Effect of nutritional energy regulation on the fate of antibiotic resistance genes during composting of sewage sludge

Plant-derived essential oil contributes to the reduction of multidrug resistance genes in the sludge composting process

Multidrug-resistant bacteria and multi-resistance genes in sludge have become a serious issue for public health. It is imperative to develop feasible and environmentally friendly methods of sludge composting to alleviate multidrug resistance genes. Plant-derived essential oil is an effective natural and eco-friendly antibacterial, which has great utilization in inhibiting pathogens in the agricultural industry. Nevertheless, the application of plant-derived essential oil to control pathogenic bacteria and antibiotic resistance in composting has not been reported. This study conducted a composting system by adding plant-derived essential oil i.e., oregano essential oil (OEO), to sludge composting. The findings indicated that multidrug resistance genes and priority pathogens (critical, high, and medium categories) were reduced by (17.0 ± 2.2)% and (26.5 ± 3.0)% in the addition of OEO (OH treatment) compared to control. Besides, the OH treatment changed the bacterial community and enhanced the gene sequences related to carbohydrate metabolism in compost microorganisms. Mantel test and variation partitioning analysis revealed that the target virulence factors (VFs), target mobile genetic elements (MGEs), and priority pathogens were the most important factors affecting multidrug resistance in composting. The OH treatment could significantly inhibit the target VFs, target MGEs, and priority pathogens, which were helpful for the suppression and elimination of multidrug resistance genes. These findings provide new insights into the regulation of multidrug resistance genes during sludge composting and a novel way to diminish the environmental risk of antibiotic resistance.

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.

Dynamics of antibiotic resistance genes and the association with bacterial community during pig manure composting with chitin and glucosamine addition

In modern ecological systems, the overuse and misuse of antibiotics have escalated the prevalence of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), positioning them as emerging environmental contaminants. Notably, composting serves as a sustainable method to recycle agricultural waste into nutrient-rich fertilizer while potentially reducing ARGs and MGEs. This study conducted a 47-day composting experiment using pig manure and corn straw, supplemented with chitin and N-Acetyl-D-glucosamine, to explore the impact of these additives on the dynamics of ARGs and MGEs, and to unravel the interplay between these genetic elements and microbial communities in pig manure composting. Results showed that adding 5% chitin into composting significantly postponed thermophilic phase, yet enhanced the removal efficiency of total ARGs and MGEs by over 20% compared to the control. Additionally, the addition of N-Acetyl-D-glucosamine significantly increased the abundance of tetracycline-resistant and sulfonamide-resistant genes, as well as MGEs. High-throughput sequencing revealed that N-Acetyl-D-glucosamine enhanced bacterial α-diversity, providing diverse hosts for ARGs and MGEs. Resistance mechanisms, predominantly efflux pumps and antibiotic deactivation, played a pivotal role in shaping the resistome of composting process. Co-occurrence network analysis identified the key bacterial phyla Proteobacteria, Firmicutes, Gemmatimonadota, and Myxococcota in ARGs and MGEs transformation and dissemination. Redundancy analysis indicated that physicochemical factors, particularly the carbon-to-nitrogen ratio emerged as critical variables influencing ARGs and MGEs. The findings lay a foundation for the developing microbial regulation method to reduce the risks of ARGs in animal manure composts.

Semi-permeable membrane-covered high-temperature aerobic composting: A review

Semi-permeable membrane-covered high-temperature aerobic composting (SMHC) is a suitable technology for the safe treatment and disposal of organic solid waste as well as for improving the quality of the final compost. This paper presents a comprehensive summary of the impact of semi-permeable membranes centered on expanded polytetrafluoroethylene (e-PTFE) on compost physicochemical properties, carbon and nitrogen transformations, greenhouse gas emission reduction, microbial community succession, antibiotic removal, and antibiotic resistance genes migration. It is worth noting that the semi-permeable membrane can form a micro-positive pressure environment under the membrane, promote the uniform distribution of air in the heap, reduce the proportion of anaerobic area in the heap, improve the decomposition rate of organic matter, accelerate the decomposition of compost and improve the quality of compost. In addition, this paper presents several recommendations for future research areas in the SMHC. This investigation aims to guide for implementation of semi-permeable membranes in high-temperature aerobic fermentation processes by systematically compiling the latest research progress on SMHC.

Co-exposure of microplastics and sulfamethoxazole propagated antibiotic resistance genes in sediments by regulating the microbial carbon metabolism

The concerns on the carriers of microplastics (MPs) on co-existing pollutants in aquatic environments are sharply rising in recent years. However, little is known about their interactions on the colonization of microbiota, especially for the spread of pathogens and antibiotic resistance genes (ARGs). Therefore, this study aimed to investigate the influences on the propagation of ARGs in sediments by the co-exposure of different MPs and sulfamethoxazole (SMX). The results showed that the presence of MPs significantly enhanced the contents of total organic carbon, while having no effects on the removal of SMX in sediments. Exposure to SMX and MPs obviously activated the microbial carbon utilization capacities based on the BIOLOG method. The propagation of ARGs in sediments was activated by SMX, which was further promoted by the presence of polylactic acid (PLA) MPs, but significantly lowered by the co-exposed polyethylene (PE) MPs. This apparent difference may be attributed to the distinct influence on the antibiotic efflux pumps of two MPs. Moreover, the propagation of ARGs may be also dominated by microbial carbon metabolism in sediments, especially through regulating the carbon sources of carboxylic acids, carbohydrates, and amino acids. This study provides new insights into the carrier effects of MPs in sediments.

