Response of antibiotic resistance genes abundance by graphene oxide during the anaerobic digestion of swine manure with copper pollution

Antibiotic resistance genes in anaerobic digestion: Unresolved challenges and potential solutions

Antimicrobial resistance (AMR) threatens public health, necessitating urgent efforts to mitigate the global impact of antibiotic resistance genes (ARGs). Anaerobic digestion (AD), known for volatile solid reduction and energy generation, also presents a feasible approach for the removal of ARGs. This review encapsulates the existing understanding of ARGs and antibiotic-resistant bacteria (ARB) during the AD process, highlighting unresolved challenges pertaining to their detection and quantification. The questions raised and discussed include: Do current ARGs detection methods meet qualitative and quantitative requirements? How can we conduct risk assessments of ARGs? What happens to ARGs when they come into co-exposure with other emerging pollutants? How can the application of internal standards bolster the reliability of the AD resistome study? What are the potential future research directions that could enhance ARG elimination? Investigating these subjects will assist in shaping more efficient management strategies that employ AD for effective ARG control.

SiO2 nanoparticles can enhance nitrogen retention and reduce copper resistance genes during aerobic composting of swine manure

SiO2 nanoparticles (SiO2 NPs) are low-cost, environmentally friendly materials with significant potential to remove pollutants from complex environments. In this study, SiO2 NPs were used for the first time as an additive in aerobic composting to enhance nitrogen retention and reduce the expression of copper resistance genes. The addition of 0.5 g kg-1 SiO2 NPs effectively reduced nitrogen loss by 72.33 % by decreasing denitrification genes (nosZ, nirK, and napA) and increasing nitrogen fixation gene (nifH). The dominant factors affecting nitrification and denitrification genes were Firmicutes and C/N ratio. Additionally, SiO2 NPs decreased copper resistance genes by 28.96 % - 37.52 % in compost products. Copper resistance genes decreased most in the treatment with 0.5 g kg-1 SiO2 NPs. In summary, 0.5 g kg-1 SiO2 NPs have the potential to reduce copper resistance genes and enhance nitrogen retention during aerobic composting, which may be used to improve compost quality.

Meta-analysis of wastewater microbiome for antibiotic resistance profiling

The microbial composition and stress molecules are main drivers influencing the development and spread of antibiotic resistance bacteria (ARBs) and genes (ARGs) in the environment. A reliable and rapid method for identifying associations between microbiome composition and resistome remains challenging. In the present study, secondary metagenome data of sewage and hospital wastewaters were assessed for differential taxonomic and ARG profiling. Subsequently, Random Forest (RF)-based ML models were used to predict ARG profiles based on taxonomic composition and model validation on hospital wastewaters. Total ARG abundance was significantly higher in hospital wastewaters (15 ppm) than sewage (5 ppm), while the resistance towards methicillin, carbapenem, and fluoroquinolone were predominant. Although, Pseudomonas constituted major fraction, Streptomyces, Enterobacter, and Klebsiella were characteristic of hospital wastewaters. Prediction modeling showed that the relative abundance of pathogenic genera Escherichia, Vibrio, and Pseudomonas contributed most towards variations in total ARG count. Moreover, the model was able to identify host-specific patterns for contributing taxa and related ARGs with >90% accuracy in predicting the ARG subtype abundance. More than >80% accuracy was obtained for hospital wastewaters, demonstrating that the model can be validly extrapolated to different types of wastewater systems. Findings from the study showed that the ML approach could identify ARG profile based on bacterial composition including 16S rDNA amplicon data, and can serve as a viable alternative to metagenomic binning for identification of potential hosts of ARGs. Overall, this study demonstrates the promising application of ML techniques for predicting the spread of ARGs and provides guidance for early warning of ARBs emergence.

High-throughput profiling the effects of zinc on antibiotic resistance genes in the anaerobic digestion of swine manure

The problem of antibiotic resistance genes (ARGs) caused by heavy metals has attracted extensive attention of human beings. Zn, a widely used feed additive, has a very high residue in swine manure, but the distribution characteristics of ARGs imposed by Zn in anaerobic digestion (AD) products are not clear. In this study, the behaviour of mobile genetic elements (MGEs), bacterial community, and their association with ARGs were determined in the presence of 125 and 1250 mg L-1 Zn in AD system of swine manure. Zn-treated enriched the abundance of ARGs, and produced some new genotypes that were not detected in CK treatment. In addition, low concentration of Zn significantly increased the relative abundance of ARGs, as compared to higher Zn and CK group. Correspondingly, the abundances of most top30 genus were highest in ZnL (125 mg L-1 Zn), followed by CK and ZnH (1250 mg L-1 Zn). Notably, network analysis showed that the relationship between ARGs and MGEs is closer than that ARGs and bacteria, suggesting that ARGs increased in Zn-treated, especially low level Zn, may be due to the amplification transfer of ARGs among varied microorganisms by horizontal transfer with MGEs. Therefore, strengthen the management of in livestock manure is crucial to control the spread of ARGs in organic fertilizers.

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

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

A systematic review of antibiotic resistance driven by metal-based nanoparticles: Mechanisms and a call for risk mitigation

Elevations in antibiotic resistance genes (ARGs) are due not only to the antibiotic burden, but also to numerous environmental pressures (e.g., pesticides, metal ions, or psychotropic pharmaceuticals), which have led to an international public health emergency. Metal-based nanoparticles (MNPs) poison bacteria while propelling nanoresistance at ambient or sub-lethal concentrations, acting as a wide spectrum germicidal agent. Awareness of MNPs driven antibiotic resistance has created a surge of investigation into the molecule mechanisms of evolving and spreading environmental antibiotic resistome. Co-occurrence of MNPs resistance and antibiotic resistance emerge in environmental pathogens and benign microbes may entail a crucial outcome for human health. In this review we expound on the systematic mechanism of ARGs proliferation under the stress of MNPs, including reactive oxygen species (ROS) induced mutation, horizontal gene transfer (HGT) relevant genes regulation, nano-property, quorum sensing, and biofilm formation and highlighting on the momentous contribution of nanoparticle released ion. As antibiotic resistance pattern alteration is closely knit with the mediate activation of nanoparticle in water, soil, manure, or sludge habitats, we have proposed a virulence and evolution based antibiotic resistance risk assessment strategy for MNP contaminated areas and discussed practicable approaches that call for risk management in critical environmental compartments.

Tracing the transfer characteristics of antibiotic resistance genes from swine manure to biogas residue and then to soil

Based on laboratory simulation experiments and metagenomic analysis, this study tracked the transmission of antibiotic resistance genes (ARGs) from swine manure (SM) to biogas residue and then to soil (biogas residue as organic fertilizer (OF) application). ARGs were abundant in SM and they were assigned to 11 categories of antibiotics. Among the 383 ARG subtypes in SM, 43 % ARG subtypes were absent after anaerobic digestion (AD), which avoided the transfer of these ARGs from SM to soil. Furthermore, 9 % of the ARG subtypes in SM were introduced into soil after amendment with OF. Moreover, 43 % of the ARG subtypes in SM were present in OF and soil, and their abundances increased slightly in the soil amended with OF. The bacterial community in the soil treated with OF was restored to its original state within 60 to 90 days, probably because the abundances of ARGs were elevated but not significantly in the soil. Network analysis identified 31 potential co-host bacteria of ARGs based on the relationships between the bacteria community members, where they mainly belonged to Firmicutes, followed by Bacteroidetes, Actinobacteria, and Proteobacteria. This study provides a basis for objectively evaluating pollution by ARGs in livestock manure for agricultural use.

