Agricultural activities affect the pattern of the resistome within the phyllosphere microbiome in peri-urban environments

Antibiotic resistome dynamics in agricultural river systems: Elucidating transmission mechanisms and associated risk to water security

Usage of antibiotics in agriculture has increased dramatically recently, significantly raising the influx of antibiotic resistance genes (ARGs) into river systems through organic manure runoff, seriously threatening water security. However, the dynamics, transmission mechanisms, and potential water security risk of ARGs, as well as their response to land use spatial scale and seasonal variations in agricultural river systems remain unclear. To address these challenges, this work employed metagenomic technique to systematically evaluate the pollution and dissemination of ARGs in overlying water and sediment within a typical agricultural catchment in China. The results demonstrated significant differences between overlying water and sediment ARGs. Overlying water dominated by multidrug ARGs exhibited higher diversity, whereas sediment predominantly containing sulfonamide ARGs had higher abundance. The dynamics of ARGs in overlying water were more responsive to seasonal variations compared to sediment due to greater changes in hydrodynamics and nutrient conditions. The profiles of ARGs in overlying water were largely regulated by microbiota, whereas mobile genetic elements (MGEs) were the main forces driving the dissemination of ARGs in sediment. The variation in dissemination mechanisms led to different resistance risks, with sediment presenting a higher resistance risk than overlying water. Furthermore, Mantel test was applied to discover the impact of land use spatial scale and composition on the transmission of ARGs in river systems. The findings showed that cultivated land within 5 km of the riverbank was the key influencing factor. Cultivated land exacerbated ARGs spread by increasing MGEs abundance and nutrient concentrations, resulting in the abundance of ARGs in high-cultivated sites being twice that in low-cultivated sites, and raising the regional water security risk, with a more pronounced effect in sediment. These findings contribute to a better understanding of ARGs dissemination in agricultural watersheds, providing a basis for implementing effective resistance control measures and ensuring water security.

Needles in haystacks: monitoring the potential escape of bioaerosolised antibacterial resistance genes from wastewater treatment plants with air and phyllosphere sampling

Wastewater treatment plants are well-known point sources of emissions of antibacterial resistance genes (ARGs) into the environment. Although most work to date has focused on ARG dispersal via effluent, aerial dispersal in bioaerosols is a poorly understood, but likely important vector for ARG dispersal. Recent evidence suggests that ARG profiles of the conifer needle phyllosphere could be used to measure bioaerosol dispersal from anthropogenic sources. Here, we assessed airborne dispersal of ARGs from wastewater treatment plants in Wales, UK and Quebec, Canada, using conifer needles as passive bioaerosol monitors. ARG profiles of wastewater were compared to those of conifer phyllosphere using high-throughput qPCR. ARG richness was significantly lower in conifer phyllosphere samples than wastewater samples, though no differences were observed across the dispersal gradients. Mean copy number of ARGs followed a similar trend. ARG profiles showed limited, but consistent patterns with increasing distance from wastewater treatment plants, but these did not align with those of wastewater samples. For example, proportional abundance of aminoglycosides decreased over the dispersal gradient in Wales, whereas mobile genetic elements showed the inverse relationship. In summary, while distinct ARG profiles exist along dispersal gradients, links to those of wastewater were not apparent.

Distinct patterns of the soil and phyllosphere antibiotic resistome in natural forest ecosystems under an altitudinal gradient

Warming affects microbial functioning of soil and the phyllosphere across global ecosystems. However, little is known about the impact of increasing temperature on antibiotic resistome profiles in natural forests. To address this issue, we investigated antibiotic resistance genes (ARGs) in both soil and the plant phyllosphere using an experimental platform established in a forest ecosystem that delivers a temperature difference of 2.1 °C along an altitudinal gradient. Principal Coordinate Analysis (PCoA) showed that there were significant differences in the composition of soil and plant phyllosphere ARGs at different altitudes (P = 0.001). The relative abundance of phyllosphere ARGs and mobile genetic elements (MGEs) and soil MGEs increased with temperature. More resistance gene classes increased in abundance in the phyllosphere (10 classes) than soil (2 classes), and a Random Forest model analysis suggested that phyllosphere ARGs were more sensitive to temperature change than soil. Increasing temperature as a direct consequence of an altitudinal gradient, and the relative abundance of MGEs were the main drivers that shaped the profiles of ARGs in the phyllosphere and soil. Biotic and abiotic factors affected phyllosphere ARGs indirectly via MGEs. This study enhances our understanding of the influence of altitude gradients on resistance genes in natural environments.