Performance of sewage sludge treatment for the removal of antibiotic resistance genes: Status and prospects

Wastewater treatment plants (WWTPs) receive wastewater containing antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs), which are predominant contributors to environmental pollution in water and soil. Of these sources, sludge is a more significant contributor than effluent. Knowing how sludge treatment affects the fate of ARGs is vital for managing the risk of these genes in both human and natural environments. This review therefore discusses the sources and transmission of ARGs in the environment and highlights the risks of ARGs in sludge. The effects of co-existing constituents (heavy metals, microplastics, etc.) on sludge and ARGs during treatment are collated to highlight the difficulty of treating sludge with complex constituents in ARGs. The effects of various sludge treatment methods on the abundances of ARGs in sludge and in soil from land application of treated sludge are discussed, pointing out that the choice of sludge treatment method should take into account various potential factors, such as soil and soil biology in subsequent land application. This review offers significant insights and explores the abundances of ARGs throughout the process of sludge treatment and disposal. Unintentional addition of antibiotic residues, heavy metals, microplastics and organic matter in sludge could significantly increase the abundance and reduce the removal efficiency of ARGs during treatment, which undoubtedly adds a barrier to the removal of ARGs from sludge treatment. The complexity of the sludge composition and the diversities of ARGs have led to the fact that no effective sludge treatment method has so far been able to completely eliminate the ecological risk of ARGs. In order to reduce risks resulting by transmission of ARGs, technical and management measures need to be implemented.

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.

Distribution and major driving elements of antibiotic resistance genes in the soil-vegetable system under microplastic stress

Microplastics (MPs) and antibiotic resistance genes (ARGs) are both enriched in soil-vegetable systems as a consequence of the prolonged use of agricultural mulches. MPs can form unique bacterial communities and provide potential hosts for ARGs. Therefore, MPs stress may promote the spread of ARGs from soil to crops. Increasing ARGs pollution in soil-vegetable system. In our research, we investigated the distribution and major driving elements of antibiotic resistance genes in the soil-vegetable system under microplastic stress. The results showed that MPs treatment decreased the relative abundance of ARGs in non-rhizosphere soil. High concentrations of MPs promoted the enrichment of tetracycline antibiotic resistance genes in rhizosphere soil. MPs treatment promoted the enrichment of ARGs and mobile genetic elements (MGEs) in lettuce tissues, and the overall abundance of ARGs in root after 0.5 %, 1 %, and 2 % (w/w, dry weight) polyethylene (PE) administration was considerably higher compared to that in the untreated group (p < 0.05). At the same time, high PE concentrations promoted the spread of sulfa ARGs from root to leaf. MPs also impacted the bacterial communities in the soil-plant system, and the changes in ARGs as well as MGEs in each part of the soil-vegetable system were significantly correlated with the bacterial diversity index (p < 0.05). Correlation analysis and network analysis showed that bacterial communities and MGEs were the main drivers of ARGs variation in soil-lettuce systems.

Spatio-temporal distribution and dynamics of antibiotic resistance genes in a water-diversion lake, China

The distribution and dynamics of antibiotic resistance genes (ARGs) in water-diversion lakes are poorly understood. In this study, two comparative in situ investigations of ARG profiles targeting water diversion (DP) and non-diversion periods (NDP) were conducted in Luoma Lake, a vital transfer node for the eastern route of the South-to-North Water Diversion Project in China. The results demonstrated significant spatiotemporal variations in ARG contamination and notable differences in the co-occurrence patterns of ARGs and bacterial communities between DP and NDP. Correlations among ARGs with the 16 S rRNA, and mobile genetic elements indicate that horizontal gene transfer (HGT) and vertical gene transfer (VGT) in NDP, but only HGT in DP, were the primary mechanisms of ARG proliferation and spread, implying that water diversion could be an essential control of the transfer pattern of ARGs in a lake environment. The null model analysis indicated that stochastic processes, with predominant driver of ecological drift in the lake mainly drove the assembly of ARGs. Partial least squares structural equation modeling was developed to analyze the causal effects of the factors in shaping ARG dynamics and identify the major driving forces in the DP and NDP.

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.

