Historical trajectories of antibiotics resistance genes assessed through sedimentary DNA analysis of a subtropical eutrophic lake. - Related Documents




#
Rank
Similarity
Title + Abs.
Year
PMID
012345
683201.0000Historical trajectories of antibiotics resistance genes assessed through sedimentary DNA analysis of a subtropical eutrophic lake. Investigating the occurrence of antibiotic-resistance genes (ARGs) in sedimentary archives provides opportunities for reconstructing the distribution and dissemination of historical (i.e., non-anthropogenic origin) ARGs. Although ARGs in freshwater environments have attracted great attention, historical variations in the diversity and abundance of ARGs over centuries to millennia remain largely unknown. In this study, we investigated the vertical change patterns of bacterial communities, ARGs and mobile genetic elements (MGEs) found in sediments of Lake Chenghai spanning the past 600 years. Within resistome preserved in sediments, 177 ARGs subtypes were found with aminoglycosides and multidrug resistance being the most abundant. The ARG abundance in the upper sediment layers (equivalent to the post-antibiotic era since the 1940s) was lower than those during the pre-antibiotic era, whereas the ARG diversity was higher during the post-antibiotic era, possibly because human-induced lake eutrophication over the recent decades facilitated the spread and proliferation of drug-resistant bacteria. Statistical analysis suggested that MGEs abundance and the bacterial community structure were significantly correlated with the abundance and diversity of ARGs, suggesting that the occurrence and distribution of ARGs may be transferred between different bacteria by MGEs. Our results provide new perspectives on the natural history of ARGs in freshwater environments and are essential for understanding the temporal dynamics and dissemination of ARGs.202438621322
682710.9999Metagenomic profiles of planktonic bacteria and resistome along a salinity gradient in the Pearl River Estuary, South China. Estuarine ecosystems undergo pronounced and intricate changes due to the mixing of freshwater and saltwater. Additionally, urbanization and population growth in estuarine regions result in shifts in the planktonic bacterial community and the accumulation of antibiotic resistance genes (ARGs). The dynamic changes in bacterial communities, environmental factors, and carriage of ARGs from freshwater to seawater, as well as the complex interrelationships among these factors, have yet to be fully elucidated. Here, we conducted a comprehensive study based on metagenomic sequencing and full-length 16S rRNA sequencing, covering the entire Pearl River Estuary (PRE) in Guangdong, China. The abundance and distribution of the bacterial community, ARGs, mobile genetic elements (MGEs), and bacterial virulence factors (VFs) were analyzed on a site-by-site basis through sampling along the salinity gradient in PRE, from upstream to downstream. The structure of the planktonic bacterial community undergoes continuous changes in response to variations in estuarine salinity, with the phyla Proteobacteria and Cyanobacteria being dominant bacterial throughout the entire region. The diversity and abundance of ARGs and MGEs gradually decreased with the direction of water flow. A large number of ARGs were carried by potentially pathogenic bacteria, especially in Alpha-proteobacteria and Beta-proteobacteria. Multi-drug resistance genes have the highest abundance and subtypes in PRE. In addition, ARGs are more linked to some MGEs than to specific bacterial taxa and disseminate mainly by HGT and not by vertical transfer in the bacterial communities. Various environmental factors, such as salinity and nutrient concentrations, have a significantly impact on the community structure and distribution of bacteria. In conclusion, our results represent a valuable resource for further investigating the intricate interplay between environmental factors and anthropogenic disturbances on bacterial community dynamics. Moreover, they contribute to a better understanding of the relative impact of these factors on the dissemination of ARGs.202337211102
