Fates of Antibiotic Resistance Genes in the Gut Microbiome from Different Soil Fauna under Long-Term Fertilization

Warming exacerbates the effects of pesticides on the soil collembolan gut microbiome and antibiotic resistome

In the context of global climate warming, studies have yet to fully clarify how pollutants affect the gut microbiome and antibiotic resistance genes (ARGs) in nontarget soil fauna. This study investigates the interactive effects of pesticide exposure (imidacloprid) and elevated temperature on the gut bacterial community and ARGs in the model soil collembolan Folsomia candida. Our results demonstrate warming exacerbates the toxicity of imidacloprid in collembolans. While exposure to both warming and pesticide significantly altered the gut microbial composition of F. candida, impairing microbial metabolic diversity and potential host defense mechanisms, it also increased collembolan mortality. This combined exposure significantly enhanced the abundance and diversity of ARGs in the collembolan gut. A notable correlation between ARGs and mobile genetic elements (MGEs) underscores the potential risk of ARG transmission. Co-occurrence network analysis identified 52 bacterial genera as potential ARG hosts. Additionally, pure-culture exposure experiments with the isolated bacterium Serratia liquefaciens revealed the adaptability of ARG hosts to pesticide and warming stress plays an important role in driving the observed increase in ARGs. In conclusion, this study highlights the synergistic effects of climate warming and pesticide contamination on nontarget soil organisms, emphasizing the potential long-term risks to soil ecosystem health and stability.

Microplastics reduced the natural attenuation of antibiotic resistance genes in fertilized soils

The prolonged application of mulch and manure in agriculture has led to significant microplastic (MP) pollution in fertilized soils, raising global concerns about its potential impacts on soil health and ecosystem function. However, the effects of MP exposure on antibiotic resistance genes (ARGs) and microbial communities in fertilized soils are unknown. Therefore, we comprehensively explored the trends and drivers of ARGs during their natural abatement under the stress of conventional and biodegradable MP addition in fertilized soils using a soil microcosm experiment and metagenomic. The findings indicated that the presence of polybutylene succinate MPs (PBS-MPs) reduced the natural attenuation rate of ARGs in fertilized soils while increasing the fraction of high-risk ARGs in soils. Microbial communities and mobile genetic elements (MGEs) mainly drove the inhibitory effect of MPs on ARG abatement. Interestingly, most potential hosts for the coexistence of ARGs, metal resistance genes (MRGs), and MGEs were annotated as pathogens, such as Escherichia spp., Salmonella spp., and Klebsiella spp. In addition, MP stress in fertilized soil may lead to long-term contamination by highly virulent and antibiotic-resistant Escherichia coli. MPs influence the distribution of carbon sources, which in turn reduces the diversity and stability of soil microbial communities, while simultaneously promoting the colonization of crucial ARG hosts, like Dyella spp. This ultimately prolonged the high-risk state for ARG proliferation in the soil. This study highlights the significant risk posed by MPs to the persistence and spread of ARGs in fertilized soils. These results provide valuable insights for managing MP contamination in agricultural systems, emphasizing the need for sustainable practices to mitigate the long-term environmental risks associated with MP pollution.

From glacier forelands to human settlements: Patterns, environmental drivers, and risks of antibiotic resistance genes

Antibiotic resistance genes (ARGs) are biological pollutants widely present in glaciers, such as ice, snow, and melt water. However, it remains unclear whether ARGs in glaciers influence their distribution in human settlements within the glacier basins. Therefore, we investigated the distribution pattern and driving factors of ARGs in the Laohugou glacier basins on the Tibetan Plateau. Using high-throughput quantitative PCR, the total abundance of ARGs in the Laohugou glacier basins ranged from 7.53 × 10⁶ to 1.83 × 10⁹ copies/g, including 128 detected ARGs across 11 classes, with aminoglycoside resistance genes being the dominant group. The abundance of ARGs exhibited a U-shaped pattern along the elevational gradient, with higher levels in glacier regions and human settlements, and the lowest abundance at mid-elevations. While glacier melting and anthropogenic disturbance are likely major contributors to this pattern, other potential mechanisms may also be involved, such as elevation-dependent microbial community composition, atmospheric deposition and release of legacy ARGs from melting permafrost and glacial ice. Together, these processes likely interact to shape the observed ARG pattern in this alpine watershed. We further verified that the distribution of ARGs was strongly correlated with microbial community structure, especially bacterial communities (r > 0.50; p < 0.05). Network analysis showed that Nitrolancea negatively correlated with several core ARGs, suggesting its potential role in regulating the spread of ARGs. Random forest analysis and structural equation modeling (SEM) indicated that, after accounting for various driving factors, organic matter and bacterial biomass were the primary drivers of increased ARG abundance. This study provides a foundation for assessing the risks of ARGs in glacier basins under global climate change, offering insights into risk mitigation strategies and guiding future ecological and public health research.

Understanding bacterial ecology to combat antibiotic resistance dissemination

The dissemination of antibiotic resistance from environmental sources is a growing concern. Despite the widespread occurrence of antibiotic resistance transmission events, there are actually multiple obstacles in the ecosystem that restrict the flow of bacteria and genes, in particular nonnegligible biological barriers. How these ecological factors help combat the dissemination of antibiotic resistance and relevant antibiotic resistance-diminishing organisms (ARDOs) deserves further exploration. This review summarizes the factors that influence the growth, metabolism, and environmental adaptation of antibiotic-resistant bacteria (ARB) and restrict the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Additionally, this review discusses the achievements in the application of ARDOs to improve biotechnology for wastewater and solid waste remediation while highlighting current challenges limiting their broader implementation.

