The behavior of antibiotic-resistance genes and their relationships with the bacterial community and heavy metals during sewage sludge composting

Applicability of intI1 as an indicator gene for securing the removal efficiency of extracellular antimicrobial resistance genes in full-scale wastewater treatment plants

Mitigating the release of extracellular antimicrobial resistance genes (exARGs) from wastewater treatment plants (WWTPs) is crucial for preventing the spread of antimicrobial resistance from human domains into the environment. This study aimed to evaluate the applicability of intI1 as a performance indicator for securing the removal of exARGs at WWTPs. We investigated the reduction of exARGs and intI1 in a full-scale WWTP, where identical wastewater was treated using conventional activated sludge (CAS) and membrane bioreactor (MBR) systems. The log reduction values (LRVs) for exARGs were lower than those for intracellular ARGs (iARGs) across all ARG species and treatment systems. LRVs for exARGs were consistently higher in the MBR than in the CAS. The intI1 exhibited lower LRVs compared to most exARGs, ensuring a minimum LRV of exARG in both CAS and MBR systems. Consequently, intI1 is an effective indicator gene for securing the removal of exARGs.

Comprehensive effects of tea branch biochar on antibiotic resistance profiles and C/N/S cycling in the compost microbiota of animal manure

The comprehensive effects of exogenous additives on microbial-driven antibiotic resistance profiles and C/N/S conversion in animal manure composting remains uncertain. This study examined whether tea branch biochar could regulate the microflora involved in antibiotic resistance and C/N/S conversion during pig and chicken manure composting. Compared with the control treatment, biochar addition prolonged the high-temperature period (>55 °C) for 1-2 days and raised the maximum temperature in chicken manure composting. Moreover, biochar addition reduced the prevalence of antibiotic resistance genes (ARGs) in both pig and chicken manure composting by up to 30 %, targeting various types of ARGs such as peptide, phenicol, and diaminopyrimidines. Additionally, the compost microbiota exhibited the overlaps of C/N/S conversion functions. Luteimonas (Xanthomonadaceae) was identified as a dominant bacterium responsible for C/N/S conversion in both pig and chicken manure composting, while also acting as a potential ARG carrier. Thus, Luteimonas is crucial in shaping antibiotic resistance profiles and C/N/S cycling in animal manure composting, indicating its role as a keystone genus. These findings suggest that tea branch biochar can mitigate the spread of ARGs from animal manure, as well as enhance nutrient cycling and compost quality.

The simultaneous addition of chitosan and peat enhanced the removals of antibiotics resistance genes during biogas residues composting

Direct reuse of biogas residue (BR) has the potential to contribute to the dissemination of antibiotic resistance genes (ARGs). Although high-temperature composting has been demonstrated as an effective method for the harmless treatment of organic waste, there is few researches on the fate of ARGs in high-temperature composting of BR. This research examined the impact of adding 5% chitosan and 15% peat on physicochemical characteristics, microbial communities, and removal of ARGs during BR-straw composting in 12 Biolan 220L composters for 48 days. Our results showed that the simultaneous addition of chitosan and peat extended the high-temperature period, and increased the highest temperature to 74 °C and germination index. These effects could be attributed to the presence of thermophilic cellulose-decomposing genera (Thermomyces and Thermobifida). Although the microbial communities differed compositionally among temperature stages, their dissimilarity drastically reduced at final stage, indicating that the impact of different treatments on microbial community composition decreases at the end of composting. Peat had a greater impact on aerobic genera capable of cellulose degradation at thermophilic stage than chitosan. Surprisingly, despite the total copy number of ARGs significantly decreased during composting, especially in the treatment with both chitosan and peat, intl1 gene abundance significantly increased 2 logs at thermophilic stage and maintained high level in the final compost, suggesting there is still a potential risk of transmission and proliferation of ARGs. Our work shed some lights on the development of waste resource utilization and emerging contaminants removal technology.

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

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

Effects of tomato straw fermentation on nutrients and bacterial community structure

Unsustainable straw treatment methods detrimentally affect the environment and ecology. Aerobic fermentation (AE) and anaerobic fermentation (AN) are environmentally friendly treatments that better utilise straw resources. In this study, high-throughput sequencing was used to investigate the effects of AE and AN on nutrient content and microbial community structure during tomato straw fermentation. Nitrate nitrogen, available phosphorus, available potassium, and fulvic acid contents following AE were 1250.04 mg/kg, 80.34 %, 161.39 %, and 49.31 %, respectively, which were higher than those following AN. Ammonium nitrogen, humic acid, and humic substance levels following AN were 309.07 %, 31.18 %, and 17.38 %, respectively, which were higher than those following AE. Firmicutes (24.76 %) and Actinobacteria (12.93 %) were more abundant following AE, whereas Proteobacteria (33.82 %) and Bacteroidetes (33.82 %) exhibited higher abundance following AN. AE more effectively eliminated pathogenic bacteria (22.01%-0.26 %) and encouraged stronger interactions between dominant bacterial genera. Redundancy and Mantel test analyses revealed that electrical conductivity and temperature were the most important environmental factors affecting bacterial communities in AE and AN, respectively. AE had a stronger effect on effective nutrient release from tomato straw, implying its greater application potential as a fertiliser. Overall, our study provides a theoretical basis for the optimisation of fermentation methods and processes.

