Sludge bio-drying: Effective to reduce both antibiotic resistance genes and mobile genetic elements

Elimination of antibiotic resistance genes and adaptive response of Firmicutes during chicken manure composting

Aerobic composting is an effective method for reducing the abundance of antibiotic resistance genes (ARGs), but its effectiveness is influenced by the complex conditions during the process. However, the impact of composting conditions on the fate of ARGs and the underlying mechanisms remains unclear. This study examined the profile of ARGs, their mobility potential, hosts, and the risk of antibiotic resistome under different chicken manure composting conditions. A total of 708 ARGs were identified, and composting reduced their relative abundance by 29.4 %-82.4 %. Composting amendments and aeration rates exhibited similar elimination efficiencies for ARGs at different levels. However, low initial moisture content (50 %) caused a rebound in ARG abundance during the maturation phase. ARGs were mainly located on plasmids. After composting, the percentage of plasmid-born ARGs decreased from 46.3 %-70.8 % to 28.4 %-49.0 %. ARGs co-localized with mobile genetic elements displayed similar trends. The tolerance of Firmicutes to low moisture content played a key role in the rebound of ARGs and variations in their mobility potential. Composting reduced antibiotic resistance and ARG mobility in pathogens. Conversely, low moisture content hindered this attenuation effect in Firmicutes, which increased antibiotic resistome risk. This study provides comprehensive insights into the fate of ARGs and highlights the environmental risks of ARGs during composting.

Bioaerosol emission characteristics and potential risks during composting: Focus on pathogens and antimicrobial resistance

In this study, we analyzed bioaerosol emission characteristics and potential risks of antimicrobial resistance (AMR) during composting using the impaction culture method and metagenomic sequencing. The results showed that the highly saturated water vapor in the emission gas mitigated particulate matter emission during the thermophilic period. About the bioaerosols, the airborne aerobic bacterial emissions were suppressed as composting enters the mature period, and the airborne fungi are usually present as single-cell or small-cell aggregates (< 3.3 µm). In addition, the microbial community structure in bioaerosols was stable and independent of composting time. Most importantly, the PM2.5 in bioaerosols contained large amounts of antibiotic resistance genes (ARGs), potential pathogens, and multidrug resistant pathogens, which were diverse and present in high concentrations. Among them, ARGs concentrations encoding 21 antibiotics ranged from - 4.50 to 0.70 ppm/m3 (Log10 ARGs). Among the 89 potential human pathogens detected, Escherichia coli, Salmonella enterica, Klebsiella pneumoniae, and Staphylococcus aureus were the only culturable potentially multidrug resistant pathogens carrying multiple ARGs encoding resistance at high concentrations (- 0.57 to 1.15 ppm/m3 (Log10 ARGs)), and were more likely to persist and multiply in oligotrophic environments. Our findings indicate that composting technology can transfer AMR from solid compost to gas phase and increase the risk of AMR transmission.

Determinants of antimicrobial resistance in biosolids: A systematic review, database, and meta-analysis

Biosolids can provide a nutrient rich soil amendment, particularly for poor soils and semi-arid or drought-prone areas. However, there are concerns that sludge and biosolids could be a source of propagation and exposure to AMR determinants such as antibiotic resistant bacteria (ARB), and antibiotic resistance genes (ARGs). To inform risk assessment efforts, a systematic literature review was performed to build a comprehensive spreadsheet database of ARB and ARG concentrations in biosolids (and some sludges specified as intended for land application), along with 69 other quantitative and qualitative meta-data fields from 68 published studies describing sampling information and processing methods that can be used for modeling purposes. Mean ARG concentrations per gram in positive samples of biosolids ranged from -5.7 log10(gene copies [gc]/g) to 12.92 log10(gc/g) (with these range values reported per dry weight), and aqueous concentrations ranged from 0.9 log10(gc/L) to 14.6 log10(gc/L). Mean ARB concentrations per gram of biosolids ranged from 2.02 log10 (colony forming units [CFU]/g) to 9.00 log10 (CFU/g) (dry weight), and aqueous concentrations ranged from 3.23 log10 (CFU/L) to 12.0 log10 (CFU/L). ARG log removal values (LRVs) during sewage sludge stabilization were calculated from a meta-analysis of mean concentrations before and after stabilization from 31 studies, ranging from -2.05 to 5.52 logs. The classes of resistance most relevant for a risk assessment corresponded to sulfonamide (sul1 and sul2), tetracycline (tetZ, tetX, tetA and tetG), beta-lactam (blaTEM), macrolide (ermB and ermF), aminoglycoside (strA and aac(6')-Ib-cr), and integron-associated (intI1). The resistance classes most relevant for ARB risk assessment included sulfonamides (sulfamethoxazole and sulfamethazine), cephalosporin (cephalothin and cefoxitin), penicillin (ampicillin), and ciprofloxin (ciprofloxacin). Considerations for exposure assessment are discussed to highlight risk assessment needs relating to antimicrobial resistance (AMR) associated with biosolids application. This study aids in prioritization of resources for reducing the spread of AMR within a One Health framework.

Disinfectant polyhexamethylene guanidine triggered simultaneous efflux pump antibiotic- and metal-resistance genes propagation during sludge anaerobic digestion

The environmental transmission of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) exerted devastating threats to global public health, and their interactions with other emerging contaminants (ECs) have raised increasing concern. This study investigated that the abundances of ARGs and MRGs with the predominant type of efflux pump were simultaneously increased (8.4-59.1%) by disinfectant polyhexamethylene guanidine (PHMG) during waste activated sludge (WAS) anaerobic digestion. The aggregation of the same microorganisms (i.e., Hymenobacter and Comamonas) and different host bacteria (i.e., Azoarcus and Thauera) were occurred upon exposure to PHMG, thereby increasing the co-selection and propagation of MRGs and ARGs by vertical gene transfer. Moreover, PHMG enhanced the process of horizontal gene transfer (HGT), facilitating their co-transmission by the same mobile genetic elements (20.2-223.7%). Additionally, PHMG up-regulated the expression of critical genes (i.e., glnB, trpG and gspM) associated with the HGT of ARGs and MRGs (i.e., two-component regulatory system and quorum sensing) and exocytosis system (i.e., bacterial secretion system). Structural equation model analysis further verified that the key driver for the simultaneous enrichment of ARGs and MRGs under PHMG stress was microbial community structure. The study gives new insights into the aggravated environmental risks and mechanisms of ECs in sludge digestion system, providing guidance for subsequent regulation and control of ECs.

Efficient elimination of antibiotic resistome in livestock manure by semi-permeable membrane covered hyperthermophilic composting

Livestock manure is a hotspot for antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), and an important contributor to antibiotic resistance in non-clinical settings. This study investigated the effectiveness and potential mechanisms of a novel composting technology, semi-permeable membrane covered hyperthermophilic composting (smHTC), in removal of ARGs and MGEs in chicken manure. Results showed that smHTC was more efficient in removal of ARGs and MGEs (92% and 93%) compared to conventional thermophilic composting (cTC) (76% and 92%). The efficient removal in smHTC is attributed to direct or indirect negative effects caused by the high temperature, including reducing the involvement of bio-available heavy metals (HMs) in co-selection processes of antibiotic resistance, decreasing the bacterial abundance and diversity, suppressing the horizontal gene transfer and killing potential ARGs hosts. Overall, smHTC can efficiently remove the resistome in livestock manure, reducing the risk to crops and humans from ARGs residues in compost products.