Gut microbiota bridges dietary nutrients and host immunity

Dietary nutrients and the gut microbiota are increasingly recognized to cross-regulate and entrain each other, and thus affect host health and immune-mediated diseases. Here, we systematically review the current understanding linking dietary nutrients to gut microbiota-host immune interactions, emphasizing how this axis might influence host immunity in health and diseases. Of relevance, we highlight that the implications of gut microbiota-targeted dietary intervention could be harnessed in orchestrating a spectrum of immune-associated diseases.

Stimulating anaerobic digestion to degrade recalcitrant organic pollutants: Potential role of conductive materials-led direct interspecies electron transfer

This review aims to provide a comprehensive understanding of the potential of CMs-dominated DIET in the degradation of recalcitrant organic pollutants in AD. The review covers the mechanisms and efficiencies of recalcitrant organic pollutant degradation by CMs-dominated DIET, the comparison of degradation pathways between DIET and chemical treatment, recent insights on DIET-enhanced degradation, and the evaluation of the potential and future development of CMs-dominated DIET. The review emphasizes the importance of coupled syntrophic microorganisms, electron flux, and physicochemical properties of CMs in enhancing the degradation performance of AD. Additionally, it highlights the advantages of DIET-led syntrophic metabolism over traditional oxidation technologies in terms of environmental friendliness and efficiency. Finally, the review acknowledges the potential risks associated with introducing CMs into AD systems and provides guidance for waste treatment and energy recovery.

Nano-Selenium inhibited antibiotic resistance genes and virulence factors by suppressing bacterial selenocompound metabolism and chemotaxis pathways in animal manure

Numerous antibiotic resistance genes (ARGs) and virulence factors (VFs) found in animal manure pose significant risks to human health. However, the effects of graphene sodium selenite (GSSe), a novel chemical nano-Selenium, and biological nano-Selenium (BNSSe), a new bioaugmentation nano-Se, on bacterial Se metabolism, chemotaxis, ARGs, and VFs in animal manure remain unknown. In this study, we investigated the effects of GSSe and BNSSe on ARGs and VFs expression in broiler manure using high-throughput sequencing. Results showed that BNSSe reduced Se pressure during anaerobic fermentation by inhibiting bacterial selenocompound metabolism pathways, thereby lowering manure Selenium pollution. Additionally, the expression levels of ARGs and VFs were lower in the BNSSe group compared to the Sodium Selenite and GSSe groups, as BNSSe inhibited bacterial chemotaxis pathways. Co-occurrence network analysis identified ARGs and VFs within the following phyla Bacteroidetes (genera Butyricimonas, Odoribacter, Paraprevotella, and Rikenella), Firmicutes (genera Lactobacillus, Candidatus_Borkfalkia, Merdimonas, Oscillibacter, Intestinimonas, and Megamonas), and Proteobacteria (genera Desulfovibrio). The expression and abundance of ARGs and VFs genes were found to be associated with ARGs-VFs coexistence. Moreover, BNSSe disruption of bacterial selenocompound metabolism and chemotaxis pathways resulted in less frequent transfer of ARGs and VFs. These findings indicate that BNSSe can reduce ARGs and VFs expression in animal manure by suppressing bacterial selenocompound metabolism and chemotaxis pathways.

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

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

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

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

Graphene oxide addition to anaerobic digestion of waste activated sludge: Impact on methane production and removal of emerging contaminants

The effect of graphene oxide on the anaerobic digestion of waste activated sludge was investigated at two graphene oxide concentrations (0.025 and 0.075 g graphene oxide per g volatile solids) using biochemical methane potential tests. The occurrence of 36 pharmaceuticals was monitored in the solid and liquid phases before and after the anaerobic treatment. The addition of graphene oxide improved the removal of most pharmaceuticals detected, even those that are considered persistent to biological degradation, such as azithromycin, carbamazepine, and diclofenac. No significant differences were observed in the final specific methane production without graphene oxide and with the lowest graphene oxide concentration, yet the highest graphene oxide concentration partially inhibited methane production. The relative abundance of antibiotic resistance genes was not affected by the graphene oxide addition. Finally, significant changes in the microbial community including bacteria and archaea were detected with graphene oxide addition.

A review of the impact of conductive materials on antibiotic resistance genes during the anaerobic digestion of sewage sludge and animal manure

The urgent need to reduce the environmental burden of antibiotic resistance genes (ARGs) has become even more apparent as concerted efforts are made globally to tackle the dissemination of antimicrobial resistance. Concerning levels of ARGs abound in sewage sludge and animal manure, and their inadequate attenuation during conventional anaerobic digestion (AD) compromises the safety of the digestate, a nutrient-rich by-product of AD commonly recycled to agricultural land for improvement of soil quality. Exogenous ARGs introduced into the natural environment via the land application of digestate can be transferred from innocuous environmental bacteria to clinically relevant bacteria by horizontal gene transfer (HGT) and may eventually reach humans through food, water, and air. This review, therefore, discusses the prospects of using carbon- and iron-based conductive materials (CMs) as additives to mitigate the proliferation of ARGs during the AD of sewage sludge and animal manure. The review spotlights the core mechanisms underpinning the influence of CMs on the resistome profile, the steps to maximize ARG attenuation using CMs, and the current knowledge gaps. Data and information gathered indicate that CMs can profoundly reduce the abundance of ARGs in the digestate by easing selective pressure on ARGs, altering microbial community structure, and diminishing HGT.

Effect of graphene and graphene oxide on antibiotic resistance genes during copper-contained swine manure anaerobic digestion

Copper is an important selectors for antibiotic resistance genes (ARGs) transfer because of metal-antibiotic cross-resistance and/or coresistance. Due to carbon-based materials' good adsorption capacity for heavy metals, graphene and graphene oxide have great potential to reduce ARGs abundance in the environment with copper pollution. To figure out the mechanics, this study investigated the effects of graphene and graphene oxide on the succession of ARGs, mobile genetic elements (MGEs), heavy metal resistance genes (HMRGs), and bacterial communities during copper-contained swine manure anaerobic digestion. Results showed that graphene and graphene oxide could reduce ARGs abundance in varying degrees with the anaerobic reactors that contained a higher concentration of copper. Nevertheless, graphene decreased the abundance of ARGs more effectively than graphene oxide. Phylum-level bacteria such as Firmicutes, Bacteroidetes, Spirochaetes, and Verrucomicrobiaat were significantly positively correlated with most ARGs. Network and redundancy analyses demonstrated that alterations in the bacterial community are one of the main factors leading to the changes in ARGs. Firmicutes, Bacteroidetes, and Spirochaetes were enriched lower in graphene reactor than graphene oxide in anaerobic digestion products, which may be the main reason that graphene is superior to graphene oxide in reduced ARGs abundance. Additionally, ARGs were close to HMRGs than MGEs in the treatments with graphene, the opposite in graphene oxide reactors. Therefore, we speculate that the reduction of HMRGs in graphene may contribute to the result that graphene is superior to graphene oxide in reduced ARGs abundance in anaerobic digestion.

