Variable effects of oxytetracycline on antibiotic resistance gene abundance and the bacterial community during aerobic composting of cow manure

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

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

The risk of viable but non-culturable (VBNC) enterococci and antibiotic resistance transmission during simulated municipal sludge composting

Sludge composting is a sludge resource utilization method that can reduce pollutants, such as pathogens. Enterococci are regarded as more reliable and conservative indicators of pathogen inactivation than fecal coliforms, which are typically used as indicators of fecal pollution. Non-spore pathogenic bacteria may enter a viable but non-culturable (VBNC) state during composting, leading to residual risk. The VBNC status of bacteria is related to their survival during composting. However, the survival mechanisms of enterococci during sludge composting remain unclear. Therefore, this study aimed to investigate the VBNC state of enterococci in different phases of simulated sludge composting and the fate of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) during the composting process. This study is expected to provide a basis for subsequent exploration of possible methods to completely inactivate enterococci and reduce ARGs during sludge composting. Culturable enterococci were reduced in the thermophilic phase of sludge composting, but the proportion of VBNC subpopulation increased. It was reported for the first time that most VBNC enterococci were killed by extending the cooling phase of sludge compost, and by prolonging the cooling phase the types of ARG were reduced. However, there was a certain quantity (approximately 104/g dry weight) of culturable and VBNC enterococci in the compost products. In addition, MGEs and ARGs exist in both bacteria and compost products, leading to the risk of spreading antibiotic-resistant bacteria and antibiotic resistance when sludge compost products are used.

Meta-analysis addressing the potential of antibiotic resistance gene elimination through aerobic composting

The significant increase in antibiotic resistance genes (ARGs) in organic solid wastes (OSWs) has emerged as a major threat to the food chain. Aerobic composting is a widely used technology for OSW management, with the potential to influence the fate of AGRs. However, the variability of the ARG elimination effects reported in different studies has highlighted the uncertainty regarding the effects of composting on ARGs. To identify the potential of composting in reducing ARG and the factors (e.g., composting technologies and physiochemical properties) influence ARG changes, a meta-analysis was conducted with a database including 4,232 observations. The abundances of ARGs and mobile genetic elements (MGEs) can be substantially reduced by 74.3% and 78.8%, respectively, via aerobic composting. During composting, the ARG levels in chicken and swine manure tended to be reduced more significantly (81.7% and 78.0%) compared to those in cattle manure (52.3%) and sewage sludge (32.6%). The reduction rate of sulfonamide resistant genes was only 35.3%, which was much lower than those of other types. MGEs and composting duration (CD) were identified as the most important factors driving ARG changes during composting. These findings provide a comprehensive insight into the effects of composting on ARG reduction, which may help prevent the transmission in food systems.

Effect of composting and storage on the microbiome and resistome of cattle manure from a commercial dairy farm in Poland

Manure from food-producing animals, rich in antibiotic-resistant bacteria and antibiotic resistance genes (ARGs), poses significant environmental and healthcare risks. Despite global efforts, most manure is not adequately processed before use on fields, escalating the spread of antimicrobial resistance. This study examined how different cattle manure treatments, including composting and storage, affect its microbiome and resistome. The changes occurring in the microbiome and resistome of the treated manure samples were compared with those of raw samples by high-throughput qPCR for ARGs tracking and sequencing of the V3-V4 variable region of the 16S rRNA gene to indicate bacterial community composition. We identified 203 ARGs and mobile genetic elements (MGEs) in raw manure. Post-treatment reduced these to 76 in composted and 51 in stored samples. Notably, beta-lactam, cross-resistance to macrolides, lincosamides and streptogramin B (MLSB), and vancomycin resistance genes decreased, while genes linked to MGEs, integrons, and sulfonamide resistance increased after composting. Overall, total resistance gene abundance significantly dropped with both treatments. During composting, the relative abundance of genes was lower midway than at the end. Moreover, higher biodiversity was observed in samples after composting than storage. Our current research shows that both composting and storage effectively reduce ARGs in cattle manure. However, it is challenging to determine which method is superior, as different groups of resistance genes react differently to each treatment, even though a notable overall reduction in ARGs is observed.

Biotic pathways of reciprocal responses between antibiotic resistance genes and inorganic nitrogen cycling genes in amoxicillin-stressed compost ecosystems

This study explored the transformation of inorganic nitrogen, the expression levels of antibiotic resistance genes (ARGs), and the regulatory mechanisms of key species on ARGs and inorganic nitrogen cycling genes (INCGs) under different levels of amoxicillin (AMX) stress. High level of AMX inhibited the accumulation of NH4+-N, which increased by 531 % relative to the initial. Moreover, AMX to some extent increased the levels of nirS and nirK, which could potentially result in nitrogen loss and the accumulation of NO2-. Actinobacteria might serve as potential hosts for ARGs during sludge composting. This stress induced a complex response between INCGs and ARGs more complex due to key species. Under high-level AMX pressure, most species associated with ARGs likely derived from nitrogen cycling functional species. To conclude, high levels of AMX stress might lead to nitrogen cycling imbalance and the dissemination of antibiotic resistance genes in composting systems.

Effects of oxytetracycline on variation in intracellular and extracellular antibiotic resistance genes during swine manure composting

This research aimed to investigate the alterations in extracellular (eARGs) and intracellular (iARGs) antibiotic resistance genes in response to oxytetracycline (OTC), and unravel the dissemination mechanism of ARGs during composting. The findings revealed both low (L-OTC) and high contents (H-OTC) of OTC significantly enhanced absolute abundance (AA) of iARGs (p < 0.05), compared to CK (no OTC). Composting proved to be a proficient strategy for removing eARGs, while AA of eARGs was significantly enhanced in H-OTC (p < 0.05). OTC resulted in an increase in AA of mobile genetic elements (MGEs), ATP levels, antioxidant and DNA repair enzymes in bacteria in compost product. Structural equation model further demonstrated that OTC promoted bacterial DNA repair and antioxidant enzyme activities, altered bacterial community and enhanced MGEs abundance, thereby facilitating iARGs dissemination. This study highlights OTC can increase eARGs and iARGs abundance, underscoring the need for appropriate countermeasures to mitigate potential hazards.

