Sheep and rapeseed cake manure promote antibiotic resistome in agricultural soil. - Related Documents




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700401.0000Sheep and rapeseed cake manure promote antibiotic resistome in agricultural soil. The application of manure in agriculture caused the emergence and spread of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in soil environments. However, the co-occurrence pattern and host diversity of ARGs and MGEs in soils amended with animal and green manures remains unclear. In this study, metagenomic assembly and binning techniques were employed to comprehensively explore the effects of sheep manure and green manure on soil microbiome, antibiotic resistomes, and ARG hosts. Both rapeseed cake manure and sheep manure increased the abundance and diversity of ARGs, with sheep manure particularly enhancing the abundance of ARGs conferring resistant to multidrug, quinolone, rifampicin, and macrolide-lincosamide-streptogramin (MLSB). Mobile genetic elements (MGEs), such as plasmids, transposases, and integrases, preferentially enhanced the potential mobility of some ARGs subtypes (i.e. sul2, aadA, qacH, and folp), facilitating the spread of ARGs. Additionally, sheep manure reshaped the bacterial community structure and composition as well as ARG hosts, some opportunistic pathogens (i.e. Staphylococcus, Streptococcus, and Pantoea) acquired antibiotic resistance and remained recalcitrant. It is concluded that rapeseed cake manure and sheep manure increased the co-occurrence of ARGs and MGEs, enriched the potential ARG hosts, and promoted the dissemination of ARGs in agricultural soils.202540633350
700710.9998Tracking resistomes, virulence genes, and bacterial pathogens in long-term manure-amended greenhouse soils. Organic manure has been implicated as an important source of antibiotic resistance genes (ARGs) in agricultural soils. However, the profiles of biocide resistance genes (BRGs), metal resistance genes (MRGs) and virulence genes (VGs) and their bacterial hosts in manure-amended soils remain largely unknown. Herein, a systematic metagenome-based survey was conducted to comprehensively explore the changes in resistomes, VGs and their bacterial hosts, mobile genetic elements (MGEs), and pathogenic bacteria in manure-amended greenhouse soils. Many manure-borne ARGs, BRGs, MRGs, VGs, and bacterial pathogens could be transferred into soils by applying manures, and their abundance and diversity were markedly positively correlated with greenhouse planting years (manure amendment years). The main ARGs transferred from manures to soils conferred resistance to tetracycline, aminoglycoside, and macrolide-lincosamide-streptogramin. Both statistical analysis and gene arrangements showed a good positive co-occurrence pattern of ARGs/BRGs/MRGs/VGs and MGEs. Furthermore, bacterial hosts of resistomes and VGs were significantly changed in the greenhouse soils in comparison with the field soils. Our findings confirmed the migration and dissemination of resistomes, VGs, and bacterial pathogens, and their accumulation and persistence were correlated with the continuous application of manures.202032298867
700520.9998The mobility, host, and co-occurrence of antibiotic resistance genes in multi-type pig manure-soil systems: Metagenome assembly analysis. Antibiotic resistance genes (ARGs) pose significant threats to public health and environmental safety, yet the mobility and hosts of ARGs in animal manure-soil systems remain poorly understood. Here, we evaluated the environmental risks of tilmicosin (TIL) and investigated ARG profiles, mobility, and drivers in pig manure-soil systems using metagenomic assembly. TIL was effectively degraded during aerobic composting and fertilization via hydroxylation, demethylation, and deglycosylation. Notably, the total abundance of ARGs significantly decreased during aerobic composting and fertilization, and manure types affected the distribution and composition of ARGs in fertilized soils. There was a special correlation between the genetic location and type of ARGs. In addition, the results showed co-localization of some specific ARGs and mobile genetic elements (MGEs) (tetA-tetR- transposase; tetR-floR- Tn3 family). A significant correlation was found between Escherichia coli and multiple ARG types, especially multidrug ARGs. Microbial community was the dominant factor driving the variations of ARGs in pig manure-soil systems, followed by MGEs, environmental factors, and antibiotic concentration. This study advances the understanding on the environmental risk assessment of TIL and elucidates the key drivers of ARG dissemination in pig manure-soil systems, providing critical insights and actionable strategies for sustainable livestock management and environmental risk control.202540865323