Uncovering the prevalence and drivers of antibiotic resistance genes in soils across different land-use types

The emergence and spread of antibiotic resistance genes (ARGs) in soil due to animal excreta and organic waste is a major threat to human health and ecosystems, and global efforts are required to tackle the issue. However, there is limited knowledge of the variation in ARG prevalence and diversity resulting from different land-use patterns and underlying driving factors in soils. This study aimed to comprehensively characterize the profile of ARGs and mobile genetic elements and their drivers in soil samples collected from 11 provinces across China, representing three different land-use types, using high-throughput quantitative polymerase chain reaction and 16S rRNA amplicon sequencing. Our results showed that agricultural soil had the highest abundance and diversity of ARGs, followed by tea plantation and forest land. A total of 124 unique ARGs were detected in all samples, with shared subtypes among different land-use patterns indicating a common origin or high transmission frequency. Moreover, significant differences in ARG distribution were observed among different geographical regions, with the greatest enrichment of ARGs found in southern China. Biotic and abiotic factors, including soil properties, climatic factors, and bacterial diversity, were identified as the primary drivers associated with ARG abundance, explaining 71.8% of total ARG variation. The findings of our study demonstrate that different land-use patterns are associated with variations in ARG abundance in soil, with agricultural practices posing the greatest risk to human health and ecosystems regarding ARGs. Our identification of biotic and abiotic drivers of ARG abundance provides valuable insights into strategies for mitigating the spread of these genes. This study emphasizes the need for coordinated and integrated approaches to address the global antimicrobial resistance crisis.

Role of microplastics in microbial community structure and functions in urban soils

Evidence from the laboratory suggests that microplastics (MPs) can harm soil microorganisms, affecting the structures and functions of microbial communities. The impact of soil MPs on microbes in actual urban environments with high human activity levels, however, has not been well reported. To investigate the MP effect on urban soil microorganisms under complex scenarios, we analyzed 42 soil samples from standardized plots of 7 urban functional zones. We report that urban green spaces are important for studying microbial diversity in the study area, and they also contribute to the global homogenization of soil microbes and genes. Bacterial communities in soils enriched with various MPs showed greater differences in OTUs than fungi. Compared to low-MP soils, most ARGs and nutrient cycling genes had similar or slightly lower abundances in soils with high levels of MPs. The coupling of pollutant factors with MPs as independent variables had significant explanatory power for both positive and negative correlations in PLS-PM analysis. Specifically, PET and PP MPs explained 3.54% and 6.03%, respectively, of the microbial community and functional genes. This study fills knowledge gaps on the effects of MPs on urban soil microbial communities in real environments, facilitating better management of urban green spaces.

Reforestation substantially changed the soil antibiotic resistome and its relationships with metal resistance genes, mobile genetic elements, and pathogens

Revealing the effects of reforestation on soil antibiotic resistome is essential for assessing ecosystem health, yet related studies remain scarce. Here, to determine the responses of the soil antibiotic resistome to reforestation, 30 pairs of cropland and forest soil samples were collected from southwestern China, a region with high environmental heterogeneity. All the forests had been derived from croplands more than one decade ago. The diversity and abundance of soil antibiotic resistance genes (ARGs), metal resistance genes (MRGs), mobile genetic elements (MGEs), and pathogens were determined by metagenomic sequencing and real-time PCR. The results showed that reforestation significantly increased soil microbial abundance and the contents of Cu, total carbon, total nitrogen, total organic carbon, and ammonium nitrogen. Nevertheless, it decreased the contents of soil Zn, Ba, nitrate nitrogen, and available phosphorus. The main soil ARGs identified in this region were vancomycin, multidrug, and bacitracin resistance genes. Reforestation significantly increased the soil ARG abundance by 62.58%, while it decreased the ARG richness by 16.50%. Reforestation exerted no significant effects on the abundance of heavy metal resistance genes and pathogens, but it doubled the abundance of MGEs. Additionally, reforestation substantially decreased the co-occurrence frequencies of ARGs with MRGs and pathogens. In contrast, the correlation between ARGs and MGEs was greatly enhanced by reforestation. Similarly, the correlations between soil ARG abundance and environmental factors were also strengthened by reforestation. These findings suggest that reforestation can substantially affect the soil antibiotic resistome and exerts overall positive effects on soil health by decreasing ARG richness, providing critical information for assessing the effects of "grain for green" project on soil health.

