Effects of passivators on antibiotic resistance genes and related mechanisms during composting of copper-enriched pig manure

Effects of swine manure mixed with circulating fluidized bed fly ash on black soldier fly (Diptera: Stratiomyidae) larvae and larval frass

Black soldier fly larvae (BSFL) were reared on mixtures of swine manure and circulating fluidized bed fly ash (CFA) in different ratios. The aim was to evaluate the impacts of insoluble inorganic matter on BSFL and larval frass. The growth performance and nutrient composition of the BSFL were measured under different treatments. The intestinal microbiota structure, morphological characteristics, and total proteolytic activity of the gut were analyzed. The larval frass was tested for nutrients and analyzed using energy-dispersive spectroscopy and scanning electron micrographs. In particular, the surface areas of microparticles from the larval frass (diameter < 0.0074 mm) were measured using Brunauer-Emmett-Teller method. It was found that CFA addition prolonged larval development and reduced the maximum larval weights. The mean larval length, crude protein, and highest larval weight showed negative regression with an increase in the CFA ratio (P < 0.05). Morphological images indicated that physical clogging might be the main influencing factor on larval growth. Moreover, the microbial diversity and complexity in the larval gut increased with CFA addition, but CFA addition had little effect on the composition of dominant phyla or genera (P > 0.05). Finally, the nutrient composition revealed that the frass met the organic fertilizer standard when the CFA addition ratio was less than 7.5%. The optimal addition ratio was 5%, at which the larvae had a more stable and healthier gut environment, but there was less of an effect on larval growth and nutrient composition. Moreover, particles from 5% CFA mixture had the highest surface area.

Challenges in alpine meadow recovery: The minor effect of grass restoration on microbial resource limitation

Microorganisms play a vital role in restoring soil multifunctionality and rejuvenating degraded meadows. The availability of microbial resources, such as carbon, nitrogen, and phosphorus, often hinders this process. However, there is limited information on whether grass restoration can alleviate microbial resource limitations in damaged slopes of high-altitude regions. This study focused on alpine bare land impacted by engineering activities, with the goal of using grass seeds to improve soil resource availability and multifunctionality. High-throughput sequencing and enzyme stoichiometry (vector analyses) were employed to analyze microbial community composition and assess resource limitations. Our findings suggested that soil carbon, nitrogen, and phosphorus contents were low, ranging from 7.67 to 12.6 g kg-1for carbon, 0.61 to 0.98 g kg-1,for nitrogen, and 0.65 to 0.78 g kg-1for phosphorus. Nevertheless, the standardized scores for high yield and resource acquisition strategies remained at 0.26 and 1.36 in the four groups, which were lower than those of the stress tolerance strategy. Microorganisms primarily employed the stress tolerance strategy, focusing on repairing injured cells rather than promoting cell growth, which suggests that microbial growth and metabolism were only marginally enhanced. Because of this strategy's limited impact on enhancing microbial community diversity and fostering a co-occurrence network, the resultant levels remained comparable to those observed in degraded meadows. In this case, microbial resource limitations persisted, with phosphorus remaining a constraint. Consequently, grass restoration alone offered limited relief for microbial resource limitations in alpine meadows, underscoring the challenges of solely relying on grass seeds to recover damaged alpine ecosystems.

Shaping rhizocompartments and phyllosphere microbiomes and antibiotic resistance genes: The influence of different fertilizer regimes and biochar application

Understanding the impact of different soil amendments on microbial communities and antibiotic resistance genes (ARGs) dissemination is crucial for optimizing agricultural practices and mitigating environmental risks. This study investigated the effects of different fertilizer regimes and biochar on plant-associated bacterial communities and ARGs dissemination. The biochar's structural and chemical characteristics were characterized using scanning electron microscopy (SEM) and Fourier-transform infrared (FTIR) spectroscopy, revealing a porous architecture with diverse functional groups. The presence of ARGs varied significantly across groups, with manure-treated samples exhibiting the greatest diversity and abundance, raising concerns about ARGs dissemination. Soil enzyme activities responded differently to treatments; manure significantly enhanced catalase, acid phosphatase, and urease activities, whereas saccharase was most responsive to chemical fertilizer. These differences are possibly responsible for the distinct microbiome structure associated with the plant's root system. The analysis of bacterial diversity and richness across rhizocompartments and the phyllosphere highlighted that manure-treated rhizospheres and phyllospheres displayed the highest species richness and diversity. Notably, Proteobacteria dominated across most treatments, with distinct shifts in bacterial phyla and genera influenced by manure and biochar applications. The LEfSe analysis identified key indicator genera specific to each group, indicating that both fertilizer type and biochar application significantly shape microbial community composition. Co-occurrence network analysis further demonstrated that manure and biochar treatments created unique microbial networks in the rhizosphere, rhizoplane, phyllosphere, and endosphere, highlighting the role of these amendments in modulating microbial interactions in plant-associated environments. These findings suggest that manure, while enhancing microbial diversity and soil enzyme activities, also increases ARGs, whereas biochar may not contribute to the spread of ARGs and fosters distinct microbial communities, offering valuable insights for sustainable agricultural practices.

SiO2 nanoparticles can enhance nitrogen retention and reduce copper resistance genes during aerobic composting of swine manure

SiO2 nanoparticles (SiO2 NPs) are low-cost, environmentally friendly materials with significant potential to remove pollutants from complex environments. In this study, SiO2 NPs were used for the first time as an additive in aerobic composting to enhance nitrogen retention and reduce the expression of copper resistance genes. The addition of 0.5 g kg-1 SiO2 NPs effectively reduced nitrogen loss by 72.33 % by decreasing denitrification genes (nosZ, nirK, and napA) and increasing nitrogen fixation gene (nifH). The dominant factors affecting nitrification and denitrification genes were Firmicutes and C/N ratio. Additionally, SiO2 NPs decreased copper resistance genes by 28.96 % - 37.52 % in compost products. Copper resistance genes decreased most in the treatment with 0.5 g kg-1 SiO2 NPs. In summary, 0.5 g kg-1 SiO2 NPs have the potential to reduce copper resistance genes and enhance nitrogen retention during aerobic composting, which may be used to improve compost quality.

Synergistic removal of total petroleum hydrocarbons and antibiotic resistance genes in Yellow River Delta wetlands contaminated soil composting regulated by biogas slurry addition

The interactive effects between the emerging contaminant antibiotic resistance genes (ARGs) and the traditional pollutant total petroleum hydrocarbons (TPHs) in contaminated soils remain unclear. The synergistic removal of TPHs and ARGs from composted contaminated soil, along with the microbial mechanisms driven by the addition of biogas slurry, have not yet been investigated. This study explored the impact of biogas slurry on the synergistic degradation mechanisms and bacterial community dynamics of ARGs and TPHs in compost derived from contaminated soil. The addition of biogas slurry resulted in a reduction of targeted ARGs and mobile genetic elements (MGEs) by 9.96%-95.70% and 13.32%-97.66%, respectively. Biogas slurry changed the succession of bacterial communities during composting, thereby reducing the transmission risk of ARGs. Pseudomonas, Cellvibrio, and Devosia were identified as core microorganisms in the synergistic degradation of ARGs and TPHs. According to the partial least squares path model, temperature and NO3- indirectly influenced the removal of ARGs and TPHs by directly regulating the abundance and composition of host microbes and MGEs. In summary, the results of this study contribute to the high-value utilization of biogas slurry and provide methodological support for the low-cost remediation of contaminated soils.