Exploring the humification process of municipal sludge in hyperthermophilic composting through metagenomic and untargeted metabolomic

Hyperthermophilic composting (HC) has been widely recognized for the advantage of high treatment efficiency for organic wastes. However, the humification process is still unclear. In this study, the humification process of HC was investigated, compared to conventional composting (CK). The results showed that the highest composting temperature, organic matter degradation rate, and humification index in HC were 92.62 °C, 23.98%, and 1.59, while those in CK were 70.23 °C, 14.49 %, and 1.04, indicating HC accelerated humification process. Moreover, the results of metagenomic and untargeted metabolomic showed that the genes and metabolisms related to carbohydrate, lipid, amino acid, fatty acid, and nucleotide were more abundant in HC. Consequently, the metabolic pathways regarding organic matter degradation and microbial reproduction were enhanced in the high temperature stage of HC, further accelerating the humification reaction in the low temperature stage. This work contributes to the comprehension of the humification mechanism in HC.

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

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

Electric Heating Promotes Sludge Composting Process: Optimization of Heating Method through Machine Learning Algorithms

Composting with electric heating has attracted extensive attention for the advantage of high treatment efficiency for sludge. However, there are challenges in investigating how electric heating affects the composting process and how to reduce its energy consumption. This study investigated the effects of different electric heating methods on composting. The highest temperature, water content reduction, organic matter reduction, and weight reduction rate in group B6 (heating in the first and second stages) were 76.00 ° C, 16.76 %, 4.90 %, and 35.45 %, respectively, indicating that electric heating promoted water evaporation and organic matter degradation. In conclusion, electric heating promoted the sludge composting process and the heating method of group B6 was optimal for composting characteristics. This work contributes to the understanding of the mechanism of electric heating promoting composting process and providing theoretical support for the engineering application of composting with electric heating.

Elucidating the role of two types of essential oils in regulating antibiotic resistance in soil

Although several approaches for reducing antibiotic resistance genes (ARGs) in soil have been proposed, the application of environmentally friendly approaches is now attracting much more attention. In the present study, two types of essential oils (EOs), namely lavender essential oil (LEO) and oregano essential oil (OEO), were selected to investigate their roles in regulating ARGs in soil. In a 28-day microcosm experiment, it was found that the different types and doses of EOs significantly changed the composition of microbial communities. The LEO treatments enriched more taxa belonging to Actinobacteria than the control, whereas the low dose of OEO reduced Actinobacteria enrichment. Besides, the control and the treatments with a high dose of LEO and OEO all significantly enriched the functional pathways related to Human Diseases, which were positively associated with ARGs. However, the low dose of these EOs helped to reduce the pathways. Because of inhibition of the functional pathways and ARG hosts, the low dose of OEO reduce the ARGs related to antibiotic efflux by 71.8% and the resistance genes to multidrug by 56.4%, but these roles did not occur in LEO treatments. These outcomes provide practical and theoretical support for the application of EOs in remediating ARG-contaminated soils.

External static magnetic field potentiates the reduction of antibiotic resistance genes during swine manure composting

Livestock and poultry manure are repositories of antibiotic resistance genes (ARGs). Accumulating evidence suggests that composting is an important way to effectively attenuate ARGs, but how to reinforce the reduction in ARGs during composting needs to be further investigated. This study explored the influence of an external static magnetic field on ARG mitigation enhancement during swine manure composting. The results showed that a total of 12 high-risk ARGs were identified. A relatively high magnetic field intensity (14.81 mT) was more effective in reducing the abundance of high-risk ARGs, and the removal rate was 20.66-100 %. It also reduced the abundance of 27.14 % of integrons, 79.44 % of insertion sequences, and 8.78 % of plasmids. Partial least squares path modeling showed that a relatively high magnetic field intensity treatment promoted the reduction in ermB by reducing the abundance of Phascolarctobacterium, Streptococcus, and insertion sequences. It also mitigated sul1 expression by reducing the abundance of Acinetobacter and integrons, and it mitigated tetM expression by decreasing Lactobacillus, Streptococcus, insertion sequences, and plasmids. These findings demonstrate that an external static magnetic field is an effective method for intensifying the reduction in ARGs, providing a feasible reference for controlling the potential ARG risk of organic waste composting.

Bioaccumulation of antibiotics and resistance genes in lettuce following cattle manure and digestate fertilization and their effects on soil and phyllosphere microbial communities

The degradation and bioaccumulation of selected antibiotics such as the sulfonamide sulfamethoxazole (SMX) and the fluoroquinolones enrofloxacin (ENR) and ciprofloxacin (CIP) were investigated in soil microcosm experiments where Lactuca sativa was grown with manure or digestate (1%) and spiked with a mixture of the three antibiotics (7.5 mg/kg each). The soil, rhizosphere and leaf phyllosphere were sampled (at 0 and 46 days) from each microcosm to analyze the antibiotic concentrations, main resistance genes (sul1, sul2, qnrS, aac-(6')-Ib-crand qepA), the intI1and tnpA mobile genetic elements and the microbial community structure.Overall results showed that SMX and CIP decreased (70-85% and 55-79%, respectively), and ENR was quite persistent during the 46-day experiment. In plant presence, CIP and ENR were partially up-taken from soil to plant. In fact the bioaccumulation factors were > 1, with higher values in manure than digestate amended soils. The most abundant gene in soil was sul2 in digestate- and aac-(6')-Ib-cr in the manure-amended microcosms. In soil, neither sulfamethoxazole-resistance (sul1 and sul2), nor fluoroquinolone-resistance (aac-(6')-Ib-cr, qepA and qnrS) gene abundances were correlated with any antibiotic concentration. On the contrary, in lettuce leaves, the aac-(6')-Ib-cr gene was the most abundant, in accordance with the fluoroquinolone bioaccumulation. Finally, digestate stimulated a higher soil microbial biodiversity, introducing and promoting more bacterial genera associated with antibiotic degradation and involved in soil fertility and decreased fluoroquinolone bioaccumulation.