Plant cultivar determined bacterial community and potential risk of antibiotic resistance gene spread in the phyllosphere

The global increased antibiotic resistance level in pathogenic microbes has posed a significant threat to human health. Fresh vegetables have been recognized to be an important vehicle of antibiotic resistance genes (ARGs) from environments to human beings. Phyllosphere ARGs have been indicated to be changed with plant species, yet the influence of plant cultivar on the phyllospheric resistome is still unclear. Here, we detected the ARGs and bacterial communities in the phyllosphere of two cultivars of cilantros and their corresponding soils using high-throughput quantitative PCR technique and bacterial 16S rRNA gene-based high-throughput sequencing, respectively. We further identified the potential bacterial pathogens and analyzed the effects of plant cultivar on ARGs, mobile genetic elements (MGEs), microbiome and potential bacterial pathogens. The results showed that the cultivars did not affect the ARG abundance and composition, but significantly shaped the abundance of MGEs and the composition structure of bacteria in the phyllosphere. The relative abundance of potential bacterial pathogens was significantly higher in the phyllosphere than that in soils. Mantel test showed that the ARG patterns were significantly correlated to the patterns of potential bacterial pathogens. Our results suggested that the horizontal gene transfer of ARGs in the phyllosphere might be different between the two cultivars of cilantro and highlighted the higher risk of phyllospheric microorganisms compared with those in soils. These findings extend our knowledge on the vegetable microbiomes, ARGs, and potential pathogens, suggesting more agricultural and hygiene protocols are needed to control the risk of foodborne ARGs.

Transfer and distribution of antibiotic resistance genes in the soil-peanut system receiving manure for years

Antibiotic resistance gene (ARG)-contaminated food from manure application is gaining widespread interest, but little is known about the distribution and uptake of ARGs in peanuts that are subjected to manure routinely. In this study, the ARG profile and bacterial community in soil and peanut plants from a 7-year manure-fertilized field were investigated using high-throughput qPCR and 16S rRNA gene sequencing. Manure application increased the abundance of ARGs in soil and peanuts by 59-72 and 4-10 fold, respectively. The abundance of ARGs from high to low was as follows: manure, shell-sphere soil, rhizosphere soil, bulk soil, stems, shells, needles, kernels, and roots. Source-tracker analyses were used to investigate the potential source of ARGs in peanut kernels, which revealed that the ARGs in peanut kernels may be primarily absorbed by the roots from the soil. The horizontal gene transfer (HGT) of ARGs was the primary factor in the spread of ARGs, and Proteobacteria were the primary agents of HGT between different parts of peanut plants. Additionally, norank_Chloroplast from the phylum Cyanobacteria was the most important contributor to the abundance of ARGs in peanut kernels. Overall, our findings fill a gap in our understanding of the distribution patterns of ARGs in peanut plants and the migratory pathways of ARGs from soil to peanut kernels.

Sustainable on-farm strategy for the disposal of antibiotic fermentation residue: Co-benefits for resource recovery and resistance mitigation

Antibiotic fermentation residue is a key issue for the sustainable operation of pharmaceutical companies, and its improper disposal may cause antibiotic resistance transfer in the environment. However, little is known about the resource recycling strategy of this pharmaceutical waste. Herein, we used hydrothermal spray-dried (HT+SD) and multi-plate dryer (MD) methods to produce bio-organic fertilizers and applied them to an internal recycling model of a field trial. The concentrations of antibiotics (penicillin, cephalosporin, and erythromycin) in the bio-fertilizer, wastewater, and exhaust gas were in the range of 0.002-0.68 mg/kg, ≤ 0.35 ng/mL, and 0.03-0.89 ng/mL, respectively. The organic matter and total nitrogen, phosphorus, and potassium contents were approximately 80% and 10%, respectively. The soil bacterial community was similar among the fertilizer treatments in the same crop cultivation. A total of 233 antibiotic resistance genes (ARGs) and 43 mobile genetic elements (MGEs) were detected, including seven Rank I ARGs and five Rank II ARGs. Random forest analysis showed that gene acc(3)-Via and plasmid trb-C were biomarkers, for which the resistance and the transfer mechanisms were antibiotic inactivation and conjugation, respectively. The results imply that AFR recycling disposal mode is a promising prospect for pharmaceutical waste management.

