bacterial communities. To address this issue, global studies have been conducted to assess the prevalence and quantities of antibiotics in various environmental components including freshwater, ocean, local sewage, and fish. These studies aim to establish effective analytical methods for identifying and measuring antibiotic residues in environmental matrices that might enable authorities to establish norms for the containment and disposal of antibiotics. This article offers a comprehensive overview of methods used to extract antibiotics from environmental matrices exploring purification techniques such as liquid-liquid extraction, solid-phase extraction, green extraction techniques, and concentration methods like lyophilization and rotary evaporation. It further highlights qualitative and quantitative analysis methods, high-performance liquid chromatography, ultra-high-performance liquid chromatography, and liquid chromatography-tandem along with analytical methods such as UV-Vis and tandem mass spectrometry for detecting and measuring antibiotics. Urgency is underscored for proactive strategies to curb antibiotic contamination, safeguarding the integrity of aquatic ecosystems and public health on a global scale.

Vermicompost: In situ retardant of antibiotic resistome accumulation in cropland soils

The dissemination of antibiotic resistance genes (ARGs) in soil has become a global environmental issue. Vermicomposting is gaining prominence in agricultural practices as a soil amendment to improve soil quality. However, its impact on soil ARGs remains unclear when it occurs in farmland. We comprehensively explored the evolution and fate of ARGs and their hosts in the field soil profiles under vermicompost application for more than 3 years. Vermicompost application increased several ARG loads in soil environment but decreased the high-risk bla-ARGs (blaampC, blaNDM, and blaGES-1) by log(0.04 - 0.43). ARGs in soil amended with vermicompost primarily occurred in topsoil (approximately 1.04-fold of unfertilized soil), but it is worth noting that their levels in the 40-60 cm soil layer were the same or even less than in the unfertilized soil. The microbial community structure changed in soil profiles after vermicompost application. Vermicompost application altered the microbial community structure in soil profiles, showing that the dominant bacteria (i.e., Proteobacteria, Actinobacteriota, Firmicutes) were decreased 2.62%-5.48% with the increase of soil depth. A network analysis further revealed that most of ARG dominant host bacteria did not migrate from surface soil to deep soil. In particular, those host bacteria harboring high-risk bla-ARGs were primarily concentrated in the surface soil. This study highlights a lower risk of the propagation of ARGs caused by vermicompost application and provides a novel approach to reduce and relieve the dissemination of ARGs derived from animals in agricultural production.

Environmentally Relevant Antibiotic Concentrations Exert Stronger Selection Pressure on River Biofilm Resistomes than AMR-Reservoir Effluents

Freshwater environments are primary receiving systems of wastewater and effluents, which carry low concentrations of antibiotics and antimicrobial-resistant (AMR) bacteria and genes. Aquatic microbial communities are thus exposed to environmentally relevant concentrations of antibiotics (ERCA) that presumably influence the acquisition and spread of environmental AMR. Here, we analyzed ERCA exposure with and without the additional presence of municipal wastewater treatment plant effluent (W) and swine manure run-off (M) on aquatic biofilm resistomes. Microscopic analyses revealed decreased taxonomic diversity and biofilm structural integrity, while metagenomic analysis revealed an increased abundance of resistance, virulence, and mobile element-related genes at the highest ERCA exposure levels, with less notable impacts observed when solely exposed to W or M effluents. Microbial function predictions indicated increased gene abundance associated with energy and cell membrane metabolism and heavy metal resistance under ERCA conditions. In silico predictions of increased resistance mechanisms did not correlate with observed phenotypic resistance patterns when whole communities were exposed to antimicrobial susceptibility testing. This reveals important insight into the complexity of whole-community coordination of physical and genetic responses to selective pressures. Lastly, the environmental AMR risk assessment of metagenomic data revealed a higher risk score for biofilms grown at sub-MIC antibiotic conditions.

Variations in antimicrobial resistance genes present in the rectal faeces of seals in Scottish and Liverpool Bay coastal waters

Antibiotic resistance genes originating from human activity are considered important environmental pollutants. Wildlife species can act as sentinels for coastal environmental contamination and in this study we used qPCR array technology to investigate the variety and abundance of antimicrobial resistance genes (ARGs), mobile genetic elements (MGEs) and integrons circulating within seal populations both near to and far from large human populations located around the Scottish and northwest English coast. Rectal swabs were taken from 50 live grey seals and nine live harbour seals. Nucleic acids were stabilised upon collection, enabling extraction of sufficient quality and quantity DNA for downstream analysis. 78 ARG targets, including genes of clinical significance, four MGE targets and three integron targets were used to monitor genes within 22 sample pools. 30 ARGs were detected, as well as the integrons intl1 and intl2 and tnpA transposase. Four β-lactam, nine tetracycline, two phenicol, one trimethoprim, three aminoglycoside and ten multidrug resistance genes were detected as well as mcr-1 which confers resistance to colistin, an important drug of last resort. No sulphonamide, vancomycin, macrolide, lincosamide or streptogramin B (MLSB) resistance genes were detected. Resistance genes were detected in all sites but the highest number of ARGs (n = 29) was detected in samples derived from grey seals on the Isle of May, Scotland during the breeding season, and these genes also had the highest average abundance in relation to the 16S rRNA gene. This pilot study demonstrates the effectiveness of a culture-independent workflow for global analysis of ARGs within the microbiota of live, free-ranging, wild animals from habitats close to and remote from human habitation, and highlights seals as a valuable indicator species for monitoring the presence, abundance and land-sea transference of resistance genes within and between ecosystems.

Source apportionment and predictable driving factors contribute to antibiotics profiles in Changshou Lake of the Three Gorges Reservoir area, China

Lakes, crucial antibiotic reservoirs, lack thorough exploration of quantitative relationships between antibiotics and influencing factors. Here, we conducted a comprehensive year-long investigation in Changshou Lake within the Three Gorges Reservoir area, China. The concentrations of 21 antibiotics spanned 35.6-200 ng/L, 50.3-348 ng/L and 0.57-57.9 ng/g in surface water, overlying water and sediment, respectively. Compared with abundant water period, surface water and overlying water displayed significantly high antibiotic concentrations in flat and low water periods, while sediment remained unchanged. Moreover, tetracyclines, fluoroquinolones and erythromycin posed notable risks to algae. Six primary sources were identified using positive matrix factorization model, with aquaculture contributing 21.2%, 22.7% and 25.4% in surface water, overlying water and sediment, respectively. The crucial predictors were screened through machine learning, redundancy analysis and Mantel test. Our findings emphasized the pivotal roles of water quality parameters, including water temperature (WT), pH, dissolved oxygen, electrical conductivity, inorganic anions (NO3⁻, Cl⁻ and F⁻) and metal cations (Ca, Mg, Fe, K and Cr), with WT influencing greatest. Total nitrogen (TN), cation exchange capacity, K, Al and Cd significantly impacted sediment antibiotics, with TN having the most pronounced effect. This study can promise valuable insights for environmental planning and policies addressing antibiotic pollution.

A landscape source-sink model to understanding the seasonal dynamics of antibiotics in soils at watershed scale

Human and veterinary antibiotics occur widely in soil ecosystems and pose a serious threat to soil health. Landscape structure can be linked to Earth surface processes and anthropogenic footprints and may influence the variability of antibiotics in soil. In this study, an improved landscape source-sink model was used to characterize source-sink structures using the location-weighted landscape index (LWLI), which can be linked to antibiotic seasonality. The topographic wetness index was employed to identify source and sink landscapes, which represent antibiotic transport pathways via topography-driven hydrological processes. The results indicate that LWLI values and antibiotic seasonality are typically higher in farmland soils than in forest and orchard soils. LWLI values exhibit significant positive correlations with antibiotic seasonality in soils (R2: 0.33-0.58). Furthermore, landscape source-sink structures have a significant influence on antibiotic seasonality between winter and other seasons in farmland soils; however, these structures affect antibiotic seasonality between summer and other seasons in forest and orchard soils. The results of this study indicate that water movement regulated by landscape structure may play a crucial role in influencing antibiotic seasonality in soils at the watershed scale, and the landscape source-sink model can be used to quantitatively evaluate antibiotic seasonality in soil environment.