Root exudates regulate soil antibiotic resistance genes via rhizosphere microbes under long-term fertilization

Organic fertilizer application promotes the prevalence of antibiotic resistance genes (ARGs), yet the factors driving temporal differences in ARG abundance under long-term organic fertilizer application remain unclear. This study investigated the temporal dynamics of ARG diversity and abundance in both bulk and rhizosphere soils over 17 years (2003-2019), and explored microbial evolution strategies, ARG hosts succession and the influence of root exudates on ARGs regulation. The results showed that the ARGs abundance in rhizosphere soil was lower than that in bulk soil under long-term fertilization, and ARGs abundance exhibited a decrease and then remained stable in rhizosphere soil over time. There was a strong association between host bacteria and dominant ARGs (p < 0.05). Structural equations demonstrated that bacterial community had a most pronounced influence on ARGs (p < 0.05), and metabolites exhibited an important mediation effect on bacterial community (p < 0.05), thereby impacting ARGs. The metabolome analysis evidenced that significant correlations were found between defensive root exudates and most ARGs abundance (p < 0.05), like, luteolin-7-glucoside was negatively correlated with tetA(58). These findings provide deeper insights into the dynamics of soil ARGs under long-term fertilization, and identify critical factors that influence ARGs colonization in soils, providing support for controlling the spread of ARGs in agriculture soils.

Case study on the relationship between transmission of antibiotic resistance genes and microbial community under freeze-thaw cycle on cold-region dairy farm

Freeze-thaw cycle (FTC) is a naturally occurring phenomenon in high-latitude terrestrial ecosystems, which may exert influence on distribution and evolution of microbial community in the soil. The relationship between transmission of antibiotic resistance genes (ARGs) and microbial community was investigated upon the case study on the soil of cold-region dairy farm under seasonal FTC. The results demonstrated that 37 ARGs underwent decrease in the abundance of blaTEM from 80.4 % for frozen soil to 71.7 % for thawed soil, and that sul2 from 8.8 % for frozen soil to 6.5 % for thawed soil, respectively. Antibiotic deactivation was identified to be closely related to the highest relative abundance of blaTEM, and the spread of sulfonamide resistance genes (SRGs) occurred mainly via target modification. Firmicutes in frozen soil were responsible for dominating the abundance of ARGs by suppressing the native bacteria under starvation effect in cold regions, and then underwent horizontal gene transfer (HGT) among native bacteria through mobile genetic elements (MGEs). The TRB-C (32.6-49.1 %) and tnpA-06 (0.27-7.5 %) were significantly increased in frozen soil, while Int3 (0.67-10.6 %) and tnpA-04 (11.1-19.4 %) were up-regulated in thawed soil. Moreover, the ARGs in frozen soil primarily underwent HGT through MGEs, i.e. TRB-C and tnpA-06, with increased number of Firmicutes serving as carrier. The case study not only demonstrated relationship between transmission of ARGs and microbial community in the soil under practically relevant FTC condition, but also emphasized the importance for formulating better strategies for preventing FTC-induced ARGs in dairy farm in cold regions.

Pollution characteristics of heavy metals, antibiotic and antibiotic resistance genes in the crested ibis and their habitat across different lifestyle and geography

Antibacterial resistance in wild animals has been increasingly reported worldwide, even though they are usually not directly exposed to clinically relevant antibiotics. Crested ibis, one of the rarest birds in the world, usually forages in paddy fields and prefer to nest and breed near villages that is greatly influenced by anthropogenic activities. We sampled the feces of crested ibises, as well as their habitat environment samples, to explore the pollution characteristics of heavy metals, antibiotics and antibiotic resistance genes (ARGs). Results showed that the pollution characteristics of heavy metals, antibiotic, ARGs and gut microbiota of crested ibis were more related by host lifestyle and habitats. Captive ibises had higher relative abundances of the total ARGs and tetracycline concentrations compared with feralization and wild ibises, while the heavy metal contents had shown the opposite result. The Characteristics of pollutants in the corresponding environmental samples also exhibited high similarity with the results of fecal samples. The relative abundances of Proteobacteria and Actinobacteria were significantly different between captive and wild individuals, while the abundance of majority bacterial genera was generally higher in wild populations. The concentrations of heavy metals in soil (Cd, Cu and Zn) and water (Cd, Cu, Zn and Cr) were both exceeded the background soil levels or surface water quality standards, suggesting multi-element contamination in the habitat. Ecological risk assessments of soils by Igeo and Er showed that the habitats of wild ibises were heavily and moderately contaminated by Cd, which would possibly pose a threat to the health of ibises. PLS-PM analysis indicated that microbial compositions and residual antibiotics had the most substantial impact on the dynamic changes in ARGs of ibis. Overall, this work provides a comprehensive understanding of the characteristics, risks of those contaminations, and their effects on the ARGs in the habitat of crested ibis.

Fate of antibiotic resistance genes and EPS defence mechanisms during simultaneous denitrification and methanogenesis, coupled with the biodegradation of multiple antibiotics under zinc stress

High-strength nitrogen and antibiotics-containing wastewater can be efficiently eliminated by simultaneous denitrification and methanogenesis (SDM). Heavy metals and antibiotics are two critical factors that can lead to horizontal transfer of antibiotic resistance genes (ARGs), which can be simultaneously detected in wastewater. Unfortunately, the impacts of heavy metals on SDM and antibiotic biodegradation have not been fully elucidated. Herein, the effects of SDM and multiple antibiotics biodegradation, extracellular polymeric substances (EPSs) and protein response mechanisms, and ARG fate under Zn(II) stress were comprehensively evaluated. The results indicated that a high level of Zn(II) (≥5 mg/L) stress significantly decreased the degradation rate of multiple antibiotics and suppressed denitrification and methanogenesis. In addition, Zn(II) exposure prompted the liberation of proteins from microbes into the EPSs, and the combination of EPSs with small molecules quenched the original fluorescent components and destroyed the protein structure. The dominant proteins can bind to both Zn(II) and multiple antibiotics through several types of chemical interactions, including metallic and hydrogen bonds, hydrophobic interactions, and salt bridges, relieving the toxicity of harmful substances. Moreover, metagenomic sequencing revealed that the abundance of zinc resistance genes (Zn-RGs), ARGs (mainly tetracyclines), and mobile genetic elements (MGEs) increased under Zn(II) stress. Mantel test illustrated that the ARGs mecD, tetT, and tetB(60) were most affected by MGEs. Moreover, molecular network analysis revealed that several MGEs can bridge metal resistance genes (MRGs) and ARGs, facilitating the horizontal transfer of ARGs. This study provides theoretical guidance for the environmental risk control of antibiotics-containing wastewater treated by an SDM system.