Can agricultural land use alter the responses of soil biota to antibiotic contamination?

Antibiotics accumulate in soils via various agricultural activities, endangering soil biota that play fundamental roles in maintaining agroecosystem function. However, the effects of land-use heterogeneity on soil biota tolerance to antibiotic stresses are not well understood. In this study, we explored the relationships between antibiotic residues, bacterial communities, and earthworm populations in areas with different land-use types (forest, maize, and peanut fields). The results showed that antibiotic levels were generally higher in maize and peanut fields than in forests. Furthermore, land use modulated the effects of antibiotics on soil bacterial communities and earthworm populations. Cumulative antibiotic concentrations in peanut fields were negatively correlated with bacterial diversity and earthworm abundance, whereas no significant correlations were detected in maize fields. In contrast, antibiotics improved bacterial diversity and richness in forest soils. Generally, earthworm populations showed stronger tolerance to antibiotics than did soil bacterial communities. Agricultural land use differentially modified the responses of the soil bacterial community and earthworm population to antibiotic contamination, and earthworms might provide an alternative for controlling antibiotic contamination.

Antimicrobial Resistance in the Environment: Towards Elucidating the Roles of Bioaerosols in Transmission and Detection of Antibacterial Resistance Genes

Antimicrobial resistance (AMR) is continuing to grow across the world. Though often thought of as a mostly public health issue, AMR is also a major agricultural and environmental problem. As such, many researchers refer to it as the preeminent One Health issue. Aerial transport of antimicrobial-resistant bacteria via bioaerosols is still poorly understood. Recent work has highlighted the presence of antibiotic resistance genes in bioaerosols. Emissions of AMR bacteria and genes have been detected from various sources, including wastewater treatment plants, hospitals, and agricultural practices; however, their impacts on the broader environment are poorly understood. Contextualizing the roles of bioaerosols in the dissemination of AMR necessitates a multidisciplinary approach. Environmental factors, industrial and medical practices, as well as ecological principles influence the aerial dissemination of resistant bacteria. This article introduces an ongoing project assessing the presence and fate of AMR in bioaerosols across Canada. Its various sub-studies include the assessment of the emissions of antibiotic resistance genes from many agricultural practices, their long-distance transport, new integrative methods of assessment, and the creation of dissemination models over short and long distances. Results from sub-studies are beginning to be published. Consequently, this paper explains the background behind the development of the various sub-studies and highlight their shared aspects.

Conifer Needle Phyllosphere as a Potential Passive Monitor of Bioaerosolised Antibiotic Resistance Genes

Monitoring antibiotic resistance genes (ARGs) is vital to the One Health approach to tackling the antibiotic resistance crisis. It has been suggested that conifer needles can be used as passive bioaerosol samplers. Here, the use of conifer needles as biomonitors of ARGs in bioaerosols was assessed as a proof-of-concept. Needles were collected from trees surrounding pig farms, villages, and forest sites in Québec, Canada. Needles were homogenised and DNA was extracted. Results of qPCR analyses showed biomass estimates were consistent across samples. Number and quantity of ARGs was significantly lower in forest sites when compared to the farm and village, comprising a distinct resistome. Consistent with previous findings, the most common ARGs were tetracyclines and sulfonamides, which were found close to agricultural activities. Although results were limited, there is great potential for using the conifer phyllosphere as a passive bioaerosol sampler. This method represents an accessible way to promote ARG surveillance over long distances from point sources.