697820.9999Climate warming increases the proportions of specific antibiotic resistance genes in natural soil ecosystems. Understanding the future distribution of antibiotic resistance in natural soil ecosystems is important to forecast their impacts on ecosystem and human health under projected climate change scenarios. Therefore, it is critical and timely to decipher the links between climate warming and antibiotic resistance, two of Earth's most imminent problems. Here, we explored the role of five-year simulated climate warming (+ 4 °C) on the diversity and proportions of soil antibiotic resistance genes (ARGs) across three seasons in both plantation and natural forest ecosystems. We found that the positive effects of warming on the number and proportions of ARGs were dependent on the sampling seasons (summer, autumn and winter), and seasonality was a key factor driving the patterns of ARG compositions in forest soils. Fifteen ARGs, conferring resistance to common antibiotics including aminoglycoside, beta-lactam, macrolide-lincosamide-streptogramin B, multidrug, sulfonamide, and tetracycline, were significantly enriched in the warming treatment. We showed that changes in soil properties and community compositions of bacteria, fungi and protists can explain the changes in soil ARGs under climate warming. Taken together, these findings advance our understanding of environmental ARGs under the context of future climate change and suggest that elevated temperature may promote the abundance of specific soil ARGs, with important implications for ecosystem and human health.202235158246
683130.9999Diversity of herbaceous plants and bacterial communities regulates soil resistome across forest biomes. Antibiotic resistance is ancient and prevalent in natural ecosystems and evolved long before the utilization of synthetic antibiotics started, but factors influencing the large-scale distribution patterns of natural antibiotic resistance genes (ARGs) remain largely unknown. Here, a large-scale investigation over 4000 km was performed to profile soil ARGs, plant communities and bacterial communities from 300 quadrats across five forest biomes with minimal human impact. We detected diverse and abundant ARGs in forests, including over 160 genes conferring resistance to eight major categories of antibiotics. The diversity of ARGs was strongly and positively correlated with the diversity of bacteria, herbaceous plants and mobile genetic elements (MGEs). The ARG composition was strongly correlated with the taxonomic structure of bacteria and herbs. Consistent with this strong correlation, structural equation modelling demonstrated that the positive effects of bacterial and herb communities on ARG patterns were maintained even when simultaneously accounting for multiple drivers (climate, spatial predictors and edaphic factors). These findings suggest a paradigm that the interactions between aboveground and belowground communities shape the large-scale distribution of soil resistomes, providing new knowledge for tackling the emerging environmental antibiotic resistance.201829687575
680940.9998High-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
682550.9998Bacteria and Antibiotic Resistance Genes (ARGs) in PM(2.5) from China: Implications for Human Exposure. Airborne transmission is one of the environmental dissemination pathways of antibiotic resistance genes (ARGs), and has critical implications for human exposure through inhalation. In this study, we focused on three regions of China to reveal some unique spatiotemporal features of airborne bacteria and ARGs in fine aerosols (PM(2.5)): (1) greater seasonal variations in the abundance of bacteria and ARGs in temperate urban Beijing than in the subtropical urban areas of the Yangtze River Delta (YRD) and Pearl River Delta (PRD) regions, with regional disparities in bacterial communities; (2) geographical fingerprints of ARG profiles independent of seasonal cycles and land-use gradients within each region; (3) region-independent associations between the targeted ARGs and limited bacterial genera; (4) common correlations between ARGs and mobile genetic elements (MGEs) across regions; and (5) PM(2.5) at the higher end of ARG enrichment across various environmental and human media. The spatiotemporally differentiated bacterial communities and ARG abundances, and the compositions, mobility, and potential hosts of ARGs in the atmosphere have strong implications for human inhalational exposure over spatiotemporal scales. By comparing other contributing pathways for the intake of ARGs (e.g., drinking water and food ingestion) in China and the U.S.A., we identified the region-specific importance of inhalation in China as well as country-specific exposure scenarios. Our study thus highlights the significance of inhalation as an integral part of the aggregate exposure pathways of environmentally disseminated ARGs, which, in turn, may help in the formulation of adaptive strategies to mitigate the exposure risks in China and beyond.201930525504