Transmission of antibiotic resistance genes through mobile genetic elements in Acinetobacter baumannii and gene-transfer prevention

Antibiotic resistance is a major global public health concern. Acinetobacter baumannii is a nosocomial pathogen that has emerged as a global threat because of its high levels of resistance to many antibiotics, particularly those considered as last-resort antibiotics, such as carbapenems. Mobile genetic elements (MGEs) play an important role in the dissemination and expression of antibiotic resistance genes (ARGs), including the mobilization of ARGs within and between species. We conducted an in-depth, systematic investigation of the occurrence and dissemination of ARGs associated with MGEs in A. baumannii. We focused on a cross-sectoral approach that integrates humans, animals, and environments. Four strategies for the prevention of ARG dissemination through MGEs have been discussed: prevention of airborne transmission of ARGs using semi-permeable membrane-covered thermophilic composting; application of nanomaterials for the removal of emerging pollutants (antibiotics) and pathogens; tertiary treatment technologies for controlling ARGs and MGEs in wastewater treatment plants; and the removal of ARGs by advanced oxidation techniques. This review contemplates and evaluates the major drivers involved in the transmission of ARGs from the cross-sectoral perspective and ARG-transfer prevention processes.

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

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

Seasonal variation in antibiotic resistance genes and bacterial phenotypes in swine wastewater during three-chamber anaerobic pond treatment

Antibiotic resistance is a global public health concern. Antibiotic usage in pigs makes swine wastewater (SW) a reservoir for antibiotic resistance genes (ARGs). SW is usually stored and treated in a three-chamber anaerobic pond (3-CAP) in medium and small pig farms in northern China. However, the yet unexplored presence of ARGs in SW during 3-CAP treatment may result in ARGs spreading into the environment if farmers apply SW to farmland as a liquid organic fertilizer. This study investigated the profiles of and changes in ARGs in SW during its treatment in 3-CAP over four seasons and analyzed the correlation between ARGs and bacterial phenotypes, along with the physicochemical parameters of the water. The results revealed that ARG abundance decreased considerably after 3-CAP treatment in April (47%), October (47%), and December (62%) but increased in May (43%) and August (73%). The ARG copies in the influent and other SW samples increased significantly from 10⁷ copies/mL in April to 10⁹ copies/mL in October and were maintained in December. The increase in ARG abundance was not as rapid as the growth of the bacterial population, resulting in lower relative abundance in October and December. Bacterial communities possessed more sul1 and tetM genes, which were also positively correlated with mobile genetic elements. After the 3-CAP treatment, 16% of antibiotics and 60% of heavy metals were removed, and both had a weak correlation with ARGs. Predicted phenotypes showed that gram-positive (G⁺) and gram-negative (G^-) bacteria have different capacities for carrying ARGs. G⁺ bacteria carry more ARGs than G^- bacteria. This study revealed the persistence of ARGs in SW after 3-CAP treatment over different seasons. Applying SW in the proper month will mitigate ARG dissemination to the environment.

Comparison of coated and uncoated trace elements on growth performance, apparent digestibility, intestinal development and microbial diversity in growing sheep

The suitable supplement pattern affects the digestion and absorption of trace minerals by ruminants. This study aimed to compare the effects of coated and uncoated trace elements on growth performance, apparent digestibility, intestinal development and microbial diversity in growing sheep. Thirty 4-month-old male Yunnan semi-fine wool sheep were randomly assigned to three treatments (n = 10) and fed with following diets: basal diet without adding exogenous trace elements (CON), basal diet plus 400 mg/kg coated trace elements (CTE, the rumen passage rate was 65.87%) and basal diet plus an equal amount of trace elements in uncoated form (UTE). Compared with the CON group, the average daily weight gain and apparent digestibility of crude protein were higher (P < 0.05) in the CTE and UTE groups, while there was no difference between the CTE and UTE groups. The serum levels of selenium, iodine and cobalt were higher (P < 0.05) in the CTE and UTE groups than those in the CON group, the serum levels of selenium and cobalt were higher (P < 0.05) in the CTE group than those in the UTE group. Compared with the CON and UTE groups, the villus height and the ratio of villus height to crypt depth in duodenum and ileum were higher (P < 0.05) in the CTE groups. The addition of trace minerals in diet upregulated most of the relative gene expression of Ocludin, Claudin-1, Claudin-2, ZO-1, and ZO-2 in the duodenum and jejunum and metal ion transporters (FPN1 and ZNT4) in small intestine. The relative abundance of the genera Christensenellaceae R-7 group, Ruminococcus 1, Lachnospiraceae NK3A20 group, and Ruminococcaceae in ileum, and Ruminococcaceae UCG-014 and Lactobacillus in colon was higher in the CTE group that in the CON group. These results indicated that dietary trace mineral addition improved the growth performance and intestinal development, and altered the structure of intestinal bacteria in growing sheep. Compared to uncoated form, offering trace mineral elements to sheep in coated form had a higher absorption efficiency, however, had little effect on improving growth performance of growing sheep.

Para-chloro-meta-xylenol reshaped the fates of antibiotic resistance genes during sludge fermentation: Insights of cell membrane permeability, bacterial structure and biological pathways

The occurrence of para-chloro-meta-xylenol (PCMX, as largely consumed antimicrobial chemicals) in waste activated sludge (WAS) would pose environmental risks for WAS utilization. This study revealed that PCMX principally prompted the abundances and diversity of antibiotic resistance genes (ARGs), particularly for the multidrug- genes (i.e., acrB and mexW), and reshaped the resistance mechanism categories during WAS fermentation process. The genotype and phenotype results indicated that PCMX upregulated abundances of transposase and increased cell permeability via disrupting WAS structure, which further facilitated the horizontal transfer of ARGs. The network and correlation analysis among ARGs, mobile genetic elements (MGEs) and genera (i.e., Sphingopyxis and Pseudoxanthomonas) verified that PCMX enriched the potential ARGs hosts associated with multidrug resistance mechanism. Also, PCMX upregulated the genes involved in ARGs-associated metabolic pathways, such as two-component (i.e., phoP and vcaM) and quorum sensing systems (i.e., lasR and cciR), which determined the ARGs proliferation via multidrug efflux pump and outer membrane proteins, and facilitated the recognition between ARGs hosts. Variance partitioning analysis (VPA) implied that the shift of microbial community contributed predominantly to the dissemination of ARGs. These findings unveiled the environmental behaviors and risks of exogenous pollutants in WAS with insightful understanding, which could guide the WAS utilization for resource recovery.

Investigating changes in the characteristics of antibiotic resistance genes at different reaction stages of high solid anaerobic digestion with pig manure

Contamination of antibiotic resistance genes (ARGs) from animals is a serious issue as they may spread to human pathogenic bacteria. The reduction of ARG contamination from livestock waste is thus essential. High solid anaerobic digestion (HSAD) is a new and effective technology although some aspects, such as change characteristics of ARGs at different reaction stages, have not been fully investigated. This study focused firstly on the variations in ARGs at different reaction stages in HSAD systems with five different starting methods: 1 natural start (the control) and 4 rapid starts by changing leachate reflux forms. The results showed that the rapid starting methods could accelerate start-up and increase biogas production by 312.5%. The starting and acidification stages showed higher microbial richness and diversity compared with the other stages. ARGs found to be reduced at acidification stage. Variation in ARGs at the starting and acidification stages was mainly driven by a combination of microbial community, mobile genetic elements (MGEs), and environmental factors; while the main contributory factors at the gas production stage were biomass and several unexplained factors. At the ending stage, the main driving factors were biomass and microbial communities. Most of the potential hosts (16/20) of the ARGs belonged to the Firmicutes phylum, which showed the lowest connections with the ARGs at the gas production stage.

