Elucidating the effect of microbial inoculum and ferric chloride as additives on the removal of antibiotic resistance genes from chicken manure during aerobic composting

Understanding bacterial ecology to combat antibiotic resistance dissemination

The dissemination of antibiotic resistance from environmental sources is a growing concern. Despite the widespread occurrence of antibiotic resistance transmission events, there are actually multiple obstacles in the ecosystem that restrict the flow of bacteria and genes, in particular nonnegligible biological barriers. How these ecological factors help combat the dissemination of antibiotic resistance and relevant antibiotic resistance-diminishing organisms (ARDOs) deserves further exploration. This review summarizes the factors that influence the growth, metabolism, and environmental adaptation of antibiotic-resistant bacteria (ARB) and restrict the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Additionally, this review discusses the achievements in the application of ARDOs to improve biotechnology for wastewater and solid waste remediation while highlighting current challenges limiting their broader implementation.

Inoculation of thermophilic bacteria from giant panda feces into cattle manure reduces gas emissions and decreases resistance gene prevalence in short-term composting

Here, thermophilic bacteria (TB) with cellulose degradation functions were screened from composting panda feces and applied to cattle manure composting. TB (Aeribacillus pallidus G5 and Parageobacillus toebii G12) inoculation led to remarkable improvement of the compost temperature, prolonging of the thermophilic stage and shortening of the composting process, resulting in increased manure harmlessness (GI ≥ 70%), compost humification, and greenhouse gas emission reduction (14.19%-22.57%), compared with the control compost, within 15 days of composting. In particular, G5 inoculation reduced NH3 emissions by 41.97% relative to control composts over 15 days. G5 was capable of rapidly colonizing in the composts, and its inoculation immediately enriched the genera of Firmicutes, and simultaneously decreased the genera of Proteobacteria, contributing to the elimination of harmful microorganisms. Notably, this strain lacked antibiotic resistance genes, and the absolute abundances of resistance genes and mobile genetic genes (MGEs) decreased the most (by 80.84%). Metagenomic analysis revealed that enzymes capable of producing CO2, N2O, and NH3 were generally inhibited, while CO2 fixation and N2O and NH3 reduction enzymes were enriched in the G5 compost, since metagenome-assembled genomes of Proteobacteria harbored more key genes and enzymes in complete pathways for producing N2O, NH3, and CO2. Moreover, Proteobacteria, such as Pseudomonas and Halopseudomonas, were the main host of resistance genes and MGEs. Overall, the gas emission could be reduced, and more efficient control of resistance genes could be achieved by inhibited the abundance of Proteobacteria during composting. This study provides a safe and effective microbial agent (A. pallidus) for manure treatment.

The addition of vermiculite reduced antibiotic resistance genes during composting: Novel insights based on reducing host bacteria abundance and inhibiting plasmid-mediated conjugative transfer

Antibiotic resistance genes (ARGs) are prevalent in raw materials used for composting. The utilization of eco-friendly materials for the removal of ARGs is regarded as an economically effective method. Therefore, this study focused on the impact of incorporating different proportions of vermiculite (0% (CK), 5% (T1), and 10% (T2)) on the dynamics of ARGs during composting. In comparison to CK, the total absolute abundances of ARGs decreased by 14.17% and 31.52% in T1 and T2, respectively. Potential human pathogenic bacteria, including Acinetobacter, Corynebacterium, and Lactobacillus, were identified as core hosts of ARGs. The addition of vermiculite effectively inhibited proliferation of ARG hosts by extending the thermophilic phase of composting and reducing bioavailable copper concentrations. Incorporation of vermiculite decreased the absolute abundances of transposons and integrons, such as intI1 and Tn916/1545, which were significantly positively correlated with most ARGs. Adding vermiculite simultaneously enhanced the removal of common environmental plasmids (e.g., Inc.P, Inc.W), and downregulated expression of genes associated with bacterial conjugation and plasmid replication (e.g., trBbp, trfAp), thereby inhibiting the dissemination of ARGs. Taken together, this study provides novel insights that the incorporation of vermiculite can effectively enhance the reduction rate of ARGs during composting by reducing the host of ARGs and inhibiting their dissemination.

Mechanisms and influencing factors of horizontal gene transfer in composting system: A review

Organic solid wastes such as livestock manure and sewage sludge are important sources and repositories of antibiotic resistance genes (ARGs). Composting, a solid waste treatment technology, has demonstrated efficacy in degrading various antibiotics and reducing ARGs. However, some recalcitrant ARGs (e.g., sul1, sul2) will enrich during the composting maturation period. These ARGs persist in compost products and spread through horizontal gene transfer (HGT). We analyzed the reasons behind the increase of ARGs during the maturation phase. It was found that the proliferation of ARG-host bacteria and HGT process play an important role. This article revealed that microbial physiological responses, environmental factors, pollutants, and quorum sensing (QS) can all influence the HGT process in composting systems. We examined the influence of these factors on HGT in the compost system and summarized potential mechanisms by analyzing the alterations in microbial communities. We comprehensively summarized the HGT hazards that these factors may present in composting systems. Finally, we summarized methods to inhibit HGT in compost, such as using additives, quorum sensing inhibitors (QSIs), microbial inoculation, and predicting HGT events. Overall, the HGT mechanism and driving force in complex composting systems are still insufficiently studied. In view of the current situation, using predictions to assess the risk of HGT in composting may be advisable.