681760.9998Distribution of Antibiotic Resistance Genes in Karst River and Its Ecological Risk. In recent years, karst water has been polluted by emerging pollutants such as antibiotics. In this study, the bacterial communities and antibiotic resistance genes (ARGs) in antibiotics contaminated karst river was studied in summer and winter. The concentration of antibiotics in winter karst river is higher than that in summer, and there are significant differences in structure of bacterial community and ARGs between karst river water samples. Aminoglycoside, beta-lactamase and multidrug are the main types of ARGs, and transposons play an important role in the spread of ARGs. The horizontal gene transfer (HGT) of ARGs between bacteria mediated by mobile genetic elements (MGEs) would cause the spread of ARGs and bring potential ecological risks. In addition, we found that the risk of antibiotic resistant pathogenic bacteria (ARPB) in winter was possibly higher than that in summer. It was suggested that the discharge of antibiotics, water amount and seasonal occurrence time of human intestinal diseases affect the risks caused by antibiotics contaminants. This study helps us to understand the transmission mechanism of ARGs and their potential seasonal ecological risks in complex karst water systems.202134392041
681670.9998The impact of microplastics on antibiotic resistance genes, metal resistance genes, and bacterial community in aquaculture environment. Microplastics are emerging contaminants. However, their effects on antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and the structure and abundance of bacterial communities, particularly pathogens, in aquaculture environments remains poorly understood. Therefore, this study investigated the effect of microplastics of different sizes on the abundance and distribution of ARGs, MRGs, and bacterial communities in aquaculture environments. The results revealed that, compared with pond water, large microplastics harbored significantly higher ARG abundances, particularly for multidrug-resistant genes; notably, level-I- and -II-risk ARGs were more prevalent on microplastics, highlighting the potential for horizontal gene transfer. Microplastics also exhibited a propensity to aggregate pathogenic bacteria such as Brucella and Pseudomonas, which could pose direct risks to aquatic product safety and public health. Network and differential network analyses revealed significant correlations between bacterial genera and ARG/MRG abundance, particularly on microplastics. Therefore, our findings suggest that microplastics act as vectors for the spread of ARGs, MRGs, and pathogens in aquaculture, potentially leading to the formation of complexes of these materials that threaten ecosystem health and human well-being. This study provides critical insights into the need for targeted management strategies to mitigate microplastic pollution in aquaculture settings.202539987738
643280.9998Antibiotic resistance genes in the coastal atmosphere under varied weather conditions: Distribution, influencing factors, and transmission mechanisms. Antibiotic resistance genes (ARGs) have escalated to levels of concern worldwide as emerging environmental pollutants. Increasing evidence suggests that non-antibiotic antimicrobial substances expedite the spread of ARGs. However, the drivers and mechanisms involved in the generation and spread of ARGs in the atmosphere remain inadequately elucidated. Co-occurrence networks, mantel test analysis, and partial least squares path modeling were used to analyze the symbiotic relationships of ARGs with meteorological conditions, atmospheric pollutants, water-soluble inorganic ions, bacteria, mobile genetic elements (MGEs), antibacterial biocide and metal resistance genes, and to identify the direct drivers of ARGs. The types and abundance of ARGs exhibited different seasonal distribution. Specifically, the types exhibited a strong alignment with the diversity of air masses terrestrial sources, while the abundance displayed a significant positive correlation with both biocide resistance genes (BRGs) and metal resistance genes (MRGs). The contribution of bacterial communities and MGEs to the generation and spread of ARGs was constrained by the low levels of antibiotics in the atmosphere and the existence of "viral intermediates". Conversely, antibacterial biocides and metals influenced mutation rates, cellular SOS responses, and oxidative stress of bacteria, consequently facilitating the generation and spread of ARGs. Moreover, the co-selection among their derivatives, resistance genes, ensured a stable presence of ARGs. The research highlighted the significant impact of residual antimicrobial substances on both the generation and spread of ARGs. Elucidating the sources of aerosols and the co-selection mechanism linking with ARGs, BRGs, and MRGs were crucial for preserving the stability of ARGs in the atmosphere.202539824332
698290.9998Viral 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