Temporal dynamics of antibiotic resistant bacteria and antibiotic resistance genes in activated sludge upon exposure to starvation

The activated sludge represents a huge reservoir for antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Owing to the wastewater fluctuation, annual maintenance and storage requirement, the activated sludge in wastewater treatment plants (WWTPs) may suffer from substrate deficiency (i.e., starvation). Whereas the starvation has been confirmed to regulate the antibiotic resistance in numerous pure bacteria, its impacts on the antibiotic resistance in activated sludge remain unclear. Here, the dynamics of sulfonamide and tetracycline ARB and corresponding ARGs in three forms including intracellular ARGs (iARGs), adsorbed extracellular ARGs (aeARGs) and free extracellular ARGs (feARGs) in activated sludge upon exposure to starvation were investigated. The results showed that, among the different electron donors (i.e., carbon, nitrogen and phosphate), carbon starvation could effectively reduce the absolute abundance of ARB and aeARGs by up to 1.68 lgs and 2.62 lgs, respectively, and released a small amount of feARGs in wastewater with the maximum value of 1.1 × 10⁵ copies/mL due to the high degree of sludge cell lysis and DNA adsorption/degradation. For the different acceptor conditions (that is, alternating anaerobic-aerobic, anaerobic, anoxic and aerobic), the anaerobic-aerobic starvation obviously mitigated the absolute abundance of ARB, aeARGs and iARGs by 0.71 lgs, 3.41 lgs and 1.35 lgs, respectively, via the substantial sludge cell lysis and DNA degradation. These findings demonstrated the response patterns and mechanisms of bacterial resistance in activated sludge to starvation stress, and thus provide clues to control the risk of antibiotic resistance in WWTPs by the starvation strategy.

Preharvest Environmental and Management Drivers of Multidrug Resistance in Major Bacterial Zoonotic Pathogens in Pastured Poultry Flocks

Due to nutritional benefits and perceived humane ways of treating the animals, the demand for antibiotic-free pastured poultry chicken has continued to be steadily rise. Despite the non-usage of antibiotics in pastured poultry broiler production, antibiotic resistance (AR) is reported in zoonotic poultry pathogens. However, factors that drive multidrug resistance (MDR) in pastured poultry are not well understood. In this study, we used machine learning and deep learning approaches to predict farm management practices and physicochemical properties of feces and soil that drive MDR in zoonotic poultry pathogens. Antibiotic use in agroecosystems is known to contribute to resistance. Evaluation of the development of resistance in environments that are free of antibiotics such as the all-natural, antibiotic-free, pastured poultry production systems described here is critical to understand the background AR in the absence of any selection pressure, i.e., basal levels of resistance. We analyzed 1635 preharvest (feces and soil) samples collected from forty-two pastured poultry flocks and eleven farms in the Southeastern United States. CDC National Antimicrobial Resistance Monitoring System guidelines were used to determine antimicrobial/multidrug resistance profiles of Salmonella, Listeria, and Campylobacter. A combination of two traditional machine learning (RandomForest and XGBoost) and three deep learning (Multi-layer Perceptron, Generative Adversarial Network, and Auto-Encoder) approaches identified critical farm management practices and environmental variables that drive multidrug resistance in poultry pathogens in broiler production systems that represents background resistance. This study enumerates management practices that contribute to AR and makes recommendations to potentially mitigate multidrug resistance and the prevalence of Salmonella and Listeria in pastured poultry.

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.

Dynamics and key drivers of antibiotic resistance genes during aerobic composting amended with plant-derived and animal manure-derived biochars

Plant-derived and animal manure-derived biochars have been used to improve the quality of compost but the differences in their effects on antibiotic resistance genes (ARGs) during composting are unclear. This study selected two types of biochar (RB and PB) produced from abundant agricultural waste to be added to the compost. Adding plant-derived RB performed better in ARGs, mobile genetic elements, and human pathogenic bacteria removal during aerobic composting, whereas adding manure-derived PB even increased ARGs abundance. Vertical gene transfer was possibly the key mechanism for persistent ARGs, and easily removed ARGs were regulated by horizontal and vertical gene transfer. Adding plant-derived RB reduced the abundances of persistent ARG hosts (e.g., Pseudomonas and Longispora) and ARG-related metabolic pathways and genes. The higher nitrogen content of manure-derived PB may have promoted the proliferation of ARG hosts. Overall, adding manure-derived biochar during composting may not be the optimal option for eliminating ARGs.

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.