Evaluation of the potential horizontal gene transfer ability during chicken manure and pig manure composting

Resistance genes have been identified as emerging pollutants due to their ability to rapidly spread in the environment through horizontal gene transfer (HGT). Microbial community serves as the pivotal factor influencing the frequency of HGT during manure composting. However, the characteristics of HGT in microbial community from different types of manure were unclear. Therefore, this study aimed to evaluate the potential risk of HGT in bacterial community through the co-composting of chicken manure and pig manure in different proportions. The experimental results showed that the abundance of sulfonamide antibiotic resistance genes and integrase genes was higher during pig manure composting than those during chicken manure composting. In addition, the addition of pig manure also increased resistance genes abundance during chicken manure composting. These results suggested that the potential HGT risk was greater during pig manure composting. Furthermore, microbial analysis of co-composting suggested that bacterial community of pig manure was more competitive and adaptable than that of chicken manure. Ultimately, statistical analysis indicated that compared to chicken manure composting, the potential ability of HGT was greater during pig manure composting. This study provided the vital theoretical support and scientific guidance for mitigating the HGT risk during manure composting.

Optimizing the management of aerobic composting for antibiotic resistance genes elimination: A review of future strategy for livestock manure resource utilization

Aerobic composting technology is an efficient, safe and practical method to reduce the residues of antibiotics and antibiotic resistance genes (ARGs) due to unreasonable disposal of livestock manure. Nowadays, it remains unclear how aerobic composting works to minimize the level of remaining antibiotics and ARGs in manure. Moreover, aerobic composting techniques even have the potential to enhance ARGs level. Therefore, this study conducted a literature review on ARGs variation during the composting process to assess the fate, migration, and risk features of antibiotics and ARGs in different livestock manure and compost. The relationship between ARGs reduction and crucial factors (temperature, heavy metal, and microbial community structures) in the composting process was discussed. The merits and limitations of different technologies used in compost was summarized. The effects on ARGs reduction in the aerobic composting process with various strategies was examined. We attempt to provide a fresh and novel viewpoint on the advancement of global aerobic composting technology.

Preference and regulation mechanism mediated via mobile genetic elements for antibiotic and metal resistomes during composting amended with nano ZVI loaded on biochar

This study assessed the effectiveness of nano zero-valent iron loaded on biochar (BC-nZVI) during swine manure composting. BC-nZVI significantly reduced the abundance of antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and mobile genetic elements (MGEs). BC-nZVI modified the preference of MGEs to carry ARGs and MRGs, and the corrosion products of BC-nZVI could destroy cell structure, hinder electron transfer between cells, and weaken the association between ARGs, MRGs, and host bacteria. Functional genes analysis revealed that BC-nZVI down-regulated the abundance of genes affecting the transmission and metabolism of ARGs and MRGs, including type IV secretion systems, transporter systems, two-component systems, and multidrug efflux pumps. Furthermore, the BC-nZVI decreased genes related to flagella and pili production and cell membrane permeability, thereby hindering the transfer of ARGs, MRGs, and MGEs in the environment. Redundancy analysis demonstrated that changes in the microbial community induced by BC-nZVI were pivotal factors impacting the abundance of ARGs, MRGs, and MGEs. Overall, this study confirmed the efficacy of BC-nZVI in reducing resistance genes during swine manure composting, offering a promising environmental strategy to mitigate the dissemination of these contaminants.

An overview of the occurrence, impact of process parameters, and the fate of antibiotic resistance genes during anaerobic digestion processes

Antibiotic resistance genes (ARGs) have emerged as a significant global health threat, contributing to fatalities worldwide. Wastewater treatment plants (WWTPs) and livestock farms serve as primary reservoirs for these genes due to the limited efficacy of existing treatment methods and microbial adaptation to environmental stressors. Anaerobic digestion (AD) stands as a prevalent biological treatment for managing sewage sludge and manure in these settings. Given the agricultural utility of AD digestate as biofertilizers, understanding ARGs' fate within AD processes is essential to devise effective mitigation strategies. However, understanding the impact of various factors on ARGs occurrence, dissemination, and fate remains limited. This review article explores various AD treatment parameters and correlates to various resistance mechanisms and hotspots of ARGs in the environment. It further evaluates the dissemination and occurrence of ARGs in AD feedstocks and provides a comprehensive understanding of the fate of ARGs in AD systems. This review explores the influence of key AD parameters such as feedstock properties, pretreatments, additives, and operational strategies on ARGs. Results show that properties such as high solid content and optimum co-digestion ratios can enhance ARG removal, while the presence of heavy metals, microplastics, and antibiotics could elevate ARG abundance. Also, operational enhancements, such as employing two-stage digestion, have shown promise in improving ARG removal. However, certain pretreatment methods, like thermal hydrolysis, may exhibit a rebounding effect on ARG levels. Overall, this review systematically addresses current challenges and offers future perspectives associated with the fate of ARGs in AD systems.