Urban green waste bulking agent is the major source of antimicrobial resistance genes persisted in home compost, not animal manure

Urban green waste and food waste are often used as bulking agents to prepare home compost in combination with animal manure in urban horticulture and community gardening. Although it is known that antimicrobial resistance genes (ARGs) persist in home compost, their origins have not been determined. In addition, the factors contributing to ARGs persistence remain unclear. In this study, we aim to (i) characterize the changes in the microbiome and antimicrobial resistome during the composting process of home compost using metagenomics shotgun sequencing, (ii) identify the source of the ARGs persisted in home compost using SourceTracker, and (iii) elucidate the collective effect of compost microbiome and environmental factors, including the physicochemical properties and antibiotics concentration of home compost, in contributing to ARG persistence using Procrustes analysis, co-occurrence network analysis, variation partitioning analysis, and structural equation modeling. SourceTracker analysis indicated that urban green waste bulking agent was the major source of the persisting ARGs in home compost instead of animal manure. Procrustes analysis and co-occurrence network analysis revealed a strong association between microbiome and antimicrobial resistome. Variation partitioning analysis and structural equation modeling suggested that physicochemical properties shaped the antimicrobial resistome directly and indirectly by influencing the microbiome. Our results indicated that the persistence of ARGs in home compost might be due to the succession of microbial species from the urban green waste bulking agent, and the physicochemical properties might have defined the compost environment to shape the microbiome in the compost, thus, in turn, the persisting antimicrobial resistome.

Enhanced removal of antibiotic resistance genes during chicken manure composting after combined inoculation of Bacillus subtilis with biochar

This study explored the combined effects of Bacillus subtilis inoculation with biochar on the evolution of bacterial communities, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs) during the composting of chicken manure. The results showed that B. subtilis inoculation combined with biochar increased bacterial abundance and diversity as well as prolonged the compost thermophilic period. Promoted organic matter biodegradation and facilitated the organic waste compost humification process, reduced the proliferation of ARGs by altering the bacterial composition. Firmicutes and Actinobacteriota were the main resistant bacteria related to ARGs and MGEs. The decrease in ARGs and MGEs was associated with the reduction in the abundance of related host bacteria. Compost inoculation with B. subtilis and the addition of biochar could promote nutrient transformation, reduce the increase in ARGs and MGEs, and increase the abundance of beneficial soil taxa.

Transfer of antibiotic resistance genes from soil to wheat: Role of host bacteria, impact on seed-derived bacteria, and affecting factors

The transfer of antibiotic resistance genes (ARGs) from soils to plants is poorly understood, especially the role of host bacteria in soils and its impact on seed-derived bacteria. Wheat (Triticum aestivum L.) was thus used to fill the gap by conducting pot experiments, with target ARGs and bacterial community analyzed. Results showed that the relative abundances of target ARGs gradually decreased during transfer of ARGs from the rhizosphere soil to root and shoot. Host bacteria in the rhizosphere soil were the primary source of ARGs in wheat. The 38, 21, and 19 potential host bacterial genera of target ARGs and intI1 in the rhizosphere soil, root, and shoot were identified, respectively, and they mainly belonged to phylum Proteobacteria. The abundance of ARGs carried by pathogenic Corynebacterium was reduced in sequence. During transfer of ARGs from the rhizosphere soil to root and shoot, some seed-derived bacteria and pathogenic Acinetobacter obtained ARGs through horizontal gene transfer and became potential host bacteria. Furthermore, total organic carbon, available nitrogen of the rhizosphere soil, water use efficiency, vapor pressure deficit, and superoxide dismutase of plants were identified as the key factors affecting potential host bacteria transfer in soils to wheat. This work provides important insights into transfer of ARGs and deepens our understanding of potential health risks of ARGs from soils to plants.

Antibiotics and antibiotic resistance gene dynamics in the composting of antibiotic fermentation waste - A review

Fate of antibiotics and antibiotic resistance genes (ARGs) during composting of antibiotic fermentation waste (AFW) is a major concern. This review article focuses on recent literature published on this subject. The key findings are that antibiotics can be removed effectively during AFW composting, with higher temperatures, appropriate bulking agents, and suitable pretreatments improving their degradation. ARGs dynamics during composting are related to bacteria and mobile genetic elements (MGEs). Higher temperatures, suitable bulking agents and an appropriate C/N ratio (30:1) lead to more efficient removal of ARGs/MGEs by shaping the bacterial composition. Keeping materials dry (moisture less than 30%) and maintaining pH stable around 7.5 after composting could inhibit the rebound of ARGs. Overall, safer utilization of AFW can be realized by optimizing composting conditions. However, further removal of antibiotics and ARGs at low levels, degradation mechanism of antibiotics, and spread mechanism of ARGs during AFW composting require further investigation.

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.

Zinc/carbon nanomaterials inhibit antibiotic resistance genes by affecting quorum sensing and microbial community in cattle manure production

This study used metagenomic sequencing to examine the effects of carbon-based zinc oxide nanoparticles (CZnONPs) and graphene-based zinc oxide nanoparticles (GZnONPs) on quorum sensing (QS), antibiotic resistance genes (ARGs) and microbial community changes during cattle manure production. The manure zinc content was significantly reduced in GZnONPs group. In the QS pathway, the autoinducer gene increases significantly in Control group, while the transporter and repressor genes experience a substantial increase in CZnONPs group. These results contributed to the significantly decreased the abundance of ARGs in GZnONPs group. The co-occurrence network analysis revealed a correlation between core ARGs and QS-related KEGG Orthology or ARGs' hosts, indicating that the selective pressure of zinc influences microbial QS, forming a unique ARG pattern in in vivo anaerobic fermentation. These findings suggest that implementing nutritional regulation in farming practices can serve as a preventive measure to mitigate the potential transmission of ARGs resulting from livestock waste.

The fates of antibiotic resistance genes and their association with cell membrane permeability in response to peroxydisulfate during composting

The aims of this study were to use metagenomics to reveal the fates of antibiotic resistance genes (ARGs) during composting under the regulation of peroxydisulfate and clarify the relationship between ARGs and cell membrane permeability. Results showed that peroxydisulfate increased cell membrane permeability by effectively regulating the expression of outer membrane protein and lipopolysaccharide related genes. Besides, it reduced polysaccharides and proteins in extracellular polymer substances by 36% and 58%, respectively, making it easier for intracellular ARGs (i-ARGs) to reach the extracellular environment, among which the absolute intracellular abundance of mphK, Erm(31), and tet(44) decreased to 1.2, 1.0, and 0.89 fold of the control, respectively. Finally, variation partitioning analysis showed that i-ARGs dominated the removal of ARGs. These results revealed that the removal of i-ARGs by activated peroxydisulfate was the key to the removal of ARGs and increased cell membrane permeability played a key role for peroxydisulfate to remove i-ARGs during composting.