Effect of thermal treatment of illite on the bioavailability of copper and zinc in the aerobic composting of pig manure with corn straw

The large amount of various types of heavy metals in animal manure applied to agricultural field has caused severe threat to the ecosystems of soil environments. In this study, the effect of thermal treatment of illite on the bioavailability of copper (Cu) and zinc (Zn) in the aerobic composting of pig manure with corn straw biochar was investigated. The objectives of this study were to characterize the variations in the bioavailability of Cu and Zn in the aerobic composting of pig manure added with illite treated with high temperatures and to identify the relatively dominant microbes involved in the formation of humus and passivation of heavy metals in pig manure composting based on 16S rRNA high-throughput sequencing analysis. The results showed that in comparison with the raw materials of pig manure, the bioavailability of Zn and Cu in the control and three experimental composting groups, i.e., group I (with untreated illite), group I-2 (with illite treated under 200°C), and group I-5 (with illite treated under 500°C), was decreased by 27.66 and 71.54%, 47.05 and 79.80%, 51.56 and 81.93%, and 58.15 and 86.60%, respectively. The results of 16S rRNA sequencing analysis revealed that in the I-5 group, the highest relative abundance was detected in Fermentimonas, which was associated with the degradation of glucose and fructose, and the increased relative abundances were revealed in the microbes associated with the formation of humus, which chelated with Zn and Cu to ultimately reduce the bioavailability of heavy metals and their biotoxicity in the compost. This study provided strong experimental evidence to support the application of illite in pig manure composting and novel insights into the selection of appropriate additives (i.e., illite) to promote humification and passivation of different heavy metals in pig manure composting.

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.

Deciphering and predicting changes in antibiotic resistance genes during pig manure aerobic composting via machine learning model

Livestock manure is one of the most important pools of antibiotic resistance genes (ARGs) in the environment. Aerobic composting can effectively reduce the spread of antibiotic resistance risk in livestock manure. Understanding the effect of aerobic composting process parameters on manure-sourced ARGs is important to control their spreading risk. In this study, the effects of process parameters on ARGs during aerobic composting of pig manure were explored through data mining based on 191 valid data collected from literature. Machine learning (ML) models (XGBoost and Random Forest) were utilized to predict the rate of ARGs changes during pig manure composting. The model evaluation index of the XGBoost model (R2 = 0.651) was higher than that of the Random Forest (R2 = 0.490), indicating that XGBoost had better prediction performance. Feature importance was further calculated for the XGBoost model, and the XGBoost black box model was interpreted by Shapley additive explanations analysis. Results indicated that the influencing factors on the ARGs variation in pig manure were sequentially divided into thermophilic period, total composting period, composting real time, and thermophilic stage average temperature. The findings gave an insight into the application of ML models to predict and decipher the ARG changes during manure composting and provided suggestions for better composting manipulation and optimization of process parameters.

A systematic review of antibiotic resistance driven by metal-based nanoparticles: Mechanisms and a call for risk mitigation

Elevations in antibiotic resistance genes (ARGs) are due not only to the antibiotic burden, but also to numerous environmental pressures (e.g., pesticides, metal ions, or psychotropic pharmaceuticals), which have led to an international public health emergency. Metal-based nanoparticles (MNPs) poison bacteria while propelling nanoresistance at ambient or sub-lethal concentrations, acting as a wide spectrum germicidal agent. Awareness of MNPs driven antibiotic resistance has created a surge of investigation into the molecule mechanisms of evolving and spreading environmental antibiotic resistome. Co-occurrence of MNPs resistance and antibiotic resistance emerge in environmental pathogens and benign microbes may entail a crucial outcome for human health. In this review we expound on the systematic mechanism of ARGs proliferation under the stress of MNPs, including reactive oxygen species (ROS) induced mutation, horizontal gene transfer (HGT) relevant genes regulation, nano-property, quorum sensing, and biofilm formation and highlighting on the momentous contribution of nanoparticle released ion. As antibiotic resistance pattern alteration is closely knit with the mediate activation of nanoparticle in water, soil, manure, or sludge habitats, we have proposed a virulence and evolution based antibiotic resistance risk assessment strategy for MNP contaminated areas and discussed practicable approaches that call for risk management in critical environmental compartments.

Metagenomic binning analyses of swine manure composting reveal mechanism of nitrogen cycle amendment using kaolin

The efficient control of nitrogen loss in composting and the enhancement of product quality have become prominent concerns in current research. The positive role of varying concentrations kaolin in reducing nitrogen loss during composting was revealed using metagenomic binning combined with reverse transcription quantitative polymerase chain reaction. The results indicated that the addition of 0.5 % kaolin significantly (P < 0.05) up-regulated the expression of nosZ and nifH on day 35, while concurrently reducing norB abundance, resulting in a reduction of NH3 and N2O emissions by 61.4 % and 17.5 %, respectively. Notably, this study represents the first investigation into the co-occurrence of nitrogen functional genes and heavy metal resistance genes within metagenomic assembly genomes during composting. Emerging evidence indicates that kaolin effectively impedes the binding of Cu/Zn to nirK and nosZ gene reductases through passivation. This study offers a novel approach to enhance compost quality and waste material utilization.

Robust PbO2 modified by co-deposition of ZrO2 nanoparticles for efficient degradation of ceftriaxone sodium

In recent years, PbO2 electrodes have received widespread attention due to their high oxygen evolution reaction (OER) activity. However, due to the brittle nature of the plating layer, it is easy to cause the active layer to fall off. Pb2+ will leach out with the electrochemical process causing secondary pollution. The starting point of this study is established to improve the stability and adhesion of the electrode coating. Electrochemical oxidation technology has the characteristics of high treatment efficiency, wide range of applications, and non-polluting environment. In this study, conventional PbO2 electrodes were modified by using co-deposition of ZrO2 nanoparticles. In addition, α-PbO2 was added to increase the stability of the electrodes. At a high current density of 1 A/cm2, the accelerated life of the pure PbO2 electrode is 648 h, the accelerated life of the PbO2-ZrO2 electrode is 1.37 times that of the pure PbO2, and the electrode with an added α-PbO2 layer is 1.69 times that of the pure PbO2 electrode. The amount of dissolved Pb2+ was only 29% of that of pure PbO2. The electrochemical performance of the electrode is evaluated by studying the degradation effect of ceftriaxone sodium (CXM). The addition of ZrO2 nanoparticles alters the particle size and deposition content of PbO2, leading to a unique crystal structure distinct from pure PbO2. Compared to conventional PbO2 electrodes, the PbO2-ZrO2 can remove chemical oxygen demand (COD) and pollutants more efficiently, removing for 59% increased by 38.47%. Therefore, PbO2-ZrO2 is of great value in the field of electrochemical degradation of industrial pollutants.

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.

Response of soil antibiotic resistance genes and bacterial communities to fresh cattle manure and organic fertilizer application

Livestock manure use in agriculture contributes to pollutants like antibiotic resistance genes (ARGs) and resistant bacteria. This practice could potentially facilitate ARGs development in soil ecosystems. Our study aimed to explore ARGs and bacterial communities in cattle manure from Ningxia beef cattle farms with varying breeding periods. We also assessed the impact of different application rates of cattle manure compost, created by mixing manure with different growing periods, on soil's physicochemical and heavy metal properties. High-throughput PCR and sequencing were used to analyze ARGs and bacterial communities. We aimed to understand ARGs dynamics in cattle manure during breeding stages and the impact of different fertilizer application rates on soil bacteria and resistance genes. We found 212 ARGs from cattle manure, spanning tetracycline, aminoglycoside, multidrug, and MLSB categories. Relative ARGs abundance was presented across breeding stages: lactation (C1), breeding (C3), pre-fattening (C4), calving (C2), and late fattening (C5). pH, total nitrogen (TN), electrical conductivity (EC), arsenic (As) and cadmium (Cd) presence significantly impacted ARGs quantity and microbial community structure in manure. Mobile genetic elements (MGEs) were the primary factor altering ARGs in manure (65.56%). Heavy metals contributed to 18.60% of ARGs changes. Manure application changed soil ARGs abundance, notably in soils with high application rates, primarily associated with aminoglycoside, multidrug and sulfonamide resistance. Soils with higher manure rates had elevated MGEs, positively correlated with most ARGs, suggesting MGEs' role in ARGs dissemination. Soil microbial community structure was influenced by fertilization, particularly with the highest application rate. Heavy metals (specifically Cd, contributing to 23.12%), microbial community changes (17.42%), and MGEs (17.38%) were the main factors affecting soil antibiotic resistance. Our study establishes a framework for understanding ARGs emergence in manure and treated soils. This informs strategies to mitigate environmental ARGs transmission and guides diverse livestock manure application and management.

