Impact of bioaccessible pyrene on the abundance of antibiotic resistance genes during Sphingobium sp.- and sophorolipid-enhanced bioremediation in soil

Antibiotic Resistance Genes in Agricultural Soils: A Comprehensive Review of the Hidden Crisis and Exploring Control Strategies

This paper aims to review the sources, occurrence patterns, and potential risks of antibiotic resistance genes (ARGs) in agricultural soils and discuss strategies for their reduction. The pervasive utilization of antibiotics has led to the accumulation of ARGs in the soil. ARGs can be transferred among microorganisms via horizontal gene transfer, thereby increasing the likelihood of resistance dissemination and heightening the threat to public health. In this study, we propose that physical, chemical, and bioremediation approaches, namely electrokinetic remediation, advanced oxidation, and biochar application, can effectively decrease the abundance of ARGs in the soil. This study also highlights the significance of various control measures, such as establishing a strict regulatory mechanism for veterinary drugs, setting standards for the control of ARGs in organic fertilizers, and conducting technical guidance and on-farm soil monitoring to reduce the environmental spread of ARGs and protect public health.

Insights into the functionality of biofilm-forming bacterial consortia as bioavailability enhancers towards biodegradation of pyrene in hydrocarbon-contaminated soil

Hydrophobic organic compounds (HOCs), such as pyrene, pose significant challenges for microbial-based remediation in soil due to limited substrate availability and the sustainability of augmented microbes. Research targets are to investigate the potential of biofilm-forming bacterial cells to enhance pyrene bioavailability and biodegradation in two different hydrocarbon-contaminated soil microcosms, employing microbiological, molecular, and chemical analysis validated through statistical tools. The microcosm augmented with strong biofilm bacterial consortia (A) significantly enhanced pyrene availability by 1-1.5% compared to the weak biofilm consortia (B) and mixed consortia (AB). Analysis of 16 S rDNA amplicons revealed notable differences in bacterial community composition between consortia A and B augmented soil, with Proteobacteria as the dominant phylum. Taxonomic composition of soil microbiome predicted enhanced xenobiotic biodegradative potential of strong biofilm consortia (A) up to 20 days, exhibiting a higher abundance of functional genes related to upstream degradative pathway of PAHs, such as naphthalene dioxygenase (nahAa), PAH dioxygenase subunit genes (nidA, nidB), extradiol dioxygenase (phdF) and aldehyde dehydrogenase (nidD). Our study highlights the significant role of biofilm-forming bacteria as "bioavailability enhancers," for high molecular weight PAHs like pyrene, in contaminated soils with their implications for designing future sustainable bioremediation programs.

An eco-evolutionary perspective on antimicrobial resistance in the context of One Health

The One Health approach musters growing concerns about antimicrobial resistance due to the increased use of antibiotics in healthcare and agriculture, with all of its consequences for human, livestock, and environmental health. In this perspective, we explore the current knowledge on how interactions at different levels of biological organization, from genetic to ecological interactions, affect the evolution of antimicrobial resistance. We discuss their role in different contexts, from natural systems with weak selection, to human-influenced environments that impose a strong pressure toward antimicrobial resistance evolution. We emphasize the need for an eco-evolutionary approach within the One Health framework and highlight the importance of horizontal gene transfer and microbiome interactions for increased understanding of the emergence and spread of antimicrobial resistance.

Micro-interfacial behavior of antibiotic-resistant bacteria and antibiotic resistance genes in the soil environment: A review

Overutilization and misuse of antibiotics in recent decades markedly intensified the rapid proliferation and diffusion of antibiotic resistance genes (ARGs) within the environment, thereby elevating ARGs to the status of a global public health crisis. Recognizing that soil acts as a critical reservoir for ARGs, environmental researchers have made great progress in exploring the sources, distribution, and spread of ARGs in soil. However, the microscopic state and micro-interfacial behavior of ARGs in soil remains inadequately understood. In this study, we reviewed the micro-interfacial behaviors of antibiotic-resistant bacteria (ARB) in soil and porous media, predominantly including migration-deposition, adsorption, and biofilm formation. Meanwhile, adsorption, proliferation, and degradation were identified as the primary micro-interfacial behaviors of ARGs in the soil, with component of soil serving as significant determinant. Our work contributes to the further comprehension of the microstates and processes of ARB and ARGs in the soil environments and offers a theoretical foundation for managing and mitigating the risks associated with ARG contamination.