Enhanced simultaneous removal of sulfamethoxazole and zinc (II) in the biochar-immobilized bioreactor: Performance, microbial structures and gene functions

Biochar-immobilized functional bacteria Bacillus SDB4 was applied for sulfamethoxazole (SMX) and zinc (Zn2+) simultaneous removal in the bioreactor. Under the optimal operating conditions of HRT of 10 h, pH of 7.0, SMX concentration of 10 mg L-1 and Zn2+ concentration of 50 mg L-1, the removal efficiencies of SMX and Zn2+ by the immobilized reactor (IR) were 97.42% and 96.14%, respectively, 20.39% and 30.15% higher than those by free bioreactor (FR). SEM-EDS and FTIR results revealed that the functional groups and light metals on the carrier promoted the biosorption and biotransformation of SMX and Zn2+ in IR. Moreover, the improvement of SMX and Zn2+ removal might be related to the abundance enhancement of functional bacteria and genes. Bacillus SDB4 responsible for SMX and Zn2+ removal was the main strain in IR and FR. Biochar increased the relative abundance of Bacillus from 32.12% in FR to 38.73% in IR and improved the abundances of functional genes (such as carbohydrate metabolism, replication and repair and membrane transport) by 1.82%-11.04%. The correlations among the physicochemical properties, microbial communities, functional genes and SMX-Zn2+ co-contaminant removal proposed new insights into the mechanisms of biochar enhanced microbial removal of antibiotics and heavy metals in biochar-immobilized bioreactors.

Risk assessment and dissemination mechanism of antibiotic resistance genes in compost

In recent years, the excessive of antibiotics in livestock and poultry husbandry, stemming from extensive industry experience, has resulted in the accumulation of residual antibiotics and antibiotic resistance genes (ARGs) in livestock manure. Composting, as a crucial approach for the utilization of manure resources, has the potential to reduce the levels of antibiotics and ARGs in manure, although complete elimination is challenging. Previous studies have primarily focused on the diversity and abundance of ARGs in compost or have solely examined the correlation between ARGs and their carriers, potentially leading to a misjudgment of the actual risk associated with ARGs in compost. To address this gap, this study investigated the transfer potential of ARGs in compost and their co-occurrence with opportunistic pathogenic bacteria by extensively analyzing metagenomic sequencing data of compost worldwide. The results demonstrated that the potential risk of ARGs in compost was significantly lower than in manure, suggesting that composting effectively reduces the risk of ARGs. Further analysis showed that the microbes shifted their life history strategy in manure and compost due to antibiotic pressure and formed metabolic interactions dominated by antibiotic-resistant microbes, increasing ARG dissemination frequency. Therefore, husbandry practice without antibiotic addition was recommended to control ARG evolution, dissemination, and abatement both at the source and throughout processing.

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.

From waste to wealth: Innovations in organic solid waste composting

Organic solid waste (OSW) is not only a major source of environmental contamination, but also a vast store of useful materials due to its high concentration of biodegradable components that can be recycled. Composting has been proposed as an effective strategy for recycling OSW back into the soil in light of the necessity of a sustainable and circular economy. In addition, unconventional composting methods such as membrane-covered aerobic composting and vermicomposting have been reported more effective than traditional composting in improving soil biodiversity and promoting plant growth. This review investigates the current advancements and potential trends of using widely available OSW to produce fertilizers. At the same time, this review highlights the crucial role of additives such as microbial agents and biochar in the control of harmful substances in composting. Composting of OSW should include a complete strategy and a methodical way of thinking that can allow product development and decision optimization through interdisciplinary integration and data-driven methodologies. Future research will likely concentrate on the potential in controlling emerging pollutants, evolution of microbial communities, biochemical composition conversion, and the micro properties of different gases and membranes. Additionally, screening of functional bacteria with stable performance and exploration of advanced analytical methods for compost products are important for understanding the intrinsic mechanisms of pollutant degradation.

Batch-fed composting of food waste: Microbial diversity characterization and removal of antibiotic resistance genes

The aim of this work was to study the impact of batch-fed strategies on bacterial communities and ARGs in compost. The findings demonstrate that batch-feeding helped maintain high temperatures in the compost pile for an extended period (above 50 °C for 18 days), which in turn facilitated water dissipation. High-throughput sequencing showed that Firmicutes played a significant role in batch-fed composting (BFC). They had a high relative abundance at the beginning (98.64%) and end (45.71%) of compost. Additionally, BFC showed promising results in removing ARGs, with reductions of 3.04-1.09 log copies/g for Aminoglycoside and 2.26-2.44 log copies/g for β_Lactamase. This study provides a comprehensive survey of BFC and demonstrates its potential for eliminating resistance contamination in compost.

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.

Metagenomic insights into dietary remodeling of gut microbiota and antibiotic resistome in meat rabbits

The gut microbiota is a repository of antibiotic resistance genes (ARGs), which may affect the health of humans and animals. The intestinal flora is affected by many factors but it is unclear how the intestinal microflora and antibiotic resistome in rabbits might change under dietary intervention. Feeding with lettuce led to the amplification and transfer of exogenous ARGs in the intestinal flora, but there were no significant differences when fed lettuces grown with different manure types. For example, the lsaC of lettuce fed with bovine, chicken and pig manure without adding organic fertilizer increased by 0.143, 0.151, 0.179 and 0.169 logs respectively after 4 weeks, and the efrB also increased by 0.074, 0.068, 0.079 and 0.106 logs respectively. Network analysis showed that Clostridium_ sensu_ stricto_ 18 was a potential host of type 6 virulence factor genes (VFGs). Mantel analysis showed that ARGs were directly influenced by mobile genetic elements (MGEs) and VFGs. Thus, feeding rabbits lettuce grown with different manure types contribute to the transmission of ARGs by remodeling the intestinal microenvironment. In addition, diet may affect exogenous ARGs to change the intestinal antibiotic resistome and possibly threaten health.

Performances of antibiotic resistance genes profile upon the action of biochar-activated peroxydisulfate in composting

In this study, the amendment of biochar-activated peroxydisulfate during composting to remove antibiotic resistance genes (ARGs) by direct (microbial community succession) and indirect methods (physicochemical factors) was analyzed. When implementing indirect methods, the synergistic effect of peroxydisulfate with biochar optimized the physicochemical habitat of compost, maintaining its moisture within a range of 62.95%-65.71%, and a pH of 6.87-7.73, and causing the compost to mature 18 days earlier than the control groups. The direct methods caused the optimized physicochemical habitat to adjust the microbial communities and reduce the abundance of most of the ARG host bacteria (Thermopolyspora, Thermobifida, and Saccharomonospora), thus inhibiting this substance's amplification. Heatmap analysis confirmed the necessary connection between physicochemical factors, microbial communities, and ARGs. Moreover, a mantel test confirmed the direct significant effect of the microbial communities on ARGs and the indirect significant effect of physicochemical factors on ARGs. The results showed that the abundance of more ARGs was down-regulated at the end of composting and regulated by biochar-activated peroxydisulfate, especially for the abundance of AbaF, tet(44), golS, and mryA, which was significantly decreased by 0.87-1.07 fold. These results provide new insights into the removal of ARGs during composting.