Magnetic biochar/quaternary phosphonium salt reduced antibiotic resistome and pathobiome on pakchoi leaves

Antibiotic resistance genes (ARGs) and human pathogenic bacteria (HPB) in leafy vegetable is a matter of concern as they can be transferred from soil, atmosphere, and foliar sprays, and poses a potential risk to public health. While traditional disinfection technologies are effective in reducing the presence of ARGs and HPB in soil. A new technology, foliar spraying with magnetic biochar/quaternary ammonium salt (MBQ), was demonstrated and applied to the leaf surface. High-throughput quantitative PCR targeting 96 valid ARGs and 16 S rRNA sequencing were used to assess its efficacy in reducing ARGs and HPB. The results showed that spraying MBQ reduced 97.0 ± 0.81% of "high-risk ARGs", associated with seven classes of antibiotic resistance in pakchoi leaves within two weeks. Water washing could further reduce "high-risk ARGs" from pakchoi leaves by 19.8%- 24.6%. The relative abundance of HPB closely related to numerous ARGs was reduced by 15.2 ± 0.23% with MBQ application. Overall, this study identified the potential risk of ARGs from leafy vegetables and clarified the significant implications of MBQ application for human health as it offers a promising strategy for reducing ARGs and HPB in leafy vegetables.

Role of a typical swine liquid manure treatment plant in reducing elements of antibiotic resistance

Biological treatment of swine liquid manure may be a favorable environment for the enrichment of bacteria carrying antibiotic resistance genes (ARGs), raising the alert about this public health problem. The present work sought to investigate the performance of a swine wastewater treatment plant (SWWTP), composed of a covered lagoon biodigester (CLB) followed by three facultative ponds, in the removal of usual pollutants, antibiotics, ARGs (blaTEM, ermB, qnrB, sul1, and tetA), and intI1. The SWWTP promoted a 70% of organic matter removal, mainly by the digester unit. The facultative ponds stood out in the solids' retention carried from the anaerobic stage and contributed to ammonia volatilization. The detected antibiotic in the raw wastewater was norfloxacin (< 0.79 to 60.55 μg L-1), and the SWWTP seems to equalize peaks of norfloxacin variation probably due to sludge adsorption. CLB reduced the absolute abundance of ARGs by up to 2.5 log, while the facultative stage does not seem to improve the quality of the final effluent in terms of resistance elements. Considering the relative abundances, the reduction rates of total and ARG-carrying bacteria appear to be similar. Finally, correlation tests also revealed that organic matter and solids control in liquid manure treatment systems could help reduce the spread of ARGs after the waste final disposal.

Biochar preparation and evaluation of its effect in composting mechanism: A review

This article provides an overview of biochar application for organic waste co-composting and its biochemical transformation mechanism. As a composting amendment, biochar work in the adsorption of nutrients, the retention of oxygen and water, and the promotion of electron transfer. These functions serve the micro-organisms (physical support of niche) and determine changes in community structure beyond the succession of composing primary microorganisms. Biochar mediates resistance genes, mobile gene elements, and biochemical metabolic activities of organic matter degrading. The participation of biochar enriched the α-diversity of microbial communities at all stages of composting, and ultimately reflects the high γ-diversity. Finally, easy and convincing biochar preparation methods and characteristic need to be explored, in turn, the mechanism of biochar on composting microbes at the microscopic level can be studied in depth.

Effect of hydrochar on antibiotic-resistance genes and relevant mechanisms during chicken manure composting

The reduction of enhanced antibiotic resistance genes (ARGs) in compost is important to mitigate the risk of ARG transmission in agricultural production. Hydrochar is used in many applications as a functional carbon material with adsorption and catalytic properties. This study investigated the effects of hydrochar addition on bacterial communities, mobile genetic elements (MGEs), and ARGs in chicken manure composting. The addition of 2%, 5%, and 10% hydrochar (dry weight) reduced the total numbers of target ARGs and MGEs in the compost products by 40.13-55.33% and 23.63-37.23%, respectively. Hydrochar changed the succession of the bacterial population during composting, lowering the abundance of potential pathogens and promoting microbial activity in amino acid and carbohydrate metabolism. A significant possible microbial host for ARGs was found to be Firmicutes. Hydrochar was found to affect the host microorganisms and MGEs directly by altering environmental factors that indirectly impacted the ARG profiles, as shown by partial least squares pathway modeling analysis. In conclusion, the addition of hydrochar to compost is a simple and effective method to promote the removal of ARGs.

Effect of bioaugmentation on tetracyclines influenced chicken manure composting and antibiotics resistance

Antibiotic residue in husbandry waste has become a serious concern. In this study, contaminated chicken manure composting was conducted to reveal the bioaugmentation effect on tetracyclines residue and antibiotics resistance genes (ARGs). The bioaugmented composting removed most of the antibiotics in 7 days. Under bioaugmentation, 96.88 % of tetracycline and 92.31 % of oxytetracycline were removed, 6.32 % and 20.93 % higher than the control (P < 0.05). The high-temperature period was the most effective phase for eliminating antibiotics. The treatment showed a long high-temperature period (7 days), while no high-temperature period was in control. After composting, the treatment showed 13.87 % higher TN (26.51 g/kg) and 13.42 % higher NO₃^--N (2.45 g/kg) than control (23.28 and 2.16 g/kg, respectively) but 12.72 % lower C/N, indicating fast decomposition and less nutrient loss. Exogenous microorganisms from bioaugmentation significantly reshaped the microbial community structure and facilitated the enrichment of genera such as Truepera and Fermentimonas, whose abundance increased by 71.10 % and 75.37 % than the control, respectively. Remarkably, ARGs, including tetC, tetG, and tetW, were enhanced by 198.77 %, 846.77 %, and 62.63 % compared with the control, while the integron gene (intl1) was elevated by 700.26 %, indicating horizontal gene transfer of ARGs. Eventually, bioaugmentation was efficient in regulating microbial metabolism, relieving antibiotic stress, and eliminating antibiotics in composting. However, the ability to remove ARGs should be further investigated. Such an approach should be further considered for treating pollutants-influenced organic waste to eliminate environmental concerns.

Effect of biochar addition on copper and zinc passivation pathways mediated by humification and microbial community evolution during pig manure composting

The mobility and bioavailability of Cu and Zn are the main threats associated with the land application of pig manure (PM) compost products. This study investigated the impacts of biochar (BC) concentration on passivation of Cu and Zn associated with the compost maturity. The results indicated that 15% and 10% BC favoured the passivation of Cu and Zn, respectively. BC promoted passivation of Cu by accelerating HA production and optimized the abundance of Firmicutes. BC promoted the passivation of Zn by increasing the high temperature peak and the corresponding pH (8-8.5). A higher level (15% and 20%) of BC altered the dominant bacterial phylum from Firmicutes to Proteobacteria. 20% BC inhibited the passivation of Cu and Zn by reducing the highest temperature and lowering the alkalinity of substrate. These results offer new insights into understanding how the addition of BC could reduce the risk of hazardous products during PM composting.