Lignocellulosic biomass-based glycoconjugates for diverse biotechnological applications

Glycoconjugates are the ubiquitous components of mammalian cells, mainly synthesized by covalent bonds of carbohydrates to other biomolecules such as proteins and lipids, with a wide range of potential applications in novel vaccines, therapeutic peptides and antibodies (Ab). Considering the emerging developments in glycoscience, renewable production of glycoconjugates is of importance and lignocellulosic biomass (LCB) is a potential source of carbohydrates to produce synthetic glycoconjugates in a sustainable pathway. In this review, recent advances in glycobiology aiming on glycoconjugates production is presented together with the recent and cutting-edge advances in the therapeutic properties and application of glycoconjugates, including therapeutic glycoproteins, glycosaminoglycans (GAGs), and nutraceuticals, emphasizing the integral role of glycosylation in their function and efficacy. Special emphasis is given towards the potential exploration of carbon neutral feedstocks, in which LCB has an emerging role. Techniques for extraction and recovery of mono- and oligosaccharides from LCB are critically discussed and influence of the heterogeneous nature of the feedstocks and different methods for recovery of these sugars in the development of the customized glycoconjugates is explored. Although reports on the use of LCB for the production of glycoconjugates are scarce, this review sets clear that the potential of LCB as a source for the production of valuable glycoconjugates cannot be underestimated and encourages that future research should focus on refining the existing methodologies and exploring new approaches to fully realize the potential of LCB in glycoconjugate production.

Bioaccessible PAH influence on distribution of antibiotic resistance genes and soil toxicity of different types of land use

For a better understanding of the dissemination of antibiotic resistance genes (ARGs) in natural microbial communities, it is necessary to study the factors influencing it. There are not enough studies showing the connection of some pollutants with the dissemination of ARGs and especially few works on the effect of polycyclic aromatic compounds (PAHs) on the spread of resistance in microbiocenosis. In this respect, the aim of the study was to determine the effect of bioaccessible PAHs on soil resistome. The toxicity and the content of bioaccessible PAHs and ARGs were studied in 64 samples of soils of different types of land use in the Rostov Region of Russia. In most soils, a close positive correlation was demonstrated between different ARGs and bioaccessible PAHs with different content of rings in the structure. Six of the seven studied ARGs correlated with the content of 2-, 3-, 4-, 5- or 6-ring PAHs. The greatest number of close correlations was found between the content of PAHs and ARGs in the soils of protected areas, for agricultural purposes, and in soils of hospitals. The diverse composition of microbial communities in these soils might greatly facilitate this process. A close correlation between various toxic effects identified with a battery of whole-cell bacterial biosensors and bioaccessible PAHs of various compositions was established. This correlation showed possible mechanisms of PAHs' influence on microorganisms (DNA damage, oxidative stress, etc.), which led to a significant increase in horizontal gene transfer and spread of some ARGs in soil microbial communities. All this information, taken together, suggests that bioaccessible PAHs can enhance the spread of antibiotic resistance genes.

Insight into the impacts and mechanisms of ketone stress on the antibiotic resistance in Escherichia coli

Accumulation of toxic organic has posed a substantial pressure on the proliferation of bacterial resistance. While aromatic organics have been demonstrated to enhance the antibiotic resistance in bacteria, no information is yet available on the effects of non-aromatic organics on the variations of bacterial resistance. Here, we investigated the effects of a typical ketone (i.e., methylisobutanone (MIBK)) on the variations of antibiotic resistance in Escherichia coli (E. coli). The results showed that the growth of resistant E. coli under environmental concentration of 50 μg/L MIBK was firstly inhibited as explained by the transient disruption in the cell membrane and then recovered possibly due to the reactive oxygen species. Exposure to 50 μg/L MIBK gradually raised the abundance of representative resistance gene (ampR) in E. coli. In contrast, the high concentration of 50 mg/L MIBK continuously inhibited the growth of resistant E. coli by disrupting cell membrane and notably promoted the proliferation of ampR through enhancing the horizontal transformation and up-regulating the expression of efflux pump gene. These findings provided the first evidence for the evolution of bacterial resistance in response to ketone organics.