Impact of uranium on antibiotic resistance in activated sludge

The emergence of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in the environment is well established as a human health crisis. The impact of radioactive heavy metals on ecosystems and ultimately on human health has become a global issue, especially for the regions suffering various nuclear activities or accidents. However, whether the radionuclides can affect the fate of antibiotic resistance in bacteria remains poorly understood. Here, the dynamics of ARB, three forms of ARGs-intracellular ARGs (iARGs), adsorbed extracellular ARGs (aeARGs), and free extracellular ARGs (feARGs)-and microbial communities were investigated following exposure to uranium (U), a representative radioactive heavy metal. The results showed that 90-d of U exposure at environmentally relevant concentrations of 0.05 mg/L or 5 mg/L significantly increased the ARB concentration in activated sludge (p < 0.05). Furthermore, 90-d of U exposure slightly elevated the absolute abundance of aeARGs (except tetO) and sulfonamide iARGs, but decreased tetracycline iARGs. Regarding feARGs, the abundance of tetC, tetO, and sul1 decreased after 90-d of U stress, whereas sul2 showed the opposite trend. Partial least-squares path model analysis revealed that the abundance of aeARGs and iARGs under U stress was predominantly driven by increased cell membrane permeability/intI1 abundance and cell membrane permeability/reactive oxygen species concentration, respectively. Conversely, the changes in feARGs abundance depended on the composition of the microbial community and the expression of efflux pumps. Our findings shed light on the variations of ARGs and ARB in activated sludge under U exposure, providing a more comprehensive understanding of antibiotic resistance risks aggravated by radioactive heavy metal-containing wastewater.

Effect of biochar with various pore characteristics on heavy metal passivation and microbiota development during pig manure composting

Understanding the porosity of biochar (BC) that promotes the heavy metal (HM) passivation during composting can contribute to the sustainable management of pig manure (PM). The current work aimed to explore the influence of BC with varying pore sizes on the physicochemical properties and morphological changes of HMs (including Zn, Cu, Cr, As, and Hg), and microbiota development during PM composting. The various pore sizes of BC were generated by pyrolyzing pine wood at 400 (T1), 500 (T2), 600 (T3) and 700 (T4) °C, respectively. The results revealed a positive correlation between specific surface area of BC and pyrolysis temperature. BC addition contributed to a significantly extended compost warming rate and duration of high-temperature period, as well as HM passivation, reflected in the decrease in Exc-Zn (63-34%) and Red-Cu (28-13%) content, and the conversion of Oxi-Cr (29-21%) and Red-Hg (16-5%) to more stable forms. Moreover, BC at T4 exhibited the best effect on Zn and Cu passivation due to the highest specific surface area (380.03 m2/g). In addition to its impact on HM passivation, BC addition improved the microbial environment during PM composting, leading to enhanced microbial diversity and richness. Notably, Chloroflexi and Bacteroidota played key roles in promoting the transformation of Exc-Cu and Red-Hg into stable forms. This phenomenon further stimulated the enhanced decomposition of organic matter (OM) when BC prepared at 600-700 °C was added. Therefore, it can be concluded that the regulation of BC porosity is an effective strategy to improve HM passivation and the overall effectiveness of PM composting.

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.

Biochar for soil remediation: A comprehensive review of current research on pollutant removal

Biochar usage in soil remediation has turned out to be an enticing topic recently. Biochar, a product formed by pyrolysis of organic waste, which is rich in carbon, has the aptitude to ameliorate climate change by sequestering carbon while also enhancing soil quality and crop yields. Two-edged implications of biochar on soil amendment are still being discussed yet, clarity on the long-term implications of biochar on soil health and the environment is not yet achieved. As a result, it is crucial to systematically uncover the pertinent information regarding biochar remediation, as this can serve as a roadmap for future research on using biochar to remediate contaminated soils in mining regions. This review endeavors to bring forth run thoroughly the latest state of research on the use of biochar in soil remediation, along with its potential benefits, limitations, challenges, and future scope. By synthesizing existing literature on biochar soil remediation, this review aims to provide insights into the potential of biochar as a sustainable solution for soil remediation. Specifically, this review will highlight the key factors that influence the effectiveness of biochar for soil remediation and the potential risks associated with its use, as well as the current gaps in knowledge and future research directions.

