Total Abundance Of Antibiotic Resistance Genes Research Articles

Temporal dynamics of microbial composition and antibiotic resistome in fermentation bed culture pig farms across various ages

The discharge from pig farms presents significant challenges to the environment and human health, specifically regarding the dissemination of antimicrobial resistance (AMR). Fermentation bed culture has emerged as an increasingly popular and environmentally friendly pig farming model in China, as it minimizes the release of harmful substances into the environment. However, there remains a limited understanding of the occurrence and dynamics of microbiome and antibiotic resistome in fermentation bed culture. Herein, we collected fermentation bed materials (FBM) from four fermentation bed culture pig farms with varying service ages and investigated their bacterial communities, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), metal resistance genes (MRGs) and potential antibiotic-resistant bacterial hosts through metagenomics. Pseudomonadota, Actinomycetota, Bacteroidota and Bacillota were identified as the dominant phyla present in the FBM. In total, we detected 258 unique ARGs in the FBM samples, with 79 core ARGs shared by all FBM samples, accounting for 95 % of the total ARG abundance. Our results revealed significant variations in microbial communities and ARG profiles across varying service ages of FBM. Compared to long-term FBW, short-term FBM exhibited higher numbers and abundances of ARGs, MRGs and MGEs, along with higher levels of potential bacterial pathogens and high-risk ARGs. Further analysis of metagenome-assembled genome (MAG) indicated that the putative hosts of ARGs primarily belonged to Pseudomonadota, Actinomycetota and Bacillota. Alarmingly, among the 80 recovered ARG-carrying MAGs, 23 MAGs encoded multi-resistance, including clinically significant species that require urgent attention. Overall, this study provided valuable insights into the temporal patterns of antibiotic resistome and bacterial communities within FBM, enhancing our understanding of FBM in pig farming. The findings could potentially contribute to the development of effective strategies for evaluating and regulating fermentation bed culture practices in pig farming.

Spatiotemporal dynamics, traceability analysis, and exposure risks of antibiotic resistance genes in PM2.5 in Handan, China.

Fine particulate matter (PM2.5) seriously affects environmental air quality and human health, and antibiotic resistance genes (ARGs) in PM2.5 posed a great challenge to clinical medicine. The year of 2013-2017 was an important 5-year period for the implementation of Air Pollution Prevention and Control Action Plan (APPCAP) in China. Here, we took Handan, a PM2.5 polluted city in northern China, as the research object and analyzed ARGs in PM2.5 in winter (January) from 2013 to 2017. The results showed that the abundance of ARGs was the highest in 2013 (3.7 × 10-2 copies/16S rRNA), and ARGs were positively correlated with air quality index (AQI) (r = 0.328, P < 0.05) and PM2.5 concentration (r = 0.377, P = 0.020 < 0.05) in the 5-year period. The ARGs carried by PM2.5 in four functional regions of sewage treatment plant, steel works, university, and park showed that sul1 and qepA had higher abundance in each functional region, and the total ARG abundance in sewage treatment plant (1.3 × 10-1 copies/16S rRNA) was the highest, while lowest in park (2.0 × 10-3 copies/16S rRNA). Potential source contribution function (PSCF) and concentration-weighted trajectory (CWT) model were used to trace the pollutants at the sampling points, which indicated that the surrounding cities contributed more than quarter to the sampling points. Therefore, regional transportation reduces the spatial distribution difference of ARGs in PM2.5. The exposure dose of ARGs in different functional regions illustrated that the total inhaled dose of ARGs in sewage treatment plant (1.7 × 105 copies/d) was the highest, while lowest in park (3.2 × 104 copies/d). This study is of great significance for assessing the distribution and sources of ARGs under the clean air initiative in China.

Reduction of mobile genetic elements determines the removal of antibiotic resistance genes during pig manure composting after thermal pretreatment

Animal manure is a primary repository of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). This work explored the efficiency of ARGs and MGEs removal during pig manure composting after thermal pretreatment (TPC) and the underlying mechanisms. TPC resulted in a decrease of 94.7% and 92.3% in the relative abundance of ARGs and MGEs which was 48.9% and 76.6% lower than control, respectively. Network analysis indicated that reductions of ARGs and MGEs in TPC were relevant to decrease in the amount and abundance of bacterial hosts. Furthermore, total ARGs abundance in TPC was correlated with that of intI1 and Tn916/1545 (P < 0.001). Redundancy analysis supported a leading role of MGEs in ARGs dynamics in TPC. Reduction of MGEs rather than bacterial hosts contributed mainly to ARGs removal in TPC, as revealed by structural equation modeling. In conclusion, TPC was an effective method to treat animal manure containing ARGs.