High-throughput profiling of antibiotic resistance genes in the Yellow River of Henan Province, China

Profiling antibiotic resistance genes (ARGs) in the Yellow River of China's Henan Province is essential for understanding the health risks of antibiotic resistance. The profiling of ARGs was investigated using high-throughput qPCR from water samples in seven representative regions of the Yellow River. The absolute and relative abundances of ARGs and moble genetic elements (MGEs) were higher in summer than in winter (ANOVA, p < 0.001). The diversity and abundance of ARGs were higher in the Yellow River samples from PY and KF than the other sites. Temperature (r = 0.470 ~ 0.805, p < 0.05) and precipitation (r = 0.492 ~ 0.815, p < 0.05) positively influenced the ARGs, while pH had a negative effect (r = - 0.462 ~ - 0.849, p < 0.05). Network analysis indicated that the pathogenic bacteria Rahnella, Bacillus, and Shewanella were the possible hub hosts of ARGs, and tnpA1 was the potential MGE hub. These findings provide insights into the factors influencing ARG dynamics and the complex interaction among the MGEs, pathogenic bacteria and environmental parameters in enriching ARGs in the Yellow River of Henan Province.

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.

Distance-decay equations of antibiotic resistance genes across freshwater reservoirs

Distance-decay (DD) equations can discern the biogeographical pattern of organisms and genes in a better way with advanced statistical methods. Here, we developed a data Compilation, Arrangement, and Statistics framework to advance quantile regression (QR) into the generation of DD equations for antibiotic resistance genes (ARGs) across various spatial scales using freshwater reservoirs as an illustration. We found that QR is superior at explaining dissemination potential of ARGs to the traditionally used least squares regression (LSR). This is because our model is based on the 'law of limiting factors', which reduces influence of unmeasured factors that reduce the efficacy of the LSR method. DD equations generated from the 99th QR model for ARGs were 'Sall = 90.03e-0.01Dall' in water and 'Sall = 92.31e-0.011Dall' in sediment. The 99th QR model was less impacted by uneven sample sizes, resulting in a better quantification of ARGs dissemination. Within an individual reservoir, the 99th QR model demonstrated that there is no dispersal limitation of ARGs at this smaller spatial scale. The QR method not only allows for construction of robust DD equations that better display dissemination of organisms and genes across ecosystems, but also provides new insights into the biogeography exhibited by key parameters, as well as the interactions between organisms and environment.

Effect of microplastics on oxytetracycline trophic transfer: Immune, gut microbiota and antibiotic resistance gene responses

Microplastics and antibiotics are prevalent and emerging pollutants in aquatic ecosystems, but their interactions in aquatic food chains remain largely unexplored. This study investigated the impact of polypropylene microplastics (PP-MPs) on oxytetracycline (OTC) trophic transfer from the shrimp (Neocaridina denticulate) to crucian carp (Carassius auratus) by metagenomic sequencing. The carrier effects of PP-MPs promoted OTC bioaccumulation and trophic transfer, which exacerbated enterocyte vacuolation and hepatocyte eosinophilic necrosis. PP-MPs enhanced the inhibitory effect of OTC on intestinal lysozyme activities and complement C3 levels in shrimp and fish, and hepatic immunoglobulin M levels in fish (p < 0.05). Co-exposure of MPs and OTC markedly increased the abundance of Actinobacteria in shrimp and Firmicutes in fish, which caused disturbances in carbohydrate, amino acid, and energy metabolism. Moreover, OTC exacerbated the enrichment of antibiotic resistance genes (ARGs) in aquatic animals, and PP-MPs significantly increased the diversity and abundance of ARGs and facilitated the trophic transfer of teta and tetm. Our findings disclosed the impacts of PP-MPs on the mechanism of antibiotic toxicity in aquatic food chains and emphasized the importance of gut microbiota for ARGs trophic transfer, which contributed to a deeper understanding of potential risks posed by complex pollutants on aquatic ecosystems.

Spread of plasmids carrying antibiotic resistance genes in soil-lettuce-snail food chain

Fertilization can change the composition of antibiotic resistance genes(ARGs) and their host bacteria in agricultural fields, while complex microbial activities help ARGs into crops and transmit them to humans through agricultural products.Therefore, this study constructed a farmland food chain with soil-lettuce-snail as a typical structure, added genetically engineered Pseudomonas fluorescens containing multidrug-resistant plasmid RP4 to track its spread in the farmland food chain, and used different fertilization methods to explore its influence on the spread and diffusion of ARGs and intl1 in the farmland food chain. It was found that exogenous Pseudomonas can enter plants from soil and pass into snails' intestines, and there is horizontal gene transfer phenomenon of RP4 plasmid in bacteria. At different interfaces of the constructed food chain, the addition of exogenous drug-resistant bacteria had different effects on the total abundance of ARGs and intl1. Fertilization, especially manure, not only promoted the spread of Pseudomonas aeruginosa and the transfer of RP4 plasmid levels, but also significantly increased the total abundance of ARGs and intl1 at all interfaces of the constructed food chain. The main ARGs host bacteria in the constructed food chain include Proteobacteria, Bacteroides, and Firmicutes, while Flavobacterium of Bacteroides is the unique potential host bacteria of RP4 plasmid. In conclusion, this study provides a reference for the risk assessment of ARGs transmitted to the human body through the food chain, and has important practical significance to reduce the antibiotic resistance contamination of agricultural products and ensure the safety of vegetable basket.

