Distribution of antibiotic resistance genes (ARGs) in anaerobic digestion and land application of swine wastewater

Fate of florfenicol and linezolid resistance genes and their bacterial hosts during two waste treatment models in swine feedlots

Florfenicol resistance genes (FRGs) are widely present in livestock farms. The aim of this study was to evaluate the removal efficiencies of FRGs as well as the relationships between FRGs, mobile genetic elements (MGEs) and bacterial communities during the natural drying (ND) and anaerobic digestion (AD) processes of manure treatment in swine farms by combining bacterial isolation, quantitative PCR and metagenomic approaches. Solid manure showed a higher abundance of FRGs than fresh manure and was the main contamination source of fexA and fexB in ND farms, whilst biogas slurry displayed a lower abundance of FRGs than the wastewater in AD farms. Moreover, fresh manure and wastewater showed a high abundance of optrA, and wastewater was the main contamination source of cfr in both ND and AD farms. Both optrA/fexA-positive enterococci and cfr/fexA-positive staphylococci were mainly isolated along the farms' treatment processes. The cfr-positive staphylococci were highly prevalent in wastewater (57.14 % - 100 %) and may be associated with nasal-derived cfr-positive porcine staphylococci. An increased abundance of Enterococcus, Jeotgalibaca and Vagococcus in the bacterial community structures may account for the high optrA abundance in wastewater and Jeotgalibaca may be another potential host of optrA. Furthermore, the abundance of FRG-related MGEs increased by 22.63 % after the ND process and decreased by 66.96 % in AD farms. A significant correlation was observed between cfr and ISEnfa4, whereas no significance was found between optrA and IS1216E, although IS1216E is the predominant insertion sequence involved in the transfer of optrA. In conclusion, manure and wastewater represented independent pollution sources of FRGs in swine farms. Associated MGEs might play a key role in the transfer and persistence of FRGs. The AD process was more efficient in the removal of FRGs than the ND method, nevertheless a longer storage of slurry may be required for a complete removal.

Livestock and poultry breeding farms as a fixed and underestimated source of antibiotic resistance genes

The excessive use of antibiotics, disinfectants, and drugs in livestock and poultry breeding has resulted in a rise in the presence of antibiotic resistance genes (ARGs). Antibiotic-resistant bacteria (ARB) and ARGs have been widely found in animal feces, farm wastewater, and farm air. ARGs can not only spread across media through adsorption and migration, but also transfer resistance across bacterial genera through horizontal gene transfer. Livestock breeding has become a fixed and unavoidable source of ARGs in the environment. Existing technologies for controlling ARGs, such as composting, disinfection, and sewage treatment, are not efficient in removing ARB and ARGs from waste. Furthermore, the remaining ARGs still possess a strong capacity for dissemination. At present, antibiotics used in animal husbandry are difficult to replace in a short period of time. The growth and potential risks of resistance genes in livestock and poultry breeding sources in the receiving environment are not yet clear. In this paper, we summarize the current situation of ARGs in the livestock and poultry breeding environment. We also explain the key environmental processes, main influencing factors, and corresponding ecological risks associated with ARGs in this environment. The advantages and disadvantages of current technologies for the removal of ARGs are primarily discussed. There is a particular emphasis on clarifying the spatiotemporal evolution patterns and environmental process mechanisms of ARGs, as well as highlighting the importance and urgency of developing efficient pollution control technologies.

Recent advances in swine wastewater treatment technologies for resource recovery: A comprehensive review

Swine wastewater (SW), characterized by highly complex organic and nutrient substances, poses serious impacts on aquatic environment and public health. Furthermore, SW harbors valuable resources that possess substantial economic potential. As such, SW treatment technologies place increased emphasis on resource recycling, while progressively advancing towards energy saving, sustainability, and circular economy principles. This review comprehensively encapsulates the state-of-the-art knowledge for treating SW, including conventional (i.e., constructed wetlands, air stripping and aerobic system) and resource-utilization-based (i.e., anaerobic digestion, membrane separation, anaerobic ammonium oxidation, microbial fuel cells, and microalgal-based system) technologies. Furthermore, this research also elaborates the key factors influencing the SW treatment performance, such as pH, temperature, dissolved oxygen, hydraulic retention time and organic loading rate. The potentials for reutilizing energy, biomass and digestate produced during the SW treatment processes are also summarized. Moreover, the obstacles associated with full-scale implementation, long-term treatment, energy-efficient design, and nutrient recovery of various resource-utilization-based SW treatment technologies are emphasized. In addition, future research prospective, such as prioritization of process optimization, in-depth exploration of microbial mechanisms, enhancement of energy conversion efficiency, and integration of diverse technologies, are highlighted to expand engineering applications and establish a sustainable SW treatment system.

Fe-Mn binary oxides improve the methanogenic performance and reduce the environmental health risks associated with antibiotic resistance genes during anaerobic digestion

Increasing evidence indicates that metal oxides can improve the methanogenic performance during anaerobic digestion (AD) of piggery wastewater. However, the impacts of composite metal oxides on the methanogenic performance and risk of antibiotic resistance gene (ARG) transmission during AD are not fully understood. In this study, different concentrations of Fe-Mn binary oxides (FMBO at 0, 250, 500, and 1000 mg/L) were added to AD to explore the effects of FMBO on the process. The methane yield was 7825.1 mL under FMBO at 250 mg/L, 35.2% higher than that with FMBO at 0 mg/L. PICRUSt2 functional predictions showed that FMBO promoted the oxidation of acetate and propionate, and the production of methane from the substrate, as well as increasing the abundances of most methanogens and genes encoding related enzymes. Furthermore, under FMBO at 250 mg/L, the relative abundances of 14 ARGs (excluding tetC and sul2) and four mobile gene elements (MGEs) decreased by 24.7% and 55.8%, respectively. Most of the changes in the abundances of ARGs were explained by microorganisms, especially Bacteroidetes (51.20%), followed by MGEs (11.98%). Thus, the methanogenic performance of AD improved and the risk of horizontal ARG transfer decreased with FMBO, especially at 250 mg/L.

Effect of wheat crops on the persistence and attenuation of antibiotic resistance genes in soil after swine wastewater application

Swine wastewater (SW) application introduces antibiotic resistance genes (ARGs) into farmland soils. However, ARG attenuation in SW-fertigated soils, especially those influenced by staple crops and soil type, remains unclear. This study investigated twelve soil ARGs and one mobile genetic element (MGE) in sandy loam, loam, and silt loam soils before and after SW application in wheat-planted and unplanted soils. The results revealed an immediate increase in the abundance of ARGs in soil by two orders of magnitude above background levels following SW application. After SW application, the soil total ARG abundance was attenuated, reaching background levels at 54 days; However, more individual ARGs were detected above the detection limit than pre-application. Among the 13 genes, acc(6')-lb, tetM, and tetO tended to persist in the soil during wheat harvest. ARG half-lives were up to four times longer in wheat-planted soils than in bare soils. Wheat planting decreased the persistence of acc(6')-lb, ermB, ermF, and intI2 but increased the persistence of others such as sul1 and sul2. Soil type had no significant impact on ARG and MGE fates. Our findings emphasize the need for strategic SW application and the consideration of crop cultivation effects to mitigate ARG accumulation in farmland soils.