Aerobic co-composting of mature compost with cattle manure: organic matter conversion and microbial community characterization

The production of organic fertilizer by aerobic composting of cattle manure is an important way of its resource utilization. This study evaluated the effects of adding mature compost on the decomposition and microbial communities in the aerobic composting of cattle manure. The addition of mature compost shortens the composting cycle and results in a final lignocellulosic degradation rate of 35%. Metagenomic analysis showed that this was due to the proliferation of thermophilic and organic matter-degrading functional microorganisms, which enhanced the activity of carbohydrate-active enzymes. With the addition of mature compost, the microbial community exhibited stronger metabolic functions, especially carbohydrate and amino acid metabolism, which are the driving forces of organic matter degradation. This study deepens the understanding of organic matter conversion and microbial community metabolic functions when mature compost is used for livestock manure composting and provides a promising technology for livestock manure composting.

Functional substitutability of native herbivores by livestock for soil carbon stock is mediated by microbial decomposers

Grazing by large mammalian herbivores impacts climate as it can favor the size and stability of a large carbon (C) pool in the soils of grazing ecosystems. As native herbivores in the world's grasslands, steppes, and savannas are progressively being displaced by livestock, it is important to ask whether livestock can emulate the functional roles of their native counterparts. While livestock and native herbivores can have remarkable similarity in their traits, they can differ greatly in their impacts on vegetation composition which can affect soil-C. It is uncertain how these similarities and differences impact soil-C via their influence on microbial decomposers. We test competing alternative hypotheses with a replicated, long-term, landscape-level, grazing-exclusion experiment to ask whether livestock in the Trans-Himalayan ecosystem of northern India can match decadal-scale (2005-2016) soil-C stocks under native herbivores. We evaluate multiple lines of evidence from 17 variables that influence soil-C (quantity and quality of C-input from plants, microbial biomass and metabolism, microbial community composition, eDNA, veterinary antibiotics in soil), and assess their inter-relationships. Livestock and native herbivores differed in their effects on several soil microbial processes. Microbial carbon use efficiency (CUE) was 19% lower in soils under livestock. Compared to native herbivores, areas used by livestock contained 1.5 kg C m^-2 less soil-C. Structural equation models showed that alongside the effects arising from plants, livestock alter soil microbial communities which is detrimental for CUE, and ultimately also for soil-C. Supporting evidence pointed toward a link between veterinary antibiotics used on livestock, microbial communities, and soil-C. Overcoming the challenges of sequestering antibiotics to minimize their potential impacts on climate, alongside microbial rewilding under livestock, may reconcile the conflicting demands from food-security and ecosystem services. Conservation of native herbivores and alternative management of livestock is crucial for soil-C stewardship to envision and achieve natural climate solutions.

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.

Coupling network of hydrogen sulfide precursors and bacteria in kitchen waste composting

This study was focused on the changes of hydrogen sulfide (H₂S), its precursors, and microorganisms associated with its transformation during the composting process of kitchen waste. The results showed that the content of cysteine (Cys) and methionine (Met) decreased by 32.3 % and 57.5 % respectively, while the content of sulfate (SO₄^2-) changed little during composting. The main release period of H₂S was during the high-temperature period of composting, Cys was its main precursor. Based on network analysis, a total of 15 core genera associated with the conversion of H₂S precursors were identified, and the transformation of the H₂S precursor was mainly influenced by Filomicrobium. Temperature, pH, and TN levels had a positive effect on Filomicrobium. It could find a balance point by controlling these three factors to reduce the production of H₂S.

Evaluation of bacterial diversity in a swine manure composting system contaminated with veterinary antibiotics (VAs)

Composting has become an alternative for the treatment of organic effluents, due to its low cost, easy handling, and a great capacity for treating swine manure. As it is a biological process, many microorganisms are involved during the composting process and act in the degradation of organic matter and nutrients and also have the ability to degrade contaminants and accelerate the transformations during composting. The objective of this work was to identify microorganisms present in the swine effluent composting system, under the contamination by most used veterinary drugs in Brazil. The composting took place for 150 days, there was an addition of 200 L of manure (these 25 L initially contaminated with 17 antibiotics) in 25 kg of eucalyptus wood shavings. The microorganisms were measured at times (0 until 150 days) and were identified by the V3-V4 regions of the 16S rRNA for Bacteria, by means of next-generation sequencing (NSG). The results show seven different bacterial phyla (Proteobacteria, Bacteroidetes, Firmicutes, Acidobacteria, Actinobacteria, Spirochaetota and Tenericutes) and 70 bacterial genera (more than 1% significance), of which the most significant ones were Pseudomonas, Sphingobacterium, Devosia, Brucella, Flavisolibacter, Sphingomonas and Nitratireductor. The genus Brucella was found during mesophilic and thermophilic phases, and this genus has not yet been reported an in article involving composting process. With the results obtained, the potential for adaptation of the bacterial community was observed, being under the influence of antibiotics for veterinary use.

Digestate from Agricultural Biogas Plants as a Reservoir of Antimicrobials and Antibiotic Resistance Genes-Implications for the Environment

Antimicrobials and antibiotic resistance genes (ARGs) in substrates processed during anaerobic digestion in agricultural biogas plants (BPs) can reach the digestate (D), which is used as fertilizer. Antimicrobials and ARGs can be transferred to agricultural land, which increases their concentrations in the environment. The concentrations of 13 antibiotics in digestate samples from biogas plants (BPs) were investigated in this study. The abundance of ARGs encoding resistance to beta-lactams, tetracyclines, sulfonamides, fluoroquinolones, macrolide-lincosamide-streptogramin antibiotics, and the integrase genes were determined in the analyzed samples. The presence of cadmium, lead, nickel, chromium, zinc, and mercury was also examined. Antimicrobials were not eliminated during anaerobic digestion. Their concentrations differed in digestates obtained from different substrates and in liquid and solid fractions (ranging from 62.8 ng/g clarithromycin in the solid fraction of sewage sludge digestate to 1555.9 ng/L doxycycline in the liquid fraction of cattle manure digestate). Digestates obtained from plant-based substrates were characterized by high concentrations of ARGs (ranging from 5.73 × 102 copies/gDcfxA to 2.98 × 109 copies/gDsul1). The samples also contained mercury (0.5 mg/kg dry mass (dm)) and zinc (830 mg/kg dm). The results confirmed that digestate is a reservoir of ARGs (5.73 × 102 to 8.89 × 1010 copies/gD) and heavy metals (HMs). In addition, high concentrations of integrase genes (105 to 107 copies/gD) in the samples indicate that mobile genetic elements may be involved in the spread of antibiotic resistance. The study suggested that the risk of soil contamination with antibiotics, HMs, and ARGs is high in farms where digestate is used as fertilizer.