Inhibition of quorum sensing serves as an effective strategy to mitigate the risks of human bacterial pathogens in soil

The coexistence of antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence factor genes (VFGs) in human bacterial pathogens (HBPs) increases their risks to ecological security and human health and no effective strategy is available. Herein, we demonstrated two typical quorum sensing (QS) interfering agents, 4-nitropyridine-N-oxide (4-NPO, a QS inhibitor) and Acylase Ⅰ (a quorum quenching (QQ) enzyme), effectively decreased the abundance of HBPs by 48.30% and 72.54%, respectively, which was accompanied by the reduction of VFGs, ARGs, and MGEs. The decrease in QS signals mediated by QS interfering agents disturbed bacterial communication and inhibited biofilm formation. More importantly, QS interfering agents reduced the intra-species and inter-species conjugation frequencies among bacteria, considerably inhibiting the dissemination of ARGs and VFGs via horizontal gene transfer. Furthermore, the QS interfering agents did not significantly affect the metabolic function of other nonpathogenic microorganisms in the soil. Collectively, our study provides an effective and eco-friendly strategy to mitigate the risks of HBPs in soil.

Effects and mechanisms of polystyrene micro- and nano-plastics on the spread of antibiotic resistance genes from soil to lettuce

Effects of microplastics (MPs) and nanoplastics (NPs) on the spread of antibiotic resistance genes (ARGs) in soil-plant systems are still unclear. To investigate the spread and mechanisms of ARGs from soil to lettuce, lettuce was exposed to soil spiked with two environmentally relevant concentrations of polystyrene MPs (100 μm) and NPs (100 nm). Results showed that microorganisms that carried ARGs in soil were increased after exposure to MPs/NPs, which led to an increase in ARGs in roots. NPs were absorbed by roots and can be transported to leaves. Analysis of transcriptomics, proteomics and metabolomics indicated that high concentration of NPs regulated the expression of related genes and proteins and improved the accumulation of flavonoids in the lettuce, therefore decreased the abundance of microorganisms that contained ARGs. Our work emphasizes the size and dose influences of MPs and NPs on the spread of ARGs from soil to plant.

Mechanisms Underlying the Overlooked Chiral Fungicide-Driven Enantioselective Proliferation of Antibiotic Resistance in Earthworm Intestinal Microbiome

From a "One Health" perspective, the global threat of antibiotic resistance genes (ARGs) is associated with modern agriculture practices including agrochemicals application. Chiral fungicides account for a considerable proportion of wildly used agrochemicals; however, whether and how their enantiomers lead to differential proliferation of antibiotic resistance in agricultural environments remain overlooked. Focused on the soil-earthworm ecosystem, we for the first time deciphered the mechanisms underlying the enantioselective proliferation of antibiotic resistance driven by the enantiomers of a typical chiral fungicide mandipropamid (i.e., R-MDP and S-MDP) utilizing a multiomic approach. Time-series metagenomic analysis revealed that R-MDP led to a significant enhancement of ARGs with potential mobility (particularly the plasmid-borne ARGs) in the earthworm intestinal microbiome. We further demonstrated that R-MDP induced a concentration-dependent facilitation of plasmid-mediated ARG transfer among microbes. In addition, transcriptomic analysis with verification identified the key aspects involved, where R-MDP enhanced cell membrane permeability, transfer ability, biofilm formation and quorum sensing, rebalanced energy production, and decreased cell mobility versus S-MDP. Overall, the findings provide novel insights into the enantioselective disruption of microbiome and resistome in earthworm gut by chiral fungicides and offer significant contributions to the comprehensive risk assessment of chiral agrochemicals in agroecosystems.

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.

Impacts of irrigation with treated livestock wastewater on the accumulation characteristic of ARGs in the farmland soil: a case study in Hohhot, China

Irrigation with treated livestock wastewater (TWW) is a promising strategy for reusing resources. However, TWW irrigation might introduce antibiotic resistant genes (ARGs) into the soil, posing environmental risks associated with antibiotic resistance. This study focuses on investigating the influence of irrigation amounts and duration on the fate of ARGs and identifies key factors driving their changes. The results showed that there were 13 ARGs in TWW, while only 5 ARGs were detected in irrigated soil. That is some introduced ARGs from TWW could not persistently exist in the soil. After 1-year irrigation, an increase in irrigation amount from 0.016 t/m2 to 0.048 t/m2 significantly enhanced the abundance of tetC by 29.81%, while ermB and sul2 decreased by 45.37% and 76.47%, respectively (p < 0.01). After 2-year irrigation, the abundance of tetC, ermB, ermF, dfrA1, and total ARGs significantly increased (p < 0.05) when the irrigation amount increased. The abundances of ARGs after 2-year irrigation were found to be 2.5-34.4 times higher than 1 year. Obviously, the irrigation years intensified the positive correlation between ARGs abundance and irrigation amount. TetC and ermF were the dominant genes resulting in the accumulation of ARGs. TWW irrigation increased the content of organic matter and total nitrogen in the soil, which affected microbial community structure. The changes of the potential host were the determining factors driving the ARGs abundance. Our study demonstrated that continuous TWW irrigation for 2 years led to a substantial accumulation of ARGs in soil.

A case for the importance of following antibiotic resistant bacteria throughout the soil food web

It is necessary to complement next-generation sequencing data on the soil resistome with theoretical knowledge provided by ecological studies regarding the spread of antibiotic resistant bacteria (ARB) in the abiotic and, especially, biotic fraction of the soil ecosystem. Particularly, when ARB enter agricultural soils as a consequence of the application of animal manure as fertilizer, from a microbial ecology perspective, it is important to know their fate along the soil food web, that is, throughout that complex network of feeding interactions among members of the soil biota that has crucial effects on species richness and ecosystem productivity and stability. It is critical to study how the ARB that enter the soil through the application of manure can reach other taxonomical groups (e.g., fungi, protists, nematodes, arthropods, earthworms), paying special attention to their presence in the gut microbiomes of mesofauna-macrofauna and to the possibilities for horizontal gene transfer of antibiotic resistant genes.