Metagenomic insights into role of red mud in regulating fate of compost antibiotic resistance genes mediated by both direct and indirect ways

In this study, the amendment of red mud (RM) in dairy manure composting on the fate of antibiotic resistance genes (ARGs) by both direct (bacteria community, mobile genetic elements and quorum sensing) and indirect ways (environmental factors and antibiotics) was analyzed. The results showed that RM reduced the total relative abundances of 10 ARGs and 4 mobile genetic elements (MGEs). And the relative abundances of total ARGs and MGEs decreased by 53.48% and 22.30% in T (with RM added) on day 47 compared with day 0. Meanwhile, the modification of RM significantly increased the abundance of lsrK, pvdQ and ahlD in quorum quenching (QQ) and decreased the abundance of luxS in quorum sensing (QS) (P < 0.05), thereby attenuating the intercellular genes frequency of communication. The microbial community and network analysis showed that 25 potential hosts of ARGs were mainly related to Firmicutes, Proteobacteria and Actinobacteria. Redundancy analysis (RDA) and structural equation model (SEM) further indicated that RM altered microbial community structure by regulating antibiotic content and environmental factors (temperature, pH, moisture content and organic matter content), which then affected horizontal gene transfer (HGT) in ARGs mediated by QS and MGEs. These results provide new insights into the dissemination mechanism and removal of ARGs in composting process.

Exploring the impact of biochar supplement on the dynamics of antibiotic resistant fungi during pig manure composting

The purpose of this study was to investigate antibiotic resistant fungal (ARF) communities in pig manure (PM) composting employing two different biochar (coconut shell-CSB and bamboo biochar-BB) as amendment. Three treatments (Control, 10% CSB and 10% BB) were designed and indicated with T1 to T3. Experimental results declared that the fungal abundance significantly reduced among the both biochar applied treatments but three dominant phyla Ascomycota, Basidiomycota and Mucoromycota were still relatively greater abundance present. There were significant differences (p < 0.05) in the relative abundance and diversity of fungi among all three treatments. Interestingly, biochar addition regulated the overall fungal community in final compost. Compared with the control group, the abundance of fungi was positively mobilized, and especially CSB showed a better effect. Conclusively, biochar has potential to inhibit and reduce the ARGs population and mobility in compost. Thus, these findings offer new insight to understand the succession of ARFs during PM composting.

Comparison of composting factors, heavy metal immobilization, and microbial activity after biochar or lime application in straw-manure composting

Composting is an efficient way of disposing agricultural solid wastes as well as passivating heavy metals (HMs). Herein, equivalent (3%) biochar (BC) or lime (LM) were applied in rice straw and swine manure composting, with no additives applied as control group (CK). The results indicated that both the additives increased NO₃^--N content, organic matter degradation, humus formation, and HM immobilization in composting, and the overall improvement of lime was more significant. In addition, the additives optimized the bacterial community of compost, especially for thermophilic and mature phase. Lime stimulated the growth of Bacillus, Peptostreptococcus, Clostridium, Turicibacter, Clostridiaceae and Pseudomonas, which functioned well in HM passivation via biosorption, bioleaching, or promoting HM-humus formation by secreting hydrolases. Lime (3%) as additive is recommended in swine manure composting to promote composting maturity and reduce HM risk. The study present theoretical guidance in improving composting products quality for civil and industrial composting.

Responsive change of crop-specific soil bacterial community to cadmium in farmlands surrounding mine area of Southeast China

In arable soils co-influenced by mining and farming, soil bacteria significantly affect metal (Cadmium, Cd) bioavailability and accumulation. To reveal the soil microecology response under this co-influence, three intersection areas (cornfield, vegetable field, and paddy field) were investigated. With a similar nutrient condition, the soils showed varied Cd levels (0.31-7.70 mg/kg), which was negatively related to the distance from mining water flow. Different soils showed varied microbial community structures, which were dominated by Chloroflexi (19.64-24.82%), Actinobacteria (15.49-31.96%), Acidobacteriota (9.46-20.31%), and Proteobacteria (11.88-14.57%) phyla. A strong correlation was observed between functional microbial taxon (e. g. Acidobacteriota), soil physicochemical properties, and Cd contents. The relative abundance of tolerant bacteria including Vicinamibacteraceae, Knoellia, Ardenticatenales, Lysobacter, etc. elevated with the increase of Cd, which contributed to the enrichment of heavy metal resistance genes (HRGs) and integration genes (intlI), thus enhancing the resistance to heavy metal pollution. Cd content rather than crop species was identified as the dominant factor that influenced the bacterial community. Nevertheless, the peculiar agrotype of the paddy field contributed to its higher HRGs and intlI abundance. These results provided fundamental information about the crop-specific physiochemical-bacterial interaction, which was helpful to evaluate agricultural environmental risk around the intersection of farmland and pollution sources.

Distribution, horizontal transfer and influencing factors of antibiotic resistance genes and antimicrobial mechanism of compost tea

Compost tea was alternatives of chemical pesticide for green agriculture, but there were no reports about antibiotic resistance genes (ARGs) in compost tea. This study investigated the effect of livestock manures, sewage sludge, their composting products and liquid fermentation on ARGs, mobile genetic elements (MGEs), metal resistance genes (MRGs) and antimicrobial properties of various compost tea. The results showed aerobic liquid fermentation reduced ARGs by 65.93 % and 45.20 % in the compost tea of chicken manure and sludge, enriched ARGs by 8.57 % and 37.41 % in the compost tea of pig manure and bovine manure, and increased MGEs and MRGs by 1.25 × 10^-5-5.53 × 10^-3 and 2.03 × 10^-5-2.03 × 10^-3 in the four compost tea. The correlation coefficient of tetracycline and sulfonamide resistance genes between compost product and compost tea were 0.98 and 0.91. aadA2-02, sul2 and tetX abundant in the compost tea were positively correlated with MGEs and MRGs. Furthermore, liquid fermentation enriched the potential host of tetracycline and vancomycin resistance genes. Tetracycline resistance genes occupied 62.7 % of total ARGs in the compost tea. Alcaligenes and Bacillus enriched by 0.78-39.31 % in the four compost tea, which metabolites had high antimicrobial activity. The potential host of ARGs accounted for 42.1 % bacteria abundance in the four compost tea.

The effects of biochar on antibiotic resistance genes (ARGs) removal during different environmental governance processes: A review

Antibiotic resistance genes (ARGs) pollution has been considered as one of the most significant emerging environmental and health challenges in the 21st century, many efforts have been paid to control the proliferation and dissemination of ARGs in the environment. Among them, the biochar performs a positive effect in reducing the abundance of ARGs during different environmental governance processes and has shown great application prospects in controlling the ARGs. Although there are increasing studies on employing biochar to control ARGs, there is still a lack of review paper on this hotspot. In this review, firstly, the applications of biochar to control ARGs in different environmental governance processes were summarized. Secondly, the processes and mechanisms of ARGs removal promoted by biochar were proposed and discussed. Then, the effects of biochar properties on ARGs removal were highlighted. Finally, the future prospects and challenges of using biochar to control ARGs were proposed. It is hoped that this review could provide some new guidance for the further research of this field.