Impacts of irrigation with treated livestock wastewater on the accumulation characteristic of ARGs in the farmland soil: a case study in Hohhot, China

Irrigation with treated livestock wastewater (TWW) is a promising strategy for reusing resources. However, TWW irrigation might introduce antibiotic resistant genes (ARGs) into the soil, posing environmental risks associated with antibiotic resistance. This study focuses on investigating the influence of irrigation amounts and duration on the fate of ARGs and identifies key factors driving their changes. The results showed that there were 13 ARGs in TWW, while only 5 ARGs were detected in irrigated soil. That is some introduced ARGs from TWW could not persistently exist in the soil. After 1-year irrigation, an increase in irrigation amount from 0.016 t/m2 to 0.048 t/m2 significantly enhanced the abundance of tetC by 29.81%, while ermB and sul2 decreased by 45.37% and 76.47%, respectively (p < 0.01). After 2-year irrigation, the abundance of tetC, ermB, ermF, dfrA1, and total ARGs significantly increased (p < 0.05) when the irrigation amount increased. The abundances of ARGs after 2-year irrigation were found to be 2.5-34.4 times higher than 1 year. Obviously, the irrigation years intensified the positive correlation between ARGs abundance and irrigation amount. TetC and ermF were the dominant genes resulting in the accumulation of ARGs. TWW irrigation increased the content of organic matter and total nitrogen in the soil, which affected microbial community structure. The changes of the potential host were the determining factors driving the ARGs abundance. Our study demonstrated that continuous TWW irrigation for 2 years led to a substantial accumulation of ARGs in soil.

Degradation kinetics of veterinary antibiotics and estrogenic hormones in a claypan soil

Veterinary antibiotics and estrogens are excreted in livestock waste before being applied to agricultural lands as fertilizer, resulting in contamination of soil and adjacent waterways. The objectives of this study were to 1) investigate the degradation kinetics of the VAs sulfamethazine and lincomycin and the estrogens estrone and 17β-estradiol in soil mesocosms, and 2) assess the effect of the phytochemical DIBOA-Glu, secreted in eastern gamagrass (Tripsacum dactyloides) roots, on antibiotic degradation due to the ability of DIBOA-Glu to facilitate hydrolysis of atrazine in solution assays. Mesocosm soil was a silt loam representing a typical claypan soil in portions of Missouri and the Central United States. Mesocosms (n = 133) were treated with a single target compound (antibiotic concentrations at 125 ng g-1 dw, estrogen concentrations at 1250 ng g-1 dw); a subset of mesocosms treated with antibiotics were also treated with DIBOA-Glu (12,500 ng g-1 dw); all mesocosms were kept at 60% water-filled pore space and incubated at 25 °C in darkness. Randomly chosen mesocosms were destructively sampled in triplicate for up to 96 days. All targeted compounds followed pseudo first-order degradation kinetics in soil. The soil half-life (t0.5) of sulfamethazine ranged between 17.8 and 30.1 d and ranged between 9.37 and 9.90 d for lincomycin. The antibiotics results showed no significant differences in degradation kinetics between treatments with or without DIBOA-Glu. For estrogens, degradation rates of estrone (t0.5 = 4.71-6.08 d) and 17β-estradiol (t0.5 = 5.59-6.03 d) were very similar; however, results showed that estrone was present as a metabolite in the 17β-estradiol treated mesocosms and vice-versa within 24 h. The antibiotics results suggest that sulfamethazine has a greater potential to persist in soil than lincomycin. The interconversion of 17β-estradiol and estrone in soil increased their overall persistence and sustained soil estrogenicity. This study demonstrates the persistence of these compounds in a typical claypan soil representing portions of the Central United States.

Poultry manure-derived microorganisms as a reservoir and source of antibiotic resistance genes transferred to soil autochthonous microorganisms

Animal husbandry is increasing yearly due to the growing demand for meat and livestock products, among other reasons. To meet these demands, prophylactic antibiotics are used in the livestock industry (i.e., poultry farming) to promote health and stimulate animal growth. However, antibiotics are not fully metabolized by animals, and they are evacuated to the environment with excreta. Animal manure is used as fertilizer to reduce the volume of waste generated in the livestock sector. However, manure often contains microorganisms harboring antibiotic resistance genes (ARGs). Then, the microbiome of manure applicate to the soil may contribute to the spread of antibiotic resistance in the environment, including autochthonous soil-dwelling microorganisms. The present study was conducted during the crops growing season in Poland (May to September 2019) to determine the influence of poultry manure as well as poultry manure supplemented with selected antibiotics on the diversity of the soil microbiome in treatments that had not been previously fertilized with manure and the ability of antibiotic-resistant bacteria to transfer ARGs to other soil bacteria. Antibiotic concentrations were elevated at the beginning of the study and decreased over time. Poultry manure induced significant changes in the structure of microbial communities in soil; the diversity of the soil microbiome decreased, and the abundance of bacterial genera Bradyrhizobium, Streptomyces, and Pseudomonas, which are characteristic of the analyzed manure, increased. Over time, soil microbial diversity was restored to the state observed before the application of manure. Genes conferring resistance to multiple drugs as well as genes encoding resistance to bacitracin and aminoglycosides were the most frequently identified ARGs in the analyzed bacteria, including on mobile genetic elements. Multidrug resistance was observed in 17 bacterial taxa, whereas ARGs were identified in 32 bacterial taxa identified in the soil microbiome. The results of the study conclude that the application of poultry manure supplemented with antibiotics initially affects soil microbiome and resistome diversity but finally, the soil shows resilience and returns to its original state after time, with most antibiotic resistance genes disappearing. This phenomenon is of great importance in sustainable soil health after manure application.

Comprehensive discovery and migration evaluation of antimicrobial drugs and their transformation products in a swine farm by target, suspect, and nontarget screening

Swine farms contaminated the surrounding environment through manure application and biogas slurry irrigation, hence causing the wide residual of multiple antimicrobial drugs (ADs) and their transformation products (TPs). This study performed target, suspect, and nontarget screening methods to comprehensively investigate the pollution profiles of ADs in a typical swine farm, and characterize the potential transformed pathway of TPs and distinguish specific reactions of different catalog of ADs. Samples of fresh feces, compost, biogas slurry, topsoil, column soil, groundwater and plants were analyzed using the database containing 98 target analytes, 679 suspected parent ADs, and ∼ 107 TPs. In total, 29 ADs were quantitively detected, and tetracyclines (TCs) were mostly frequently detected ADs with the concentrations up to 4251 ng/g in topsoil. Soil column investigation revealed that doxycycline (DOX) and tetracycline (TC) in soil could migrate to depths of approximately 1 m in soil. Suspect screening identified 75 parent ADs, with 10 being reported for the first time in environmental media. Semi-quantification of ADs revealed that one of the less-concerned ADs, clinafloxacin, was detected to exceed 5000 ng/L in biogas slurry, suggesting that significant attentions should be paid to these less-concerned ADs. Moreover, 314 TPs was identified, and most of them were found to undergo microbial/enzymatic metabolism pathways. Overall, our study displays a comprehensive overview of ADs and their TPs in swine farming environments, and provides an inventory of crucial list that worthy of concern. The results emphasize the need to quantify the levels and distribution of previously overlooked ADs and their TPs in livestock farms.