Tracking antibiotic resistance through the environment near a biosolid spreading ground: Resistome changes, distribution, and metal(loid) co-selection

The application of urban wastewater treatment plants (WWTPs) products to agricultural lands has contributed to the rising level of antibiotic resistance and drawn a critical public health concern. It has not been thoroughly investigated at which spatial scales a biosolid applied area as a potentially predominant source affects surrounding soil resistomes. This study investigated distribution and impact of WWTP biosolids treated with anaerobic digestion on an agricultural area. Heterotrophic plate counts (HPCs) and quantitative polymerase chain reaction (qPCR) were performed for detection of selected antibiotic-resistant bacteria (ARB), selected antibiotic resistance genes (ARGs), intI1 genes, and 16S rRNA genes. Biosolid samples contained significantly higher levels of selected ARGs than the raw agricultural soils (p < 0.05). The average relative abundances of intI1, sul1, bla_SHV, and ermB genes were significantly higher in biosolid-amended soils than nearby agricultural soils (p < 0.05). Spatial interpolation analysis of relative gene abundances of intI1, sul1, sul2, and tetW across the studied area further indicated directional trends towards the northwest and southeast directions, highlighting possible airborne spread. Concentrations of Co, Cu, Ni, and Fe were found to be significantly and positively correlated with relative abundances of intI1, sul1, and tetW genes (p < 0.05). The resistance ratios of culturable antibiotic-resistant bacteria in agricultural soils with biosolid amendments were generally identical to those without biosolid amendments. This study will advance the understanding of the antibiotic resistome in agricultural soils impacted by long-term waste reuse and inform the evaluation strategies for future biosolids application and management.

Conurbation size drives antibiotic resistance along the river

With growing concerns about antibiotic resistance, the tracking of antibiotic resistance genes (ARGs) in urban waterways will facilitate our increased understanding of the impact of urbanization on ARGs dissemination. In the current study, we assessed the ARGs profiles and antibiotic resistome in water samples along the Jiulong River basin, a distance of 250 km, to better understand the impact of anthropogenic activities. A total of 244 ARGs and 12 MGEs were detected from 21 sampling sites. Both relative and absolute abundance of the observed resistome decreased with increasing distance from urban areas. Ordinary least-squares (OLS) regression revealed that both the relative and absolute resistome abundance were positively correlated with city size. The resistome had several inputs and outputs and Fast Expectation Maximization Microbial Source Tracking (FEAST), suggested that the majority of the antibiotic resistome originated from anthropogenic activities. A total of 8 ARGs and 20 microbial OTUs were considered as biomarkers that differentiated the location of sampling sites. Bacterial communities were significantly correlated with ARGs according to Procrustes analysis and Mantel test, which was also supported by a co-occurrence network. Variation partitioning analysis revealed that ARG profiles were driven by multiple factors. Although antibiotic resistome abundance significantly increased near urban conurbations, overall resistome abundance decreased as the river flowed downstream. Our study highlights the effect of conurbation size on antibiotic resistance profiles within the river basin and the potential resilience of rivers to recover from ARGs contamination.

Spatial and temporal dynamics of microbiomes and resistomes in broiler litter stockpiles

Farmers apply broiler chicken litter to soils to enrich organic matter and provide crops with nutrients, following varying periods of stockpiling. However, litter frequently harbors fecal-derived microbial pathogens and associated antibiotic resistance genes (ARGs), and may be a source of microbial contamination of produce. We coupled a cutting-edge Loop Genomics long-read 16S rRNA amplicon-sequencing platform with high-throughput qPCR that targeted a suite of ARGs, to assess temporal (five time points over a 60-day period) and spatial (top, middle and bottom layers) microbiome and resistome dynamics in a broiler litter stockpile. We focused on potentially pathogenic species from the Enterobacteriaceae, Enterococcaceae and Staphylococcaceae families associated with food-borne disease. Bacterial diversity was significantly lower in the middle of the stockpile, where targeted pathogens were lowest and Bacillaceae were abundant. E. coli was the most abundant Enterobacteriaceae species, and high levels of the opportunistic pathogen Enterococcus faecium were detected. Correlation analyses revealed that the latter was significantly associated with aminoglycoside (aac(6′)-Ib(aka aacA4), aadA5), tetracycline (tetG), vancomycin (vanC), phenicol (floR) and MLSB (mphB) resistance genes. Staphylococcaceae were primarily non-pathogenic, but extremely low levels of the opportunistic pathogen S. aureus were detected, as was the opportunistic pathogen S. saprophyticus, which was linked to vancomycin (vanSA, vanC1), MLSB (vatE, ermB) and tetracycline (tetK) resistance genes. Collectively, we found that stockpile microbiomes and resistomes are strongly dictated by temporal fluctuations and spatial heterogeneity. Insights from this study can be exploited to improve stockpile management practice to support sustainable antimicrobial resistance mitigation policies in the future.

