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

Maturity phase is crucial for removing antibiotic resistance genes during composting: novel insights into dissolved organic matter-microbial symbiosis system

Composting is widely regarded as an effective method for reducing antibiotic resistance genes (ARGs) in livestock and poultry manure. However, the critical mechanisms of ARGs in different composting phase are still unclear. In this study, normal composting and two types of rapid composting (without mature phase) were used to analyze the removal of ARGs and the succession of dissolved organic matter (DOM). Compared to normal composting, rapid composting reactivated tetracyclines, sulfonamide, and quinolones resistance genes during the maturation phase and reduced the total ARGs removal rates by 45.58 %-57.87 %. Humus-like components could inhibit the proliferation of ARGs, and the enrichment of protein-like components increased abundances of Pusillimonas, Persicitalea, and Pseudomonas, indirectly reducing the removal. This study is the first to demonstrate the contribution of DOM and microbial community to ARGs removal, emphasizing the importance of the maturation phase for ARGs elimination. This research provides guidance for producing safe compost products.

Manure input propagated antibiotic resistance genes and virulence factors in soils by regulating microbial carbon metabolism

Antibiotic resistance genes (ARGs) and virulence factors (VFs) in soils represent a significant threat to ecological security and human health. The carbon-rich soil formed by manure fertilization provides an energy source for soil microbes. However, we still know little about how microbial-dominated carbon metabolism affects ARGs and VFs proliferation in soils subjected to long-term fertilization and irrigation practices in wheat-maize system. Here, we investigated soil microbial carbon metabolism, ARGs and VFs distribution, and microbial composition in soils under 9-year of different fertilization and irrigation managements during wheat growing period. Results showed that manure (M) increased total abundance of soil ARGs by 5.9 %-8.0 % and 2.1 %-4.8 % and VFs by 5.4 %-7.5 % and 2.0 %-4.9 % compared to no fertilizer (CK) and NPK fertilizer (C), respectively, regardless of irrigation. M enriched more number of ARGs and VFs types, and increased abundance of host microbes involved in carbon fixation and carbon degradation, such as Streptomyces, Lysobacter and Agromyces. M increased abundance of carbohydrate-active enzymes (CAZymes) and carbon cycle functional pathways, as well as microbial carbon metabolism capacity. Partial least squares path modeling and correlation analysis showed that microbial diversity, CAZymes, carbon cycle functional pathways (particularly carbon fixation and degradation) and microbial carbon metabolism capacity of microbial community had direct positive effects on the proliferation and spread of ARGs and VFs. In conclusion, our results highlight the importance of microbial mediated carbon metabolism in driving the dissemination of ARGs and VFs in soils under long-term manure application.

Association of infrastructure and operations with antibiotic resistance potential in the dairy environment in India

The dairy industry in developing countries is often associated with inappropriate use of antibiotics and the subsequent contamination of the environment with co-selectors of antibiotic resistance. However, the specific factors in dairy farm environments that influence antibiotic resistance levels and the subsequent exposure risks to farm workers are unknown. We examined the link between the infrastructure and operations of the dairy farm and the antibiotic resistance potential in India, which is the highest producer and consumer of dairy products globally. We sampled sixteen dairy farms in the Dehradun district, India, that varied in their herd size, infrastructure, and operational features during winter, summer, and monsoon. We collected samples of dung, manure, wastewater, manure-amended, and control soil from these farms. We quantified six antibiotic resistance genes (ARGs) (sul1, sul2, parC, mcr5, ermF, and tetW), an integron integrase gene cassette (intI1), and 16S rRNA gene copies as an indicator for total bacterial count. We observed that the infrastructure and the operations of the dairy farms were significantly associated with antibiotic resistance potential in the dairy environment. For example, with increased ventilation and exposure to external weather, the levels of sul2 (x͂=10-1.63) and parC (x͂=10-4.24) in manure increased. When farmers administered antibiotics without veterinary consultation, the relative levels of intI1 (x͂=10-2.36), sul2 (x͂=10-1.58), and tetW (x͂=10-3.04) in manure were lower than the cases where professional advice was sought. Small-scale farms had lower relative ARG levels than medium- and large-scale farms, except for mcr5 (x͂=10-3.98) in wastewater. In different sample types, the relative ARG levels trended as manure-amended soil (x͂=10-2.34) > wastewater (x͂=10-2.90)> manure (x͂=10-3.39)> dung (x͂=10-2.54). ARGs correlated with the marker for horizontal gene transfer, intI1, which exacerbates overall antibiotic resistance levels. Exposure assessment showed that the agriculture farm workers working in manure-amended agriculture farms are exposed to higher antibiotic resistance potential than dairy farm workers, who manually handle dung. Our study showed that the link between the dairy infrastructure (ventilation and floor type) and operations (scale of operation and veterinary consultation) and the antibiotic resistance potential in the dairy farm environment was statistically significant. This knowledge paves the way for designing interventions that can minimize the antibiotic resistance potential on dairy farms and in affected environments and thus reduce the public health burden of antibiotic-resistant infections in the dairy industry and dairy workers in India.

Mechanism of reducing antibiotic resistance genes by nano-selenium during composting: insight into host microorganisms and a two-component system

Nano-selenium (nano-Se) makes up for the low biological activity and high toxicity of inorganic selenium, and is widely used as a novel Se fertilizer in agriculture. This study investigated the effects of different concentrations of nano-Se on Antibiotic resistance genes (ARGs) and host microorganisms during aerobic composting of cow manure. The results showed that high-concentration nano-Se had excellent effects on ARG removal, effectively inhibiting the dominant ARG subtypes such as aada and tetA(48). Transposase was the mobile genetic element (MGE) that deserves the most attention, which maintained a relatively high abundance in each sample. Antibiotic efflux-transposase had the highest abundance of all ARG resistance mechanism-MGE types. At the end of composting, antibiotic efflux-transposase abundance in group Se_H decreased by 7.14 %, 21.96 %, and 54.92 %, respectively, compared with groups CK, Se_L, and Se_M. High-concentration nano-Se inhibited the activity of transposase to reduce the risk of horizontal transmission of antibiotic efflux ARGs. Proteobacteria and Actinobacteria were the main ARG host microorganisms, and Actinobacteria had a lower tolerance threshold for nano-Se. Network analysis and Mantel testing demonstrated that high-concentration nano-Se could weaken the association between host microorganisms and the ARG subtypes. Structural equation models showed that high-concentration nano-Se regulated the transfer of ARGs primarily by stimulating signal transduction in host microorganisms. Thus, the addition of proper concentrations of nano-Se during aerobic composting of cow manure was effective in reducing ARG exposure risk by regulating transposase and host microorganisms.