Unravelling the mechanisms of antibiotic and heavy metal resistance co-selection in environmental bacteria

The co-selective pressure of heavy metals is a contributor to the dissemination and persistence of antibiotic resistance genes in environmental reservoirs. The overlapping range of antibiotic and metal contamination and similarities in their resistance mechanisms point to an intertwined evolutionary history. Metal resistance genes are known to be genetically linked to antibiotic resistance genes, with plasmids, transposons, and integrons involved in the assembly and horizontal transfer of the resistance elements. Models of co-selection between metals and antibiotics have been proposed, however, the molecular aspects of these phenomena are in many cases not defined or quantified and the importance of specific metals, environments, bacterial taxa, mobile genetic elements, and other abiotic or biotic conditions are not clear. Co-resistance is often suggested as a dominant mechanism, but interpretations are beset with correlational bias. Proof of principle examples of cross-resistance and co-regulation has been described but more in-depth characterizations are needed, using methodologies that confirm the functional expression of resistance genes and that connect genes with specific bacterial hosts. Here, we comprehensively evaluate the recent evidence for different models of co-selection from pure culture and metagenomic studies in environmental contexts and we highlight outstanding questions.

The response and factors of microbial aerosol emission from the sludge bio-drying process

Exposure to high levels of microbial contaminants during waste disposal leads to the development of various diseases, including respiratory symptoms and gastrointestinal infections. In this study, the emissions of airborne bacteria and fungi during the process of sludge bio-drying were investigated. The recorded emission levels of airborne bacteria and fungi were 2398 ± 1307 CFU/m3 and 1963 ± 468 CFU/m3, respectively. Viable bacteria were sized between 1.1 and 3.3 μm, while fungal particles were concentrated between 2.1 and 4.7 μm. High-throughput sequencing was used to conduct a microbial population assay, and correlation analysis was performed to estimate the relationship between key factors and bioaerosol emissions. The main bacteria identified were Bacillus sp., Lysinibacillus sp. YS11, unclassified Enterobacteriaceae, Brevundimonas olei, and Achromobacter sp.; the primary types of fungi were Aspergillus ochraceus, Gibberella intricans, Fusarium concentricum, Aspergillus qinqixianii, and Alternaria sp.; and the dominant opportunistic pathogens were Bacillus anthracis and Aspergillus ochraceus. At lower moisture and temperature levels, airborne bacterial concentrations were higher, especially the release of fine particles. In addition, moisture content had a significant impact on the microbial population in bioaerosols. This study provides insights into strategies for controlling bioaerosols in the exhaust gases of the sludge bio-drying process.

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.

Antibiotic resistance genes fate during food waste management - Comparison between thermal treatment, hyperthermophilic composting, and anaerobic membrane bioreactor

The fate of eight different antibiotic resistance genes (ARGs) in food waste (sul1, sul2, tetO, tetW, ermF, ermB, ampC, oxa-1), intI1, and rpoB were monitored during thermal treatment (pyrolysis and incineration), hyperthermophilic composting, and anaerobic membrane bioreactor (AnMBR) treatment. ARGs in food waste ranged from 2.9 × 106 to 3.5 × 109 copies/kg with ampC being the least abundant and sul1 being the most abundant. Thermal treatment achieved removal below detection limits of all ARGs. Only two ARGs (sul1 and ampC) persisted in hyperthermophilic composting. While all genes except for ermB decreased in the AnMBR effluent relative to the food waste feed, sul1 remained at relatively high abundance. Biosolids on the contrary, accumulated tetO, ampC and sul2 in all tested operating conditions. Thermal treatment, despite limited resource recovery, provides the most effective mitigation of ARG risk in food waste.

Risk control of antibiotics, antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) during sewage sludge treatment and disposal: A review

Sewage sludge is an important reservoir of antibiotics, antibiotic resistance genes (ARGs), and antibiotic resistant bacteria (ARB) in wastewater treatment plants (WWTPs), and the reclamation of sewage sludge potentially threats human health and environmental safety. Sludge treatment and disposal are expected to control these risks, and this review summarizes the fate and controlling efficiency of antibiotics, ARGs, and ARB in sludge involved in different processes, i.e., disintegration, anaerobic digestion, aerobic composting, drying, pyrolysis, constructed wetland, and land application. Additionally, the analysis and characterization methods of antibiotics, ARGs, and ARB in complicate sludge are reviewed, and the quantitative risk assessment approaches involved in land application are comprehensively discussed. This review benefits process optimization of sludge treatment and disposal, with regard to environmental risks control of antibiotics, ARGs, and ARB in sludge. Furthermore, current research limitations and gaps, e.g., the antibiotic resistance risk assessment in sludge-amended soil, are proposed to advance the future studies.

Antibiotic and heavy metal resistance genes in sewage sludge survive during aerobic composting

Municipal sewage sludge has been generated in increasing amounts with the acceleration of urbanization and economic development. The nutrient rich sewage sludge can be recycled by composting that has a great potential to produce stabilized organic fertilizer and substrate for plant cultivation. However, little is known about the metals, pathogens and antibiotic resistance transfer risks involved in applying the composted sludge in agriculture. We studied changes in and relationships between heavy metal contents, microbial communities, and antibiotic resistance genes (ARGs), heavy metal resistance genes (HMRGs) and mobile genetic elements (MGEs) in aerobic composting of sewage sludge. The contents of most of the analyzed heavy metals were not lower after composting. The bacterial α-diversity was lower, and the community composition was different after composting. Firmicutes were enriched, and Proteobacteria and potential pathogens in the genera Arcobacter and Acinetobacter were depleted in the composted sludge. The differences in bacteria were possibly due to the high temperature phase during the composting which was likely to affect temperature-sensitive bacteria. The number of detected ARGs, HMRGs and MGEs was lower, and the relative abundances of several resistance genes were lower after composting. However, the abundance of seven ARGs and six HMRGs remained on the same level after composting. Co-occurrence analysis of bacterial taxa and the genes suggested that the ARGs may spread via horizontal gene transfer during composting. In summary, even though aerobic composting is effective for managing sewage sludge and to decrease the relative abundance of potential pathogens, ARGs and HMRGs, it might include a potential risk for the dissemination of ARGs in the environment.