The source, fate and prospect of antibiotic resistance genes in soil: A review

Antibiotic resistance genes (ARGs), environmental pollutants of emerging concern, have posed a potential threat to the public health. Soil is one of the huge reservoirs and propagation hotspot of ARGs. To alleviate the potential risk of ARGs, it is necessary to figure out the source and fate of ARGs in the soil. This paper mainly reviewed recent studies on the association of ARGs with the microbiome and the transmission mechanism of ARGs in soil. The compositions and abundance of ARGs can be changed by modulating microbiome, soil physicochemical properties, such as pH and moisture. The relationships of ARGs with antibiotics, heavy metals, polycyclic aromatic hydrocarbons and pesticides were discussed in this review. Among the various factors mentioned above, microbial community structure, mobile genetic elements, pH and heavy metals have a relatively more important impact on ARGs profiles. Moreover, human health could be impacted by soil ARGs through plants and animals. Understanding the dynamic changes of ARGs with influencing factors promotes us to develop strategies for mitigating the occurrence and dissemination of ARGs to reduce health risks.

What role does organic fertilizer actually play in the fate of antibiotic resistome and pathogenic bacteria in planting soil?

Organic fertilizer increase antibiotic resistance genes (ARGs) and bacterial pathogens have widely documented. However, how organic fertilizer is involved in changing soil ARGs and pathogenic bacteria after long-term (≥5 years) application remains unclear. Herein, the ARGs and pathogenic bacteria were compared in organic fertilized soils (AF) and non-fertilized soils (NF), and the contribution of input sources (organic fertilizer, irrigation water, air and background soil) on soil ARGs also was determined in this study. Results showed that the abundances of some ARGs, such as vanR and aac(6')-I in AF, were significantly higher than these of NF (p < 0.05). And a relatively higher abundance of potential pathogens, especially, Salmonella enterica and Stenotrophomonas maltophilia, in AF was observed. This indicated that organic fertilizer application can maintain a high level of some soil ARGs and pathogenic bacteria for at least 5 years. Traceability analysis unearthed that organic fertilizer application mainly increased its own contribution to soil ARGs from 1.16% to 9.05%, as well reduced the contribution of background soil, suggesting that the increase in soil ARGs may be partly attributable to organic fertilizer inputs. Notably, organic fertilizer application did not significantly alter the contribution ratio of input sources to microorganisms, but there was a clear change in the composition of soil microorganisms, which meant that the effect of the input source on the microorganism may emanate from other factors, rather than direct inputs. Subsequent structural equation demonstrated that organic fertilizer application significantly enhanced the effect of environmental factors on ARGs, and also indirectly increased the influence of communities on ARGs. Collectively, under the long-term fertilization, the role of organic fertilizers on soil ARGs not just stems from its own input, and also dominates the influence of environmental factors on ARGs. This study elucidates main causes for the difference in ARGs in AF vs. NF and enlightens actual role of organic fertilizer in them.

Metabolomics reveals the mechanism of tetracycline biodegradation by a Sphingobacterium mizutaii S121

Contamination by tetracycline residues has adverse influences on the environment and is considered a pressing issue. Biodegradation is regarded as a promising way to treat tetracycline residues in the environment. Here, strain Sphingobacterium mizutaii S121, which could degrade 20 mg/L tetracycline completely within 5 days, was isolated from contaminated soil. The characteristics of tetracycline degradation by strain S121 were investigated under various culture conditions. Response surface methodology was used to predict the maximum tetracycline degradation ratio, which can be obtained under the following conditions: 31.36 °C, pH of 7.15, and inoculum volume of 5.5% (v/v). Furthermore, extracellular tetracycline biodegradation products and intracellular metabolic pathways of S121 were detected by ultraperformance liquid chromatography-quadrupole-time-of-flight-mass spectrometry (UPLC-Q-TOF-MS) and UHPLC-quadrupole electrospray (QE)-MS, respectively. The results identified eight possible degradation products, and three putative degradation pathways were proposed. In addition, exposure to tetracycline produced significant influences on metabolic pathways such as pyrimidine, purine, taurine and hypotaurine metabolism and lysine degradation. Consequently, the intracellular metabolic pathway response of S121 in the presence of tetracycline was proposed. These findings are presented for the first time, which will facilitate a comprehensive understanding of the mechanism of tetracycline degradation. Moreover, strain S121 can be a promising bacterium for tetracycline bioremediation.