Residual enrofloxacin in cattle manure increased persistence and dissemination risk of antibiotic resistance genes during anaerobic digestion

Anaerobic digestion is a common approach to dispose and recycle livestock manures, and the agricultural application of anaerobic digestives represents an important pathway of spreading antibiotic resistance genes (ARGs) from livestock manures to soils. Enrofloxacin is a clinically important fluoroquinolone antibiotic with high residual concentrations in livestock manure, and propagation of fluoroquinolone resistance genes poses a huge risk to public health. Compared with other antibiotics, enrofloxacin is relatively durable in anaerobic digestion system. However, its effect on the persistence of ARGs during anaerobic digestion and its mechanism are not clear. In this study, we investigated effects of 0, 4, and 8 mg/L enrofloxacin on the abundance, persistence, and transferring risk of five plasmid-mediated fluroquinolone ARGs and five typic clinically important non-fluoroquinolone ARGs during cattle manure digestion. The responses of integrons and microbial communities to enrofloxacin were assessed to uncover the underlying mechanisms. All the ten detected ARGs were highly persistent in anaerobic digestion, among them seven ARGs increased over 8.2 times after digestion. Network analysis revealed that the potential hosts of ARGs were critical functional taxa during anaerobic digestion, which can explain the high persistence of ARGs. Residual enrofloxacin significantly increased the abundance of aac(6')-ib-cr, sul1, intI1, and intI2 throughout the digestion, but had no impact on the other ARGs, demonstrating its role in facilitating horizontal gene transfer of the plasmid-mediated aac(6')-ib-cr. The influence of enrofloxacin on microbial communities disappeared at the end of digestion, but the ARG profiles remained distinctive between the enrofloxacin treatments and the control, suggesting the high persistence of enrofloxacin induced ARGs. Our results suggested the high persistence of ARGs in anaerobic digestion system, and highlighted the role of residual enrofloxacin in livestock manure in increasing dissemination risk of fluroquinolone resistance genes.

Environmental drivers and interaction mechanisms of heavy metal and antibiotic resistome exposed to amoxicillin during aerobic composting

The environmental accumulation and spread of antibiotic resistance pose a major threat to global health. Aerobic composting has become an important hotspot of combined pollution [e.g., antibiotic resistance genes (ARGs) and heavy metals (HMs)] in the process of centralized treatment and resource utilization of manure. However, the interaction mechanisms and environmental drivers of HMs resistome (MRGs), antibiotic resistance (genotype and phenotype), and microbiome during aerobic composting under the widely used amoxicillin (AMX) selection pressure are still poorly understood. Here, we investigated the dynamics of HMs bioavailability and their MRGs, AMX-resistant bacteria (ARB) and antibiotic resistome (ARGs and intI1), and bacterial community to decipher the impact mechanism of AMX by conducting aerobic composting experiments. We detected higher exchangeable HMs and MRGs in the AMX group than the control group, especially for the czrC gene, indicating that AMX exposure may inhibit HMs passivation and promote some MRGs. The presence of AMX significantly altered bacterial community composition and AMX-resistant and -sensitive bacterial structures, elevating antibiotic resistome and its potential transmission risks, in which the proportions of ARB and intI1 were greatly increased to 148- and 11.6-fold compared to the control group. Proteobacteria and Actinobacteria were significant biomarkers of AMX exposure and may be critical in promoting bacterial resistance development. S0134_terrestrial_group was significantly negatively correlated with bla_TEM and czrC genes, which might play a role in the elimination of some ARGs and MRGs. Except for the basic physicochemical (MC, C/N, and pH) and nutritional indicators (NO₃ ^--N, NH₄ ⁺-N), Bio-Cu may be an important environmental driver regulating bacterial resistance during composting. These findings suggested the importance of the interaction mechanism of combined pollution and its synergistic treatment during aerobic composting need to be emphasized.

Effect of homemade compound microbial inoculum on the reduction of terramycin and antibiotic resistance genes in terramycin mycelial dreg aerobic composting and its mechanism

In order to tackle the issue of terramycin mycelial dreg (TMD) diagnosis and removal of terramycin and antibiotic resistance genes (ARGs), this study adopted aerobic composting (AC) technology and added homemade compound microbial inoculum (HCMI) to promote the AC of TMD and enhance the removal of terramycin and ARGs. The findings demonstrated that terramycin residue could be basically harmless after AC. Moreover, HCMI not only reduced QacB and tetH but also increased the degradation rates of VanRA, VanT, and dfrA24 by 40.81%, 5.65%, and 54.18%, respectively. The HCMI improved the removal rate of ARG subtypes to a certain extent. According to redundancy analysis, during AC, the succession of the microbial community had a stronger influence on the variance of ARG subtype than the environmental conditions. Differences in the abundance of various bacteria due to changes in temperature may be an intrinsic mechanism for the variation of ARG subtypes.

Temporal dynamic of antibiotic resistance genes in the Zaohe-Weihe hyporheic zone: driven by oxygen and bacterial community

The widespread spread of antibiotic resistance genes (ARGs) in hyporheic zone (HZ) has become an emerging environmental problem due to their potentially harmful nature. In this research, three different oxygen treatment systems were set up to study the effects of oxygen changes on the abundance of ARGs in the HZ. In addition, the effects of temperature and salinity on ARGs were investigated under aerobic and anaerobic systems, respectively. The bacterial community composition of sediment samples and the relationship with ARGs were analyzed. The explanation ratio and causality of the driving factors affecting ARGs were analyzed using variation partitioning analysis (VPA) and structural equation model (SEM). The relative abundance of ARGs and mobile genetic elements (MGEs) in the anaerobic system increased significantly, which was higher than that in the aerobic system and the aerobic-anaerobic interaction system. The experiment of salinity and temperature also further proved this result. There were many bacterial communities that affected tetracycline and sulfonamide ARGs in sediments, and these host bacteria are mainly concentrated in Proteobacteria, Firmicutes and Bacteroidetes. VPA and SEM further revealed that the abundance of ARGs was mainly influenced by changes in bacterial communities and oxygen conditions, and horizontal gene transfer (HGT) of MGEs also had a positive effect on the spread of ARGs. Those findings suggest that complex oxygen conditions in the HZ alter bacterial communities and promote MGEs-mediated horizontal transfer, which together lead to the spread of ARGs. This study has value as a reference for formulating effective strategies to minimize the propagation of ARGs in underground environment.