Effect of reactor operation modes on mitigating antibiotic resistance genes (ARGs) and methane production from hydrothermally-pretreated pig manure

Numerous efforts have been made to enhance the performance of anaerobic digestion (AD) for accelerating renewable energy generation, however, it remains unclear whether the intensified measures could enhance the proliferation and transmissions of antibiotic resistance genes (ARGs) in the system. This study assessed the impact of an innovative pig manure AD process, which includes hydrothermal pretreatment (HTP) and a two-stage configuration with separated acidogenic and methanogenic phases, on biomethane (CH4) production and ARGs dynamics. Results showed that HTP significantly increase CH4 production from 0.65 to 0.75 L/L/d in conventional single-stage AD to 0.82 and 0.91 L/L/d in two-stage AD. This improvement correlated with a rise in the relative abundance of Methanosarcina, a key methanogenesis microorganism. In the two-stage AD, the methanogenic stage offered an ideal environment for methanogens growth, resulting in substantially faster and higher CH4 production by about 10% compared to single-stage AD. Overall, the combined use of HTP and the two-stage AD configuration enhanced CH4 production by 40% compared to traditional single-stage AD. The abundance and diversity of ARGs were significantly reduced in the acidogenic reactors after HTP. However, the ARGs levels increased by about two times in the following methanogenesis stage and reached similar or higher levels than in single stage AD. The erm(F), erm(G), ant(6)-Ia, tet(W), mef(A) and erm(B) were the six main ARGs with significant differences in relative abundances in various treatments. The two-stage AD mode could better remove sul2, but it also had a rebound which elevated the risk of ARGs to the environment and human health. Network analysis identified pH and TVFAs as critical factors driving microbial communities and ARG proliferation in the new AD process. With the results, this study offers valuable insights into the trade-offs between AD performance enhancement and ARG-related risks, pinpointing essential areas for future research and practical improvements.

Tracing the transfer characteristics of antibiotic resistance genes from swine manure to biogas residue and then to soil

Based on laboratory simulation experiments and metagenomic analysis, this study tracked the transmission of antibiotic resistance genes (ARGs) from swine manure (SM) to biogas residue and then to soil (biogas residue as organic fertilizer (OF) application). ARGs were abundant in SM and they were assigned to 11 categories of antibiotics. Among the 383 ARG subtypes in SM, 43 % ARG subtypes were absent after anaerobic digestion (AD), which avoided the transfer of these ARGs from SM to soil. Furthermore, 9 % of the ARG subtypes in SM were introduced into soil after amendment with OF. Moreover, 43 % of the ARG subtypes in SM were present in OF and soil, and their abundances increased slightly in the soil amended with OF. The bacterial community in the soil treated with OF was restored to its original state within 60 to 90 days, probably because the abundances of ARGs were elevated but not significantly in the soil. Network analysis identified 31 potential co-host bacteria of ARGs based on the relationships between the bacteria community members, where they mainly belonged to Firmicutes, followed by Bacteroidetes, Actinobacteria, and Proteobacteria. This study provides a basis for objectively evaluating pollution by ARGs in livestock manure for agricultural use.

Variations in antibiotic resistance genes during long-term operation of an upflow anaerobic sludge blanket reactor

Antibiotic resistance genes (ARGs) have been widely detected in the environment. Anaerobic digestion (AD) has the potential ability to remove ARGs, and a comprehensive study is needed on the variations in ARGs during AD. In this study, variations in antibiotic resistance genes (ARGs) and microbial communities were investigated during the long-term operation of an upflow anaerobic sludge blanket (UASB) reactor. An antibiotic mixture of erythromycin, sulfamethoxazole and tetracycline was added to the UASB influent and the operation period was 360 days. The abundances of 11 ARGs and class 1 integron-integrase gene were detected in the UASB reactor, and the correlation between the ARGs and the microbial community was analyzed. The composition of ARGs indicated that the main ARGs in the effluent were sul1, sul2, and sul3, whereas the main ARG in the sludge was tetW. Correlation analysis indicated a negative correlation between microorganisms and ARGs in the UASB. In addition, most of ARGs showed a positive correlation with norank_f_Propionibacteriaceae and Clostridum_sensu_stricto_6, which were identified as potential hosts. These findings may help develop a feasible strategy for removing ARGs from aquatic environments during anaerobic digestion.

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.

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

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

A review on the effects of discharging conventionally treated livestock waste to the environmental resistome

Globally, animal production has developed rapidly as a consequence of the ongoing population growth, to support food security. This has consequently led to an extensive use of antibiotics to promote growth and prevent diseases in animals. However, most antibiotics are not fully metabolized by these animals, leading to their excretion within urine and faeces, thus making these wastes a major reservoir of antibiotics residues, antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) in the environment. Farmers normally depend on conventional treatment methods to mitigate the environmental impact of animal waste; however, these methods are not fully efficient to remove the environmental resistome. The present study reviewed the variability of residual antibiotics, ARB, as well as ARGs in the conventionally treated waste and assessed how discharging it could increase resistome in the receiving environments. Wherein, considering the efficiency and environmental safety, an addition of pre-treatments steps with these conventional treatment methods could enhance the removal of antibiotic resistance agents from livestock waste.

Role of suspended solids on the co-precipitation of pathogenic indicators and antibiotic resistance genes with struvite from digested swine wastewater

Struvite recovered from wastewater contains high concentration of fecal indicator bacteria (FIB), porcine adenoviruses (PAdV) and antibiotic resistance genes (ARGs), becoming potential resources of these microbial hazards. Understanding the precipitation behavior of pathogenic indicators and ARGs with suspended solids (SS) will provide the possible strategy for the control of co-precipitation. In this study, SS was divided into high-density SS (separated by centrifugation) and low-density SS (further separated by filtration), and the role of SS on the co-precipitation of FIB, PAdV and ARGs was investigated. The distribution analysis showed that 35.5-73.0% FIB, 79.6% PAdV and 64.5-94.8% ARGs existed in high-density SS, while the corresponding values were 26.9-64.4%, 11.7% and 3.5-24.3% in low-density SS. During struvite generation, 82.7-96.9% FIB, 75.5% PAdV and 56.3-86.5% ARGs were co-precipitated into struvite. High-density SS contributed 20.7-68.5% FIB, 63.9% PAdV and 38.7-87.2% ARGs co-precipitation, and the corresponding contribution of low-density SS was 31.4-79.2%, 3.9% and 6.2-54.7%. Moreover, the precipitated SS in struvite obviously decreased inactivation efficiency of FIB and ARGs in drying process. These results provide a potential way to control the co-precipitation and inactivation of FIB, PAdV and ARGs in struvite through removing high-density SS prior to struvite recovery.

Mitigation effects and microbial mechanism of two ecological earthworms on the uptake of chlortetracycline and antibiotic resistance genes in lettuce

The contamination of greenhouse vegetable soils with antibiotics and antibiotic resistance genes (ARGs), caused by the application of livestock and poultry manure, is a prominent environmental problem. In this study, the effects of two ecological earthworms (endogeic Metaphire guillelmi and epigeic Eisenia fetida) on the accumulation and transfer of chlortetracycline (CTC) and ARGs in a soil-lettuce system were studied via pot experiments. The results revealed that earthworm application accelerated the removal of the CTC from the soil and lettuce roots and leaves, with the CTC content reducing by 11.7-22.8 %, 15.7-36.1 %, and 8.93-19.6 % compared with that of the control, respectively. Both earthworms significantly reduced the CTC uptake by lettuce roots from the soil (P < 0.05) but did not change the CTC transfer efficiency from the roots to leaves. The high-throughput quantitative PCR results showed that the relative abundance of ARGs in the soil and lettuce roots and leaves decreased by 22.4-27.0 %, 25.1-44.1 %, and 24.4-25.4 %, respectively, with the application of earthworms. Earthworm addition decreased the interspecific bacterial interactions and the relative abundance of mobile genetic elements (MGEs), which helped reduce the dissemination of ARGs. Furthermore, some indigenous soil antibiotic degraders (Pseudomonas, Flavobacterium, Sphingobium, and Microbacterium) were stimulated by the earthworms. The results of redundancy analysis indicated that the bacterial community composition, CTC residues, and MGEs were the main parameters affecting the distribution of ARGs, accounting for 91.1 % of the total distribution. In addition, the bacterial function prediction results showed that the addition of earthworms reduced the abundance of some pathogenic bacteria in the system. Overall, our findings imply that earthworm application can substantially reduce the accumulation and transmission risk of antibiotics and ARGs in soil-lettuce systems, providing a cost-effective soil bioremediation practice for addressing antibiotic and ARGs contamination to guarantee the safety of vegetables and human health.