Effects of co-selection of antibiotic-resistance and metal-resistance genes on antibiotic-resistance potency of environmental bacteria and related ecological risk factors

The inadequate elimination of micropollutants in wastewater treatment plants (WWTP), cause to increase in the incidence of antibiotic resistant bacterial strains. Growth of microbial pathogens in WWTP is one of the serious public health problems. The widespread and simultaneous emergence of antibiotic resistance genes (ARGs) and heavy metal resistance genes (HMRGs) in the environment with heavy metals create persistent and selective pressure for co-selection of both genes on environmental microorganisms. Co-localization of ARGs and HMRGs on the same horizontal mobile genetic elements (MGEs) allows the spreading of numerous antibiotic-resistant strains of bacteria in aquatic and terrestrial environment. The biofilm formation and colonization potential of environmental bacteria leads to the co-selection of multi-antibiotic resistance and multi-metal tolerance. Horizontal gene transfer (HGT), co-localization of both ARGs and HMRGs on the same MGEs, and the shared resistomes are important bacteria-associated ecological risks factors, which reduce the effectiveness of antibiotics against bacterial infections.

Dynamic changes of microbial community and moisture ratio during bio-drying of sludge after electro-dewatering

Using electro-dewatering as the pretreatment process for sludge bio-drying can improve the dewatering performance. It was innovatively investigated including the microbial mechanism and the kinetics of moisture removal by bio-drying with electro-dewatered sludge in this study. Two bio-drying processes using electro-dewatered sludge (EDS) and sludge added cornstalk conditioner (CSS) were compared. Microbial community analysis showed that the abundance of Bacteroidetes increased from 4.21% to 16.67% after electro-dewatering. The dominant phyla were Bacteroidetes (36.79%), Proteobacteria (32.35%), and Actinobacteria (24.58%) at the end of EDS bio-drying. Network analysis revealed that the co-occurrence patterns in EDS included 40 nodes and 97 edges. The prediction results of the Kyoto Encyclopedia of Genes and Genomes demonstrated that the relative abundances of carbohydrate metabolism and metabolism of terpenoids and polyketides in sludge decreased, while the relative abundances of lipid metabolism, xenobiotic biodegradation and metabolism increased after electro-dewatering. Five thin layer drying kinetic models were analyzed to estimate the bio-drying kinetic parameters. The Page's model could be better fitted to the results and the highest R² was 0.9570 in the EDS. The new coefficients k (0.1637) and n (1.2097) were obtained. The results provided mechanism and data support for exploring and applying bio-drying technology after sludge electro-dewatering.

Metagenomic analysis reveals the microbial degradation mechanism during kitchen waste biodrying

Biodrying is a treatment to remove moisture using bio-heat generated during organic degradation. Organic matter degradation and microbial metabolism were studied during the whole kitchen waste biodrying, using metagenomic analysis. After the 25-day biodrying process, carbohydrate, protein and lipid contents decreased by 83.7%, 27.8% and 79.3%, respectively, and their degradation efficiencies increased after the thermophilic phase. Lipase activity exceeded 10 mmol d^-1 g^-1 throughout biodrying. Cellulase and lipase activities recovered by 2.21% and 5.77%, respectively, after the thermophilic phase, while the protease activity had a maximum increment of 347%. Metabolic analysis revealed that carbohydrate, amino acid and lipid metabolism was possibly inhibited by the high temperature, but the relative abundances of related predicted functions recovered by more than 0.9%, 7% and 11%, respectively, by the end of biodrying. Protein function prediction suggests that β-oxidation, fatty acid biosynthesis, and the degradation of cellulose and chitin were possibly enhanced during the thermophilic phase. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that leucine, isoleucine and lysine could ultimately degraded to acetyl-CoA. Weissella, Aeribacillus and Bacillus were the genera with the most enriched functional genes during the whole biodrying process. These findings help elucidate the microbial degradation processes during biodrying, which provides further scientific support for improving the application of biodrying products.

Ferric chloride further simplified the horizontal gene transfer network of antibiotic resistance genes in anaerobic digestion

The role of ferric chloride (FC) on the reduction of antibiotic resistance genes (ARGs) in anaerobic digestion (AD) system was investigated from the perspective of vertical (VGT) and horizontal gene transfer (HGT) network through the high-throughput qPCR (HT-qPCR). Although FC showed limited impacts on methane production in AD of swine manure, the tetracycline and MLSB resistance genes were specifically reduced at the end, where tetQ of antibiotic target protection and ermF of antibiotic target alteration contributed the most to the reduction. Both VGT and HGT network were divided into three modules, and the complexity of HGT network was largely reduced along with AD, where the HGT connection was reduced from 683 (Module III) to 172 (Module I), and FC addition could further reduce the relative abundance of ARG hosts in Module I. The contribution of VGT and HGT to the changes of ARGs in AD was further deciphered, and although the VGT reflected by the changes of microbial community contributed the most to the dynamics of ARGs (68.0 %), the HGT contribution could further be reduced by the FC addition. This study provided a new perspective on the fate of ARGs response to the FC addition in the AD system.

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.

Intra-/extra-cellular antibiotic resistance responses to sewage sludge composting and salinization of long-term compost applied soils

Municipal sewage sludge, a reservoir of antibiotic resistance genes (ARGs), is usually composted as fertilizer for agricultural application especially in arid and semi-arid areas. The evolution patterns of intracellular ARGs (iARGs) and extracellular ARGs (eARGs) during composting and their responses to soil salinization after long-term compost application kept unclear previously, which were systematically studied in the current study. The variation and dissemination risk of eARGs and iARGs with the salinization of farmland soils was also evaluated. Extra/intra-cellular ARGs relative abundance varied drastically through composting process. Generally, the relative abundance of the cell-free eARGs (f-eARGs) and the cell-adsorbed eARGs (a-eARGs) were 4.62 and 3.54 folds (median) higher than that of iARGs, respectively, during the entire composting process, which held true even before the sludge composting (false discovery rate, FDR p < 0.05). There was no significant difference in relative abundance between f-eARGs and a-eARGs. The relative abundance of eARGs gradually decreased with composting time but was relatively higher than iARGs. It was worth noting that iARGs rebounded in the maturation phase. However, an over ten-year application of the eARG-rich compost led to much more severe contamination of iARGs than eARGs in soil. Soil salinization caused remarkable rise of eARGs by 943.34-fold (FDR p < 0.05). The variation of ARGs during composting and soil salinization was closely related to the change of microbial community structure. In compost, the bacterial communities mainly interacting with ARGs were the Firmicutes (54 unique and 35 shared core genera); and the bacterial communities playing major roles in ARGs during soil salinization were Proteobacteria (116 unique and 53 shared core genera) and Actinobacteria (52 unique and 27 shared core genera). These findings are important for assessing the transmission risk of ARGs in compost application to farmland in arid and semi-arid areas.