Effect of sulfamethazine on anaerobic digestion of manure mediated by biochar

Antibiotic contamination from animal production and wastewater treatment process will release antibiotic resistant genes to the environment and potentially threaten human health. Meanwhile, the residual antibiotic in manure could have inactive impacts on anaerobic digestion (AD). This study explores the effect of sulfamethazine on manure AD mediated by biochar. The results show that biochar weakens the adverse effects of sulfamethazine on AD by adsorption sulfamethazine during the initial stage (0-3 days) of AD and promoting the growth of hydrolytic bacteria (especially Firmicutes and Bacteroidetes) and methanogens (especially Methanothrix and Methanosarcina). Besides, the presence of biochar improves the biogas production capacity of AD and promotes microbial diversity and community richness. Thus, the addition of biochar greatly reduces sulfamethazine and is testified to be a desirable strategy to mitigate the inhibition of sulfamethazine on AD.

Enhanced removal of antibiotic resistance genes and human bacterial pathogens during anaerobic digestion of dairy manure via addition of manure biochar

In this study, the response of antibiotic resistance genes (ARGs), mobile gene elements (intI1), and human bacterial pathogens (HBPs) to addition of manure biochar (1-10 g/L) was studied in anaerobic digestion (AD) at 20-55 °C for treating dairy manure. Twelve ARGs comprising five tetracycline resistance genes, two sulfonamide resistance genes, two macrolide resistance genes, three β-lactam antibiotic resistance genes, and intI1 were analyzed by quantitative PCR. High-throughput sequencing data were matched against a database of putative 538 HBPs. Significant removal of ARGs (except for tetO and ermB) and intI1 was observed in all the samples. Manure biochar resulted in significant removal of ARGs and HBPs; however, negative effects were also observed in some conditions. This is the first study to provide to explore the fates of ARGs and HBPs by adding manure biochar to AD.

Exploration of machine learning algorithms for predicting the changes in abundance of antibiotic resistance genes in anaerobic digestion

The land application of digestate from anaerobic digestion (AD) is considered a significant route for transmitting antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) to ecosystems. To date, efforts towards understanding complex non-linear interactions between AD operating parameters with ARG/MGE abundances rely on experimental investigations due to a lack of mechanistic models. Herein, three different machine learning (ML) algorithms, Random Forest (RF), eXtreme Gradient Boosting (XGBoost), and Artificial Neural Network (ANN), were compared for their predictive capacities in simulating ARG/MGE abundance changes during AD. The models were trained and cross-validated using experimental data collected from 33 published literature. The comparison of model performance using coefficients of determination (R²) and root mean squared errors (RMSE) indicated that ANN was more reliable than RF and XGBoost. The mode of operation (batch/semi-continuous), co-digestion of food waste and sewage sludge, and residence time were identified as the three most critical features in predicting ARG/MGE abundance changes. Moreover, the trained ANN model could simulate non-linear interactions between operational parameters and ARG/MGE abundance changes that could be interpreted intuitively based on existing knowledge. Overall, this study demonstrates that machine learning can enable a reliable predictive model that can provide a holistic optimization tool for mitigating the ARG/MGE transmission potential of AD.

Electron shuttles enhanced the removal of antibiotics and antibiotic resistance genes in anaerobic systems: A review

The environmental and epidemiological problems caused by antibiotics and antibiotic resistance genes have attracted a lot of attention. The use of electron shuttles based on enhanced extracellular electron transfer for anaerobic biological treatment to remove widespread antibiotics and antibiotic resistance genes efficiently from wastewater or organic solid waste is a promising technology. This paper reviewed the development of electron shuttles, described the mechanism of action of different electron shuttles and the application of enhanced anaerobic biotreatment with electron shuttles for the removal of antibiotics and related genes. Finally, we discussed the current issues and possible future directions of electron shuttle technology.

A critical review of process parameters influencing the fate of antibiotic resistance genes in the anaerobic digestion of organic waste

The overuse and inappropriate disposal of antibiotics raised severe public health risks worldwide. Specifically, the incomplete antibiotics metabolism in human and animal bodies contributes to the significant release of antibiotics into the natural ecosystems and the proliferation of antibiotic-resistant bacteria carrying antibiotic-resistant genes. Moreover, the organic feedstocks used for anaerobic digestion are often highly-rich in residual antibiotics and antibiotic-resistant genes. Hence, understanding their fate during anaerobic digestion has become a significant research focus recently. Previous studies demonstrated that various process parameters could considerably influence the propagation of the antibiotic-resistant genes during anaerobic digestion and their transmission via land application of digestate. This review article scrutinizes the influences of process parameters on antibiotic-resistant genes propagation in anaerobic digestion and the inherent fundamentals behind their effects. Based on the literature review, critical research gaps and challenges are summarized to guide the prospects for future studies.

Identification of factors affecting removal of antibiotic resistance genes in full-scale anaerobic digesters treating organic solid wastes

Efficiencies of removing antibiotic resistance genes (ARGs) and intI1 were explored using eight full-scale anaerobic digesters. The digesters demonstrated different characteristics on the basis of substrate types (food waste, manure or sludge); configuration (single or two-stage); temperature (psychrophilic, mesophilic or thermophilic); hydraulic retention time (HRT) (9.7-44 days); and operation mode (continuous stirred tank reactor or plug flow reactor). Digesters' configuration or operating parameters showed a greater effect on abundance of ARGs than the type of input substrate. Redundancy analysis (RDA) accounted for 85.2% of the total variances and digesters with the same configuration and operational conditions showed similar performance for removal of ARGs. The highest efficiencies of removing ARGs (99.99%) were observed in two-stage thermophilic digesters with relatively long HRTs (32 days). The lowest removal efficiency (97.93%) was observed in single-stage mesophilic with relatively short HRTs (9.7 days), likely due to vertical and horizontal gene transfer.

Insights into the associations of copper and zinc with nitrogen metabolism during manure composting with shrimp shell powder

The application of shrimp shell powder (SSP) in manure composting can promote the maturation of compost and reduce the associated environmental risk. This study investigated the response of adding SSP at different levels (CK: 0, L: 5%, M: 10%, and H: 15%) on heavy metal resistance genes (MRGs), nitrogen functional genes, enzymes, and microorganisms. SSP inhibited nitrification and denitrification via decreasing the abundances of functional genes and key enzymes related to Cu, Zn, and MRGs. The nitrate reductase and nitrous-oxide reductase in the denitrification pathway were lower under H. Phylogenetic trees indicated that Burkholderiales sp. had strong relationships with OTU396 and OTU333, with important roles in the nitrogen cycle and plant growth. Redundancy analysis and structural equation modeling showed the complex response between heavy metal and nitrogen that bio-Cu and bio-Zn had positive significantly relationships with nirK-type and amoA-type bacteria, and amoA-type bacteria might be hotspot of cueO.

