Long-term manure inputs induce a deep selection on agroecosystem soil antibiotic resistome

Critical insights into the Hormesis of antibiotic resistome in saline soil: Implications from salinity regulation

Soil is recognized as an important reservoir of antibiotic resistance genes (ARGs). However, the effect of salinity on the antibiotic resistome in saline soils remains largely misunderstood. In this study, high-throughput qPCR was used to investigate the impact of low-variable salinity levels on the occurrence, health risks, driving factors, and assembly processes of the antibiotic resistome. The results revealed 206 subtype ARGs across 10 categories, with medium-salinity soil exhibiting the highest abundance and number of ARGs. Among them, high-risk ARGs were enriched in medium-salinity soil. Further exploration showed that bacterial interaction favored the proliferation of ARGs. Meanwhile, functional genes related to reactive oxygen species production, membrane permeability, and adenosine triphosphate synthesis were upregulated by 6.9%, 2.9%, and 18.0%, respectively, at medium salinity compared to those at low salinity. With increasing salinity, the driver of ARGs in saline soils shifts from bacterial community to mobile gene elements, and energy supply contributed 28.2% to the ARGs at extreme salinity. As indicated by the neutral community model, stochastic processes shaped the assembly of ARGs communities in saline soils. This work emphasizes the importance of salinity on antibiotic resistome, and provides advanced insights into the fate and dissemination of ARGs in saline soils.

Body size: A hidden trait of the organisms that influences the distribution of antibiotic resistance genes in soil

Body size is a key life-history trait of organisms, which has important ecological functions. However, the relationship between soil antibiotic resistance gene (ARG) distribution and organisms' body size has not been systematically reported so far. Herein, the impact of organic fertilizer on the soil ARGs and organisms (bacteria, fungi, and nematode) at the aggregate level was analyzed. The results showed that the smaller the soil aggregate size, the greater the abundance of ARGs, and the larger the body size of bacteria and nematodes. Further analysis revealed significant positive correlations of ARG abundance with the body sizes of bacteria, fungi, and nematodes, respectively. Additionally, the structural equation model demonstrated that changes in soil fertility mainly regulate the ARG abundance by affecting bacterial body size. The random forest model revealed that total phosphorus was the primary soil fertility factor influencing the body size of organisms. Therefore, these findings proposed that excessive application of phosphate fertilizers could increase the risk of soil ARG transmission by increasing the body size of soil organisms. This study highlights the significance of organisms' body size in determining the distribution of soil ARGs and proposes a new disadvantage of excessive fertilization from the perspective of ARGs.

Deciphering soil resistance and virulence gene risks in conventional and organic farming systems

Organic farming is a sustainable agricultural practice emphasizing natural inputs and ecological balance, and has garnered significant attention for its potential health and environmental benefits. However, a comprehensive evaluation of the emergent contaminants, particularly resistance and virulence genes within organic farming system, remains elusive. Here, a total of 36 soil samples from paired conventional and organic vegetable farms were collected from Jiangsu province, China. A systematic metagenomic approach was employed to investigate the prevalence, dispersal capability, pathogenic potential, and drivers of resistance and virulence genes across both organic and conventional systems. Our findings revealed a higher abundance of antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and virulence factor genes (VFGs) in organic farming system, with ARGs exhibiting a particularly notable increase of 10.76% compared to the conventional one. Pathogens such as Pseudomonas aeruginosa, Escherichia coli, and Mycobacterium tuberculosis were hosts carrying all four gene categories, highlighting their potential health implications. The neutral community model captured 77.1% and 71.9% of the variance in community dynamics within the conventional and organic farming systems, respectively, indicating that stochastic process was the predominant factor shaping gene communities. The relative smaller m value calculated in organic farming system (0.021 vs 0.023) indicated diminished gene exchange with external sources. Moreover, farming practices were observed to influence the resistance and virulence gene landscape by modifying soil properties, managing heavy metal stress, and steering mobile genetic elements (MGEs) dynamics. The study offers insights that can guide agricultural strategies to address potential health and ecological concerns.