Pangenomic and functional investigations for dormancy and biodegradation features of an organic pollutant-degrading bacterium Rhodococcus biphenylivorans TG9

Environmental bacteria contain a wealth of untapped potential in the form of biodegradative genes. Leveraging this potential can often be confounded by a lack of understanding of fundamental survival strategies, like dormancy, for environmental stress. Investigating bacterial dormancy-to-degradation relationships enables improvement of bioremediation. Here, we couple genomic and functional assessment to provide context for key attributes of the organic pollutant-degrading strain Rhodococcus biphenylivorans TG9. Whole genome sequencing, pangenome analysis and functional characterization were performed to elucidate important genes and gene products, including antimicrobial resistance, dormancy, and degradation. Rhodococcus as a genus has strong potential for degradation and dormancy, which we demonstrate using R. biphenylivorans TG9 as a model. We identified four Resuscitation-promoting factor (Rpf) encoding genes in TG9 involved in dormancy and resuscitation. We demonstrate that R. biphenylivorans TG9 grows on fourteen typical organic pollutants, and exhibits a robust ability to degrade biphenyl and several congeners of polychlorinated biphenyls. We further induced TG9 into a dormant state and demonstrated pronounced differences in morphology and activity. Together, these results expand our understanding of the genus Rhodococcus and the relationship between dormancy and biodegradation in the presence of environmental stressors.

Temporal changes of microbial community structure and nitrogen cycling processes during the aerobic degradation of phenanthrene

Phenanthrene (PHE) is frequently detected in worldwide soils. But it is still not clear that how the microbial community succession happens and the nitrogen-cycling processes alter during PHE degradation. In this study, the temporal changes of soil microbial community composition and nitrogen-cycling processes during the biodegradation of PHE (12 μg g^-1) were explored. The results showed that the biodegradation of PHE followed the second-order kinetics with a half-life of 7 days. QPCR results demonstrated that the bacteria numbers increased by 67.1%-194.7% with PHE degradation, whereas, no significant change was observed in fungi numbers. Thus, high-throughput sequencing based on 16 S rRNA was conducted and showed that the abundances of Methylotenera, Comamonadaceae, and Nocardioides involved in PHE degradation and denitrification were significantly increased, while those of nitrogen-metabolism-related genera such as Nitrososphaeraceae, Nitrospira, Gemmatimonadacea were decreased in PHE-treated soil. Co-occurrence network analysis suggested that more complex interrelations were constructed, and Proteobacteria instead of Acidobacteriota formed intimate associations with other microbes in responding to PHE exposure. Additionally, the abundances of nifH and narG were significantly up-regulated in PHE-treated soil, while that of amoA especially AOAamoA was down-regulated. Finally, correlation analysis found several potential microbes (Methylotenera, Comamonadaceae, and Agromyces) that could couple PHE degradation and nitrogen transformation. This study confirmed that PHE could alter microbial community structure, change the native bacterial network, and disturb nitrogen-cycling processes.

Tapping the Role of Microbial Biosurfactants in Pesticide Remediation: An Eco-Friendly Approach for Environmental Sustainability

Pesticides are used indiscriminately all over the world to protect crops from pests and pathogens. If they are used in excess, they contaminate the soil and water bodies and negatively affect human health and the environment. However, bioremediation is the most viable option to deal with these pollutants, but it has certain limitations. Therefore, harnessing the role of microbial biosurfactants in pesticide remediation is a promising approach. Biosurfactants are the amphiphilic compounds that can help to increase the bioavailability of pesticides, and speeds up the bioremediation process. Biosurfactants lower the surface area and interfacial tension of immiscible fluids and boost the solubility and sorption of hydrophobic pesticide contaminants. They have the property of biodegradability, low toxicity, high selectivity, and broad action spectrum under extreme pH, temperature, and salinity conditions, as well as a low critical micelle concentration (CMC). All these factors can augment the process of pesticide remediation. Application of metagenomic and in-silico tools would help by rapidly characterizing pesticide degrading microorganisms at a taxonomic and functional level. A comprehensive review of the literature shows that the role of biosurfactants in the biological remediation of pesticides has received limited attention. Therefore, this article is intended to provide a detailed overview of the role of various biosurfactants in improving pesticide remediation as well as different methods used for the detection of microbial biosurfactants. Additionally, this article covers the role of advanced metagenomics tools in characterizing the biosurfactant producing pesticide degrading microbes from different environments.