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

Comprehensive studies of the effects of various physical and chemical variables (including heavy metals), antibiotics, and microorganisms in the environment on antibiotic resistance genes are rare. We collected sediment samples from the Shatian Lake aquaculture area and surrounding lakes and rivers located in Shanghai, China. The spatial distribution of sediment ARGs was assessed by metagenomic analysis that revealed 26 ARG types (510 subtypes), dominated by Multidrug, β-lactam, Aminoglycoside, Glycopeptides, Fluoroquinolone, and Tetracyline. Redundancy discriminant analysis indicated that antibiotics (SAs and MLs) in the aqueous environment and sediment along with water TN and TP were the key variables affecting the abundance distribution of total ARGs. However, the main environmental drivers and key influences differed among the different ARGs. For total ARGs, the environmental subtypes affecting their structural composition and distribution characteristics were mainly antibiotic residues. Procrustes analysis showed a significant correlation between ARGs and microbial communities in the sediment in the survey area. Network analysis revealed that most of the target ARGs were significantly and positively correlated with microorganisms, and a small number of ARGs (e.g., rpoB, mdtC, and efpA) were highly significantly and positively correlated with microorganisms (e.g., Knoellia, Tetrasphaera, and Gemmatirosa). Potential hosts for the major ARGs included Actinobacteria, Proteobacteria, and Gemmatimonadetes. Our study provides new insight and a comprehensive assessment of the distribution and abundance of ARGs and the drivers of ARG occurrence and transmission.

Hyper-thermophilic anaerobic pretreatment enhances the removal of transferable oxazolidinone and phenicol cross-resistance gene optrA in enterococci

The extensive use of florfenicol in poultry industry results in the emergence of optrA gene, which also confers resistance to clinically important antibiotic linezolid. This study investigated the occurrence, genetic environments, and removal of optrA in enterococci in mesophilic (37 °C) and thermophilic (55 °C) anaerobic digestion systems, and a hyper-thermophilic (70 °C) anaerobic pretreatment system for chicken waste. A total of 331 enterococci were isolated and analyzed for antibiotic resistance against linezolid and florfenicol. The optrA gene was frequently detected in enterococci from chicken waste (42.7%) and effluents from mesophilic (72%) and thermophilic (56.8%) reactors, but rarely detected in the hyper-thermophilic (5.8%) effluent. Whole-genome sequencing revealed that optrA-carrying Enterococcus faecalis sequence type (ST) 368 and ST631 were the dominant clones in chicken waste, and they remained dominant in mesophilic and thermophilic effluents, respectively. The plasmid-borne IS1216E-fexA-optrA-erm(A)-IS1216E was the core genetic element for optrA in ST368, whereas chromosomal Tn554-fexA-optrA was the key one in ST631. IS1216E might play a key role in horizontal transfer of optrA due to its presence in different clones. Hyper-thermophilic pretreatment removed enterococci with plasmid-borne IS1216E-fexA-optrA-erm(A)-IS1216E. A hyper-thermophilic pretreatment is recommended for chicken waste to mitigate dissemination of optrA from animal waste to the environment.

Occurrence and prevalence of antibiotic resistance genes in apple orchard after continual application of anaerobic fermentation residues of pig manure

Fermented organic fertilizers made from pig manure contaminated with antibiotics are widely used in fruit tree production. However, their effects on the residual antibiotics and the spread of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in apple orchards are still largely unknown. In the present study, we detected 100 ARGs and 10 MGEs that were transferred from pig manure to an apple orchard. Compared with the original pig manure, significantly greater concentrations of tetracycline, chlortetracycline, oxytetracycline, sulfadiazine, and salfamethyldiazine were observed in anaerobic fermentation residues of the pig manure. The total relative abundance levels of ARGs on the apple pericarp surface, in the orchard soil treated with biogas slurry, and in the orchard soil treated with biogas residue were 122.5, 5.2, 1.4 times higher than those in pristine soil, respectively, which were primarily attributed to the increase in the relative abundance of some ARG subtypes, including blaCTX-M, blaTEM, ermC, sul2, tetO, vgaB, and vgb. Long-term biogas slurry and biogas residue applications to orchard soil enriched bioaccumulation of 10 ARGs and 1 MGEs on the apple pericarp surface with 67.98 the highest factor. This research indicates that the application of anaerobic fermentation residues of pig manure promoted the spread of ARGs in the soil and fruits and increased the level of ARG pollution in the orchard. Results of this study highlight the importance of assessing the ecological safety of organic fertilizers from the perspective of ARGs and indicate that efforts should be devoted to further reducing ARG levels in pig manure before its application to farmland.

Biotransformation of sulfamethoxazole (SMX) by aerobic granular sludge: Removal performance, degradation mechanism and microbial response

Aerobic granular sludge (AGS) is a promising biotechnology for the treatment of antibiotic-rich wastewater. However, little is known about the antibiotics degradation mechanism and microbial response in a sulfamethoxazole (SMX)-loaded AGS system. Herein, the results of a continuous 240 days test suggested that 0.5-5 mg/L of SMX could be thoroughly removed by AGS via adsorption and degradation. The degradation pathway of SMX involved the hydrolysis of the sulfonamide bond and cleavage of NS or CS bonds, subsequently leading to the production of small molecular substances (e.g. benzene and 5-methyl-isoxazole). In terms of the AGS system, it exhibited a strong resistance to 0.5 mg/L of SMX, while 1 and 5 mg/L of SMX significantly inhibited the microbial growth, declined the nitrification efficiency, weakened the sludge settleability, and triggered the excessive growth of filamentous bacteria. Besides, the secretion of extracellular polymer substances was suppressed by 57.3% when increasing the SMX concentration from 0.5 to 5 mg/L, which was not conducive to the system stability. The long-term presence of SMX enhanced the proliferation of antibiotics resistance genes (sul1and sul2) and exerted a strong selection pressure on the microbial community, especially with Thiothrix being the dominating genus. Overall, this study elucidated that AGS qualified promising application prospects in the removal of SMX present in wastewater, but SMX at high concentrations posed great adverse impacts on the performance of the AGS system, which causes concern when treating SMX rich wastewaters.

Seasonal variation in antibiotic resistance genes and bacterial phenotypes in swine wastewater during three-chamber anaerobic pond treatment

Antibiotic resistance is a global public health concern. Antibiotic usage in pigs makes swine wastewater (SW) a reservoir for antibiotic resistance genes (ARGs). SW is usually stored and treated in a three-chamber anaerobic pond (3-CAP) in medium and small pig farms in northern China. However, the yet unexplored presence of ARGs in SW during 3-CAP treatment may result in ARGs spreading into the environment if farmers apply SW to farmland as a liquid organic fertilizer. This study investigated the profiles of and changes in ARGs in SW during its treatment in 3-CAP over four seasons and analyzed the correlation between ARGs and bacterial phenotypes, along with the physicochemical parameters of the water. The results revealed that ARG abundance decreased considerably after 3-CAP treatment in April (47%), October (47%), and December (62%) but increased in May (43%) and August (73%). The ARG copies in the influent and other SW samples increased significantly from 10⁷ copies/mL in April to 10⁹ copies/mL in October and were maintained in December. The increase in ARG abundance was not as rapid as the growth of the bacterial population, resulting in lower relative abundance in October and December. Bacterial communities possessed more sul1 and tetM genes, which were also positively correlated with mobile genetic elements. After the 3-CAP treatment, 16% of antibiotics and 60% of heavy metals were removed, and both had a weak correlation with ARGs. Predicted phenotypes showed that gram-positive (G⁺) and gram-negative (G^-) bacteria have different capacities for carrying ARGs. G⁺ bacteria carry more ARGs than G^- bacteria. This study revealed the persistence of ARGs in SW after 3-CAP treatment over different seasons. Applying SW in the proper month will mitigate ARG dissemination to the environment.

Removal of antibiotic resistance genes during livestock wastewater treatment processes: Review and prospects

Antibiotic resistance genes (ARGs) are emerging pollutants that have received extensive attention. Many different types of ARGs exist in livestock wastewater. If not effectively treated, they can threaten animal production, public health and the ecological safety of the surrounding environment. To address the high risk of livestock wastewater contamination by ARGs, the effects of different wastewater treatment processes on ARGs and their influencing factors and mechanisms are reviewed herein. Additionally, the current problems associated with removal of ARGs are discussed, and future research is proposed.