700630.9998Metagenomic 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.202337409977
682340.9997Metagenomic assembly and binning analyses the prevalence and spread of antibiotic resistome in water and fish gut microbiomes along an environmental gradient. The pristine river and urban river show an environmental gradient caused by anthropogenic impacts such as wastewater treatment plants and domestic wastewater discharges. Here, metagenomic and binning analyses unveiled antibiotic resistance genes (ARGs) profiles, their co-occurrence with metal resistance genes (MRGs) and mobile genetic elements (MGEs), and their host bacteria in water and Hemiculter leucisculus samples of the river. Results showed that the decrease of ARG abundances from pristine to anthropogenic regions was attributed to the reduction of the relative abundance of multidrug resistance genes in water microbiomes along the environmental gradient. Whereas anthropogenic impact contributed to the enrichment of ARGs in fish gut microbiomes. From pristine to anthropogenic water samples, the dominant host bacteria shifted from Pseudomonas to Actinobacteria. Potential pathogens Vibrio parahaemolyticus, Enterobacter kobei, Aeromonas veronii and Microcystis aeruginosa_C with multiple ARGs were retrieved from fish gut microbes in lower reach of Ba River. The increasing trends in the proportion of the contigs carrying ARGs (ARCs) concomitant with plasmids along environmental gradient indicated that plasmids act as efficient mobility vehicles to enhance the spread of ARGs under anthropogenic pressures. Moreover, the higher co-occurrence of ARGs and MRGs on plasmids revealed that anthropogenic impacts accelerated the co-transfer potential of ARGs and MRGs and the enrichment of ARGs. Partial least squares path modeling revealed anthropogenic contamination could shape fish gut antibiotic resistome mainly via affecting ARG host bacteria in water microbiomes, following by ARGs co-occurrence with MGEs and MRGs in gut microbiomes. This study enhanced our understanding of the mechanism of the anthropogenic activities on the transmission of antibiotic resistome in river ecosystem and emphasized the risk of ARGs and pathogens transferring from an aquatic environment to fish guts.202235716556
698250.9997Viral Communities Suppress the Earthworm Gut Antibiotic Resistome by Lysing Bacteria on a National Scale. Earthworms are critical in regulating soil processes and act as filters for antibiotic resistance genes (ARGs). Yet, the geographic patterns and main drivers of earthworm gut ARGs remain largely unknown. We collected 52 earthworm and soil samples from arable and forest ecosystems along a 3000 km transect across China, analyzing the diversity and abundance of ARGs using shotgun metagenomics. Earthworm guts harbored a lower diversity and abundance of ARGs compared to soil, resulting in a stronger distance-decay rate of ARGs in the gut. Greater deterministic assembly processes of ARGs were found in the gut than in soil. The earthworm gut had a lower frequency of co-occurrence patterns between ARGs and mobile genetic elements (MGEs) in forest than in arable systems. Viral diversity was higher in the gut compared to soil and was negatively correlated with bacterial diversity. Bacteria such as Streptomyces and Pseudomonas were potential hosts of both viruses and ARGs. Viruses had negative effects on the diversity and abundance of ARGs, likely due to the lysis on ARG-bearing bacteria. These findings provide new insights into the variations of ARGs in the earthworm gut and highlight the vital role of viruses in the regulation of ARGs in the soil ecosystem.202439037720
692760.9997Manure application: A trigger for vertical accumulation of antibiotic resistance genes in cropland soils. The application of livestock manure increases the dissemination risk of antibiotic resistance genes (ARGs) in farmland soil environment. However, the vertical migration behavior and driving factor of ARGs in manured soil under swine manure application remains undefined. Here, the dynamics of ARGs, mobile genetic elements (MGEs) and bacterial communities in different soil depths (0 - 80 cm) with long-term swine manure application were tracked and conducted using real-time qPCR. Results showed that long-term application of swine manure remarkably facilitated the vertical accumulation of ARGs and MGEs, in particular that the relative abundance of bla(ampC) showed significant enrichment with increasing depth. ARGs abundance was similar in the three fields with long-term application of swine manure. (p＞0.05). Procrustes analysis indicated that microbial communities were the dominant drivers of ARGs variation in topsoil, and the changes of environmental factors played a vital role in vertical migration ARGs in cropland soils. Additionally, the variation patterns of high-risk ARGs (i.e., bla(ampC), bla(TEM-1)) were influenced by the dominant bacteria (Actinomycetes) and pH. This study illustrated that the swine manure application promoted the vertical migration of ARGs, including multidrug resistance determinants, highlighting the ecological risk caused by long-term manure application.202235483148