Preparation of spiramycin fermentation residue derived biochar for effective adsorption of spiramycin from wastewater

Spiramycin (SPI) fermentation residue (SFR) is classified as hazardous waste in China because of the residual antibiotics in it. SFR disposal in the traditional way is costly and wasteful of resources. In this study, pyrolysis method was adopted to covert SFR to biochar for SPI removal from wastewater, and the SPI adsorption performance was investigated. The results showed that the optimal pyrolysis temperature was 700 °C as the prepared biochar BC700 exhibited the highest SPI removal efficiency. The specific surface area of BC700 was 451.68 m²/g, and the maximum adsorption capacity was 147.28 mg/g. The adsorption mechanism involved electrostatic interaction, pore filling, π-π interaction, hydrogen bonding, and the participation of C-C and O-CO functional groups in the adsorption. No residual SPI was detected in BC700 indicating the detoxification of SFR was achieved. Moreover, after recycling for 5 times, the SPI removal efficiency was still higher than 80.0%. Therefore, this study could provide a promising method for SFR disposal.

Variation of Soil Microbial Community and Sterilization to Fusarium oxysporum f. sp. niveum Play Roles in Slightly Acidic Electrolyzed Water-Alleviated Watermelon Continuous Cropping Obstacle

It is critical to exploit technologies for alleviating watermelon continuous cropping obstacle which frequently occurs and results in the limiting production and economic losses of watermelon. This study aimed to explore the effects of slightly acidic electrolyzed water (SAEW) on watermelon continuous cropping obstacles. The results showed that SAEW significantly improved the growth of watermelon seedlings cultivated in continuous cropping soil and caused a mass of changes to the diversity of the soil microbial community. Compared with Con, SAEW decreased the diversity index of bacteria by 2%, 0.48%, and 3.16%, while it increased the diversity index of fungus by 5.68%, 10.78%, and 7.54% in Shannon, Chao1, and ACE index, respectively. Besides, the enrichment level of Fusarium oxysporum f. sp. niveum (FON) was remarkably downregulated by 50.2% at 14 days of SAEW treatment, which could decrease the incidence of Fusarium wilt disease. The wet and dry weights of FON mycelia in the fluid medium were depressed more than 93%, and the number of FON colonies in continuous cropping soil was reduced by 83.56% with SAEW treatment. Additionally, a strong correlation between watermelon, FON, and SAEW was presented by correlation analysis. Furthermore, the content of endogenous reactive oxygen species (ROS) was over quadruply increased by SAEW, which may contribute to the sterilizing effect of SAEW on FON. Taken together, our findings demonstrated that exogenous SAEW could alter the soil microbial diversity and decrease the accumulation of FON, which improved the growth of watermelon seedlings and finally alleviated continuous cropping obstacles of watermelon.

Metagenomic Insights Into the Changes of Antibiotic Resistance and Pathogenicity Factor Pools Upon Thermophilic Composting of Human Excreta

In times of climate change, practicing a form of sustainable, climate-resilient and productive agriculture is of primordial importance. Compost could be one form of sustainable fertilizer, which is increasing humus, water holding capacity, and nutrient contents of soils. It could thereby strengthen agriculture toward the adverse effects of climate change, especially when additionally combined with biochar. To get access to sufficient amounts of suitable materials for composting, resources, which are currently treated as waste, such as human excreta, could be a promising option. However, the safety of the produced compost regarding human pathogens, pharmaceuticals (like antibiotics) and related resistance genes must be considered. In this context, we have investigated the effect of 140- and 154-days of thermophilic composting on the hygienization of human excreta and saw dust from dry toilets together with straw and green cuttings with and without addition of biochar. Compost samples were taken at the beginning and end of the composting process and metagenomic analysis was conducted to assess the fate of antibiotic resistance genes (ARGs) and pathogenicity factors of the microbial community over composting. Potential ARGs conferring resistance to major classes of antibiotics, such as beta-lactam antibiotics, vancomycin, the MLS_B group, aminoglycosides, tetracyclines and quinolones were detected in all samples. However, relative abundance of ARGs decreased from the beginning to the end of composting. This trend was also found for genes encoding type III, type IV, and type VI secretion systems, that are involved in pathogenicity, protein effector transport into eukaryotic cells and horizontal gene transfer between bacteria, respectively. The results suggest that the occurrence of potentially pathogenic microorganisms harboring ARGs declines during thermophilic composting. Nevertheless, ARG levels did not decline below the detection limit of quantitative PCR (qPCR). Thresholds for the usage of compost regarding acceptable resistance gene levels are yet to be evaluated and defined.

Plant-scale hyperthermophilic composting of sewage sludge shifts bacterial community and promotes the removal of organic pollutants

The dissipation of toxic organic pollutants during plant-scale hyperthermophilic composting and the influence of microbial community remain unclear. The results of plant-scale hyperthermophilic composting of municipal sludge with green waste showed that the residual concentrations of polyaromatic hydrocarbons, phthalates, polybrominated diphenyl ethers were <5 mg/kg and decreased over time, with the removal percentages from 12.1% to 51.2% during seven days of composting. High-throughput sequencingreveals that hyperthermophilic composting significantly reduced the diversity (e.g., observed species, chao1 and Shannon index) of bacterial community, shifting their structure and functions. The relative abundances of dominant phyla Proteobacteria and Firmicutes declined significantly, while those of extremophilic and heat-resisting phyla Deinococcus-Thermus and Chloroflexi increased dramatically. Some genera capable of degrading organic pollutants presented stably in sludge composts. Moreover, hyperthermophilic composting enriched the bacterial functions related to degradation and metabolism of cellulose and xenobiotics pollutants, which promoted the dissipation of organic pollutants and humification.