6883100.9998Metagenomic insights into the profile of antibiotic resistomes in sediments of aquaculture wastewater treatment system. To meet the rapidly growing global demand for aquaculture products, large amounts of antibiotics were used in aquaculture, which might accelerate the evolution of antibiotic-resistant bacteria (ARB) and the propagation of antibiotic genes (ARGs). In our research, we revealed the ARGs profiles, their co-occurrence with mobile genetic elements (MGEs), and potential hosts in sediments of a crab pond wastewater purification system based on metagenomic analysis. The residual antibiotic seems to increase the propagation of ARGs in the crab pond, but there was no clear relationship between a given antibiotic type and the corresponding resistance genes. The effect of aquaculture on sediment was not as profound as that of other anthropogentic activities, but increased the relative abundance of sulfonamide resistance gene. A higher abundance of MGEs, especially plasmid, increased the potential ARGs dissemination risk in crab and purification ponds. Multidrug and sulfonamide resistance genes had greater potential to transfer because they were more frequently carried by MGEs. The horizontal gene transfer was likely to occur among a variety of microorganisms, and various ARGs hosts including Pseudomonas, Acinetobacter, Escherichia, and Klebsiella were identified. Bacterial community influenced the composition of ARG hosts, and Proteobacteria was the predominant hosts. Overall, our study provides novel insights into the environmental risk of ARGs in sediments of aquaculture wastewater treatment system.202234963542
6976110.9998Unveiling the critical role of overlooked consumer protist-bacteria interactions in antibiotic resistance gene dissemination in urban sewage systems. Antibiotic resistance genes (ARGs) are emerging contaminants of significant concern due to their role in facilitating the spread of antibiotic resistance, especially high-risk ARGs, which are characterized by high human accessibility, gene mobility, pathogenicity, and clinical availability. Studies have shown that cross-domain interactions, such as those between consumer protists (consumers) and bacteria, can influence bacterial diversity, distribution, and function through top-down control. The consumers-bacteria interactions may also affect the occurrence and distribution of ARGs, yet this has been scarcely explored in field investigations. We conducted a city-scale investigation of ARGs, protists, and bacterial communities across each unit of the urban sewage system (USS), including 49 sewage pumping stations (SW), as well as influent (IF), activated sludge (AS), and effluent (EF) from seven wastewater treatment plants. Interestingly, consumers-bacteria interactions, as indicated by indices of bipartite relevance networks (i.e., connectedness and cohesion), increased from SW and IF to AS and EF. Structural equation modelling (SEM) revealed that consumers-bacteria interactions had a greater influence on the abundance of total ARGs and high-risk ARGs than seasonal or environmental factors. Notably, the total effects of consumers-bacteria interactions in SEM were significant (P < 0.05) and comparable in both IF and EF, even with the decrease in ARG abundance from IF to EF. This suggests a potential risk of ARG spread to the environment, facilitated by consumer protists in the EF. Additionally, the relevance network also demonstrated an increasing trend in the relationships between consumer protists and potential hosts of high-risk ARGs from raw sewage (SW and IF) to AS and EF. Overall, this study emphasizes the importance of integrating multitrophic microbial interactions to better understand and mitigate the dissemination of ARGs in sewage systems.202539662352
6826120.9998Impact of land use on antibiotic resistance genes and bacterial communities in rivers. River ecosystems support essential ecosystem functions and services, including supplying water for domestic, agricultural, and industrial activities, provisioning of hydropower and fisheries, supporting navigation and recreational activities, and regulating water quality. In recent decades, the presence and spread of antibiotic resistance genes (ARGs) have emerged as a key threat to ecosystem health and human well-being. Rivers that are surrounded by human-modified landscapes serve as primary repositories and sources of ARGs. However, our understanding of the relationship between the diversity of ARGs and land use remain limited. We collected 30 sediment samples from five rivers in Ningbo, China, and then classified the sampling sites into two groups (i.e., group A with low levels of human impacts and group B with intense human impact) based on land use in their upstream areas. In total, we found 31 types of ARGs and 148 phyla of bacteria in the samples. ARGs abundance had a positive relationship with the levels of anthropogenic activities, and exhibited significant difference between the two groups. Co-occurrence networks showed that the interrelationship between bacteria and ARGs was more complex in group B than in group A. Moreover, Structural Equation Modeling (SEM) revealed that anthropogenic activity not only posed direct effect on ARGs but also indirectly affected ARGs through bacteria. Our results underscore the profound impacts of land-use changes on the diversity of ARGs, bacteria communities, and their relationships, which highlight the need for integrating ARGs in river assessments in regions with human-dominated land use.202540154785
