Environmental analysis of typical antibiotic-resistant bacteria and ARGs in farmland soil chronically fertilized with chicken manure

Effects of hydrothermal treatment on the reduction of antibiotic-resistant Escherichia coli and antibiotic resistance genes and the fertilizer potential of liquid product from cattle manure

In this study, the reduction in the abundance of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) and the fertilizer potential of liquid products from hydrothermally treated cattle manure were investigated. Hydrothermal treatment (HTT) was conducted under different reaction temperatures (125, 150, 175 and 200 °C) and retention times (60, 90 and 120 min). The total organic carbon (TOC) and total nitrogen (TN) of the liquid product increased with increasing reaction temperature. The germination index (GI), a measure of the percentage of germination, exceeded 90 % at 125, 150, and 175 °C in diluted samples, while it decreased to 18 % at 200 °C. Although a longer retention time contributed to an increase in TOC of liquid products, it did not increase the GI values. The liquid product should be diluted or adjusted before use as fertilizer to prevent phytotoxicity. In our analysis of ARB and ARGs, E. coli and antibiotic-resistant E. coli were completely reduced after HTT, except for the operating conditions of 125 °C and 60 min. Although both a higher reaction temperature and longer retention time tended to be better for the reduction of ARGs and intI1, it was found that the longer retention time is much more effective than the higher reaction temperature. The reduction of target ARGs and intI1 was 2.9-log under175 °C and 120 min. Comprehensively considering the fertilizer potential of liquid product and the reduction of ARB and ARGs, 175 °C of reaction temperature and 120 min of retention time of operating conditions for HTT were recommended.

Pyrite from acid mine drainage promotes the removal of antibiotic resistance genes and mobile genetic elements in karst watershed with abundant calcium carbonate

More information is needed to fully comprehend how acid mine drainage (AMD) affects the phototransformation of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in karst water and sewage-irrigated farmland soil with abundant carbonate rocks (CaCO3) due to increasing pollution of AMD formed from pyrite (FeS2). The results showed FeS2 accelerated the inactivation of ARB with an inactivation of 8.7 log. Notably, extracellular and intracellular ARGs and mobile genetic elements (MGEs) also experienced rapid degradation. Additionally, the pH of the solution buffered by CaCO3 significantly influenced the photo-inactivation of ARB. The Fe2+ in neutral solution was present in Fe(II) coordination with strong reducing potential and played a crucial role in generating •OH (7.0 μM), which caused severe damage to ARB, ARGs, and MGEs. The •OH induced by photo-Fenton of FeS2 posed pressure to ARB, promoting oxidative stress response and increasing generation of reactive oxygen species (ROS), ultimately damaging cell membranes, proteins and DNA. Moreover, FeS2 contributed to a decrease in MIC of ARB from 24 mg/L to 4 mg/L. These findings highlight the importance of AMD in influencing karst water and sewage-irrigated farmland soil ecosystems. They are also critical in advancing the utilization of FeS2 to inactivate pathogenic bacteria.

Effect of composting and storage on the microbiome and resistome of cattle manure from a commercial dairy farm in Poland

Manure from food-producing animals, rich in antibiotic-resistant bacteria and antibiotic resistance genes (ARGs), poses significant environmental and healthcare risks. Despite global efforts, most manure is not adequately processed before use on fields, escalating the spread of antimicrobial resistance. This study examined how different cattle manure treatments, including composting and storage, affect its microbiome and resistome. The changes occurring in the microbiome and resistome of the treated manure samples were compared with those of raw samples by high-throughput qPCR for ARGs tracking and sequencing of the V3-V4 variable region of the 16S rRNA gene to indicate bacterial community composition. We identified 203 ARGs and mobile genetic elements (MGEs) in raw manure. Post-treatment reduced these to 76 in composted and 51 in stored samples. Notably, beta-lactam, cross-resistance to macrolides, lincosamides and streptogramin B (MLSB), and vancomycin resistance genes decreased, while genes linked to MGEs, integrons, and sulfonamide resistance increased after composting. Overall, total resistance gene abundance significantly dropped with both treatments. During composting, the relative abundance of genes was lower midway than at the end. Moreover, higher biodiversity was observed in samples after composting than storage. Our current research shows that both composting and storage effectively reduce ARGs in cattle manure. However, it is challenging to determine which method is superior, as different groups of resistance genes react differently to each treatment, even though a notable overall reduction in ARGs is observed.

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.

Degradation kinetics of veterinary antibiotics and estrogenic hormones in a claypan soil