Joint effects of bacterium and biochar in remediation of antibiotic-heavy metal contaminated soil and responses of resistance gene and microbial community

Soils containing both veterinary antibiotics (VAs) and heavy metals necessitate effective remediation approaches, and microbial and molecular levels of the results should be further examined. Here, a novel material combining waste fungus chaff-based biochar (WFCB) and Herbaspirillum huttiense (HHS1) was established to immobilize copper (Cu) and zinc (Zn) and degrade oxytetracycline (OTC) and enrofloxacin (ENR). Results showed that the combined material exhibited high immobilization of Cu (85.5%) and Zn (64.4%) and great removals of OTC (41.9%) and ENR (40.7%). Resistance genes including tet(PB), tetH, tetR, tetS, tetT, tetM, aacA/aphD, aacC, aadA9, and czcA were reduced. Abundances of potential hosts of antibiotic resistance genes (ARGs) including phylum Proteobacteria and genera Brevundimonas and Rhodanobacter were altered. Total phosphorus and pH were the factors driving the VA degrading microorganisms and potential hosts of ARGs. The combination of WFCB and HHS1 can serve as an important bioresource for immobilizing heavy metals and removing VAs in the contaminated soil.

Elucidating the beneficial effects of diatomite for reducing abundances of antibiotic resistance genes during swine manure composting

Diatomite (DE) has been used for nitrogen conservation during the composting of feces but its effects on antibiotic resistance genes (ARGs) and the associated mechanisms are still unclear. In this study, DE was added at three different proportions (0%, 4%, and 8%) to swine manure during composting. The results showed that adding DE helped to reduce the abundances of ARGs and the maximum decrease (88.99%) occurred with the highest dose. DE amendment promoted the transformation of reducible copper into a more stable form, i.e., the residual fraction, which reduced the selective pressure imposed by copper and further decreased the abundances of ARGs. Tn916/1545 and intI1 were critical genetic components related to ARGs, and thus the reductions in the abundances of ARGs may be attributed to the suppression of horizontal transfer due to the decreased abundances of mobile genetic elements (MGEs). The microbial community structure (bacterial abundance and diversity) played key role in the evolution of ARGs. DE could enhance the competition between hosts and non-hosts of ARGs by increasing the bacterial community diversity. Compared with CK, DE amendment optimized the bacterial community by reducing the abundances of the potential hosts of ARGs and pathogens such as Corynebacterium, thereby improving the safety of the compost product. In addition, KEGG function predictions revealed that adding DE inhibited the metabolic pathway and genes related to ARGs. Thus, composting with 8% DE can reduce the risk of ARG transmission and improve the practical value for agronomic applications.

Biochar can mitigate co-selection and control antibiotic resistant genes (ARGs) in compost and soil

Heavy metals (HMs) contamination raises the expression of antibiotic resistance (AR) in bacteria through co-selection. Biochar application in composting improves the effectiveness of composting and the quality of compost. This improvement includes the elimination and reduction of antibiotic resistant genes (ARGs). The use of biochar in contaminated soils reduces the bioaccessibility and bioavailability of the contaminants hence reducing the biological and environmental toxicity. This decrease in contaminant bioavailability reduces contaminants induced co-selection pressure. Conditions which favour reduction in HMs bioavailable fraction (BF) appear to favour reduction in ARGs in compost and soil. Biochar can prevent horizontal gene transfer (HGT) and can eliminate ARGs carried by mobile genetic elements (MGEs). This effect reduces maintenance and propagation of ARGs. Firmicutes, Proteobacteria, and Actinobacteria are the major bacteria phyla identified to be responsible for dissipation, maintenance, and propagation of ARGs. Biochar application rate at 2-10% is the best for the elimination of ARGs. This review provides insight into the usefulness of biochar in the prevention of co-selection and reduction of AR, including challenges of biochar application and future research prospects.

Unveiling the occurrence, hosts and mobility potential of antibiotic resistance genes in the deep ocean

As emerging microbial contaminants, antibiotic resistance genes (ARGs) are widely reported in the neritic zone. However, the profiles of ARGs in the deep ocean have not yet been fully resolved. In this study, the distribution, hosts, and mobility potential of ARGs at different water depths in the Western Pacific (WP) were investigated and compared to those in Bohai Sea (BH) waters using environmental parameter measurements, amplicon sequencing, metagenomic assembly and binning approaches. Our results showed that the top eight most abundant known ARG types in WP and BH waters were multidrug (39.85%), peptide (14.98%), aminoglycoside (11.33%), macrolide-lincosamide-streptogramin (MLS, 4.06%), tetracycline (3.74%), beta-lactam (3.12%), fluoroquinolone (1.79%) and rifamycin (1.24%). The ARGs observed in mesopelagic and bathypelagic waters were abundant and diverse as those observed in neritic waters, indicating that deep-sea water could be another environmental reservoir for ARGs. For deep-sea ARGs, members from classes Gammaproteobacteria (70%) and Alphaproteobacteria (21.1%) were the most important potential hosts. In addition, mobile genetic element analysis suggested that the ARG migration potential in dee sea water (> 1000 m) was relatively high. Overall, our findings expanded the understanding of ARGs in deep seawater and provided guidance for ARG pollution control and risk prediction.

Insights into the associations of copper and zinc with nitrogen metabolism during manure composting with shrimp shell powder

The application of shrimp shell powder (SSP) in manure composting can promote the maturation of compost and reduce the associated environmental risk. This study investigated the response of adding SSP at different levels (CK: 0, L: 5%, M: 10%, and H: 15%) on heavy metal resistance genes (MRGs), nitrogen functional genes, enzymes, and microorganisms. SSP inhibited nitrification and denitrification via decreasing the abundances of functional genes and key enzymes related to Cu, Zn, and MRGs. The nitrate reductase and nitrous-oxide reductase in the denitrification pathway were lower under H. Phylogenetic trees indicated that Burkholderiales sp. had strong relationships with OTU396 and OTU333, with important roles in the nitrogen cycle and plant growth. Redundancy analysis and structural equation modeling showed the complex response between heavy metal and nitrogen that bio-Cu and bio-Zn had positive significantly relationships with nirK-type and amoA-type bacteria, and amoA-type bacteria might be hotspot of cueO.

Effect of antibiotic mixtures on the characteristics of soluble microbial products and microbial communities in upflow anaerobic sludge blanket

Two upflow anaerobic sludge blanket reactors (UASBs) were used to investigate the effects of three antibiotic mixtures (erythromycin, sulfamethoxazole, and tetracycline) on reactor performance, soluble microbial products (SMPs) composition and microbial community. One reactor (UASB_antibiotics) was fed with antibiotic mixtures, whereas another reactor (UASB_control) was used as a control without the addition of antibiotic mixtures. Compared with those in UASB_control, UASB_antibiotics show lower chemical oxygen demand removal efficiency and biogas content. A higher removal efficiency of antibiotic mixtures was obtained in first few stages in UASB_antibiotics. The SMPs composition of effluent from the two reactors did not differ significantly, and the main components were protein-like substances, which produced higher fluorescence intensity in UASB_antibiotics. Gas chromatography-mass spectrometry analysis revealed that the main compounds identified as SMPs (<580 Da) were alkanes, aromatics and esters, with only 20% similarity of SMPs between UASB_antibiotics and UASB_control. Antibiotics had a significant effect on the microbial community structure. Notably, in UASB_control, hydrogenotrophic methanogens, key microorganisms in anaerobic digestion, had an obvious advantage at all stages compared with UASB_antibiotics, whereas acetoclastic methanogen exhibited the opposite pattern. The above results demonstrated that antibiotic mixtures influenced the effluent quality during anaerobic treatment of synthetic wastewater, resulting in changes in the microbial community structure. This study clarified the effect of antibiotic mixtures on the operation of UASBs. It could contribute to identifying potential strategies for improving effluent quality in anaerobic treatment.