Bioaccumulation of Manure-borne antibiotic resistance genes in carrot and its exposure assessment

The effect of manure application on the distribution and accumulation of antibiotic resistance genes (ARGs) in tissue of root vegetables remains unclear, which poses a bottleneck in assessing the health risks from root vegetables due to application of manure. Towards this goal, experiments were conducted in pots to investigate the distribution and bioaccumulation of ARGs in carrot tissues due to application of pig manure. The 144 ARGs targeting nine types of antibiotics were quantified by high throughput qPCR in the soil and plant samples. The rhizosphere was a hot spot for ARGs enrichment in the manured soil. The abundance, diversity, and bioaccumulation factors of ARGs in the phyllosphere were significantly higher than those of carrot root skin and tuber. Manure application increased bioaccumulation of 12 ARGs and 2 MGEs in carrot tuber with 124 the highest factor. The application of manure increased transfer of 10 ARGs and 3 MGEs from carrot skin to inner tuber by factors of 0.1-11.8. The average gene copy number of ARGs of per gram carrot root was about 4.8 × 10⁴ and 1.1 × 10⁶ in the control and the manured treatment, respectively. Children and adults may co-ingest 2.7 × 10⁷ and 3.2 × 10⁷ of ARGs copies/d from carrots grown with pig manure, using estimated human intake values. However, peeling may reduce the intake of ARGs by 28-91% and of MGEs by 46-59%. In conclusion, the application of pig manure increased the accumulation of ARGs in the skin of carrots, whereas peeling was an effective strategy to reduce the risk.

Multiple 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.

Diversity and abundance of antibiotic resistance genes in rhizosphere soil and endophytes of leafy vegetables: Focusing on the effect of the vegetable species

Antibiotic resistance genes (ARGs) in the endophytes of vegetables represent a potential route of human exposure to the soil resistome. However, the effect of vegetable species on the endophytic ARG profiles is unclear, hampering our understanding of how ARGs migrate into the soil-vegetable system and their potential health risks. Here, we planted four leafy vegetables (cilantro, endive, lettuce, and pak choi), which are commonly eaten raw, and analyzed the resistomes and microbiomes in three sample types (rhizosphere soil, root, and leaf endophytes). A total of 150 ARG subtypes were detected using high-throughput quantitative PCR. Vegetable species had a significant effect on ARG diversity and abundance, and pak choi accumulated more ARGs in its associated microbiome than the other three vegetables. The bacterial community was the primary factor shaping ARG profiles and was significantly correlated with ARG subtypes. We identified aadE, tet(34), and vanSB as shared ARGs among leaves of the four vegetables; the bacterial families correlated with tet(34) and vanSB were also shared across the vegetables and belonged to Proteobacteria. This study deepens our understanding of how endophytic ARG profiles vary among different vegetables and highlights the potential health risk associated with consuming these vegetables raw.

Transmission Routes of the Microbiome and Resistome from Manure to Soil and Lettuce

The land application of animal manure can introduce manure microbiome and resistome to croplands where food crops are grown. The objective of this study was to characterize the microbiome and resistome on and in the leaves of lettuce grown in manured soil and identify the main transmission routes of microbes and antibiotic resistance genes (ARGs) from soil to the episphere and endosphere of lettuce. Shotgun metagenomic results show that manure application significantly altered the composition of the microbiome and resistome of surface soil. SourceTracker analyses indicate that manure and original soil were the main source of the microbiome and resistome of the surface soil and rhizosphere soil, respectively. Manure application altered the microbiome and resistome in the episphere of lettuce (ADONIS p < 0.05), and surface soil accounted for ∼81% of the microbes and ∼62% of the ARGs in episphere. Manure application had limited impacts on the microbiome and resistome in the endosphere (ADONIS p > 0.05). Our results show that manure-borne microbes and ARGs reached the episphere primarily through surface soil and some epiphytic microbes and ARGs further entered the endosphere. Our findings can inform the development of pre- and postharvest practices to minimize the transmission of manure-borne resistome from food crops to consumers.