Tracing the transfer characteristics of antibiotic resistance genes from swine manure to biogas residue and then to soil

Based on laboratory simulation experiments and metagenomic analysis, this study tracked the transmission of antibiotic resistance genes (ARGs) from swine manure (SM) to biogas residue and then to soil (biogas residue as organic fertilizer (OF) application). ARGs were abundant in SM and they were assigned to 11 categories of antibiotics. Among the 383 ARG subtypes in SM, 43 % ARG subtypes were absent after anaerobic digestion (AD), which avoided the transfer of these ARGs from SM to soil. Furthermore, 9 % of the ARG subtypes in SM were introduced into soil after amendment with OF. Moreover, 43 % of the ARG subtypes in SM were present in OF and soil, and their abundances increased slightly in the soil amended with OF. The bacterial community in the soil treated with OF was restored to its original state within 60 to 90 days, probably because the abundances of ARGs were elevated but not significantly in the soil. Network analysis identified 31 potential co-host bacteria of ARGs based on the relationships between the bacteria community members, where they mainly belonged to Firmicutes, followed by Bacteroidetes, Actinobacteria, and Proteobacteria. This study provides a basis for objectively evaluating pollution by ARGs in livestock manure for agricultural use.

The soil-microbe-plant resistome: A focus on the source-pathway-receptor continuum

The One World, One Health concept implies that antibiotic resistance (AR) in the soil-microbe-plant resistome is intricately linked to the human resistome. However, the literature is mainly confined to sources and types of AR in soils or microbes, but comprehensive reviews tracking AR in the soil-microbe-plant resistome are limited. The present review applies the source-pathway-receptor concept to understand the sources, behaviour, and health hazards of the soil-microbe-plant resistome. The results showed that the soil-microbe-plant system harbours various antibiotic-resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and mobile genetic elements (MGEs). Anthropogenic sources and drivers include soil application of solid waste, wastewater, biosolids, and industrial waste. Water-, wind-, and human-driven processes and horizontal gene transfer circulate AR in the soil-microbe-plant resistome. The AR in bulk soil, soil components that include soil microorganisms, soil meso- and macro-organisms, and possible mechanisms of AR transfer to soil components and ultimately to plants are discussed. The health risks of the soil-microbe-plant resistome are less studied, but potential impacts include (1) the transfer of AR to previously susceptible organisms and other resistomes, including the human resistome. Overall, the study tracks the behaviour and health risks of AR in the soil-plant system. Future research should focus on (1) ecological risks of AR at different levels of biological organization, (2) partitioning of AR among various phases of the soil-plant system, (3) physico-chemical parameters controlling the fate of AR, and (4) increasing research from low-income regions particularly Africa as most of the available literature is from developed countries.

Deciphering the Role of WWTPs in Cold Environments as Hotspots for the Dissemination of Antibiotic Resistance Genes

Cold environments are the most widespread extreme habitats in the world. However, the role of wastewater treatment plants (WWTPs) in the cryosphere as hotspots in antibiotic resistance dissemination has not been well established. Hence, a snapshot of the resistomes of WWTPs in cold environments, below 5 °C, was provided to elucidate their role in disseminating antibiotic resistance genes (ARGs) to the receiving waterbodies. The resistomes of two natural environments from the cold biosphere were also determined. Quantitative PCR analysis of the aadA, aadB, ampC, blaSHV, blaTEM, dfrA1, ermB, fosA, mecA, qnrS, and tetA(A) genes indicated strong prevalences of these genetic determinants in the selected environments, except for the mecA gene, which was not found in any of the samples. Notably, high abundances of the aadA, ermB, and tetA(A) genes were found in the influents and activated sludge, highlighting that WWTPs of the cryosphere are critical hotspots for disseminating ARGs, potentially worsening the resistance of bacteria to some of the most commonly prescribed antibiotics. Besides, the samples from non-disturbed cold environments had large quantities of ARGs, although their ARG profiles were highly dissimilar. Hence, the high prevalences of ARGs lend support to the fact that antibiotic resistance is a common issue worldwide, including environmentally fragile cold ecosystems.

A review on the effects of discharging conventionally treated livestock waste to the environmental resistome

Globally, animal production has developed rapidly as a consequence of the ongoing population growth, to support food security. This has consequently led to an extensive use of antibiotics to promote growth and prevent diseases in animals. However, most antibiotics are not fully metabolized by these animals, leading to their excretion within urine and faeces, thus making these wastes a major reservoir of antibiotics residues, antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) in the environment. Farmers normally depend on conventional treatment methods to mitigate the environmental impact of animal waste; however, these methods are not fully efficient to remove the environmental resistome. The present study reviewed the variability of residual antibiotics, ARB, as well as ARGs in the conventionally treated waste and assessed how discharging it could increase resistome in the receiving environments. Wherein, considering the efficiency and environmental safety, an addition of pre-treatments steps with these conventional treatment methods could enhance the removal of antibiotic resistance agents from livestock waste.