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

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

Inoculation with thermophiles enhanced the food waste bio-drying and complicated interdomain ecological networks between bacterial and fungal communities

Bio-drying is a practical approach for treating food waste (FW). However, microbial ecological processes during treatment are essential for improving the dry efficiency, and have not been stressed enough. This study analyzed the microbial community succession and two critical periods of interdomain ecological networks (IDENs) during FW bio-drying inoculated with thermophiles (TB), to determine how TB affects FW bio-drying efficiency. The results showed that TB could rapidly colonize in the FW bio-drying, with the highest relative abundance of 5.13%. Inoculating TB increased the maximum temperature, temperature integrated index and moisture removal rate of FW bio-drying (55.7 °C, 219.5 °C, and 86.11% vs. 52.1 °C, 159.1 °C, and 56.02%), thereby accelerating the FW bio-drying efficiency by altering the succession of microbial communities. The structural equation model and IDEN analysis demonstrated that TB inoculation complicated the IDENs between bacterial and fungal communities by significantly and positively affecting bacterial communities (b = 0.39, p < 0.001) and fungal communities (b = 0.32, p < 0.01), thereby enhancing interdomain interactions between bacteria and fungi. Additionally, inoculation TB significantly increased the relative abundance of keystone taxa, including Clostridium sensu stricto, Ochrobactrum, Phenylobacterium, Microvirga and Candida. In conclusion, the inoculation of TB could effectively improve FW bio-drying, which is a promising technology for rapidly reducing FW with high moisture content and recovering resources from it.

Wheat straw pyrochar more efficiently decreased enantioselective uptake of dinotefuran by lettuce and dissemination of antibiotic resistance genes than hydrochar in an agricultural soil

Remediation of soils pollution caused by dinotefuran, a chiral pesticide, is indispensable for ensuring human food security. In comparison with pyrochar, the effect of hydrochar on enantioselective fate of dinotefuran, and antibiotic resistance genes (ARGs) profiles in the contaminated soils remain poorly understood. Therefore, wheat straw hydrochar (SHC) and pyrochar (SPC) were prepared at 220 and 500 °C, respectively, to investigate their effects and underlying mechanisms on enantioselective fate of dinotefuran enantiomers and metabolites, and soil ARG abundance in soil-plant ecosystems using a 30-day pot experiment planted with lettuce. SPC showed a greater reduction effect on the accumulation of R- and S-dinotefuran and metabolites in lettuce shoots than SHC. This was mainly resulted from the lowered soil bioavailability of R- and S-dinotefuran due to adsorption/immobilization by chars, together with the char-enhanced pesticide-degrading bacteria resulted from increased soil pH and organic matter content. Both SPC and SHC efficiently reduced ARG levels in soils, owing to lowered abundance of ARG-carrying bacteria and declined horizontal gene transfer induced by decreased dinotefuran bioavailability. The above results provide new insights for optimizing char-based sustainable technologies to mitigate pollution of dinotefuran and spread of ARGs in agroecosystems.

Joint toxicity mechanisms of perfluorooctanoic acid and sulfadiazine on submerged macrophytes and periphytic biofilms

Hazardous chemicals, such as perfluoroalkyl substances (PFASs) and antibiotics, coexist in aquatic environments and pose a severe threat to aquatic organisms. However, research into the toxicity of these pollutants on submerged macrophytes and their periphyton is still limited. To assess their combined toxicity, Vallisneria natans (V. natans) was exposed to perfluorooctanoic acid (PFOA) and sulfadiazine (SD) at environmental concentrations. Photosynthetic parameters such as chlorophyll a, chlorophyll b, total chlorophyll, and carotenoids were lower in the SD exposure group, indicating that SD had a significant effect on the photosynthesis of aquatic plants. Single and combined exposures effectively induced antioxidant responses, with increases in superoxide dismutase, peroxidase activities, and ribulose-1,5-bisphosphate carboxylase concentrations, as well as malondialdehyde content. Accordingly, antagonistic toxicity was assessed between PFOA and SD. Furthermore, metabolomics revealed that V. natans improved stress tolerance through changes in enoic acid, palmitic acid, and palmitoleoyloxymyristic acid related to the fatty acid metabolism pathway responding to the coexisting pollutants. Additionally, PFOA and SD in combination induced more effects on the microbial community of biofilm. The alternation of α- and β-D-glucopyranose polysaccharides and the increased content of autoinducer peptides and N-acylated homoserine lactones indicated that PFOA and SD changed the structure and function of biofilm. These investigations provide a broader perspective and comprehensive analysis of the responses of aquatic plants and periphyton biofilms to PFAS and antibiotics in the environment.

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.

Biochar preparation and evaluation of its effect in composting mechanism: A review

This article provides an overview of biochar application for organic waste co-composting and its biochemical transformation mechanism. As a composting amendment, biochar work in the adsorption of nutrients, the retention of oxygen and water, and the promotion of electron transfer. These functions serve the micro-organisms (physical support of niche) and determine changes in community structure beyond the succession of composing primary microorganisms. Biochar mediates resistance genes, mobile gene elements, and biochemical metabolic activities of organic matter degrading. The participation of biochar enriched the α-diversity of microbial communities at all stages of composting, and ultimately reflects the high γ-diversity. Finally, easy and convincing biochar preparation methods and characteristic need to be explored, in turn, the mechanism of biochar on composting microbes at the microscopic level can be studied in depth.