Veterinary antibiotics and estrogens are excreted in livestock waste before being applied to agricultural lands as fertilizer, resulting in contamination of soil and adjacent waterways. The objectives of this study were to 1) investigate the degradation kinetics of the VAs sulfamethazine and lincomycin and the estrogens estrone and 17β-estradiol in soil mesocosms, and 2) assess the effect of the phytochemical DIBOA-Glu, secreted in eastern gamagrass (Tripsacum dactyloides) roots, on antibiotic degradation due to the ability of DIBOA-Glu to facilitate hydrolysis of atrazine in solution assays. Mesocosm soil was a silt loam representing a typical claypan soil in portions of Missouri and the Central United States. Mesocosms (n = 133) were treated with a single target compound (antibiotic concentrations at 125 ng g-1 dw, estrogen concentrations at 1250 ng g-1 dw); a subset of mesocosms treated with antibiotics were also treated with DIBOA-Glu (12,500 ng g-1 dw); all mesocosms were kept at 60% water-filled pore space and incubated at 25 °C in darkness. Randomly chosen mesocosms were destructively sampled in triplicate for up to 96 days. All targeted compounds followed pseudo first-order degradation kinetics in soil. The soil half-life (t0.5) of sulfamethazine ranged between 17.8 and 30.1 d and ranged between 9.37 and 9.90 d for lincomycin. The antibiotics results showed no significant differences in degradation kinetics between treatments with or without DIBOA-Glu. For estrogens, degradation rates of estrone (t0.5 = 4.71-6.08 d) and 17β-estradiol (t0.5 = 5.59-6.03 d) were very similar; however, results showed that estrone was present as a metabolite in the 17β-estradiol treated mesocosms and vice-versa within 24 h. The antibiotics results suggest that sulfamethazine has a greater potential to persist in soil than lincomycin. The interconversion of 17β-estradiol and estrone in soil increased their overall persistence and sustained soil estrogenicity. This study demonstrates the persistence of these compounds in a typical claypan soil representing portions of the Central United States.

Assessing the Effect of Oxytetracycline on the Selection of Resistant Escherichia coli in Treated and Untreated Broiler Chickens

Oxytetracycline (OTC) is administered in the poultry industry for the treatment of digestive and respiratory diseases. The use of OTC may contribute to the selection of resistant bacteria in the gastrointestinal tract of birds or in the environment. To determine the effect of OTC on the selection of resistant Escherichia coli strains post-treatment, bacteria were isolated from droppings and litter sampled from untreated and treated birds. Bacterial susceptibility to tetracyclines was determined by the Kirby-Bauer test. A total of 187 resistant isolates were analyzed for the presence of tet(A), (B), (C), (D), (E), and (M) genes by PCR. Fifty-four strains were analyzed by PFGE for subtyping. The proportion of tetracycline-resistant E. coli strains isolated was 42.88%. The susceptibility of the strains was treatment-dependent. A high clonal diversity was observed, with the tet(A) gene being the most prevalent, followed by tet(C). Even at therapeutic doses, there is selection pressure on resistant E. coli strains. The most prevalent resistance genes were tet(A) and tet(C), which could suggest that one of the main mechanisms of resistance of E. coli to tetracyclines is through active efflux pumps.

Immobilization of Bacillus Thuringiensis and applicability in removal of sulfamethazine from soil

Microbial degradation is considered an essential and promising treatment for sulfadimidine contamination of soil. To address the low colonization rates and inefficiencies of typical antibiotic-degrading bacteria, sulfamethazine (SM2)-degrading strain H38 is converted into immobilized bacteria in this study. Results show that the removal rate of SM2 by immobilized strain H38 reaches 98% at 36 h, whereas the removal rate of SM2 by free bacteria reaches 75.2% at 60 h. In addition, the immobilized bacteria H38 exhibits tolerance to a wide range of pH (5-9) and temperature (20 °C-40 °C). As the amount of inoculation increases and the initial concentration of SM2 decreases, the removal rate of SM2 by the immobilized strain H38 increases gradually. Laboratory soil remediation tests show that the immobilized strain H38 can remove 90.0% of SM2 from the soil on the 12th day, which exceeds the removal by free bacteria by 23.9% in the same period. Additionally, the results show that the immobilized strain H38 enhances the overall activity of microorganisms in SM2-contaminated soil. Compared with the SM2 only (control group containing no bacteria) and free bacterial treatment groups, the gene expression levels of ammonia-oxidizing archaea, ammonia-oxidizing bacteria, cbbLG, and cbbM increased significantly in the treatment group with immobilized strain H38. This study shows that immobilized strain H38 can reduce the effect of SM2 on soil ecology to a greater extent than free bacteria, while providing safe and effective remediation.

Effect of sulfamethazine on the horizontal transfer of plasmid-mediated antibiotic resistance genes and its mechanism of action

As a new type of environmental pollutant, antibiotic resistance genes (ARGs) pose a huge challenge to global health. Horizontal gene transfer (HGT) represents an important route for the spread of ARGs. The widespread use of sulfamethazine (SM2) as a broad-spectrum bacteriostatic agent leads to high residual levels in the environment, thereby increasing the spread of ARGs. Therefore, we chose to study the effect of SM2 on the HGT of ARGs mediated by plasmid RP4 from Escherichia coli (E. coli) HB101 to E. coli NK5449 as well as its mechanism of action. The results showed that compared with the control group, SM2 at concentrations of 10 mg/L and 200 mg/L promoted the HGT of ARGs, but transfer frequency decreased at concentrations of 100 mg/L and 500 mg/L. The transfer frequency at 200 mg/L was 3.04 × 10^-5, which was 1.34-fold of the control group. The mechanism of SM2 improving conjugation transfer is via enhancement of the mRNA expression of conjugation genes (trbBP, trfAP) and oxidative stress genes, inhibition of the mRNA expression of vertical transfer genes, up regulation of the outer membrane protein genes (ompC, ompA), promotion of the formation of cell pores, and improvement of the permeability of cell membrane to promote the conjugation transfer of plasmid RP4. The results of this study provide theoretical support for studying the spread of ARGs in the environment.