Environmental health hazards of untreated livestock wastewater: potential risks and future perspectives

Due to technological and economic limitations, waste products such as sewage and manure generated in livestock farming lack comprehensive scientific and centralized treatment. This leads to the exposure of various contaminants in livestock wastewater, posing potential risks to both the ecological environment and human health. This review evaluates the environmental and physical health risks posed by common pollutants in livestock wastewater and outlines future treatment methods to mitigate these risks. Residual wastes in livestock wastewater, including pathogenic bacteria and parasites surviving after epidemics or diseases on various farms, along with antibiotics, organic wastes, and heavy metals from farming activities, contribute to environmental damage and pose risks to human health. As the livestock industry's development increasingly impacts society's future negatively, addressing the issue of residual wastes in livestock wastewater discharge becomes imperative. Ongoing advancements in wastewater treatment systems are consistently updating and refining practices to effectively minimize waste exposure at the discharge source, mitigating risks to environmental ecology and human health. This review not only summarizes the "potential risks of livestock wastewater" but also explores "the prospects for the development of wastewater treatment technologies" based on current reports. It offers valuable insights to support the long-term and healthy development of the livestock industry and contribute to the sustainable development of the ecological environment.

Greenhouse gas emission characteristics and influencing factors of agricultural waste composting process: A review

China, being a major agricultural nation, employs aerobic composting as an efficient approach to handle agricultural solid waste. Nevertheless, the composting process is often accompanied by greenhouse gas emissions, which are known contributors to global warming. Therefore, it is urgent to control the formation and emission of greenhouse gases from composting. This study provides a comprehensive analysis of the mechanisms underlying the production of nitrous oxide, methane, and carbon dioxide during the composting process of agricultural wastes. Additionally, it proposes an overview of the variables that affect greenhouse gas emissions, including the types of agricultural wastes (straw, livestock manure), the specifications for compost (pile size, aeration). The key factors of greenhouse gas emissions during composting process like physicochemical parameters, additives, and specific composting techniques (reuse of mature compost products, ultra-high-temperature composting, and electric-field-assisted composting) are summarized. Finally, it suggests directions and perspectives for future research. This study establishes a theoretical foundation for achieving carbon neutrality and promoting environmentally-friendly composting practices.

Sustainable management and valorization of biomass wastes using synthetic microbial consortia

In response to the persistent expansion of global resource demands, considerable attention has been directed toward the synthetic microbial consortia (SMC) within the domain of microbial engineering, aiming to address the sustainable management and valorization of biomass wastes. This comprehensive review systematically encapsulates the most recent advancements in research and technological applications concerning the utilization of SMC for biomass waste treatment. The construction strategies of SMC are briefly outlined, and the diverse applications of SMC in biomass wastes treatment are explored, with particular emphasis on its potential advantages in waste degradation, hazardous substances control, and high value-added products conversion. Finally, recommendations for the future development of SMC technology are proposed, and prospects for its sustainable application are discussed.

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.

Reduction of mobile genetic elements determines the removal of antibiotic resistance genes during pig manure composting after thermal pretreatment

Animal manure is a primary repository of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). This work explored the efficiency of ARGs and MGEs removal during pig manure composting after thermal pretreatment (TPC) and the underlying mechanisms. TPC resulted in a decrease of 94.7% and 92.3% in the relative abundance of ARGs and MGEs which was 48.9% and 76.6% lower than control, respectively. Network analysis indicated that reductions of ARGs and MGEs in TPC were relevant to decrease in the amount and abundance of bacterial hosts. Furthermore, total ARGs abundance in TPC was correlated with that of intI1 and Tn916/1545 (P < 0.001). Redundancy analysis supported a leading role of MGEs in ARGs dynamics in TPC. Reduction of MGEs rather than bacterial hosts contributed mainly to ARGs removal in TPC, as revealed by structural equation modeling. In conclusion, TPC was an effective method to treat animal manure containing ARGs.

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.

Biochar as functional amendment for antibiotic resistant microbial community survival during hen manure composting

The study aim was to reveal the mechanism of impact of two type biochar on composting of hen manure (HM) and wheat straw (WS). Biochar derived from coconut shell and bamboo used as additives to reduce antibiotic resistant bacteria (ARB) in HM compost. The results manifested that effect of biochar amendment was significant to reduce ARB in HM composting. Compared with control, the microbial activity and abundance were increased in both biochar applied treatment, and bacterial community was changed. Additionally, network analysis revealed that biochar amendment increased the quantity of microorganisms related to organic matter degrading. Among them, coconut shell biochar (CSB) played a pioneering role to mitigate ARB to better exert its effects. Structural correlation analysis showed that CSB reduce ARB mobility and promote organic matter degradation via improving beneficial bacterial community structure. Overall, composting with participation of biochar amendment stimulated antibiotic resistance bacterial dynamics. These results evidence practical value for scientific research and lay the foundation for agricultural promotion of composting.