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.

Intensive management facilitates bacterial invasion on soil microbial community

Intensive management has greatly altered natural forests, especially forests around the world are increasingly being converted into economic plantations. Soil microbiota are critical for community functions in all ecosystems, but the effects of microbial disturbance during economic plantation remain unclear. Here, we used Escherichia coli O157:H7, a model pathogenic species for bacterial invasion, to assess the invasion impacts on the soil microbial community under intensive management. The E. coli invasion was tracked for 135 days to explore the instant and legacy impacts on the resident community. Our results showed that bamboo economic plantations altered soil abiotic and biotic properties, especially increasing pH and community diversity. Higher pH in bamboo soils resulted in longer pathogen survivals than in natural hardwood soils, indicating that pathogen suppression during intensive management should arouse our attention. A longer invasion legacy effect on the resident community (P < 0.05) were found in bamboo soils underlines the need to quantify the soil resilience even when the invasion was unsuccessful. Deterministic processes drove community assembly in bamboo plantations, and this selection acted more strongly during by E. coli invasion than in hardwood soils. We also showed more associated co-occurrence patterns in bamboo plantations, suggesting more complex potential interactions within the microbial community. Apart from community structure, community functions are also strongly related to the resident species associated with invaders. These findings provide new perspectives to understand intensive management facilitates the bacterial invasion, and the impacts would leave potential risks on environmental and human health.

Long-term field application of manure induces deep selection of antibiotic resistomes in leaf endophytes of Chinese cabbage

Antibiotic resistomes in leaf endophytes of vegetables threaten human health through the food chain. However, little is known about the ability of long-term manure fertilization to impact the deep selection of antibiotic resistance genes (ARGs) in leaf endophytes of vegetables planted in different types of soils. Here, by high-throughput quantitative PCR, we characterized the ARGs of leaf endophytes of Chinese cabbage (Brassica pekinensis (Lour.) Rupr.) grown in long-term (14 year) manure-amended acidic, neutral and calcareous soils. In total, 87 ARGs and 4 mobile genetic elements (MGEs) were detected in all the samples. Manure fertilization significantly increased the ARG numbers and normalized abundance in leaf endophytes, especially in acidic soil. Moreover, in acidic soil, manure application also led to a higher increase in the normalized abundance of opportunist and specialist ARGs, and more opportunist and specialist ARGs posed a high risk according to their risk ranks. Random forest analysis revealed that Proteobacteria and MGEs were the major drivers affecting the normalized abundance of opportunist and specialist ARGs in both acidic and neutral soils, respectively. In calcareous soil, Cyanobacteria and Actinobacteria were the most important contributors. Collectively, this study expands our knowledge about the deep selection of plant resistomes under long-term manure application.

pH drives the spatial variation of antibiotic resistance gene profiles in riparian soils at a watershed scale

Owing to convenient water access, riparian areas are often sites for intensive livestock breeding industries and agriculture, which can increase the spread of antibiotic resistance genes (ARGs). However, studies on ARG profiles in riparian soils are limited and there is little information regarding the factors influencing ARGs at a watershed scale. Here, we analyzed ARG profiles, bacterial communities, and soil properties in riparian soils under different land-use types. A total of 124 ARGs and 25 mobile genetic elements (MGEs) were detected in the riparian soils, which covered almost all major classes of antibiotics. Non-metric multidimensional scaling analysis showed that both the distance to the water reservoir and land-use types played important roles in shaping ARG profiles in riparian soils at a watershed scale. Downstream soils harbored three times the abundance of ARGs compared with upstream and midstream soils. Distance-decay analysis indicated that the similarity of ARG profiles and bacterial community composition decreased significantly with the increase of geographical distance (p < 0.001). When taking the land-use type into consideration, the relative abundance and diversity of ARGs and MGEs in orchard and farmland soils were significantly higher than those in wasteland soils. This indicated that anthropogenic activities can also affect ARG patterns in riparian soils. MGE abundance was identified as major driving factors of ARG profiles. In addition, among all the examined soil properties, soil pH was found to be more important than nutrients and organic carbon in shaping ARG profiles. Our findings provide valuable data on ARG distribution in riparian soils in a reservoir catchment and highlight downstream soils is crucial for ensuring water source security.