Metagenomic Analysis of the Long-Term Synergistic Effects of Antibiotics on the Anaerobic Digestion of Cattle Manure

The conversion of cattle manure into biogas in anaerobic digestion (AD) processes has been gaining attention in recent years. However, antibiotic consumption continues to increase worldwide, which is why antimicrobial concentrations can be expected to rise in cattle manure and in digestate. This study examined the long-term synergistic effects of antimicrobials on the anaerobic digestion of cattle manure. The prevalence of antibiotic resistance genes (ARGs) and changes in microbial biodiversity under exposure to the tested drugs was investigated using a metagenomic approach. Methane production was analyzed in lab-scale anaerobic bioreactors. Bacteroidetes, Firmicutes, and Actinobacteria were the most abundant bacteria in the samples. The domain Archaea was represented mainly by methanogenic genera Methanothrix and Methanosarcina and the order Methanomassiliicoccales. Exposure to antibiotics inhibited the growth and development of methanogenic microorganisms in the substrate. Antibiotics also influenced the abundance and prevalence of ARGs in samples. Seventeen types of ARGs were identified and classified. Genes encoding resistance to tetracyclines, macrolide–lincosamide–streptogramin antibiotics, and aminoglycosides, as well as multi-drug resistance genes, were most abundant. Antibiotics affected homoacetogenic bacteria and methanogens, and decreased the production of CH4. However, the antibiotic-induced decrease in CH4 production was minimized in the presence of highly drug-resistant microorganisms in AD bioreactors.

New insights of anaerobic performance, antibiotic resistance gene removal, microbial community structure: applying graphite-based materials in wet anaerobic digestion

The addition of carbonaceous materials into anaerobic digestion (AD) has gained widespread attention due to their significant effects on anaerobic performance and antibiotic resistance gene (ARG) removal. This study selected graphite, graphene, and graphene oxide (GO) as additives to investigate variations in AD performance, ARG removal, microbial community diversity and structure in wet AD systems. The results indicated that the addition of graphite-based materials in wet AD systems could increase degradation of solid organic matters by 0.91%-3.41% and utilization of soluble organic fractions by 10.43%-13.67%, but could not stimulate methane production. After the addition of graphite and graphene, ARG removal rates were effectively increased to 90.85% and 94.22%, respectively. However, the total ARG removal rate was reduced to 77.46% with the addition of GO. In addition, the microbial diversity in the wet AD process was enhanced with the addition of GO only, graphite and graphene led to a reduction in it. As for bacterial community, graphite and graphene increased the abundance of Thermotogae from 43.43% to 57.42% and 58.74%, while GO increased the abundance of Firmicute from 49.90% to 56.27%. For the archaeal community, the proportion of hydrogenotrophic methanogens was improved when adding each graphite-based material; however, only GO increased Methanosaeta that was acetoclastic methanogens. Finally, methanogens were found as the ARG host, and ARGs that belong to the same subtype might exist in the same host bacteria.

Co-selective Pressure of Cadmium and Doxycycline on the Antibiotic and Heavy Metal Resistance Genes in Ditch Wetlands

Abuse of heavy metals and antibiotics results in the dissemination of metal resistance genes (MRGs) and antibiotic resistance genes (ARGs). Ditch wetlands are important sinks for heavy metals and antibiotics. The relationships between bacterial communities and MRG/ARG dissemination under dual stresses of heavy metals and antibiotics remain unclear. The responses of MRGs and ARGs to the co-selective pressure of cadmium (Cd) and doxycycline (DC) in ditch wetlands were investigated after 7-day and 84-day exposures. In ecological ditches, residual rates of Cd and DC varied from 0.4 to –5.73% and 0 to –0.61%, respectively. The greatest total relative abundance of ARGs was observed in the Cd 5 mg L^–1 + DC 50 mg L^–1 group. A significant level of DC (50 mg L^–1) significantly reduced the total relative abundances of MRGs at a concentration of 5 mg L^–1 Cd stress. Redundancy analysis indicated that Cd and DC had strong positive effects on most ARGs and MRGs after a 7-day exposure. Meanwhile, the class 1 integron gene (intI1) exhibited strong positive correlations with most ARGs and cadmium resistance genes (czcA) after an 84-day exposure. Network analysis showed that Acinetobacter and Pseudomonas were the potential dominant host genera for ARGs and MRGs, and tetracycline resistance genes (tetA), czcA, and intI1 shared the same potential host bacteria Trichococcus after an 84-day exposure.

When dewatered swine manure-derived biochar meets swine wastewater in anaerobic digestion: A win-win scenario towards highly efficient energy recovery and antibiotic resistance genes attenuation for swine manure management

This work explored the feasibility of dewatered swine manure-derived biochar (DSMB) as an additive to facilitate anaerobic digestion (AD) of swine wastewater for energy recovery and antibiotic resistance genes (ARG) attenuation enhancements. With 20 g/L DSMB assistance, the methanogenic lag time of swine wastewater was shortened by 17.4-21.1%, and the maximum CH₄ production rate increased from 40.8 mL/d to 48.3-50.5 mL/d, among which DSMB prepared under 300 °C exhibited a better performance than that prepared under 500 °C and 700 °C. Integrated analysis of DSMB electrochemical properties, microbial electron transfer system activity, and microbial community succession revealed the potential of DSMB-300 to act as redox-active electron transfer mediators between syntrophic microbes to accelerate syntrophic methanogenesis via potential direct interspecies electron transfer. Meanwhile, DSMB preparation by pyrolysis dramatically reduced ARG abundance by almost 4 logs. Adding DSMB into AD not only strengthened the attenuation efficiency of ARG in the original swine wastewater, but also effectively controlled the potential risk of horizontal gene transfer by mitigating 74.8% of the mobile gene elements abundance. Accordingly, we proposed a win-win scenario for bio-waste management in swine farms, highlighting the more advanced energy recovery and ARG attenuation compared to the current status.

The effect of carbon-based copper nanocomposites on Microcystis aeruginosa and the movability of antibiotic resistance genes in urban water

The presence of Microcystis aeruginosa (M. aeruginosa) can affect the transference of antibiotic resistance genes (ARGs), and the presence of carbon-based copper nanocomposites (CCN) can affect the growth of M. aeruginosa. However, the effect of CCN on M. aeruginosa and ARGs is not fully understood. In this study, metagenomic sequencing was employed to analyze the movability of ARGs, their potential transfer, and possible hosts in photobioreactor treating urban water. The results uggested that 20 mg/L of CCN changed the composition and abundance of microorganisms in urban water, significantly promoted the flocculation of M aeruginosa, and decreased the composing proportion of Cyanophyta sp. and M aeruginosa. The results indicated that 20 mg/L of CCN significantly decreased the absolute abundance and ARGs proportions which mediated by plasmids (32.7 %). Furthermore, the lower co-occurrence probability of ARGs and mobile genetic elements (MGEs) suggested that 20 mg/L of CCN weakened the movability potential of ARGs mediated by MGEs such as plasmids. Among the 452 metagenome-assembled genomes (MAGs), 95 MAGs belonging to 41 bacterial categories were identified as possible ARG hosts. These results will provide insights into the control of harmful cyanobacteria and the management of ARGs in urban water.