Effects of soil habitat changes on antibiotic resistance genes and related microbiomes in paddy fields

The changes of paddy soil habitat profoundly affect the structure and function of soil microorganisms, but how this process drives the growth and spread of manure- derived antibiotic resistance genes (ARGs) after entering the soil is unclear. Herein, this study explored the environmental fate and behavior of various ARGs in the paddy soil during rice growth period. Results showed that most ARG abundances in flooded soil was lower than that in non-flooded soil during rice growth (decreased by 33.4 %). And soil dry-wet alternation altered microbial community structure in paddy field (P < 0.05), showing that Actinobacteria and Firmicutes increased in proportion under non-flooded conditions, and Chloroflexi, Proteobacteria and Acidobacteria evolved into the dominant groups in flooded soil. Meanwhile, the correlation between ARGs and bacterial communities was stronger than that with mobile genetic elements (MGEs) in both flooded and non-flooded paddy soils. Furthermore, soil properties, especially oxidation reduction potential (ORP), were proved to be an essential factor in regulating the variability of ARGs in the whole rice growth stage by structural equation model, with a direct influence (λ = 0.38, P < 0.05), following by similar effects of bacterial communities and MGEs (λ = 0.36, P < 0.05; λ = 0.29, P < 0.05). This study demonstrated that soil dry-wet alternation effectively reduced the proliferation and dissemination of most ARGs in paddy fields, providing a novel agronomic measure for pollution control of antibiotic resistance in farmland ecosystem.

Long-term impacts of conservation pasture management in manuresheds on system-level microbiome and antibiotic resistance genes

Animal manure improves soil fertility and organic carbon, but long-term deposition may contribute to antibiotic resistance genes (ARGs) entering the soil-water environment. Additionally, long-term impacts of applying animal manure to soil on the soil-water microbiome, a crucial factor in soil health and fertility, are not well understood. The aim of this study is to assess: (1) impacts of long-term conservation practices on the distribution of ARGs and microbial dynamics in soil, and runoff; and (2) associations between bacterial taxa, heavy metals, soil health indicators, and ARGs in manures, soils, and surface runoff in a study following 15 years of continuous management. This management strategy consists of two conventional and three conservation systems, all receiving annual poultry litter. High throughput sequencing of the 16S ribosomal RNA was carried out on samples of cattle manure, poultry litter, soil, and runoff collected from each manureshed. In addition, four representative ARGs (intl1, sul1, ermB, and blactx-m-32) were quantified from manures, soil, and runoff using quantitative PCR. Results revealed that conventional practice increased soil ARGs, and microbial diversity compared to conservation systems. Further, ARGs were strongly correlated with each other in cattle manure and soil, but not in runoff. After 15-years of conservation practices, relationships existed between heavy metals and ARGs. In the soil, Cu, Fe and Mn were positively linked to intl1, sul1, and ermB, but trends varied in runoff. These findings were further supported by network analyses that indicated complex co-occurrence patterns between bacteria taxa, ARGs, and physicochemical parameters. Overall, this study provides system-level linkages of microbial communities, ARGs, and physicochemical conditions based on long-term conservation practices at the soil-water-animal nexus.

Long-term field application of manure induces deep selection of antibiotic resistomes in leaf endophytes of Chinese cabbage

Antibiotic resistomes in leaf endophytes of vegetables threaten human health through the food chain. However, little is known about the ability of long-term manure fertilization to impact the deep selection of antibiotic resistance genes (ARGs) in leaf endophytes of vegetables planted in different types of soils. Here, by high-throughput quantitative PCR, we characterized the ARGs of leaf endophytes of Chinese cabbage (Brassica pekinensis (Lour.) Rupr.) grown in long-term (14 year) manure-amended acidic, neutral and calcareous soils. In total, 87 ARGs and 4 mobile genetic elements (MGEs) were detected in all the samples. Manure fertilization significantly increased the ARG numbers and normalized abundance in leaf endophytes, especially in acidic soil. Moreover, in acidic soil, manure application also led to a higher increase in the normalized abundance of opportunist and specialist ARGs, and more opportunist and specialist ARGs posed a high risk according to their risk ranks. Random forest analysis revealed that Proteobacteria and MGEs were the major drivers affecting the normalized abundance of opportunist and specialist ARGs in both acidic and neutral soils, respectively. In calcareous soil, Cyanobacteria and Actinobacteria were the most important contributors. Collectively, this study expands our knowledge about the deep selection of plant resistomes under long-term manure application.

Persistence of Antibiotic Resistance Genes Varies with Particle Size and Substrate Conditions in Recirculating Streams

Antibiotic resistance (AR) determinants are enriched in animal manures, a significant portion of which is land-applied as a soil amendment or as fertilizer, leading to potential AR runoff and microbial pollution in adjacent surface waters. To effectively inform AR monitoring and mitigation efforts, a thorough understanding and description of the persistence and transport of manure-derived AR in flowing waters are needed. We used experimental recirculating mesocosms to assess water-column removal rates of antibiotic resistance genes (ARGs) originating from a cow manure slurry collected from a dairy farm. We quantified the effect of three benthic (i.e., bottom) substrate variations and particle sizes of manure slurry on water column removal rates. Overall, we observed variation in ARG behavior across substrate treatments and particle sizes. For ARGs associated with small particles, removal rates were higher in mesocosms with a substrate. tetW was typically removed at the highest rates across particle size and treatment, followed by ermB and bla_TEM. Our data suggests that both substrate character and particle size exert control on the fate and transport of ARGs in surface waters, laying the foundation for future research in this area to establish a predictive framework for AR persistence and fate in flowing waters.

Critical Evaluation of Two Qualitative Analytical Approaches for Multiclass Determination of Veterinary Drugs in Bovine Muscle Using UHPLC-Q-Orbitrap: The Wind of Change in Brazilian Monitoring

Food safety is recognized as a main requirement for consumers, food industries, and official laboratories. Here, we present the optimization and screening qualitative validation of two multianalyte methods in bovine muscle tissues by ultra-high-performance liquid chromatography coupled to high-resolution mass spectrometry with an Orbitrap-type analyzer, operated with a heated ionization source in positive and negative mode. This aims for not only the simultaneous detection of veterinary drugs regulated in Brazil but also the prospection of antimicrobials not yet monitored. Two different sample preparation procedures were applied: method A-generic solid-liquid extraction with 0.1% formic acid (v/v) in an aqueous solution of EDTA 0.1% (w/v)-acetonitrile-methanol (1:1:1, v/v/v), followed by an additional ultrasound-assisted extraction and method B-QuEChERS. In both procedures, selectivity showed satisfactory conformity. From a detection capability (CCβ) equivalent to ½ the maximum residue limit, >34% of the analyte resulted in a false positive rate of <5%, preponderant by the QuEChERS method, which exhibited a higher yield of the sample. The results showed the potential application of both procedures in the routine analysis of foods by official laboratories, enabling the expansion of this methodological portfolio as well as its analytical scopes, thus optimizing the control of residues of veterinary drugs in the country.

Influence of manure application method on veterinary medicine losses to water

Veterinary medicines are routinely used within modern animal husbandry, which results in frequent detections within animal manures and slurries. The application of manures to land as a form of organic fertiliser presents a pathway by which these bioactive chemicals can enter the environment. However, to date, there is limited understanding regarding the influence of commonly used manure application methods on veterinary medicine fate in soil systems. To bridge this knowledge gap, a semi-field study was conducted to assess the influence of commonly used application methods such as, broadcast, chisel sweep, and incorporation on veterinary medicine losses to waters. A range of veterinary medicines were selected and applied as a mixture; these were enrofloxacin, florfenicol, lincomycin, meloxicam, oxytetracycline, sulfadiazine, trimethoprim and tylosin. All the assessed veterinary medicines were detected within surface runoff and leachates, and the concentrations generally decreased throughout the irrigation period. The surface runoff concentrations ranged from 0.49 to 183.47 μg/L and 2.26-236.83 μg/L for the bare soil and grass assessments respectively. The leachate concentrations ranged from 0.04 to 309.66 μg/L and 0.33-37.79 μg/L for the bare soil and grass assessments respectively. More advanced application methods (chisel sweep) were found to significantly reduce the mass loads of veterinary medicines transported to surface runoff and leachate by 13-56% and 49-88% over that of broadcast. Incorporating pig slurries reduced the losses further with surface runoff and leachate losses being 13-56% and 49-88% lower than broadcast. Our results show that manure application techniques have a significant effect on veterinary medicine fate in the environment and as such these effects should be considered in the decision-making processes for the management of manures as well as from a risk mitigation perspective for aquatic compartments.