Composting temperature directly affects the removal of antibiotic resistance genes and mobile genetic elements in livestock manure

The high antibiotic resistance gene (ARGs) contents in livestock manure pose a potential risk to environment and human health. The heap composting with an ambient temperature and thermophilic composting are two methods for converting livestock manure into fertilizer. This study investigated the variations in ARGs and mobile genetic elements (MGEs) and revealed potential mechanisms for ARGs removal using the two composting methods. The ARGs abundance were enriched by 44-fold in heap composting, among them, the macrolide-resistance genes increased significantly. On the contrary, the ARGs were removed by 92% in thermophilic composting, among them, tetracycline-resistance genes decreased by 97%. The bacterial hosts of ARGs were associated with the variations of ARGs and MGEs. The tetO was correlated with the most diverse bacteria in heap composting, and Bacteroidetes was the major host bacteria. While tetT was correlated with the most diverse bacteria in thermophilic composting, and Proteobacteria was the major host bacteria. Structural equation models showed that the enrichment of ARGs in heap composting was mainly correlated with bacterial communities, whereas, the removal of ARGs in thermophilic composting was directly affect by MGEs. Composting temperature directly affected the variations in ARGs. Higher and lower temperatures significantly decreased and increased, respectively, ARGs and MGEs abundance levels.

Clarifying the beneficial effects of plant growth-promoting rhizobacteria for reducing abundances of antibiotic resistance genes during swine manure composting

This study investigated the effects on antibiotic resistance genes (ARGs) and the related mechanisms of different plant growth-promoting rhizobacteria (PGPR) inoculation strategies during composting: no inoculation (CK), inoculation in initial phase (T1), inoculation in cooling phase (T2), and inoculation in both initial and cooling phases (T3). After composting, the total relative abundances (RAs) of ARGs decreased by 0.26 and 0.03 logs under T3 and T2, respectively, but increased by 0.05 and 0.22 logs under T1 and CK. The abundances of eight ARGs were lowest under T3, including some high risk ARGs with clinical importance. Bioavailable Cu significantly affected the readily removed ARGs, and PGPR inoculation decreased the bioavailability of Cu. T3 reduced the abundances of potential pathogen hosts, inhibited horizontal gene transfer by reducing the RAs of mobile gene elements (0.48 logs), and downregulated the expression of genes related to ARG propagation, thereby decreasing the ecological risk of ARGs.

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.

Short-term biodrying achieves compost maturity and significantly reduces antibiotic resistance genes during semi-continuous food waste composting inoculated with mature compost

Food waste (FW) is important object of resource utilization and source of antibiotic resistance genes (ARGs). This study investigated the effects of biodrying combined with inoculating mature compost (B&M) on the composting efficiency, succession of bacterial communities and their links with metabolism functions as well as the fate of ARGs during FW composting. The results showed that B&M could rapidly raise and maintain high relative abundance of Bacillaceae (66.59-94.44%) as well as composting temperature (45.86-65.86 ℃), so as to achieve the final maturity of FW composting in a short time by regulating microbial carbohydrate (14.02-15.31%) and amino acid metabolism (10.33-12.47%). Network analysis demonstrated that high temperature could effectively inhibit the proliferation and spread of potential bacterial hosts of ARGs and integrons including Lactobacillaceae, Enterobacteriaceae, Leuconostocaceae and Corynebacteriaceae during the first two days of composting. As a result, B&M significantly reduced the absolute (72.09-99.47%) and relative abundances (0.31-2.44 logs) of nearly all ARGs especially ermB, tetM, bla_CTX-M and bla_OXA. Present study deepened the knowledge of ARGs variation, succession and metabolism functions of bacterial communities when B&M processes were used for FW composting, suggesting a promising technology for reducing the transmission risk of ARGs and reaching maturity of FW composting.

Triclosan enriched resistance genes more easily than copper in the presence of environmental tetracycline in aerobic granular sludge system

Triclosan (TCS) and copper (Cu²⁺) were exposed to aerobic granular sludge (AGS) system treating wastewater containing environmental tetracycline, respectively, to explore the different biochemical responses, more importantly, the fates of resistance genes (RGs) in AGS system. The results showed that TCS and Cu²⁺ could significantly inhibit the N and P removal in AGS system by reducing several key functional genes, including amoA gene of ammonia-oxidizing bacteria, Nitrospira and phosphorus accumulating organisms 16S rRNA genes. TCS caused higher degree of RGs' enrichment than Cu²⁺, which made the average total relative abundance of RGs of 1.38 ± 0.73 and 0.78 ± 0.24 in TCS and Cu system, respectively. Cu²⁺ could induce a wider range of horizontal gene transfer than TCS, leading to the detections of more potential hosts harboring RGs in Cu system. Cu system seemed to have stronger repair, immunity and defense ability than TCS system, which enabled it to have sufficient ability to trigger protection mechanism to realize self-protection, eventually the RGs also were controlled. Integron (intI1 and intI3) and plasmids (trb-C and IncQ) might cooperate with microorganisms and water quality parameters to enhance the enrichment of RGs in TCS system, however this interaction among various environmental factors was not obvious in Cu system, which might be responsible for the lower abundance of RGs. The increasing levels of TCS and Cu²⁺ in wastewater should be paid more attentions during the treatment of wastewater containing environmental tetracycline by AGS system. Especially for TCS, it had the ability to enrich RGs more easily than Cu²⁺, which should be prevented from entering wastewater treatment plants as far as possible, to avoid more serious proliferation and dissemination of various RGs.

Potential threat of antibiotics resistance genes in bioleaching of heavy metals from sediment

Bioleaching is considered a promising technology for remediating heavy metals pollution in sediments. During bioleaching, the pressure from the metals bioleached is more likely to cause the spread of antibiotic resistance genes (ARGs). The changes in abundance of ARGs in two typical heavy metal bioleaching treatments using indigenous bacteria or functional bacteria agent were compared in this study. Results showed that both treatments successfully bioleached heavy metals, with a higher removal ratio of Cu with functional bacteria agent. The absolute abundances of most ARGs decreased by one log unit after bioleaching, particularly tetR (p = 0.02) and tetX (p = 0.04), and intI1 decreased from 10⁶ to 10⁴ copies/g. As for the relative abundance, ARGs in the non-agent treatment increased from 3.90 × 10^-4 to 1.67 × 10^-3 copies/16S rRNA gene copies (p = 0.01), and in the treatment with agent, it reached 6.65 × 10^-2 copies/16S rRNA gene copies, and intI1 relative abundance was maintained at 10^-3 copies/16S rRNA gene copies. The relative abundance of ARGs associated with efflux pump mechanism and ribosomal protection mechanism increased the most. The co-occurrence network indicated that Cu bioleached was the environmental factor determining the distribution of ARGs, Firmicutes might be the potential hosts of ARGs. Compared to bioleaching with indigenous bacteria, the addition of functional bacteria agent engendered a decrease in microbial alpha diversity and an increase in the amount of Cu bioleached, resulting in a higher relative abundance of ARGs. Heavy metal pollution can be effectively removed from sediments using the two bioleaching treatments, however, the risk of ARGs propagation posed by those procedures should be considered, especially the treatment with functional bacteria agents. In the future, an economical and efficient green technology that simultaneously reduces both the absolute abundance and relative abundance of ARGs should be developed.