Thermophilic Composting of Human Feces: Development of Bacterial Community Composition and Antimicrobial Resistance Gene Pool

In times of climate change, practicing sustainable, climate-resilient, and productive agriculture is of primordial importance. Compost from different resources, now treated as wastes, could be one form of sustainable fertilizer creating a resilience of agriculture to the adverse effects of climate change. However, the safety of the produced compost regarding human pathogens, pharmaceuticals, and related resistance genes must be considered. We have assessed the effect of thermophilic composting of dry toilet contents, green cuttings, and straw, with and without biochar, on fecal indicators, the bacterial community, and antibiotic resistance genes (ARGs). Mature compost samples were analyzed regarding fecal indicator organisms, revealing low levels of Escherichia coli that are in line with German regulations for fertilizers. However, one finding of Salmonella spp. exceeded the threshold value. Cultivation of bacteria from the mature compost resulted in 200 isolates with 36.5% of biosafety level 2 (BSL-2) species. The majority is known as opportunistic pathogens that likewise occur in different environments. A quarter of the isolated BSL-2 strains exhibited multiresistance to different classes of antibiotics. Molecular analysis of total DNA before and after composting revealed changes in bacterial community composition and ARGs. 16S rRNA gene amplicon sequencing showed a decline of the two most abundant phyla Proteobacteria (start: 36-48%, end: 27-30%) and Firmicutes (start: 13-33%, end: 12-16%), whereas the abundance of Chloroflexi, Gemmatimonadetes, and Planctomycetes rose. Groups containing many human pathogens decreased during composting, like Pseudomonadales, Bacilli with Bacillus spp., or Staphylococcaceae and Enterococcaceae. Gene-specific PCR showed a decline in the number of detectable ARGs from 15 before to 8 after composting. The results reveal the importance of sufficiently high temperatures lasting for a sufficiently long period during the thermophilic phase of composting for reducing Salmonella to levels matching the criteria for fertilizers. However, most severe human pathogens that were targeted by isolation conditions were not detected. Cultivation-independent analyses also indicated a decline in bacterial orders comprising many pathogenic bacteria, as well as a decrease in ARGs. In summary, thermophilic composting could be a promising approach for producing hygienically safe organic fertilizer from ecological sanitation.

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

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

Industrial Composting of Sewage Sludge: Study of the Bacteriome, Sanitation, and Antibiotic-Resistant Strains

Wastewater treatment generates a huge amount of sewage sludge, which is a source of environmental pollution. Among the alternatives for the management of this waste, industrial composting stands out as one of the most relevant. The objective of this study was to analyze the bacterial population linked to this process and to determine its effectiveness for the reduction, and even elimination, of microorganisms and pathogens present in these organic wastes. For this purpose, the bacteriome and the fecal bacteria contamination of samples from different sewage sludge industrial composting facilities were evaluated. In addition, fecal bacteria indicators and pathogens, such as Salmonella, were isolated from samples collected at key stages of the process and characterized for antibiotic resistance to macrolide, β-lactam, quinolone, and aminoglycoside families. 16S rRNA phylogeny data revealed that the process clearly evolved toward a prevalence of Firmicutes and Actinobacteria phyla, removing the fecal load. Moreover, antibiotic-resistant microorganisms present in the raw materials were reduced, since these were isolated only in the bio-oxidative phase. Therefore, industrial composting of sewage sludge results in a bio-safe final product suitable for use in a variety of applications.

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

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

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

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

Nitrogen transformation and dynamic changes in related functional genes during functional-membrane covered aerobic composting

The effects of functional membrane covering (FMC) on nitrogen transformation and related functional genes during aerobic composting were investigated by performing a comparable experiment. The FMC increased the pile temperature, promoted compost maturity, and decreased nitrogen loss. The FMC reduced NH₃ and N₂O emissions by 7.34% and 26.27%, respectively. The water film and the micro-positive pressure environment under the membrane effectively prevented NH₃ escaping. The FMC up-regulated the amoA gene copy number (promoting NH₃/NH₄⁺ oxidation). The reduction of N₂O emission by the FMC was mainly related to denitrifying genes (nirK, nirS, and nosZ). The FMC down-regulated the nirK and nirS gene copy numbers, but up-regulated the nosZ gene copy number. Pearson correlation analysis indicated that the functional membrane characteristics and differences between the composting pile environments caused by the FMC significantly affected the nitrogen forms and the related functional genes. The FMC strongly decreased nitrogen emissions and therefore conserved nitrogen.