Swine-manure composts induce the enrichment of antibiotic-resistant bacteria but not antibiotic resistance genes in soils

Composting is a common and effective strategy for reducing antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) from animal manure. However, it is unclear whether the advantages of composting for the control of ARGs and ARB can be further increased in land application. This study investigated the fate of ARB and ARGs after land application of swine-manure composts (SMCs) to three different soil types (red soil, loess and black soil). The results showed that although the SMCs caused an increase in the abundance of total ARGs in the soil in the short period, they significantly reduced (p < 0.01) the abundance of total ARGs after 82 days compared to the control. The decay rate of ARGs reflected by the half-life times (t1/2) varied by soil type, with red soil being the longest. The SMCs mainly introduced ermF, tetG and tetX into the soils, while these ARGs quickly declined to the control level. Notably, SMCs increased the number of ARB in the soils, especially for cefotaxime-resistant bacteria. Although SMCs only affected the microbiome significantly during the early stage (p < 0.05), it took a much longer time for the microbiome to recover compared to the control. Statistical analysis indicated that changes in the microbial community contributed more to the fate of ARGs during SMCs land application than other factors. Overall, it is proposed that the advantages of ARGs control in the composting process for swine manure can be further increased in land application, but it can still bring some risks in regard to ARB.

Metagenomic Profiles of Yak and Cattle Manure Resistomes in Different Feeding Patterns before and after Composting.

Antibiotic resistance is a global threat to public health, with antibiotic resistance genes (ARGs) being one of the emerging contaminants; furthermore, animal manure is an important reservoir of biocide resistance genes (BRGs) and metal resistance genes (MRGs). However, few studies have reported differences in the abundance and diversity of BRGs and MRGs between different types of animal manure and the changes in BRGs and MRGs before and after composting. This study employed a metagenomics-based approach to investigate ARGs, BRGs, MRGs, and mobile genetic elements (MGEs) of yak and cattle manure before and after composting under grazing and intensive feeding patterns. The total abundances of ARGs, clinical ARGs, BRGs, MRGs, and MGEs were lower in the manure of grazing livestock than in the manure of the intensively fed group. After composting, the total abundances of ARGs, clinical ARGs, and MGEs in intensively fed livestock manure decreased, whereas those of ARGs, clinical ARGs, MRGs, and MGEs increased in grazing livestock manure. The synergy between MGEs mediated horizontal gene transfer and vertical gene transmission via host bacteria proliferation, which was the main driver that altered the abundance and diversity of ARGs, BRGs, and MRGs in livestock manure and compost. Additionally, tetQ, IS91, mdtF, and fabK were potential indicators for estimating the total abundance of clinical ARGs, BRGs, MRGs, and MGEs in livestock manure and compost. These findings suggest that grazing livestock manure can be directly discharged into the fields, whereas intensively fed livestock manure should be composted before returning to the field. IMPORTANCE The recent increase in the prevalence of antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and metal resistance genes (MRGs) in livestock manure poses risks to human health. Composting is known to be a promising technology for reducing the abundance of resistance genes. This study investigated the differences and changes in the abundances of ARGs, BRGs, and MRGs between yak and cattle manure under grazing and intensive feeding patterns before and after composting. The results indicate that the feeding pattern significantly affected the abundances of resistance genes in livestock manure. Manure in intensive farming should be composted before being discharged into the field, while grazing livestock manure is not suitable for composting due to an increased number of resistance genes.