A sustainable and economic strategy to reduce risk antibiotic resistance genes during poultry manure bioconversion by black soldier fly Hermetia illucens larvae: Larval density adjustment

Black soldier fly (Hermetia illucens) larvae (BSFL) are common insects that are known for bioconversion of organic waste into a sustainable utilization resource. However, a strategy to increase antibiotic resistance gene (ARG) elimination in sustainable and economic ways through BSFL is lacking. In the present study, different larval densities were employed to assess the mcr-1 and tetX elimination abilities, and potential mechanisms were investigated. The application and economic value of each larval density were also analyzed. The results showed that the 100 larvae cultured in 100 g of manure group had the best density because the comprehensive disadvantage evaluation ratio was the lowest (14.97%, good bioconversion manure quality, low ARG deposition risk and reasonable larvae input cost). Further investigation showed that mcr-1 could be significantly decreased by BSFL bioconversion (4.42 ×10⁷ copies/g reduced to 4.79 ×10⁶-2.14 ×10⁵ copies/g)(P＜0.05); however, mcr-1 was increasingly deposited in the larval gut with increasing larval density. The tetX abundance was stabilized by BSFL bioconversion, except that the abundance at the lowest larval density increased (1.22 ×10¹⁰ copies/g increase, 34-fold). Escherichia was the host of mcr-1 and tetX in all samples, especially in fresh manure; Alcaligenes was the host of tetX in bioconversion manure; and the abundance of Alcaligenes was highly correlated with the pH of bioconversion manure. The pH of bioconversion manure was extremely correlated with the density of larvae. Klebsiella and Providencia were both hosts of tetX in the BSF larval gut, and Providencia was also the host of mcr-1 in the BSF larval gut. The density of larvae influenced the bioconversion manure quality and caused the ARG host abundance to change to control the abundance of ARGs, suggesting that larval density adjustment was a useful strategy to manage the ARG risk during BSFL manure bioconversion.

Antibiotic resistance genes alternation in soils modified with neutral and alkaline salts: interplay of salinity stress and response strategies of microbes

Growing evidence points to the pivotal roles of salt accumulation in mediating antibiotic resistance genes (ARGs) spread in soil, whereas how salt mediates ARGs dissemination remains unknown. Herein, the effects of neutral or alkaline (Ne/Al) salt at low, moderate and high levels (Ne/Al-L, Ne/Al-M, Ne/Al-H) on the dissemination of ten typical ARGs in soils were explored, by simultaneously considering the roles of salinity stress and response strategies of microbes. In the soils amended with Ne/Al-L and Al-M salt, the dissemination of ARGs was negligible and the relative abundances of ARGs and mobile genetic elements (MGEs) were decreased. However, Ne-M and Al-H salt contributed to the dissemination of ARGs in soils, with the significantly increased absolute and relative abundances of ARGs and MGEs. In Ne-H soil, although the absolute abundance of ARGs declined drastically due to serious oxidative damage, their relative abundances were promoted. The facilitated ARGs transfer was potentially related to the excessive generation of intracellular reactive oxygen species and increased activities of DNA repair enzymes involved in SOS system. In addition, the activated intracellular protective response including quorum sensing and energy metabolism largely provided essential factors for ARGs dissemination. The co-occurrence of ARGs and over-expressed salt-tolerant genes in specific halotolerant bacteria further suggested the selection of salt stress on ARGs. Moreover, less disturbance of alkaline salt than neutral salt on ARGs evolution was observed, due to the lower abiotic stress and selective pressure on microbes. This study highlights that soil salinity-sodicity could dose-dependently reshape the dissemination of ARGs and community structure of microbes, which may increase the ecological risks of ARGs in agricultural environment.

Mechanism of a double-channel nitrogen-doped lignin-based carbon on the highly selective removal of tetracycline from water

A high-performance nitrogen-doped lignin-based carbon material (ILAC-N) was synthesized using industrial lignin and urea by hydrothermal and activation, as an absorbent of tetracycline hydrochloride (TC). The results showed that the ILAC-N comprises a double-channeled structure with micro and mesopores. It exhibits an excellent adsorption capacity of TC across a wide pH range (pH 2-11), with the highest adsorption capacity of 1396 mg g^-1 at 323 K. Tests in actual wastewater showed that the TC removal rate by ILAC-N exceeded 97.4%. Moreover, it maintained a removal rate of 84% after 10 regeneration cycles, revealing its high reusability. Mechanisms suggested that pore filling and π-π interaction played a critical role in this process. In conclusion, ILAC-N can be broadly applied to livestock manure and pharmaceutical wastewater treatment, owing to its high adsorption capacity, good adsorption properties across a wide pH range, excellent reusability. Furthermore, this research opens a new path for lignin utilization.

Bioleaching rather than chemical conditioning using Fe[III]/CaO or polyacrylamide mitigates antibiotic resistance in sludge composting via pre-removing antibiotic resistance genes and limiting horizontal gene transfer

Conditioning can drastically improve the dewaterability of sewage sludge and is widely practiced in most wastewater treatment plants (WWTPs). Sludge conditioning was also reported as a crucial step in sludge treatment to attenuate antibiotic resistance, but it remains unclear whether the attenuated antibiotic resistance by conditioning treatments would guarantee low abundance of antibiotic resistance genes (ARGs) in the compost products of municipal sewage sludge. Herein, the impacts of three conditioning treatments, including bioleaching and chemical conditioning using Fe[III]/CaO or polyacrylamide (PAM), on the abundances of 20 ARGs and 4 mobile genetic elements (MGEs) during conventional aerobic composting of dewatered sludge were investigated. It was found that the absolute and relative abundances of total ARGs in compost product of bioleached sludge accounted for only 13.8%-28.8% of that in compost products of un-conditioned, Fe[III]/CaO-conditioned, or PAM-conditioned sludges. Besides, bioleaching conditioning resulted in the lowest abundances of ARG subtypes and ARG-associated bacteria in the sludge compost product. The shift of ARG profiles in the bioleached sludge composting can be mainly ascribed to the ARG-associated bacteria, while the MGEs drove the ARG profiles during conventional composting of un-conditioned sludge and the two chemically conditioned sludge. Thus, bioleaching conditioning is superior to the chemical conditioning using Fe[III]/CaO or PAM in mitigating antibiotic resistance in sludge compost products, which was contributed by the pre-removal of ARGs prior to composting treatment and the potential limitation of ARGs transfer during conventional composting.