Stabilization of lead in polluted sediment based on an eco-friendly amendment strategy: Microenvironment response mechanism

Stabilization is the most important remediation mechanisms for sediment polluted heavy metals. However, little research has been done on the identification of microenvironmental response and internal correlation, as well as synergistic mechanisms during heavy metal remediation. This study aims to investigate the inner response mechanisms of microenvironment after the lead (Pb) are gradually stabilized in sediment. An eco-friendly amendment strategy which firstly used 100% biodegradable sophorolipids (SOP) to modify chlorapatite (ClAP) for the fabrication of SOP@nClAP was applied in this study. The stabilization efficiency of Pb was significantly improved by SOP@nClAP compared with ClAP. Most importantly, the high-throughput sequencing showed that the dominant species in the sediment changed with the stabilization of Pb. The decrease of Proteobacteria and increase of Firmicutes, especially the Sedimentibacter within the phylum Firmicute directly suggested that large amounts of Pb were stabilized. This research is not only devoted to stabilize Pb in sediment by eco-friendly amendment strategy, but also keep a watchful eye on microenvironment response mechanisms during the Pb stabilization in sediment. Therefore, this study lays a foundation for the future application of more heavy metal amendment strategies in the sediment environment and improves the possibility of large-scale site amendment.

Microbial glycoconjugates in organic pollutant bioremediation: recent advances and applications

The large-scale application of organic pollutants (OPs) has contaminated the air, soil, and water. Persistent OPs enter the food supply chain and create several hazardous effects on living systems. Thus, there is a need to manage the environmental levels of these toxicants. Microbial glycoconjugates pave the way for the enhanced degradation of these toxic pollutants from the environment. Microbial glycoconjugates increase the bioavailability of these OPs by reducing surface tension and creating a solvent interface. To date, very little emphasis has been given to the scope of glycoconjugates in the biodegradation of OPs. Glycoconjugates create a bridge between microbes and OPs, which helps to accelerate degradation through microbial metabolism. This review provides an in-depth overview of glycoconjugates, their role in biofilm formation, and their applications in the bioremediation of OP-contaminated environments.

Enrichment of antibiotic resistance genes (ARGs) in polyaromatic hydrocarbon-contaminated soils: a major challenge for environmental health

Polyaromatic hydrocarbons (PAHs) are widely spread ecological contaminants. Antibiotic resistance genes (ARGs) are present with mobile genetic elements (MGE) in the bacteria. There are molecular evidences that PAHs may induce the development of ARGs in contaminated soils. Also, the abundance of ARGs related to tetracycline, sulfonamides, aminoglycosides, ampicillin, and fluoroquinolones is high in PAH-contaminated environments. Genes encoding the efflux pump are located in the MGE and, along with class 1 integrons, have a significant role as a connecting link between PAH contamination and enrichment of ARGs. The horizontal gene transfer mechanisms further make this interaction more dynamic. Therefore, necessary steps to control ARGs into the environment and risk management plan of PAHs should be enforced. In this review, influence of PAH on evolution of ARGs in the contaminated soil, and its spread in the environment, has been described. The co-occurrence of antibiotic resistance and PAH degradation abilities in bacterial isolates has raised the concerns. Also, presence of ARGs in the microbiome of PAH-contaminated soil has been discussed as environmental hotspots for ARG spread. In addition to this, the possible links of molecular interactions between ARGs and PAHs, and their effect on environmental health has been explored.

Polycyclic aromatic hydrocarbons, antibiotic resistance genes, toxicity in the exposed to anthropogenic pressure soils of the Southern Russia

The influence of anthropogenic pollution, particularly with polycyclic aromatic hydrocarbons (PAHs) on soil toxicity and spread of antibiotic resistance genes (ARGs) is extremely important nowadays. We studied 20 soil samples from a technogenically polluted site, municipal solid wastes (MSW) landfills, and rural settlements in the southwestern part of the Rostov Region of Russia. A close correlation was established between the results of biosensor testing for integral toxicity, the content of genes for the biodegradation of hydrocarbons, and the concentration of PAHs in soils. The relation between the quantitative content of ARGs and the qualitative and quantitative composition of PAHs has not been registered. Soils subjected to different types of the anthropogenic pressure differed in PAHs composition. The technogenic soils are the most polluted ones. These soils are enriched with 5 ring PAHs and carry the maximum variety of assayed ARGs, despite the fact that they do not receive household or medical waste.