Impact of environment on transmission of antibiotic-resistant superbugs in humans and strategies to lower dissemination of antibiotic resistance

Antibiotics are the most efficient type of therapy developed in the twentieth century. From the early 1960s to the present, the rate of discovery of new and therapeutically useful classes of antibiotics has significantly decreased. As a result of antibiotic use, novel strains emerge that limit the efficiency of therapies in patients, resulting in serious consequences such as morbidity or mortality, as well as clinical difficulties. Antibiotic resistance has created major concern and has a greater impact on global health. Horizontal and vertical gene transfers are two mechanisms involved in the spread of antibiotic resistance genes (ARGs) through environmental sources such as wastewater treatment plants, agriculture, soil, manure, and hospital-associated area discharges. Mobile genetic elements have an important part in microbe selection pressure and in spreading their genes into new microbial communities; additionally, it establishes a loop between the environment, animals, and humans. This review contains antibiotics and their resistance mechanisms, diffusion of ARGs, prevention of ARG transmission, tactics involved in microbiome identification, and therapies that aid to minimize infection, which are explored further below. The emergence of ARGs and antibiotic-resistant bacteria (ARB) is an unavoidable threat to global health. The discovery of novel antimicrobial agents derived from natural products shifts the focus from chemical modification of existing antibiotic chemical composition. In the future, metagenomic research could aid in the identification of antimicrobial resistance genes in the environment. Novel therapeutics may reduce infection and the transmission of ARGs.

Metagenomic Profiles of Yak and Cattle Manure Resistomes in Different Feeding Patterns before and after Composting

Antibiotic resistance is a global threat to public health, with antibiotic resistance genes (ARGs) being one of the emerging contaminants; furthermore, animal manure is an important reservoir of biocide resistance genes (BRGs) and metal resistance genes (MRGs). However, few studies have reported differences in the abundance and diversity of BRGs and MRGs between different types of animal manure and the changes in BRGs and MRGs before and after composting. This study employed a metagenomics-based approach to investigate ARGs, BRGs, MRGs, and mobile genetic elements (MGEs) of yak and cattle manure before and after composting under grazing and intensive feeding patterns. The total abundances of ARGs, clinical ARGs, BRGs, MRGs, and MGEs were lower in the manure of grazing livestock than in the manure of the intensively fed group. After composting, the total abundances of ARGs, clinical ARGs, and MGEs in intensively fed livestock manure decreased, whereas those of ARGs, clinical ARGs, MRGs, and MGEs increased in grazing livestock manure. The synergy between MGEs mediated horizontal gene transfer and vertical gene transmission via host bacteria proliferation, which was the main driver that altered the abundance and diversity of ARGs, BRGs, and MRGs in livestock manure and compost. Additionally, tetQ, IS91, mdtF, and fabK were potential indicators for estimating the total abundance of clinical ARGs, BRGs, MRGs, and MGEs in livestock manure and compost. These findings suggest that grazing livestock manure can be directly discharged into the fields, whereas intensively fed livestock manure should be composted before returning to the field. IMPORTANCE The recent increase in the prevalence of antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and metal resistance genes (MRGs) in livestock manure poses risks to human health. Composting is known to be a promising technology for reducing the abundance of resistance genes. This study investigated the differences and changes in the abundances of ARGs, BRGs, and MRGs between yak and cattle manure under grazing and intensive feeding patterns before and after composting. The results indicate that the feeding pattern significantly affected the abundances of resistance genes in livestock manure. Manure in intensive farming should be composted before being discharged into the field, while grazing livestock manure is not suitable for composting due to an increased number of resistance genes.

Graphene nano zinc oxide reduces the expression and release of antibiotic resistance-related genes and virulence factors in animal manure

Animal manure contains many antibiotic resistance genes (ARGs) and virulence factors (VFs), posing significant health threats to humans. However, the effects of graphene nano zinc oxide (GZnONP), a zinc bioaugmentation substitute, on bacterial chemotaxis, ARGs, and VFs in animal manure remain scanty. Herein, the effect of GZnONP on the in vivo anaerobic expression of ARGs and VFs in cattle manure was assessed using high-throughput sequencing. Results showed that GZnONP inhibited bacterial chemotaxis by reducing the zinc pressure under anaerobic fermentation, altering the microbial community structure. The expression of ARGs was significantly lower in GZnONP than in zinc oxide and nano zinc oxide (ZnONP) groups. The expression of VFs was lower in the GZnONP than in the zinc oxide and ZnONP groups by 9.85 % and 13.46 %, respectively. Co-occurrence network analysis revealed that ARGs and VFs were expressed by the Spirochaetes phylum, Paraprevotella genus, and Treponema genus et al. The ARGs-VFs coexistence was related to the expression/abundance of ARGs and VFs genes. GZnONP reduces the abundance of certain bacterial species by disrupting chemotaxis, minimizing the transfer of ARGs and VFs. These findings suggest that GZnONP, a bacterial chemotaxis suppressor, effectively reduces the expression and release of ARGs and VFs in animal manure.

Microbial inoculants enhance the persistence of antibiotic resistance genes in aerobic compost of food waste mainly by altering interspecific relationships

The effects of microbial inoculants on ARG removal in composting are poorly understood. Here, a co-composting method for food waste and sawdust amended with different microbial agents (MAs) was designed. The results show that the compost without MA unexpectedly achieved the best ARG removal. The addition of MAs markedly increased the abundance of tet, sul and multidrug resistance genes (p < 0.05). Structural equation modeling demonstrated that MAs can enhance the contribution of the microbial community to ARG changes by reshaping community structure and altering the ecological niche, causing the proliferation of individual ARGs, an effect related to the MA component. Network analysis revealed that inoculants weakened the correlation between ARGs and community but increased the linkage between ARGs and core species, suggesting that inoculant-induced ARG proliferation may correspond with gene exchange occurring mainly between core species. The outcome provides new insights into MA application for ARG removal in waste treatment.