Zero valent iron improved methane production and specifically reduced aminoglycoside and tetracycline resistance genes in anaerobic digestion

It is unadvisable to discuss the antibiotic resistance genes (ARGs) reduction in anaerobic digestion (AD) system neglecting its main purpose-methane production. The methane production improvement coupling with antibiotic resistance genes (ARGs) reduction in anaerobic digestion (AD) by zero valent iron (ZVI) were simultaneously investigated. Whether the role of ZVI on the ARGs fate was random or specific was clarified through the high-throughput qPCR (HT-qPCR). Results indicated that ZVI improved methane production and ARGs reduction by 23.9% and 25.0%, respectively. The improved methane production was associated with chemical reaction and variances of microbial community caused by ZVI, where DIET between Petrimonas, Clostridium and Syntrophomonas, Methanosarcina was established along with ACAS being enriched. ZVI specifically, not randomly, facilitated the reduction of aminoglycoside resistance genes of antibiotic inactivation and tetracycline resistance genes of ribosomal protection proteins. The specifical reduction could be attributed to enzyme activity inhibition and intracellular ionic disturbance caused by higher amounts of ZVI, although most of ARGs fate could be well explained by microbial community which contributed the most to ARGs dynamics as a whole. ZVI-based AD was a promising way for the improvement of methane production coupling ARGs reduction.

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.

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.

Dissipation of antibiotic resistance genes in manure-amended agricultural soil

Soil antibiotic resistance due to animal manure application is of great concern in recent years. Little is known about the fate of antibiotic resistance genes (ARGs) in agricultural soils associated with long-term manure application. Here we used soil microcosms to investigate the dissipation of ARGs and the change of bacterial community in agricultural soil originated from a vegetable field which had received 24 years' swine manure application. Soil microcosms were conducted at different soil moistures and with or without biochar over a testing period of two years in lab. Results showed that continuous manure application induced an accumulation of ARGs in soil, wherein the dissipation of ARGs differed from those in non-manure amended soil. ARGs persisted in soils at least two years, although their abundance declined gradually. Meanwhile, soil moisture and biochar had significant impact on the fate of ARGs. ARGs dissipated faster in soil with higher moisture. Biochar amendment contributed to the maintenance of bacterial diversity. Within the two years of simulation experiment, biochar enhanced soil ARG retention as they dissipated slowly in the soil amended with biochar. Succession of microbial community may have sustained the transfer and resilience of ARGs. This study provides insight into the dissipation of antibiotic resistance genes in manure-applied agricultural soil.

Attenuation effects of iron on dissemination of antibiotic resistance genes in anaerobic bioreactor: Evolution of quorum sensing, quorum quenching and dynamics of community composition

Zero valent iron (ZVI) coupled with bioreactors is arising as a promising technology for antibiotic resistance genes (ARGs) mitigation, whereas the succession and behaviors of microbes caused by ZVI in relieving ARGs propagation remain unclear. Herein, the effects of ZVI on microbial quorum sensing (QS), quorum quenching (QQ) system and community dynamics were examined in anaerobic bioreactor fed with oxytetracycline (tet), to illustrate the roles of evolutive microbial communication and community composition in ARGs attenuation. With the addition of 5 g/L ZVI, the total absolute abundance of tet ARGs was retarded by approximate 95% and 72% in sludge and effluent after 25 days operation. The abundance of mobile genetic elements and the heredity of antibiotic resistant bacteria revealed the declined horizontal and vertical transfer of ARGs, which directly led to the reduced ARGs propagation. Potential mechanisms are that the positive effects of ZVI on QQ activity via the functional bacteria enrichment inhibited QS system and thus ARGs transfer. Partial least--squares path modeling further demonstrated that ARGs abundance was strongly limited by the dynamics of bacterial composition and thereby less frequent microbial communication. These results provide new insights into the mechanisms of antibiotic resistome remission in anaerobic bioreactor modified by ZVI.

Airborne and indigenous microbiomes co-drive the rebound of antibiotic resistome during compost storage

Composting is widely used to reduce the abundance of antibiotic resistance genes (ARGs) in solid waste. While ARG dynamics have been extensively investigated during composting, the fate and abundance of residual ARGs during the storage remain unexplored. Here, we tested experimentally how ARG and mobile genetic element (MGE) abundances change during compost storage using metagenomics, quantitative PCR and direct culturing. We found that 43.8% of ARGs and 39.9% of MGEs quickly recovered already during the first week of storage. This rebound effect was mainly driven by the regrowth of indigenous, antibiotic-resistant bacteria that survived the composting. Bacterial transmission from the surrounding air had a much smaller effect, being most evident as MGE rebound during the later stages of storage. While hyperthermophilic composting was more efficient at reducing the relative abundance of ARGs and MGEs, relatively greater ARG rebound was observed during the storage of hyperthermophilic compost, exceeding the initial levels of untreated sewage sludge. Our study reveals that residual ARGs and MGEs left in the treated compost can quickly rebound during the storage via airborne introduction and regrowth of surviving bacteria, highlighting the need to develop better storage strategies to prevent the rebound of ARGs and MGEs after composting.

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.

The change of water content and role of microbe in the sludge drying process

In this study, the pure terephthalic acid sludge was treated by a drying process which was an economical and environmentally method. The water change and metabolic pathways for bacterial community function prediction were analyzed. The microbial community changes were studied by high-throughput sequencing to draw the dynamic succession model. Then multiple statistics was used to determine the key factors of the reduction. The results showed that the main stage of water loss in the PTA sludge drying process was the high temperature period where the water lost by evaporation accounted for more than 90% of the total removal. The main metabolic pathways for bacterial community function were amino acid (7.72%-8.71% of Kyoto encyclopedia of genes and genomes relative abundance and 8.26%-9.51% of Cluster of orthologous groups of proteins relative abundance) and carbohydrate metabolism. The model describing the dynamic succession of microbial communities showed that the dominant bacteria changed from Nitrospira, Novosphingobium and Azohydromonas to Pseudomonas, Paeniglutamicibac and Pelotomaculum. The key factors for water loss were Gemmatimonas, Novosphingobium and Azohydromonas with the correlation coefficients of 0.887, 0.772, 0.783, respectively; the key factors for dry matter loss were Pelotomaculum, total organic matter, dissovlved organic carbon and carbon/nitrogen ratio; the key factors for toxic substance loss were Brevundimonas, Novosphingobium and Gemmatimonas. These results provided theoretical support for the application and demonstration for hazardous waste sludge reduction.

Insights into the effects of Zn exposure on the fate of tylosin resistance genes and dynamics of microbial community during co-composting with tylosin fermentation dregs and swine manure

Though heavy metals are widely reported to induce antibiotic resistance propagation, how antibiotic resistance changes in response to heavy metal abundances remains unclearly. In this study, the tylosin fermentation dregs (TFDs) and swine manure co-composting process amended with two exposure levels of heavy metal Zn were performed. Results showed that the bioavailable Zn contents decreased 2.6-fold averagely, and the removal percentage of total tylosin resistance genes was around 23.5% after the co-composting completed. Furthermore, the tylosin resistance genes and some generic bacteria may exhibited a hormetic-like dose-response with the high-dosage inhibition and low dosage stimulation induced by bioavailable Zn contents during the co-composting process, which represented a beneficial aspect of adaptive responses to harmful environmental stimuli. This study provided a comprehensive understanding and predicted risk assessment for the Zn-contaminate solid wastes deposal and suggested that low levels of Zn or other heavy metals should receive more attention for their potential to the induction of resistance bacteria and propagation of antibiotic resistance genes.