Characteristics of resistome and bacterial community structure in constructed wetland during dormant period: A fullscale study from Annan wetland

As a green technology, constructed wetlands (CWs) can provide a low-cost solution for wastewater treatment. Either as a standalone treatment or integrated with conventional treatment, nutrients, antibiotic resistant bacteria (ARB)/antibiotic resistance genes (ARGs) can be removed by CW efficiently. While, few studies have focused on characteristics of resistome and bacterial community (BC) structure in CW during dormant period. Therefore, in this study, Annan CW (a full-scale hybrid CW) was selected to characterize resistome and BC during dormant period. The profiles of bacteria / ARGs were monitored in combination of shotgun sequencing and metagenomic assembly analysis. And multidrug ARGs are the most abundant in Annan CW, and surface flow wetland had the relatively high ARG diversity and abundance compared with subsurface flow wetland and the front pond. The most dominant phylum in CW is Proteobacteria, while the other dominant phylum in three parts have different order. COD, TP, TN, ARGs, and mobile genetic genes (MGEs) were removed by subsurface flow CW with better performance, but virulent factors (VFs) were removed by surface flow CW with better performance. Based on the spatiotemporal distribution of ARGs, the internal mechanism of ARGs dynamic variation was explored by the redundancy analysis (RDA) and variation partitioning analysis (VPA). BCs, MGEs and environmental factors (EFs) were responsible for 45.6 %, 28.3 % and 15.4 % of the ARGs variations. Among these factors, BCs and MGEs were the major co-drivers impacting the ARG profile, and EFs indirectly influence the ARG profile. This study illustrates the specific functions of ARG risk elimination in different CW components, promotes a better understanding of the efficiency of CWs for the reduction of ARG and ARB, contributing to improve the removal performance of constructed wetlands. And provide management advice to further optimize the operation of CWs during dormant period.

Fate of antibiotic resistance genes and class 1 integrons during sludge treatment using pilot-scale anaerobic digestion with thermal hydrolysis pretreatment

This work evaluated the fate of antibiotic resistance genes (ARGs) and class 1 integron gene in sewage sludge before and after pilot-scale thermal hydrolysis pretreatment (THP) and subsequent mesophilic anaerobic digestion (AD) treatment. Variables investigated include THP temperatures, feedstock types, and AD solids retention times. Real-time polymerase chain reaction was performed to quantify the ARGs in feedstocks, THP and AD effluent. Results show that THP significantly (t test, p < 0.05) reduced the absolute abundances of most ARGs, with the reduction ranging from 0.03 to 3.09 log units. Rebound effects of ARGs in the subsequent AD were observed and were relevant with tested variables; shorter solids retention time (10 days) and higher THP temperature (165 ℃) can significantly reduce ARGs in AD effluent. These findings provide references about the effects of the THP and AD on the control of ARG spread from sewage sludge to environments.

Removal behavior and key drivers of antibiotic resistance genes in two full-scale leachate treatment plants

Leachate is a critical reservoir of antibiotic resistance genes (ARGs) and its proper treatment is closely related to human health and ecosystem safety. Here, we used high-throughput qPCR to explore the removal behavior of ARGs in two full-scale leachate treatment plants (LTPs) where biological treatment and membrane filtration processes were integrated. A total of 286 ARGs and 55 mobile genetic elements (MGEs) were detected, with aminoglycoside, multidrug and MLSB resistance genes being the most prevalent and abundant. Anaerobic digestion was found to be an important pretreatment process for leachate, while anoxic/aerobic tanks in membrane bioreactor (MBR) acted as incubators for ARGs due to their significant proliferation effect on ARGs. Integrated membrane filtration (UF-NF-RO) excelled in ARGs removal with absolute abundances reduced by 3 to 6 orders of magnitude, from about 10⁹ copies/mL in raw leachate to 10³-10⁵ copies/mL in effluents. Our results also showed that leachate treatment processes significantly altered the composition of ARGs and bacterial communities. Procrustes analysis and network analysis revealed strong associations between microbes and ARGs, with several hub genes and bacterial genera identified. Structural equation models (SEMs) indicated that bacterial composition, MGEs and basic water properties were the key drivers shaping ARGs dynamics in the raw leachate, biological system and filtration system, respectively. Notably, several pathogens (e.g., Klebsiella, Vibrio, Aeromonas) were closely correlated with ARGs in raw leachate and may amplify the dissemination risks of ARGs. Moreover, insertion sequences in biological systems would accelerate the horizontal gene transfer of ARGs. In short, this study provides new insights into the mechanisms of ARGs removal and dissemination behavior in industrial-scale LTPs.

Metagenomic analysis reveals antibiotic resistance genes and virulence factors in the saline-alkali soils from the Yellow River Delta, China

The propagation of antibiotic resistance genes (ARGs) and virulence factors (VFs) in the saline-alkali soils and associated environmental factors remains unknown. In this study, soil samples from the Yellow River Delta, China with four salinity gradients were characterized by their physiochemical properties, and shotgun metagenomic sequencing was used to identify the ARGs and VFs carried by microorganisms. Soil salinization significantly reduced the relative abundances of Solirubrobacterales, Propionibacteriales, and Micrococcales, and quorum sensing in microorganisms. The number of ARGs and VFs significantly decreased in medium and high saline-alkali soils as compared with that in non-saline-alkali soil, however, the ARGs of Bacitracin, and the VFs of iron uptake system, adherence, and stress protein increased significantly in saline-alkali soils. Spearman analysis showed that the ARGs of fluoroquinolone, tetracycline, aminoglycoside, beta-lactam, and tigecycline were positively correlated with soil pH. Similarly, we observed an increased contribution to the ARGs and VFs by taxa belonging to Solirubrobacterales and Gemmatimonadales, respectively. The control plot was mainly improved from saline-alkali land through application of animal manure, which tended to contain large amounts of ARGs and VFs in this study. Further studies are needed to observe ARGs and VFs in the saline-alkali land for multiple years and speculate the potential risks caused by varied ARGs and VFs to the soil ecosystem and human health.

Enhanced removal of antibiotic resistance genes and human bacterial pathogens during anaerobic digestion of dairy manure via addition of manure biochar

In this study, the response of antibiotic resistance genes (ARGs), mobile gene elements (intI1), and human bacterial pathogens (HBPs) to addition of manure biochar (1-10 g/L) was studied in anaerobic digestion (AD) at 20-55 °C for treating dairy manure. Twelve ARGs comprising five tetracycline resistance genes, two sulfonamide resistance genes, two macrolide resistance genes, three β-lactam antibiotic resistance genes, and intI1 were analyzed by quantitative PCR. High-throughput sequencing data were matched against a database of putative 538 HBPs. Significant removal of ARGs (except for tetO and ermB) and intI1 was observed in all the samples. Manure biochar resulted in significant removal of ARGs and HBPs; however, negative effects were also observed in some conditions. This is the first study to provide to explore the fates of ARGs and HBPs by adding manure biochar to AD.

Metagenomic insights into the antibiotic resistomes of typical Chinese dairy farm environments

Antibiotic resistance genes (ARGs) in the environment pose a threat to human and animal health. Dairy cows are important livestock in China; however, a comprehensive understanding of antibiotic resistance in their production environment has not been well clarified. In this study, we used metagenomic methods to analyze the resistomes, microbiomes, and potential ARG bacterial hosts in typical dairy farm environments (including feces, wastewater, and soil). The ARGs resistant to tetracyclines, MLS, β-lactams, aminoglycoside, and multidrug was dominant in the dairy farm ecosystem. The abundance and diversity of total ARGs in dairy feces and wastewater were significantly higher than in soil (P < 0.05). The same environmental samples from different dairy have similar resistomes and microbiomes. A high detection rate of tet(X) in wastewater and feces (100% and 71.4%, respectively), high abundance (range from 5.74 to 68.99 copies/Gb), and the finding of tet(X5) challenged the clinical application of the last antibiotics resort of tigecycline. Network analysis identified Bacteroides as the dominant genus in feces and wastewater, which harbored the greatest abundance of their respective total ARG coverage and shared ARGs. These results improved our understanding of ARG profiles and their bacterial hosts in dairy farm environments and provided a basis for further surveillance.