6884130.9998The changes in antibiotic resistance genes during 86 years of the soil ripening process without anthropogenic activities. This study aimed to reveal the baseline of natural variations in antibiotic resistance genes (ARGs) in soil without anthropogenic activities over the decades. Nine soil samples with different time of soil formation were taken from the Yancheng Wetland National Nature Reserve, China. ARGs and mobile genetic elements (MGEs) were characterized using metagenomic analysis. A total of 196 and 192 subtypes of ARGs were detected in bulk soil and rhizosphere, respectively. The diversity and abundance of ARGs were stable during 69 years probably due to the alkaline pH soil environment but not due to antibiotics. Increases in ARGs after 86 years were probably attributed to more migrant birds inhabited compared with other sampling sites. Multidrug was the most abundant type, and largely shared by soil samples. It was further shown that soil samples could not be clearly distinguished, suggesting a slow process of succession of ARGs in the mudflat. The variation partitioning analysis revealed that the ARG profile was driven by the comprehensive effects exhibited by the bacterial community, MGEs, and environmental factors. Besides, pathogenic bacteria containing ARGs mediated by migrant birds in the area with 86 years of soil formation history nearing human settlements needed special attention. This study revealed the slow variations in ARGs in the soil ripening process without anthropogenic activities over decades, and it provided information for assessing the effect of human activities on the occurrence and dissemination of ARGs.202133228990
6830140.9998Heavy 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
6814150.9998Watershed urbanization enhances the enrichment of pathogenic bacteria and antibiotic resistance genes on microplastics in the water environment. Microplastics (MPs) serve as vectors for microorganisms and antibiotic resistance genes (ARGs) and contribute to the spread of pathogenic bacteria and ARGs across various environments. Patterns of microbial communities and ARGs in the biofilm on the surface of MPs, also termed as plastisphere, have become an issue of global concern. Although antibiotic resistome in the plastisphere has been detected, how watershed urbanization affects patterns of potential pathogens and ARGs in the microplastic biofilms is still unclear. Here, we compared the bacterial communities, the interaction between bacterial taxa, pathogenic bacteria, and ARGs between the plastisphere and their surrounding water, and revealed the extensive influence of urbanization on them. Our results showed that bacterial communities and interactions in the plastisphere differed from those in their surrounding water. Microplastics selectively enriched Bacteroidetes from water. In non-urbanized area, the abundance of Oxyphotobacteria was significantly (p < 0.05) higher in plastisphere than that in water, while α-Proteobacteria was significantly (p < 0.05) higher in plastisphere than those in water of urbanized area. Pathogenic bacteria, ARGs, and mobile genetic elements (MGEs) were significantly (p < 0.05) higher in the urbanized area than those in non-urbanized area. MPs selectively enriched ARG-carrying potential pathogens, i.e., Klebsiella pneumoniae and Enterobacter cloacae, and exhibited a distinct effect on the relative abundance of ARG and pathogens in water with different urbanization levels. We further found ARGs were significantly correlated to MGEs and pathogenic bacteria. These results suggested that MPs would promote the dissemination of ARGs among microbes including pathogenic bacteria, and urbanization would affect the impact of MPs on microbes, pathogens, and ARGs in water. A high level of urbanization could enhance the enrichment of pathogens and ARGs by MPs in aquatic systems and increase microbial risk in aquatic environments. Our findings highlighted the necessity of controlling the spread of ARGs among pathogens and the usage of plastic products in ecosystems of urban areas.202236108884