Higher impact resistance and lower antibiotic resistance genes proliferation rate in shortcut nitrification-denitrification process under long-term antibiotics selection pressure

Shortcut nitrification–denitrification (SCND) has been widely concerned due to its high nitrogen removal efficiency and low operating cost. However, little information is available on the fate of antibiotic resistance genes (ARGs) in SCND process. This study investigates the dynamics of nitrogen removal and ARGs between SCND and full nitrification–denitrification (FND) under long-term selective pressure conditions of tetracycline and sulfadiazine. The study explores the response patterns of extracellular polymers, microbial activity, and microbial community. Results show that the SCND process exhibits 9.14% higher extracellular polymers and 119.07% higher respiratory activity than FND process, resulting in better TN removal performance (67.16% vs. 49.24%) and stronger impact resistance. Compared to Phase I (0 µg/L) and Phase II (100 µg/L), the relative abundance of total ARGs experienced a sharp increase in Phase III (500 µg/L). The SCND process maintains a lower total ARGs abundance than the FND process in water phase. Specifically, in phase III, the relative abundance of intI1 and ARGs in the FND process are 0.04–2.1 logs and 0.66–1.60 logs higher than that of the SCND process in sludge and water phases, respectively. More denitrifying microbes (>40%) are enriched in the SCND process, while it changes to hydrolytic acidification bacteria (>20%) in the FND process. The Partial Least Squares Path Modeling reveals that microbial community and microbial activity play a crucial role in ARGs transmission, with microbial activity exerting greater influence. Additionally, potential pathogenic bacteria including Clostridium, Gemnobacter, Klebsiella, Enternobacter, Aeromonas, Burkholderia are identified, and SCND over FND process shows better inhibition effect on potential pathogenic bacteria proliferation (0.022% vs 0.080%). This study provides new insights into removing traditional pollutants and ARGs simultaneously from wastewater treatment system.

Comparative insight into the effects of different carbon source supplement on antibiotic resistance genes during whole-run and short-cut nitrification-denitrification processes.

Mature landfill leachate is known for nitrogen-removal challenging and meantime was considered as an important sink of antibiotic resistance genes (ARGs). The added external carbon sources, enabling the short-cut nitrification and denitrification, may facilitate the proliferation of bacteria that possibly carry ARGs. However, this speculation has yet to be studied. Here, we explored the effects of glucose, sodium acetate, and methanol supplements on ARGs during whole-run and short-cut treatment processes. The results showed that sodium acetate supplement during short-cut process efficiently reduced the abundances of total ARGs (0.84-1.99 copies/16S rRNA) and integrons (0.59-1.20 copies/16S rRNA), which were highly enhanced by methanol addition during whole-run treatment process (total ARGs: 3.60-11.01 copies/16S rRNA, integrons: 1.20-4.69 copies/16S rRNA). Indirect gradient analysis showed that the variation of ARGs was not correlated with the supplement of different external carbon source. Correlation analysis indicated that dominant intl1 (55.99 ± 17.61% of integrons) showed positively significant correlations with all detected ARGs expect for sul2 and ermB (p < 0.05), suggesting the significant role on ARGs dissemination. Redundancy analysis illustrated that the potential hosts of intl1, intl2, sul1, tetQ, tetM, mefA, and mexF were dominant Bacteroidetes and Actinobacteria. Interestingly, the numbers and significant extent of correlations under the supplement of sodium acetate during short-cut denitrification process were obviously declined, and it was in accordance with ARGs reduced by sodium acetate supplement, suggesting sodium acetate displayed the efficient ARGs reduction during short-cut process. In summary, this study provides a comparative understanding of the effects on ARGs by different carbon source supplements during nitrification-denitrification processes of leachate; sodium acetate is the optimal carbon source.

Antibiotic resistance genes are closely linked with bacterial functions during anoxic-oxic treatment process of pig wastewater

The distribution of antibiotic resistance genes (ARGs) during the anoxic-oxic (A/O) treatment process of pig wastewater was studied by metagenomics. Subsequently, the relationships among bacterial communities, functions and ARGs were analyzed. During the A/O treatment processes, 314 ARG subtypes belonging to 15 ARG types were detected. The dominant ARG types were multidrug, MLS, peptide, glycopeptide, beta-lactam, aminoglycoside and tetracycline resistance genes. The resistance genes MexS, oleC, tetA(48), rphB, macB and smeS can be used as index factors to predict the total abundance of ARGs by a linear function. The functional bacterial genera and genes involved in C-, N- and S-cycling had significant positive correlations with some ARGs, suggesting that functional bacteria were potential ARG hosts. In addition, network analysis suggested that OprM was positively correlated with carbon and nitrogen metabolism. Presumably, functional bacteria containing ARGs may protect the removal process of pollutants in pig farm wastewater. This study highlighted the profiles of ARGs in pig farm wastewater A/O treatment processes and their complex interactions with bacterial functions, and provided an important reference for resolving the contradiction between pollutant removal and antibiotic resistance prevention and control in pig farm wastewater.

