Calcined Eggshell Waste for Mitigating Soil Antibiotic-Resistant Bacteria/Antibiotic Resistance Gene Dissemination and Accumulation in Bell Pepper

Nitrogen-Doped Carbon Dots Facilitate CRISPR/Cas for Reducing Antibiotic Resistance Genes in the Environment

The continued acquisition and propagation of antibiotic resistance genes (ARGs) in the environment confound efforts to manage the global rise in antibiotic resistance. Here, CRISPR-Cas9/sgRNAs carried by nitrogen-doped carbon dots (NCDs) were developed to precisely target multi-"high-risk" ARGs (tet, cat, and aph(3')-Ia) commonly detected in the environment. NCDs facilitated the delivery of Cas9/sgRNAs to Escherichia coli (E. coli) without cytotoxicity, achieving sustained elimination of target ARGs. The elimination was optimized using different weight ratios of NCDs and Cas9 protein (1:1, 1:20, and 1:40), and Cas9/multi sgRNAs were designed to achieve multi-cleavage of ARGs in either a single strain or mixed populations. Importantly, NCDs successfully facilitated Cas9/multi sgRNAs for resensitization of antibiotic-resistant bacteria in soil (approaching 50%), whereas Cas9/multi sgRNAs alone were inactivated in the complex environment. This work highlights the potential of a fast and precise strategy to minimize the reservoir of antibiotic resistance in agricultural system.

Utilising calcined eggshell waste as a multifunctional sustainable agent as a nano-adsorbent, photocatalyst and priming elicitor

Since waste-to-value approach and having potential benefits in several applications, eggshell-derived calcium oxide (ECaO) produced from eggshells is attracting attention in the recent research. ECaO nanoparticles (NPs) were investigated here for its dual purpose in cleaning wastewater and as a nanopriming agent, since catalysts have an impact on seedlings even after being dumped in the soil. The initial comparison was between the adsorption capacities of naturally occurring ECaO and chemically synthesised CaO (CCaO), demonstrating that ECaO NPs had a higher adsorption capacity due to its greater porosity. Congo Red utilises ECaO NPs for both adsorption and photodegradation. Adsorption equilibrium was achieved with 93.4% in just 6 min, but photocatalysis requires 120 min to break down 95% of Congo Red, which is reduced to 45 min in sono-photocatalysis. Second, the priming impact of ECaO NPs on germination was investigated using monocot and dicot seeds. In contrast to phytotoxic effects at higher loadings, 50 mg/l of ECaO NPs demonstrated quicker floral development, stronger seedling growth and higher chlorophyll content.

Elucidating the role of two types of essential oils in regulating antibiotic resistance in soil

Although several approaches for reducing antibiotic resistance genes (ARGs) in soil have been proposed, the application of environmentally friendly approaches is now attracting much more attention. In the present study, two types of essential oils (EOs), namely lavender essential oil (LEO) and oregano essential oil (OEO), were selected to investigate their roles in regulating ARGs in soil. In a 28-day microcosm experiment, it was found that the different types and doses of EOs significantly changed the composition of microbial communities. The LEO treatments enriched more taxa belonging to Actinobacteria than the control, whereas the low dose of OEO reduced Actinobacteria enrichment. Besides, the control and the treatments with a high dose of LEO and OEO all significantly enriched the functional pathways related to Human Diseases, which were positively associated with ARGs. However, the low dose of these EOs helped to reduce the pathways. Because of inhibition of the functional pathways and ARG hosts, the low dose of OEO reduce the ARGs related to antibiotic efflux by 71.8% and the resistance genes to multidrug by 56.4%, but these roles did not occur in LEO treatments. These outcomes provide practical and theoretical support for the application of EOs in remediating ARG-contaminated soils.