Overview of Direct and Indirect Effects of Antibiotics on Terrestrial Organisms

Antibiotics (ABs) have made it possible to treat bacterial infections, which were in the past untreatable and consequently fatal. Regrettably, their use and abuse among humans and livestock led to antibiotic resistance, which has made them ineffective in many cases. The spread of antibiotic resistance genes (ARGs) and bacteria is not limited to nosocomial environments, but also involves water and soil ecosystems. The environmental presence of ABs and ARGs is a hot topic, and their direct and indirect effects, are still not well known or clarified. A particular concern is the presence of antibiotics in agroecosystems due to the application of agro-zootechnical waste (e.g., manure and biosolids), which can introduce antibiotic residues and ARGs to soils. This review provides an insight of recent findings of AB direct and indirect effects on terrestrial organisms, focusing on plant and invertebrates. Possible changing in viability and organism growth, AB bioaccumulation, and shifts in associated microbiome composition are reported. Oxidative stress responses of plants (such as reactive oxygen species production) to antibiotics are also described.

Transmission mechanisms of antibiotic resistance genes in arsenic-contaminated soil under sulfamethoxazole stress

Numerous studies have revealed the spread mechanism of antibiotic resistance genes (ARGs) in single antibiotic-contaminated soils. However, the comprehensive impacts of heavy metals and antibiotics on ARGs and the underlying mechanisms are still unknown. Here, high-throughput quantitative PCR and high-throughput sequencing were used to investigate changes in ARGs and bacterial communities under various sulfamethoxazole (SMX) regimes (0, 1, 10, 50 mg kg^-1) in arsenic (As) contaminated soils. The study found that the abundances of ARGs, mobile genetic elements (MGEs), and heavy metal resistance genes (HMRGs) significantly increased in the soil fortified at 10 and 50 mg kg^-1 SMX concentrations. The ARGs abundance increased with the increase in the MGEs abundance. Many significant positive correlations between various ARGs subtypes and HMRGs subtypes were found. These results indicate that the HMRGs and MGEs positively contributed to the enrichment of ARGs in As-contaminated soils under SMX stress. Meanwhile, the abundance of copiotrophic (Actinobacteriota) reduced and oligotrophic (Gemmatimonadota) increased, indicating that the life history strategy of the community changed. In addition, Gemmatimonadota was positively correlated to ARGs, HMRGs, and MGEs, suggesting that Gemmatimonadota, which can cope with As and SMX stress, was the host for resistance genes in the soil. Finally, the study found that MGEs play a determinant role in ARGs proliferation due to the direct utilization of HGT, and the indirect effect for ARGs spread under a co-selection mechanism of ARGs and HMRGs, while the bacterial community showed indirect influences by altering environmental factors to act on MGEs. Collectively, this study revealed new insights into the mechanisms of resistance gene transmission under combined SMX and As contamination in soil ecosystems.

Metagenomic next generation sequencing for studying antibiotic resistance genes in the environment

Bacterial antimicrobial resistance (AMR) is a persisting and growing threat to human health. Characterization of antibiotic resistance genes (ARGs) in the environment is important to understand and control ARG-associated microbial risks. Numerous challenges exist in monitoring ARGs in the environment, due to the extraordinary diversity of ARGs, low abundance of ARGs with respect to the complex environmental microbiomes, difficulties in linking ARGs with bacterial hosts by molecular methods, difficulties in achieving quantification and high throughput simultaneously, difficulties in assessing mobility potential of ARGs, and difficulties in determining the specific AMR determinant genes. Advances in the next generation sequencing (NGS) technologies and related computational and bioinformatic tools are facilitating rapid identification and characterization ARGs in genomes and metagenomes from environmental samples. This chapter discusses NGS-based strategies, including amplicon-based sequencing, whole genome sequencing, bacterial population-targeted metagenome sequencing, metagenomic NGS, quantitative metagenomic sequencing, and functional/phenotypic metagenomic sequencing. Current bioinformatic tools for analyzing sequencing data for studying environmental ARGs are also discussed.

Distribution and transmission of β-lactamase resistance genes in meal-to-milk chain on dairy farm

Antibiotics have been widely used in animal husbandry, which leads to high risk of food-borne transfer of antibiotic resistance genes (ARGs). The present study investigated the distribution of β-lactamase resistance genes (β-RGs) on dairy farm in the Songnen Plain of western Heilongjiang Province, China, to provide mechanistic insights into food-borne transmission of β-RGs through "meal-to-milk" chain under practically relevant circumstances. The results demonstrated that the abundance of β-RGs (91%) was much higher than that of other ARGs in the livestock farms. The blaTEM exhibited the content as high as 94.55% among all ARGs, and higher than 98% blaTEM was detected in meal, water and milk sample. The metagenomic taxonomy analysis indicated that the blaTEM should be carried by tnpA-04 (7.04%) and tnpA-03 (1.48%) hosted in Pseudomonas genus (15.36%) and Pantoea (29.02%) genus. Both tnpA-04 and tnpA-03 in the milk sample were identified to be the key mobile genetic elements (MGEs) responsible for transferring blaTEM along the "meal-manure-soil-surface water-milk" chain. The ARGs transfer across ecological boundaries underscored the need to evaluate potential dissemination of high-risk Proteobacteria and Bacteroidetes carried by humans and animals. They were capable of producing expanded-spectrum β-lactamases (ESBLs) and destroying commonly used antibiotics, leading to possible risk of food-borne horizontal transmission of ARGs. This study not only has important environmental implications for identifying the pathway for ARGs transfer, but also highlights the demand for appropriate policy toward safe regulation of dairy farm and husbandry products.