683070.9997Heavy metal could drive co-selection of antibiotic resistance in terrestrial subsurface soils. Terrestrial surface ecosystems are important sinks for antibiotic resistance genes (ARGs) due to the continuous discharge of contaminants from human-impacted ecosystems. However, the abundance and resistance types of ARGs and their influencing factors in terrestrial subsurface soils are not well known. In this study, we investigated the abundance and diversity of ARGs, and their correlations with metal resistance genes (MRGs), mobile genetic elements (MGEs), bacteria, and heavy metals in subsurface soils using high throughput quantitative PCR and metagenomic sequencing approaches. Abundant and diverse ARGs were detected with high spatial heterogeneity among sampling sites. Vertically, there was no significant difference in ARG profiles between the aquifer and non-aquifer soils. Heavy metals were key factors shaping ARG profiles in soils with high heavy metal contents, while they showed no significant effect in low contents. Moreover, heavy metals could trigger the proliferation of antibiotic resistance by increasing MGE abundance or influencing bacterial communities. Metagenomic analysis also revealed the widespread co-occurrence of ARGs and MRGs, with heavy metals possibly enhancing the co-selection of ARGs and MRGs in soils with high heavy metal contents. This study highlighted the heavy metal-driven co-selection of ARGs and revealed the occurrence of ARG pollution in terrestrial subsurface soils.202133858075
682980.9997Metagenomic insights into the characteristics and co-migration of antibiotic resistome and metal(loid) resistance genes in urban landfill soil and groundwater. The heavy metals and antibiotic resistance genes (ARGs) in landfills showed a significant correlation; however, the relationship between metal(loid) resistance genes (MRGs) and ARGs in contaminated environments, as well as whether they co-migrate with human pathogenic bacteria (HPB), remains unclear. This study is the first to report the characteristics and co-migration of ARGs and MRGs in the soil and groundwater of aged urban landfill sites. Our findings indicated that quinolone, efflux, and macrolide-lincosamide-streptogramin represented the most abundant ARGs identified. Notably, ARG abundance was higher in groundwater compared to soil, with subtype diversity reflecting a similar trend; however, microbial diversity in soil was greater. Metagenome-assembled genomes data indicated a higher risk of antibiotic-resistant HPB in groundwater. It is imperative to focus on HPB that co-carry ARGs and MRGs alongside mobile genetic elements (MGEs), such as Ralstonia pickettii and Pseudomonas stutzeri. Genes conferring resistance to copper and mercury, as well as MGEs such as qacEdelta and intI1, played a critical role in promoting horizontal gene transfer of antibiotic resistance. MRG may promote ARG migration by affecting the permeability of the cell membrane. Procrustes analysis revealed a strong similarity (87 %) between heavy metals and MRG structures. Variance partitioning analyses demonstrated that both heavy metals and biological factors jointly governed landfill ARGs (96.2 %), exerting a more substantial influence in groundwater than in soil. This study serves as a reference for managing landfill, while emphasizing the importance of addressing the co-migration of MRGs and ARGs in pathogens when controlling the spread of risks.202540614847
691690.9997Mobile genetic elements in potential host microorganisms are the key hindrance for the removal of antibiotic resistance genes in industrial-scale composting with municipal solid waste. During the municipal solid waste (MSW) composting, antibiotic resistance genes (ARGs) could be one of the concerns to hinder the application of MSW composting. However, the understanding of enrichment and dissemination of ARGs during the industrial-scale composting is still not clear. Hence, this study aimed to investigate the ARG distributions at different stages in an industrial-scale MSW composting plant. Seven target ARGs and four target mobile genetic elements (MGEs) and bacterial communities were investigated. The abundances of ARGs and MGEs increased during two aerobic thermophilic stages, but they decreased in most ARGs and MGEs after composting. Network analysis showed that potential host bacteria of ARGs were mainly Firmicutes and Actinobacteria. The reduction of potential host bacteria was important to remove ARGs. MGEs were an important factor hindering ARG removal. Water-extractable S and pH were two main physicochemical factors in the changes of microbial community and the abundance of ARGs.202031962245