Hormetic Effect of Pyroligneous Acids on Conjugative Transfer of Plasmid-mediated Multi-antibiotic Resistance Genes within Bacterial Genus

Spread of antibiotic resistance genes (ARGs) by conjugation poses great challenges to public health. Application of pyroligneous acids (PA) as soil amendments has been evidenced as a practical strategy to remediate pollution of ARGs in soils. However, little is known about PA effects on horizontal gene transfer (HGT) of ARGs by conjugation. This study investigated the effects of a woody waste-derived PA prepared at 450°C and its three distillation components (F1, F2, and F3) at different temperatures (98, 130, and 220°C) on conjugative transfer of plasmid RP4 within Escherichia coli. PA at relatively high amount (40-100 μL) in a 30-mL mating system inhibited conjugation by 74-85%, following an order of PA > F3 ≈ F2 ≈ F1, proving the hypothesis that PA amendments may mitigate soil ARG pollution by inhibiting HGT. The bacteriostasis caused by antibacterial components of PA, including acids, phenols, and alcohols, as well as its acidity (pH 2.81) contributed to the inhibited conjugation. However, a relatively low amount (10-20 μL) of PA in the same mating system enhanced ARG transfer by 26-47%, following an order of PA > F3 ≈ F2 > F1. The opposite effect at low amount is mainly attributed to the increased intracellular reactive oxygen species production, enhanced cell membrane permeability, increased extracellular polymeric substance contents, and reduced cell surface charge. Our findings highlight the hormesis (low-amount promotion and high-amount inhibition) of PA amendments on ARG conjugation and provide evidence for selecting an appropriate amount of PA amendment to control the dissemination of soil ARGs. Moreover, the promoted conjugation also triggers questions regarding the potential risks of soil amendments (e.g., PA) in the spread of ARGs via HGT.

Electrochemical properties of roots determine antibiotic adsorption on roots

The adsorption behaviors and transfer pathways of antibiotics in plant-soil system are greatly influenced by the electrochemical properties of both soil particles and plant roots. However, the effects of roots electrochemical properties on antibiotic adsorption are largely unknown. Here, the fresh soybean, maize, and wheat roots with different electrochemical properties were obtained from hydroponic cultivation, and the adsorption processes and mechanisms of doxycycline, tetracycline, sulfadiazine, and norfloxacin on roots under various environmental conditions were investigated. Results showed that the adsorption amount of antibiotics on roots increased with the initial concentration of antibiotics. The coexisting low-molecular weight organic acids and anions inhibited the antibiotic adsorption on roots. The soybean roots performed strong adsorption ability compared with the maize and wheat roots driven by the variations in root electrochemical properties. This study demonstrates the significance of electrochemical interactions between antibiotics and roots in plant-soil system and can contribute to the more accurate risk assessment and effective pollution control of antibiotics.

Biochar can mitigate co-selection and control antibiotic resistant genes (ARGs) in compost and soil

Heavy metals (HMs) contamination raises the expression of antibiotic resistance (AR) in bacteria through co-selection. Biochar application in composting improves the effectiveness of composting and the quality of compost. This improvement includes the elimination and reduction of antibiotic resistant genes (ARGs). The use of biochar in contaminated soils reduces the bioaccessibility and bioavailability of the contaminants hence reducing the biological and environmental toxicity. This decrease in contaminant bioavailability reduces contaminants induced co-selection pressure. Conditions which favour reduction in HMs bioavailable fraction (BF) appear to favour reduction in ARGs in compost and soil. Biochar can prevent horizontal gene transfer (HGT) and can eliminate ARGs carried by mobile genetic elements (MGEs). This effect reduces maintenance and propagation of ARGs. Firmicutes, Proteobacteria, and Actinobacteria are the major bacteria phyla identified to be responsible for dissipation, maintenance, and propagation of ARGs. Biochar application rate at 2-10% is the best for the elimination of ARGs. This review provides insight into the usefulness of biochar in the prevention of co-selection and reduction of AR, including challenges of biochar application and future research prospects.