Bacterial abundance and antimicrobial resistance prevalence carried by adult house flies (Diptera: Muscidae) at Kansas dairy and beef cattle operations

House flies (Musca domestica L.) are filth-breeding pests of urban and rural environments around the world. Frequenting microbe-rich substrates for nutritional and reproductive needs, house flies pose a risk to human and animal health through their carriage and transmission of pathogenic and antimicrobial resistant bacteria (AMR). Adult house flies were collected from Kansas beef and dairy cattle operations to assess factors influencing bacterial abundance and AMR incidence flies. Aerobic culturable bacteria and suspected coliforms (SC) were enumerated from fly homogenate cultured on nonselective (tryptic soy agar) and selective (violet-red bile agar VRBA) media, respectively. Unique morphotypes of SC isolates were screened for tetracycline resistance and tested for resistance to 4 additional antibiotics to identify multi-drug resistant (MDR) isolates. Female house flies carried greater abundances of both culturable bacteria and SC than male flies. Abiotic factors such as ambient and soil temperatures correlated with culturable bacteria and SC abundances in flies, but farm type correlated only with SC abundance and trends of resistance phenotypes observed in SC isolates. Male and female flies from both farm types carried one or more AMR and MDR SC isolates (73.02% AMR and 31.09% MDR). The majority of AMR and MDR bacteria were Escherichia/Shigella sp., which possessed the widest range of phenotypic resistance variability found in our study. Our results further emphasize the role house flies play in harboring bacteria of risk to human and animal health and identified factors of potential use for the development of strategies to mitigate house fly transmission of bacterial pathogens and AMR within confined cattle operations.

Regulation of antibiotic resistance gene rebound by degrees of microecological niche occupation by microbiota carried in additives during the later phases of swine manure composting

The occupation of microecological niches (MNs) by bacteria carrying lower antibiotic resistance genes (ARGs) has been demonstrated an effective strategy for reducing ARGs in compost, thereby mitigating the associated land use risks. In this study, humus soil (HS), matured compost (MC), and their respective isolated microbial agents (HSM and MCM), which exhibit varying abundances of ARGs, were introduced as additives after the thermophilic phase to investigate their influence on ARG removal and the mechanisms underlying effective MN occupation. The addition of HS resulted in the most favorable outcomes, including the highest carbon degradation, minimized nitrogen loss, and an 83.16 % reduction in ARG abundance during the later composting stages. In comparison, ARG rebound levels were 61.77 %-285.33 % across other treatments and 729.23 % in the control. Distinct dominant bacterial genera and potential ARG-host bacterial communities were observed, which varied with different additives and contributed to MN occupation dynamics. The addition of the HS additive intensified competition among non-host bacteria, and diversified the interactions both between genes and between bacteria. These changes suppressed horizontal gene transfer (HGT) mediated by mobile genetic elements (MGEs) and altered the abundance and composition of both dominant and non-dominant potential host species. Furthermore, it shifted the relative importance of key physicochemical parameters, collectively enhancing ARG removal during composting. These findings elucidate the mechanisms by which MN adjustments contribute to ARG reduction, providing actionable insights for designing composting strategies that mitigate environmental ARG dissemination risks more effectively.

Humus Soil Inhibits Antibiotic Resistance Gene Rebound in Swine Manure Composting by Modulating Microecological Niches

Aerobic composting is widely used for the degradation of organic matter, simultaneously reducing the presence of antibiotic resistance genes (ARGs) in swine manure. However, the phenomenon of abundance rebound or even enrichment of ARGs is still a problem. The effect and mechanism of humus soil (Hs) on ARG reduction by adding it into the piles (0% for the control group (CK); 10% for S1 group; 20% for S2 group; and 30% for S3 group) after the thermophilic phase of composting was investigated. The results indicated that Hs promoted organic matter degradation and nitrogen loss. During days 15-36, the greatest reduction of 69.91% in total ARG abundance was observed in S2, while the abundance rebounded by 222.75% in CK and decreased only 13.71% in S3. With the 20% Hs addition, 85.42% abundance reduction for mobile genetic elements (MGEs) and 100% removal rates for aadA5, aadA9, sul1, sul2, and tetX were achieved. Moreover, the addition of Hs immediately changed the bacterial community structure of the substrate and varied the bacterial community successional direction in the treatments. Additionally, significantly positive correlations (|r| > 0.6; p < 0.05) were found between the top 20 genera and ARGs. The potential host bacteria for ARGs changed from Lactobacillus, Fermentimonas, Pusillimonas, and Ruminofilibacter in CK to Lactobacillus, Romboutsia, and Streptococcus in S2, highlighting the shift and reduction in host bacteria driven by Hs, which, in turn, influenced the abundance variations in ARGs. This study verified the feasibility of inhibiting the rebound of ARG abundance effectively by influencing the microecological niche in the pile, offering an approach for promoting a reduction in ARGs in animal wastes.

Antibiotic resistance genes in the coastal atmosphere under varied weather conditions: Distribution, influencing factors, and transmission mechanisms

Antibiotic resistance genes (ARGs) have escalated to levels of concern worldwide as emerging environmental pollutants. Increasing evidence suggests that non-antibiotic antimicrobial substances expedite the spread of ARGs. However, the drivers and mechanisms involved in the generation and spread of ARGs in the atmosphere remain inadequately elucidated. Co-occurrence networks, mantel test analysis, and partial least squares path modeling were used to analyze the symbiotic relationships of ARGs with meteorological conditions, atmospheric pollutants, water-soluble inorganic ions, bacteria, mobile genetic elements (MGEs), antibacterial biocide and metal resistance genes, and to identify the direct drivers of ARGs. The types and abundance of ARGs exhibited different seasonal distribution. Specifically, the types exhibited a strong alignment with the diversity of air masses terrestrial sources, while the abundance displayed a significant positive correlation with both biocide resistance genes (BRGs) and metal resistance genes (MRGs). The contribution of bacterial communities and MGEs to the generation and spread of ARGs was constrained by the low levels of antibiotics in the atmosphere and the existence of "viral intermediates". Conversely, antibacterial biocides and metals influenced mutation rates, cellular SOS responses, and oxidative stress of bacteria, consequently facilitating the generation and spread of ARGs. Moreover, the co-selection among their derivatives, resistance genes, ensured a stable presence of ARGs. The research highlighted the significant impact of residual antimicrobial substances on both the generation and spread of ARGs. Elucidating the sources of aerosols and the co-selection mechanism linking with ARGs, BRGs, and MRGs were crucial for preserving the stability of ARGs in the atmosphere.

Industrial-scale aerobic composting with the addition of Paenibacillus mucilaginosus: Improving product quality and removing antibiotic resistance genes

This study comprehensively investigated the effects of adding Paenibacillus mucilaginosus to industrial-scale compost on compost quality, microbial community dynamics, and antibiotic resistance genes (ARGs). The results of this investigation unequivocally demonstrated that the inclusion of Paenibacillus mucilaginosus prolonged the thermophilic phase of composting, thereby enhancing organic matter decomposition and facilitating nitrogen fraction conversion. Moreover, the inoculation of Paenibacillus mucilaginosus altered the microbial community structure during the rapid heating and thermophilic stages. Significantly, the removal rates of tetM, tetR, and sul1 were 99.84%, 99.68%, and 97.61%, respectively, with inoculation increasing these rates by 8.94%, 9.85%, and 9.34%, respectively, compared to the control (P < 0.05). These findings highlighted the efficacy of incorporating Paenibacillus mucilaginosus into industrial-scale compost as a potent strategy to enhance nutrient transformation processes and mitigate ARG activity.