Using HRMS fingerprinting to explore micropollutant contamination in soil and vegetables caused by swine wastewater irrigation

Livestock wastewater has been reused for agricultural irrigation to save water and fertilise the soil. However, micropollutants excreted by livestock animals may contaminate the soil and crops through livestock wastewater irrigation. This study employed high-resolution mass spectrometry (HRMS) to facilitate broad-scope suspect screening of soil and vegetables and identify changes in micropollutant fingerprints caused by swine wastewater irrigation. Field trials were performed to simulate the practical cultivation of small leafy vegetables. Soil and pak choi were irrigated with groundwater, a reasonable amount of swine wastewater, and excessive swine wastewater (three times the reasonable amount) and were sampled at three time points. The samples were extracted using organic solvents and analysed with a liquid chromatography-quadrupole-time-of-flight HRMS system. The molecular features were compared to over 3000 micropollutants in commercial libraries. The relative concentrations of suspect micropollutants among the irrigation groups were compared using multivariate and univariate analyses. The marker micropollutants that increased with swine wastewater irrigation were rigorously identified based on the MS/MS spectra. Fifty-three micropollutants were frequently found in the soil (n = 54) and 36 in the pak choi (n = 53). Partial least squares discriminant analysis (PLS-DA) models revealed significant differences in the micropollutant fingerprints in the soil among the three irrigation groups, but not in the pak choi. Eight micropollutants with variable importance in projection scores above 1.0 in the PLS-DA model and significantly higher relative concentrations (p < 0.05) in the soil irrigated with swine wastewater were confirmed as markers. Besides veterinary drugs and their metabolites, cinnamic acid and phenylalanine were the markers relevant to swine feed that were not previously reported. Nevertheless, accumulations of micropollutants in the soil or contamination of the pak choi due to swine wastewater irrigation were not found under the trial conditions.

Antibiotic resistome in groundwater and its association with mountain springs and river

The distribution of antibiotic resistance genes (ARGs) in water sources potentially threatens drinking water safety. However, the sources of antibiotic resistome in groundwater are still under-investigated. Here, we evaluated the profiles of antibiotic resistome in peri-urban groundwater and its associated water sources (river and mountain spring) to characterize the antibiotic resistome from natural water sources on groundwater resistome. A total of 261 antibiotic resistome were detected in groundwater, mountain spring, and river samples. The relative abundances of ARGs and mobile genetic elements (MGEs) were significantly higher in the river samples than in spring water and groundwater samples. The resistome profiles were similar between groundwater and spring water but differed from the river samples. According to source tracking results, the groundwater resistome was likely to be derived from springs (28.0%-50.0%) and rivers (28.6%-48.6%), which share the same trend for the source tracking of bacterial communities. Bacterial α-diversity, bacterial β-diversity, and MGEs directly or indirectly affected the ARGs in groundwater samples. Although the abundance of groundwater resistome was not elevated by river and spring water, groundwater resistomes were diverse and may be derived from both river and spring water. We highlight the importance of groundwater resistome and its association with potential water sources, providing a better understanding and basis for the effective control of the ARG proliferation and dissemination in groundwater from exogenous water bodies in the future.

Exploring antibiotic resistance load in paddy-upland rotation fields amended with commercial organic and chemical/slow release fertilizer

Agricultural fertilization caused the dissemination of antibiotic resistance genes (ARGs) in agro-ecological environment, which poses a global threat to crop-food safety and human health. However, few studies are known about the influence of different agricultural fertilization modes on antibiotic resistome in the paddy-upland rotation soils. Therefore, we conducted a field experiment to compare the effect of different fertilization (chemical fertilizer, slow release fertilizer and commercial organic fertilizer replacement at various rates) on soil antibiotic resistome in paddy-upland rotation fields. Results revealed that a total of 100 ARG subtypes and 9 mobile genetic elements (MGEs) occurred in paddy-upland rotation soil, among which MDR-ARGs, MLSB-ARGs and tet-ARGs were the dominant resistance determinants. Long-term agricultural fertilization remarkably facilitated the vertical accumulation of ARGs, in particular that bla _ampC and tetO in relative abundance showed significant enrichment with increasing depth. It's worth noting that slow release fertilizer significantly increased soil ARGs, when comparable to manure with 20% replacing amount, but chemical fertilizer had only slight impact on soil ARGs. Fertilization modes affected soil microbial communities, mainly concentrated in the surface layer, while the proportion of Proteobacteria with the highest abundance decreased gradually with increasing depth. Furthermore, microbial community and MGEs were further proved to be essential factors in regulating the variability of ARGs of different fertilization modes by structural equation model, and had strong direct influence (λ = 0.61, p < 0.05; λ = 0. 55, p < 0.01). The results provided scientific guidance for reducing the spreading risk of ARGs and control ARG dissemination in agricultural fertilization.

Vegetative buffer strips show limited effectiveness for reducing antibiotic transport in surface runoff

Vegetative buffer strips (VBS) have been demonstrated to effectively reduce loads of sediment, nutrients, and herbicides in surface runoff, but their effectiveness for reducing veterinary antibiotic (VA) loads in runoff has not been well documented. The objective of this study was to determine the effectiveness of VBS vegetation and width on surface runoff loads of the VAs sulfamethazine (SMZ) and lincomycin (LIN). Experimental design of the plots (1.5 × 25 m) was a two-way factorial with four vegetation treatments (tall fescue [Festuca aruninacea Schreb.]; tall fescue with switchgrass [Panicum virgatum L.] hedge; warm-season native grass mix; and continuous fallow control), and four buffer widths (0, 2, 5, and 9 m). Turkey litter spiked with SMZ and LIN was applied to the source area (upper 7 m) of each plot, and runoff was collected at each width. Runoff was generated with a rotating boom simulator. Results showed VA loads in runoff at the 0-m sampler ranged from 3.8 to 5.9% of applied, and overall VA transport in runoff was predominately in the dissolved phase (90% for SMZ and 99% for LIN). Among vegetation treatments, only tall fescue significantly reduced loads of SMZ and LIN compared with the control, with load reductions of ∼30% for both VAs. Estimated field-scale reductions in VA loads showed that source-to-buffer area ratios (SBARs) of 10:1 to 20:1 reduced VA loads by only 7 to 16%. Overall, the grass VBS tested here were less effective at reducing SMZ and LIN loads in surface runoff than has been previously demonstrated for sediment, nutrients, and herbicides.

Effect of live and inactivated Chlamydomonas reinhardtii on the removal of tetracycline in aquatic environments

With the development of medical drugs, the widely used tetracycline has brought many adverse effects on the ecosystem and human health. Tetracycline pollution of water environment is becoming more and more serious, and has become an emerging environmental problem. As single celled organisms, microalgae are not only model organisms for risk assessment of aquatic ecosystems, but also can efficiently purify sewage. Microalgae-mediated pollutant remediation has attracted more and more attention from researchers. In this paper, Chlamydomonas reinhardtii (C. reinhardtii) was used to remove tetracycline in aqueous solution, and the removal efficiency and mechanism of microalgae on tetracycline were studied. The results showed that the removal rates of tetracycline by active and inactivated microalgae at a density of 5 × 10⁶ cells·mL^-1 were 81.9% and 89.8%, respectively. C. reinhardtii removed tetracycline through biosorption and nonmetabolic processes. Microalgal cell supernatant and hydroxyl radicals could significantly promote the removal of tetracycline. The positively charged tetracycline was electrostatically adsorbed on the microalgae surface and extracellular polymeric substances. Microalgae biomass can promote the production of ROS and enhance the ability of microalgae to remove tetracycline.