Neglected Drivers of Antibiotic Resistance: Survival of Extended-Spectrum β-Lactamase-Producing Pathogenic Escherichia coli from Livestock Waste through Dormancy and Release of Transformable Extracellular Antibiotic Resistance Genes under Heat Treatment

Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae has caused a global pandemic with high prevalence in livestock and poultry, which could disseminate into the environment and humans. To curb this risk, heat-based harmless treatment of livestock waste was carried out. However, some risks of the bacterial persistence have not been thoroughly assessed. This study demonstrated that antibiotic-resistant bacteria (ARB) could survive at 55 °C through dormancy, and simultaneously transformable extracellular antibiotic resistance genes (eARGs) would be released. The ESBL-producing pathogenic Escherichia coli CM1 from chicken manure could enter a dormant state at 55 °C and reactivate at 37 °C. Dormant CM1 had stronger β-lactam resistance, which was associated with high expression of β-lactamase genes and low expression of outer membrane porin genes. Resuscitated CM1 maintained its virulence expression and multidrug resistance and even had stronger cephalosporin resistance, which might be due to the ultra-low expression of the porin genes. Besides, heat at 55 °C promoted the release of eARGs, some of which possessed a certain nuclease stability and heat persistence, and even maintained their transformability to an Acinetobacter baylyi strain. Therefore, dormant multidrug-resistant pathogens from livestock waste will still pose a direct health risk to humans, while the resuscitation of dormant ARB and the transformation of released eARGs will jointly promote the proliferation of ARGs and the spread of antibiotic resistance.

Shifts in bacterial diversity characteristics during the primary and secondary fermentation stages of bio-compost inoculated with effective microorganisms agent

Microbial inoculation was an effective way to improve product quality of composting and solve traditional composting shortage. However, the effect mechanism of microbial inoculation on compost microorganisms remains unclear. Here, Shifts in bacterial community, metabolic function and co-occurrence network during the primary and secondary fermentation stages of bio-compost inoculated with effective microorganisms (EM) agent were analyzed by high-throughput sequencing and network analysis. Microbial inoculation promoted organic carbon transformation in early stage of secondary fermentation (days 27 to 31). The beneficial biocontrol bacteria were main dominant genera at the second fermentation stage. Microbial inoculation can be good for the survival of beneficial bacteria. Inoculation with microbes promoted amino acid, carbohydrate and lipid metabolism, and inhibited energy metabolism and citrate cycle (TCA cycle). Microbial inoculation could enhance complexity of bacterial network and enhance mutual cooperation among bacteria during composting.

Pretreatment and composting technology of agricultural organic waste for sustainable agricultural development

With the continuous development of agriculture, Agricultural organic waste (AOW) has become the most abundant renewable energy on earth, and it is a hot spot of research in recent years to realize the recycling of AOW to achieve sustainable development of agricultural production. However, lignocellulose, which is difficult to degrade in AOW, greenhouse gas emissions, and pile pathogenic fungi and insect eggs are the biggest obstacles to its return to land use. In response to the above problems researchers promote organic waste recycling by pretreating AOW, controlling composting conditions and adding other substances to achieve green return of AOW to the field and promote the development of agricultural production. This review summarizes the ways of organic waste treatment, factors affecting composting and problems in composting by researchers in recent years, with a view to providing research ideas for future related studies.

Phosphorus functional microorganisms and genes: A novel perspective to ascertain phosphorus redistribution and bioavailability during copper and tetracycline-stressed composting

There is limited information on the phosphorus availability under copper and tetracycline-amended composting: Insights into microbial communities and genes. Thus, this work investigated the phosphorus redistribution and transformation, illustrated the variation in microbial communities and genes, and ascertained the multiple action-patterns among which within copper and tetracycline-amended composting. Phosphorus bioavailability reduced by 8.96 % ∼ 13.10 % due to the conservation of Ex-P to Ca-P. Copper and tetracycline showed a significant effect on fungal succession, but not to bacteria, as well as inhibited the phosphorus functional genes in fungal communities, while accelerated it in bacterial communities. Under the copper/tetracycline-stressed conditions, bacterial Firmicutes could promote the mineralization of organic phosphorus, and bacterial Proteobacteria might facilitate the dissolution of inorganic phosphorus. These findings could provide theoretical guidance for the further research on phosphorus bioavailability ascribed to microbial communities and genes.

Fate of Horizontal-Gene-Transfer Markers and Beta-Lactamase Genes during Thermophilic Composting of Human Excreta

Thermophilic composting is a suitable treatment for the recycling of organic wastes for agriculture. However, using human excreta as feedstock for composting raises concerns about antibiotic resistances. We analyzed samples from the start and end of a thermophilic composting trial of human excreta, together with green cuttings and straw, with and without biochar. Beta-lactamase genes bla_CTX-M, bla_IMP, and bla_TEM conferring resistance to broad-spectrum beta-lactam antibiotics, as well as horizontal gene transfer marker genes, intI1 and korB, were quantified using qPCR. We found low concentrations of the beta-lactamase genes in all samples, with non-significant mean decreases in bla_CTX-M and bla_TEM copy numbers and a mean increase in bla_IMP copy numbers. The decrease in both intI1 and korB genes from start to end of composting indicated that thermophilic composting can decrease the horizontal spread of resistance genes. Thus, thermophilic composting can be a suitable treatment for the recycling of human excreta.