Metagenomic insights into the influence of mobile genetic elements on ARGs along typical wastewater treatment system on pig farms in China

The wastewater treatment processes (WTP) on pig farms are heavily contaminated by antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) play an important role in shaping ARG profiles. Here we first employed metagenomic sequencing to follow the diversities and shifts of ARG associated mobile genetic elements (AAMGEs) including insertion sequences (ISs) and plasmids along the WTP for three pig farms in southeast China. The IS average relative abundance rose from the initial pig feces source to the wastewater storage lagoon (WSL) but decreased in the influent and rose in the effluent of the anaerobic digestor (AD). In contrast, plasmids were eliminated rapidly along this process. These results indicated that the AD reduced plasmid copies while IS abundance increased. We found a great diversity ISs, including IS91, ISNCY, IS630 and IS701, were large contributors to the transfer of multi-drug resistance. In addition, the tetracycline resistance genes co-occurred with a greater diversity of ISs than other ARG classes and this likely contributed to the high abundance of tetracycline resistance genes we found. The transfer of ARGs mediated by MGEs along the WTP of pig farms was a key contributor for the ARGs persistence in the environment of pig farms. Collectively, our findings demonstrated different fates for ISs and plasmids along the WTP for pig farms and suggested that AAMGE monitoring served as an important role in controlling ARGs in pig waste.

Alteration of Manure Antibiotic Resistance Genes via Soil Fauna Is Associated with the Intestinal Microbiome

Livestock wastes contain high levels of antibiotic resistance genes (ARGs) and a variety of human-related pathogens. Bioconversion of livestock manure using larvae of the beetle Protaetia brevitarsis is an effective technique for waste reduction and value creation; however, the fate of manure ARGs during gut passage and interaction with the gut microbiome of P. brevitarsis remains unclear. To investigate this, we fed P. brevitarsis with dry chicken manure for 6 days and measured bacterial community dynamics and ARG abundance and diversity along the P. brevitarsis gut tract using high-throughput quantitative PCR and metagenomics approaches. The diversity of ARGs was significantly lower in larval midgut, hindgut, and frass than in raw chicken manure, and around 80% of pathogenicity-related genes (PRGs) exhibited reduced abundance. Network analysis demonstrated that Bacteroidetes and Firmicutes were the key bacterial phyla associated with ARG reduction. Metagenomic analysis further indicated that ARGs, mobile genetic elements (MGEs), and PRGs were simultaneously attenuated in the hindgut, implicating a decreased likelihood for horizontal gene transfer (HGT) of ARGs among bacteria and pathogens during manure bioconversion. Our findings demonstrated that the attenuation of ARGs is strongly associated with the variation of the gut microbiome of P. brevitarsis, providing insights into mechanisms of risk mitigation of ARG dissemination during manure bioconversion. IMPORTANCE Saprophagous fauna like the oriental edible beetle (P. brevitarsis) plays a fundamental role in converting organic wastes into biofertilizer. Accumulating evidence has shown that soil fauna can reduce the abundance of ARGs, although the underlying mechanism of ARG reduction is still unclear. In our previous research, we found a large reduction of ARGs in vegetable roots and leaves from frass compared with raw manure, providing a promising biofertilizer for soil-vegetable systems. Therefore, in this study, temporal dynamic changes in the microbiomes of the donor (chicken manure) and host (P. brevitarsis) were investigated, and we found a close association between the gut microbiome and the alteration of ARGs. These results shed new light on how the insect gut microbiome can mitigate manure-borne ARGs and provide insights into the bioconversion process via a typical member of the saprophagous fauna, P. brevitarsis.

Dynamic distribution and driving mechanisms of antibiotic resistance genes in a human-intensive watershed

Accelerated urbanization has promoted urban watersheds as important reservoirs of antibiotic resistance genes (ARGs); yet the biogeographical patterns and driving mechanisms of ARGs at the watershed scale remain unclear. Here, we examined the dynamic distribution of ARGs in a human-intensive watershed (including city, river and lake systems) over different seasons in a temperate region, as well as revealed the key factors shaping ARGs dynamics through structural equation models (SEMs). High diversity and abundance of ARGs were detected in sediments and surface water, with aminoglycoside, beta-lactamase and multidrug resistance genes dominating. PCoA showed distinct ARGs variations between the two phases. Seasonal changes and regional functions had significant impacts on the distribution patterns of ARGs. More diverse ARGs were detected in winter, while higher ARGs abundances were observed in spring and summer. The city system showed the highest level of ARGs contamination and was mainly derived from wastewater and human/animal feces based on SourceTracker analysis and ARGs indicators. Notably, watershed restoration could significantly mitigate the ARGs pollution status and improve biodiversity in the aquatic environment. Network analysis identified several hub ARGs and bacterial genera, which helped to infer potential bacterial hosts carrying ARGs. Furthermore, ARGs indicators provided insights to trace ARGs sources. SEMs indicated that bioavailable heavy metals and nutrients can greatly shape ARGs dynamics in regions with high-intensity human activities, while the microbial community and MGEs dominate the fate of ARGs in less human-impacted regions. More attention should be given to control heavy metals and nutrients to curb the spread of ARGs. Overall, this study highlights the environmental fate of ARGs and provides novel strategies to mitigate ARGs pollution in the human-intensive watershed.

Occurrence and transfer characteristics of blaCTX-M genes among Escherichia coli in anaerobic digestion systems treating swine waste

Livestock waste is a known reservoir of Escherichia coli (E. coli) carrying clinically important CTX-M-type extended-spectrum β-lactamase genes (bla_CTX-M), however, the occurrence and transfer characteristics of bla_CTX-M genes during anaerobic digestion (AD) remain unclear. Herein, four full-scale and two parallel lab-scale AD systems treating swine waste under ambient and mesophilic conditions were investigated by both molecular- and culture-based methods to reveal the occurrence and transfer behaviors of bla_CTX-M genes during AD. Real-time TaqMan polymerase chain reaction revealed 1.3 × 10⁴-6.8 × 10⁵ and 3.0 × 10⁴-7.0 × 10⁵ copies/mL of bla_CTX-M groups 1 and 9 in all feeding substrates. While AD reduced the absolute abundance of groups 1 and 9 by 0.63-2.24 and 0.08-1.30 log (P < 0.05), 5.0 × 10²-4.1 × 10³ and 1.1 × 10⁴-3.5 × 10⁴ copies/mL of groups 1 and 9 remained in the anaerobic effluent, respectively. In total, 141 bla_CTX-M-carrying E. coli isolates resistant to cefotaxime were obtained from the AD reactors. Whole-genome sequencing showed that bla_CTX-M-65 mainly carried by E. coli ST155 was the most frequently detected group 9 subtype in the feeding substrate; whereas bla_CTX-M-14 associated with the dominant clones E. coli ST6802 and ST155 became the major subtype in AD effluent. Furthermore, bla_CTX-M-14 was flanked by ΔIS26 upstream and ΔIS903B downstream. The ΔIS26-bla_CTX-M-14-ΔIS903B element was mainly located on the IncHI2 plasmid in E. coli ST48 and ST6802 and also the IncFIB plasmid in ST155 in anaerobic effluent. Conjugation assays showed that the plasmids harboring bla_CTX-M-14 could be successfully transferred at a frequency of 10^-3-10^-2 cells per recipient cell. This study revealed that bla_CTX-M genes remained in both the full-scale and lab-scale AD effluents of swine waste. Thus, additional efforts should be implemented to block the discharge and spread of antibiotic resistance genes to the environment.