Effect of photocatalysis on the physicochemical properties of liquid digestate

Antibiotic residues pose a risk to the agricultural application of liquid digestate. In our previous study, photocatalysis was employed to degrade the antibiotics in liquid digestate and observed that the removal efficiency of TC, OTC, and CTC was up to 94.99%, 88.92%, and 95.52%, respectively, at the optimal experimental level, demonstrating the feasibility of this technology. In this study, the liquid digestate after photocatalysis was analyzed to evaluate the effect of photocatalysis on the nutrients, phytotoxicity, and bacterial community of liquid digestate. The results showed that photocatalysis had little effect on the major nutrients TN, TP, and TK in liquid digestate. However, photocatalysis could cause an increase in tryptophan substances as well as soluble microbial by-products and a decrease in humic acid substances in the liquid digestate. The toxicity of liquid digestate after photocatalysis exhibited an increasing trend followed by a decreasing trend, and the liquid digestate after photocatalysis for 2 h had a promoting effect on seed germination and root growth. The richness, diversity, and evenness of bacterial communities in liquid digestate were decreased as a result of photocatalysis. The dominant species in the liquid digestate was dramatically changed by photocatalysis, and the antibiotic concentration also had a major effect on the dominant species in the liquid digestate after photocatalysis. After photocatalysis for 2 h, the dominant species in the liquid digestate changed from Firmicutes to Proteobacteria.

Evaluation of bacterial diversity in a swine manure composting system contaminated with veterinary antibiotics (VAs)

Composting has become an alternative for the treatment of organic effluents, due to its low cost, easy handling, and a great capacity for treating swine manure. As it is a biological process, many microorganisms are involved during the composting process and act in the degradation of organic matter and nutrients and also have the ability to degrade contaminants and accelerate the transformations during composting. The objective of this work was to identify microorganisms present in the swine effluent composting system, under the contamination by most used veterinary drugs in Brazil. The composting took place for 150 days, there was an addition of 200 L of manure (these 25 L initially contaminated with 17 antibiotics) in 25 kg of eucalyptus wood shavings. The microorganisms were measured at times (0 until 150 days) and were identified by the V3-V4 regions of the 16S rRNA for Bacteria, by means of next-generation sequencing (NSG). The results show seven different bacterial phyla (Proteobacteria, Bacteroidetes, Firmicutes, Acidobacteria, Actinobacteria, Spirochaetota and Tenericutes) and 70 bacterial genera (more than 1% significance), of which the most significant ones were Pseudomonas, Sphingobacterium, Devosia, Brucella, Flavisolibacter, Sphingomonas and Nitratireductor. The genus Brucella was found during mesophilic and thermophilic phases, and this genus has not yet been reported an in article involving composting process. With the results obtained, the potential for adaptation of the bacterial community was observed, being under the influence of antibiotics for veterinary use.

Exploring the abundance and influencing factors of antimicrobial resistance genes in manure plasmidome from swine farms

Plasmids play a critical role in the dissemination of antimicrobial resistance genes (ARGs), however, a systematical understanding of ARGs originated from plasmids in swine production is currently lacking. Herein, quantitative polymerase chain reaction was applied to determine the prevalence of ten ARGs and the class1 integron gene intI1 of plasmid source in swine manure from 44 farms in Sichuan, Hubei and Hebei provinces, China. All assayed ARGs were observed in plasmid DNA samples, and the average absolute abundance of aac(6')-Ib-cr, bla_NDM, bla_CTX-M, optrA, ermB, floR, mcr-1, qnrS, tetM, sul1 and intI1 were 7.09, 2.90, 4.67, 6.62, 7.55, 7.14, 4.08, 4.85, 7.16, 7.11 and 8.07 of 10 log copies/gram, respectively. IntI1 showed a high correlation (r > 0.8, P < 0.01) with the abundance of aac(6')-Ib-cr and sul1 in swine manure. Moreover, the farm scale (i.e., herd population) and geographical location were not found to be critical factors influencing the absolute abundance of ARGs of plasmid DNA in swine farms. However, the concentrations of florfenicol, Cu, Zn, Fe, total phosphorus (TP) and total potassium (TK) demonstrated a significant correlation with the abundance of several ARGs. Particularly, Cu and Zn had high correlations with optrA and bla_CTX-M, respectively. Our results demonstrated that antibiotics, heavy metals and environmental nutrients are likely jointly contributing to the long-term persistence of ARGs in swine production. This study provides insights into the abundance and influencing factors of ARGs from swine manure, which is of significance for assessing and reducing the public health risks in livestock production.

Effects of Oxytetracycline/Lead Pollution Alone and in the Combined Form on Antibiotic Resistance Genes, Mobile Genetic Elements, and Microbial Communities in the Soil

The application of livestock manure is the leading cause of antibiotic and heavy metal pollution in agricultural soil. However, the effects of oxytetracycline (OTC) and lead (Pb) pollution in the single or combined form on antibiotic resistance genes (ARGs) in the soil need to be further studied. This study was planned to investigate the effects of OTC and Pb application on ARGs, mobile genetic elements (MGEs), and bacterial abundance in the soil. The relative abundance of ARGs and MGEs increased by 0.31-fold and 0.03-fold after the addition of 80 mg kg^-1 Pb to the soil, and by 0.49-fold and 0.03-fold after the addition of 160 mg kg^-1 Pb. In addition, under the premise of the existence of OTC, the inhibitory effect of a low concentration of Pb on ARG is stronger than that of a high concentration of Pb, resulting in a lower abundance of ARGs. The abundance of ARGs and MGEs increased by 0.11-fold and 0.17-fold after the addition of OTC (30 mg kg^-1) to the soil at a Pb concentration of 80 mg kg^-1 and by 0.18-fold and 0.04-fold at a Pb concentration of 160 mg kg^-1. The addition of OTC and Pb in the soil also decreased the many bacterial communities such as Bacteroidetes, Proteobacteria, Acidobacteria, and Firmicutes. Redundancy analysis (RDA) showed that organic matter content and pH were positively correlated with the abundance of ARGs and MGEs. At the same time, electrical conductivity (EC) had a negative correlation with the abundance of ARGs and MGEs in the soil. Intl1 was significantly associated with tetB, sul1, tetQ, sul2, and sul3. Network analysis illustrated that Actinobacteria, Bacteroidetes, and Proteobacteria were the main host bacteria causing changes in the abundance of ARGs and MGEs, and they were also predominant phylum in the culture environment. This conclusion can provide a reference for the related research of ARGs in soil.