Interactions between fungi and bacteria hosts carrying MGEs is dominant for ARGs fate during manure mesophilic composting

The mycelial networks of fungi promote the interaction between the originally isolated bacteria, thereby potentially enhancing the exchange of nutrients and the horizontal transfer of genetic materials. However, the driving effect of fungi on antibiotic resistance genes (ARGs) during mesophilic facultative composting is still unclear. This study aims to elucidate the changes in ARGs and underlying mechanisms during the mesophilic composting of manure. Results indicated that reduction rates of ARGs in sheep and pig manure over a 90-day composting period were 34.68% and 60.10%, respectively. The sul1, sul2 and tetX were identified as recalcitrant ARGs in both composting treatments, with the additional unique recalcitrant gene addA observed in sheep manure. Fungal communities appeared to have a more significant influence on the cooperation between bacteria and fungi. Massive fungi interacted intensively with bacterial hosts carrying both ARGs and mobile genetic elements (MGEs). In sheep and pig manure, there were 53 and 38 potential bacterial hosts (genus level) carrying both ARGs and MGEs, associated close interactions with fungi. Structural equation modeling revealed that compost properties influence ARGs by affecting the abundance of core fungi and the hosts carrying MGEs, and that core fungi could also impact ARGs by influencing the bacterial hosts carrying MGEs. Core fungi have the potential to facilitate the horizontal transfer of ARGs by enhancing bacterial network interactions.

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

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

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.

Deciphering basic and key traits of bio-pollutants in a long-term reclaimed water headwater urban stream

Reclaimed water has been recognized as a stable water resource for ecological replenishment in riverine environment. However, information about the bio-pollutants spatial and temporal distributions and the associated risk in this environment remains insufficient. Herein, the bio-pollutant profile in a long-term reclaimed water headwater urban stream, including antibiotic resistance genes (ARGs), mobile genetic elements and pathogens, were revealed by metagenomics. Notably, the temporal variation in bio-pollutant levels exceeded spatial fluctuations, possibly due to the varied rainfall intensity. Specially, multidrug resistance genes and Acinetobacter baumannii (A. baumannii) were the dominant ARGs and pathogens, respectively, exhibiting higher abundance in the dry season, especially in the downstream of the receiving point, where the bio-risk also peaked. A. baumannii and Ralstonia solanacearum were found to be the main plasmids contributors inducing the horizontal gene transfer process in this stream. Overall, A. baumannii contributed over 50 % bio-risk values in most samples, indicating that it was the "overlord" in this headwater urban stream. This study revealed characteristics of bio-pollutants in a typical long-term reclaimed water headwater urban stream, highlighting the superiority of A. baumannii in bio-pollutants, which should be a key consideration in the bio-pollutants surveillance for reclaimed waters.

Distribution of antibiotic resistance genes and their pathogen hosts in duck farm environments in south-east coastal China

Livestock farms are major reservoirs of antibiotic resistance genes (ARGs) that are discharged into the environment. However, the abundance, diversity, and transmission of ARGs in duck farms and its impact on surrounding environments remain to be further explored. Therefore, the characteristics of ARGs and their bacterial hosts from duck farms and surrounding environment were investigated by using metagenomic sequencing. Eighteen ARG types which consist of 823 subtypes were identified and the majority conferred resistance to multidrug, tetracyclines, aminoglycosides, chloramphenicols, MLS, and sulfonamides. The floR gene was the most abundant subtype, followed by sul1, tetM, sul2, and tetL. ARG abundance in fecal sample was significantly higher than soil and water sample. Our results also lead to a hypothesis that Shandong province have been the most contaminated by ARGs from duck farm compared with other four provinces. PcoA results showed that the composition of ARG subtypes in water and soil samples was similar, but there were significant differences between water and feces samples. However, the composition of ARG subtypes were similar between samples from five provinces. Bacterial hosts of ARG subtypes were taxonomically assigned to eight phyla that were dominated by the Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. In addition, some human bacterial pathogens could be enriched in duck feces, including Enterococcus faecium, Acinetobacter baumannii, and Staphylococcus aureus, and even serve as the carrier of ARGs. The combined results indicate that a comprehensive overview of the diversity and abundance of ARGs, and strong association between ARGs and bacterial community shift proposed, and benefit effective measures to improve safety of antibiotics use in livestock and poultry farming. KEY POINTS: • ARG distribution was widespread in the duck farms and surroundings environment • ARG abundance on the duck farms was significantly higher than in soil and water • Human bacterial pathogens may serve as the vectors for ARGs.

Risk level and removal performance of antibiotic resistance genes and bacterial pathogens in static composting with different temperatures

The effect of different levels of temperature on resistance genes is not clear in mesophilic static composting (<50 °C). This study conducted livestock manure composting with different temperature gradients from 20 to 50 °C, it was found that the reduction rates of risk rank-I antibiotic resistance genes (from 3 % to 66 %), metal resistance genes (from -50 % to 76 %) and bacterial pathogens (from 72 % to 91 %) all increased significantly with increasing temperature from 20 to 50°C. The vulnerability of bacterial communities increased significantly, and the assembly process of bacterial communities changed from deterministic to stochastic with the increase of composting temperature. Higher temperature could accelerate the removal of thermolabile resistance genes hosts or pathogenic hosts carrying mobile genetic elements by directly or indirectly affecting organic acids content. Therefore, for soil safety, the temperature of the manure recycling process should be increased as much as possible.

Efficient reduction of antibiotic resistance genes and mobile genetic elements in organic waste composting via fenton-like treatment

Livestock manure harbors antibiotic resistance genes (ARGs), and aerobic composting (AC) is widely adopted for waste management. However, mitigating ARG resurgence in later stages remains challenging. This work aims to curb ARGs rebounding through a Fenton-like reaction during food waste and swine manure co-composting. Results revealed that 0.025 % zerovalent iron (ZVI) + 0.5 % hydrogen peroxide (H2O2) facilitated maximum ARG, mobile genetic elements (MGEs), and 16 s rRNA removal with reductions of 2.68, 2.69, and 1.4 logs. Spectroscopic analysis confirmed Fenton-like reaction and cell apoptosis analysis indicated that 0.025 % ZVI and 0.5 % H2O2 treatment had the maximum early apoptosis, least observed, and normal cells on day 30. Redundancy analysis highlighted the influence of bacterial communities and physicochemical properties on ARGs, with MGEs playing a crucial role in Fenton treatments. Our findings suggest incorporating ZVI and H2O2 in composting can significantly reduce ARGs and enhance waste management practices.