Removal of Diverse and Abundant ARGs by MF-NF Process from Pig Manure and Digestate

Antimicrobial resistances are emerging as one main threat to worldwide human health and are expected to kill 10 million people by 2050. Intensive livestock husbandry, along with biogas digestate, are considered as one of the biggest ARG reservoirs. Despite major concerns, little information is available on the diversity and abundance of various ARGs in small to large scale pig farms and biogas digestate slurry in Germany, followed by their consequent removal using microfiltration (MF)-nanofiltration (NF) process. Here, we report the identification and quantification of 189 ARGs in raw manure and digestate samples, out of which 66 ARGs were shared among manures and 53 ARGs were shared among both manure and digestate samples. The highest reported total ARG copy numbers in a single manure sampling site was 1.15 × 10⁸ copies/100 µL. In addition, we found the absolute concentrations of 37 ARGs were above 10⁵ copies/100 μL. Filtration results showed that the highly concentrated ARGs (except aminoglycoside resistance ARGs) in feed presented high log retention value (LRV) from 3 to as high as 5 after the MF-NF process. Additionally, LRV below 2 was noticed where the initial absolute ARG concentrations were ≤10³ copies/100 μL. Therefore, ARG removal was found to be directly proportional to its initial concentration in the raw manure and in digestate samples. Consequently, some ARGs (tetH, strB) can still be found within the permeate of NF with up to 10⁴ copies/100 μL.

Tracking antibiotic resistance through the environment near a biosolid spreading ground: Resistome changes, distribution, and metal(loid) co-selection

The application of urban wastewater treatment plants (WWTPs) products to agricultural lands has contributed to the rising level of antibiotic resistance and drawn a critical public health concern. It has not been thoroughly investigated at which spatial scales a biosolid applied area as a potentially predominant source affects surrounding soil resistomes. This study investigated distribution and impact of WWTP biosolids treated with anaerobic digestion on an agricultural area. Heterotrophic plate counts (HPCs) and quantitative polymerase chain reaction (qPCR) were performed for detection of selected antibiotic-resistant bacteria (ARB), selected antibiotic resistance genes (ARGs), intI1 genes, and 16S rRNA genes. Biosolid samples contained significantly higher levels of selected ARGs than the raw agricultural soils (p < 0.05). The average relative abundances of intI1, sul1, bla_SHV, and ermB genes were significantly higher in biosolid-amended soils than nearby agricultural soils (p < 0.05). Spatial interpolation analysis of relative gene abundances of intI1, sul1, sul2, and tetW across the studied area further indicated directional trends towards the northwest and southeast directions, highlighting possible airborne spread. Concentrations of Co, Cu, Ni, and Fe were found to be significantly and positively correlated with relative abundances of intI1, sul1, and tetW genes (p < 0.05). The resistance ratios of culturable antibiotic-resistant bacteria in agricultural soils with biosolid amendments were generally identical to those without biosolid amendments. This study will advance the understanding of the antibiotic resistome in agricultural soils impacted by long-term waste reuse and inform the evaluation strategies for future biosolids application and management.

The role of iron-based nanoparticles (Fe-NPs) on methanogenesis in anaerobic digestion (AD) performance

Several strategies have been proposed to improve the performance of the anaerobic digestion (AD) process. Among them, the use of various nanoparticles (NPs) (e.g. Fe, Ag, Cu, Mn, and metal oxides) is considered one of the most effective approaches to enhance the methanogenesis stage and biogas yield. Iron-based NPs (zero-valent iron with paramagnetic properties (Fe⁰) and iron oxides with ferromagnetic properties (Fe₃O₄/Fe₂O₃) enhance microbial activity and minimise the inhibition effect in methanogenesis. However, comprehensive and up-to-date knowledge on the function and impact of Fe-NPs on methanogens and methanogenesis stages in AD is frequently required. This review focuses on the applicative role of iron-based NPs (Fe-NPs) in the AD methanogenesis step to provide a comprehensive understanding application of Fe-NPs. In addition, insight into the interactions between methanogens and Fe-NPs (e.g. role of methanogens, microbe interaction and gene transfer with Fe-NPs) beneficial for CH₄ production rate is provided. Microbial activity, inhibition effects and direct interspecies electron transfer through Fe-NPs have been extensively discussed. Finally, further studies towards detecting effective and optimised NPs based methods in the methanogenesis stage are reported.

Bloom of tetracycline resistance genes in mudflats following fertilization is attributed to the increases in the shared potential hosts between soil and organic fertilizers

A field experiment was carried out in mudflats adjacent to the Yellow Sea, China, amended with sewage sludge and vermicompost by one-time input at different rates to reveal the fates of tetracycline resistance genes (TRGs) and their potential hosts in the soils. Quantitative PCR results showed that soils added with either sludge or vermicompost had more abundant TRGs compared with the non-fertilized soil. This situation was more obvious in sludge fertilized soils especially at high application rates. Vermicompost exhibited a promising outlook for improvement of the mudflats. The abundances of intI1 in the non-fertilized soils were significantly higher than those in fertilizers and fertilized soils. The potential hosts for intI1 were not shared with other TRGs-contained hosts, indicating that intI1 had little effects on the dissemination of TRGs in the mudflats. Moreover, the exclusive hosts for TRGs in fertilizers were not higher than those in the non-fertilized soils, illustrating little effects of fertilization on the introduction of exogenous TRGs into soil. The shared hosts between soil and fertilizers were highest among four possible sources, contributing vastly to the bloom of TRGs following fertilization. It was also shown that different organic fertilizers caused distinct categories of shared potential hosts for TRGs. RDA analysis further indicated that the abundances of the shared potential hosts were affected by soil nutrients. These results suggested that the development of TRGs in soil following fertilization depended on the shared potential hosts with similar ecological niches between soil and fertilizers.

Responses of methane production, microbial community and antibiotic resistance genes to the mixing ratio of gentamicin mycelial residues and wheat straw in anaerobic co-digestion process

Anaerobic co-digestion (AcoD) of gentamicin mycelial residues (GMRs), a kind of nitrogen-rich biowaste, and wheat straw (WS) is an attractive technology for the recycling of GMRs. However, the effects of the co-substrate ratio on methane production, system stability and antimicrobial resistance during co-digestion remain unclear. Thus, this study aimed to fill in the blanks through AcoD of GMRs and WS with different mixing ratios (1:0, 2:1, 1:1, 1:2, 0:1, VS basis) via batch tests. Results showed that AcoD facilitated methane production than mono anaerobic digestion and reduced the accumulation of the toxic substances, such as ammonia nitrogen and humic-like substances. The maximum methane production was obtained at the reactors with the mixing ratio of 1:1 and 1:2 (R-1:1 and R-1:2), which matched with the relative abundance of key enzymes related to methanogenesis predicted by PICRUSt. Microbial community analysis indicated that Methanosaeta was the most dominant methanogen in the AcoD reactors. The highest relative abundance of Methanosaeta (45.1%) was obtained at R-1:1 due to the appropriate AcoD conditions, thus, providing greater possibilities for high stability of AcoD system. Additionally, AcoD of the GMRs and WS under the mixing ratio of 1:1 and 1:2 did not prompt the increase of antibiotic resistance genes (ARGs). Not only that, the likelihood of horizontal gene transfer declined in R-1:1 due to the weaker connection and transport between host and recipient bacteria. Findings of this study suggested that the suitable mixing ratio of GMRs and WS contributes to methane production and system stability, and reduces the dissemination risks of ARGs.

Microbial community structures and antibiotic biodegradation characteristics during anaerobic digestion of chicken manure containing residual enrofloxacin

To explore the interaction between the residual antibiotic in animal manure and biological treatment, the effect of enrofloxacin (ENR) on the anaerobic digestion of chicken manure, and biodegradation rate of ENR was studied under the condition of actual residual ENR content of 0, 8, 16 and 32 mg/kg·TS. The results showed that the addition of ENR increased the total biogas production, especially 8 mg/kg·TS promoted the anaerobic reaction obviously, and the corresponding cumulative biogas production was increased by 15.33%. However, in the presence of 32 mg/kg·TS, the biogas production rate was reduced and the peak period of biogas production was delayed. The results of enzyme activities determination and 16S rRNA sequencing showed that ENR had different effects on archaea and bacteria. The residual ENR could promote hydrolysis reactions in the anaerobic system, but could inhibit acetoclastic methanogens, and the relative abundance of Methanosaeta declined by 7.22‒12.41%. The first-order kinetic model showed that the half-life period of ENR in the anaerobic digestion system was 9.16‒10.83 days, and the biodegradation rate exceeded 80% after the treatment. This study can bring important information for the management of animal manure in the future.