Effects of tetracycline, sulfonamide, fluoroquinolone, and lincosamide load in pig slurry on lettuce: Agricultural and human health implications

The application of pig slurry as fertilizer in agriculture provides nutrients, but it can also contain veterinary medicines, including antibiotic residues (ABs), which can have an ecotoxicological impact on agroecosystems. Furthermore, uptake, translocation, and accumulation of ABs in crops can mobilize them throughout the food chain. This greenhouse study aims to assess AB uptake from soil fertilized with pig slurry and its phenotypical effects on Lactuca sativa L. The plants were cropped in loamy clay soil dosed at 140 kg total N/ha and containing antibiotics (lincomycin, sulfadiazine, oxytetracycline, and enrofloxacin) at different concentration levels (0, 0.05, 0.5, 5, 50, and 500 mg/kg fresh weight, fw). Whereas sulfadiazine (11.8 ng/g fw) was detected in lettuce leaves at the intermediate doses (0.5 mg/kg), lincomycin and its transformation products (hydroxy/sulfate) were only detected at the 50 mg/kg fw dose. In addition, increased AB doses in the pig slurry resulted in decreased lettuce fresh weight and lipid and carbohydrate content and became lethal to lettuce at the highest AB concentrations (500 mg/kg fw). Nevertheless, even at higher doses, the AB content in lettuce following pig-slurry fertilization did not pose any direct significant human health risk (total hazard quotient<0.01). However, the promotion of antimicrobial resistance in humans due to the intake of these vegetables cannot be ruled out.

Subsurface Manure Injection Reduces Surface Transport of Antibiotic Resistance Genes but May Create Antibiotic Resistance Hotspots in Soils

Compared to surface application, manure subsurface injection reduces surface runoff of nutrients, antibiotic resistant microorganisms, and emerging contaminants. Less is known regarding the impact of both manure application methods on surface transport of antibiotic resistance genes (ARGs) in manure-amended fields. We applied liquid dairy manure to field plots by surface application and subsurface injection and simulated rainfall on the first or seventh day following application. The ARG richness, relative abundance (normalized to 16s rRNA), and ARG profiles in soil and surface runoff were monitored using shotgun metagenomic sequencing. Within 1 day of manure application, compared to unamended soils, soils treated with manure had 32.5-70.5% greater ARG richness and higher relative abundances of sulfonamide (6.5-129%) and tetracycline (752-3766%) resistance genes (p ≤ 0.05). On day 7, soil ARG profiles in the surface-applied plots were similar to, whereas subsurface injection profiles were different from, that of the unamended soils. Forty-six days after manure application, the soil ARG profiles in manure injection slits were 37% more diverse than that of the unamended plots. The abundance of manure-associated ARGs were lower in surface runoff from manure subsurface injected plots and carried a lower resistome risk score in comparison to surface-applied plots. This study demonstrated, for the first time, that although manure subsurface injection reduces ARGs in the runoff, it can create potential long-term hotspots for elevated ARGs within injection slits.

Global review of macrolide antibiotics in the aquatic environment: Sources, occurrence, fate, ecotoxicity, and risk assessment

The extensive use of macrolide antibiotics (MCLs) has led to their frequent detection in aquatic environments, affecting water quality and ecological health. In this study, the sources, global distribution, environmental fate, ecotoxicity and global risk assessment of MCLs were analyzed based on recently published literature. The results revealed that there are eight main sources of MCLs in the water environment. These pollution sources resulted in MCL detection at average or median concentrations of up to 3847 ng/L, and the most polluted water bodies were the receiving waters of wastewater treatment plants (WWTPs) and densely inhabited areas. Considering the environmental fate, adsorption, indirect photodegradation, and bioremoval may be the main attenuation mechanisms in natural water environments. N-demethylation, O-demethylation, sugar and side chain loss from MCL molecules were the main pathways of MCLs photodegradation. Demethylation, phosphorylation, N-oxidation, lactone ring hydrolysis, and sugar loss were the main biodegradation pathways. The median effective concentration values of MCLs for microalgae, crustaceans, fish, and invertebrates were 0.21, 39.30, 106.42, and 28.00 mg/L, respectively. MCLs induced the generation of reactive oxygen species, that caused oxidative stress to biomolecules, and affected gene expression related to photosynthesis, energy metabolism, DNA replication, and repair. Moreover, over 50% of the reported water bodies represented a medium to high risk to microalgae. Further studies on the development of tertiary treatment technologies for antibiotic removal in WWTPs, the combined ecotoxicity of antibiotic mixtures at environmental concentration levels, and the development of accurate ecological risk assessment models should be encouraged.

Effects of drying strategies on sporulation and titer of microbial ecological agents with Bacillus subtilis

Drying operation is beneficial to the preservation and transportation of microbial ecological agents. In this study, drying kinetics and water distribution variations in solid biomass medium during hot air drying (HAD) and vacuum freeze drying (VFD) were systematically investigated. Meanwhile, the effects of different drying strategies on the sporulation of Bacillus subtilis and the titer of microbial ecological agents were compared. The results showed that both HAD and VFD induced rapid water removal from the solid biomass medium. VFD retained bound water and maintained the porous structure of the solid medium. Both HAD and VFD induced sporulation. The expression level of sporulation-regulatory genes spo0A, sigF, and sigE followed the order 80°C-HAD > 60°C-HAD > VFD. The spore number in the medium after 80°C-HAD drying for 6 h was 0.72 × 10¹⁰/g dry medium, which was 9.1 and 12.5% larger than that of the medium with 60°C-HAD and VFD, respectively. Therefore, 80°C-HAD is an effective drying strategy for promoting sporulation, which improves the titer of microbial ecological agents with B. subtilis.

Environmental impacts of mass drug administration programs: exposures, risks, and mitigation of antimicrobial resistance

Mass drug administration (MDA) of antimicrobials has shown promise in the reduction and potential elimination of a variety of neglected tropical diseases (NTDs). However, with antimicrobial resistance (AMR) becoming a global crisis, the risks posed by widespread antimicrobial use need to be evaluated. As the role of the environment in AMR emergence and dissemination has become increasingly recognized, it is likewise crucial to establish the role of MDA in environmental AMR pollution, along with the potential impacts of such pollution. This review presents the current state of knowledge on the antimicrobial compounds, resistant organisms, and antimicrobial resistance genes in MDA trials, routes of these determinants into the environment, and their persistence and ecological impacts, particularly in low and middle-income countries where these trials are most common. From the few studies directly evaluating AMR outcomes in azithromycin MDA trials, it is becoming apparent that MDA efforts can increase carriage and excretion of resistant pathogens in a lasting way. However, research on these outcomes for other antimicrobials used in MDA trials is sorely needed. Furthermore, while paths of AMR determinants from human waste to the environment and their persistence thereafter are supported by the literature, quantitative information on the scope and likelihood of this is largely absent. We recommend some mitigative approaches that would be valuable to consider in future MDA efforts. This review stands to be a valuable resource for researchers and policymakers seeking to evaluate the impacts of MDA.

Field study on loss of tetracycline antibiotics from manure-applied soil and their risk assessment in regional water environment of Guangzhou, China

Tetracycline antibiotics (TCs) introduced into agricultural fields via manure application tend to accumulate in soils and further reach water environments via surface runoff and leachate, posing potential risks to regional water environment. This study investigated the loss of tetracycline (TC), oxytetracycline (OTC), and chlortetracycline (CTC) in surface runoff and leachate samples collected from a vegetable farmland with manure application in Guangzhou, South China. A risk assessment method was constructed for evaluating the ecological and health risks of manure-associated antibiotics released from soil into water environment. The results showed that the concentrations of three TCs in surface runoff, 30-cm leachate, and 60-cm leachate after the first rainfall event were 2.79-35.97, 1.71-18.44, and 0.4-2.66 μg/L, respectively, which all decreased with sampling depth and the time after rainfall events. Up to 0.13% of TCs were transported into the surface water through surface runoff, while less than 0.01% of TCs were transported into the groundwater through leachate at 60 cm. OTC had a higher total mass percentage (0.13%) into surface water via runoff than CTC (0.11%) and TC (0.07%) likely due to its smallest K_d value and largest input mass. Based on loss percentages, their predicted environmental concentrations (PEC) ranged from 4.87 (TC) to 16.91 (OTC) ng/L in regional surface water and 1.42 (TC) to 5.20 (CTC) ng/L in regional groundwater. The risk assessment based on PEC results suggested non-negligible health risk (HQ > 1.0 × 10^-6) and low ecological risk (RQ < 0.1) in both regional surface water and groundwater, drawing concerns on the potential hazards of TCs released from manure-amended soil into water environments.