Ecological Responses of Maize Rhizosphere to Antibiotics Entering the Agricultural System in an Area with High Arsenicals Geological Background

Metal(loid)s can promote the spread and enrichment of antibiotic resistance in the environmental ecosystem through a co-selection effect. Little is known about the ecological effects of entering antibiotics into the environment with long-term metal(loid)s' resistance profiles. Here, cow manure containing oxytetracycline (OTC) or sulfadiazine (SA) at four concentrations (0 (as control), 1, 10, and 100 mg/kg) was loaded to a maize cropping system in an area with high a arsenicals geological background. Results showed that exogenous antibiotics entering significantly changed the nutrient conditions, such as the concentration of nitrate nitrogen, ammonium nitrogen, and available phosphorus in the maize rhizosphere soil, while total arsenic and metals did not display any differences in antibiotic treatments compared with control. Antibiotics exposure significantly influenced nitrate and nitrite reductase activities to reflect the inhibition of denitrification rates but did not affect the soil urease and acid phosphatase activities. OTC treatment also did not change soil dehydrogenase activities, while SA treatment posed promotion effects, showing a tendency to increase with exposure concentration. Both the tested antibiotics (OTC and SA) decreased the concentration of arsenite and arsenate in rhizosphere soil, but the inhibition effects of the former were higher than that of the latter. Moreover, antibiotic treatment impacted arsenite and arsenate levels in maize root tissue, with positive effects on arsenite and negative effects on arsenate. As a result, both OTC and SA treatments significantly increased bioconcentration factors and showed a tendency to first increase and then decrease with increasing concentration. In addition, the treatments decreased translocation capacity of arsenic from roots to shoots and showed a tendency to increase translocation factors with increasing concentration. Microbial communities with arsenic-resistance profiles may also be resistant to antibiotics entering.

Distribution of quinolone and macrolide resistance genes and their co-occurrence with heavy metal resistance genes in vegetable soils with long-term application of manure

The spread of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) has become an increasingly serious global public health issue. This study investigated the distribution characteristics and influencing factors of ARB and ARGs in greenhouse vegetable soils with long-term application of manure. Five typical ARGs, four heavy metal resistance genes (MRGs), and two mobile genetic elements (MGEs) were quantified by real-time quantitative polymerase chain reaction (qPCR). The amount of ARB in manure-improved soil greatly exceeded that in control soil, and the bacterial resistance rate decreased significantly with increases in antibiotic concentrations. In addition, the resistance rate of ARB to enrofloxacin (ENR) was lower than that of tylosin (TYL). Real-time qPCR results showed that long-term application of manure enhanced the relative abundance of ARGs in vegetable soils, and the content and proportion of quinolone resistance genes were higher than those of macrolide resistance genes. Redundancy analysis (RDA) showed that qepA and qnrS significantly correlated with total and available amounts of Cu and Zn, highlighting that certain heavy metals can influence persistence of ARGs. Integrase gene intI1 correlated significantly with the relative abundance of qepA, qnrS, and ermF, suggesting that intI1 played an important role in the horizontal transfer of ARGs. Furthermore, there was a weakly but not significantly positive correlation between specific detected MRGs and ARGs and MGEs. The results of this study enhance understanding the potential for increasing ARGs in manure-applied soil, assessing ecological risk and reducing the spread of ARGs.

Influence of site-specific factors on antibiotic resistance in agricultural soils of Yangtze River Delta: An integrated study of multi-factor modeling

Agricultural soils are important reservoirs for antibiotic resistance genes (ARGs), which is closely linked to soil microorganisms. Environmental factors and co-existed pollutants may function as promoters or inhibitors for ARG proliferation to influence the agriculture green development. However, research focusing on the interaction of potential environmental drivers and ARGs is still lacking in agricultural soils. Here, we explored the microbial profile in 241 soil samples in Yangtze River Delta, and analyzed the relationship of microbial structures, ARGs, and typical site-specific factors. We found that the abundance of most ARGs was negatively correlated with the ratio of fungi and bacteria (F/B), whereas positively correlated with the ratio of gram-positive and gram-negative microbes (G⁺/G^-). The co-occurrence network revealed significant associations among 18 site-specific factors, including 6 meteorological factors, 5 soil physicochemical properties, 5 co-existed organic pollutants, and 2 co-existed heavy metals. Random forest analysis demonstrated that F/B was mainly influenced by soil organic matters and co-existed polychlorinated biphenyls, while G⁺/G^- was predominately regulated by soil total phosphorus and moisture content, which possibly resulting in their difference relationship with ARG abundance. Besides, the contribution of meteorological factors (>30%) in the explanation for F/B and G⁺/G^- structures was the highest among all the site-specific factors. Together with path analysis showing meteorological factors probably affecting the ARG abundance through direct positive ways or indirect paths via physicochemical properties, microbial structure, and co-existed organic pollutants, we considered meteorological factors as the potential promoters for ARG proliferation. Collectively, these results increase our understanding of agricultural soils as hotspots of ARGs, and highlight the underappreciated role of meteorological factors as potential promoters for soil ARGs, providing reference for us to regulate ARG pollution scientifically to improve the development of green agriculture.