The effects of functional groups on the sorption of naphthalene on microplastics

Ubiquitous microplastics were recognized as an ideal carrier for polycyclic aromatic hydrocarbons (PAHs) to spread in nature or transfer to biota, thus posing risks to human health. However, little is known about how the functional groups in PAH derivatives influence their sorption onto microplastics as compared to parent PAHs. This study investigated the sorption of naphthalene (NAP) and its derivatives onto polystyrene microspheres with (MP-COOH) or without (MP) surface modification of the carboxyl group. NAP derivatives with charged groups (e.g., -NH₂, -OH and -COOH) reached the sorption equilibrium more early than NAP and its derivative with an uncharged group (e.g., -CH₃), whereas their sorption capacities (K_d = 6.0-8.4 L/g for MP, K_d = 4.5-6.3 L/g for MP-COOH) were significantly lower than that of the latter (K_d = 11.6-12.0 L/g for MP, K_d = 9.4-10.0 L/g for MP-COOH). The inhibition of charged groups on sorption could be attributed to their facilitation on molecular polarity and, thus, their lower hydrophobicity (LogK_OW) since hydrophobicity was the crucial factor controlling the sorption of NAP and NAP derivatives onto both MP and MP-COOH. Computational modeling further showed that charged functional groups would weaken the π-π interaction or strengthen the repulsion between NAP or NAP derivative molecule and MP or MP-COOH molecule, which might also contribute to the suppressed sorption. This study provides new insight into the affinity of PAH derivatives with microplastics, which, therefore, improves our understanding of the environmental fates of microplastics and the organic pollutants.

World within world: Intestinal bacteria combining physiological parameters to investigate the response of Metaphire guillelmi to tetracycline stress

Due to the abusive usage of antibiotics in animal husbandry, a large amount of residual antibiotics has been released into the environment, therein posing great threat against both environment security and public health. Therefore, it is of great significance to investigate the toxicity of antibiotics on the widely-applied bioindicator-earthworm. In this work, the physiological parameters and the intestinal bacteria community of Metaphire guillelmi were monitored simultaneously to evaluate their sensitivity to the tetracycline (TC) exposure. As expected, the antioxidant enzyme activity and coelomocyte apoptosis acted fairly well as biomarkers for the TC toxicity. In contrast, the intestinal bacteria of Metaphire guillelmi responded varyingly to different TC doses. When TC concentration increased from 0 to 35.7 μg cm^-2, the percentage of the Proteobacteria phylum declined significantly from 85.5% to 34.4%, while the proportions of the Firmicutes, Planctomycetes and Atinomycete phyla clearly increased (p < 0.05). Meanwhile, the levels of TC resistance genes tetA, tetC, and tetW increased with the increasing TC concentration, in contrast to the declined abundance in denitrifying genes nirS and nosZ (p < 0.05). By analyzing the correlation between the antioxidant enzyme activity and the dominant intestinal bacteria in the worm gut, it is interesting to found that the four dominant bacteria genera Mesorhizobium, Aliihoeflea, Romboutsia, and Nitrospira are the promising bioindicator of TC stress due to their sensitive response. This work shed novel light on evaluating the ecotoxicological risks posed by residual TC in environment by using a combination of physiological parameters and intestinal bacterial activity in earthworms.

Potential risks of antibiotic resistant bacteria and genes in bioremediation of petroleum hydrocarbon contaminated soils

Bioremediation represents a sustainable approach to remediating petroleum hydrocarbon contaminated soils. One aspect of sustainability includes the sourcing of nutrients used to stimulate hydrocarbon-degrading microbial populations. Organic nutrients such as animal manure and sewage sludge may be perceived as more sustainable than conventional inorganic fertilizers. However, organic nutrients often contain antibiotic residues and resistant bacteria (along with resistance genes and mobile genetic elements). This is further exacerbated since antibiotic resistant bacteria may become more abundant in contaminated soils due to co-selection pressures from pollutants such as metals and hydrocarbons. We review the issues surrounding bioremediation of petroleum-hydrocarbon contaminated soils, as an example, and consider the potential human-health risks from antibiotic resistant bacteria. While awareness is coming to light, the relationship between contaminated land and antibiotic resistance remains largely under-explored. The risk of horizontal gene transfer between soil microorganisms, commensal bacteria and/or human pathogens needs to be further elucidated, and the environmental triggers for gene transfer need to be better understood. Findings of antibiotic resistance from animal manures are emerging, but even fewer bioremediation studies using sewage sludge have made any reference to antibiotic resistance. Resistance mechanisms, including those to antibiotics, have been considered by some authors to be a positive trait associated with resilience in strains intended for bioremediation. Nevertheless, recognition of the potential risks associated with antibiotic resistant bacteria and genes in contaminated soils appears to be increasing and requires further investigation. Careful selection of bacterial candidates for bioremediation possessing minimal antibiotic resistance as well as pre-treatment of organic wastes to reduce selective pressures (e.g., antibiotic residues) are suggested to prevent environmental contamination with antibiotic-resistant bacteria and genes.