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.

Effects of microbial inoculant and additives on pile composting of cow manure

Composting is an effective method of recycling organic solid waste, and it is the key process linking planting with recycling. To explore the reuse of agricultural organic solid waste as a resource in the Yellow River Delta, the effects of microbial inoculant and different additives (calcium superphosphate, biochar, tomato straw, rice husk, and sugar residue) on pile composting of cow dung were studied to obtain the best composting conditions. The results showed that microbial inoculant and additives all played positive roles in the process of aerobic composting, and the experimental groups outperformed the control groups without any additives. For discussion, the microbial inoculant promoted rapid pile body heating more than the recovery materials alone, and the effects on aerobic composting were related to the organic matter of substrates and biochar. After being composted, all the materials were satisfactorily decomposed. Degradation of additives into humic acid might serve as electron shuttles to promote thorough organic matter decomposition. These results provide a scientific basis data for industrial composting of organic solid waste processed by on-site stacking, and provide a reference for researcher and practitioners for studying the applications of microbial inoculant on aerobic composting.

Sensitive response mechanism of ARGs and MGEs to initial designed temperature during swine manure and food waste co-composting

The rapid aerobic composting process has been used to reduce organic wastes, but the associated risks of antibiotic resistance genes (ARGs) need to evaluate in an efficient way. The primary objective of this work was to explore the underlying mechanism of initial adjustment in composting temperature on the variation of ARGs, mobile genetic elements (MGEs), and microbial composition during co-composting. The co-composting was initially externally heated (T2) for 5 days. The results showed that ARGs abundance in conventional composting (T1) was reduced by 49.36%, while multidrug was enriched by 86.16% after a period of 30 days. While in T2 ARGs were removed by 79.46% particularly the fraction of sulfonamide, multidrug, and vancomycin resistance genes were >90% without rebounding of any ARGs. Whereas, MGEs were reduced by 68.12% and 93.62% in T1 and T2, while the half-lives of ARGs and MGEs were lower in T2 compared to T1 (86.3%,86.7%). T2 also affected the metabolism function by regulating carbohydrate metabolism (9.62-10.39%) and amino acid metabolism (9.92-10.93%). Apart from this, the potential human pathogenic bacteria Pseudomonas was reduced by 90.6% in T2 and only 32.9% in T1 respectively. Network analysis showed that Ureibacillus, Weissella, Corynebacterium, Escherichia-Shigella, Acinetobacter were the main host of multiple genes. Structural equation models exhibited that bacterial communities were mainly responsible for the enrichment of ARGs in T1, whereas, it was directly affected by MGEs in T2. Similarly, ARGs variation was directly related to composting temperature. With this simple strategy, ARGs associated risk can be significantly reduced in composting.

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.

Insight into the role of biogenic manganese oxides-assisted gravity-driven membrane filtration systems toward emerging contaminants removal

Effective water purification technologies are required to remove emerging contaminants (ECs) and prevent their extensive occurrence in rural areas. In this work, coupling gravity-driven membrane (GDM) filtration with biogenic manganese oxides (BioMnOx) in the biofouling layer was utilized for treating water containing SMX. Comparisons between BioMnOx-GDM (with BioMnOx) and Control-GDM (without BioMnOx) indicated that BioMnOx could significantly promote the removal of DOC, NH₄⁺-N, and fluorescent pollutants due to its strong oxidating capacity and high biological activity. The formation of BioMnOx increased the abundance of SMX-degrading bacteria, enriched the metabolic pathway and mineralization rate of SMX, and effectively promoted the remove of SMX. More importantly, BioMnOx facilitated the removal of antibiotic resistance genes (ARGs) in the GDM, because it increased the link between microorganisms and reduced the concentration of SMX, thus reduced the expression of ARGs. LB-EPS played an important role in the membrane fouling. Compared with the Control-GDM, the concentration of LB-EPS in BioMnOx-GDM decreased, which was beneficial to alleviate membrane fouling. Although a thicker biofouling layer (1774.88 μm vs.775.54 μm) was formed in BioMnOx-GDM, the biofilm with higher porosity (64.93% vs. 41.24%) had a more positive effect on the flux. Overall, BioMnOx could improve the pollutant removal and stable flux level of the GDM system. BioMnOx-GDM effectively avoided the risks brought by ECs and ensured water safety in rural areas.

Current status and future perspective of antimicrobial-resistant bacteria and resistance genes in animal-breeding environments

The emergence and spread of antimicrobial-resistant bacteria (ARB) and antimicrobial resistance genes (ARGs) are a global public health concern. ARB are transmitted directly or indirectly from animals to humans. The importance of environmental transmission of ARB and ARGs has recently been demonstrated, given the relationships between compost, livestock wastewater, insects, and wildlife. In addition, companion animals and their surrounding environments (veterinary hospitals and homes with companion animals) should be considered owing to their close relationship with humans. This review discusses the current status and future perspectives of ARB and ARGs in animal-breeding environments.

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.