Dynamics of Diversity and Abundance of Sulfonamide Resistant Bacteria in a Silt Loam Soil Fertilized by Compost

Although composting is effective in deactivating antibiotic substances in manure, the influence of compost fertilization on the occurrence and dissemination of antibiotic resistance in arable soils remains to be controversial. Herein, the abundance and diversity of two sulfonamide resistance genes (sul1 and sul2) in soil fertilized by compost spiked with two concentrations of sulfadiazine (1 and 10 mg kg⁻¹) were studied intensively by qPCR and high throughput sequencing based on a two-month microcosm experiment. The concentration of sulfadiazine decreased rapidly after spiking from 25% at Day 1 to less than 2.7% at Day 60. Relative abundance of both sul1 and sul2 were significantly higher in soil amended with compost than the non-amended control at Day 1 and slightly decreased with incubation time except for sul2 in the S10 treatment. Soil bacterial communities were transiently shifted by compost fertilization regardless of the presence of sulfadiazine. Relative abundance of genera in three hubs positively interlinked with sul1 and sul2 were significantly higher in compost treated soil than the control at Day 1, 7 and 21, but not at Day 60. High throughput sequencing analyses revealed that most detected (>67% in relative abundance) sul1 and sul2 genotypes sharing >99% similarity with those found in gammaproteobacterial pathogens frequently were commonly present in compost and soil. These results indicated that compost fertilization might increase the abundance rather than diversity of sulfadiazine-resistant populations in soil, which may be facilitated by the presence of sulfadiazine.

Enhanced removal of antibiotic resistance genes and mobile genetic elements during swine manure composting inoculated with mature compost

Livestock manure is a major source of antibiotic resistance genes (ARGs) that enter the environment. This study assessed the effects of inoculation with mature compost (MC) on the fates of ARGs and the bacterial community during swine manure composting. The results showed that MC prolonged the thermophilic period and promoted the decomposition of organic matter, which was due to the rapid growth and reproduction of thermophilic bacteria (Bacillus, Thermobifida, and Thermobacillus). MC significantly reduced the relative abundances of ARGs (1.02 logs) and mobile genetic elements (MGEs) (1.70 logs) after composting, especially sulfanilamide resistance genes. The total ARGs removal rate was 1.11 times higher in MC than the control. Redundancy analysis and structural equation modeling showed that horizontal gene transfer mediated by MGEs (ISCR1 and intI1) was the main direct factor related to the changes in ARGs during composting, whereas the C/N ratio and pH were the two most important indirect factors. Network analysis showed that members of Firmicutes comprising Romboutsia, Clostridisensu_stricto_1, and Terrisporobacter were the main bacterial hosts of ARGs and MGEs. MC reduced the risk of ARGs transmission by decreasing the abundances of bacterial hosts. Thus, MC is a promising strategy for reducing the proliferation risk of ARGs.

Occurrence and dissipation mechanism of organic pollutants during the composting of sewage sludge: A critical review

Sewage sludge contains various classes of organic pollutants, limiting its land application. Sludge composting can effectively remove some organic pollutants. This review summarizesrecent researches on concentration changes and dissipation of different organic pollutants including persistent organic pollutants during sludge composting, and discusses their dissipation pathways and the current understanding on dissipation mechanism. Some organic pollutants like PAHs and phthalates were removed mainly through biodegradation or mineralization, and their dissipation percentages were higher than those of PCDD/Fs and PCBs. Nevertheless, some recalcitrant organic pollutants could be sequestrated in organic fractions of sludge mixtures, and their levels and ARG abundance even increased after sludge composting in some studies, posing potential risks for land application. This review demonstrated that microbial community and their corresponding degradation for organic pollutants were influenced by different pollutants, bulking agents, composting methods and processes. Further research perspectives on removing organic pollutants during sludge composting were highlighted.

Does lipid stress affect performance, fate of antibiotic resistance genes and microbial dynamics during anaerobic digestion of food waste?

The dissemination of antibiotic resistance genes (ARGs) in food waste (FW) disposal can pose severe threats to public health. Lipid is a primary composition in FW, while whether lipid stress can affect ARGs dynamics during anaerobic digestion (AD) process of FW is uncertain. This study focused on the impacts of lipid stress on methane production, fate of ARGs and its microbial mechanisms during AD of FW. Results showed that high lipid content increased methane yield but prolonged hydrolysis and lag time of methane production compared to AD of FW without oil. Moreover, variations of ARGs were more susceptible to lipid stress. Lipid stress could facilitate the reduction of total ARGs abundances compared to the group without oil, particularly restraining the proliferation of sul1, aadA1 and mefA in AD systems (P < 0.05). Mantel test suggested that integrons (intl1 and intl2) were significantly correlated with all detected ARGs (r: 0.33, P < 0.05), indicating that horizontal gene transfer mediated by integrons could be the driving force on ARGs dissemination. Network analysis suggested that Firmicutes, Bacteroidetes, Synergistetes and Proteobacteria were the main potential hosts of ARGs. In addition, under the lipid stress, the reduction of host bacteria was responsible for the elimination of several specific ARGs, thereby affecting ARGs profiles. These findings firstly deciphered ARGs dynamics and their driving factors responding to lipid stress during anaerobic biological treatment of FW.