Individual and combined applications of biochar and pyroligneous acid mitigate dissemination of antibiotic resistance genes in agricultural soil

Remediation of agricultural soils polluted with antibiotic resistance genes (ARGs) is important for protecting food safety and human health. However, the feasibility of co-application of biochar and pyroligneous acid, two multifunctional soil amendments, for mitigating dissemination of soil ARGs is unknown. Thus, a woody biochar (BC450) and its by-product, pyroligneous acid (PA450) simultaneously produced at 450 °C from blended wood wastes, were used to compare their individual and combined effects on soil ARG abundance using a 65-day pot experiment planted with leafy vegetable Brassica chinensis L. The individual and combined applications of PA450 and BC450 significantly reduced the absolute abundance of ARGs by 65.7-81.4% and 47.5-72.9% in the corresponding rhizosphere and bulk soil. However, the co-application showed little synergistic effect, probably due to the counteractive effect of BC450 on the PA450-mitigated soil ARG proliferation, resulted from the promoted soil bacterial growth and/or adsorption of antimicrobial components of PA450 by BC450. The decreased abundances of mobile genetic element intI1 and Tn916/1545 in the PA450 treatments demonstrated the potential of PA450 for weakening horizontal gene transfer (HGT). Furthermore, weakened HGT by individual PA450, lowered availability of heavy metals by individual BC450, and different bacterial community (e.g., reduced ARGs bacterial host) together with improved soil properties from co-application of PA450 and BC450 all contributed to the reduced ARG level. This study highlighted the feasibility of co-applications of biochar and pyroligneous acid amendment for mitigating soil ARG pollution. These findings provide important information for developing eco-friendly technologies using biochar and pyroligneous acid in remediating ARG-contaminated soils.

Pyroligneous acid mitigated dissemination of antibiotic resistance genes in soil

Strategies to mitigate the spread of antibiotic resistance genes (ARGs) in soils are urgently needed. Therefore, a pristine pyroligneous acid (PA) from pyrolyzing blended woody waste at 450 °C and its three fractions distilled at 98, 130, and 220 °C (F1, F2, and F3) were used to evaluate their feasibility of reducing ARGs in soil. Application of PA, F2, and F3 effectively decreased the relative ARG abundance by 22.4-75.4% and 39.7-66.7% in the rhizosphere and bulk soil relative to control, respectively, and the removal efficiency followed an order of F3 > PA > F2. Contrarily, F1 increased the abundance of ARGs. The decreased abundance of two mobile genetic elements and impaired conjugative transfer of RP4 plasmid in the presence of PA, F2 and F3 demonstrated that the weakened horizontal gene transfer (HGT) contributed to the reduced ARG level. Variation partitioning analysis and structural equation models confirmed that ARG reduction was primarily driven by the weakened HGT, followed by the decreased co-selection of heavy metals and shifted bacterial community (e.g., reduced potential host bacteria of ARGs). Our findings provide practical and technical support for developing PA-based technology in remediating ARG-contaminated soil to ensure food safety and protect human health.

Tracking resistomes, virulence genes, and bacterial pathogens in long-term manure-amended greenhouse soils

Organic manure has been implicated as an important source of antibiotic resistance genes (ARGs) in agricultural soils. However, the profiles of biocide resistance genes (BRGs), metal resistance genes (MRGs) and virulence genes (VGs) and their bacterial hosts in manure-amended soils remain largely unknown. Herein, a systematic metagenome-based survey was conducted to comprehensively explore the changes in resistomes, VGs and their bacterial hosts, mobile genetic elements (MGEs), and pathogenic bacteria in manure-amended greenhouse soils. Many manure-borne ARGs, BRGs, MRGs, VGs, and bacterial pathogens could be transferred into soils by applying manures, and their abundance and diversity were markedly positively correlated with greenhouse planting years (manure amendment years). The main ARGs transferred from manures to soils conferred resistance to tetracycline, aminoglycoside, and macrolide-lincosamide-streptogramin. Both statistical analysis and gene arrangements showed a good positive co-occurrence pattern of ARGs/BRGs/MRGs/VGs and MGEs. Furthermore, bacterial hosts of resistomes and VGs were significantly changed in the greenhouse soils in comparison with the field soils. Our findings confirmed the migration and dissemination of resistomes, VGs, and bacterial pathogens, and their accumulation and persistence were correlated with the continuous application of manures.