Effect of biochar addition on the dynamics of antibiotic resistant bacteria during the pig manure composting

In present study, the taxonomic variation of antibiotic resistant bacteria (ARB) in pig manure (PM) composting with coconut shell biochar (CSB) and bamboo biochar (BB) addition was investigated. The experiment was divided into three treatments: T1 (as control or without biochar amendment), T2 was added 10% coconut shell biochar and T3 supplemented with 10% bamboo biochar. The initial feed stock were properly homogenized using a mechanical crusher. PM and wheat straw (WS) were mixed in a 5: 1 dry weight ratio to adjust the initial carbon/nitrogen ratio 25:1, bulk density to ~0.5 (kg/L) and ~60% moisture content, respectively. This experiment was lasted for 42 days. The results indicated the bacterial communities in the three treatments were more different in terms of relative abundance and diversity of dominant bacteria. The control group had the highest abundance of Kingdome bacteria. The changes in ARB was noticed by variation in the relative abundances of Actinobacteria, Proteobacteria, Firmicutes and Bacteroidota. At the end of composting (on day 42), the total RAs of ARB at the class, order, and family levels were considerably reduced in T2 and T3 by ~35.78-38.75%, 36.42-40.63% and 45.82-47.70%, respectively. But in T1 was decreased by 6.16-8.62%, 7.93-8.72% and 8.70-10.15%, as compared with the day 0 sample. However, the CSB was much more effective to reduce 55 to 60% of ARB than T3 or BB applied treatment has 40 to 42% ARB reduction, while control has certainly very less RAa of ARB reduction. Finally, the biochar amendment was significant approach to mitigate the total ARB abundance in compost and it's further used for organic farming purposes.

Antibiotics and antibiotic resistance genes in landfills: A review

Landfill are important reservoirs of antibiotics and antibiotic resistance genes (ARGs). They harbor diverse contaminants, such as heavy metals and persistent organic chemicals, complex microbial consortia, and anaerobic degradation processes, which facilitate the occurrence, development, and transfer of ARGs and antibiotic resistant bacteria (ARB). The main concern is that antibiotics and developed ARGs and ARB may transfer to the local environment via leachate and landfill leakage. In this paper, we provide an overview of established studies on antibiotics and ARGs in landfills, summarize the origins and distribution of antibiotics and ARGs, discuss the linkages among various antibiotics, ARGs, and bacterial communities as well as the influencing factors of ARGs, and evaluate the current treatment processes of antibiotics and ARGs. Finally, future research is proposed to fill the current knowledge gaps, which include mechanisms for the development and transmission of antibiotic resistance, as well as efficient treatment approaches for antibiotic resistance.

Effects of H3PO4 modified biochar on heavy metal mobility and resistance genes removal during swine manure composting

In this research, static composting treatments of swine manure with forced ventilation were conducted to study the effects of biochar (BC) and H₃PO₄ modified biochar (BP) addition on heavy metals (HMs) stabilization, profiles of antibiotic resistance genes (ARGs), heavy metals resistance genes (MRGs) and bacterial communities during swine manure composting. After 42 days of the composting, compared to control (CK), BC and BP decreased the concentration of diethylenetriamine pentaacetic acid extractable Cu and Zn by 12.04%, 15.15% and 26.91%, 36.50%, respectively. Furthermore, BC and BP treatments reduced the total abundances of nine ARGs by 4.02% and 66.21%, and five MRGs by 53.66% and 58.81%, compared to CK in the compost product. Network analysis and square structural equation model analysis revealed that the decrease of ARGs and MRGs in BP treatment was related tothe change in bacterial community during the composting, rather than differences in co-selection pressure.

Effects of mineral additives on antibiotic resistance genes and related mechanisms during chicken manure composting

In this study, two typical minerals (diatomite and bentonite) were applied during composting, and their influences on antibiotics, antibiotic resistance genes (ARGs), intI1 and the bacterial communities were investigated. The relative abundance of total ARGs decreased by 53.72% and 59.54% in diatomite and bentonite addition compared with control on day 42. The minerals addition also reduced the relative abundance of intI1, as much as 41.41% and 59.81% in diatomite and bentonite treatments. Proteobacteria and Firmicutes were the dominant candidate hosts of the major ARGs. There was a significant correlation between total ARGs and intI1 during the composting. Structural equation models further demonstrated that intI1 and antibiotics were the predominant direct factors responsible for ARG variations, and composting properties and bacterial community composition also shifted the variation of ARG profiles by influencing intI1. Overall, these findings suggest that diatomite and bentonite could decrease the potential proliferation of ARGs in chicken manure.

Response of antibiotic resistance to the co-exposure of sulfamethoxazole and copper during swine manure composting

Heavy metals driven co-selection of antibiotic resistance in soil and water bodies has been widely concerned, but the response of antibiotic resistance to co-existence of antibiotics and heavy metals in composting system is still unknown. Commonly used sulfamethoxazole and copper were individually and jointly added into four reactors to explore their effects on antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), heavy metal resistance genes (MRGs) and bacterial community structure. The abundance of total ARGs and MGEs were notably decreased by 68.64%-84.95% and 91.27-97.38%, respectively, after the composting. Individual addition of sulfamethoxazole, individual addition of copper, simultaneously addition of sulfamethoxazole and copper increased the abundance of ARGs and MGEs throughout the composting period. Co-exposure of sulfamethoxazole and copper elevated the total abundance of ARGs by 1.17-1.51 times by the end of the composting compared to individual addition of sulfamethoxazole or copper. Network analysis indicated that the shifts in potential host bacteria determined the ARGs variation. Additionally, MGEs and MRGs had significant effects on ARGs, revealing that horizontal gene transfer and heavy metals induced co-resistance could promote ARGs dissemination.

Fate of antibiotic resistance genes in industrial-scale rapid composting of pharmaceutical fermentation residue: The role implications of microbial community structure and mobile genetic elements

Composting is an effective technology to recycle organic solid waste as a green resource. However, pharmaceutical fermentation residue (PFR) contains a variety of pollutants, such as residual drug and antibiotic resistance genes (ARGs), which limits the green cycle of using PFR as a resource. To promote the green recycling of PFR, this study evaluated the characteristics of abundance and the response relationship of ARGs during the process of rapid composting. Different rapid composting samples were collected, and DNA was extracted from each sample. The absolute abundance of ARGs was quantified using quantitative PCR, and the microbial community structure was identified using high-throughput sequencing. The results showed that ermB, ermF, tetM and tetQ were reduced by 89.55%, 15.10%, 89.55%, and 82.30% respectively, and only sul2 increased by approximately 5-fold. Mobile genetic elements (MGEs) directly affected the changes in abundance of ARGs. As typical MGEs, intl1 and intl2 decreased by 3.40% and 54.32%, respectively. Potential host microorganisms important factors that affected ARGs and MGEs. A network analysis indicated that the potential host microorganisms were primarily distributed in Firmicutes and Proteobacteria at the phylum level. The pH and content of water-extractable sulfur were physicochemical parameters that substantially affected the abundance of potential host microorganisms through redundancy analysis. Industrial-scale rapid composting could reduce the number of ARGs and shorten the composting cycle, which merits its popularization and application.