6885160.9998Abundant bacteria shaped by deterministic processes have a high abundance of potential antibiotic resistance genes in a plateau river sediment. Recent research on abundant and rare bacteria has expanded our understanding of bacterial community assembly. However, the relationships of abundant and rare bacteria with antibiotic resistance genes (ARGs) remain largely unclear. Here, we investigated the biogeographical patterns and assembly processes of the abundant and rare bacteria from river sediment at high altitudes (Lhasa River, China) and their potential association with the ARGs. The results showed that the abundant bacteria were dominated by Proteobacteria (55.4%) and Cyanobacteria (13.9%), while the Proteobacteria (33.6%) and Bacteroidetes (18.8%) were the main components of rare bacteria. Rare bacteria with a large taxonomic pool can provide function insurance in bacterial communities. Spatial distribution of persistent abundant and rare bacteria also exhibited striking differences. Strong selection of environmental heterogeneity may lead to deterministic processes, which were the main assembly processes of abundant bacteria. In contrast, the assembly processes of rare bacteria affected by latitude were dominated by stochastic processes. Abundant bacteria had the highest abundance of metabolic pathways of potential drug resistance in all predicted functional genes and a high abundance of potential ARGs. There was a strong potential connection between these ARGs and mobile genetic elements, which could increase the ecological risk of abundant taxa and human disease. These results provide insights into sedimental bacterial communities and ARGs in river ecosystems.202236406442
6977170.9998Tracking virulence genes and their interaction with antibiotic resistome during manure fertilization. Antibiotic resistance genes, collectively termed as antibiotic resistome, are regarded as emerging contaminants. Antibiotics resistome can be highly variable in different environments, imposing environmental safety concern and public health risk when it is in conjunction with pathogenic bacteria. However, it remains elusive how pathogenic bacteria interact with antibiotic resistome, making it challenging to assess microbial risk. Here, we examined the presence and relative abundance of bacterial virulence genes representing potential pathogens in swine manure, compost, compost-amended soil, and unamended agricultural soil in five suburban areas of Beijing, China. The absolute abundances of virulence genes were marginally significantly (p < 0.100) increased in compost-amended soils than unamended soil, revealing potential health risks in manure fertilization. The composition of potential pathogens differed by sample types and was linked to temperature, antibiotics, and heavy metals. As antibiotics can confer pathogens the resistance to clinic treatment, it was alarming to note that virulence genes tended to co-exist with antibiotic resistance genes, as shown by prevalently positive links among them. Collectively, our results demonstrate that manure fertilization in agriculture might give rise to the development of potentially antibiotic-resistant pathogens, unveiling an environmental health risk that has been frequently overlooked.202235810986
6829180.9998Metagenomic 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
6974190.9998Comparison of soil and grass microbiomes and resistomes reveals grass as a greater antimicrobial resistance reservoir than soil. Grasslands cover a large proportion of global agricultural landmass used to feed herbivores and ruminants and link the environment to the food chain via animals onto humans. However, most scientific studies of antimicrobial resistance and microbiomes at the environmental - animal nexus have focused on soil or vegetables rather than grasslands. Based on previous microbiome phyllosphere-soil studies we hypothesised that the microbiome and resistomes across soil and grass would have a core of shared taxa and antimicrobial resistance genes (ARGs), but that in addition each would also have a minority of unique signatures. Our data indicated grass contained a wider variety and higher relative abundance of ARGs and mobile genetic elements (MGEs) than soil with or without slurry amendments. The microbiomes of soil and grass were similar in content but varied in the composition proportionality. While there were commonalities across many of the ARGs present in soil and on grass their correlations with MGEs and bacteria differed, suggesting a source other than soil is also relevant for the resistome of grass. The variations in the relative abundances of ARGs in soil and on grass also indicated that either the MGEs or the bacteria carrying the ARGs comprised a higher relative abundance on grass than in soil. We conclude that while soil may be a source of some of these genes it cannot be the source for all ARGs and MGEs. Our data identifies grass as a more diverse and abundant reservoir of ARGs and MGEs in the environment than soil, which is significant to human and animal health when viewed in the context of grazing food animals.202336191722