6810100.9997Heavy metals and microbiome are negligible drivers than mobile genetic elements in determining particle-attached and free-living resistomes in the Yellow River. Suspended particles in water can shelter both microorganisms and contaminants. However, the emerging pollutants antibiotic resistance genes (ARGs) in free-living (FL) or particle-attached (PA) bacteria in aquatic environments are less explored. In this study, we compared the free-living and particle-attached ARGs during four seasons in the Yellow River using high-throughput quantitative PCR techniques and 16S rRNA gene sequencing. Our results demonstrated that both the free-living water and particles were dominated by tetracycline and beta-lactamase resistance genes. The PA-ARGs had a higher absolute abundance than FL-ARGs in the Yellow River, regardless of the season. Both PA-ARGs and FL-ARGs had the highest absolute abundance and diversity during winter. Mobile genetic elements (MGEs) were the dominant driver for both size-fractionated ARGs. However, the microbiome had less influence on PA-ARG profiles than the FL-ARG profiles, while the effects of the heavy metals on ARGs were negligible. The community assembly of both FL-ARG and PA-ARG can be explained by neutral processes. Several opportunistic pathogens (e.g., Escherichia coli) associated with human health exhibited a higher relative abundance in the particles than during a free-living lifestyle. Parts of these pathogens were potential ARG hosts. As such, it is important to monitor the ARGs and opportunistic pathogens from size-fractionated bacteria and develop targeted strategies to manage ARG dissemination and opportunistic pathogens to ensure public health.202234736202
6809110.9997High-throughput profiling of antibiotic resistance gene dynamic in a drinking water river-reservoir system. The rapid construction of reservoir in river basin generates a river-reservoir system containing an environmental gradient from river system to reservoir system in modern aquatic environment worldwide. Profiles of antibiotic resistance genes (ARGs) in river-reservoir system is essential to better understand their dynamic mechanisms in aquatic eco-environment. In this study, we investigated the diversity, abundance, distribution of ARGs and mobile genetic elements (MGEs) in a representative river-reservoir system using high-throughput quantitative PCR, as well as ranked the factors (e.g. antibiotics, bacterial biomass, bacteria communities, and MGEs) influencing the patterns of ARGs based on structural equation models (SEMs). Seasonal variations in absolute abundance of ARGs and MGEs exhibited similar trends with local rainfall, suggesting that seasonal runoff induced by the rainfall potentially promote the absolute abundance of ARGs and MGEs. In contrast, environmental gradient played more important roles in the detected number, relative abundance, distribution pattern of ARGs and MGEs in the river-reservoir system. Moreover, environmental gradient also made the co-occurrence patterns associated with ARGs subtypes, MGEs and bacteria genera in river system different from those in reservoir system. The SEMs revealed that MGEs contributed the most to shape the ARG profiles. Overall, our findings provide novel insights into the mechanisms of environmental gradient on ARGs dynamics in river-reservoir system, probably via influencing the MGEs, antibiotics, pathogenic bacteria community and nonpathogenic bacteria community.201930447523