Land Use Influences Antibiotic Resistance in the Microbiome of Soil Collembolans Orchesellides sinensis

Numerous studies have investigated the composition and diversity of antibiotic resistance genes (ARGs) in multiple environments but the pattern of ARGs in field-collected soil fauna remains poorly understood. In the present study soil collembolans were collected from six sites with three different land use types (parkway land, park land, and arable land) and 285 ARGs and 10 mobile genetic elements (MGEs) in the microbiome of these "wild" collembolans were quantified by high-throughput quantitative PCR. A total of 76 unique ARGs and 5 MGEs were detected. There were significant differences between collection sites in the antibiotic resistome in the collembolans. Land use significantly altered the distribution patterns of collembolan ARGs. Thirty shared ARGs and three shared MGEs were identified. The co-occurrences of shared resistomes were largely random, and more positive relationships were found in the coassociation network. Partial redundancy analysis confirms that the changes in bacterial communities explained 27.77% of the variation in ARGs. These findings suggest that resistance genes are pervasive in the microbiome associated with the field collembolan and the activity of the collembolans may contribute to the spread and dissemination of resistance genes in the environment, an aspect of ARGs that has until now been largely overlooked.

Changes in tetracycline partitioning and bacteria/phage-comediated ARGs in microplastic-contaminated greenhouse soil facilitated by sophorolipid

The emerging mixed contamination of antibiotics and microplastics in greenhouse soil has made the control of antibiotic resistant gene (ARG) transmission a novel challenge. In this work, surfactant sophorolipid was applied to enhance the dissipation of tetracycline (TC) and tet genes in the presence of microplastics in greenhouse soil. During 49days of incubation, soil bacteria and phages were both found to be the crucial reservoirs of ARGs. Meanwhile, microplastic's presence significantly inhibited the dissipation of TC and ARGs in the soil. However, sophorolipid application was proved to outweigh the negative impact caused by microplastic existence, and lead to the highest dissipation of soil TC and ARGs. Significant positive correlation was detected between the dissipation rate of water-soluble and exchangeable TC content and bacteria/phage co-mediated ARG levels. This also held true between the two fractions of soil TC and the ratio of ARG level in the bacteria to that in the phages (B_ARGs/P_ARGs). The opposite impacts of microplastic presence and sophorolipid amendment on the TC/ARG dissipation found in this work provides new information for understanding ARG transmission between bacteria and phages in the mixed contaminated greenhouse soil.

An underappreciated hotspot of antibiotic resistance: The groundwater near the municipal solid waste landfill

Landfills are so far the most common practice for the disposals of municipal solid waste (MSW) worldwide. Since MSW landfill receives miscellaneous wastes, including unused/expired antibiotics and bioactive wastes, it gradually becomes a huge potential bioreactor for breeding antibiotic resistance. Antibiotic resistance genes (ARGs) in landfill can flow to the environment through leakage of landfill leachate and pose a risk to public health. Using high throughput quantitative Polymerase Chain Reaction (HT-qPCR), we investigated the prevalence, diversity of ARGs and its association with various mobile genetic elements (MGEs) in MSW landfill groundwater. Totally 171 unique ARGs (belonging to 9 ARG types, encompassing 3 major resistance mechanisms) and 8 MGEs (6 transposase genes, and 2 integron-integrase genes) were identified. The normalized abundance of ARG was ranging from 0.24 to 5.66 copies/cell with multidrug, beta-lactams and tetracycline resistance genes being the most abundant ARG types. The co-occurrence pattern and significant correlation between MGEs and ARGs, indicated that MGEs may play an important role in the persistence and proliferation of ARGs. A Mantel test and Procrustes analysis suggested that ARG profiles were significantly correlated with bacterial community. Variation partitioning analysis (VPA) further demonstrated that bacterial community shifts contribute 65.8% of the total ARG variations. Additionally network analysis revealed that 15 bacterial taxa at family level might be the potential hosts of ARGs. These findings provide evidence that groundwater near MSW landfill is an underappreciated hotspot of antibiotic resistance and contribute to the spread of ARGs via the flowing contaminated groundwater.