Production of medium chain fatty acids from fermentation of antibiotic residuals: Fate of antibiotic resistance genes

The potential of antibiotic resistance genes (ARGs) amplification restricts the biological recovery of antibiotic fermentation residues (AFRs) through two-stage anaerobic fermentation. This study explored the fate of ARGs during the fermentation of AFRs that comprising of acidification and chain elongation (CE). Results showed that with the alteration of fermentation process from acidification to CE, microbial richness was significantly increased, total abundance of ARGs was slightly decreased by 1.84%, and the significant negative correlations between ARGs and microbes were increased, implied the inhibitory effect of CE microbes to ARGs amplification. However, the total abundance of mobile genetic elements (MGEs) was increased by 24.5%, indicating that the potential of gene horizontal transfer of ARGs increased. This work suggested that two-stage anaerobic fermentation could effectively restrict the ARGs amplification, but more concerns are needed for the long-term dissemination of ARGs.

Granular activated carbon remediates antibiotic resistance propagation and methanogenic inhibition induced by polystyrene nanoplastics in sludge anaerobic digestion

Nano/microplastics (NPs/MPs) in sewage sludge can induce oxidative stress to the anaerobic digestion (AD) and also proliferate antibiotic resistance genes (ARGs). Recently, granular activated carbon (GAC) has been used as an additive to enhance methane production in AD via direct interspecies electron transfer (DIET); however, its impact on AD exposed to NPs/MPs is yet to be studied. This study examined the effect of GAC (5 and 15 g/L) on sludge AD exposed to 150 µg/L of polystyrene nanoplastics (PsNPs). PsNPs decreased methane yield by 32.3% due to elevated levels of reactive oxygen species. However, GAC addition counteracted this adverse effect and improved methane production, attributed to the potential enrichment of DIET-active microbes and the adsorption of PsNPs by GAC. Moreover, GAC reduced the total abundance of ARGs, which was increased by PsNPs exposure. Thus, GAC can provide dual benefits in mitigating methanogenic inhibition caused by PsNPs and ARG spread.

A global perspective on compositions, risks, and ecological genesis of antibiotic resistance genes in biofilters of drinking water treatment plants

Antibiotic resistance genes (ARGs) in biofilters of drinking water treatment plants (DWTPs) are regarded to be a remarkable potential health risk to human. A global survey on ARGs in biofilters may help evaluate their risk features as a whole. This study aims to explore the compositions, risks, and ecological genesis of ARGs in the biofilters of DWTPs. In total, 98 metagenomes of DWTP biofilters were collected from Sequence Read Archive (SRA) of National center for Biotechnology Information (NCBI), and the main ARG types were recognized, with multidrug, bacitracin, and beta-lactam as the first three types. Source water types (surface water vs. groundwater) were found to significantly influence antibiotic resistome, overpassing biofilter media and locations. Although ARG abundances of surface water biofilters were approximately five times higher than that of groundwater biofilters, the risk pattern of ARGs was highly similar between surface water biofilters and groundwater biofilters, and up to 99.61% of the ARGs on average belong to the least risk and unassessed ranks, and only 0.23% the highest risk rank. Monobactam biosynthesis pathway and prodigiosin biosynthesis pathway, two antibiotics biosynthesis pathways, were observed to be positively correlated with several ARG types and total ARG abundance in samples of surface water and groundwater biofilters, respectively, suggesting their potential roles in ecological genesis of ARGs. Overall, the results of this study would deepen our understanding of the ARG risks in biofilters of DWTPs and shed light on their ecological genesis inside.