Effects of graphite, graphene, and graphene oxide on the anaerobic co-digestion of sewage sludge and food waste: Attention to methane production and the fate of antibiotic resistance genes

This study explored and compared the influence of graphite, graphene, and graphene oxide (GO) on the performance of anaerobic co-digestion fed with sewage sludge and food waste, the variations of antibiotic resistance genes (ARGs), and the evolution of microbial community. Graphene exhibited the best performance for improving methane production and organic degradation, which increased by 36.09% and 23.07% compared with control group. The experimental results showed that graphene had the greatest influence on the removal efficiency of blaOXA-1, macrolide resistance genes (ermF and ermB), and some tetracycline resistance genes (tetQ and tetX); however, the removal efficiency of sulfonamide resistance genes (sul1 and sul2), intI1, and some tetracycline resistance genes (tetM, tetO, and tetW) were highest when GO was added. Network analysis indicated that the host cells of mefA, ermB, and tetO were different from other ARG host cells; moreover, graphene controlled the horizontal transfer of ARGs between microbial communities.

Effects of chlorine disinfectants on the microbial community structure and the performance of anaerobic digestion of swine manure

The residual chlorine disinfectants (CDs) in swine slurry could negatively impact the anaerobic digestion (AD). The objective of this study was to investigate the effects of CDs on mesophilic and thermophilic AD. The results indicated that CDs exerted inhibition effects on methanogenesis at the initial stage of mesophilic AD, leading to the extension of lag time from 0.62 days for control to 0.85, 1.9, 3.8, and 5.5 days with the increasing CDs concentrations of 50, 100, 200, and 400 mg/L, respectively. Under thermophilic condition, the inhibition effects reduced significantly at the initial stage but a decrease of CMP_u at later stage was observed. The microbial analysis revealed that CDs resulted in the enrichment of chlorine-resistant bacteria (Clostridum_sensu_stricto_1) and archaea (Methanosarcina). Addition of activated carbon (AC), zero-valent iron (ZVI) and biochar (BC) was evaluated for alleviating the inhibitions of CDs and proved to be feasible strategies to alleviate the inhibited AD.

Trace metals and animal health: Interplay of the gut microbiota with iron, manganese, zinc, and copper

Metals such as iron, manganese, copper, and zinc are recognized as essential trace elements. These trace metals play critical roles in development, growth, and metabolism, participating in various metabolic processes by acting as cofactors of enzymes or providing structural support to proteins. Deficiency or toxicity of these metals can impact human and animal health, giving rise to a number of metabolic and neurological disorders. Proper breakdown, absorption, and elimination of these trace metals is a tightly regulated process that requires crosstalk between the host and these micronutrients. The gut is a complex system that serves as the interface between these components, but other factors that contribute to this delicate interaction are not well understood. The gut is home to trillions of microorganisms and microbial genes (the gut microbiome) that can regulate the metabolism and transport of micronutrients and contribute to the bioavailability of trace metals through their assimilation from food sources or by competing with the host. Furthermore, deficiency or toxicity of these metals can modulate the gut microenvironment, including microbiota, nutrient availability, stress, and immunity. Thus, understanding the role of the gut microbiota in the metabolism of manganese, iron, copper, and zinc, as well as in heavy metal deficiencies and toxicities, and vice versa, may provide insight into developing improved or alternative therapeutic strategies to address emerging health concerns. This review describes the current understanding of how the gut microbiome and trace metals interact and affect host health, particularly in pigs.

Fate of antibiotic resistance genes during high solid anaerobic digestion with pig manure: Focused on different starting modes

As an emerging technology, high solid anaerobic digestion (HSAD) was usually hampered by the long lag phase of methane production. A reasonable starting mode enabled fast startup in HSAD, which was scarcely reported. This study established 5 starting modes for HSAD with pig manure. The results showed that system T4 (biogas slurry once and then autologous leachate reflux) had the shortest lag phase. Starting modes had a total effect of 36.6% on gas production, among which 17.1% affected gas production directly and 19.5% affected it through other factors. About 12/17 of antibiotic resistance genes (ARGs) and 3 mobile genetic elements (MGEs) were effectively reduced during HSAD. System T4 had the highest microbial diversity and the largest number of unique OTUs. MGEs explained most for ARGs variation (>50%), followed by microbial community. Most of the potential host genera for ARGs belonged to Firmicutes phyla, which could be decreased by starting modes.

Fate of antibiotic resistance genes and metal resistance genes during the thermophilic fermentation of solid and liquid swine manures in an ectopic fermentation system

Environmental pollution due to resistance genes from livestock manure has become a serious issue that needs to be resolved. However, little studies focused on the removal of resistance genes in simultaneous processing of livestock feces and urine. This study investigated the fate of antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and class 1 integron-integrase gene (intI1) during thermophilic fermentation of swine manure in an ectopic fermentation system (EFS), which has been regarded as a novel system for efficiently treating both feces and urine. The abundances of MRGs and tetracycline resistance genes were 34.44-97.71% lower in the EFS. The supplementation of heavy metals significantly increased the abundance of intI1, with the enhancement effect of copper being more prominent than that of zinc. The highest abundances of resistance genes and intI1 were observed at high Cu levels (A2), indicating that Cu can increase the spreading of resistance genes through integrons. Network analysis revealed the co-occurrence of ARGs, MRGs, and intI1, and these genes potentially shared the same host bacteria. Redundancy analysis showed that the bacterial community explained most of the variations in ARGs, and environmental factors had influences on ARGs abundances by modulating the bacterial community composition. The decreased Sphingomonas, Comamonas, Acinetobacter, Lactobacillus, Bartonella, Rhizobium, and Bacteroides were mainly responsible for the reduced resistance genes. These results demonstrate that EFS can reduce resistance genes in simultaneous processing of livestock feces and urine.

Dispersion of Antibiotic Resistance Genes (ARGs) from stored swine manure biogas digestate to the atmosphere

Biogas digestate is a reservoir of antibiotic resistance genes (ARGs) and could pose a high health risk to both human and animals if the host microorganisms of ARGs become aerosolized. The purpose of this study was to investigate the diversity and relative abundance characteristics of aerosol-loaded ARGs from biogas digestate during storage, and to explore whether the change of ARGs in biogas digestate directly affect the dispersion of aerosol-loaded ARGs. This study reported for the first time that 28 of 42 ARG subtypes detected in the biogas digestate could be dispersed to the atmosphere via aerosol dispersion in a lab-scale dynamic emission vessels experiment. The relative abundance or diversity of ARGs in aerosols were different from that in biogas digestate, and no significant correlation were observed between the relative abundance of ARGs in biogas digestate and aerosols. The dominant ARGs were tetracycline resistance genes in biogas digestate and β-lactam resistance genes in aerosols. The process of biogas digestate storage reduced the total relative abundance of targeted ARGs in biogas digestate, decreased by 0.35 copies/16S rRNA after 30 days of storage, but increased the abundance of some ARG subtypes, including tetM, tetX, tetQ, tetS, ermF and sul2. High-concerned ARGs, including NDM-1, mcr-1 and vancomycin resistance genes (including vanA, vanB, vanRA and vanSA), were found in biogas digestate, and NDM-1 and vanB were also detected in aerosols. These results indicated a potential risk of ARGs dispersion during biogas digestate storage. Further research on the dispersion of ARGs from biogas digestate is required to elucidate the emission mechanism and develop mitigation measures.