Agricultural land-use change and rotation system exert considerable influences on the soil antibiotic resistome in Lake Tai Basin

In this study, we use high-throughput quantitative polymerase chain reaction approaches to comprehensively assess the effects of agricultural land-use change on the antibiotic resistome of agricultural runoffs after rainfalls in Lake Tai Basin. For the first time in this region, our findings show that orchard runoffs harbored more diverse and abundant antibiotic resistance genes (ARGs) than traditional cropland runoffs. Network analysis demonstrated that orchard runoffs possessed a strong ability for ARG dissemination via horizontal gene transfer. These results suggest that residents might be exposed to a higher public health threat than before. Moreover, the present study confirmed that the rice-wheat rotation system plays a key role in regulating the soil antibiotic resistome profile. Using 16S rRNA high-throughput sequencing technology, this study clarified the relationships between the antibiotic resistome and soil microbiome composition. Finally, we discuss the key environmental factors driving changes in the soil antibiotic resistome. In summary, this study gives insight into the dissemination of environmental ARGs to the people living in the Lake Tai Basin.

Seasonal change is a major driver of soil resistomes at a watershed scale

Soils harbor the most diverse naturally evolved antibiotic resistomes on Earth that threaten human health, ecosystem processes, and food security. Yet the importance of spatial and temporal variability in shaping the distribution of soil resistomes is not well explored. Here, a total of 319 topsoil samples were collected at a watershed scale during four seasons (spring to winter) and high-throughput quantitative PCR (HT-qPCR) was used to characterize the profiles of soil antibiotic resistance genes (ARGs). A significant and negative correlation was observed between soil ARG profiles and seasonal dissimilarity, which along with seasonally dependent distance-decay relationships highlight the importance of seasonal variability in shaping soil antibiotic resistomes. Significant, though weak, distance-decay relationships were identified in spring, summer and winter, for ARG similarities with geographic distances. There were also strong interactions between specific soil ARGs and Actinobacteria, Firmicutes and Proteobacteria. Moreover, we found that the relative abundance of soil Actinobacteria, Firmicutes and Proteobacteria correlated significantly with annual mean temperature and annual mean precipitation at a watershed scale. A random forest model showed that seasonal change rather than spatial variation was the most important predictor of the composition of soil ARGs. Together, these results constitute an advance in our understanding of the relative importance of spatial and temporal variability in shaping soil ARG profiles, which will provide novel insights allowing us to forecast their distribution under a changing environment.

Diverse and abundant antibiotic resistance genes in mangrove area and their relationship with bacterial communities - A study in Hainan Island, China

Antibiotic resistance genes (ARGs) are emerging contaminants in the environment and have been highlighted as a worldwide environmental and health concern. As important participants in the biogeochemical cycles, mangrove ecosystems are subject to various anthropogenic disturbances, and its microbiota may be affected by various contaminants such as ARGs. This study selected 13 transects of mangrove-covered areas in Hainan, China for sediment sample collection. The abundance and diversity of ARGs and mobile genetic elements (MGEs) were investigated using high-throughput quantitative polymerase chain reaction (HT-qPCR), and high-throughput sequencing was used to study microbial structure and diversity. A total of 179 ARGs belonging to 9 ARG types were detected in the study area, and the detection rates of vanXD and vatE-01 were 100%. The abundance of ARGs was 8.30 × 10⁷-6.88 × 10⁸ copies per g sediment (1.27 × 10^-2-3.39 × 10^-2 copies per 16S rRNA gene), which was higher than similar studies, and there were differences in the abundance of ARGs in these sampling transects. The multidrug resistance genes (MRGs) accounted for the highest proportion (69.0%), which indicates that the contamination of ARGs in the study area was very complicated. The ARGs significantly positively correlated with MGEs, which showed that the high level of ARGs was related to its self-enhancement. The dominant bacteria at the genus level were Desulfococcus, Clostridium, Rhodoplanes, Bacillus, Vibrio, Enterococcus, Sedimentibacter, Pseudoalteromonas, Paracoccus, Oscillospira, Mariprofundus, Sulfurimonas, Aminobacterium, and Novosphingobium. There was a significant positive correlation between 133 bacterial genera and some ARGs. Chthoniobacter, Flavisolibacter, Formivibrio, Kaistia, Moryella, MSBL3, Perlucidibaca, and Zhouia were the main potential hosts of ARGs in the sediments of Hainan mangrove area, and many of these bacteria are important participants in biogeochemical cycles. The results contribute to our understanding of the distribution and potential hosts of ARGs and provide a scientific basis for the protection and management of Hainan mangrove ecosystem.