Elevated CO2 alleviated the dissemination of antibiotic resistance genes in sulfadiazine-contaminated soil: A free-air CO2 enrichment study

Climate change affects soil microbial communities and their genetic exchange, and subsequently modifies the transfer of antibiotic resistance genes (ARGs) among bacteria. However, how elevated CO2 impacts soil antibiotic resistome remains poorly characterized. Here, a free-air CO2 enrichment system was used in the field to investigate the responses of ARGs profiles and bacterial communities to elevated CO2 (+200 ppm) in soils amended with sulfadiazine (SDZ) at 0, 0.5 and 5 mg kg−1. Results showed that SDZ exposure induced the co-occurrence of beta-lactamase and tetracycline resistance genes, and SDZ at 5 mg kg−1 enhanced the abundance of aminoglycoside, sulfonamide and multidrug resistance genes. However, elevated CO2 weakened the effects of SDZ at 0.5 mg kg−1 following an observed reduction in the total abundance of ARGs and mobile genetic elements. Additionally, elevated CO2 significantly decreased the abundance of vancomycin resistance genes and alleviated the stimulation of SDZ on the dissemination of aminoglycoside resistance genes. Correlation analysis and structural equation models revealed that elevated CO2 could directly influence the spread of ARGs or impose indirect effects on ARGs by affecting soil properties and bacterial communities. Overall, our results furthered the knowledge of the dissemination risks of ARGs under future climate scenarios.

Enrichment of antibiotic resistant genes and pathogens in face masks from coastal environments

Face masks (FMs) are essential to limit the spread of the coronavirus during pandemic, a considerable of which are accumulated on the coast. However, limited is known about the microbial profile in the biofilm of the face masks (so-called plastisphere) and the impacts of face masks on the surrounding environments. We herein performed face mask exposures to coastal sediments and characterized the microbial community and the antibiotic resistome. We detected 64 antibiotic-resistance genes (ARGs) and 12 mobile gene elements (MGEs) in the plastisphere. Significant enrichments were found in the relative abundance of total ARGs in the plastisphere compared to the sediments. In detail, the relative abundance of tetracycline, multidrug, macrolide-lincosamide-streptogramin B (MLSB), and phenicol-resistant genes had increased by 5–10 times. Moreover, the relative abundance of specific hydrocarbonoclastic bacteria (e.g., Polycyclovorans sp.), pathogens (e.g., Pseudomonas oleovorans), and total MGEs significantly increased in the sediments after face mask exposure, which was congruent with the alteration of pH value and metal concentrations in the microcosms. Our study demonstrated the negative impacts of FMs on coastal environments regardless of the profiles of ARGs or pathogens. These findings improved the understanding of the ecological risks of face masks and underlined the importance of beach cleaning.

Phytostabilization mitigates antibiotic resistance gene enrichment in a copper mine tailings pond.

Mining-impacted environments are distributed globally and have become increasingly recognized as hotspots of antibiotic resistance genes (ARGs). However, there are currently no reports on treatment technologies to deal with such an important environmental problem. To narrow this knowledge gap, we implemented a phytostabilization project in an acidic copper mine tailings pond and employed metagenomics to explore ARG characteristics in the soil samples. Our results showed that phytostabilization decreased the total ARG abundance in 0-10cm soil layer by 75%, which was companied by a significant decrease in ARG mobility, and a significant increase in ARG diversity and microbial diversity. Phytostabilization was also found to drastically alter the ARG host composition and to significantly reduce the total abundance of virulence factor genes of ARG hosts. Soil nutrient status, heavy metal toxicity and SO42- concentration were important physicochemical factors to affect the total ARG abundance, while causal mediation analysis showed that their effects were largely mediated by the changes in ARG mobility and microbial diversity. The increase in ARG diversity associated with phytostabilization was mainly mediated by a small subgroup of ARG hosts, most of which could not be classified at the genus level and deserve further research in the future.

Metagenomics insights into the effects of lactic acid bacteria inoculation on the biological reduction of antibiotic resistance genes in alfalfa silage

Antibiotic resistance genes (ARGs) are a new type of pollutant and pose major threats to public health. However, the distribution and transmission risk of ARGs in alfalfa silage as the main forage for ruminants have not been studied. This study first deciphered the effects of Lactobacillus plantarum MTD/1 or Lactobacillus buchneri 40788 inoculations on distribution and transmission mechanism of ARGs in alfalfa silage by metagenomics. Results showed that multidrug and bacitracin resistance genes were the dominant ARGs in ensiled alfalfa. The natural ensiling process increased the abundances of bacitracin, beta_lactam, and aminoglycoside in alfalfa silage with 30% DM, and vancomycin in alfalfa silage with 40% DM. Meanwhile, prolonged wilting increased ARG enrichment in fresh alfalfa. Interestingly, alfalfa silage inoculated with L. plantarum MTD/1 or L. buchneri 40788 reduced the abundances of total ARG, and multidrug, MLS, vancomycin, aminoglycoside, tetracycline, and fosmidomycin resistance genes by reductions of the host bacteria and the enrichment of ARGs located in the plasmid. The hosts of ARG in alfalfa silage were mainly derived from harmful bacteria or pathogens, and some of the clinical ARGs were observed in alfalfa silage. Basically, the combined effect of microbes, MGEs, and fermentation quality was the major driver of ARG transfer and dissemination in microecosystem of ensiling, where the microbes appeared to be the crucial factor. In summary, inoculation with the present lactic acid bacteria could reduce ARG abundance in ensiled alfalfa, and a better effect was observed in L. plantarum-treated silage than in L. buchneri treated silage.