Fates of intracellular and extracellular antibiotic resistance genes during the cattle farm wastewater treatment process

Cattle farm wastewater, as a significant reservoir for antibiotic resistance genes (ARGs), has received wide attention. Intracellular and extracellular ARGs (iARGs and eARGs) were detected during wastewater treatment, including solid-liquid separation, anaerobic regulation, upflow anaerobic sludge blanket (UASB) digestion, an anoxic-oxic-anoxic-oxic (A²O²) process, a membrane bioreactor (MBR), and ozone disinfection. Ten abundant ARGs were chosen as the target ARGs according to metagenomic sequencing. The concentrations of the total target iARGs and eARGs were 6.12 × 10⁷ and 3.24 × 10⁶ copy numbers/mL in raw wastewater, and then 3.79 × 10³ and 3.95 × 10⁵ copy numbers/mL in final effluent, because UASB, A²O², MBR and ozone disinfection can gradually reduce the concentrations of most ARGs. The concentrations of ARGs were positively correlated with almost all wastewater quality indicators. Positive correlation was also observed between iARGs and Bacteroidetes, Firmicutes and Spirochaetes, indicating that the bacteria in these three phyla might be the main hosts of ARGs. Wastewater quality indicators and bacterial community composition affected the distribution and removal of ARGs during cattle wastewater treatment.

A Review on Constructed Treatment Wetlands for Removal of Pollutants in the Agricultural Runoff

Constructed wetland (CW) is a popular sustainable best management practice for treating different wastewaters. While there are many articles on the removal of pollutants from different wastewaters, a comprehensive and critical review on the removal of pollutants other than nutrients that occur in agricultural field runoff and wastewater from animal facilities, including pesticides, insecticides, veterinary medicine, and antimicrobial-resistant genes are currently unavailable. Consequently, this paper summarized recent findings on the occurrence of such pollutants in the agricultural runoff water, their removal by different wetlands (surface flow, subsurface horizontal flow, subsurface vertical flow, and hybrid), and removal mechanisms, and analyzed the factors that affect the removal. The information is then used to highlight the current research gaps and needs for resilient and sustainable treatment systems. Factors, including contaminant property, aeration, type, and design of CWs, hydraulic parameters, substrate medium, and vegetation, impact the removal performance of the CWs. Hydraulic loading of 10–30 cm/d and hydraulic retention of 6–8 days were found to be optimal for the removal of agricultural pollutants from wetlands. The pollutants in agricultural wastewater, excluding nutrients and sediment, and their treatment utilizing different nature-based solutions, such as wetlands, are understudied, implying the need for more of such studies. This study reinforced the notion that wetlands are effective for treating agricultural wastewater (removal > 90%) but several research questions remain unanswered. More long-term research in the actual field utilizing environmentally relevant concentrations to seek actual impacts of weather, plants, substrates, hydrology, and other design parameters, such as aeration and layout of wetland cells on the removal of pollutants, are needed.

Chlortetracycline alters microbiota of gut or faeces in pigs and leads to accumulation and migration of antibiotic resistance genes

In this study, we investigated the effect of long-term use of chlortetracycline (CTC) on the gut microbiota composition and metabolism profiles in pigs, and the variation of antibiotic resistance genes (ARGs) and microbial communities in faeces and manure during aerobic composting (AC) and anaerobic digestion (AD). The pigs were fed the same basal diet supplemented with or without 75 mg/kg CTC, and fresh faeces of 30-, 60-, 90-, and 120-day-old pigs were collected from the CTC group. The results showed that CTC reduced the diversity of the gut microbiota significantly and changed its structure. Metabolomics analysis of intestinal contents revealed 23 differentially abundant metabolites, mainly organic acids, carbohydrates, and amino acids. Metabolic pathways, such as the TCA cycle, propionate metabolism, and pyruvate metabolism, were changed. From 30 to 120 days of age, the amount of CTC residues in faeces and the abundance of 3 tetracycline resistance genes increased significantly, and it was positively correlated with tetC, tetG, tetW, sul1 and intI2. CTC residue levels and ARGs abundance gradually decreased with fermentation time, and AC was better than AD at reducing ARGs abundance. The results suggest that in-feed CTC can reduce the diversity of the gut microbiota, change the structure, function and metabolism of the bacterial community, and increase the abundance of ARGs in faeces.

Effects of graphite, graphene, and graphene oxide on the anaerobic co-digestion of sewage sludge and food waste: Attention to methane production and the fate of antibiotic resistance genes

This study explored and compared the influence of graphite, graphene, and graphene oxide (GO) on the performance of anaerobic co-digestion fed with sewage sludge and food waste, the variations of antibiotic resistance genes (ARGs), and the evolution of microbial community. Graphene exhibited the best performance for improving methane production and organic degradation, which increased by 36.09% and 23.07% compared with control group. The experimental results showed that graphene had the greatest influence on the removal efficiency of blaOXA-1, macrolide resistance genes (ermF and ermB), and some tetracycline resistance genes (tetQ and tetX); however, the removal efficiency of sulfonamide resistance genes (sul1 and sul2), intI1, and some tetracycline resistance genes (tetM, tetO, and tetW) were highest when GO was added. Network analysis indicated that the host cells of mefA, ermB, and tetO were different from other ARG host cells; moreover, graphene controlled the horizontal transfer of ARGs between microbial communities.

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.

Aerobic Composting and Anaerobic Digestion Decrease the Copy Numbers of Antibiotic-Resistant Genes and the Levels of Lactose-Degrading Enterobacteriaceae in Dairy Farms in Hokkaido, Japan

Efficient methods for decreasing the spread of antimicrobial resistance genes (ARGs) and transfer of antimicrobial-resistant bacteria (ARB) from livestock manure to humans are urgently needed. Aerobic composting (AC) or anaerobic digestion (AD) are widely used for manure treatment in Japanese dairy farms. To clarify the effects of AC and AD on antimicrobial resistance, the abundances of antimicrobial (tetracycline and cefazolin)-resistant lactose-degrading Enterobacteriaceae as indicator bacteria, copy numbers of ARGs (tetracycline resistance genes and β-lactamase coding genes), and concentrations of residual antimicrobials in dairy cow manure were determined before and after treatment. The concentration of tetracycline/cefazolin-resistant lactose-degrading Enterobacteriaceae was decreased over 1,000-fold by both AC and AD. ARGs such as tetA, tetB, and bla TEM were frequently detected and their copy numbers were significantly reduced by ∼1,000-fold by AD but not by AC. However, several ARG copies remained even after AD treatment. Although concentrations of the majority of residual antimicrobials were decreased by both AC and AD, oxytetracycline level was not decreased after treatment in most cases. In addition, 16S rRNA gene amplicon-based metagenomic analysis revealed that both treatments changed the bacterial community structure. These results suggest that both AC and AD could suppress the transmission of ARB, and AD could reduce ARG copy numbers in dairy cow manure.

Contributions of meat waste decomposition to the abundance and diversity of pathogens and antibiotic-resistance genes in the atmosphere

Airborne transmission of antibiotic-resistance genes (ARGs) in landfill and acquisition of antibiotic resistance by pathogenic bacteria are posing potential threat to human and environmental health. However, little is known about contribution of waste decomposition to airborne ARGs and pathogens during landfilling of household waste. Herein, the dynamic changes of microbial communities and ARGs were comparatively investigated in leachate and bioaerosol during the decomposition of chicken, fish, and pork wastes. Results found that chicken and pork decomposition could result in emitting high abundance of bioaerosol and pathogen, while fish fermentation will lead to high airborne microbial activity. The main pathogens were Bacilli, Burkholderia-Paraburkholderia and Mycobacterium in bioaerosols, but were Wohlfahrtiimonas, Peptoniphilus and Fusobacterium in leachate, suggesting that the ability of aerosolization of bacteria in leachate was independent of their abundance and diversity. Whereas, diversity and relative abundance of ARGs in leachate were significantly higher than bioaerosol. Moreover, the relative abundance of ARGs in leachate and bioaerosols was not completely relevant. The changes of pathogenic community contributed significantly to the prevalence of ARGs in bioaerosol and leachate. The results will define the contribution of household waste decomposition to airborne pathogen and ARG distribution and provide foundation for airborne bacterial exposure risk and control in landfill.