Understanding flow patterns from the field - Controlled laboratory experiments on the transport behavior of veterinary antibiotics in the presence of liquid manure

The main entry path of veterinary antibiotics to the environment is the application of liquid manure on agricultural land. Along with the manure, they can infiltrate into soils and leach into groundwater. As the environmental behavior of veterinary antibiotics is strongly affected by the process of sorption, the comprehensive knowledge regarding their sorption behavior is key to a reliable risk assessment. However, the flow patterns in field experiments are influenced by several factors that can hardly be distinguished, while most of the sorption studies on veterinary antibiotics were designed without manure or as batch experiments, which means that the effects of manure on the transport behavior of the antibiotic substances remained unaccounted for. In order to understand the results from a previous field experiment and concurrently fill the identified knowledge gap, a column experiment was performed to investigate the effects of manure on the transport of sulfamethazine, sulfadiazine, tetracycline, and lincomycin in soil. Results show that sulfamethazine and sulfadiazine were highly mobile in both the presence and absence of manure, while tetracycline did not appear at the outlet of any column. Despite their high mobility, in the presence of manure the sulfonamides were slightly delayed compared to the conservative tracer as was also seen during the previous field experiment. Lincomycin transport was already delayed in the absence of manure. Furthermore, in the presence of manure, lincomycin was delayed by 4.5 times relative to the tracer, which clearly underlined the influence of manure on the transport of lincomycin and offers an explanation why lincomycin has barely been detected in the long-term field experiment. However, in contrast to the results obtained in the field experiment, the recovery rates were the same in presence and absence of manure for both sulfonamides and lincomycin, probably due to reduced degradation at the applied concentration level.

Resistome and mobilome in surface runoff from manured soil as affected by setback distance

Land application of livestock manure introduces antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) into the soil environment. The objectives of this study were to examine the changes of resistome and mobilome in runoff and soil as a function of setback distance, i.e., the distance between manured soil and surface water, and to quantify the contributions of manure and background soil to the ARGs and MGEs in surface runoff. The resistome and mobilome in runoff and soil from a field-scale plot study were characterized using a high throughput quantitative polymerase chain reaction (HT-qPCR) array. It was estimated that a setback distance of ~40 m is required to reduce the total abundance of ARGs and MGEs in runoff from amended plots to that in control runoff. The resistome and mobilome of the soil in the setback region was not affected by manure-borne ARGs and MGEs. SourceTracker analyses revealed that background soil gradually became the predominant source of the ARGs and MGEs in runoff as setback distance increased. The results demonstrate how manure-borne ARGs and MGEs dissipated in agricultural runoff with increasing setback distance and had limited impacts on the resistome and mobilome of soil within the setback region.

Transport of Veterinary Antibiotics in Farmland Soil: Effects of Dissolved Organic Matter

The application of manure as a fertiliser to farmland is regarded as a major source of veterinary antibiotic (VA) contamination in the environment. The frequent detection of such emerging contaminants and their potential adverse impacts on the ecosystem and human health have provoked increasing concern for VA transport and fate. Extrinsic dissolved organic matter (DOM) may be introduced into farmland soil along with Vas, and thus exert significant effects on the transport of VAs via hydrological processes upon rainfall. The leaching of VAs can be either enhanced or reduced by DOM, depending on the nature, mobility, and interactions of VAs with DOM of different origins. From the aspect of the diversity and reactivity of DOM, the state-of-the-art knowledge of DOM-VA interactions and their resulting effects on the sorption-desorption and leaching of VAs in farmland soil was reviewed. Spectroscopic techniques for examining the extent of binding and reactive components of DOM with VAs are summarized and their usefulness is highlighted. Models for simulating VA transport under the effects of DOM were also reviewed. It is suggested that distinct impacts of DOM of various organic fertiliser/amendment origins should be considered for predicting the transport of VAs in farmland soil.

Environmental contamination in a high-income country (France) by antibiotics, antibiotic-resistant bacteria, and antibiotic resistance genes: Status and possible causes

Antimicrobial resistance (AMR) is a major global public health concern, shared by a large number of human and animal health actors. Within the framework of a One Health approach, actions should be implemented in the environmental realm, as well as the human and animal realms. The Government of France commissioned a report to provide policy and decision makers with an evidential basis for recommending or taking future actions to mitigate AMR in the environment. We first examined the mechanisms that underlie the emergence and persistence of antimicrobial resistance in the environment. This report drew up an inventory of the contamination of aquatic and terrestrial environments by AMR and antibiotics, anticipating that the findings will be representative of some other high-income countries. Effluents of wastewater treatment plants were identified as the major source of contamination on French territory, with spreading of organic waste products as a more diffuse and incidental contamination of aquatic environments. A limitation of this review is the heterogeneity of available data in space and time, as well as the lack of data for certain sources. Comparing the French Measured Environmental Concentrations (MECs) with predicted no effect concentrations (PNECs), fluoroquinolones and trimethoprim were identified as representing high and medium risk of favoring the selection of resistant bacteria in treated wastewater and in the most contaminated rivers. All other antibiotic molecules analyzed (erythromycin, clarithromycin, azithromycin, tetracycline) were at low risk of resistance selection in those environments. However, the heterogeneity of the data available impairs their full exploitation. Consequently, we listed indicators to survey AMR and antibiotics in the environment and recommended the harmonization of sampling strategies and endpoints for analyses. Finally, the objectives and methods used for the present work could comprise a useful example for how national authorities of countries sharing common socio-geographic characteristics with France could seek to better understand and define the environmental dimension of AMR in their particular settings.

Environmental heterogeneity determines the response patterns of microbially mediated N-reduction processes to sulfamethoxazole in river sediments

The widespread occurrence of antibiotics in aquatic ecosystems leads to potential ecological risks to organisms, in turn affecting microbially mediated processes. Here, we investigated the response of dominant N-reduction processes to the frequently detected antibiotic sulfamethoxazole (SMX) along the Chaobai River with regional environmental heterogeneity, including denitrification, anaerobic ammonium oxidation (anammox), dissimilatory nitrate reduction to ammonium (DNRA), and nitrous oxide (N₂O) release. We found two divergent SMX response patterns for denitrification in contrasting scenarios of geochemical properties. In the context of low nitrate and carbon, SMX weakened denitrification with a slightly stimulation first. Whereas SMX directly inhibited denitrification when nitrate and carbon were sufficient. High SMX concentration suppressed anammox (26-72%) and DNRA activities (48-84%) via restraining the activities of anammox and DNRA bacteria. Notably, SMX increased the contribution of denitrification to N-reduction at the expense of DNRA to N-reduction, leading to a shift in nitrogen conversion towards denitrification. Additionally, SMX stimulated N₂O emission (up to 91%) due to superior restraint on process of N₂O reduction to N₂ and an incline for N-reduction towards denitrification, thereby exacerbating greenhouse effect. Our results advance the understanding of how nitrogen cycling is affected by SMX in aquatic ecosystems with environmental heterogeneity.

Modeling the vertical transport of antibiotic resistance genes in agricultural soils following manure application

Antibiotic resistance genes (ARGs) may be introduced to agricultural soil through the land application of cattle manure. During a rainfall event, manure-borne ARGs may infiltrate into subsurface soil and leach into groundwater. The objective of this study was to characterize and model the vertical transport of manure-borne ARGs through soil following the land application of beef cattle manure on soil surface. In this study, soil column experiments were conducted to evaluate the influence of manure application on subsurface transport of four ARGs: erm(C), erm(F), tet(O) and tet(Q). An attachment-detachment model with the decay of ARGs in the soil was used to simulate the breakthrough of ARGs in leachates from the control column (without manure) and treatment (with manure) soil columns. Results showed that the first-order attachment coefficient (k_a) was five to six orders of magnitude higher in the treatment column than in the control column. Conversely, the first-order detachment and decay coefficients (k_d and μ_s) were not significantly changed due to manure application. These findings suggest that in areas where manure is land-applied, some manure-borne bacteria-associated ARGs will be attached to the soil, instead of leaching to groundwater in near terms.