Impacts of organic materials amendment on the soil antibiotic resistome in subtropical paddy fields.

The organic material amendment has been proven to change the soil antibiotic resistance genes (ARGs) profile, which may threaten human health through the food chain, but the effects and mechanisms of different organic materials on ARGs in paddy soils are less explored. In this study, a field experiment was set up with the treatments of conventional chemical fertilization (NPK) and common organic material amendment [rice straw (RS), swine manure (SM), and biochar (BC)] to explore the effects and mechanisms. In total, 84 unique ARGs were found across the soil samples with different organic material amendments, and they conferred resistance to the major antibiotic classes. Compared with NPK, SM significantly increased the detected number and relative abundance of ARGs. A higher detected number of ARGs than NPK was observed in BC, whereas BC had a lower relative abundance of ARGs than NPK. Compared with NPK, a detected number decrease was observed in RS, although abundance showed no significant differences. Compared with other treatments, a higher detected number and relative abundance of mobile genetic elements (MGEs) were observed in BC, indicating a higher potential for horizontal gene transfer. There were significantly positive relationships between the relative abundances of total ARGs and MGEs and the bacterial abundance. The network analysis suggested the important role of MGEs and bacterial communities in shaping the ARGs profile. Mantel test and redundancy analysis (RDA) suggested that soil carbon, nitrogen, and C/N were the major chemical drivers of the ARGs profile. The risk of ARGs spreading to the food chain should be considered when applying SM and biochar, which shifted the ARGs and MGEs profiles, respectively. Pre-treatment measures need to be studied to reduce the dissemination of ARGs in paddy fields.

Heavy Metal Content and Resistance Gene Abundance and Related Properties in the Surface Soil around Qinghai Lake

Soil heavy metal pollution and the prevalence of resistance genes have been a global concern, and thus many studies have reported the content of heavy metals and resistance genes in soils; however, the contents of heavy metals and antibiotic resistance genes (ARGs) in the soil in highland areas is still unclear. In this study, the environmental residues and distribution of heavy metals and resistance genes in the soil in Qinghai were analyzed, and the relationship between the concentration of heavy metals and antibiotic resistance genes in the soil was explored. Among the soil samples, the content of heavy metal zinc was the highest ［mean: (50.27±19.88) mg·kg-1］, followed by the content of heavy metal cadmium ［mean: (30.27±9.45) mg·kg-1］, and the content of heavy metal mercury was the lowest ［mean: (0.027±0.019) mg·kg-1］. The subtypes of heavy metal resistance genes in soils were mainly czcA, merA, and merP, whose main function was to be responsible for developing mercury resistance. The relative abundance of β-lactamase resistance genes (0.1505) was the highest in soil, accounting for 47.54% of the total abundance of ARGs; tetracycline resistance genes accounted for 16.93% of the total abundance of ARGs, FCA accounted for approximately 14.56%, and MLSB accounted for approximately 8.77%. The diversity and relative abundance of movable genetic elements (MGEs) were low, and only the [STBX]tnpA01[STBZ] gene was detected; intl[STBX]1[STBZ] and intl[STBX]2[STBZ] were not detected. Correlation studies showed that Cu content (r=-0.533, P=0.006) and Hg (r=0.692, P=0.006) in soil were significantly negatively correlated with altitude, whereas other heavy metals were not significantly correlated with altitude. In addition, heavy metal content was significantly correlated with soil type (P<0.05). There was a significant positive correlation between heavy metal mercury content in soils and czcA (r=0.692, P=0.006), merA (r=0.816, P=0.007), and merP (r=0.594, P=0.02). The results of this study elucidated the occurrence and distribution of heavy metals and ARGs in the Tibetan Plateau region and found that the content of heavy metals in the soil was significantly related to resistance genes.