A review of bacteriophage therapy for pathogenic bacteria inactivation in the soil environment

The emerging contamination of pathogenic bacteria in the soil has caused a serious threat to public health and environmental security. Therefore, effective methods to inactivate pathogenic bacteria and decrease the environmental risks are urgently required. As a century-old technique, bacteriophage (phage) therapy has a high efficiency in targeting and inactivating pathogenic bacteria in different environmental systems. This review provides an update on the status of bacteriophage therapy for the inactivation of pathogenic bacteria in the soil environment. Specifically, the applications of phage therapy in soil-plant and soil-groundwater systems are summarized. In addition, the impact of phage therapy on soil functioning is described, including soil function gene transmission, soil microbial community stability, and soil nutrient cycling. Soil factors, such as soil temperature, pH, clay mineral, water content, and nutrient components, influence the survival and activity of phages in the soil. Finally, the future research prospects of phage therapy in soil environments are described.

Soil oxytetracycline exposure alters the microbial community and enhances the abundance of antibiotic resistance genes in the gut of Enchytraeus crypticus

Gut microbiota make an important contribution to the health of soil invertebrates. Many studies have focused on effects of antibiotics on soil invertebrates. Influence from antibiotics on the gut microbiota of non-target soil fauna is rarely reported and the abundance of antibiotics resistance genes (ARGs) in the gut is poorly understood. Here, 10 μg·g^-1 of oxytetracycline (OTC) (environmentally relevant concentration) was added in soil, used Enchytraeus crypticus as soil model worm was tested for the response to oxytetracycline. The results showed that although soil OTC exposure did not cause a change in E. crypticus growth, mortality or reproduction, it did result in bioaccumulation of OTC in E. crypticus body tissues. The OTC treatment induced a shift in the composition and diversity of the gut microbiota of E. crypticus when compared to the control treatment. Specifically, the relative abundance of Proteobacteria declined significantly from 52.2% to 32.4% after OTC exposure (P = 0.028), but the relative abundance of Planctomycetes was significantly elevated from 28.1% to 45.8% (P = 0.002). It is noteworthy that soil OTC exposure significantly enhanced the abundance and number of tetracycline-related ARGs in the E. crypticus gut. These results suggest that change in E. crypticus gut microbiota has potential as an indicator of soil antibiotic pollution, and E. crypticus gut may act as a receiver and mediator of ARGs resulting from soil antibiotic pollution.

Bacteriophages as Environmental Reservoirs of Antibiotic Resistance

Although antibiotic resistance represents a significant and growing public health concern, the contribution of bacteriophages (phages) to the mobilization of antibiotic resistance genes (ARGs) in the environment has not been extensively studied. Recent studies, however, suggest that phages play an important role in the acquisition, maintenance, and spread of ARGs than previously expected. This Opinion article offers an update on the contribution of phages to environmental antibiotic resistance. A better understanding of the mechanisms and factors that promote antibiotic resistance may significantly contribute to the implementation of control strategies.

Comparing polyvalent bacteriophage and bacteriophage cocktails for controlling antibiotic-resistant bacteria in soil-plant system

Antibiotic resistant pathogenic bacteria (ARPB) residual in soil-plant system has caused serious threat against public health and environmental safety. Being capable of targeted lysing host bacteria, phage therapy has been proposed as promising method to control the ARPB contamination in environments. In this study, microcosm trials were performed to investigate the impact of various phage treatments on the dissipation of tetracycline resistant Escherichia coli K-12 and chloramphenicol resistant Pseudomonas aeruginosa PAO1 in soil-carrot system. After 70 days of incubation, all the four phage treatments significantly decreased the abundance of the pathogenic bacteria and the corresponding antibiotic resistance genes (tetW and cmlA) in the soil-carrot system (p < 0.05), following the order of the cocktail phage treatment (phages ΦYSZ1 + ΦYSZ2) > the polyvalent phage (ΦYSZ3 phage with broad host range) treatment > host-specific phage (ΦYSZ2 and ΦYSZ1) treatments > the control. In addition, the polyvalent phage treatment also exerted positive impact on the diversity and stability of the bacterial community in the system, suggesting that this is an environmentally friendly technique with broad applications in the biocontrol of ARPB/ARGs in soil-plant system.