Ecological insight into antibiotic resistome of ion-adsorption rare earth mining soils from south China by metagenomic analysis

Antibiotic resistome has led to growing global threat to public health. Rare earth elements play important roles in modern society and mining activity for them has caused serious impact on soil ecosystems. However, antibiotic resistome in, especially, ion-adsorption rare earth-related soils is still poorly understood. In this work, soils were collected from ion-adsorption rare earth mining areas and adjacent regions of south China and metagenomic analysis was employed for profile, driving factors and ecological assembly of antibiotic resistome in the soils. Results show prevalence of antibiotic resistance genes conferring resistance to tetracycline/fluoroquinolone (adeF), peptide (bcrA), aminoglycoside (rpsL), tetracycline (tet(A)) and mupirocin (mupB) in ion-adsorption rare earth mining soils. Profile of antibiotic resistome is accompanied by its driving factors, i.e., physicochemical properties (La, Ce, Pr, Nd and Y of rare earth elements in 12.50-487.90 mg kg^-1), taxonomy (Proteobacteria, Actinobacteria) and mobile genetic elements (MGEs, plasmid pYP1, Transposase_20). Variation partitioning analysis and partial least-squares-path modeling demonstrate that taxonomy is the most important individual contributor and pose most direct/indirect effect to antibiotic resistome. Further, null model analysis reveals stochastic processes as dominant ecological assembly of antibiotic resistome. This work advances our knowledge on antibiotic resistome with emphasis on ecological assembly in ion-adsorption rare earth-related soils for ARGs mitigation, mining management and mine restoration.

Tracking soil resistance and virulence genes in rice-crayfish co-culture systems across China

Rice-crayfish co-culture (RC) has been widely and rapidly promoted as a sustainable agricultural system in many countries. The accumulation of crayfish residues could enhance soil organic matters; however, impacts of this integrated farming model on the dissemination and pathogenicity of resistance and virulence genes remain poorly understood. Here, we characterized antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), metal resistance genes (MRGs) and virulence factor genes (VFGs) using metagenomic methods in paired RC and rice monoculture (RM) systems across China. The RC model did not increase the abundance of soil ARGs, BRGs, MRGs, or VFGs in comparison to the RM model, but selectively enriched 35 subtypes of these potential resistance and virulence genes. Network analysis revealed that resistance and virulence genes had a higher number of connections with mobile genetic elements (MGEs) in the RC system than that in the RM system, suggesting a higher horizontal transfer potential of these genes. Moreover, the RC model had a higher abundance of human opportunistic pathogens such as Salmonella enterica, Vibrio cholerae, and Shigella dysenteriae which were potential hosts of VFGs such as phoP, fleS, and gspE, suggesting a potential threat to human health. We further unraveled that stochastic process was the main driver of the assembly of resistance and virulence genes in the RC system. The abundance of ARGs and VFGs were primarily associated with microbial community compositions, while the abundance of BRGs and MRGs were mainly associated with that of MGEs. Taken together, our results suggest that the RC model has potential to cause the dissemination and pathogenicity of resistance and virulence genes, which has important implications for the control of soil-borne biological risks and the strategic management of sustainable agriculture.

Shifts of Antibiotic Resistomes in Soil Following Amendments of Antibiotics-Contained Dairy Manure

Dairy manure is a nutrition source for cropland soils and also simultaneously serves as a contamination source of antibiotic resistance genes (ARGs). In this study, five classes of antibiotics including aminoglycosides, beta-lactams, macrolides, sulfonamides, and tetracyclines, were spiked in dairy manure and incubated with soil for 60 days. The high throughput qPCR and 16S rRNA amplicon sequencing were used to detect temporal shifts of the soil antibiotic resistomes and bacterial community. Results indicated dairy manure application increased the ARG abundance by 0.5-3.7 times and subtype numbers by 2.7-3.7 times and changed the microbial community structure in soils. These effects were limited to the early incubation stage. Selection pressure was observed after the addition of sulfonamides. Bacterial communities played an important role in the shifts of ARG profiles and accounted for 44.9% of the resistome variation. The incubation period, but not the different antibiotic treatments, has a strong impact on the bacteria community. Firmicutes and Bacteroidetes were the dominant bacterial hosts for individual ARGs. This study advanced our understanding of the effect of dairy manure and antibiotics on the antibiotic resistome in soils and provided a reference for controlling ARG dissemination from dairy farms to the environment.