Assessment of veterinary antibiotics from animal manure-amended soil to growing alfalfa, alfalfa silage, and milk

Using animal manure as organic fertilizer to grow fodder crops is causing public health concerns because animal manure is the major reservoir of veterinary antibiotics. In this study, we used a mathematical model to estimate the risk of human exposure to veterinary antibiotics when using swine manure as organic fertilizer to grow alfalfa (Medicago sativa L.). Alfalfa was planted in a greenhouse and fertilized with swine manure spiked with oxytetracycline (OTC, at 0, 150, and 1500 mg/kg of manure), ofloxacin (OFL, at 0, 15, and 150 mg/kg), or sulfamonomethoxine (SMM, at 0, 5, 15 and 150 mg/kg). Alfalfa was harvested at the budding stage and ensiled for 60 days. Results showed that OTC and OFL could be detected in the alfalfa root, stem, and leaf with a concentration ranging from 8.85 to 59.17 μg OTC /kg and from 1.50 to 4.10 μg OFL/kg dry matter, but SMM could only be detected in the root ranging from 29.10 to 63.75 μg/kg dry matter. The ensiling for 60 days decreased the OFL concentration by 68.7% but only slightly decreased the OTC concentration. The maximum daily exposures of humans to OTC and OFL through liquid milk consumption were estimated to be 5.84E-8 and 1.63E-8 μg, respectively, both of which are well below the intake levels of OTC (72 μg) and OFL (54 μg) mandated by the European Union. The results of the present study indicate that using swine manure as organic fertilizer to grow alfalfa poses a limited risk for human exposure to veterinary antibiotics through the consumption of liquid milk.

A review targeting veterinary antibiotics removal from livestock manure management systems and future outlook

Veterinary antibiotics (VAs) contamination has been considered as a worldwide environmental and health concern in recent decades. This paper reviewed the variability of contents of VAs and their release from the animal breeding industry into the surrounding environment along with the performance of the manure treatment technologies. The data collected revealed that VAs were mostly excreted in animal feces and observed in manure, soil, water, and sediment. The findings illustrate the disparity of VAs in excretion rates, consumption, and their residues in the environment with relatively high distribution for tetracyclines, fluoroquinolones, and sulfonamides. Anaerobic digestion has a capacity to remove of 73% VAs while manure composting and constructed wetlands can remove 84.7%, and 90% VAs. Due to the profound effect of antibiotics on the environment, further research and intensive management strategies for livestock manure need to be designed to improve the removal efficiency and manure management technologies.

Occurrence, effects and behaviour of the antibiotic lincomycin in the agricultural and aquatic environment - A review

Lincomycin, an antibiotic commonly used in veterinary medicine, is frequently detected within the agricultural environment. The active compound enters the aquatic environment after manure application via infiltration or surface run-off, where it may negatively affect non-target organisms and contribute to the development and spread of resistant genes. However, a review on the fate of lincomycin within the agricultural and aquatic environment is lacking. Hence, to provide an overview, the main part of this paper summarizes the current literature on the occurrence, effects and behaviour of lincomycin in all relevant environmental compartments, including manure, soil, surface water and groundwater. Lincomycin was regularly detected in all environmental compartments and even in the food chain, appeared to sorb temporarily and mainly in its cationic microspecies, and dissipated after time periods that could cover days, months, or years, depending on the compartment and conditions. As noticed during the literature research conducted, information on the attenuation of lincomycin in terms of biological degradation in the aquatic environment is widely lacking, although it seems that biodegradation is the major removal mechanism. Therefore, a laboratory study, implemented by means of batch experiments, was carried out in order to evaluate the biological degradation of lincomycin in the aquatic environment. First order degradation started after a start-up phase of 10-14 days with a degradation rate constant of 0.55 d^-1 and a half-life time of 30 h. Further, the degradation rate constant was found to be independent of initial concentrations as long as concentrations did not exceed a concentration level at which the bacteria were inhibited, as it was the case in this study at a concentration of 10 mg L^-1. Biodegradation was confirmed as an important degradation pathway for LIN in the aquatic environment.

Investigating antibiotics, antibiotic resistance genes in soil, groundwater and vegetables in relation to agricultural field - Applicated with lincomycin mycelial residues compost

Antibiotic mycelial residue, a kind of organic bio-waste, after composting with the subsequent land application is an effective way to achieve its resource utilization. However, its influences on soil quality and ecological safety in the practical agricultural field and related environmental media, e.g., groundwater and vegetables, remain investigated. In the present study, a field experiment with vegetable plants was conducted to study the influences of lincomycin mycelial residue compost (LMRC) on soil quality, and antibiotics and ARGs' fate. In particular, soil physicochemical properties and microbial community composition were analyzed. Moreover, antibiotics and ARGs' evolution in soil, vegetable, and groundwater were determined. The results showed that the LMRC amendment enhanced soil fertility with the increases of organic matter, total nitrogen, and available P/K. Enzyme activities except catalase and urease were promoted, and they were positively related to the LMRC application ratio. Soil microbial community composition presented temporary shifts as LMRC added, and the low application amount soil showed no significant difference with control at the end of the experiment. Similarly, lincomycin concentration in soil was far lower than the background, and it decreased below the predicted no-effect concentration in groundwater. Besides, the detected lincomycin in pakchoi grew in 0.5% and 1% LMRC amended soil was lower than acceptable daily intake (30 μg/kg). Low application rate (0.5%) of LMRC caused no significant changes of tested ARGs in soil, vegetables, and groundwater. Information obtained from this study provides reasonable application strategies for LMRC that with environmental acceptable antibiotic and ARGs.

Bacterial communities regulate temporal variations of the antibiotic resistome in soil following manure amendment

The increasing emergence of antibiotic-resistant genes (ARGs) represents a global threat to human health. Land application of animal manure is known to contribute considerably to the propagation and dispersal of antibiotic resistance in agro-ecosystems. Yet, the primary determinants of the fate of the soil resistome remain obscure. In this study, a pot experiment was conducted to examine temporal changes in ARGs, mobile genetic elements (MGEs), and bacterial communities in a weakly developed loamy soil (an entisol known as calcareous purple soil) upon addition of pig or chicken manure. On the day of manure application, substantial increases in the diversity and relative abundance of ARGs were observed in soil amended with raw pig manure. At the same time, no obvious changes were observed for soil amended with chicken manure. Antibiotic resistance in pig manure-amended soils rapidly decreased over time to a level that was still higher than that of unamended soil at 100 days after manure application. The results of the Mantel test and Procrustes analysis indicated that ARG profiles in soil were significantly correlated with the structure of the bacterial phylogeny. Variation partitioning analysis further revealed that the bacterial community played a major role in regulating the temporal changes in ARGs in soil following manure application. Increased numbers and relative abundances of MGEs and their significant positive correlations with ARGs were observed, which suggest that a potential contribution from lateral gene transfer to the persistence and spread of ARGs should not be overlooked. Overall, our findings provide a better understanding of the mechanisms underlying the dynamics of ARGs in entisols following manure application and have practical implications for managing manure applications in entisols of the study area and other areas.

Role played by the environment in the emergence and spread of antimicrobial resistance (AMR) through the food chain

The role of food-producing environments in the emergence and spread of antimicrobial resistance (AMR) in EU plant-based food production, terrestrial animals (poultry, cattle and pigs) and aquaculture was assessed. Among the various sources and transmission routes identified, fertilisers of faecal origin, irrigation and surface water for plant-based food and water for aquaculture were considered of major importance. For terrestrial animal production, potential sources consist of feed, humans, water, air/dust, soil, wildlife, rodents, arthropods and equipment. Among those, evidence was found for introduction with feed and humans, for the other sources, the importance could not be assessed. Several ARB of highest priority for public health, such as carbapenem or extended-spectrum cephalosporin and/or fluoroquinolone-resistant Enterobacterales (including Salmonella enterica), fluoroquinolone-resistant Campylobacter spp., methicillin-resistant Staphylococcus aureus and glycopeptide-resistant Enterococcus faecium and E. faecalis were identified. Among highest priority ARGs bla CTX -M, bla VIM, bla NDM, bla OXA -48-like, bla OXA -23, mcr, armA, vanA, cfr and optrA were reported. These highest priority bacteria and genes were identified in different sources, at primary and post-harvest level, particularly faeces/manure, soil and water. For all sectors, reducing the occurrence of faecal microbial contamination of fertilisers, water, feed and the production environment and minimising persistence/recycling of ARB within animal production facilities is a priority. Proper implementation of good hygiene practices, biosecurity and food safety management systems is very important. Potential AMR-specific interventions are in the early stages of development. Many data gaps relating to sources and relevance of transmission routes, diversity of ARB and ARGs, effectiveness of mitigation measures were identified. Representative epidemiological and attribution studies on AMR and its effective control in food production environments at EU level, linked to One Health and environmental initiatives, are urgently required.