Insights into the fates of plasmids and antimicrobial resistance genes during swine manure treatment and related factors based on plasmidome and metagenome analyses

Swine manure treatment plants are important reservoirs of plasmid-harboring antibiotic resistance genes (ARGs) and physicochemical contaminants, but the changes in the abundances of plasmids and ARGs, and their interactions with the physicochemical properties of manure, are still unclear. Thus, in the present study, plasmidome and metagenome analyses were conducted for samples collected at different stages in the swine manure treatment process. The results indicated that anaerobic digestion and aerobic digestion were the most efficient stages for reducing the abundances of ARGs in swine manure. However, the plasmids associated with ARGs were not effectively removed in these stages. Through the whole treatment process, the IncL/M, IncQ1, IncHI2A, IncA/C, and IncN plasmid groups had strong correlations (r > 0.8, P < 0.01) with most ARG types, thereby indicating that these plasmids play important roles in the persistence of ARGs in this environment. Furthermore, the pH, total nitrogen, total phosphorus, and four heavy metals (Cu, Zn, As, and Fe) significantly affected the abundances of seven ARG subtypes (tetB(P), ant(6)-Ia, tet44, aph(3'')-Ib, mefB, tet(L), and tet(39)). In particular, florfenicol had the most positive correlations with ARGs. Our results indicated that nutrients, heavy metals, and antibiotics all contributed to the presence and persistence of plasmid-harboring ARGs. This study provides insights into the fate of plasmids and ARGs, and related factors during the swine manure treatment process, thereby facilitating the development of a new treatment technique for removing ARGs and reducing the public health risk associated with livestock production.

Co-doped Fe-MIL-100 as an adsorbent for tetracycline removal from aqueous solution

In the study, Fe-MIL-100 was modified by adding Co²⁺ in the synthesis process; Co/Fe-MIL-100 was successfully synthesized and used to adsorb tetracycline. The addition of Co²⁺ increased the thermal stability of Fe-MIL-100 without changing the crystal structure. It was found that Co/Fe-MIL-100 exhibited satisfactory performance in tetracycline removal, the tetracycline removal efficiency reached almost 100% in the initial concentration range of 10-40 mg/L, and it still reached 82.38% under the condition of 60 mg/L tetracycline. Besides, the factors of tetracycline concentration, pH and inorganic anion on removal efficiency were explored. The coexistence of inorganic anion decreased the adsorption capacity of tetracycline due to the competitive adsorption. CO₃^2- had a more obvious inhibition effect on the adsorption efficiency of tetracycline than Cl^-. The fitting correlation coefficient of Langmuir model was higher and the kinetics better fitted by pseudo-second-order, respectively. As a result of its high removal efficiency and excellent recycling performance, it has great potential in application fields such as removing tetracycline from wastewater.

Industrial aerobic composting and the addition of microbial agents largely reduce the risks of heavy metal and ARG transfer through livestock manure

Composting is an effective and necessary modality in the recycling of agricultural wastes such as livestock manure, furfural, and straw. However, the risks of heavy metals (HMs) and antibiotic resistance genes (ARGs) during industrial-scale composting process have not been adequately assessed, especially with the addition of bacterial agents. In this study, changes in HMs toxicity, ARGs propagation and microbial community structure during industrial-scale aerobic composting of livestock manure were firstly investigated with various substrates addition. Moreover, the effect of the addition of bacterial agents (Bacillus strains) was evaluated. The results showed that industrial aerobic composting process could immobilize various HMs with different extents and significantly reduce the levels of ARGs such as intl1 and oqxB genes. The addition of Bacillus strains could further reduce the levels of most detected ARGs and the bioavailability of Cu and Cr, and the relative abundance of ereA and tetA was undetectable in some materials. After composting, the main bacterial community structures were similar among different substrates irrespective of bacterial agents and indicated that the composting process was the main driver for their change. This study provides a scientific reference for the safe reuse of livestock manure.

Distribution and Transfer of Antibiotic Resistance Genes in Coastal Aquatic Ecosystems of Bohai Bay

Antibiotic resistance genes (ARGs) are abundant in diverse ecosystems and the resistome may constitute a health threat for humans and animals. It is necessary to uncover ARGs and the accumulation mechanisms from different environmental sources. Various habitats, such as soil, seawater and fish intestines, could overflow a considerable amount of ARGs and the horizontal transfer of ARGs may occur in these environments. Thus, we assessed the composition and abundance of ARGs in seawater, soil and intestinal tracts of Cynoglossus semilaevis collected from different sites in Bohai Bay (China), including a natural area and three fish farms, through a high-throughput qPCR array. In total, 243 ARGs were uncovered, governing the resistance to aminoglycoside, multidrug, beta-lactamase, macrolide lincosamide streptomycin B (MLSB), chloramphenicol, sulfonamide, tetracycline, vancomycin and other antibiotics. The action mechanisms of these ARGs were mainly antibiotic deactivation, efflux pump and cellular protection. Importantly, similar ARGs were detected in different samples but show dissimilar enrichment levels. ARGs were highly enriched in the fish farms compared to the natural sea area, with more genes detected, while some ARGs were detected only in the natural sea area samples, such as bacA-02, tetL-01 and ampC-06. Regarding sample types, water samples from all locations shared more ARGs in common and held the highest average level of ARGs detected than in the soil and fish samples. Mobile genetic elements (MGEs) were also detected in three sample types, in the same trend as ARGs. This is the first study comparing the resistome of different samples of seawater, soil and intestines of C. semilaevis. This study contributes to a better understanding of ARG dissemination in water sources and could facilitate the effective control of ARG contamination in the aquatic environment.