In situ analysis of antibiotic resistance genes in anaerobically digested dairy manure and its subsequent disposal facilities

The metagenomic and quantitative polymerase chain reaction approaches were combined to evaluate the profiles of ARGs and plasmids in anaerobically digested dairy manure in situ and reveal the persistence and elevation of typical ARGs and plasmids in its subsequent disposal facilities in CAFOs, respectively. Our results indicated that the typical ARGs and plasimd were mainly sul2, mefa, tetm-01, tetm-02, tetw, aph3iiia, and clostridioides difficile strain 12,038 plasmid unnamed in CAFOs, some of which greatly enriched in AD residue after its storage, especially sul1 and sul2. Meantime, the AD slurry recycling introduced the bacteria carrying ARGs into soil, especially Romboutsia genus, which greatly enriched sul2, tetm-01, tetm-02, aphiiia, and mefa. In the present study, ARGs occurrence, persistence and distribution were understood through in situ analysis of their profiles during dairy manure AD treatment and subsequent disposals in CAFOs, which are helpful for controlling the potential environmental risks from dairy manure recycling.

Tracking antibiotic resistance gene transfer at all seasons from swine waste to receiving environments

Antibiotic resistance genes (ARGs) in livestock farms have attracted a growing attention with potential effects on human health. As one of the most important organic fertilizer, swine waste provided an ideal environment for understanding the dissemination and accumulation of ARGs in agricultural ecosystems. Here we conducted a year-round follow-up trace from swine waste to receiving environments, with the purpose of revealing the contamination profiles and ecological risks of ARGs at different seasons. Results indicated that a variety of common ARGs and even high-risk ARGs (i.e., bla_ampC, bla_OXA-1, bla_TEM-1 and mcr-1) were prevalent from swine waste to farmland soil, with changing in various degrees from season to season. Regarding the occurrence pattern of ARGs, tetracycline resistance genes (tet-ARGs) were predominant genes at four seasons in all fresh pig feces, swine manure, manured soil and wastewater. The levels of most ARGs in solid waste were reduced at a different degree via natural composting, and the removal effect was best in summer, while ARGs decreased poorly after wastewater treatment, especially in winter (up to 10^-1 copies/16S copies in the residual level), which increased the possibility of propagation to receiving environment. This concern was also validated by the investigation on farmland environment with long-term application of manure, where causing an increase in ARG abundances in soils (approximately 0.9-32.7 times). To our knowledge, this study is the first to demonstrate the distribution pattern of ARGs from swine waste to its receiving farmland environment at all seasons on this integrity chain.

Enhanced removal of antibiotic resistance genes and mobile genetic elements during swine manure composting inoculated with mature compost

Livestock manure is a major source of antibiotic resistance genes (ARGs) that enter the environment. This study assessed the effects of inoculation with mature compost (MC) on the fates of ARGs and the bacterial community during swine manure composting. The results showed that MC prolonged the thermophilic period and promoted the decomposition of organic matter, which was due to the rapid growth and reproduction of thermophilic bacteria (Bacillus, Thermobifida, and Thermobacillus). MC significantly reduced the relative abundances of ARGs (1.02 logs) and mobile genetic elements (MGEs) (1.70 logs) after composting, especially sulfanilamide resistance genes. The total ARGs removal rate was 1.11 times higher in MC than the control. Redundancy analysis and structural equation modeling showed that horizontal gene transfer mediated by MGEs (ISCR1 and intI1) was the main direct factor related to the changes in ARGs during composting, whereas the C/N ratio and pH were the two most important indirect factors. Network analysis showed that members of Firmicutes comprising Romboutsia, Clostridisensu_stricto_1, and Terrisporobacter were the main bacterial hosts of ARGs and MGEs. MC reduced the risk of ARGs transmission by decreasing the abundances of bacterial hosts. Thus, MC is a promising strategy for reducing the proliferation risk of ARGs.

Role of anaerobic sludge digestion in handling antibiotic resistant bacteria and antibiotic resistance genes - A review

Currently, anaerobic sludge digestion (ASD) is considered not only for treating residual sewage sludge and energy recovery but also for the reduction of antibiotic resistance genes (ARGs). The current review highlights the reasons why antibiotic resistant bacteria (ARB) and ARGs exist in ASD and how ASD performs in the reduction of ARB and ARGs. ARGs and ARB have been detected in ASD with some reports indicating some of the ARGs can be completely removed during the ASD process, while other studies reported the enrichment of ARB and ARGs after ASD. This paper reviews the performance of ASD based on operational parameters as well as environmental chemistry. More studies are needed to improve the performance of ASD in reducing ARGs that are difficult to handle and also differentiate between extracellular (eARGs) and intracellular ARGs (iARGs) to achieve more accurate quantification of the ARGs.

Comparison of an integrated short-cut biological nitrogen removal process with magnetic coagulation treating swine wastewater and food waste digestate

An integration of two processes, magnetic coagulation (MC) and short-cut biological nitrogen removal (SBNR), coupled with a sequencing batch membrane bioreactor (SMBR) controlled by an automatic real-time control strategy (RTC), was developed to treat different characteristics of high strength wastewater. The treatment efficiency and microbial community-diversity of the proposed method was evaluated and investigated using swine wastewater and food waste (FW) digestate. The MC showed high removal of TSS (89.1 ± 1.5%, 92.21 ± 1.8%), turbidity (90.58 ± 2.1%, 95.1 ± 2.1%), TP (88.5 ± 1.9%, 92.1 ± 1.5%), phosphate (87.76 ± 1.6%, 91.22 ± 1.5%), and SMBR achieved stable and excellent removal of COD (96.05 ± 0.2%, 97.39 ± 0.2%), TN (97.30 ± 0.3%, 97.44 ± 0.3%) andNH₄⁺-N (99.07 ± 0.2%, 98.54 ± 0.2%) for swine wastewater and FW digestate, respectively. The effluent COD andNH₄⁺-N concentrations were found to meet their discharge standards. The microbial community comparison showed similar diversity and richness, and genus Diaphorobacter and Thaurea were dominant in denitritation, and Nitrosomonas was dominant in nitritation treating both swine wastewater and FW digestate.

Fate of disposable face masks in high-solids anaerobic digestion: Experimental observations and review of potential environmental implications

Face masks became a part of our daily life amid the global COVID-19 (SARS-CoV-2) pandemic. Most of the face masks are made for single-use and primarily disposed of in garbage bins with other non-recyclable wastes. To date, little is known about how disposable face masks in municipal solid waste (MSW) would interfere with high-solids anaerobic digestion (HSAD) in waste management facilities. Here, we first report preliminary results from a lab experiment conducted with the organic fraction of municipal solid waste (OFMSW) amended with used disposable face masks. The lab-scale HSAD systems were operated with percolate recirculation comparable to commercial HSAD systems typically used for full-scale processing of OFMSW. The results suggested that the presence of face masks in OFMSW could negatively affect methane productivity and kinetics. In the digesters amended with face masks, total cumulative methane production decreased by up to 18%, along with a 12-29% decrease in maximum methane production rates than the control digester (without face masks). Moreover, lag phases increased by 7-14%. The results also suggested that the type of polymeric materials used in face masks would be more critical than their total number/loading in the digester, which warrants further investigation. The visual inspection of digestate showed that the face masks were mostly undegraded after 40 days of operation. Much remains unknown about how the undegraded face masks will affect the digestate management practices, such as composting, land application, and landfilling. However, the review of existing literature suggested that they can be a potential source of plastic and microplastic pollution and amplify transmission of antibiotic resistance genes to the ecosystem. In summary, this study underscores the importance of developing safe and reliable disposal guidelines and management plans for single-use face masks.