Intraspecific and interspecific quorum sensing of bacterial community affects the fate of antibiotic resistance genes during chicken manure composting under penicillin G stress

In this study, the effects of penicillin G (PENG) on the fate of bacterial communities and β-lactamase antibiotic resistance genes (ARGs) during chicken manure composting were assessed, to illustrate the roles of PENG in ARGs behavior. The results showed that the total absolute abundances of 9 ARGs and 4 mobile genetic elements (MGEs) was significantly increased by PENG (P < 0.05). Dozens of potential hosts for ARGs were predominantly affiliated with Firmicutes, Proteobacteria, and Actinobacteria. Meanwhile, the higher concentration of PENG significantly increased the abundance of luxI and luxS in quorum sensing (QS) (P < 0.05), which enhanced the frequency of inter/intraspecific gene "communication." Redundancy analysis and structural equation modeling further revealed that QS had a strong regulatory role in horizontal gene transfer of ARGs mediated via MGEs. These results provide new insight into the mechanism of ARGs propagation in aerobic composting modified by PENG.

Insight into the evolution of antibiotic resistance genes and microbial community during spiramycin fermentation residue composting process after thermally activated peroxydisulfate pretreatment

Previous research has been demonstrated that the residual unextracted antibiotics in spiramycin fermentation residue (SFR) could be efficiently removed by thermally activated peroxodisulfate (TAP) pretreatment, indicating the improvement of biodegradability. This study aimed to investigate the effect of TAP pretreatment on the succession of bacterial community and fate of antibiotic resistance genes (ARGs) during SFR composting. Results indicated that TAP pretreatment increased the composting temperature and promoted the decomposition of organic matters. Furthermore, TAP pretreatment could increase bacterial alpha diversity and significantly reduce the relative abundance of ARGs (1.13-1.75 times) and mobile genetic elements (MGEs) (1.13-1.32 times) after composting. The compost of pretreated SFR by TAP could reduce the enrichment of ARGs and MGEs in the bacterial community, especially the rRNA methylase genes of ermB (4-142-folds). Redundancy analysis showed that Actinobacteria, Bacteroidetes, Proteobacteria and horizontal gene transfer mediated by MGEs (intI1) was positively related to the changes in ARGs (accounted for 97.4%). Network analysis showed that Firmicutes was the main bacterial hosts of ARGs and MGEs. These findings demonstrated that TAP pretreatment combined composting was a promising strategy for SFR safe treatment and disposal that could reduce the proliferation and transfer of ARGs.

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.

Influence of microbial inoculants on co-composting of lignocellulosic crop residues with farm animal manure: A review

The rapidly developing agro-industry generates huge amounts of lignocellulosic crop residues and animal manure worldwide. Although co-composting represents a promising and cost-effective method to treat various agricultural wastes simultaneously, poor composting efficiency prolongs total completion time and deteriorates the quality of the final product. However, supplementation of the feedstock with beneficial microorganisms can mitigate these negative effects by facilitating the decomposition of recalcitrant materials, enhancing microbial enzyme activity, and promoting maturation and humus formation during the composting process. Nevertheless, the influence of microbial inoculation may vary greatly depending on certain factors, such as start-up parameters, structure of the feedstock, time of inoculation, and composition of the microbial cultures used. The purpose of this contribution is to review recent developments in co-composting procedures involving different lignocellulosic crop residues and farm animal manure combined with microbial inoculation strategies. To evaluate the effectiveness of microbial additives, the results reported in a large number of peer-reviewed articles were compared in terms of composting process parameters (i.e., temperature, microbial activity, total organic carbon and nitrogen contents, decomposition rate of lignocellulose fractions, etc.) and compost characteristics (humification, C/N ratio, macronutrient content, and germination index). Most studies confirmed that the use of microbial amendments in the co-composting process is an efficient way to facilitate biodegradation and improve the sustainable management of agricultural wastes. Overall, this review paper provides insights into various inoculation techniques, identifies the limitations and current challenges of co-composting, especially with microbial inoculation, and recommends areas for further research in this field.

The effects of electric field assisted composting on ammonia and nitrous oxide emissions varied with different electrolytes

Enhancing electron transfer through directly elevating electric potential has been verified to reduce gaseous emissions from composting. Reducing electric resistance of composting biomass might be a choice to further strengthening electron transfer. Here, the effects of chemical electrolytes addition on gaseous Nitrogen emission in electric field assistant composting were investigated. Results suggest that adding acidic electrolyte (ferric chloride) significantly reduced ammonia (NH3) emission by 72.1% but increased nitrous oxide (N2O) emission (by 24-fold) (P < 0.05), because of a dual effect on nitrifier activity: i) an elevated abundance and proportion of ammonia oxidizing bacteria Nitrosomonadaceae, and ii) delayed growth of nitrite oxidizing bacteria. Neutral and alkaline electrolytes had no negative or positive effect on N2O or NH3 emission. Hence, there is a potential trade-off between NH3 and N2O mitigation if using ferric chloride as acidic electrolyte, and electrolyte addition should aim to enhance electron production promote N2O mitigation.