Bloom of tetracycline resistance genes in mudflats following fertilization is attributed to the increases in the shared potential hosts between soil and organic fertilizers

A field experiment was carried out in mudflats adjacent to the Yellow Sea, China, amended with sewage sludge and vermicompost by one-time input at different rates to reveal the fates of tetracycline resistance genes (TRGs) and their potential hosts in the soils. Quantitative PCR results showed that soils added with either sludge or vermicompost had more abundant TRGs compared with the non-fertilized soil. This situation was more obvious in sludge fertilized soils especially at high application rates. Vermicompost exhibited a promising outlook for improvement of the mudflats. The abundances of intI1 in the non-fertilized soils were significantly higher than those in fertilizers and fertilized soils. The potential hosts for intI1 were not shared with other TRGs-contained hosts, indicating that intI1 had little effects on the dissemination of TRGs in the mudflats. Moreover, the exclusive hosts for TRGs in fertilizers were not higher than those in the non-fertilized soils, illustrating little effects of fertilization on the introduction of exogenous TRGs into soil. The shared hosts between soil and fertilizers were highest among four possible sources, contributing vastly to the bloom of TRGs following fertilization. It was also shown that different organic fertilizers caused distinct categories of shared potential hosts for TRGs. RDA analysis further indicated that the abundances of the shared potential hosts were affected by soil nutrients. These results suggested that the development of TRGs in soil following fertilization depended on the shared potential hosts with similar ecological niches between soil and fertilizers.

Quantification of antibiotic resistance genes and mobile genetic in dairy manure

Background

Antibiotic resistance genes (ARGs) are considered to be emerging environmental contaminants of concern potentially posing risks to human and animal health, and this research studied the prevalence of antimicrobial resistance in dairy manure.

Methods

This study is focused on investigating prevalence of ARGs in California dairy farm manure under current common different manure management. A total of 33 manure samples were collected from multiple manure treatment conditions: (1) flushed manure (FM), (2) fresh pile (FP), (3) compost pile (CP), (4) primary lagoon (PL), and (5) secondary lagoon (SL). After DNA extraction, all fecal samples were screened by PCR for the presence of eight ARGs: four sulfonamide ARGs (sulI, sulII, sulIII, sulA), two tetracycline ARGs (tetW, tetO), two macrolide-lincosamide-streptogramin B (MLS_B) ARGs (ermB, ermF). Samples were also screened for two mobile genetic elements (MGEs) (intI1, tnpA), which are responsible for dissemination of ARGs. Quantitative PCR was then used to screen all samples for five ARGs (sulII, tetW, ermF, tnpA and intI1).

Results

Prevalence of genes varied among sample types, but all genes were detectable in different manure types. Results showed that liquid-solid separation, piling, and lagoon conditions had limited effects on reducing ARGs and MGEs, and the effect was only found significant on tetW (p = 0.01). Besides, network analysis indicated that sulII was associated with tnpA (p < 0.05), and Psychrobacter and Pseudomonas as opportunistic human pathogens, were potential ARG/MGE hosts (p < 0.05). This research indicated current different manure management practices in California dairy farms has limited effects on reducing ARGs and MGEs. Improvement of different manure management in dairy farms is thus important to mitigate dissemination of ARGs into the environment.

Diversity and distribution of antibiotic resistance genes associated with road sediments transported in urban stormwater runoff

Recently, increasing attention has been paid to antibiotic resistance genes (ARGs) in urban stormwater runoff. However, there were little data on the diversity and distribution of ARGs associated with road sediments transported in runoff. The investigation of ARGs diversity showed that sulfonamide resistance genes (sul2 and sul3) occupied 61.7%-82.3% of total ARGs in runoff. The analysis of ARGs distribution in particulate matter (PM) implied that both tetQ and trbC existed mainly in PM with size of 150-300 μm, but other ARGs and mobile genetic elements (MGEs) were dominant in PM with size <75 μm. The discussion of potential hosts indicated that target genes (ermF, blaOXA1/blaOXA30, ermC, qnrA, sul2, tnpA-01, intI2, tetW, intI1, sul3, trbC) had the strongest subordinate relationship with Proteobacteria at phylum level and Enterobacter at genus level. The effect evaluation of ARGs distribution suggested that 13 kinds of ARGs were positively correlated with Pr/PS and Zeta potential, resulting in the more ARGs in PM with smaller size (<75 μm).