Effects of cadmium and copper mixtures on antibiotic resistance genes in rhizosphere soil

The evolvement and development of antibiotic resistance in microorganisms may be influenced by metals; however, it is still unclear how cadmium (Cd) and copper (Cu) combined affect the distribution and presence of antibiotic-resistance genes (ARGs) in rhizosphere soil. The aims of this research were to (1) compare the distribution patterns of bacterial communities and ARGs in response to the effects of Cd and Cu both separately and combined; (2) explore the possible mechanisms underlying the variation in soil bacterial communities and ARGs in addition to the combined effects of Cd, Cu, and various environmental variables (nutrients, pH, etc.); and (3) provide a reference for assessing the risks of metals (Cd and Cu) and ARGs. The findings showed that the multidrug resistance genes acrA and acrB and the transposon gene intI-1 were present in high relative abundance in bacterial communities. Cadmium and Cu had a substantial interaction effect on the abundance of acrA, whereas Cu had a notable main effect on the abundance of intI-1. According to the network analysis, the strong links between bacterial taxa and specific ARGs revealed that most ARGs were hosted by Proteobacteria, Actinobacteria, and Bacteroidetes. According to structural equation modeling, Cd had a larger effect on ARGs than Cu. Compared to previous analyses of ARGs, bacterial community diversity had little effect on ARGs in this study. Overall, the results may have important consequences for determining the possible hazard of soil metals and extend the understanding of how Cd and Cu co-select ARGs in rhizosphere soils.

Antibiotic resistance in soil-plant systems: A review of the source, dissemination, influence factors, and potential exposure risks

As an emerging environmental contaminant, the widespread of antibiotic resistance has caused a series of environmental issues and human health concerns. A load of antibiotic residues induced by agricultural practices have exerted selective pressure to bacterial communities in the soil-plant system, which facilitated the occurrence and dissemination of antibiotic resistance genes (ARGs) through horizontal gene transfer. As a result, the enrichment of ARGs within crops at harvest under the influence of food ingestion could lead to critical concerns of public health. In this review, the prevalence and dissemination of antibiotic resistance in the soil-plant system are highlighted. Moreover, different underlying mechanisms and detection methods for ARGs transfer between the soil environment and plant compartments are summarized and discussed. On the other hand, a wide range of influencing factors for the transfer and distribution of antibiotic resistance within the soil-plant system are also presented and discussed. In response to exposure of antibiotic residues and resistomes, corresponding hazard identification assessments have been summarized, which could provide beneficial guides of the toxicological tolerance for the general population. Finally, further research priorities for detection and management ARGs spread are also suggested.

Metagenomic analysis reveals patterns and hosts of antibiotic resistance in different pig farms

In actual production environments, antibiotic-resistant genes (ARGs) are abundant in pig manure, which can form transmission chains through animals, the environment, and humans, thereby threatening human health. Therefore, based on metagenomic analysis methods, ARGs and mobile genetic elements (MGEs) were annotated in pig manure samples from 6 pig farms in 3 regions of Shanxi Province, and the potential hosts of ARGs were analyzed. The results showed that a total of 14 ARG types were detected, including 182 ARG subtypes, among which tetracycline, phenol, aminoglycoside, and macrolide resistance genes were the main ones. ARG profiles, MGE composition, and microbial communities were significantly different in different regions as well as between different pig farms. In addition, Anaerobutyricum, Butyrivibrio, and Turicibacter were significantly associated with multiple ARGs, and bacteria such as Prevotella, Bacteroides, and the family Oscillospiraceae carried multiple ARGs, suggesting that these bacteria are potential ARG hosts in pig manure. Procrustes analysis showed that bacterial communities and MGEs were significantly correlated with ARG profiles. Variation partitioning analysis results indicated that the combined effect of MGEs and bacterial communities accounted for 64.08% of resistance variation and played an important role in ARG profiles. These findings contribute to our understanding of the dissemination and persistence of ARGs in actual production settings, and offer some guidance for the prevention and control of ARGs contamination.

Characterization of microbial community, ecological functions and antibiotic resistance in estuarine plastisphere

The plastisphere is a new ecological niche. Compared to the surrounding water, microbial community composition associated with the plastisphere is known to differ with functional consequences. Here, this study characterized the bacterial and fungal communities associated with four types of plastisphere (polyethylene, polystyrene, polypropylene and polyvinyl chloride) in an estuarine habitat; assessed ecological functions including carbon, nitrogen, phosphorus and sulfur cycling, and determined the presence of antibiotic resistance genes (ARGs) and human pathogens. Stochastic processes dominated the community assembly of microorganisms on the plastisphere. Several functional genera related to nutrient cycling were enriched in the plastisphere. Compared to surrounding water and other plastisphere, the abundances of carbon, nitrogen and phosphorus cycling genes (cdaR, nosZ and chpy etc.) and ARGs (aadA2-1, cfa and catB8 etc.) were significantly increased in polyvinyl chloride plastisphere. In contrast, the polystyrene plastisphere was the preferred substrate for several pathogens being enriched with for example, Giardia lamblia 18S rRNA, Klebsiella pneumoniae phoE and Legionella spp. 23S rRNA. Overall, this study showed that different plastisphere had different effects on ecological functions and health risk in estuaries and emphasizes the importance of controlling plastic pollution in estuaries. Data from this study support global policy drivers that seek to reduce plastic pollution and offer insights into ecological functions in a new ecological niche of the Anthropocene.