7002120.9997Response of soil antibiotic resistance genes and bacterial communities to fresh cattle manure and organic fertilizer application. Livestock manure use in agriculture contributes to pollutants like antibiotic resistance genes (ARGs) and resistant bacteria. This practice could potentially facilitate ARGs development in soil ecosystems. Our study aimed to explore ARGs and bacterial communities in cattle manure from Ningxia beef cattle farms with varying breeding periods. We also assessed the impact of different application rates of cattle manure compost, created by mixing manure with different growing periods, on soil's physicochemical and heavy metal properties. High-throughput PCR and sequencing were used to analyze ARGs and bacterial communities. We aimed to understand ARGs dynamics in cattle manure during breeding stages and the impact of different fertilizer application rates on soil bacteria and resistance genes. We found 212 ARGs from cattle manure, spanning tetracycline, aminoglycoside, multidrug, and MLSB categories. Relative ARGs abundance was presented across breeding stages: lactation (C1), breeding (C3), pre-fattening (C4), calving (C2), and late fattening (C5). pH, total nitrogen (TN), electrical conductivity (EC), arsenic (As) and cadmium (Cd) presence significantly impacted ARGs quantity and microbial community structure in manure. Mobile genetic elements (MGEs) were the primary factor altering ARGs in manure (65.56%). Heavy metals contributed to 18.60% of ARGs changes. Manure application changed soil ARGs abundance, notably in soils with high application rates, primarily associated with aminoglycoside, multidrug and sulfonamide resistance. Soils with higher manure rates had elevated MGEs, positively correlated with most ARGs, suggesting MGEs' role in ARGs dissemination. Soil microbial community structure was influenced by fertilization, particularly with the highest application rate. Heavy metals (specifically Cd, contributing to 23.12%), microbial community changes (17.42%), and MGEs (17.38%) were the main factors affecting soil antibiotic resistance. Our study establishes a framework for understanding ARGs emergence in manure and treated soils. This informs strategies to mitigate environmental ARGs transmission and guides diverse livestock manure application and management.202339492397
7028130.9997Metagenomic insights to effective elimination of resistomes in food waste composting by lime addition. Food waste contains abundant resistomes, including antibiotic and heavy metal resistance genes (ARGs and MRGs), which pose risks to the environment and human health. Composting can be used for food waste treatment, but it fails to effectively eliminate these resistomes. Thus, this study investigated the performance of lime to regulate the dynamics and mobility of ARGs and MRGs in food waste composting by metagenomics. Genome-resolved analysis was further conducted to identify the ARGs and MRGs hosts and their horizontal gene transfer (HGT) events. Results showed that lime addition at 1 % (wet weight) could significantly promote temperature and pH increase to sterilize hosts, particularly pathogen bacteria (e.g. Acinetobacter johnsonii and Enterobacter cloacae), thus reducing the abundance of resistomes by more than 57.1 %. This sterilization notably reduced the number of mobile ARGs and MRGs driven by mobile genetic elements (MGEs). The contribution of MGEs located on chromosomal sequences to horizontally transfer ARGs and MRGs was significantly higher than that on mobilizable plasmids. Further analysis indicated that the reduced resistomes by lime was mainly attributed to effective sterilization of hosts rather than decreased HGT diversity. Thus, this study provides valuable insights into use lime as a low-cost control of resistomes in waste recycling.202541061540
6822140.9997River contamination shapes the microbiome and antibiotic resistance in sharpbelly (Hemiculter leucisculus). Animals living in urban river systems play critical roles in the dissemination of microbiome and antibiotic resistance that poses a strong threat to public health. This study provides a comprehensive profile of microbiota and antibiotic resistance genes (ARGs) of sharpbelly (Hemiculter leucisculus) and the surrounding water from five sites along the Ba River. Results showed Proteobacteria, Firmicutes and Fusobacteria were the dominant bacteria in gut of H. leucisculus. With the aggravation of water pollution, bacterial biomass of fish gut significantly decreased and the proportion of Proteobacteria increased to become the most dominant phylum eventually. To quantify the contributions of influential factors on patterns of gut microbiome with structural equation model (SEM), water bacteria were confirmed to be the most stressors to perturb fish gut microbiome. SourceTracker model indicated that deteriorating living surroundings facilitated the invasion of water pathogens to fish gut eco-environments. Additionally, H. leucisculus gut is an important reservoir of ARGs in Ba River with relative abundance up to 9.86 × 10(-1)/copies. Among the ARGs, tetracycline and quinolone resistance genes were detected in dominant abundance. Deterioration of external environments elicited the accumulation of ARGs in fish gut. Intestinal class I integron, environmental heavy metal residues and gut bacteria were identified as key drivers of intestinal ARGs profiles in H. leucisculus. Analysis of SEM and co-occurrence patterns between ARGs and bacterial hosts indicated that class I integron and bacterial community played vital roles in ARGs transmission through water-fish pathway. In general, this study highlighted hazards of water contamination to microbiome and ARGs in aquatic animals and provided a new perspective to better understand the bacteria and ARGs dissemination in urban river ecosystems.202133120330