Reducing water use by alternate-furrow irrigation with livestock wastewater reduces antibiotic resistance gene abundance in the rhizosphere but not in the non-rhizosphere

Livestock wastewater is rich in nutrients but may contain antibiotics and antibiotic resistance genes (ARGs). Their discharge to watercourses or soil may result in proliferation of ARGs. Irrigation with wastewater appears to be the most feasible option of disposing of it. One efficient irrigation technology used in arid regions is alternate-furrow irrigation (AFI) by alternately drying part of the plant roots for a prolonged period to physiologically reduce transpiration without compromising yield. However, the extent to which AFI with wastewater influences the concentration of antibiotics and spread of ARGs in soil is poorly understood. The purpose of this paper is to investigate how AFI using swine wastewater alters antibiotic kinetics and ARGs abundance under different irrigation rates, using pepper as the model plant. We examined three AFI treatments using 50%, 65% and 80% of the amount of water employed in sufficient conventional furrow irrigation. Each treatment had a groundwater irrigation control. The results showed that antibiotic concentrations and relative ARGs abundance in the top 20 cm of soil did not increase with the irrigation amount, although they were higher than those in the groundwater-irrigated soils. The relative ARGs abundance in the soil was modulated by irrigation amount and reducing the irrigation amount in AFI reduced ARGs dispersion only in rhizosphere. When the soil moisture was close to field capacity, ARGs were more abundant in rhizosphere than in non-rhizosphere, possibly because the rhizosphere is rich in microbes and increasing antibiotic concentrations due to an increase in irrigation rate favors antibiotic-resistant microbiome in competing for substrates. These, however, were not mirrored in the relative ARGs abundance in the roots. These results have important implications as it revealed that reducing the input of antibiotics and ARGs into soil with AFI does not necessarily reduce ARGs proliferation.

Inactivation of antibiotic-resistant bacteria by chlorine dioxide in soil and shifts in community composition

Antibiotic-resistant bacteria are common widespread in soil and the most resistant species isStaphylococcus aureus.Sphingomonas,ArthrobacterandMassiliaare sensitive to ClO₂.MicromonosporaceaeandThaumarchaeotaare more resistant to ClO₂.

Coexistence and association between heavy metals, tetracycline and corresponding resistance genes in vermicomposts originating from different substrates

Coexistence of antibiotics/heavy metals and the overexpression of resistance genes in the vermicompost has become an emerging environmental issue. Little is known about the interaction and correlation between chemical pollutants and biological macromolecular compounds. In this study, three typical vermicompost samples were selected from the Yangtze River Delta region in China to investigate the antibiotic, heavy metal and corresponding antibiotic resistance genes (ARGs) and heavy metal resistance genes (HRGs). The results indicated the prevalence of tetracycline (TC), copper (Cu), zinc (Zn), cadmium (Cd), corresponding TC-resistance genes (tetA, tetC, tetW, tetM, tetO, and tetS) and HRGs (copA, pcoA, cusA, czcA, czcB, and czcR) in the three vermicompost samples. In addition, the ARG level was positively associated with the water-soluble TC fraction in the vermicompost, and it was same between the HRG abundance and exchangeable heavy metal content (p < 0.05). Moreover, a positive correlation was found between ARG and HRG abundance in the vermicompost samples, suggesting a close regulation mechanism involving the expression of both genes. The result obtained here could provide new insight into the controlling risk of heavy metals, TC, and relevant resistance genes mixed contamination in the vermicompost.