Effect of immobilized anthraquinone-2-sulfonate on antibiotic resistance genes and microbial community in biofilms of anaerobic reactors

Quinone compounds could significantly accelerate anaerobic biotransformation of refractory pollutants. However, the effect of quinone compounds application on the propagation of antibiotic resistance genes (ARGs) in the bio-treatment of these pollutants-containing wastewater is not available. In this study, the catalytic performance of anthraquinone-2-sulfonate immobilized on polyurethane foam (AQS-PUF), changes of ARGs, mobile gene elements (MGEs) and microbial community structure attached on AQS-PUF and PUF in the up-flow anaerobic bioreactors were investigated. The results showed that AQS-PUF could significantly accelerate the decolorization of azo dye RR X-3B. Meanwhile, metagenomics analysis showed that the total absolute abundance of ARGs increased in the presence of the immobilized AQS. Among ARGs, the number of the efflux pump-encoding ARGs in the biofilm of AQS-PUF accounted for 35.7% of the total ARGs, which was slightly higher than that of PUF (32.1%) due to the presence of the immobilized AQS. The relative abundances of ARGs conferring resistance to MLS (macrolide, lincosamide and streptogramin), tetracycline and sulfonamide, which were deeply concerned, reduced 10%, 21.7% and 7.3% in the presence of the immobilized AQS, respectively. Moreover, the immobilized AQS resulted in the decreased relative abundance of plasmids, transposons and class I integrons. Among the detected 31 ARG subtypes located in MGEs, the relative abundances of only lnuF, msrE and mphD in the biofilm of AQS-PUF were over 2-fold higher compared with those in the biofilm of PUF. However, the three ARGs and their host Gammaproteobacteria was not dominant in microbial community. The relative abundances of more ARGs including MLS (lnuB and EreA), tetracycline (tetH) resistance genes located in MGEs decreased, which was attributed to the decreased relative abundance of their hosts. These studies showed that the addition of the immobilized AQS (around 0.25 mM) had a beneficial effect on reducing the spread of ARGs during dyeing wastewater bio-treatment.

Addition of nanoparticles increases the abundance of mobile genetic elements and changes microbial community in the sludge anaerobic digestion system

This study explored the fate of mobile genetic elements (MGEs) in anaerobic digestion (AD) system with four nanoparticles (NPs) added, including carbon NPs, Al₂O₃ NPs, ZnO NPs, and CuO NPs. 16S rRNA amplicon sequencing and quantitative PCR to investigate the microbial community, MGEs abundance and the potential host in the AD process. The results of high-throughput sequencing showed that ZnO NPs and CuO NPs significantly reduced the microbial diversity and significantly changed the microbial community structure. Simultaneously, the absolute abundance of MGEs increased by 145.01%, 159.67%, 354.70%, and 132.80% on the carbon NPs, Al₂O₃ NPs, ZnO NPs, and CuO NPs. The enrichment rate of tnpA-03 in ZnO NPs group was the highest, which could reach up to 2854.80%. Co-occurrence analysis revealed that Proteobacteria harbored the vast majority of MGEs followed by Firmicutes. Redundancy analysis and variation partitioning analysis showed that metabolites were the main factors that shifted the succession of bacterial communities. Moreover, there were significant positive correlations between metabolites and part MGEs (such as tnpA-01, tnpA-02, tnpA-03, tnpA-04, tnpA-05, tnpA-07 and ISCR1). This study provides a new perspective that NPs increase the risk of antibiotic resistance through MGEs during AD process.

Estimating the risks from phthalate esters and metal(loid)s in cultivated edible fungi from Jingmen, Central China

Cultivated mushrooms inevitably absorb phthalate esters (PAEs) and potentially toxic metal(loid)s from plastic grow bags and substrate. The associated harm to consumers should be further clarified. This study measured six priority PAEs and nine metal(loid)s in eight mushroom varieties from greenhouses near Jingmen, Hubei, central China. The averaged total target PAE was between 8.60 ± 1.55 and 27.20 ± 5.90 mg kg^-1 dry weight. Levels of di-n-butyl phthalate in all samples and those of di-(2-ethylhexyl) phthalate in four mushroom species exceeded the maximum residual amount of China. Compared with the maximum levels of contaminants for foods in China, Cd in one and Pb in four mushroom species exceeded the limits. The estimated weekly intake of As, Cd, Cu, Hg, and Pb for different age groups was higher than the provisional tolerable weekly intake; however, there was no significant carcinogenic risks based on assessment of single or combined PAEs and metal(loid)s.

Microbiological safety and antibiotic resistance risks at a sustainable farm under large-scale open-air composting and composting toilet systems

This study evaluated the microbial safety and antibiotic resistance risks of a sustainable ecological farm under large-scale open-air composting (OC) and green composting toilet systems (CT). Samples of livestock manure, compost, soil, vegetables, and rainwater were analysed to determine the best treatment of wastes and risk assessment of land application. Results showed that pathogenic bacteria (PB) in livestock manure was significantly greater than that in the surrounding topsoil, while the distribution of bacteria resistant to amoxicillin (AMX), tetracycline (TC), and amoxicillin-tetracycline (AMX- TC) was the opposite through long-term resistance selection pressure. E. coli and Enterococcus were the dominant pathogens in feces and surrounding soil, respectively, and AMX-resistant bacteria dominated soil, compost, and vegetable samples. Overall, while OC may significantly increase antibiotic resistance and effectively remove fecal PB, CT offers faster consumption with greater antibiotic resistant bacteria (ARB) removal but more PB. Moreover, PB and ARB were concentrated in mature compost, soil in planting areas, vegetables, and rainwater. In farm soil and vegetables, AMX-resistant and AMX-TC-resistant bacterial communities displayed similar composition. These findings may explain the main pathways of PB transmission, migration and accumulation of ARB in farms, and the potential risks to human health through the food chain.

Changes and distributions of antibiotic resistance genes in liquid and solid fractions in mesophilic and thermophilic anaerobic digestion of dairy manure

This study mainly explored the changes and distributions of antibiotic resistance genes (ARGs) in liquid fraction (L_F) and solid fraction (S_F) in anaerobic digestion (AD) of dairy manure. After mesophilic and thermophilic AD, the copy numbers of ARGs in L_F decreased by 0.06-1.80 logs while those in S_F increased by 0.08-7.85 logs, suggesting the enrichment of ARGs in S_F. Statistical analysis elucidated that high total solids promoted the enrichment of ARGs in S_F. The increased abundances of genera such as Ruminofilibacter, Treponema and Sphaerochaeta in S_F were responsible for the enrichment of most ARGs. These insights demonstrated the digested solid had the potential risks to promote the spread of ARGs in the environment, and the digested solid of livestock manure should be post-treated before the application.