Effects of Oxytetracycline/Lead Pollution Alone and in the Combined Form on Antibiotic Resistance Genes, Mobile Genetic Elements, and Microbial Communities in the Soil

The application of livestock manure is the leading cause of antibiotic and heavy metal pollution in agricultural soil. However, the effects of oxytetracycline (OTC) and lead (Pb) pollution in the single or combined form on antibiotic resistance genes (ARGs) in the soil need to be further studied. This study was planned to investigate the effects of OTC and Pb application on ARGs, mobile genetic elements (MGEs), and bacterial abundance in the soil. The relative abundance of ARGs and MGEs increased by 0.31-fold and 0.03-fold after the addition of 80 mg kg^-1 Pb to the soil, and by 0.49-fold and 0.03-fold after the addition of 160 mg kg^-1 Pb. In addition, under the premise of the existence of OTC, the inhibitory effect of a low concentration of Pb on ARG is stronger than that of a high concentration of Pb, resulting in a lower abundance of ARGs. The abundance of ARGs and MGEs increased by 0.11-fold and 0.17-fold after the addition of OTC (30 mg kg^-1) to the soil at a Pb concentration of 80 mg kg^-1 and by 0.18-fold and 0.04-fold at a Pb concentration of 160 mg kg^-1. The addition of OTC and Pb in the soil also decreased the many bacterial communities such as Bacteroidetes, Proteobacteria, Acidobacteria, and Firmicutes. Redundancy analysis (RDA) showed that organic matter content and pH were positively correlated with the abundance of ARGs and MGEs. At the same time, electrical conductivity (EC) had a negative correlation with the abundance of ARGs and MGEs in the soil. Intl1 was significantly associated with tetB, sul1, tetQ, sul2, and sul3. Network analysis illustrated that Actinobacteria, Bacteroidetes, and Proteobacteria were the main host bacteria causing changes in the abundance of ARGs and MGEs, and they were also predominant phylum in the culture environment. This conclusion can provide a reference for the related research of ARGs in soil.

Composting effect and antibiotic removal under a new temperature control strategy

The main objective of this study was to investigate the feasibility of a new temperature control strategy in the co-composting process to accelerate operation cycle and remove antibiotics from mixed organic wastes. The evaluation of the composting process showed that composting with temperature control (TC) was completed within 14 days. The final compost of TC exhibited a 10% higher degradation of organic matters, more humus formation and 11.25% lower heavy metals concentration than conventional composting (CC), which fully met the Chinese National Agricultural Organic Fertilizer Standard requirements. The degradation extent and kinetic of macrolides, tetracyclines, sulfonamides and fluoroquinolones showed that the removal efficiency of total antibiotics in TC was 23.58% higher than CC, with less half-life, which was significantly correlated with higher temperature. Particularly, the highest removal was observed for sulfonamides (87.45%) in TC, the half-life of which was reduced by 75.95% compared with CC. The higher degradation rate was attributed to enhanced decomposition of unstable antibiotics and degrading activity of microbes at high temperature. The microbiological analysis showed that the external heating led to a distinct composition and succession of bacterial community in TC. Firmicutes, Proteobacteria, Actinobacteriota and Bacteroidota were dominant and the emergence of Patescibacteria and Chloroflexi at cooling period in TC proved that the later composting environment was in an oligotrophic state. Current research provided a promising rapid composting approach for high-quality fertilizer production and antibiotic management in organic waste disposal.

Fate of resistome components and characteristics of microbial communities in constructed wetlands and their receiving river

Currently, most researches focus on that constructed wetlands (CWs) achieve desirable removal of antibiotics, antibiotic resistance genes (ARGs) and human pathogens. However, few studies have assessed the fate of resistome components, especially the behavior and cooccurrence of ARGs, mobile genetic elements (MGEs) and virulence factors (VFs). Therefore, characteristics of microbial communities (MCs) in CWs and their receiving rivers also deserve attention. These factors are critical to water ecological security. This study used two CWs to explore the fate of resistome components and characteristics of MCs in the CWs and their receiving river. Eleven samples were collected from the two CWs and their receiving river. High-throughput profiles of ARGs and microbial taxa in the samples were characterized. 31 ARG types consisting of 400 subtypes with total relative abundance 42.63-84.94× /Gb of sequence were detected in CWs, and 62.07-88.08× /Gb of sequence in river, evidencing that ARG pollution covered CWs and the river, and implying huge potential risks from ARGs. MGEs and VFs were detected, and tnpA, IS91 and intI1 were the three dominant MGEs, while Flagella. Type IV pili and peritrichous flagella were main VFs. Both CWs can remove ARGs, MGEs and VFs efficiently. However, some ARGs were difficult to remove, such as sul1 and sul2, and certain ARGs remained in the effluent of the CWs. The co-occurrence of ARGs, MGEs, and VFs implies the risk of antibiotic resistance and dissemination of ARGs. Eighty-five types of human pathogen were detected in the river samples, particularly Pseudomonas aeruginosa, Bordetella bronchiseptica, Aeromonas hydrophila and Helicobacter pylori. Correlation analysis indicated that MCs had significant effects on the profiles of ARGs in the water environment. This study reveals potential risks of the reuse of reclaimed water, and illustrates the removal ability of ARGs and related elements by CWs. This study will be helpful for monitoring and managing resistomes in water environments.

Succession of the microbial communities and metabolic functions in composting or deep burial processing of dead chickens

1. This study examined the effects of composting and deep burial techniques on degradation efficiency of dead chickens. Different raw materials (crushed branches or rape straws) and disinfectants (quicklime or bleaching powder) were applied in composting and deep burial process, respectively. The whole process lasted for 90 d in both summer and winter.2. High throughput sequencing displayed that Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria and Deinococcus-Thermus were the most dominant bacterial phyla during the experiment. The relative abundance of Firmicutes dwindled gradually with prolonged composting duration, while Proteobacteria, Bacteroidetes and Deinococcus-Thermous increased gradually over time.3. The bacterial functions identified from the KEGG pathway showed that amino acid and carbohydrate metabolism were the major microbial metabolic pathways that determined final degradation efficiency. At the end of the trial, the decomposition status of chicken carcasses and faecal coliforms were measured.4. The results demonstrated that the optimum decomposition effect was obtained in composting compared with other treatment groups. Low ambient temperature reduced degradation efficiency, due to restricted microbial activity. In addition, faecal coliforms were not completely removed by the deep burial process of dead chickens in winter.5.These findings provide a theoretical basis for the feasibility of composting chicken carcasses instead of deep burial.