'Agricultural Waste to Treasure' - Biochar and eggshell to impede soil antibiotics/antibiotic resistant bacteria (genes) from accumulating in Solanum tuberosum L

Soil contamination with antibiotics and antibiotic resistant bacteria/genes (ARB/ARGs) has becoming an emerging environmental problem. Moreover, the mixed pollutants' transfer and accumulation from soil to tuberous vegetables has posed a great threat against food security and human health. In this work, the application of two absorbing materials (maize biochar and sulfate modified eggshell) was able to reduce the poisonous effect of soil antibiotics on potato root system by stimulate the dissipation of water-soluble antibiotics in soil; and also improve food quality by increasing potato starch, protein, fat, and vitamins. Meanwhile, both amendments could effectively decrease the classes and the accumulative abundance of ARB and ARGs (sulI, sulII, catI, catII, ermA, ermB) in the edible parts of potato. The lowest abundance of ARGs was detected in the biochar application treatment, with the accumulative ARG level of 8.9 × 10² and 7.2 × 10² copies mL^-1 in potato peel (sull + catI + ermA) and tuberous root (sulI), respectively. It is the first study to demonstrate the feasibility of biochar and eggshell derived from agricultural wastes as green absorbing materials to reduce soil antibiotic, ARB, and ARGs accumulation risk in tuberous vegetable.

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.

Feasibility of sulfate-calcined eggshells for removing pathogenic bacteria and antibiotic resistance genes from landfill leachates

High abundance of human pathogen and antibiotic resistance genes (ARGs) in landfill leachate has become an emerging threat against human health. Therefore, sulfate- and calcination-modified eggshells as green agricultural bioresource were applied to test the feasibility of removing pathogenic bacteria and ARGs from leachate. The highest removal of Escherichia coli (E. coil) and gentamycin resistant gene (gmrA) from artificial contaminated landfill leachate was achieved by the application of eggshell with combined treatment of sulfate and calcination. The 16S and gmrA gene copies of E. coil declined significantly from 1.78E8±8.7E6 and 4.12E8±5.9E6 copies mL^-1 to 1.32E7±2.6E6 and 2.69E7±7.2E6 copies mL^-1, respectively, within 24h dynamic adsorption equilibrium process (p<0.05). Moreover, according to the Langmuir kinetic model, the greatest adsorption amount (1.56×10⁹ CFU E. coil per gram of modified eggshells) could be obtained at neutral pH of 7.5. The optimal adsorption eggshells were then screened to the further application in three typical landfill leachates in Nanjing, eastern China. Significant decrease in species and abundance of pathogenic bacteria and ARGs (tet, sul, erm, qnr, and ampC) indicated its great efficiency to purify landfill leachates. This study demonstrated that sulfate-calcined eggshells can be an environmentally-friendly and highly efficient bioadsorbent to the management of reducing dissemination risk of pathogen and ARGs in landfill leachate.

Adaptation to Biocides Cetrimide and Chlorhexidine in Bacteria from Organic Foods: Association with Tolerance to Other Antimicrobials and Physical Stresses

Chlorhexidine (CH) and quaternary ammonium compounds (QAC), such as cetrimide (CE), are widely used as disinfectants because of their broad antimicrobial spectrum. However, their frequent use for disinfection in different settings may promote bacterial drug resistance against both biocides and clinically relevant antibiotics. This study analyzes the effects of stepwise exposure to cetrimide (CE) and chlorhexidine (CH) of bacteria from organic foods and previously classified as biocide-sensitive. Gradual exposure of these strains to biocides resulted in mainly transient decreased antimicrobial susceptibility to other antibiotics and to biocides. Biocide-adapted bacteria also exhibit alterations in physiological characteristics, mainly decreased heat tolerance, or gastric acid tolerance in CE-adapted strains, while bile resistance does not seem to be influenced by biocide adaptation. Results from this study suggest that changes in membrane fluidity may be the main mechanism responsible for the acquisition of stable tolerance to biocides.