Removal of sulfamethazine and Cu2+ by Sakaguchia cladiensis A5: Performance and transcriptome analysis

To reduce the potential risks of contamination of antibiotics and heavy metals to ecological environment and human safety, biological removal of these composite pollutants is the focus of much study. One previously identified isolate, Sakaguchia cladiensis A5, was used to decompose sulfamethazine (SMZ) and adsorb Cu²⁺. The ability of A5 to remove SMZ was enhanced by pre-induced culture, which reached 49.8% on day 9. The removal of SMZ could be also increased to 37.6% on day 3 in the presence of Cu²⁺, but only to 12.2% in the system without Cu²⁺. The biosorption of Cu²⁺ mainly occurred on the cell walls, while the biodegradation of SMZ was inside the cells. By comparative transcriptome analysis for A5, 1270 and 2220 differentially expressed genes (DEGs) were identified after treating single SMZ and SMZ/Cu²⁺, respectively. The Gene expression pattern analysis suggested a suppression of transcriptional changes in A5 responding to SMZ/Cu²⁺ as compared to under the sole stress of SMZ. The DEGs functional enrichment analysis suggested that the antioxidant and sulfate assimilation pathways played a key role on SMZ biodegradation and Cu²⁺ biosorption. The DEGs of proteins CAT, PRDX5, SAT, and CYSC were up-regulated to facilitate the resistance of A5 against oxidative toxicity of Cu²⁺. Moreover, the protein MET30 activated by Cu²⁺ was also overexpressed to promote the transmembrane transport of SMZ, such that A5 could decompose SMZ more effectively in SMZ/Cu²⁺ system. The results of this study would provide new insights into the mechanism of biodegradation and biosorption of SMZ/Cu²⁺.

Antibiotic resistance gene transfer during anaerobic digestion with added copper: Important roles of mobile genetic elements

The abuse of heavy metals as feed additives in livestock is widespread and it might aggravate the spread of antibiotic resistance genes (ARGs) in the environment. However, the mechanisms that allow heavy metals to increase the transmission of ARGs in the environment remain unclear. Cu is the heavy metal present at the highest concentration in livestock manure, and thus Cu was selected to investigate the responses of ARGs to heavy metals. The effects of the microbial communities, mobile genetic elements (MGEs), and heavy metal resistance genes (HMRGs) on ARGs were determined in the presence of 75 and 227 mg L^-1 Cu in a swine manure anaerobic digestion (AD) system. In the AD products, the presence of residual Cu (75 and 227 mg L^-1) increased the total ARGs, HMRGs, and some MGEs, and the higher Cu selected more ARGs than the lower Cu treatment. The results demonstrated that Cu could promote the co-selection of HMRGs, ARGs, and MGEs. The different levels of Cu did not change the bacterial community composition, but they influenced the abundances of bacteria during AD. Network analysis showed that the presence of Cu increased the co-occurrence of specific bacteria containing ARGs, HMRGs, and MGEs. Furthermore, the co-occurrence of MGEs and ARGs increased greatly compared with that of HMRGs and ARGs. Therefore, compared HMRGs, the increased MGEs had the main effect on increasing of ARGs.

Swine Manure Composting With Compound Microbial Inoculants: Removal of Antibiotic Resistance Genes and Their Associations With Microbial Community

In this study, compound microbial inoculants, including three Bacillus strains and one Yeast strain, were inoculated into swine manure composting to explore the effects on antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), microbial community structure, and pathogenic bacteria. The results indicated that the abundances of the detected ARGs ranged from 3.6 × 10³ to 1.13 × 10⁸ copies/g. The ARGs with the highest abundance was sul2, and the lowest was blaCTX. Composting removes most of the ARGs and MGEs by 22.8-99.7%. These ARGs were significantly reduced during the thermophilic phase of compost. The removal rate of ARGs at the different layers of compost pile was different as follows: middle layer > upper layer > lower layer. But some ARGs proliferated significantly in the maturation phase of compost, especially the sulfonamide resistance genes. Compound microbial inoculants increased the temperature of compost, accelerated water loss, nitrogen fixation, and increased the removal rate of β-lactamase resistance genes, the transposon gene tn916 and part of tetracycline resistance genes by 3.7-23.8% in compost. Compound microbial inoculants changed the community structure and increased the Bacillus abundance in the thermophilic phase of compost. And it was helpful for removing pathogens during composting. The addition of compound microbial inoculants causes the decrease of Firmicutes and the increase of Bacteroidetes, which may be related to the removal and proliferation of ARGs.

Speciation, toxicity mechanism and remediation ways of heavy metals during composting: A novel theoretical microbial remediation method is proposed

Heavy metals (HM) pollution is a major limitation to the application of composting products. Therefore, mitigating the toxicity of HM has attracted wide attention during composting. The toxicity of HM is mainly acted on microorganisms during composting, and the toxicity of different HM speciation is obviously various. There are many pathways to change the speciation to reduce the toxicity during composting. Therefore, in this review, the speciation distribution, toxicity mechanism and remediation ways of HM during composting were discussed in order to better solve HM pollution. The microbial remediation technology holds enormous potential to remediate for HM without damaging composting, however, it is hard to extract HM. The innovation of this review was to outline microbial remediation strategies for HM during composting based on two mechanisms of microbial remediation: extracellular adsorption and intracellular sequestration, to solve the problem how to extract microbial agents from the compost. Ultimately, a novel theoretical method of microbial remediation was proposed to remove HM from the compost.

Changes in sediment microbial diversity following chronic copper-exposure induce community copper-tolerance without increasing sensitivity to arsenic

Sediment microbial communities were exposed for 21 days to an environmental concentration of copper to assess Cu-induced composition changes and resulting effects on microbial sensitivity to acute Cu and As toxicity. Chronic Cu exposure reduced the diversity of the bacterial and archaeal communities from Day 0 to Day 21. The pollution-induced community tolerance concept (PICT) predicts that loss of the most sensitive taxa and gain of more tolerant ones should increase the capacity of Cu-exposed communities to tolerate acute Cu toxicity. Although diversity loss and functional costs of adaptation could have increased their sensitivity to subsequent toxic stress, no increased sensitivity to As was observed. PICT responses varied according to heterotrophic activity, selected as the functional endpoint for toxicity testing, with different results for Cu and As. This suggests that induced tolerance to Cu and As was supported by different species with different metabolic capacities. Ecological risk assessment of contaminants would gain accuracy from further research on the relative contribution of tolerance acquisition and co-tolerance processes on the functional response of microbial communities.

Fate of antibiotic resistance genes during high-solid anaerobic co-digestion of pig manure with lignite

Lignite could be used to promote methane production during high-solid anaerobic co-digestion (HS-AcoD) of pig manure, however, the effects of lignite amendment on the fate of ARGs during HS-AcoD are unknown. Here, we explored the influence of lignite (0%, 8%, 16%, 32%, and 64%) on the fate of ARGs during HS-AcoD of pig manure. The results showed that 16% lignite reduced the absolute abundance of ARGs by 28.71% compared with the 0% lignite treatment. Variation partitioning analysis suggested the combined effect of microbial community, mobile genetic elements (MGEs) and environmental factors was the major driver shaping the pattern of ARGs. The potential hosts of ARGs were Bifidobacterium, Lactobacillus, Tissierella and Streptococcus. Structural equation models analysis suggested lignite indirectly impacted the pattern of ARGs by significantly reducing the abundance of microbial community and MGEs. These findings give an insight into the mechanistic understanding of the lignite influence on the reduction of ARGs during HS-AcoD.