Do Long-Term Conservation Pasture Management Practices Influence Microbial Diversity and Antimicrobial Resistant Genes in Runoff?

Runoff from land-applied manure and poultry litter is one mechanism by which manure-borne bacteria are transported over large distances in the environment. There is a global concern that antimicrobial resistant (AMR) genes may be transmitted through the food chain from animal manures to soil to surface water. However, details are lacking on the ecology of AMR genes in water runoff as well as how conservation management practices may affect the runoff microbiome or minimize the movement of AMR genes. The aim of this study was to identify microbial community structure and diversity in water runoff following 14-years of poultry litter and cattle manure deposition and to evaluate the amount of AMR genes under five conventional and conservation pasture management strategies. Since 2004, all watersheds received annual poultry litter at a rate of 5.6 Mg ha⁻¹ and were consistently managed. Surface runoff samples were collected from each watershed from 2018 to 2019, characterized using Illumina 16S rRNA gene amplicon sequencing and enumerated for four AMR-associated genes (ermB, sulI, intlI, and bla_ctx-m-32) using quantitative PCR. Overall, long-term pasture management influenced water microbial community structure, with effects differing by year (p < 0.05). Bacterial richness (Chao1 index) was influenced by pasture management, with the lowest richness occurring in the control (nearby non-agricultural water source) and the greatest under fields that were hayed (no cattle presence). Runoff bacterial richness in watersheds increased following poultry litter applications, indicating poultry litter is a possible source of bacteria and altered runoff community structure. The bla_ctx-m-32 gene was not detected in any surface water sample. The remaining three AMR genes were absent in the non-agricultural control, but present in agricultural samples. However, there was no impact (p > 0.05) from pasture management on the abundance of these genes, indicating both conventional and conservation practices have similar ecologies for these targets; however, there was a greater detection of sulI genes from runoff in continuously grazed systems in 2019, with hay being lowest in 2019. Results illustrate that the edge of field buffer strips may increase bacterial richness in water runoff, but these changes in richness do not greatly impact target AMR genes in the United States largest land-use category.

Changes and distributions of antibiotic resistance genes in liquid and solid fractions in mesophilic and thermophilic anaerobic digestion of dairy manure

This study mainly explored the changes and distributions of antibiotic resistance genes (ARGs) in liquid fraction (L_F) and solid fraction (S_F) in anaerobic digestion (AD) of dairy manure. After mesophilic and thermophilic AD, the copy numbers of ARGs in L_F decreased by 0.06-1.80 logs while those in S_F increased by 0.08-7.85 logs, suggesting the enrichment of ARGs in S_F. Statistical analysis elucidated that high total solids promoted the enrichment of ARGs in S_F. The increased abundances of genera such as Ruminofilibacter, Treponema and Sphaerochaeta in S_F were responsible for the enrichment of most ARGs. These insights demonstrated the digested solid had the potential risks to promote the spread of ARGs in the environment, and the digested solid of livestock manure should be post-treated before the application.

Treated wastewater irrigation promotes the spread of antibiotic resistance into subsoil pore-water

In the present study, we investigated the impact of treated wastewater (TWW) irrigation on the prevalence of antibiotic resistance genes (ARGs) in subsoil pore-water, a so-far under-appreciated matrix. We hypothesized that TWW irrigation increases ARG prevalence in subsoil pore-water. This hypothesis was tested using a multiphase approach, which consisted of sampling percolated subsoil pore-water from lysimeter-wells of a real-scale TWW-irrigated field, operated for commercial farming practices, and controlled, laboratory microcosms irrigated with freshwater or TWW. We monitored the abundance of six selected ARGs (sul1, bla_OXA-58, tetM, qnrS, bla_CTX-M-32 and bla_TEM), the intI1 gene associated with mobile genetic elements and an indicator for anthropogenic pollution and bacterial abundance (16S rRNA gene) by qPCR. The bacterial load of subsoil pore water was independent of both, irrigation intensity in the field study and irrigation water type in the microcosms. Among the tested genes in the field study, sul1 and intI1 exhibited constantly higher relative abundances. Their abundance was further positively correlated with increasing irrigation intensity. Controlled microcosm experiments verified the observed field study results: the relative abundance of several genes, including sul1 and intI1, increased significantly when irrigating with TWW compared to freshwater irrigation. Overall, TWW irrigation promoted the spread of ARGs and intI1 in the subsoil pore-water, while the bacterial load was maintained. The combined results from the real-scale agricultural field and the controlled lab microcosms indicate that the dissemination of ARGs in various subsurface environments needs to be taken into account during TWW irrigation scenarios.

Multimedia mass balance approach to characterizing the transport potential of antibiotics in soil-plant systems following manure application

Antibiotics are ubiquitous in agro-ecosystems worldwide, which can pose remarkable risks to ecological security and human health. However, comprehensive evaluation on the multimedia fate and transport potential of antibiotics in soil-plant systems is still lacking. A mass balance approach was performed to gain insights into the transport and fate of antibiotics in soil-plant systems following manure application. Our results showed that more than 99 % of antibiotics were released from applied manure fertilizer into the soil-plant system. Antibiotic concentrations in soil and plant compartments increased over 120 days. Most of the antibiotics persisted in soil (about 65 %), while less than 0.1 % accumulated in the plants. Rainfall-induced runoff, subsurface interflow and soil water infiltration were alternative transport pathways for antibiotics in soil-plant systems although their contributions were limited. Dissipation was the main removal pathway for antibiotics accounting for about 33 % of total input mass. Tetracyclines had higher mass proportion in soil following by quinolones, whereas most of sulfonamides and macrolides were dissipated. Mass balance approach based on tracking environmental fates of antibiotics can facilitate the understandings in the source comparisons and mitigation strategies, and therefore provide insights to inform modeling and limiting the transport of manure-borne antibiotics to neighboring environmental compartments.

Effects of land use and rainfall on sequestration of veterinary antibiotics in soils at the hillslope scale

Veterinary antibiotics have been detected as contaminants of emerging concern in soil environment worldwide. Animal manure is frequently applied to agricultural fields to improve soil fertility, which can result in introducing large amount of antibiotics into soil environment. However, few attempts have been made to identify the spatial and temporal dynamics of veterinary antibiotics in soil at the hillslope scale with different land uses. This study was performed to explore the pattern and variability of veterinary antibiotics in the soil in response to rainfall events. Results showed that higher concentrations of veterinary antibiotics were generally found in cropland (292.6 ± 280.1 ng/g) and orchard (228.1 ± 230.5 ng/g) than in forestland (13.5 ± 9.9 ng/g). After rainfall events, antibiotics accumulated in the soil at the positions where manure was applied, especially under high-intensity rainfall conditions. However, the antibiotic concentration in soil slightly increased from the top to the bottom of hills, thus indicating the restricted contribution of runoff to antibiotic transport, especially under low-intensity rainfall conditions. In addition, most antibiotics were sequestered in the surface soil (0-10 cm), and higher antibiotic concentrations were observed in deep soil (20-40 cm) in cropland than orchard. The soil aggregate, organic matter, and clay content played important roles in antibiotic sequestration along the hillslope subject to low-, medium-, and large-amount rainfall events, respectively. This study identified that land use, rainfall conditions, and soil structures jointly affect the spatial and temporal variability of antibiotics in soils on hillslopes.