A comprehensive review on agricultural waste utilization through sustainable conversion techniques, with a focus on the additives effect on the fate of phosphorus and toxic elements during composting process

The increasing trend of using agricultural wastes follows the concept of "waste to wealth" and is closely related to the themes of sustainable development goals (SDGs). Carbon-neutral technologies for waste management have not been critically reviewed yet. This paper reviews the technological trend of agricultural waste utilization, including composting, thermal conversion, and anaerobic digestion. Specifically, the effects of exogenous additives on the contents, fractionation, and fate of phosphorus (P) and potentially toxic elements (PTEs) during the composting process have been comprehensively reviewed in this article. The composting process can transform biomass-P and additive-born P into plant available forms. PTEs can be passivated during the composting process. Biochar can accelerate the passivation of PTEs in the composting process through different physiochemical interactions such as surface adsorption, precipitation, and cation exchange reactions. The addition of exogenous calcium, magnesium and phosphate in the compost can reduce the mobility of PTEs such as copper, cadmium, and zinc. Based on critical analysis, this paper recommends an eco-innovative perspective for the improvement and practical application of composting technology for the utilization of agricultural biowastes to meet the circular economy approach and achieve the SDGs.

Biosafety assessment of laying hens fed different treatments of black soldier flies (Hermetia illucens) under doxycycline stress

The black soldier fly (BSF, Hermetia illucens) is a resource insect that can utilize livestock and poultry feces. However, BSFs may also increase the risk of transmission of antibiotic resistance genes (AGRs) that are widespread in livestock and poultry farm environments. Therefore, we aimed to evaluate the biosecurity risks of different BSF treatments in the laying chicken food chain using the "chicken manure-BSF-laying hens" model. Our results indicated that different BSF treatments significantly affected antibiotic residue, ARGs, MGEs, bacterial antibiotic resistance, and bacterial microbial community composition in the food chain of laying hens fed BSFs. These risks can be effectively reduced through starvation treatment and high-temperature grinding treatment. Comprehensive risk assessment analysis revealed that starvation combined with high-temperature milling (Group H) had the greatest effect.

Dynamics of antibiotic resistance genes during manure composting: Reduction in herbivores manure and accumulation in carnivores

The elevated levels of antibiotic resistance genes (ARGs) in livestock manure represent a significant threat to both the environment and human health. Composting has been recognized as an effective strategy to mitigate the abundance of ARGs in manure. However, notable rebounds in ARGs abundance have been observed during this process. This study explored the changes in ARGs abundance and the underlying influencing factors during the composting of carnivore (chicken and pig) and herbivore (sheep and cow) manures, along with mushroom residues. The findings revealed that the total relative abundance of ARGs increased by 6.96 and 10.94 folds in chicken and pig manure composts, respectively, whereas it decreased by a remarkable 91.72% and 98.37% in sheep and cow manure composts. Nitrogen content emerged as the primary physicochemical factors governing the abundance of ARGs in chicken and pig manure composts. Conversely, carbon content played a pivotal role in determining ARGs abundance in chicken and pig manure composts. Furthermore, the presence of dominant hosts, such as Corynebacterium, Bacillus, and Clostridium, along with emerging bacteria like Thermobifida, Saccharomonospora, and Actinomadura, contributed significantly to the enrichment of total ARGs, including tetG, tetO, tetX, and sul2, in chicken and pig manure composts. The coexistence of these genes with mobile genetic elements and a plethora of host bacteria, coupled with their high abundance, renders them particularly high-risk ARGs. On the other hand, the observed decrease in the abundance of total ARGs in sheep and cow manure composts can be attributed to the decline in the population of host bacteria, specifically Atopostipes, Psychrobacter, and Corynebacterium. Collectively, these results provide crucial insights into the management of ARGs risks and offer essential theoretical support for enhancing the safe utilization of organic fertilizer in agriculture.

Mechanisms for more efficient antibiotics and antibiotic resistance genes removal during industrialized treatment of over 200 tons of tylosin and spectinomycin mycelial dregs by integrated meta-omics

To mitigate the environmental risks posed by the accumulation of antibiotic mycelial dregs (AMDs), this study first attempted over 200 tons of mass production fermentation (MP) using tylosin and spectinomycin mycelial dregs alongside pilot-scale fermentation (PS) for comparison, utilizing the integrated-omics and qPCR approaches. Co-fermentation results showed that both antibiotics were effectively removed in all treatments, with an average removal rate of 92%. Antibiotic resistance gene (ARG)-related metabolic pathways showed that rapid degradation of antibiotics was associated with enzymes that inactivate macrolides and aminoglycosides (e.g., K06979, K07027, K05593). Interestingly, MP fermentations with optimized conditions had more efficient ARGs removal because homogenization permitted faster microbial succession, with more stable removal of antibiotic resistant bacteria and mobile genetic elements. Moreover, Bacillus reached 75% and secreted antioxidant enzymes that might inhibit horizontal gene transfer of ARGs. The findings confirmed the advantages of MP fermentation and provided a scientific basis for other AMDs.

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

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

Enhancing C and N turnover, functional bacteria abundance, and the efficiency of biowaste conversion using Streptomyces-Bacillus inoculation

Microbial inoculation plays a significant role in promoting the efficiency of biowaste conversion. This study investigates the function of Streptomyces-Bacillus Inoculants (SBI) on carbon (C) and nitrogen (N) conversion, and microbial dynamics, during cow manure (10% and 20% addition) and corn straw co-composting. Compared to inoculant-free controls, inoculant application accelerated the compost's thermophilic stage (8 vs 15 days), and significantly increased compost total N contents (+47%) and N-reductase activities (nitrate reductase: +60%; nitrite reductase: +219%). Both bacterial and fungal community succession were significantly affected by DOC, urease, and NH4+-N, while the fungal community was also significantly affected by cellulase. The contribution rate of Cupriavidus to the physicochemical factors of compost was as high as 83.40%, but by contrast there were no significantly different contributions (∼60%) among the top 20 fungal genera. Application of SBI induced significant correlations between bacteria, compost C/N ratio, and catalase enzymes, indicative of compost maturation. We recommend SBI as a promising bio-composting additive to accelerate C and N turnover and high-quality biowaste maturation. SBI boosts organic cycling by transforming biowastes into bio-fertilizers efficiently. This highlights the potential for SBI application to improve plant growth and soil quality in multiple contexts.

Devitalization of Bacteria in Composted Cattle Manure with Natural Additives and Risk for Environment

Nowadays, there is an effort to improve the effectiveness of the composting process, supported by the addition of various supplements to reduce soil nutrition losses and increase soil remediation. The aim of this study was to examine the devitalization effect of natural additives like zeolite-clinoptilolite and its combination with hydrated lime in composted cattle manure on indicator and pathogen bacteria. The composting process was running in three static piles of cattle manure mixed with wheat straw (control, zeolite-lime, and zeolite) for 126 days. Composted manure substrates were determined for physicochemical (temperature, pH, nitrogen and phosphorus content, C/N, organic matter, and moisture) and microbiological analyses (Salmonella spp., indicator bacteria). The effects of additives were reflected in changes in physicochemical factors, e.g., an increase in temperature (<53 °C) or pH (<9.3). According to Pearson correlation, these changes (pH, Nt, Pt) resulted in a significant decrease (p < 0.001) of indicator bacteria (two or three orders) in zeolite pile or zeolite-lime pile. Die-off of Salmonella spp. in the zeolite-lime pile was indicated within 41 days; in other piles, this occurred on day 63. Our results can aid in further optimizing the composting of cattle manure in order to lower environmental pollution and the risk of human infection.