Microbial community structure and antibiotic resistance profiles in sediments with long-term aquaculture history

The aim of this investigation was to examine the microbial populations and their resistance patterns towards antibiotics, including the impact of nitrogen metabolism in response to the reintroduction of antibiotics, as well as the presence of resistance genes in sediments from shrimp ponds that have been utilized for extended periods of 5, 15, and over 30 years. Results showed that the sediments exhibited a high prevalence of Proteobacteria, Bacteroidetes, Planctomycetes, Chloroflexi, and Oxyphotobacteria as the most abundant bacterial phyla, accounting for 70.35-77.43% of the total bacterial community. The five most abundant phyla of fungi detected in all sediments, namely Rozellomycota, Ascomycota, Aphelidiomycota, Basidiomycota, and Mortierellomycota, constituted 24.26-32.54% of the total fungal community. It was highly probable that the Proteobacteria and Bacteroidetes phyla serve as the primary reservoir of antibiotic-resistant bacteria (ARB) in the sediment, which included various genera like Sulfurovum, Woeseia, Sulfurimonas, Desulfosarcina, and Robiginitalea. Among these genera, Sulfurovum appeared to be the most widespread in the sediment of aquaculture ponds that have been in operation for more than three decades, while Woeseia dominated in ponds that have been recently reclaimed and have a 15-year aquaculture history. Antibiotic resistance genes (ARGs) were categorized into seven distinct groups according to their mechanism of action. The prevalence of multidrug-resistant ARGs was found to be the highest among all types, with an abundance ranging from 8.74 × 10^-2 to 1.90 × 10^-1 copies per 16S rRNA gene copies. The results of a comparative analysis of sediment samples with varying aquaculture histories indicated that the total relative abundance of ARGs was significantly diminished in sediment with a 15-year aquaculture history as opposed to sediment with either a 5-year or 30-year aquaculture history. Another assessment of antibiotic resistances in aquaculture sediments involved an examination of the effects of reintroducing antibiotics on nitrogen metabolism processes. The findings revealed that the rates of ammonification, nitrification, and denitrification in the sediment with a history of 5 years and 15 years, decreased as the concentration of oxytetracycline increased from 1 to 300, and 2000 mg/kg, and inhibitory effects were found to be less pronounced in sediments with a 5-year history compared to those with a 15-year history. In contrast, oxytetracycline exposure led to a significant decrease in the rates of these processes in aquaculture pond sediments with a >30 years of aquaculture history across all the concentrations tested. The emergence and dissemination of antibiotic resistance profiles in aquaculture environments requires attention in future aquaculture management.

The role of pretreatments in handling antibiotic resistance genes in anaerobic sludge digestion - A review

Sludge is among the most important reservoirs of antibiotic resistance genes (ARGs), which would cause potential environmental risks with the sludge utilization. Currently, anaerobic digestion (AD) is effective to simultaneously realize the resource recovery and pollutants removal, including antibiotic resistance genes (ARGs), and various pretreatments are used to enhance the performance. Recently, plentiful publications have focused on the effects of pretreatment on ARGs removal, but the contradictory results are often obtained, and a comprehensive understanding of the research progress and mechanisms is essential. This study summarizes various pretreatment techniques for improving AD efficiency and ARGs reduction, investigates promising performance in ARGs removal when pretreatments combined with AD, and analyzes the potential mechanisms accounting for ARGs fates. The results showed that although thermal hydrolysis pretreatment showed the best performance in ARGs reduction during the pretreatment process, the significant rebound of ARGs would occur in the subsequent AD process. Conversely, ozone pretreatment and alkali pretreatment had no significant effect on ARGs abundance in the pretreatment stage, but could enhance ARGs removal by 15.6-24.3 % in the subsequent AD. Considering the efficiency and economic effectiveness, free nitrous acid pretreatment would be a promising and feasible option, which could enhance methane yield and ARGs removal by up to 27 % and 74.5 %, respectively. Currently, the factors determining ARGs fates during pretreatment and AD processes included the shift of microbial community, mobile genetic elements (MGEs), and environmental factors. A comprehensive understanding of the relationship between the fate of ARGs and pretreatment technologies could be helpful for systematically evaluating various pretreatments and facilitating the development of emerging and effective pretreatment techniques. Moreover, given the effectiveness, economic efficiency and environmental safety, we called for the applications of modern analysis approaches such as metagenomic and machine learning on the optimization of pretreatment conditions and revealing underlying mechanisms.

Sulfur enhancement effects for uranium bioleaching in column reactors from a refractory uranium ore

The feasibility of sulfur enhancement for uranium bioleaching in column reactors was assessed with a designed mixed Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans and Leptospirillum ferriphilum from a refractory uranium ore. The uranium extraction reached 86.2% with the sulfur enhancement (1 g/kg) in 77 days leaching process, increased by 12.6% vs. the control without sulfur addition. The kinetic analysis showed that uranium bioleaching with sulfur enhancement in columns followed an internal diffusion through the product layer-controlled model. Ore residue characteristics indicated that sulfur enhancement could strengthen the porosity of passivation layer, improving the ore permeability. Notably, bacterial community analysis showed that sulfur enhancement at 1 g/kg could make the iron-oxidizing and sulfur-oxidizing bacteria on the ore surface maintain a good balance (approx. 1:1), and thus decomposing ore more effectively. Lastly, a possible mechanism model for uranium bioleaching with sulfur enhancement was proposed.