Responses of bacterial communities and antibiotic resistance genes to nano-cellulose addition during pig manure composting

Treatment with exogenous additives during composting can help to alleviate the accumulation of antibiotic resistance genes (ARGs) caused by the direct application of pig manure to farmland. In addition, nano-cellulose has an excellent capacity for adsorbing pollutants. Thus, the effects of adding 300, 600, and 900 mg/kg nano-cellulose to compost on the bacterial communities, mobile genetic elements (MGEs), and ARGs were determined in this study. After composting, treatment with nano-cellulose significantly reduced the relative abundance of ARGs, which was lowest in the compost product with 600 mg/kg added nano-cellulose. Nano-cellulose inhibited the rebound in ARGs from the cooling period to the maturity period, and weakened the selective pressure of heavy metals on microorganisms by passivating bio-Cu. The results also showed that MGEs explained most of the changes in the abundances of ARGs, and MGEs had direct effects on ARGs. The addition of 600 mg/kg nano-cellulose reduced the abundances of bacterial genera associated with ermQ, tetG, and other genes, and the number of links (16) between ARGs and MGEs was lowest in the treatment with 600 mg/kg added nano-cellulose. Therefore, adding 600 mg/kg nano-cellulose reduced the abundances of ARGs by affecting host bacteria and MGEs. The results obtained in this study demonstrate the positive effect of nano-cellulose on ARG pollution in poultry manure, where adding 600 mg/kg nano-cellulose was most effective at reducing the abundances of ARGs.

The fate of antibiotic resistance genes and their influential factors during excess sludge composting in a full-scale plant

The alteration of antibiotic resistance genes (ARGs) during sludge composting has been less studied in a full-scale plant, causing the miss of practical implications for understanding/managing ARGs. Therefore, this study tracked the changes of ARGs and microbial communities in a full-scale plant engaged in excess sludge composting and then explored the key factors regulating ARGs through a series of analyses. After composting, the absolute and relative abundance of ARGs decreased by 91.90% and 66.57%, respectively. Additionally, pathway analysis showed that MGEs, composting physicochemical properties were the most vital factors directly influencing ARGs. Finally, network analysis indicated that Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria were the main hosts of ARGs. Based on these findings, it can be known that full-scale composting could reduce ARGs risk to an extent.

Performance of full-scale aerobic composting and anaerobic digestion on the changes of antibiotic resistance genes in dairy manure

Understanding the different performances of full-scale active composting (AC) and anaerobic digestion (AD) on the changes of antibiotic resistance genes (ARGs) in dairy manure is crucial to uncover the dissemination risks of ARGs in post-biotreated manure. In this regard, metagenomic sequencing was deployed to reveal the variations of ARGs in dairy manure in an intensive dairy farm. Results showed that the total abundance of ARGs increased from 150.64 reads/ng DNA to 204.06 reads/ng DNA in dairy manure, and it is mainly attributed to the contributions of AC (85.49%) rather than AD (14.51%). In AC, more ARG subtypes were induced and the dominant ARG subtypes were shifted completely, probably due to the enrichment of Proteobacteria and Actinobacteria which could be the hosts of multiple ARGs. These results inspire us to further evaluate the dissemination risks of ARGs along the route from composted manure to soil and to plants.

Disentangling the Effects of Physicochemical, Genetic, and Microbial Properties on Phase-Driven Resistome Dynamics during Multiple Manure Composting Processes

Composting alters manure-derived antibiotic resistance genes (ARGs) to a certain extent, which is largely dependent upon the composting phase, manure type, microbial phylogeny, and physicochemical properties. However, little is known about how these determinants influence the fate and dynamics of ARGs as well as the mechanisms underlying the ecological process of ARGs during composting. Here, we investigated the temporal patterns of ARGs and their correlations with a series of physicochemical, genetic, and microbial properties during pilot-scale composting of chicken, maggot, bovine, and swine manure. We detected 237 ARGs, 71 of which were co-occurring across all four composting processes and accounted for >80% of the sum of resistome abundance. In support of this ARG co-occurrence, variance partition analyses demonstrated that the manure type explained less resistome variations (5.6%) than the composting phase (21.6%). During the phase-driven resistome dynamics, ARGs showed divergent variations in abundance, and certain beta-lactams and multidrug ARGs were consistently enriched across multiple manure composting processes. Correlation analyses all led to the conclusion that the divergent ARG variations during composting were attributable to the unequal effects of physicochemical properties, mobile elements, and succession of indigenous microbiota, whereas antibiotic residues' effects were marginal. Ultimately, this study determines the relative importance of various key determinants in the phase-driven divergence of ARGs during multiple manure composting processes and demonstrates a clear need to evaluate risks posed by enriched ARGs toward their receiving environments.

Antibiotic resistance genes in layer farms and their correlation with environmental samples

Livestock farms are generally considered to be the important source of antibiotic resistance genes (ARGs). It is important to explore the spread of ARGs to reduce their harm. This study analyzed 13 resistance genes belonging to 7 types in 68 samples of layer manure including different stages of layer breeding, layer manure fertilizer, and soil from 9 laying hen farms in Guangdong Province. The detection rate of antibiotic resistance genes was extremely high at the layer farm in manure (100%), layer manure fertilizer (100%), and soil (> 95%). The log counts of antibiotic resistance genes in layer manure (3.34-11.83 log copies/g) were significantly higher than those in layer manure fertilizer (3.45-9.80 log copies/g) and soil (0-7.69 log copies/g). In layer manure, ermB was the most abundant antibiotic resistance gene, with a concentration of 3.19 × 10⁹- 6.82 × 10¹¹ copies/g. The average abundances of 5 antibiotic resistance genes were above 10¹⁰ copies/g in the descending order ermB, sul2, tetA, sul1, and strB. The relative abundances of ARGs in layer manure samples from different breeding stages ranked as follows: brooding period (BP), late laying period (LL), growing period (GP), early laying period (EL), and peak laying period (PL). There was no significant correlation between the farm scale and the abundance of antibiotic resistance genes. Moreover, the farther away from the layer farm, the lower the abundance of antibiotic resistance genes in the soil. We also found that compost increases the correlation between antibiotic resistance genes, and the antibiotic resistance genes in soil may be directly derived from layer manure fertilizer instead of manure. Therefore, when applying layer manure fertilizer to cultivated land, the risk of antibiotic resistance genes pollution should be acknowledged, and in-depth research should be conducted on how to remove antibiotic resistance genes from layer manure fertilizer to control the spread of antibiotic resistance genes.

Chitosan as additive affects the bacterial community, accelerates the removals of antibiotics and related resistance genes during chicken manure composting

Manures, storages for antibiotic resistance genes (ARGs), pollute soil and water as well as endanger human health. Recently, we have been searching a better solution to remove antibiotics and ARGs during aerobic composting. Here, the dynamics of chitosan addition on the profiles of 71 ARGs, bacterial communities, chlortetracycline (CTC), ofloxacin (OFX) were investigated in chicken manure composting and compared with zeolite addition. Chitosan addition effectively reduces antibiotics contents (CTC under detection limit, OFX 90.96%), amounts (18) and abundance (56.7%, 11.1% higher than zeolite addition) of ARGs and mobile genetic elements (MGEs) after 42 days composting. Network analysis indicated that a total of 27 genera strains assigned into 4 phyla (Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes) were the potential hosts of ARGs. Redundancy analysis (RDA) demonstrated that bacterial community succession is the main contributor in the variation of ARGs. Overall, chitosan addition may effect bacterial composition by influencing physic-chemical properties and the concentration of antibiotics, Cu²⁺, Zn²⁺ to reduce the risk of ARG transmission. This study gives a new strategy about antibiotics and ARGs removal from composting on the basis of previous studies.

Key factors driving the fate of antibiotic resistance genes and controlling strategies during aerobic composting of animal manure: A review

Occurrence of antibiotic resistance genes (ARGs) in animal manure impedes the reutilization of manure resources. Aerobic composting is potentially effective method for resource disposal of animal manure, but the fate of ARGs during composting is complicated due to the various material sources and different operating conditions. This review concentrates on the biotic and abiotic factors influencing the variation of ARGs in composting and their potential mechanisms. The dynamic variations of biotic factors, including bacterial community, mobile genetic elements (MGEs) and existence forms of ARGs, are the direct driving factors of the fate of ARGs during composting. However, most key abiotic indicators, including pH, moisture content, antibiotics and heavy metals, interfere with the richness of ARGs indirectly by influencing the succession of bacterial community and abundance of MGEs. The effect of temperature on ARGs depends on whether the ARGs are intracellular or extracellular, which should be paid more attention. The emergence of various controlling strategies renders the composting products safer. Four potential removal mechanisms of ARGs in different controlling strategies have been concluded, encompassing the attenuation of selective/co-selective pressure on ARGs, killing the potential host bacteria of ARGs, reshaping the structure of bacterial community and reducing the cell-to-cell contact of bacteria. With the effective control of ARGs, aerobic composting is suggested to be a sustainable and promising approach to treat animal manure.