Multiple driving factors contribute to the variations of typical antibiotic resistance genes in different parts of soil-lettuce system

The application of manure compost may cause the transmission of antibiotic resistance genes (ARGs) in agroecological environment, which poses a global threat to public health. However, the driving factors for the transmission of ARGs from animal manure to agroecological systems remains poorly understood. Here, we explored the spatiotemporal variation in ARG abundance and bacterial community composition as well as relative driving factors in a soil-lettuce system amended with swine manure compost. The results showed that ARGs abundance had different variation trends in soil, lettuce phylloplane and endophyere after the application of swine manure compost. The temporal variations of total ARGs abundance had no significant different in soil and lettuce phylloplane, while lettuce endosphere enriched half of ARGs to the highest level at harvest. There was a significant linear correlation between ARGs and integrase genes (IGs). In contrast to the ARGs variation trend, the alpha diversity of soil and phylloplane bacteria showed increasing trends over planting time, and endosphere bacteria remained stable. Correlation analysis showed no identical ARG-related genera in the three parts, but the shared Proteobacteria, Pseudomonas, Halomonas and Chelativorans, from manure compost dominated ARG profile in the soil-lettuce system. Moreover, redundancy analysis and structural equation modelling showed the variations of ARGs may have resulted from the combination of multiple driving factors in soil-lettuce system. ARGs in soil were more affected by the IGs, antibiotic and heavy metals, and bacterial community structure and IGs were the major influencing factors of ARG profiles in the lettuce. The study provided insight into the multiple driving factors contribute to the variations of typical ARGs in different parts of soil-lettuce system, which was conducive to the risk assessment of ARGs in agroecosystem and the development of effective prevention and control measures for ARGs spread in the environment.

Antimicrobial resistance in integrated agroecosystems: State of the science and future opportunities

As the Journal of Environmental Quality (JEQ) celebrates 50 years of publication, the division of environmental microbiology is one of the newest additions to the journal. During this time, significant advances in understanding of the interconnected microbial community and impact of the microbiome on natural and designed environmental systems have occurred. In this review, we highlight the intractable challenge of antimicrobial resistance (AMR) on humans, animals, and the environment, with particular emphasis on the role of integrated agroecosystems and by highlighting contributions published in JEQ. From early studies of phenotypic resistance of indicator organisms in waters systems to current calls for integrating AMR assessment across "One Health," publications in JEQ have advanced our understanding of AMR. As we reflect on the state of the science, we emphasize future opportunities. First, integration of phenotypic and molecular tools for assessing environmental spread of AMR and human health risk continues to be an urgent research need for a one health approach to AMR. Second, monitoring AMR levels in manure is recommended to understand inputs and potential spread through agroecosystems. Third, baseline knowledge of AMR levels is important to realize the impact of manure inputs on water quality and public health risk; this can be achieved through background monitoring or identifying the source-related genes or organisms. And finally, conservation practices designed to meet nutrient reduction goals should be explored for AMR reduction potential.

Antibiotic resistance genes in layer farms and their correlation with environmental samples

Livestock farms are generally considered to be the important source of antibiotic resistance genes (ARGs). It is important to explore the spread of ARGs to reduce their harm. This study analyzed 13 resistance genes belonging to 7 types in 68 samples of layer manure including different stages of layer breeding, layer manure fertilizer, and soil from 9 laying hen farms in Guangdong Province. The detection rate of antibiotic resistance genes was extremely high at the layer farm in manure (100%), layer manure fertilizer (100%), and soil (> 95%). The log counts of antibiotic resistance genes in layer manure (3.34-11.83 log copies/g) were significantly higher than those in layer manure fertilizer (3.45-9.80 log copies/g) and soil (0-7.69 log copies/g). In layer manure, ermB was the most abundant antibiotic resistance gene, with a concentration of 3.19 × 10⁹- 6.82 × 10¹¹ copies/g. The average abundances of 5 antibiotic resistance genes were above 10¹⁰ copies/g in the descending order ermB, sul2, tetA, sul1, and strB. The relative abundances of ARGs in layer manure samples from different breeding stages ranked as follows: brooding period (BP), late laying period (LL), growing period (GP), early laying period (EL), and peak laying period (PL). There was no significant correlation between the farm scale and the abundance of antibiotic resistance genes. Moreover, the farther away from the layer farm, the lower the abundance of antibiotic resistance genes in the soil. We also found that compost increases the correlation between antibiotic resistance genes, and the antibiotic resistance genes in soil may be directly derived from layer manure fertilizer instead of manure. Therefore, when applying layer manure fertilizer to cultivated land, the risk of antibiotic resistance genes pollution should be acknowledged, and in-depth research should be conducted on how to remove antibiotic resistance genes from layer manure fertilizer to control the spread of antibiotic resistance genes.

Antibiotics, Multidrug-Resistant Bacteria, and Antibiotic Resistance Genes: Indicators of Contamination in Mangroves?

Multidrug-resistant bacteria and antibiotic resistance genes can be monitored as indicators of contamination in several environments. Mangroves are among the most productive ecosystems, and although they can be resilient to the action of climate phenomena, their equilibrium can be affected by anthropogenic activities. Regarding the presence and persistence of multidrug-resistant bacteria in mangroves, it is common to think that this ecosystem can function as a reservoir, which can disperse the antibiotic resistance capacity to human pathogens, or serve as a filter to eliminate drug-resistant genes. The possible impact of anthropogenic activities carried out near mangroves is reviewed, including wastewater treatment, food production systems, leisure, and tourism. Adverse effects of antibiotic resistance genes or multidrug-resistant bacteria, considered as emerging contaminants, have not been reported yet in mangroves. On the contrary, mangrove ecosystems can be a natural way to eliminate antibiotics, antibiotic-resistant bacteria, and even antibiotic-resistant genes from the environment. Although mangroves’ role in decreasing antibiotics and antibiotic resistance genes from the environment is being proposed, the mechanisms by which these plants reduce these emerging contaminants have not been elucidated and need further studies. Additionally, further evaluation is needed on the effects of antibiotics and antibiotic-resistant bacteria in mangroves to generate an analysis of the human contribution to the degradation of this specific ecosystem as well as to define if these contaminants can be used as indicators of contamination in mangrove ecosystems.