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

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

High nitrogen addition after the application of sewage sludge compost decreased the bioavailability of heavy metals in soil

Nitrogen (N) fertilizer is highly significant in agricultural production, but long-term N addition causes changes in quality indicators, such as soil organic matter (SOM), thus affecting the absorption and accumulation of organic pollutants. Therefore, paying more attention to organic fertilizers in the development of green agriculture is necessary. However, the accumulation of heavy metals (HMs) contained in organic fertilizers (especially sewage sludge compost (SSC)) in the soil can cause environmental contamination, but how this cumulative reaction changes with the long-term N addition remains unclear. Here the SSC impact on the bioavailability of five typical HMs (cadmium-Cd, chromium-Cr, copper-Cu, lead-Pb and arsenic-As) in the soil-plant system before and after SSC application was demonstrated through a field study in soils with different application rates of 0, 100 and 300 kg N ha^-1yr^-1, respectively. Our results showed that SSC application increased the concentration of most HMs in soil profiles and plant systems (wheat roots and grains), but the accumulation rate of HMs and most bioaccumulation values (BAC-bioaccumulation coefficient and BCF-bioconcentration factor) in plant systems were both lower in high-N addition soil than that in the low-N group. Moreover, speciation distribution results further indicated that SSC application increased the LB (liable available form, including F1-water soluble, F2-ion exchangeable, and F3-bound to carbonates) form of HMs and decreased the PB (potentially available form, including F4-humic acids and F6-fraction bound to organic matter) form of HMs in high-N addition soil, respectively. Those results suggested that HM bioavailability in high-N addition soil was lower than that in low-N addition soil when applied with SSC. Overall, this study found that increasing soil N content can inhibit the bioavailability of HMs when applying SSC, providing suggestions for optimizing the trialability and risk assessment of SSC application.

Fates of antibiotic resistance genes and bacterial/archaeal communities of activated sludge under stress of copper: Gradient increasing/decreasing exposure modes

Effect of copper (Cu) on antibiotic resistance genes (ARGs) and bacterial/archaeal community of activated sludge under gradient increasing (0.5-10 mg/L) or decreasing exposure (10-0.5 mg/L) modes was explored. Here, 29 genes were detected among 48 selected ARGs and mobile gene elements (MGEs). Two exposure modes showed dissimilar effects on ARGs and distribution was more affected by environmental concentrations of Cu, which promoted transmission of ARGs (multiple drug resistance and sulfonamide). Cellular protection was main resistance mechanism, which was less inhibited than efflux pumps. The tnpA-02, as main MGE, interacted closely with ARGs (sul2, floR, etc.). Gradient increasing exposure mode had more effects on bacterial/archaeal structure and composition. Bacteria were main hosts for specific ARGs and tnpA-02, while archaea carried multiple ARGs (cmx(A), adeA, etc.), and bacteria (24.24 %) contributed more to changes of ARGs than archaea (19.29 %). This study clarified the impacts of Cu on the proliferation and transmission of ARGs.

Microbial community succession in soils under long-term heavy metal stress from community diversity-structure to KEGG function pathways

Currently, understanding the structure and function of the microbial community is the key step in artificially constructing microbial communities to control soil heavy metal pollution. Abundant/rare microbial communities play different roles in different levels of concentrations. However, the correlation between heavy metals and rare/abundant subgroups is poorly understood. In this study, we used a metagenomics approach to comprehensively investigate the evolutionary changes in microbial diversity, structure, and function under different heavy metal concentration stress in soils surrounding gold tailings. The results show that the main pollutants were Pb, As, and Zn. Indigenous microorganisms have different responses to heavy metal concentrations. Bacteria are the main components of indigenous microorganisms, mainly including Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria. With the increase of heavy metal pollution, the relative abundance of Proteobacteria increased, and that of Actinobacteria decreased. Archaea was significantly inhibited by heavy metal stress and was more sensitive to heavy metal concentration. The response of fungi to heavy metal concentration was not obvious. The results of KEGG pathways showed that carbon fixation was inhibited with increasing heavy metal concentrations, while nitrogen metabolism was in contrast. Abundant subcommunity had a greater correlation mainly with metal resistance mechanisms, and rare subcommunity plays a key role for soil nutrient cycling such as N, S cycling in soils contaminated. Overall, this study provides a comprehensive analysis of the effects of heavy metal stress at different concentrations on microorganisms in farmland around gold tailings and reveals the relationship between heavy metals on KEGG pathways.