Insights into the beneficial effects of woody peat for reducing abundances of antibiotic resistance genes during composting

Antibiotic resistance genes (ARGs) in manure endangered human health, while heavy metals in manure will pose selective pressure on ARGs. This study explored the effects on ARGs of adding woody peat during composting at different ratios (0 (CK), 5% (T1), and 15% (T2)). After composting, the relative abundances of 8/11 ARGs were 6.97-38.09% and 10.73-54.31% lower in T1 and T2, respectively, than CK. The bioavailable Cu content was 1.40% and 18.40% lower in T1 and T2, respectively, than CK. Network analysis showed that ARGs, mobile genetic elements (MGEs), and metal resistance genes possessed common potential host bacteria, such as Streptococcus, Dietzia, and Corynebacterium_1. Environmental factors, especially bioavailable Cu, and MGEs accounted for 80.75% of the changes in the abundances of ARGs. In conclusion, 15% Woody peat is beneficial to decrease the bioavailable Cu content and weaken horizontal gene transfer for controlling the spread of ARGs during composting.

The quality of compost was improved by low concentrations of fulvic acid owing to its optimization of the exceptional microbial structure

The influence of different concentrations of fulvic acid at 0, 100, 200, and 400 mg/kg was evaluated during the course of composting with straw and mushroom residues as substrates. The optimal concentration of fulvic acid is 100 mg/Kg based on microbial characteristics, chemical parameters, and germination index testing. Nearly 80% of the microbial taxa responded significantly to fulvic acid over the composting period, with a dynamic change of the co-occurrence network from complex to simple and then to complex. Fulvic acid accelerated the progress of composting and reduced the emission of gases at the thermophilic phase. The optimal concentration of fulvic acid enriched the beneficial microorganisms Aeribacillus, Oceanobacillus, and Rhodospirillaceae, and decreased the abundances of pathogenic microorganisms Corynebacterium, Elizabethkingia, and Sarcocystidae. This study indicates a new strategy to optimize the composting process using the biostimulant fulvic acid.

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.

Proliferation of antibiotic-resistant microorganisms and associated genes during composting: An overview of the potential impacts on public health, management and future

Antibiotic residues together with non-antibiotic drugs and heavy metals act as a selective pressure for the spread of antibiotic-resistant microorganisms (ARMs), antibiotic-resistant genes (ARGs), and mobile genetic elements (MGEs) during composting of livestock manure. ARMs, ARGs and MGEs have become emerging contaminants since they are regularly implicated in the majority of compost produced from livestock manure. The prevalence of these contaminants in agricultural soil receiving compost has drawn huge attention globally due to the risks they pose to the total environment. Although a large body of literature exists on the application of composting methods in minimizing the relative abundance of these contaminants, there is a paucity of information on the robustness, limitations and opportunities and threats of various composting protocols currently deployed. To address this knowledge gap, the current review compiled literature on the origin and mechanisms of the proliferation of ARMs, ARGs, and MGEs during composting of livestock manure. The effectiveness of current composting protocols in the reduction or removal of emerging contaminants was evaluated. Furthermore, the potential environmental impacts and human health risks of these contaminants following land application of compost were also presented. Finally, we propose some strategic approaches for the reduction of ARGs and MGEs during composting of livestock manure.

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.

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.

Mechanism concerning the occurrence and removal of antibiotic resistance genes in composting product with ozone post-treatment

The soil application of composting product will probably cause the spread of antibiotic resistance genes (ARGs) to environment, thereby it is crucial to remove ARGs in composting product. Ozone was adopted for the first time as a post-treatment method to remove the ARGs in composting product in this study. Ozone treatment significantly removed the total ARGs and mobile genetic elements (MGEs) once ozonation process finished. After 10-day storage stage, although the amount of total intracellular ARGs and MGEs increased, the total extracellular ARGs and MGEs decreased in the ozone-treated compost product. Correlation analysis revealed that the reduction in intracellular 16S rRNA contributed to intracellular tetQ and tetW removal, while the variations of other ARGs after ozonation related to MGEs abundance. Network analysis suggested that the reduction of potential host bacteria, as well as the decline in NH₄⁺-N and TOC after the ozonation, contributed to the intracellular ARGs removal.

In-feed antibiotic use changed the behaviors of oxytetracycline, sulfamerazine, and ciprofloxacin and related antibiotic resistance genes during swine manure composting

The dynamics of oxytetracycline (OTC), sulfamerazine (SM1), ciprofloxacin (CIP) and related antibiotic resistance genes (ARGs) during swine manure composting were compared between manure collected from swine fed a diet containing these three antibiotics (T_D) and manure directly spiked with these drugs (T_S). The composting removal efficiency of OTC (94.9 %) and CIP (87.8 %) in the T_D treatment was significantly higher than that of OTC (83.8 %, P <  0.01) and CIP (83.9 %, P <  0.05) in the T_S treatment, while SM1 exhibited no significant difference (P >  0.05) between the two treatments. Composting effectively reduced the majority of ARGs in both T_D and T_S types of manure, especially tetracycline resistance genes (TRGs). Compared with the T_S treatment, the abundance of some ARGs, such as tetG, qepA, sul1 and sul2, increased dramatically up to 309-fold in the T_D treatment. The microbial composition of the composting system changed significantly during composting due to antibiotic feeding. Redundancy analysis suggested that the abundance of ARGs had a considerable impact on alterations in the physicochemical parameters (C/N, pH and temperature) and bacterial communities (Actinobacteria, Proteobacteria and Firmicutes) during the composting of swine manure.