Factors Affecting the Bioaccessibility and Intestinal Transport of Difenoconazole, Hexaconazole, and Spirodiclofen in Human Caco-2 Cells Following in Vitro Digestion

This study examined how gastrointestinal conditions affect pesticide bioaccessibility and intestinal transepithelial transport of pesticides (difenoconazole, hexaconazole, and spirodiclofen) in humans. We used an in vitro model combining human gastric and intestinal digestion, followed with Caco-2 cell model for human intestinal absorption. Bioaccessibility of three tested pesticides ranged from 25.2 to 76.3% and 10.6 to 79.63% in the gastric and intestinal phases, respectively. A marked trend similar to the normal distribution was observed between bioaccessibility and pH, with highest values observed at pH 2.12 in gastric juice. No significant differences were observed with increasing digestion time; however, a significant negative correlation was observed with the solid-liquid (S/L) ratio, following a logarithmic equation. R² ranged from 0.9198 to 0.9848 and 0.9526 to 0.9951 in the simulated gastric and intestinal juices, respectively, suggesting that the S/L ratio is also a major factor affecting bioaccessibility. Moreover, significant dose- and time-response effects were subsequently observed for intestinal membrane permeability of difenoconazole, but not for hexaconazole or spirodiclofen. This is the first study to demonstrate the uptake of pesticides by human intestinal cells, aiding quantification of the likely effects on human health and highlighting the importance of considering bioaccessibility in studies of dietary exposure to pesticide residues.

Human migration activities drive the fluctuation of ARGs: Case study of landfills in Nanjing, eastern China

Landfills are perfect sites to study the effect of human migration on fluctuation of antibiotic resistance genes (ARGs) as they are the final destination of municipal waste. For example, large-scale human migration during the holidays is often accompanied by changes in waste dumping having potential effects on ARG abundance. Three landfills were selected to examine fluctuation in the abundance of fifteen ARGs and Intl1 genes for 14 months in Nanjing, eastern China. Mass human migration, the amount of dumped waste and temperature exerted the most significant effects on bimonthly fluctuations of ARG levels in landfill sites. As a middle-sized cosmopolitan city in China, millions of college students and workers migrate during holidays, contributing to the dramatic increases in waste production and fluctuation in ARG abundances. In line with this, mass migration explained most of the variation in waste dumping. The waste dumping also affected the bioaccessibility of mixed-compound pollutants that further positively impacted the level of ARGs. The influence of various bioaccessible compounds on ARG abundance followed the order: antibiotics>nutrients>metals>organic pollutants. Concentrations of bioaccessible compounds were more strongly correlated with ARG levels compared to total compound concentrations. Improved waste classification and management strategies could thus help to decrease the amount of bioaccessible pollutants leading to more effective control for urban ARG dissemination.

Effect of biochar amendment on the control of soil sulfonamides, antibiotic-resistant bacteria, and gene enrichment in lettuce tissues

Considering the potential threat of vegetables growing in antibiotic-polluted soil with high abundance of antibiotic-resistant genes (ARGs) against human health through the food chain, it is thus urgent to develop novel control technology to ensure vegetable safety. In the present work, pot experiments were conducted in lettuce cultivation to assess the impedance effect of biochar amendment on soil sulfonamides (SAs), antibiotic-resistant bacteria (ARB), and ARG enrichment in lettuce tissues. After 100 days of cultivation, lettuce cultivation with biochar amendment exhibited the greatest soil SA dissipation as well as the significant improvement of lettuce growth indices, with residual soil SAs mainly existing as the tightly bound fraction. Moreover, the SA contents in roots and new/old leaves were reduced by one to two orders of magnitude compared to those without biochar amendment. In addition, isolate counts for SA-resistant bacterial endophytes in old leaves and sul gene abundances in roots and old leaves also decreased significantly after biochar application. However, neither SA resistant bacteria nor sul genes were detected in new leaves. It was the first study to demonstrate that biochar amendment can be a practical strategy to protect lettuce safety growing in SA-polluted soil with rich ARB and ARGs.