Distribution of antibiotic, heavy metals and antibiotic resistance genes in livestock and poultry feces from different scale of farms in Ningxia, China

With the rapid development of livestock and poultry breeding industries, pollution problems caused by the discharge of animal feces have become increasingly severe. Nevertheless, there are limited investigations about nutrients and pollutants in animal feces from different scale of farms, especially in Northwest China. Here we investigated nutrients content, 19 antibiotics, 7 heavy metals, 329 antibiotic resistance genes (ARGs) and 35 mobile genetic elements (MGEs) in six main livestock and poultry feces collected from 5 coastal regions of Ningxia. Pig and chicken feces exhibited higher levels of nutrients content, but antibiotics, heavy metals, ARGs and MGEs were also more abundant than those in cattle and sheep feces. Chlortetracycline hydrochloride and doxycycline hyclate were the most commonly used antibiotic, which detected with the highest rate and concentrations, especially in broiler, layer and pig feces. Strong positive correlations were found among different ARGs or between ARGs and MGEs, indicated the risk of horizontal gene transfer of ARGs. Residual antibiotic and heavy metals significantly affect the abundance of ARGs. Feeding mode and the scales of the animal farms served little effect on the distribution of the pollutants (including residual antibiotics, heavy metals, MGEs and ARGs), which were significantly different among animal types. Use of antibiotics and heavy metals should be strictly regulated, especially in chicken and pig farms, in order to control contaminants and reduce potential risks to the environment.

Impact of Anthropogenic Activities on the Dissemination of ARGs in the Environment-A Review

Over the past few decades, due to the excessive consumption of drugs in human and veterinary medicine, the antimicrobial resistance (AR) of microorganisms has risen considerably across the world, and this trend is predicted to intensify. Many worrying research results indicate the occurrence of pools of AR, both directly related to human activity and environmental factors. The increase of AR in the natural environment is mainly associated with the anthropogenic activity. The dissemination of AR is significantly stimulated by the operation of municipal facilities, such as wastewater treatment plants (WWTPs) or landfills, as well as biogas plants, agriculture and farming practices, including animal production and land application of manure. These activities entail a risk to public health by spreading bacteria resistant to antimicrobial products (ARB) and antibiotic resistance genes (ARGs). Furthermore, subinhibitory concentrations of antimicrobial substances additionally predispose microbial consortia and resistomes to changes in particular environments that are permeated by these micropollutants. The current state of knowledge on the fate of ARGs, their dissemination and the complexity of the AR phenomenon in relation to anthropogenic activity is inadequate. This review summarizes the state-of-the-art knowledge on AR in the environment, in particular focusing on AR spread in an anthropogenically altered environment and related environmental consequences.

The combined effect of an integrated reclaimed water system on the reduction of antibiotic resistome

The reuse of urban reclaimed water is conducive to alleviate the current serious shortage of water resources. However, antibiotic resistance genes (ARGs) in reclaimed water have received widespread attention due to their potential risks to public health. Deciphering the fate of ARGs in reclaimed water benefits the development of effective strategies to control resistome risk and guarantees the safety of water supply of reclaimed systems. In this study, the characteristics of ARGs in an integrated reclaimed water system (sewage treatment plant-constructed wetland, STP-CW) in Beijing (China) have been identified using metagenomic assembly-based analysis, as well as the combined effect of the STP-CW system on the reduction of antibiotic resistome. Results showed a total of 29 ARG types and 813 subtypes were found in the reclaimed water system. As expected, the STP-CW system improved the removal of ARGs, and about 58% of ARG subtypes were removed from the effluent of the integrated STP-CW system, which exceeded 43% for the STP system and 37% for the CW system. Although the STP-CW system had a great removal on ARGs, abundant and diverse ARGs were still found in the downstream river. Importantly, network analysis revealed the co-occurrence of ARGs, mobile genetic elements and virulence factors in the downstream water, implying potential resistome dissemination risk in the environment. Source identification with SourceTracker showed the STP-effluent was the largest contributor of ARGs in the downstream river, with a contribution of 45%. Overall, the integrated STP-CW system presented a combined effect on the reduction of antibiotic resistome, however, the resistome dissemination risk was still non-negligible in the downstream reclaimed water. This study provides a comprehensive analysis on the fate of ARGs in the STP-CW-river system, which would benefit the development of effective strategies to control resistome risk for the reuse of reclaimed water.

A Comprehensive Study of the Microbiome, Resistome, and Physical and Chemical Characteristics of Chicken Waste from Intensive Farms

The application of chicken waste to farmland could be detrimental to public health. It may contribute to the dissemination of antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) from feces and their subsequent entry into the food chain. The present study analyzes the metagenome and resistome of chicken manure and litter obtained from a commercial chicken farm in Poland. ARB were isolated, identified, and screened for antibiogram fingerprints using standard microbiological and molecular methods. The physicochemical properties of the chicken waste were also determined. ARGs, integrons, and mobile genetic elements (MGE) in chicken waste were analyzed using high-throughput SmartChip qPCR. The results confirm the presence of many ARGs, probably located in MGE, which can be transferred to other bacteria. Potentially pathogenic or opportunistic microorganisms and phytopathogens were isolated. More than 50% of the isolated strains were classified as being multi-drug resistant, and the remainder were resistant to at least one antibiotic class; these pose a real risk of entering the groundwater and contaminating the surrounding environment. Our results indicate that while chicken manure can be sufficient sources of the nutrients essential for plant growth, its microbiological aspects make this material highly dangerous to the environment.