The 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.

Microbial functional traits in phyllosphere are more sensitive to anthropogenic disturbance than in soil

Soil-plant microbiome plays a critical role in the regulation of terrestrial ecosystem function and service, including biogeochemical cycling and primary production. The lack of knowledge regarding the differences in microbial functional traits, i.e. the functional genes related to carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) cycles, between soil and plant microbiomes hampers our prediction of the terrestrial nutrient cycling processes under the pressure of anthropogenic disturbance. Herein, a quantitative microbial element cycling (QMEC) method and amplicon sequencing was employed to characterize CNPS cycling genes and microbial communities in soil and plant samples collected from peri-urban farmland with high anthropogenic disturbance and forest ecosystem with minimal disturbance. The soil-plant system harbored a diverse array of CNPS cycling genes, which were significantly more abundant in soil than in phyllosphere. The overall CNPS gene profiles in farmland samples was distinct from that of forest samples in both soil and plant phyllosphere. Farmland samples had a lower abundance of CNPS cycling genes than forest samples, indicating that intensive agricultural management practices may consequently compromise the biogeochemical cycling potential of nutrients. Significant positive correlations between the abundance of CNPS cycling genes and microbial diversity were observed in phyllosphere microbiome but not in soil, suggesting that the functional redundancy in soil microbiome may be higher than that of phyllosphere microbiome. Taken together, we provide experimental evidence for the substantial impacts of anthropogenic disturbance on CNPS cycling genes in the soil-plant system and necessitate future efforts to unravel the plant microbiome diversity and functionality under the pressure of global changes.

Microbiome and antibiotic resistome in household dust from Beijing, China

We spend ever-increasing time indoors along with urbanization; however, the geographical distribution patterns of microbiome and antibiotic resistome, and their driving forces in household environment remains poorly characterized. Here, we surveyed the bacterial and fungal communities, and the resistome in settled dust gathered from 82 homes located across Beijing, China, employing Illumina sequencing and high-throughput quantitative PCR techniques. There was no clear geographical distribution pattern in dust-related bacterial communities although a slight but significant (P < 0.05) distance-decay relationship occurred in its community similarity; by contrast, a relatively distinct geographical clustering and a stronger distance-decay relationship were observed in fungal communities at the local scale. The cross-domain (bacteria versus fungi) relationships in the microbiome of the dust samples were mostly observed as robust co-occurrence correlations. The bacterial communities were dominated by Proteobacteria and Actinobacteria phyla, with human skin, soil and plants being potential major sources. The fungal communities largely comprised potential allergens (a median 61% of the fungal sequences), with Alternaria genus within Ascomycota phylum being the most predominant taxa. The profile of dust-related bacterial communities was mainly affected by housing factors related to occupants and houseplants, while that of fungal communities was determined by georeferenced environmental factors, particularly vascular plant diversity. Additionally, a great diversity (1.96 on average for Shannon index) and normalized abundance (2.22 copies per bacterial cell on average) of antibiotic resistance genes were detected across the dust samples, with the dominance of genes resistant to vancomycin and Macrolide-Lincosamide-Streptogramin B. The resistome profile exhibited no distinct geographical pattern, and was primarily driven by certain bacterial phyla and occupancy-related factors. Overall, we underline the significance of anthropogenic impacts and house location in structuring bacterial and fungal communities inside homes, respectively, and suggest that household dust is an overlooked reservoir for antibiotic resistance.