6925150.9996Multiple driving factors contribute to the variations of typical antibiotic resistance genes in different parts of soil-lettuce system. The application of manure compost may cause the transmission of antibiotic resistance genes (ARGs) in agroecological environment, which poses a global threat to public health. However, the driving factors for the transmission of ARGs from animal manure to agroecological systems remains poorly understood. Here, we explored the spatiotemporal variation in ARG abundance and bacterial community composition as well as relative driving factors in a soil-lettuce system amended with swine manure compost. The results showed that ARGs abundance had different variation trends in soil, lettuce phylloplane and endophyere after the application of swine manure compost. The temporal variations of total ARGs abundance had no significant different in soil and lettuce phylloplane, while lettuce endosphere enriched half of ARGs to the highest level at harvest. There was a significant linear correlation between ARGs and integrase genes (IGs). In contrast to the ARGs variation trend, the alpha diversity of soil and phylloplane bacteria showed increasing trends over planting time, and endosphere bacteria remained stable. Correlation analysis showed no identical ARG-related genera in the three parts, but the shared Proteobacteria, Pseudomonas, Halomonas and Chelativorans, from manure compost dominated ARG profile in the soil-lettuce system. Moreover, redundancy analysis and structural equation modelling showed the variations of ARGs may have resulted from the combination of multiple driving factors in soil-lettuce system. ARGs in soil were more affected by the IGs, antibiotic and heavy metals, and bacterial community structure and IGs were the major influencing factors of ARG profiles in the lettuce. The study provided insight into the multiple driving factors contribute to the variations of typical ARGs in different parts of soil-lettuce system, which was conducive to the risk assessment of ARGs in agroecosystem and the development of effective prevention and control measures for ARGs spread in the environment.202134562788
6983160.9996Deciphering Potential Roles of Earthworms in Mitigation of Antibiotic Resistance in the Soils from Diverse Ecosystems. Earthworms are capable of redistributing bacteria and antibiotic resistance genes (ARGs) through soil profiles. However, our understanding of the earthworm gut microbiome and its interaction with the antibiotic resistome is still lacking. Here, we characterized the earthworm gut and soil microbiome and antibiotic resistome in natural and agricultural ecosystems at a national scale, and microcosm studies and field experiments were also employed to test the potential role of earthworms in dynamics of soil ARGs. The diversity and structure of bacterial communities were different between the earthworm gut and soil. A significant correlation between bacterial community dissimilarity and spatial distance between sites was identified in the earthworm gut. The earthworm gut consistently had lower ARGs than the surrounding soil. A significant reduction in the relative abundance of mobile genetic elements and dominant bacterial phylotypes that are the likely hosts of ARGs was observed in the earthworm gut compared to the surrounding soil, which might contribute to the decrease of ARGs in the earthworm gut. The microcosm studies and field experiments further confirmed that the presence of earthworms significantly reduced the number and abundance of ARGs in soils. Our study implies that earthworm-based bioremediation may be a method to reduce risks associated with the presence of ARGs in soils.202133977709