Microbial cooperation promotes humification to reduce antibiotic resistance genes abundance in food waste composting

Antibiotic resistance genes (ARGs) fate in a full-scale Food waste (FW) facility was investigated. Results showed that with the changes in ARGs, microbial networks could be naturally divided into two clusters, named as the ARGs increasing group (AI group) and the ARGs decreasing group (AD group). The significant difference between two groups (i.e. stronger microbial competition in the AI group and stronger microbial cooperation in the AD group) implied that the variation in ARGs over time were caused by a switch between competition and cooperation. These results indicated that microbial competition might increase ARGs abundance, while cooperation might reduce it. Meanwhile, structural-equation-model (SEM model) showed that humification indexes (e.g. GI value) was an indicator for characterizing microbial interactions and ARGs. The results of the linear model further confirmed that mature compost (GI values > 92.6 %) could reduce the risk of ARGs.

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

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

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.

Fate and exposure risk of florfenicol, thiamphenicol and antibiotic resistance genes during composting of swine manure

Livestock manure is an important source of antibiotic resistance genes (ARGs) spreading to the environment, posing a potential threat to human health. Here, we investigated the dissipation of florfenicol (FF) and thiamphenicol (TAP), and their effects on the bacterial community, mobile genetic elements (MGEs), and ARGs during composting. The results indicated that FF and TAP dissipated rapidly in compost, with half-life values of 5.1 and 1.6 d, respectively. However, FF could not be completely removed during composting. The FF and TAP residues in manure could reduce the elimination of ARGs and MGEs during composting, and had a negative effect on the physicochemical factors of the compost. Significant correlations were found between floR and intI1, indicating that floR in manure may more easily diffuse to the soil environment. Meanwhile, the presence of FF in manure could increase the abundance of floR. Network analysis showed that Proteobacteria and Firmicutes were the dominant bacterial communities and important potential pathogen hosts carrying ARGs. The predicted environmental concentration of FF in the soil was over 100 μg kg^-1, which indicates that FF poses a potential risk to the natural environment, and we verified this result through field experiments. The results showed that FF dissipated in the soil after it migrated from manure to soil. In contrast, TAP in manure posed lower environmental risk. This study highlights that changed in composting conditions may control the rate of removal of ARGs. Further studies are needed to investigate the best environmental conditions to achieve a faster degradation of FF and a more comprehensive elimination of ARGs during composting.

Exploring the effects of heavy metal passivation under Fenton-like reaction on the removal of antibiotic resistance genes during composting

This study aims to explore the succession of microbes carrying antibiotic resistance genes (ARGs), the relationship between heavy metal speciation and ARGs via Fenton-like reaction during composting. The results indicated that the passivation of Cu and Ni was more prominent, and the Fenton-like reaction promoted exceptionally the passivation of Zn, Ni and Mn. The removals of macrolides-lincosamids-streptogramins (MLS), aminoglycoside and tetracycline resistance genes were induced with the composting process, but the relative abundance of bacitracin resistance genes increased. Additionally, Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes were main carriers and disseminators of ARGs, and the Fenton-like reaction improved the contribution degree of Proteobacteria to bacitracin, tetracycline and aminoglycoside resistance genes. Redundancy analysis revealed the passivation of heavy metal contributed to the removal of tetracycline, MLS and aminoglycoside resistance genes. Conclusively, the Fenton-like reaction promoted the passivation of Zn, Ni and Mn, and controlled the abundance of bacitracin resistance genes in composting.

Metagenomic assembly reveals hosts and mobility of common antibiotic resistome in animal manure and commercial compost

BACKGROUND

Antibiotics and antibiotic resistance genes (ARGs) used in intensive animal farming threaten human health worldwide; however, the common resistome, ARG mobility, and ARG host composition in different animal manures and mixed manure composts remain unclear. In the present study, metagenomic assembly and cross-sample mapping were used to comprehensively decipher the common resistome and its potential mobility and hosts in animal manure and composts.

RESULTS

In total, 201 ARGs were shared among different animal (layer, broiler, swine, beef cow, and dairy cow) manures and accounted for 86-99% of total relative abundance of ARGs. Except for multidrug, sulfonamide, and trimethoprim resistance genes, the relative abundance of most ARGs in composts was significantly lower than that in animal manure. Procrustes analysis indicated that antibiotic residues positively correlated with ARG composition in manure but not in composts. More than 75% ARG subtypes were shared between plasmids and chromosomes in our samples. Transposases could play a pivotal role in mediating the transfer of ARGs between different phyla in animal manure and composting. Cross-sample mapping to contigs carrying ARGs showed that the hosts of common resistome in manure had preference on animal species, and the dominant genus of ARG host shifted from Enterococcus in manure to Pseudomonas in composts. The broad host range and linking with diverse mobile genetic elements (MGEs) were two key factors for ARGs, such as sul1 and aadA, which could survive during composting. The multidrug resistance genes represented the dominant ARGs in pathogenic antibiotic-resistant bacteria in manure but could be effectively controlled by composting.

CONCLUSIONS

Our experiments revealed the common resistome in animal manure, classified and relative quantified the ARG hosts, and assessed the mobility of ARGs. Composting can mitigate ARGs in animal manure by altering the bacterial hosts; however, persistent ARGs can escape from the removal because of diverse host range and MGEs. Our findings provide an overall background for source tracking, risk assessment, and control of livestock ARGs.