Antibiotic and metal resistance genes are closely linked with nitrogen-processing functions in municipal solid waste landfills

Landfilled antibiotics and metals were related to the occurrences of their resistance genes, whose decade-long development in leachates with the dynamic landfilling environmental conditions, especially with the varying nitrogen contents, has yet to be studied. Here, we sampled leachates from five representative municipal solid waste landfills in China. The total concentrations of antibiotics (5000 - 50000 ng/L) and metals (10 - 60 mg/L) in leachates were significantly different among different sites and they were only closely related to sulfonamide and tetracycline resistance genes (P < 0.05). Regarding the abundance of subtype resistance genes, sul1 and ermB were dominant antibiotic resistance genes (ARGs) and terc, arsc, and mer were dominant heavy metal resistance genes (HMRGs); and meanwhile the observed huge variations of these genes appeared to be related to environmental factors like nitrate and pH (P < 0.05). The GeoChip results further indicated that more than 85% of sequenced ARGs/HMRGs and nitrogen processing genes, particularly of the denitrification genes, were hosted by the same bacterial species, such as Pseudomonas sp. and Bacillus sp., which belonged to the predominant phylum in leachates. These results extended our knowledge about the linkages among ARGs, HMRGs and nitrogen-processing functions in leachates.

The fate of antibiotic resistance genes in cow manure composting: shaped by temperature-controlled composting stages

Current work for animal manure processing is not up to the required standards and hence are not supposed to reflect the actual performance in antibiotic resistance control. As a result, this study carried out temperature-controlled aerobic composting, with sulfamethoxazole (SMX) as a typical antibiotic. The results of four different treatments demonstrated that temperature, water content, C/N ratio, EC, and pH showed no significant (p > 0.05) difference. Antibiotic resistance genes (ARGs) significantly decreased in the initial 10 days of the thermophilic phase, but the abundance of sul1 and sul2 increased greatly after 30 days. Moreover, ARGs were closely related with each other during the late stages of composting. A noteworthy effect of composting properties, especially temperature on bacterial community, which then had a positive effect on ARGs abundances. These findings provided evidence that the standard composting was still insufficient to control antibiotic resistance.

Critical insight into the fate of antibiotic resistance genes during biological treatment of typical biowastes

Antibiotic resistance genes (ARGs) in biowaste, such as livestock manure and excess activated sludge, pose potential threat to human and ecological health when applied to agricultural fields. Biological treatment approaches, such as thermophilic composting/vermicomposting and anaerobic digestion, widely adopted to stabilize biowaste have demonstrated significant effects on the fate of ARGs. However, the influence of these biological treatments on ARGs is not known. This review summarizes the occurrence of ARGs in biowaste and the impact of thermophilic composting, vermicomposting, and anaerobic digestion on the fate of ARGs with discussion on factors, including substrate properties, pretreatments, additives, and operational parameters, associated with ARGs during biological treatment of biowaste. Finally, this review explores the research implications and proposes new avenues in the field of biological treatment of organic waste.

Composting of oxytetracycline fermentation residue in combination with hydrothermal pretreatment for reducing antibiotic resistance genes enrichment

Hydrothermal pretreatment can efficiently remove the residual antibiotics in oxytetracycline fermentation residue (OFR), but its effect on antibiotic resistance genes (ARGs) during composting remains unclear. This study compared the shifts in bacterial community and evolutions in ARGs and integrons during different composting processes of OFRs with and without hydrothermal pretreatment. The results demonstrated that hydrothermal pretreatment increased the bacterial alpha diversity at the initial phase, and increased the relative abundances of Proteobacteria and Actinobacteria but decreased that of Bacteroidetes at the final phase by inactivating mycelia and removing residual oxytetracycline. Composting process inevitably elevated the abundance and relative abundance of ARGs. However, the increase in ARGs was significantly reduced by hydrothermal pretreatment, because the removal of oxytetracycline decreased their potential host bacteria and inhibited their horizontal gene transfer. The results demonstrated that hydrothermal pretreatment is an efficient strategy to reduce the enrichment of ARGs during the OFR composting.

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

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

Lignite as additives accelerates the removal of antibiotic resistance genes during poultry litter composting

Antibiotic resistance genes (ARGs) in animal manure are a great threat to human health. This study investigated the effects of lignite addition at three levels (5%, 10%, 15% w/w) on the profiles of ARGs and the bacterial communities during poultry litter composting. Lignite addition effectively promoted the removal of manure-borne ARGs. After 65 days of composting, the relative abundances of ARGs decreased by 8.9% in control (no lignite), and by 15.8%, 27.7% and 41.5% in 5%, 10% and 15% lignite treatments, respectively. Although the total mobile genetic elements were enriched after composting, the enrichment of the intI-1 gene was significantly lower in the 10% and 15% lignite treatments compared with control. Network analysis indicated that Actinobacteria and Firmicutes were potential bacterial hosts for ARGs. Redundancy analysis showed that bacterial community succession played a key role in the shifts of ARGs. Taken together, this study provides evidence that lignite as additives promoted the removal efficacy of ARGs during composting of poultry litter.

Enhanced removal of antibiotic resistance genes and mobile genetic elements during sewage sludge composting covered with a semi-permeable membrane

Transmission of antibiotic resistance genes (ARGs) via air media, such as particulate matter, has been intensively investigated due to human exposure through inhalation. However, whether particulate matter originating from the atmospheric environment of composting plants can impact ARG abundance during composting is unknown. Here, we investigated the effects of the atmospheric environment of composting plants on ARG abundance during sewage sludge composting using semi-permeable membrane-covered thermophilic composting (smTC) and conventional thermophilic composting (cTC). After smTC treatment, the total abundances of ARGs and mobile genetic elements (MGEs) decreased by 42.1 % and 38.1 % compared with those of the initial phase, respectively, but they increased by 4.5- and 1.6-fold after cTC, respectively. This result suggested that smTC was more efficient at decreasing ARGs and MGEs than cTC, mainly due to a significant reduction in bacterial contamination from the atmospheric environment of composting plants that accelerated the resurgence of ARGs and MGEs. Furthermore, culture experiments demonstrated that the abundance and diversity of antibiotic-resistant bacteria during the mature phase of smTC were also significantly (P <  0.05) lower than those in the cTC treatment. Thus, covering composting with a semi-permeable membrane could decrease the risk of ARGs spreading.

The fate of antibiotic resistance genes during co-composting of swine manure with cauliflower and corn straw

Composting is not completely effective in reducing antibiotic resistance genes (ARGs) in animal manure. This work studied the effects of different treatment conditions on the fate of ARGs in composting swine manure with cauliflower and corn straw as bulking agents. The results showed that the addition of microbial agents or the ratio of corn stalks to cauliflower (1:12) could significantly decrease the absolute abundances of most ARGs (an average of 480 times) compared with the control treatment. Principal component analysis indicated that bacterial communities were significantly correlated with ARG abundance, suggesting that microbial communities have an impact on ARG variation during co-composting. Redundancy and Network analysis confirmed the changing patterns of individual ARGs (qnrS, bla_AmpC, bla_TEM-1) were influenced by the selectivity of host bacteria (Pseudomonas, Klebsiella, and Halocella) and environmental variables (TN, NH₃-N, TOC, and pH). These findings helped to optimize composting conditions, thereby reducing the risk of ARGs spread.