Investigating fungal community characteristics in co-composted cotton stalk and various livestock manure products

Agricultural wastes, comprising cotton straw and livestock manure, can be effectively managed through aerobic co-composting. Nevertheless, the quality and microbial characteristics of co-composting products from different sources remain unclear. Therefore, this study utilized livestock manure from various sources in Xinjiang, China, including herbivorous sheep manure (G), omnivorous pigeon manure (Y), and pigeon-sheep mixture (GY) alongside cotton stalks, for a 40-day co-composting process. We monitored physicochemical changes, assessed compost characteristics, and investigated fungal community. The results indicate that all three composts met established composting criteria, with compost G exhibiting the fastest microbial growth and achieving the highest quality. Ascomycota emerged as the predominant taxon in three compost products. Remarkably, at the genus level, the biomarker species for G, Y, and GY are Petromyces and Cordyceps, Neurospora, and Neosartorya, respectively. Microorganisms play a pivotal role in organic matter degradation, impacting nutrient composition, demonstrating significant potential for the decomposition and transformation of compost components. Redundancy analysis indicates that potassium, total organic carbon, and C:N are key factors influencing fungal communities. This study elucidates organic matter degradation in co-composting straw and livestock manure diverse sources, optimizing treatment for efficient agricultural waste utilization and sustainable practices.

Occurrence and dissemination of antibiotic resistance genes in the Yellow River basin: focused on family farms

As an emerging contaminant, antibiotic resistance genes (ARGs) have attracted growing attention, owing to their widespread dissemination and potential risk in the farming environment. However, ARG pollution from family livestock farms in the Yellow River basin, one of the main irrigation water sources in the North China Plain, remains unclear. Herein, we targeted 21 typical family farms to assess the occurrence patterns of ARGs in livestock waste and its influence on ARGs in receiving environment by real-time quantitative PCR (qPCR). Results showed that common ARGs were highly prevalent in family livestock waste, and tet-ARGs and sul-ARGs were the most abundant in these family farms. Most ARG levels in fresh feces of different animals varied, as the trend of chicken farms (broilers > laying hens) > swine farms (piglets > fattening pigs > boars and sows) > cattle farms (dairy cattle > beef cattle). The effect of natural composting on removing ARGs for chicken manure was better than that for cattle manure, while lagoon storage was not effective in removing ARGs from family livestock wastewater. More troublesomely, considerable amounts of ARGs were discharged with manure application, further leading to the ARG increase in farmland soil (up to 58-119 times), which would exert adverse impacts on human health and ecological safety.

Is the application of organic fertilizers becoming an undeniable source of microplastics and resistance genes in agricultural systems?

The application of organic fertilizers is becoming an undeniable source of microplastics and antibiotic resistance genes (ARGs) in agricultural soils. The complex microbial activity further transfers resistance genes and their host bacteria to agricultural products and throughout the entire food chain. Therefore, the current main focus is on reducing the abundance of microplastics and ARGs in organic fertilizers at the source, as well as managing microplastics and ARGs in soil. The control of microplastic abundance in organic fertilizers is currently only achieved through pre-composting selection and other methods. However, there are still many shortcomings in the research on the distribution characteristics, propagation and diffusion mechanisms, and control technologies of ARGs, and some key scientific issues still need to be urgently addressed. The high-temperature composting of organic waste can effectively reduce the abundance of ARGs in organic fertilizers to a certain extent. However, it is also important to consider the spread of ARGs in residual antibiotic-resistant bacteria (ARB). This article systematically explores the pathways and interactions of microplastics and resistance genes entering agricultural soils through the application of organic fertilizers. The removal of microplastics and ARGs from organic fertilizers was discussed in detail. Based on the limitations of existing research, further investigation in this area is expected to provide valuable insights for the development and practical implementation of technologies aimed at reducing soil microplastics and resistance genes.

Urea addition as an enhanced strategy for degradation of petroleum contaminants during co-composting of straw and pig manure: Evidences from microbial community and enzyme activity evaluation

Alterations in microbial community succession patterns and enzyme activities by petroleum pollutants during co-composting of straw and swine manure with the supplementary nitrogen source are unclear. In this study, urea was added into co-composting systems, and the removal performance of petroleum, microbial enzyme activity and community changes were investigated. Results showed that the polyphenol oxidase and catalase activities which were both related to the degradation of petroleum contaminants were accordingly increased from 20.65 to 30.31 U/g and from 171.87 to 231.86 U/g due to urea addition. The removal efficiency of petroleum contaminants in composting with urea increased from 45.06% to 82.29%. The addition of urea increased the diversity and abundance of petroleum-degrading microorganisms, and enhanced microbial linkages. This study provides a novel strategy for the degradation of petroleum hydrocarbon as well as a new insight into the effect of urea on both microbial processes and composting phases.

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.

Metagenomics-assembled analysis revealed the characteristics of antibiotic resistome and community coalescence in the soils irrigated with different irrigation materials

Antibiotic resistance has received widespread attention in recent years. Soil irrigation and fertilization are routine agricultural practices, but also lead to the spread of antibiotic resistance genes (ARGs) in soil-crop system such as via resistome coalescence. Despite community coalescence being ubiquitous and important in natural ecosystems, little research has been done to investigate resistome coalescence during soil irrigation activities. In this study, the characteristics of antibiotic resistome and community coalescence in the soils irrigated with different irrigation materials (wastewater, wastewater-river water, and wastewater-manure) have been revealed by utilizing microcosm experiments and high-throughput sequencing-based metagenomic assembly approaches. Results showed irrigation and coalescence changed soil quality and resistome. Totally, 789 unique ARGs were identified in the irrigation system, including some emerging ARGs. The abundance and diversity of ARGs increased in the coalesced soils, mainly due to the newly imported ARGs from irrigation materials. Relatively, the soils irrigated with wastewater and manure showed higher level of ARGs. Irrigation with the mixtures containing river water caused greater loss of indigenous taxa, while the community structure of mixing treatment with manure changed more dramatically. Interestingly, the succession of community in coalesced soils was influenced by transient competition for resources and ecological niche width, and the highest abundance and diversity of microorganisms and ARGs were found in the initial phase of coalescence, followed by a gradual succession towards the original community. With increasement of wastewater in the irrigation materials, the soil community showed a stepwise change rather than linear change. Notably, natural deposit of irrigation materials reduced their impacts on the ARGs in the coalesced soils. Findings provide new insights into the resistome coalescence during agricultural practices for reducing the spread risks of ARGs.

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.