Investigation on the treatment effect of slope wetland on pollutants under different hydraulic retention times

This work was aimed at investigating the feasibility of the slope wetland system (SWs) for improving the polluted river water. According to the characteristics of polluted river water with different hydraulic retention time (HRT) changes, a field simulation device was set up. In this experiment, a SWs simulation device was set up to study pollutant removal of SWs under different hydraulic conditions. It was found that the effect of mixed fillers (zeolite and ceramsite) as the bed was better than that of the gravel fillers as the bed. The improvement of each treatment index was about 5% (P < 0.05). When HRT = 5 days, the removal rate of chemical oxygen demand (COD) was 28.02%, total nitrogen (TN) was 32.99%, ammonia nitrogen (NH₃-N) was 32.49%, and total phosphorus (TP) was 38.15%. At the same time, it was found that the characteristic moderate extension of HRT is conducive to the removal of pollutants in SWs. The growth of plants in the environment of the gravel matrix was worse than that of mixed fillers (zeolite and ceramsite). It was found that physical adsorption was the main form of pollution removal on the SWs fillers by Fourier infrared spectrum (FTIR) analysis. Based on the analysis of the microbial community in the packing of the device, it is indicated that the enrichment of microorganisms appeared during the experiment, forming the dominant bacteria against the polluted river water.

Alleviating soil degradation caused by watermelon continuous cropping obstacle: Application of urban waste compost

Soil degradation caused by watermelon continuous cropping obstacle is a serious problem in China. Compost, as a soil conditioner, has great potential in improving soil degradation. In order to explore how compost affects the soil quality under continuous cropping obstacle, associations among soil chemical characteristics, microbial community structures and agronomic variables were analyzed and compared. Results showed that soil pH, available potassium, alkali-hydrolyzable nitrogen and organic matter changed significantly after using maize straw compost and sludge compost, which indicated the feasibility of composts as soil remediations. This is also reflected on the significant changes of soil microbial community. Mizugakiibacter, as the main reason of watermelon continuous cropping obstacle, decreased significantly after using compost products. It also showed a negative connection with most chemical characteristics. Rhodanobacter and Galbibacter increased significantly after using compost products, which were positively related to most chemical characteristics. The increase of them was helpful to reduce Mizugakiibacter. Beneficial bacteria were positively related to beneficial fungi (Chaetomium and Chrysosporium). The increase of them and the decrease of Verticillium also helped to improve microbial community structure. The results indicated that compost as a useful and inexpensive technique could alleviate soil degradation caused by watermelon continuous cropping obstacle.

Changes in the characteristics of dissolved organic matter during sludge treatment: A critical review

Dissolved organic matter (DOM) of sludge is a heterogeneous mixture of high to low molecular weight organic substances which is including proteinaceous compounds, carbohydrates, humic substances, lipids, lignins, organic acids, organic micropollutants and other biological derived substances generated during wastewater treatment. This paper reviews definition, composition, quantification, and transformation of DOM during different sludge treatments, and the complex interplay of DOM with microbial communities. In anaerobic digestion, anaerobic digestion-refractory organic matter, particularly compounds showing polycyclic steroid-like, alkane and aromatic structures can be generated after pretreatment. During dewatering, the DOM fraction of low molecular weight proteins (< 20,000 Dalton) is the key parameter deteriorating sludge dewaterability. During composting, decomposition and polymerization of DOM occur, followed by the formation of humic substances. During landfill treatment, the composition of DOM, particularly humic substances, are related with leachate quality. Finally, suggestions are proposed for a better understanding of the transformation and degradation of DOM during sludge treatment. Future work in sludge studies needs the establishment and implementation of definitions for sample handling and the standardization of DOM methods for analysis, including sample preparation and fractionation, and data integration. A more detailed knowledge of DOM in sludge facilitates the operation and optimization of sludge treatment technologies.

Insights into factors driving the transmission of antibiotic resistance from sludge compost-amended soil to vegetables under cadmium stress

Sludge compost is often used as a fertilizer for crops, although it might be enriched with antibiotic resistance genes (ARGs) and heavy metals that cannot be removed through composting. A robust understanding of the factors affecting the transmission of ARGs to vegetables grown in soils treated with sludge products is lacking. In this study, target ARGs in the bulk and rhizosphere soils and endophytes of shallots under heavy metal stress (i.e., Cd) were assessed, and the factors driving the transmission of ARGs were identified. Cd stress resulted in an increase in the relative abundances of target ARGs in the bulk and rhizosphere soils and endophytes. The driving factors were different in soils and plants under different degrees of Cd stress. The fungal community composition was the main driving factor of ARG variation in both bulk and rhizosphere soils. Moreover, endophytic bacteria played a crucial role in transferring ARGs to plants. Higher Cd stress promoted the transfer of most target ARGs from the below-ground plant parts to the above-ground parts. These findings indicate that application of sludge contaminated with heavy metals, such as Cd, can facilitate the dissemination of ARGs into vegetables, which must be considered while assessing the risks to public health.