The effects of biochar on antibiotic resistance genes (ARGs) removal during different environmental governance processes: A review

Antibiotic resistance genes (ARGs) pollution has been considered as one of the most significant emerging environmental and health challenges in the 21st century, many efforts have been paid to control the proliferation and dissemination of ARGs in the environment. Among them, the biochar performs a positive effect in reducing the abundance of ARGs during different environmental governance processes and has shown great application prospects in controlling the ARGs. Although there are increasing studies on employing biochar to control ARGs, there is still a lack of review paper on this hotspot. In this review, firstly, the applications of biochar to control ARGs in different environmental governance processes were summarized. Secondly, the processes and mechanisms of ARGs removal promoted by biochar were proposed and discussed. Then, the effects of biochar properties on ARGs removal were highlighted. Finally, the future prospects and challenges of using biochar to control ARGs were proposed. It is hoped that this review could provide some new guidance for the further research of this field.

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.

Cadmium stress efficiently enhanced meropenem degradation by the meropenem- and cadmium-resistant strain Pseudomonas putida R51

The β-lactam antibiotic meropenem (MEM) is widely used in infectious disease treatment and consequently can be released into the environment, causing environmental pollution. In this study, Pseudomonas putida strain R51 was isolated from the wastewater of a poultry farm and found to efficiently degrade MEM. The genome of strain R51 contains a variety of heavy metal and antibiotic resistance genes, including the metallo-β-lactamase gene (JQN61_03315) and cadmium resistance gene cadA (JQN61_19995). Under cadmium stress, the degradation rate of MEM increased significantly in strain R51. Transcriptional analysis revealed that the expression of JQN61_03315 and cadA significantly increased under cadmium stress and that the expression of many genes associated with heavy metal and antibiotic resistance also changed significantly. Molecular docking analysis suggested that metallo-β-lactamase JQN61_03315 binds to MEM. In addition, no plasmid was found in strain R51, and no mobile genetic elements were found nearby JQN61_03315. In conclusion. we proposed that JQN61_03315 was responsible for the degradation of MEM, that the expression of this gene was induced under cadmium stress, and that strain R51 can be used for bioremediation of MEM without the risk for the transmission of the MEM resistance gene. These findings will have importance for studying the microbial degradation of MEM in the presence of heavy metal pollutants.

Biochar can mitigate co-selection and control antibiotic resistant genes (ARGs) in compost and soil

Heavy metals (HMs) contamination raises the expression of antibiotic resistance (AR) in bacteria through co-selection. Biochar application in composting improves the effectiveness of composting and the quality of compost. This improvement includes the elimination and reduction of antibiotic resistant genes (ARGs). The use of biochar in contaminated soils reduces the bioaccessibility and bioavailability of the contaminants hence reducing the biological and environmental toxicity. This decrease in contaminant bioavailability reduces contaminants induced co-selection pressure. Conditions which favour reduction in HMs bioavailable fraction (BF) appear to favour reduction in ARGs in compost and soil. Biochar can prevent horizontal gene transfer (HGT) and can eliminate ARGs carried by mobile genetic elements (MGEs). This effect reduces maintenance and propagation of ARGs. Firmicutes, Proteobacteria, and Actinobacteria are the major bacteria phyla identified to be responsible for dissipation, maintenance, and propagation of ARGs. Biochar application rate at 2-10% is the best for the elimination of ARGs. This review provides insight into the usefulness of biochar in the prevention of co-selection and reduction of AR, including challenges of biochar application and future research prospects.

The dissimilarity of antibiotic and quorum sensing inhibitor on activated sludge nitrification system: Microbial communities and antibiotic resistance genes

Effects of antibiotics (azithromycin, AZM, 1-40 mg/L) and quorum sensing inhibitor (QSI, 2(5H)-furanone, 1-40 mg/L) combined pollution with environmental concentration of copper on bacterial/archaeal community and antibiotic resistance genes (ARGs) in activated sludge system were explored. QSI inhibited nitrification more obviously than AZM. AZM and QSI were synergistic inhibitions on bacterial diversity, and AZM inhibited bacterial compositions more than QSI. While, QSI had more impacts on archaeal diversity/compositions. Less interactions among bacteria and archaea communities with Aquimonas as keystone genus. Functional differences in bacteria/archaea communities were little, and AZM had more effects on metabolism. AZM mainly affected nitrifying bacteria (Candidatus Nitrospira nitrificans and Nitrosomonas). Specific denitrifying bacteria were enriched by AZM (Brevundimonas, 1.76-31.69%) and QSI (Comamonas, 0.61-9.61%), respectively. AZM enriched ARGs more easily than QSI and they were antagonistic to proliferation of ARGs. Bacteria were main hosts of ARGs (macrolide-lincosamide-streptogramin B, other/efflux, etc.) and archaea (Methanosphaerula, Methanolobus) carried multiple ARGs.