Microbial Multitrophic Communities Drive the Variation of Antibiotic Resistome in the Gut of Soil Woodlice (Crustacea: Isopoda)

Multitrophic communities inhabit in soil faunal gut, including bacteria, fungi, and protists, which have been considered a hidden reservoir for antibiotic resistance genes (ARGs). However, there is a dearth of research focusing on the relationships between ARGs and multitrophic communities in the gut of soil faunas. Here, we studied the contribution of multitrophic communities to variations of ARGs in the soil woodlouse gut. The results revealed diverse and abundant ARGs in the woodlouse gut. Network analysis further exhibited strong connections between key ecological module members and ARGs, suggesting that multitrophic communities in the keystone ecological cluster may play a pivotal role in the variation of ARGs in the woodlouse gut. Moreover, long-term application of sewage sludge significantly altered the woodlice gut resistome and interkingdom communities. The variation portioning analysis indicated that the fungal community has a greater contribution to variations of ARGs than bacterial and protistan communities in the woodlice gut after long-term application of sewage sludge. Together, our results showed that changes in gut microbiota associated with agricultural practices (e.g., sewage sludge application) can largely alter the gut interkingdom network in ecologically relevant soil animals, with implications for antibiotic resistance, which advances our understanding of the microecological drivers of ARGs in terrestrial ecosystem.

Does Plant Identity Affect the Dispersal of Resistomes Above and Below Ground?

Resistomes are ubiquitous in natural environments. Previous studies have shown that both the plant phyllosphere and soil-borne nematodes were reservoirs of above- and below-ground resistomes, respectively. However, the influence of plant identity on soil, nematode, and phyllosphere resistomes remains unclear. Here, a microcosm experiment was used to explore the characteristics of bacterial communities and resistomes in soil, nematode, and phyllosphere associated with six different plant identities (Lactuca sativa, Cichorium endivia, Allium fistulosum, Coriandrum sativum, Raphanus sativus, and Mesembryanthemum crystallinum). A total of 222 antibiotic resistance genes (ARGs) and 7 mobile genetic elements (MGEs) were detected by high-throughput quantitative PCR from all samples. Plant identity not only significantly affected the diversity of resistomes in soil, nematode, and phyllosphere but also influenced the abundance of resistomes in nematodes. Shared bacteria and resistomes indicated a possible pathway of resistomes transfer through the soil-nematode-phyllosphere system. Structural equation models revealed that plant identity had no direct effect on phyllosphere ARGs, but altered indirectly through complex above- and below-ground interactions (soil-plant-nematode trophic transfer). Results also showed that bacteria and MGEs were key factors driving the above- and below-ground flow of resistomes. The study extends our knowledge about the top-down and bottom-up dispersal patterns of resistomes.

Effects of biofertilizer on soil microbial diversity and antibiotic resistance genes

Spread of antibiotic resistance or the presence of antibiotic resistance genes (ARGs) in pathogens is a globally recognized threat to human health. Numerous studies have shown that application of organic fertilizers may increase the risk of ARGs, however, the risk of resistance genes associated with biofertilizers is largely unknown. To investigate whether biofertilizer application introduces ARGs to the soil, we used high-throughput quantitative polymerization chain reaction (HT-qPCR) to explore the effect of biofertilizer application over three years on soil ARGs in three orchards with different locations in China. Redundancy analysis showed specific and significant differences in the beta diversity of soil bacteria and fungi between treatments (fertilizer vs. no fertilizer). One-way ANOVA analysis revealed findings of the main driver of the significant difference in microbial community structure between fertilizer and control treatment was the change in soil properties following the application of biofertilizer. A total of 139 ARGs and 27 MGEs (mobile genetic elements), and 46 ARGs and 6 MGEs from 11 major taxa were detected in biofertilizer and soil samples, respectively. Only the samples from Guangxi had significant differences in the detected number of ARGs and MGEs between fertilization and control. Through structural equation modeling (SEM), we found that soil properties indirectly affected ARGs by shaping bacterial diversity, while bacterial abundance directly affected ARGs. Biofertilizer application did not significantly alter the relative abundance of ARGs in soil due to the complexity of the soil environment and competition between exogenous and native microorganisms. This study provided new insights into the spread of the antibiotic resistome of the soil through biofertilizer applications.

An integrated multidisciplinary-based framework for characterizing environmental risks of heavy metals and their effects on antibiotic resistomes in agricultural soils

In this study, a new integrated multidisciplinary-based framework has been proposed to better understand the environmental risks of heavy metals (HMs) in agricultural soils. The source apportionment results revealed by a multilinear engine model were incorporated into the geochemical indexes and the probabilistic health risk assessment models for identifying the source-oriented risks of HMs in the environment. High-throughput sequencing-based metagenomic assembly analysis was used for characterizing the prevalence and dissemination risk of antibiotic resistomes and their associations with the geochemical enrichment of HMs in the soils. Results showed agricultural and industrial activities were the main sources of HMs in the environment. Although the soils were contaminated moderately by HMs and the health risks posed by soil metals were negligible for both adult and children, source-oriented risk evaluation suggested agricultural activities contributed relatively higher contamination and health risks than the other sources. Notably, abundant and diverse antibiotic resistant genes, mobile gene elements, virulence factors, and antibiotic-resistant bacterial pathogens were identified in the agricultural soils, as well as their co-occurrences on the same contigs, implying a non-negligible resistome risk. Further, statistical and network analyses showed the geochemical enrichment of HMs exerted significant effects on the antibiotic resistomes in the environment.

Eco-risk management of tylosin fermentation residues using vermicomposting

Tylosin fermentation residues (TFR) pose an ecotoxicological risk through antibiotic resistant bacteria (ARBs) and their corresponding genes (ARGs). This study evaluated the ecotoxicity of TFR to soil biological activity, and further explored the mechanisms of vermicomposting to reduce the toxicological risk. The results showed that tylosin (TYL) was moderately degradable with a half-life (t_1/2) of 37.5 d, inducing 28-44% inhibition rate of nitrogen transformation in soil, and the EC₅₀ of earthworm avoidance was 880 mg/kg. The 30-d vermicomposting reduced the pH and OM content, while increased the EC and TN content, accelerated compost maturation (C/N ratio up to 20), and enriched the microbial community. ARGs were reduced by earthworm through removal of TYL (>70% degradation, t_1/2 of <20 d), inhibiting abundance of intI1 and ARBs. We conclude that vermicomposting is an efficient method for TFR treatment and its eco-risk management.