Effect of biochar on antibiotics and antibiotic resistance genes variations during co-composting of pig manure and corn straw

Pig manure is a reservoir of antibiotics and antibiotic resistance genes (ARGs). The effect of biochar on the variations in physicochemical properties, bacterial communities, antibiotics, ARGs, and mobile genetic elements (MGEs) of compost product during co-composting of pig manure and corn straw have been investigated in this study. Compared with the control treatment (CK), biochar addition accelerated the increase in pile temperature and prolonged the high temperature period (>55°C) for 2 days. Under biochar influence, organic matter degradation, NH₄⁺-N conversion and NO₃⁻-N production was accelerated, and dissolved total organic carbon (DOC) and dissolved total nitrogen (DTN) utilization by microorganisms were enhanced. Biochar addition altered the microbial community and promoted the vital activity of Actinobacteria in the later composting stage. The antibiotics removal efficiency (except danofloxacin and enrofloxacin) was accelerated in the early composting stage (1–14 days) by biochar addition, the pile temperature had a positive effect on antibiotics removal, and the total antibiotics removal efficiency in CK and CK+Biochar treatments was 69.58% and 78.67% at the end of the composting process, respectively. The absolute abundance of most of the ARGs in the CK+Biochar treatment was lower than that in the CK treatment during composting, and the ARGs removal mainly occurred in the early (1–14 days) and later (28–50 days) stages. Biochar addition reduced the absolute abundance of MGEs (intI1, intI2) in the compost product, and most of the ARGs had a significant positive correlation with MGEs. Network analysis and redundancy analysis showed that ARGs and MGEs occurred in various host bacteria (Firmicutes, Actinobacteria, Bacteroidetes, Proteobacteria, and Halanaerobiaeota), and that DTN and NH₄⁺-N are the main factors regulating the changes in bacterial communities, antibiotics, ARGs, and MGEs during composting. Moreover, MGEs contributed the most to the variation in ARGs. In summary, biochar addition during composting accelerated antibiotics removal and inhibited accumulation and transmission of ARGs. The results of this study could provide theoretical and technical support for biochar application for antibiotics and ARGs removal during livestock and poultry manure composting.

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.

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.

Independent and combined effects of antibiotic stress and EM microbial agent on the nitrogen and humus transformation and bacterial community successions during the chicken manure composting

This study aimed to investigate the independent and combined effects of antibiotic and EM microbial agent on the nitrogen and humus (HS) transformations as well as the bacterial community successions during the chicken manure and rice husk composting. EM microbial agent accelerated the oxytetracycline (OTC) degradation, but slowed down the norfloxacin (NOR) degradation. OTC inhibited the TN retention and promoted the HS accumulation, both NOR and EM microbial agent inhibited the TN retention and HS accumulation, while EM microbial agent showed an antagonistic effect on TN immobilization with antibiotics and reduced the impacts of antibiotics on HS. Obvious bacterial community successions occurred. Firmicutes were related to HS transformation, while Firmicutes, Actinobacteriota and Proteobacteria were associated with nitrogen conversion. NOR promoted the transformations of NH₄⁺-N to NO₃^--N and FA to HA. The findings provided theoretical data for the recycle of antibiotic-contaminated manure and the efficient production of high-quality compost.

Migration of antibiotic resistance genes and evolution of flora structure in the Xenopus tropicalis intestinal tract with combined exposure to roxithromycin and oxytetracycline

The intestinal flora is one of the most important environments for antibiotic resistance development, owing to its diverse mix of bacteria. An excellent medicine model organism, Xenopus tropicalis, was selected to investigate the spread of antibiotic resistance genes (ARGs) in the intestinal bacterial community with single or combined exposure to roxithromycin (ROX) and oxytetracycline (OTC). Seventeen resistance genes (tetA, tetB, tetE, tetM, tetO, tetS, tetX, ermF, msrA, mefA, ereA, ereB, mphA, mphB, intI1, intI2, intI3) were detected in the intestines of Xenopus tropicalis living in three testing tanks (ROX tanks, OTC tanks, ROX + OTC tanks) and a blank tank for 20 days. The results showed that the relative abundance of total ARGs increased obviously in the tank with single stress but decreased in the tank with combined stress, and the genes encoding the macrolide antibiotic efflux pump (msrA), phosphatase (mphB) and integron (intI2, intI3) were the most sensitive. With the aid of AFM scanning, DNA was found to be scattered short chain in the blank, became extended or curled and then compacted with the stress from a single antibiotic, and was compacted and then fragmented with combined stress, which might be the reason for the variation of the abundance of ARGs with stress. The ratio of Firmicutes/Bacteroides related to diseases was increased by ROX and OTC. The very significant correlation between intI2 and intI3 with tetS (p ≤ 0.001) hinted at a high risk of ARG transmission in the intestines. Collectively, our results suggested that the relative abundance of intestinal ARGs could be changed depending on the intestinal microbiome and DNA structures upon exposure to antibiotics at environmental concentrations.

Risk of horizontal transfer of intracellular, extracellular, and bacteriophage antibiotic resistance genes during anaerobic digestion of cow manure

The fate of intracellular antibiotic resistance genes (iARGs), extracellular ARGs (eARGs) and bacteriophage ARGs (bARGs) during anaerobic digestion (AD) of cow manure is unclear. Thus, the characteristics of iARGs, eARGs and bARGs during mesophilic AD (MAD) and thermophilic AD (TAD) of cow manure were investigated. The absolute abundances of iARGs decreased by 69.82% after TAD. After MAD and TAD, the total absolute abundances of eARGs increased by 63.5 times and 67.6 times, respectively, whereas those of the bARGs increased by 47.60% and 59.22%. eARGs were mainly derived from the non-specific lysis of Firmicutes, Bacteroidetes, while bacteriophages had a wide range of hosts. The variations in iARGs, eARGs and bARGs were affected by the microbial hosts but also directly driven by physicochemical factors (e.g., pH). Overall, the findings of this study revealed that there may be a risk of eARGs and bARGs disseminating during the AD of cow manure.

Effects of multiple antibiotics residues in broiler manure on composting process

At present, the effect of multiple antibiotics on aerobic composting process and its mechanism are not clear. So in this study, broiler manure containing different doses of Doxycycline (DOX) and Gatifloxacin (GAT) were used as raw materials and mixed with rice hull for aerobic composting, and the effects of the combination of multiple antibiotics on the process parameters of broiler manure composting and the succession of bacterial and fungal community structures were systematically analyzed. Our results showed that at the initial period of composting, the combination of multiple antibiotics led to a delayed temperature and pH increase (T1: 57.0 °C, T2: 48.3 °C, T3: 45.5 °C on Day 3 for temperature and T1: 7.44, T2: 7.1, T3: 6.88 on Day 5 for pH), and a slow total nitrogen decrease (T1: 1.56%, T2: 1.82%, T3: 1.74% on Day 5). Although these effects decreased gradually with the degradation of antibiotics, the relative abundance of Actinobacteriota (T1: 13.29%, T2: 10.57%, T3: 8.99%) and Bacteroidota (T1:27.52%, T2:40.03%, T3:39.81%)) were still influenced by multiple antibiotic residuals until the end of composting period. Higher levels of antibiotics had more lasting effects on the bacterial community (T3 > T2). However, the combination of these two antibiotics did not significantly promote or inhibit the succession of the fungal community structure. The heatmaps showed that composting stage had a greater effect on the microbial community structures than antibiotics. The results provided a theoretical reference for composting broiler manure containing DOX and GAT.