Short-term biodrying achieves compost maturity and significantly reduces antibiotic resistance genes during semi-continuous food waste composting inoculated with mature compost

Food waste (FW) is important object of resource utilization and source of antibiotic resistance genes (ARGs). This study investigated the effects of biodrying combined with inoculating mature compost (B&M) on the composting efficiency, succession of bacterial communities and their links with metabolism functions as well as the fate of ARGs during FW composting. The results showed that B&M could rapidly raise and maintain high relative abundance of Bacillaceae (66.59-94.44%) as well as composting temperature (45.86-65.86 ℃), so as to achieve the final maturity of FW composting in a short time by regulating microbial carbohydrate (14.02-15.31%) and amino acid metabolism (10.33-12.47%). Network analysis demonstrated that high temperature could effectively inhibit the proliferation and spread of potential bacterial hosts of ARGs and integrons including Lactobacillaceae, Enterobacteriaceae, Leuconostocaceae and Corynebacteriaceae during the first two days of composting. As a result, B&M significantly reduced the absolute (72.09-99.47%) and relative abundances (0.31-2.44 logs) of nearly all ARGs especially ermB, tetM, bla_CTX-M and bla_OXA. Present study deepened the knowledge of ARGs variation, succession and metabolism functions of bacterial communities when B&M processes were used for FW composting, suggesting a promising technology for reducing the transmission risk of ARGs and reaching maturity of FW composting.

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.

Impacts of combined pollution under gradient increasing and gradient decreasing exposure modes on activated sludge: Microbial communities and antibiotic resistance genes

The responses of microbial communities and antibiotic resistance genes (ARGs) to azithromycin and copper combined pollution under gradient increasing (from 0.5 to 10 mg/L) and decreasing exposure (from 10 to 0.5 mg/L) modes were investigated. Nitrification was inhibited more obviously under gradient increasing exposure mode. Responses of archaeal community and function structure were more obvious than bacteria under both exposure modes. The dominant bacterial and archaeal compositions (Hyphomicrobium, Euryarchaeota, etc.) were affected by two exposure modes, except some rare archaea (Methanoregula and Methanosarcina). There were more positive correlations between bacteria and archaea, and Nitrospira was keystone genus. Ammonia-oxidizing archaea (0.37-3.06%) and complete ammonia oxidizers (Nitrospira_ENR4) were enriched, and Nitrososphaera_viennensis was closely related to denitrifying genes (napA/B, nosZ, etc.). 50 ARG subtypes were detected and specific ARG subtypes (aac, ImrA, etc.) proliferated in two exposure modes. Bacteria and archaea were common hosts for 24 ARGs and contributed to their shifts.

Advancements in detection and removal of antibiotic resistance genes in sludge digestion: A state-of-art review

Sludge from wastewater treatment plants can act as a repository and crucial environmental provider of antibiotic resistance genes (ARGs). Over the past few years, people's knowledge regarding the occurrence and removal of ARGs in sludge has broadened remarkably with advancements in molecular biological techniques. Anaerobic and aerobic digestion were found to effectively achieve sludge reduction and ARGs removal. This review summarized advanced detection and removal techniques of ARGs, in the last decade, in the sludge digestion field. The fate of ARGs due to different sludge digestion strategies (i.e., anaerobic and aerobic digestion under mesophilic or thermophilic conditions, and in combination with relevant pretreatment technologies (e.g., thermal hydrolysis pretreatment, microwave pretreatment and alkaline pretreatment) and additives (e.g., ferric chloride and zero-valent iron) were systematically summarized and compared in this review. To date, this is the first review that provides a comprehensive assessment of the state-of-the-art technologies and future recommendations.

Chicken manure-based bioponics: Effects of acetic acid supplementation on nitrogen and phosphorus recoveries and microbial communities

Bioponics has the potential to recover nutrients from organic waste streams, such as chicken manure and digestate with high volatile fatty acid (VFA) contents through crop production. Acetic acid, a dominant VFA, was supplemented weekly (0, 500, 1000, and 1500 mg/L) in a chicken manure-based bioponic system, and its effect on the performance of bioponics (e.g., plant yield and nitrogen and phosphorus availabilities) was examined. Microbial communities were analyzed using 16S rRNA gene sequencing, and the functional gene abundances were predicted using PICRUSt. Although acetic acid negatively affected plant yield, no significant difference (p > 0.05) was noted in the average nitrogen or phosphorus concentration. In terms of nutrient recovery, the bioponic systems still functioned well, although higher concentrations of acetic acid decreased plant yield and altered the bacterial communities in plant roots and chicken manure sediments. These data suggest that an acetic acid concentration of < 500 mg/L or a longer loading interval is recommended for the effective operation of chicken manure and digestate-based bioponics.