Enzymatic pretreatment mitigates the dissemination of antibiotic resistance genes via regulating microbial populations and gene expressions during food waste fermentation

Food waste (FW) has been recognized as essential reservoir for resource recovery via anaerobic fermentation, which could also bring the potential risk of antibiotic resistance genes (ARGs) dissemination. Although the structural deficiency of FW could be stimulated by enzymatic pretreatment to enhance fermentation efficiency, the influences of enzymatic pretreatment on ARGs fate and microbial metabolic pathways involved in ARGs dissemination have rarely been reported. This work proved that enzymatic pretreatment could effectively decrease the total abundance of ARGs (reduced by 13.8%-24.5%) during long-term FW fermentation. It was found that enzymatic pretreatment significantly reduced the ARGs belonging to the efflux pump, which might be ascribed to its ability to increase membrane permeability. Furthermore, enzymatic pretreatment was in favor of reducing microbial diversity and various potential ARGs host (e.g., Methanosarcina, Clostridium, Prevotella, Parabacteroides). Also, this pretreatment remarkably up-regulated the genetic expressions involved in ABC transporter (e.g., eryF and mntA) and down-regulated the genetic expressions that participated in DNA replication, two-component systems (e.g., uphA and cckA), and quorum sensing (e.g., rpfF and lsrG), thereby decreasing ARGs transmission. This study would expand the insight of the influences of pretreatment method on ARGs fate during FW fermentation, and offer practical guidance on the sustainable management of FW.

Metagenomic insights into role of red mud in regulating fate of compost antibiotic resistance genes mediated by both direct and indirect ways

In this study, the amendment of red mud (RM) in dairy manure composting on the fate of antibiotic resistance genes (ARGs) by both direct (bacteria community, mobile genetic elements and quorum sensing) and indirect ways (environmental factors and antibiotics) was analyzed. The results showed that RM reduced the total relative abundances of 10 ARGs and 4 mobile genetic elements (MGEs). And the relative abundances of total ARGs and MGEs decreased by 53.48% and 22.30% in T (with RM added) on day 47 compared with day 0. Meanwhile, the modification of RM significantly increased the abundance of lsrK, pvdQ and ahlD in quorum quenching (QQ) and decreased the abundance of luxS in quorum sensing (QS) (P < 0.05), thereby attenuating the intercellular genes frequency of communication. The microbial community and network analysis showed that 25 potential hosts of ARGs were mainly related to Firmicutes, Proteobacteria and Actinobacteria. Redundancy analysis (RDA) and structural equation model (SEM) further indicated that RM altered microbial community structure by regulating antibiotic content and environmental factors (temperature, pH, moisture content and organic matter content), which then affected horizontal gene transfer (HGT) in ARGs mediated by QS and MGEs. These results provide new insights into the dissemination mechanism and removal of ARGs in composting process.

Effects of heavy metals and antibiotics on antibiotic resistance genes and microbial communities in soil

With rapid developments in livestock and poultry farming, antibiotics and heavy metals are entering the soil environment as feed additives. However, their relationships with antibiotic resistance genes (ARGs), microorganisms, and environmental factors are unclear. In this study, cadmium (Cd) and sulfadiazine (SD) were selected as representative heavy metal and antibiotic substances, respectively, to investigate the relationships among environmental factors, microorganisms, mobile genetic elements (MGEs), and ARGs. Addition of Cd and SD, both individually and in combination, increased the abundances of total ARGs and MGEs. The abundance of total ARGs increased by 0.89-fold and 1.06-fold in C2 and C8 (only-Cd-added groups), 1.61-fold and 6.53-fold in S10 and S100 (only-SD-added groups), and 7.29-fold, 7.62-fold, 2.32-fold, and 6.80-fold in C2S10, C2S100, C8S10, and C8S100 (groups with Cd and SD in combinations), respectively. Proteobacteria and Bacteroidetes were the most abundant bacterial phyla. MGEs (especially intI1) had the greatest impact on ARGs and played a crucial role in their propagation and expression. Exploring the effects of heavy metals and antibiotics in soil on ARGs is important for comprehensively assessing their ecological and environmental risks to ARGs.