Risk characteristics of resistome coalescence in irrigated soils and effect of natural storage of irrigation materials on risk mitigation

Irrigation and fertilization are the routinely agricultural practices but also cause resistome coalescence, by which the entire microbiomes from irrigation materials invade soil microbial community, to transfer antibiotic resistance genes (ARGs) in the coalesced soils. Although studies have reported the effect of irrigation or fertilization on the prevalence and spread of ARGs in soils, risk characteristics of resistome coalescence in irrigation system remain to be demonstrated and few has shown whether natural storage of irrigation materials will reduce resistance risks. To fill the gaps, two microscopic experiments were conducted for deeply exploring resistance risks in the soils irrigated with wastewater and manure fertilizer from a perspective of community coalescence by metagenomic analysis, and to reveal the effect of natural storage of irrigation materials on the reduction of resistance risks in the coalesced soils. Results showed irrigation and coalescence significantly increased the abundance and diversity of ARGs in the soils, and introduced some emerging resistance genes into the coalesced community, including mcr-type, tetX, qacB, and an array of genes conferring resistance to carbapenem. Procrustes analysis demonstrated microbial community was significantly correlated with the ARGs in coalesced soils, and variance partitioning analysis quantified its dominant role on shaping resistome profile in the environment. Besides ARGs, abundant and diverse mobile genetic elements (MGEs) were also identified in the coalesced soils and co-existed on the ARG-carrying contigs, implying potential transfer risk of ARGs in the irrigation system. Further, the analysis of metagenome-assembled genomes (MAGs) confirmed the risk by recovering 358 ARGs-carrying MAGs and identifying the resistant bacteria that co-carried multiple ARGs and MGEs. As expected, the natural storage of irrigation water and manure fertilizer reduced about 27%-54% of ARGs, MGEs and virulence factors in the coalesced soils, thus caused the soils to move towards lower resistance risks to a certain extent.

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.

Dynamics of antibiotic resistance genes and bacterial community during pig manure, kitchen waste, and sewage sludge composting

Organic solid wastes (OSWs) are important reservoirs for antibiotic resistance genes (ARGs). Aerobic composting transforms OSWs into fertilizers. In this study, we investigated ARGs dynamics and their driving mechanisms in three OSW composts: pig manure (PM), kitchen waste (KC), and sewage sludge (SG). The dominant ARGs were different in each OSW, namely tetracycline, aminoglycoside, and macrolide resistance (PM); tetracyclines and aminoglycosides (KC); and sulfonamides (SG). ARGs abundance decreased in PM (71%) but increased in KC (5.9-fold) and SG (1.3-fold). Interestingly, the ARGs abundance was generally similar in all final composts, which was contributed to the similar bacterial community in final composts. In particular, sulfonamide and β-lactam resistant genes removed (100%) in PM, while sulfonamide in KC (38-fold) and tetracycline in SG (5-fold) increased the most. Additionally, ARGs abundance rebounded during the maturation period in all treatments. Firmicutes, Proteobacteria, and Actinobacteria were the main ARGs hosts. Several persistent and high-risk genes included tetW, aadA, aadE, tetX, strB, tetA, mefA, intl1, and intl2. The structural equation models showed ARGs removal was mainly affected by physicochemical parameters and bacterial communities in PM, the ARGs enrichment in KC composting correlated with increased mobile genetic elements (MGEs). In general, thermophilic aerobic composting can inhibit the vertical gene transfer (VGT) of pig manure and horizontal gene transfer (HGT) of sludge, but it increases the HGT of kitchen waste, resulting in a dramatic increase of ARGs in KC compost. More attention should be paid to the ARGs risk of kitchen waste composting.

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.

Insights into the reduction of antibiotic-resistant bacteria and mobile antibiotic resistance genes by black soldier fly larvae in chicken manure

The increasing prevalence of antibiotic-resistant bacteria (ARB) from animal manure has raised concerns about the potential threats to public health. The bioconversion of animal manure with insect larvae, such as the black soldier fly larvae (BSFL, Hermetia illucens [L.]), is a promising technology for quickly attenuating ARB while also recycling waste. In this study, we investigated BSFL conversion systems for chicken manure. Using metagenomic analysis, we tracked ARB and evaluated the resistome dissemination risk by investigating the co-occurrence of antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and bacterial taxa in a genetic context. Our results indicated that BSFL treatment effectively mitigated the relative abundance of ARB, ARGs, and MGEs by 34.9%, 53.3%, and 37.9%, respectively, within 28 days. Notably, the transferable ARGs decreased by 30.9%, indicating that BSFL treatment could mitigate the likelihood of ARG horizontal transfer and thus reduce the risk of ARB occurrence. In addition, the significantly positive correlation links between antimicrobial concentration and relative abundance of ARB reduced by 44.4%. Moreover, using variance partition analysis (VPA), we identified other bacteria as the most important factor influencing ARB, explaining 20.6% of the ARB patterns. Further analysis suggested that antagonism of other bacteria on ARB increased by 1.4 times, while nutrient competition on both total nitrogen and crude fat increased by 2.8 times. Overall, these findings provide insight into the mechanistic understanding of ARB reduction during BSFL treatment of chicken manure and provide a strategy for rapidly mitigating ARB in animal manure.

Evaluating the potential of biodegradation of swine manure through rotary drum composting utilizing different bulking agents

The rapid expansion of the pig industry and the concurrent increase in pig units have posed a significant waste management challenge, particularly in the form of piggery waste. In this study, the potential of three different bulking agents (sawdust, dry leaves, and rice straw) for the biodegradation of piggery waste was evaluated through rotary drum composting (RDC). Following the composting time of 20 days, evaluations of macro and micronutrient concentrations and the C/N ratio revealed stable, matured compost that could be used in farming. However, the saw dust amended RDC (RDC1) outperformed among the studied trails; the total nitrogen content of 1.54%, total phosphorus of 7.68 g kg-1, and total potassium of 23.45 g kg-1 demonstrated the bioproduct produced through RDC1 resulted in superior-quality end product achieved in only 20 days in comparison with other bulking agents studied. Further, the outcomes of the study can serve the swine livestock sector through effective bioconversion of the waste.

Relating bacterial dynamics and functions to greenhouse gas and odor emissions during facultative heap composting of four kinds of livestock manure

Although facultative heap composting is widely used in small and medium-sized livestock farms in China, there are few studies on greenhouse gas (GHG) and odor emissions from this composting system. This study focused on GHG and odor emissions from facultative heap composting of four types of livestock manure and revealed the relationship between the gaseous emissions and microbial communities. Results showed that pig, sheep, and cow manure reached high compost maturity (germination index (GI) > 70%), whereas chicken manure had higher phytotoxicity (GI = 0.02%) with higher electrical conductivity and a lower carbon/nitrogen ratio. The four manure types significantly differed in the total GHG emission, with the following pattern: pig manure (308 g CO2-eq·kg-1) > cow manure (146 g CO2-eq·kg-1) > chicken manure (136 g CO2-eq·kg-1) > sheep manure (95 g CO2-eq·kg-1). Bacterium with Fermentative, Methanotrophy and Nitrite respiratory functions (e.g. Pseudomonas and Lactobacillus) are enriched within the pile so that more than 90% of the GHGs are produced in the early (days 0-15) and late (days 36-49) composting periods. CO2 contributed more than 90% in the first 35 d, N2O contributed 40-75% in the late composting period, and CH4 contributed less than 8.0%. NH3 and H2S emissions from chicken and pig manure were 4.8 times those from sheep and cow manure. Overall, the gas emissions from facultative heap composting significantly differed among the four manure types due to the significant differences in their physicochemical properties and microbial communities.