Variations of earthworm gut bacterial community composition and metabolic functions in coastal upland soil along a 700-year reclamation chronosequence

Most ecosystem functions attributed to earthworms are mediated by their internal microbiomes, and these are sensitive to disturbances in the external environment. However, few studies have focused on the response of the earthworm gut microbiome to soil chronosequence. Here, we used 16S rRNA high-throughput sequencing and high-throughput quantitative PCR to investigate the variations in bacterial communities and functional gene abundance in earthworm (Lumbricina sp.) guts and upland soils under 700 years of cultivation. Our results indicated that 700 years of upland cultivation significantly shaped bacterial communities and increased functional traits of microbes in earthworm guts, which were more sensitive to cultivation age compared to the surrounding soils. The earthworm gut bacterial community changed rapidly over the first 300 years of cultivation and then changed slowly in the following centuries. Along with the cultivation age, we also observed that the earthworm gut microbiota was successive towards a copiotrophic strategy (e.g., Xanthobacteraceae, Nocardioidaceae, Hyphomicrobiaceae, and Bacillaceae) and higher potential functions (e.g., ureC, nirS, nosZ, phoD, and pqqC). Furthermore, canonical correspondence analysis further revealed that soil pH, C:N ratio, soil organic carbon, and total nitrogen were key abiotic drivers shaping earthworm gut bacterial communities. Taken together, this study reveals the succession of bacterial communities and potential functions in earthworm guts within 700 years of upland cultivation, which may provide a broader space for us to rationally exploit and utilize the interactions between soil and earthworm gut microbiotas to benefit the soil nutrient cycling process.

Electrocatalytic inactivation of antibiotic resistant bacteria and control of antibiotic resistance dissemination risk

Antibiotic resistance in environmental matrices becomes urgently significant for public health and has been considered as an emerging environmental contaminant. In this work, the ampicillin-resistant Escherichia coli (AR E. coli) and corresponding resistance genes (bla_TEM-1) were effectively eliminated by the electrocatalytic process, and the dissemination risk of antibiotic resistance was also investigated. All the AR E. coli (∼8 log) was inactivated and 8.17 log bla_TEM-1 was degraded by the carbon nanotubes/agarose/titanium (CNTs/AG/Ti) electrode within 30 min. AR E. coli was inactivated mainly attributing to the damage of cell membrane, which was attacked by reactive oxygen species and subsequent leakage of intracellular cytoplasm. The bla_TEM-1 was degraded owing to the strand breaking in the process of electrocatalytic degradation. Furthermore, the dissemination risk of antibiotic resistance was effectively controlled after being electrocatalytic treatment. This study provided an effective electrocatalytic technology for the inactivation of antibiotic resistant bacteria and control of antibiotic resistance dissemination risk in the aqueous environment.

Evidence for Long-Term Anthropogenic Pollution: The Hadal Trench as a Depository and Indicator for Dissemination of Antibiotic Resistance Genes

Knowledge of the distribution and dissemination of antibiotic resistance genes (ARGs) is essential for understanding anthropogenic impacts on natural ecosystems. The transportation of ARGs via aquatic environments is significant and has received great attention, but whether there has been anthropogenic ARG pollution to the hadal ocean ecosystem has not been well explored. For investigating ecological health concerns, we profiled the ARG occurrence in sediments of the Mariana Trench (MT) (10 890 m), the deepest region of the ocean. Metagenomic-based ARG profiles showed a sudden increase of abundance and diversity in the surface layer of MT sediments reaching 2.73 × 10^-2 copy/cell and 81 subtypes, and a high percentage of ∼63.6% anthropogenic pollution sources was predicted by the Bayesian-modeling classification method. These together suggested that ARG accumulation and anthropogenic impacts have already permeated into the bottom of the deepest corner on the earth. Moreover, six ARG-carrying draft genomes were retrieved using a metagenomic binning strategy, one of which assigned as Streptococcus was identified as a potential bacterial host to contribute to the ARG accumulation in MT, carrying ermF, tetM, tetQ, cfxA2, PBP-2X, and PBP-1A. We propose that the MT ecosystem needs further long-term monitoring for the assessment of human impacts, and our identified three biomarkers (cfxA2, ermF, and mefA) could be used for the rapid monitoring of anthropogenic pollution. Together our findings imply that anthropogenic pollution has penetrated into the deepest region of the ocean and urge for better pollution control to reduce the risk of ARG dissemination to prevent the consistent accumulation and potential threat to the natural environment.

How can fertilization regimes and durations shape earthworm gut microbiota in a long-term field experiment?

The positive roles of earthworms on soil functionality has been extensively documented. The capacity of the earthworm gut microbiota on decomposition and nutrient cycling under long-term fertilization in field conditions has rarely been studied. Here, we report the structural, taxonomic, and functional responses of Eisenia foetida and Pheretima guillelmi gut microbiota to different fertilization regimes and durations using 16S rRNA gene-based Illumina sequencing and high-throughput quantitative PCR techniques. Our results revealed that the core gut microbiota, especially the fermentative bacteria were mainly sourced from the soil, but strongly stimulated with species-specificity, potential benefits for the host and soil health. The functional compositions of gut microbiota were altered by fertilization with fertilization duration being more influential than fertilization regimes. Moreover, the combination of organic and inorganic fertilization with the longer duration resulted in a higher richness and connectivity in the gut microbiota, and also their functional potential related to carbon (C), nitrogen, and phosphorus cycling, particularly the labile C decomposition, denitrification, and phosphate mobilization. We also found that long-term inorganic fertilization increased the abundance of pathogenic bacteria in the P. guillelmi gut. This study demonstrates that understanding earthworm gut microbiota can provide insights into how agricultural practices can potentially alter soil ecosystem functions through the interactions between soil and earthworm gut microbiotas.