Additive quality influences the reservoir of antibiotic resistance genes during chicken manure composting

Aerobic composting is commonly used to dispose livestock manure and is an efficient way to reduce antibiotic resistance genes (ARGs). Here, the effects of different quality substrates on the fate of ARGs were assessed during manure composting. Results showed that the total relative abundances of ARGs and intI1 in additive treatments were lower than that in control, and high quality treatment with low C/N ratio and lignin significantly decreased the relative abundance of tetW, ermB, ermC, sul1 and sul2 at the end of composting. Additionally, higher quality treatment reduced the relative abundances of some pathogens such as Actinomadura and Pusillimonas, and some thermotolerant degrading-related bacteria comprising Pseudogracilibacillus and Sinibacillus on day 42, probably owing to the change of composting properties in piles. Structural equation models (SEMs) further verified that the physiochemical properties of composting were the dominant contributor to the variations in ARGs and they could also indirectly impact ARGs by influencing bacterial community and the abundance of intI1. Overall, these findings indicated that additives with high quality reduced the reservoir of antibiotic resistance genes of livestock manure compost.

Distribution of genetic elements associated with antibiotic resistance in treated and untreated animal husbandry waste and wastewater

Animal breeding for meat production based on swine, cattle, poultry, and aquaculture is an activity that generates several impacts on the environment, among them the spread of antibiotic resistance. There is a worldwide concern related to the massive use of antibiotics, which causes selective pressure on the microbial community, triggering bacteria that contain "antibiotic resistance genes." According to the survey here presented, antibiotic resistance-related genes such as tetracyclines (tet), erythromycin (erm), and sulfonamides (sul), as well as the genetic mobile element interferon (int), are the most reported genetic elements in qualitative and quantitative studies of swine, cattle, poultry, and aquaculture manure/wastewater. It has been observed that biological treatments based on waste composting and anaerobic digestion are effective in ARG removal, particularly for tet, bla, erm, and qnr (quinolone) genes. On the other hand, sul and intI genes were more persistent in such treatments. Tertiary treatments, such advanced oxidative processes, are suitable strategies to improve ARG reduction. In general temperature, hydraulic retention time, and penetration of sunlight are the main operational parameters for ARG reduction in treatments applied to animal waste, and therefore attention should be addressed to optimize their efficacy regarding ARG removal. Despite being reduced, the presence of ARG in treated effluents and in biosolids indicates that there is a potential risk of antibiotic resistance spread in nature, especially through the release of treated livestock waste into the environment.

Fate of antibiotic resistance genes and metal resistance genes during the thermophilic fermentation of solid and liquid swine manures in an ectopic fermentation system

Environmental pollution due to resistance genes from livestock manure has become a serious issue that needs to be resolved. However, little studies focused on the removal of resistance genes in simultaneous processing of livestock feces and urine. This study investigated the fate of antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and class 1 integron-integrase gene (intI1) during thermophilic fermentation of swine manure in an ectopic fermentation system (EFS), which has been regarded as a novel system for efficiently treating both feces and urine. The abundances of MRGs and tetracycline resistance genes were 34.44-97.71% lower in the EFS. The supplementation of heavy metals significantly increased the abundance of intI1, with the enhancement effect of copper being more prominent than that of zinc. The highest abundances of resistance genes and intI1 were observed at high Cu levels (A2), indicating that Cu can increase the spreading of resistance genes through integrons. Network analysis revealed the co-occurrence of ARGs, MRGs, and intI1, and these genes potentially shared the same host bacteria. Redundancy analysis showed that the bacterial community explained most of the variations in ARGs, and environmental factors had influences on ARGs abundances by modulating the bacterial community composition. The decreased Sphingomonas, Comamonas, Acinetobacter, Lactobacillus, Bartonella, Rhizobium, and Bacteroides were mainly responsible for the reduced resistance genes. These results demonstrate that EFS can reduce resistance genes in simultaneous processing of livestock feces and urine.

Enhanced control of sulfonamide resistance genes and host bacteria during thermophilic aerobic composting of cow manure

Traditional composting has already shown a certain effect in eliminating antibiotic residues, antibiotic-resistant bacteria (ARBs), and antibiotic resistance genes (ARGs). It is worth noting that the rebounding of ARGs and the succession of the bacterial community during conventional aerobic composting are still serious threats. Considering the probable risk, improved and adaptable technologies are urgently needed to control antibiotic resistance efficiently. This study monitored how thermophilic aerobic composting affected the ARGs, as well as the bacterial diversity during the composting of cow manure spiked with sulfamethoxazole (SMX) at different concentrations. Results showed that the degradation of SMX was enhanced during thermophilic aerobic composting (control > SMX25 > SMX50 > SMX100) and was no longer detected after 20 days of composting. High temperature or heat significantly stimulated the rebounding of certain genes. After 35 days, the abundance of detected genes (sul2, sulA, dfrA7, and dfrA1) significantly decreased (p < 0.05) in control and antibiotic-spiked treatments, except for sul1. The addition of three concentrations of SMX elicited a sharp effect on bacterial diversity, and microbial structure in SMX25 led to significant differences with others (p < 0.05). The network analysis revealed more rigorous interactions among ARGs and abundant genera, suggesting that the host of ARGs potentially increased at low concentrations of SMX. Especially, genera g_norank_f__Beggiatoaceae, Ruminiclostridium, Caldicoprobacter, g_norank_o_MBA03, Hydrogenispora, and Ruminiclostridium_1 were major potential hosts for sul1. In conclusion, the rebounding of ARGs could be intermitted partially, and more efficient control of antibiotic resistance could be achieved in the thermophilic composting compared to conventional methods.

Synergistic impacts of Cu2+ on simultaneous removal of tetracycline and tetracycline resistance genes by PSF/TPU/UiO forward osmosis membrane

Cu²⁺, tetracycline (TC), and corresponding tetracycline resistance genes (TRGs) are common micropollutants in aquaculture wastewater, which have great impact on environment and human health. In this study, we developed a thin-film nanocomposite (TFN) forward osmosis (FO) membrane with an electrospinning thermoplastic polyurethane/polysulfone (PSF/TPU) substrate and a UiO-66-NH₂ particle interlayer modified active layer. The effects of Cu²⁺ concentration on the synergetic removal of TC and TRGs (e.g., tetA/M/X/O/C, int1, and 16 S rRNA gene) were analyzed to determine the role of Cu²⁺ in FO process. The rejection mechanism was also analyzed in depth. Results demonstrated that the rejection of TC and Cu²⁺ was 99.53% and 97.99%. The rejection of TRGs exceeded 90% (specifically, over 99% for tetC) at a Cu²⁺ concentration of 500 μg/L when 0.5 M (NH₄)₂HPO₄ was used as draw solution. Complexation reaction between Cu²⁺ and TC, electrostatic interaction, and the adsorption of Cu²⁺ on membrane surface were the main contributing factors for the high rejection efficiencies. Altogether, the as-prepared FO membrane holds great potential for simultaneously removing heavy metals, antibiotics, and resistance genes in real wastewater.