Novel Electrochemical Pretreatment for Preferential Removal of Nonylphenol in Industrial Wastewater: Biodegradability Improvement and Toxicity Reduction

Preferential pretreatment of nonylphenol (NP) before biological treatment is of great significance due to its horizontal gene transfer effect and endocrine disruption activity. A novel molecular imprinting high-index facet SnO₂ (MI-SnO_2, HIF) electrode is designed. NP was effectively removed from industrial wastewater at 1.8 V with totally suppressing human estrogen activity. The ratio of 5 day biological oxygen demand to chemical oxygen demand (BOD₅/COD_Cr) was enhanced to 0.412 from 0.186 after preferential pretreatment. The effluent concentration of NP was 6.4 μg L^-1 after further simulating anaerobic-anoxic-oxic treatment, which was about 1/10 of that without pretreatment. This preferential electrochemical pretreatment is interpreted as prior adsorption and enrichment of target pollutants on the MI-SnO_2, HIF surface. The reactive oxygen species and subsequent oxidation products were investigated by in situ electron paramagnetic resonance and electrochemical infrared spectroscopy. The degradation pathway of NP was further analyzed by liquid chromatography-mass spectrometry. This unique pretreatment method for a complex tannery wastewater system has irreplaceable status because no methods with similar advantages have been reported, expecting to be widely used in preferential pretreatment of toxic contaminants blended with highly concentrated nontoxic organics.

Efficient reduction of antibiotic residues and associated resistance genes in tylosin antibiotic fermentation waste using hyperthermophilic composting

Insufficient removal of antibiotics and antibiotic resistance genes (ARGs) from waste products can increase the risk of selection for antibiotic resistance in non-clinical environments. While composting is an efficient way to reduce ARGs, most conventional methods are ineffective at processing highly contaminated antibiotic fermentation waste. Here we explored the efficacy and underlying mechanisms of hyperthermophilic composting at removing tylosin antibiotic fermentation residues (TFR) and associated ARGs and mobile genetic elements (MGEs; plasmids, integrons and transposon). Hyperthermophilic composting removed 95.0% of TFR, 75.8% of ARGs and 98.5% of MGEs and this reduction mainly occurred after extended exposure to temperatures above 60 °C for at least 6 days. Based on sequencing and culture-dependent experiments, reduction in ARGs and MGEs was strongly associated with a decrease in the number of bacterial taxa that were initially associated with ARGs and MGEs. Moreover, we found 94.1% reduction in plasmid genes abundances (ISCR1 and IncQ-oriV) that significantly correlated with reduced ARGs during the composting, which suggests that plasmids were the main carriers for ARGs. We verified this using direct culturing to show that ARGs were more often found in plasmids during the early phase of composting. Together these results suggest that hyperthermophilic composting is efficient at removing ARGs and associated resistance genes from antibiotic fermentation waste by decreasing the abundance of antibiotic resistance plasmids and associated host bacteria.

Bacterial community changes and antibiotic resistance gene quantification in microbial electrolysis cells during long-term sulfamethoxazole treatment

In this study, sulfamethoxazole served as the electron donor for microbial electrolysis cells. After 6 months of operation, the removal efficiencies of sulfamethoxazole in three microbial electrolysis cells were 77.60%, 87.55%, and 92.53% for a 3-day period and were directly proportional to the initial added concentrations. However, the removal efficiencies in the microbial electrolysis cells with open circuits and without microorganisms were only 51% and 8%, respectively. Higher sulfamethoxazole concentrations and sustained electrical stimulation caused faster bioelectrochemical reactions, thereby enhancing sulfamethoxazole degradation. Bacterial community analysis revealed that Proteobacteria and Synergistetes, which are the main functional phyla, proliferated with increased antibiotic concentrations. The qPCR results indicated that the copy numbers of antibiotic resistance genes and integrons in microbial electrolysis cell biofilms and effluents were distinctly lower than those in traditional biological treatment systems. Thus, the generation and dissemination of antibiotic resistance genes might be a diminished challenge in microbial electrolysis cells.

Environmental media exert a bottleneck in driving the dynamics of antibiotic resistance genes in modern aquatic environment

With the rapid construction of dams worldwide, reservoir system has become a representation of modern aquatic environment. However, the profiles of antibiotic resistance genes (ARGs) and associated factor influencing their dynamics in modern aquatic environment (e.g., water phase, sediment phase, and soil phase) are largely unknown. Here, we comprehensively characterized the diversity, abundance, distribution of ARGs in a large drinking water reservoir using high-throughput quantitative PCR, as well as ranked the factors (e.g., mobile genetic elements (MGEs), bacteria community, bacterial biomass, antibiotics, and basic properties) influencing the profiles of ARGs on the basis of structural equation models (SEMs). Water phase was prone to harbor more diverse ARGs as compared to sediment phase and soil phase, and soil phase in drawdown area was a potential reservoir and hotspot for ARGs. Environmental media partially affected the ARG diversity in modern aquatic environment, while it observably influenced the distributions of ARGs and MGEs and their co-occurrence patterns. The pathways for the proliferation and spread of ARGs in water phase were both the horizontal gene transfer (HGT) and vertical gene transfer (VGT), while the dominant pathways in sediment phase and soil phase were the HGT and VGT, respectively. The SEMs demonstrated that MGEs contributed the most to drive the ARG dynamics in both water phase and sediment phase, while the most dominant factor for this in soil phase was bacterial community. Overall, environmental media exerted a bottleneck in driving the dynamics of ARGs in modern aquatic environment probably via diversifying the MGEs, bacterial community, bacterial biomass, antibiotics and basic properties.

Sludge bio-drying followed by land application could control the spread of antibiotic resistance genes

The process of sludge bio-drying has been adopted in response to the increasing amount of residual sewage sludge. It has been demonstrated that sludge bio-drying effectively reduces both antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), whereas ermF, tetX, and sulII become enriched in response to the dynamic development of the microbial community. The present study further demonstrated that the land application of sludge bio-drying products under current application rate did not cause an increase in the abundance of quantified ARGs in the soil but the persistence of ARB should be paid attention. Although land application introduced ermF, tetX, and tetG into the soil, these soon decreased to control levels. Furthermore, the decay rate varied between soil types, with red soil being the most persistent based on kinetics modeling. The fate of ARGs could also be attributed to the dynamics of the microbial community during land application, and the genus Parasegetibacter, which can degrade extracellular DNA, might play a key role in the control of ARGs. In summary, sludge bio-drying following land application could constitute an effective means of controlling the spread of ARGs, and microbial community changes contributed the most to the fate of the ARGs during the entire treatment chain (residual sewage sludge → bio-drying process → land application).