6973170.9996Carbendazim shapes microbiome and enhances resistome in the earthworm gut. BACKGROUND: It is worrisome that several pollutants can enhance the abundance of antibiotic resistance genes (ARGs) in the environment, including agricultural fungicides. As an important bioindicator for environmental risk assessment, earthworm is still a neglected focus that the effects of the fungicide carbendazim (CBD) residues on the gut microbiome and resistome are largely unknown. In this study, Eisenia fetida was selected to investigate the effects of CBD in the soil-earthworm systems using shotgun metagenomics and qPCR methods. RESULTS: CBD could significantly perturb bacterial community and enrich specific bacteria mainly belonging to the phylum Actinobacteria. More importantly, CBD could serve as a co-selective agent to elevate the abundance and diversity of ARGs, particularly for some specific types (e.g., multidrug, glycopeptide, tetracycline, and rifamycin resistance genes) in the earthworm gut. Additionally, host tracking analysis suggested that ARGs were mainly carried in some genera of the phyla Actinobacteria and Proteobacteria. Meanwhile, the level of ARGs was positively relevant to the abundance of mobile genetic elements (MGEs) and some representative co-occurrence patterns of ARGs and MGEs (e.g., cmx-transposase and sul1-integrase) were further found on the metagenome-assembled contigs in the CBD treatments. CONCLUSIONS: It can be concluded that the enhancement effect of CBD on the resistome in the earthworm gut may be attributed to its stress on the gut microbiome and facilitation on the ARGs dissemination mediated by MGEs, which may provide a novel insight into the neglected ecotoxicological risk of the widely used agrochemicals on the gut resistome of earthworm dwelling in soil. Video abstract.202235436900
7168180.9996Insights into microbial contamination in multi-type manure-amended soils: The profile of human bacterial pathogens, virulence factor genes and antibiotic resistance genes. Concerns regarding biological risk in environment have garnered increasing attention. Manure has been believed to be a significant source of antibiotic resistance genes (ARGs) in agricultural soil. Nevertheless, the profile of microbial contamination including ARGs, virulence factor genes (VFGs) and human bacterial pathogens (HBPs) in different manure-amended soils remain largely unknown. Here, we conducted the systematic metagenome-based study to explore changes in resistome, VFGs and HBPs in soils treated by frequently-used manures. The results revealed that many manure-borne ARGs, VFGs, and HBPs could be spreaded into soils, and their diversity and abundance were significantly different among chemical fertilizer, pig manure, chicken manure, cow dung and silkworm excrement application. A total of 157 potential HBPs accounting about 1.33% of total bacteria were detected. The main ARGs transferred from manures to soil conferred resistance to vancomycin and macrolide-lincosamide-streptogramin. The series analysis revealed positive co-occurrence patterns of ARGs-HBPs, VFGs-HBPs and ARGs-VFGs. Microbial contamination were more serious in pig manure and silkworm excrement sample than in the other samples, implying the usage of these two manures increased the risk of HBPs and dissemination of ARGs. This study confirmed the prevalence and discrepancy of resistome, VFGs and HBPs in different manure-amended soils.202235728317
7025190.9996Aerobic composting as an effective cow manure management strategy for reducing the dissemination of antibiotic resistance genes: An integrated meta-omics study. Livestock manure is considered as an important source for spreading antibiotic resistance genes (ARGs) into the environment, and therefore poses a direct threat to public health. Whereas the effects of reused manure on soil microbial communities and ARGs have been studied extensively, comprehensive characterizations of microbial communities and ARGs of manure produced by different management methods are not well understood. Here, we analyzed the fate of microbial communities and ARGs of cow manure treated by three conventional management strategies: aerobic composting, mechanical drying and precipitation, applying an integrated-omics approach combining metagenomics and metaproteomics. Integrated-omics demonstrated that composted manure contained the lowest diversity of microbial community and ARGs compared with manure treated by other two strategies. Quantitative PCR methods revealed that the abundances of ARGs were reduced by over 83 % after composting for 14 days, regardless of the season. Besides, the potential ARG hosts Acinetobacter and Pseudomonas dominating mechanical drying process were sharply decreased in abundances after composting. The significant co-occurrence networks among bacteria, ARGs and transposase gene tnpA-01 in composting samples indicated the important role of these bacteria in the dissemination of ARGs. These findings offer insight into potential strategies to control the spread of ARGs during livestock manure reuse.202031884359