The Effect of Organic Solid Waste Compost on Soil Properties, Growth, and Yield of Swiss Chard Crop (Beta vulgaris L.)

In Dilla town and the university compound, huge amounts of biodegradable solid waste (BDSW), which include food and farm and yard wastes, are generated from student and staff cafeterias and animal farms. Improper treatment and disposal of this waste resulted in contamination of surface water and soil, air pollution, and spreading of diseases. On the other hand, soil fertility of most arable lands of Dilla Zuria woreda is highly depleted due to low levels of soil fertility management practices and inorganic-based farming. These factors make a considerable contribution to the degradation of fertile soil and reduction of yield. Thus, the management of BDSW through composting is important to minimize environmental problems and improve the soil fertility of arable lands. However, the effects of BSWC compost on plant growth and crop yield are highly variable in different studies. This study aimed to evaluate the effect of food waste compost (FWC) and leaf yard compost (LYC) at different application rates on the soil properties, growth, and yield responses of Swiss chard (Beta vulgaris L.). Food waste, leaf and yard waste, and animal dung were collected and composted in a heap-composting method. The produced organic amendments were applied to soil at an application rate of 5, 10, and 15 t/ha, respectively. Two harvesting times were considered, and at each leaf harvesting time, plant growth parameters (height, leaf number, leaf area, and fresh weight) were analyzed; after the second harvesting time, soil properties were analyzed. Results indicated that increasing rates of FWC significantly (p < 0.001) increased the plant height, leaf area, and fresh yield of Swiss chard. The application of 15 t/ha of FWC also increased SOC, TN, available P, and CEC. Food waste was recycled through composting as a soil amendment to improve soil properties and the yield of Swiss chard.

Effects of magnesium-modified biochar on antibiotic resistance genes and microbial communities in chicken manure composting

Abatement of antibiotic resistance genes (ARGs) in livestock manure by composting has attracted attention. This study investigated the effect of adding magnesium-modified biochar (MBC) on ARGs and microbial communities in chicken manure composting. Twelve genes for tetracyclines, sulfonamides, and macrolides, and mobile genetic elements were measured in the compost pile. The results showed that after 45 days of the composting, the treatment groups of MBC had longer high temperature periods, significantly higher germination indices (GI) and lower phytotoxicity. There were four major dominant phyla (Firmicutes, Actinobacteriota, Proteobacteria, and Bacteroidota) in the compost. The abundance of Firmicutes decreased significantly during the compost cooling period; tetracycline resistance genes demonstrated an extremely significant positive correlation with Firmicutes, showing a trend of the same increase and decrease with composting time; tetT, tetO, tetM, tetW, ermB, and intI2 were reduced in the MBC group; the total abundance of resistance genes in the 2% MBC addition group was 0.67 times that of the control; Proteobacteria and Chloroflexi were also significantly lower than the other treatment groups. Most ARGs were significantly associated with mobile genetic elements (MGEs); MBC can reduce the spread and diffusion of ARGs by reducing the abundance of MGEs and inhibiting horizontal gene transfer (HGT).

Advanced approaches for resource recovery from wastewater and activated sludge: A review

Due to resource scarcity, current industrial systems are switching from waste treatment, such as wastewater treatment and biomass, to resource recovery (RR). Biofuels, manure, pesticides, organic acids, and other bioproducts with a great market value can be produced from wastewater and activated sludge (AS). This will not only help in the transition from a linear economy to a circular economy, but also contribute to sustainable development. However, the cost of recovering resources from wastewater and AS to produce value-added products is quite high as compared to conventional treatment methods. In addition, most antioxidant technologies remain at the laboratory scale that have not yet reached the level at industrial scale. In order to promote the innovation of resource recovery technology, the various methods of treating wastewater and AS to produce biofuels, nutrients and energy are reviewed, including biochemistry, thermochemistry and chemical stabilization. The limitations of wastewater and AS treatment methods are prospected from biochemical characteristics, economic and environmental factors. The biofuels derived from third generation feedstocks, such as wastewater are more sustainable. Microalgal biomass are being used to produce biodiesel, bioethanol, biohydrogen, biogas, biooils, bioplastics, biofertilizers, biochar and biopesticides. New technologies and policies can promote a circular economy based on biological materials.

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.

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.

Reductions in abundances of intracellular and extracellular antibiotic resistance genes by SiO2 nanoparticles during composting driven by mobile genetic elements

Applying exogenous additives during the aerobic composting of livestock manure is effective for slowing down the spread of antibiotic resistance genes (ARGs) in the environment. Nanomaterials have received much attention because only low amounts need to be added and they have a high capacity for adsorbing pollutants. Intracellular ARGs (i-ARGs) and extracellular ARGs (e-ARGs) comprise the resistome in livestock manure but the effects of nanomaterials on the fates of these different fractions during composting are still unclear. Thus, we investigated the effects of adding SiO₂ nanoparticles (SiO₂NPs) at four levels (0 (CK), 0.5 (L), 1 (M), and 2 g/kg (H)) on i-ARGs, e-ARGs, and the bacterial community during composting. The results showed that i-ARGs represented the main fraction of ARGs during aerobic composting of swine manure, and their abundance was lowest under M. Compared with CK, M increased the removal rates of i-ARGs and e-ARGs by 17.9% and 100%, respectively. SiO₂NPs enhanced the competition between ARGs hosts and non-hosts. M optimized the bacterial community by reducing the abundances of co-hosts (Clostridium_sensu_stricto_1, Terrisporobacter, and Turicibacter) of i-ARGs and e-ARGs (by 96.0% and 99.3%, respectively) and killing 49.9% of antibiotic-resistant bacteria. Horizontal gene transfer dominated by mobile genetic elements (MGEs) played a key role in the changes in the abundances of ARGs. i-intI1 and e-Tn916/1545 were key MGEs related closely to ARGs, and the maximum decreases of 52.8% and 100%, respectively, occurred under M, which mainly explained the decreased abundances of i-ARGs and e-ARGs. Our findings provide new insights into the distribution and main drivers of i-ARGs and e-ARGs, as well as demonstrating the possibility of adding 1 g/kg SiO₂NPs to reduce the propagation of ARGs.

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

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

Metagenomic binning analyses of pig manure composting reveal potential antibiotic-degrading bacteria and their risk of antibiotic resistance genes

Antibiotic-degrading bacteria are commonly used to treat antibiotic contamination, but the antibiotic resistance genes (ARGs) they carry are often overlooked. This study used metagenomic assembly and binning analyses to explore potential antibiotic-degrading bacteria and their ARGs during pig manure composting. The result showed that 35 metagenome-assembled genomes (MAGs) mainly containing alkyl-aryl transferase and decarboxylase genes involved in the removal of antibiotics. Multidrug (124), β-lactam (67), macrolide-lincosamide-streptogramin (MLS) (64), and tetracycline (43) were the central ARG types detected in the 35 MAGs. Furthermore, the risk of ARGs was evaluated using the arg_ranker framework, and 19 MAGs were found to contain intermediate-high-risk ARGs with human-associated-enrichment, gene transferability, and host pathogenicity. Bin 34 of the genus of Geofilum had the highest ARG risk. Bin 6, Bin 11 and Bin 14 of the genus of Limnochorda, Chelatococcus and Niabella, had a lower ARG risk and were considered as potential antibiotic-degrading bacteria.

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.

Antibiotic resistant genes in the environment-exploring surveillance methods and sustainable remediation strategies of antibiotics and ARGs

Antibiotic Resistant Genes (ARGs) are an emerging environmental health threat due to the potential change in the human microbiome and selection for the emergence of antibiotic resistant bacteria. The rise of antibiotic resistant bacteria has caused a global health burden. The WHO (world health organization) predicts a rise in deaths due to antibiotic resistant infections. Since bacteria can acquire ARGs through horizontal transmission, it is important to assess the dissemination of antibioticresistant genes from anthropogenic sources. There are several sources of antibiotics, antibiotic resistant bacteria and genes in the environment. These include wastewater treatment plants, landfill leachate, agricultural, animal industrial sources and estuaries. The use of antibiotics is a worldwide practice that has resulted in the evolution of resistance to antibiotics. Our review provides a more comprehensive look into multiple sources of ARG's and antibiotics rather than one. Moreover, we focus on effective surveillance methods of ARGs and antibiotics and sustainable abiotic and biotic remediation strategies for removal and reduction of antibiotics and ARGs from both terrestrial and aquatic environments. Further, we consider the impact on public health as this problem cannot be addressed without a global transdisciplinary effort.

Phytotoxicity of farm livestock manures in facultative heap composting using the seed germination index as indicator

Static facultative heap composting of animal manure is widely used in China, but there is almost no systematic research on the phytotoxicity of the produced compost. Here, we evaluated the phytotoxic variation in compost produced by facultative heap composting of four types of animal manure (chicken manure, pig manure, sheep manure, and cattle manure) using different plant seeds (cucumber, radish, Chinese cabbage, and oilseed rape) to determine germination index (GI). The key factors that affected GI values were identified, including the dynamics of the phytotoxicity and microbial community during heap composting. Sensitivity to toxicity differed depending on the type of plant seed used. Phytotoxicity during facultative heap composting, evaluated by the GI, was in the order: chicken manure (0-6.6 %) < pig manure (14.4-90.5 %) < sheep manure (46.0-93.0 %) < cattle manure (50.2-105.8 %). Network analysis showed that the volatile fatty acid (VFA) concentration was positively correlated with Firmicutes abundance, and NH₄⁺-N was correlated with Actinobacteria, Proteobacteria, and Bacteroidetes. More bacteria were stimulated to participate in conversions of dissolved organic carbon, dissolved nitrogen, VFA, and ammonia-nitrogen (NH₄⁺-N) in sheep manure heap composting than that in other manure. The GI was most affected by VFA in chicken manure and cattle manure heap composting, while NH₄⁺-N was the main factor affecting the GI in pig manure and sheep manure compost. The dissolved carbon and nitrogen content and composition, as well as the core and proprietary microbial communities, were the primary factors that affected the succession of phytotoxic substances in facultative heap composting, which in turn affected GI values. In this study, the key pathways of livestock manure composting that affected GI and phytotoxicity were found and evaluated, which provided new insights and theoretical support for the safe use of organic fertilizer.

Simultaneous reductions in antibiotic, antibiotic resistance genes and nitrogen loss during bioaugmentation tylosin fermentation dregs co-composting

Considering the main problems presented in the typical solid wastes antibiotic fermentation dregs (AFDs) composting that the residual antibiotics could result in the propagation of antibiotic resistance genes (ARGs), and the reduced value of agronomic production caused by the ammonia gas (NH₃) emissions. This study established a bio-augmented tylosin fermentation dregs (TFDs) aerobic co-composting system to investigate the effects of a novel isolated high-efficiency strain Klebsiella sp. TN-1 inoculation on tylosin degradation, reduction in ammonia emissions, and ARG abundances during this process. Results showed that the application of strain Klebsiella sp. TN-1 extended the thermophilic stage and promoted compost maturity. Moreover, bio-enhanced co-composting with strain Klebsiella sp. TN-1 led to a totally degradation of tylosin, and removed most of ARGs, metal resistance genes (MRGs) and mobile genetic elements (MGEs), and also effectively reduce ammonia emission by 49.76 %.via increasing ammoxidation rates. Principal co-ordinates analysis further suggested that the strain Klebsiella sp. TN-1 had little influence on the bacterial community composition, while the changes of other physical and chemical properties during this process were the main reasons for the evolution of bacterial community and propagation of ARGs in the TFDs co-composting. This study suggests the potential of the bio-enhanced strain Klebsiella sp. TN-1 for antibiotic biodegradation and its application for nitrogen conservation in the AFDs co-composting process, which could decrease the risk of ARGs spreading and make compost products more secure.

Deciphering discriminative antibiotic resistance genes and pathogens in agricultural soil following chemical and organic fertilizer

Fertilizers containing rich nutrients can change the profiles of antibiotic resistant pathogens (ARPs) and antibiotic resistance genes (ARGs) in receiving soils; however, the discriminative ARGs and ARPs in agricultural soil following different fertilizer applications remain unknown. Using metagenomic sequencing combined with binning approach, the present study investigated the discriminative ARGs and ARPs under various fertilizer applications (chemical and organic fertilizer) in a 8-year field experiment. VanR, multidrug ARG transporter, vanS, ermA, and arnA were the discriminative ARGs in the chemical fertilizer group, whereas rosB, multidrug transporter, mexW, and aac(3)-I were enhanced in the organic fertilizer group. The metagenomic binning approach revealed that both fertilizer applications caused pathogen proliferation. Chemical fertilizer caused the increase in the pathogenic genus Luteimonas, and organic fertilizer facilitated the proliferation of the pathogenic genera Dokdonella and Pseudomonas. The pathogenic species Pseudomonas_H sp014836765, carrying mexW and multidrug transporter, was enriched only in the organic fertilizer group, indicating that it was a discriminative ARP in the organic fertilizer group. Our results demonstrated that fertilizer application, particularly organic fertilizer application, can facilitate the proliferation of ARGs and ARPs in the receiving soil, posing the risk of the development and spread of soil-borne ARPs.