Effect of copper and zinc as sulfate or nitrate salts on soil microbiome dynamics and blaVIM-positive Pseudomonas aeruginosa survival

The exposure of soil to metals and to antibiotic resistant bacteria may lead to the progressive deterioration of soil quality. The persistence of antibiotic resistant bacteria or antibiotic resistance genes in soil can be influenced by the microbial community or by soil amendments with metal salts. This work assessed the effect of soil amendment with copper and zinc, as sulfate or nitrate salts, on the fate of a carbapenem-resistant (bla_VIM⁺) hospital effluent isolate of Pseudomonas aeruginosa (strain H1FC49) and on the variations of the microbial community composition. Microcosms with soil aged or not with copper and zinc salts (20 mM), and inoculated with P. aeruginosa H1FC49 were monitored at 0, 7, 14 and/or 30 days, for community composition (16S rRNA gene amplicon) and strain H1FC49 persistence. Data on culturable P. aeruginosa, quantitative PCR of the housekeeping gene ecf, and the presumably acquired genes bla_VIM⁺ and integrase (intI1), and community composition were interpreted based on descriptive statistics and multivariate analysis. P. aeruginosa and the presumably acquired genes, were quantifiable in soil for up to one month, in both metal-amended and non-amended soil. Metal amendments were associated with a significant decrease of bacterial community diversity and richness. The persistence of P. aeruginosa and acquired genes in soils, combined with the adverse effect of metals on the bacterial community, highlight the vulnerability of soil to both types of exogenous contamination.

We and herbivores eat endophytes

Health depends on the diet and a vegetal diet promotes health by providing fibres, vitamins and diverse metabolites. Remarkably, plants may also provide microbes. Fungi and bacteria that reside inside plant tissues (endophytes) seem better protected to survive digestion; thus, we investigated the reported evidence on the endophytic origin of some members of the gut microbiota in animals such as panda, koala, rabbits and tortoises and several herbivore insects. Data examined here showed that some members of the herbivore gut microbiota are common plant microbes, which derived to become stable microbiota in some cases. Endophytes may contribute to plant fibre or antimetabolite degradation and synthesis of metabolites with the plethora of enzymatic activities that they display; some may have practical applications, for example, Lactobacillus plantarum found in the intestinal tract, plants and in fermented food is used as a probiotic that may defend animals against bacterial and viral infections as other endophytic-enteric bacteria do. Clostridium that is an endophyte and a gut bacterium has remarkable capabilities to degrade cellulose by having cellulosomes that may be considered the most efficient nanomachines. Cellulose degradation is a challenge in animal digestion and for biofuel production. Other endophytic-enteric bacteria may have cellulases, pectinases, xylanases, tannases, proteases, nitrogenases and other enzymatic capabilities that may be attractive for biotechnological developments, indeed many endophytes are used to promote plant growth. Here, a cycle of endophytic-enteric-soil-endophytic microbes is proposed which has relevance for health and comprises the fate of animal faeces as natural microbial inoculants for plants that constitute bacterial sources for animal guts.

Effects of two ecological earthworm species on tetracycline degradation performance, pathway and bacterial community structure in laterite soil

This study explored the change of tetracycline degradation efficiency, metabolic pathway, soil physiochemical properties and degraders in vermiremediation by two earthworm species of epigeic Eisenia fetida and endogeic Amynthas robustus. We found a significant acceleration of tetracycline degradation in both earthworm treatments, and 4-epitetracycline dehydration pathway was remarkably enhanced only by vermiremediation. Tetracycline degraders from soils, earthworm intestines and casts were different. Ralstonia and Sphingomonas were potential tetracycline degraders in soils and metabolized tetracycline through direct dehydration pathway. Degraders in earthworm casts (Comamonas, Acinetobacter and Stenotrophomonas) and intestines (Pseudomonas and Arthrobacter) dehydrated 4-epitetracycline into 4-epianhydrotetracycline. More bacterial lineages resisting tetracycline were found in earthworm treatments, indicating the adaptation of soil and intestinal flora under tetracycline pressure. Earthworm amendment primarily enhanced tetracycline degradation by neutralizing soil pH and consuming organic matters, stimulating both direct dehydration and epimerization-dehydration pathways. Our findings proved that vermicomposting with earthworms is effective to alter soil microenvironment and accelerate tetracycline degradation, behaving as a potential approach in soil remediation at tetracycline contaminated sites.

Improving the Properties of Degraded Soils from Industrial Areas by Using Livestock Waste with Calcium Peroxide as a Green Oxidizer

Over the past years, the treatment and use of livestock waste has posed a significant problem in environmental engineering. This paper outlines a new approach to application of calcium peroxide (CaO₂) as a green oxidizer and microbiocidal agent in the treatment of poultry manure. It also presents the application of pretreated waste in improvement of degraded soils in industrial areas. The CCD (Central Composite Design) and RSM (Response Surface Methodology) were employed for optimizing the process parameters (CaO₂ concentration 1.6–8.4 wt %, temperature 5.2–38.8 °C and contact time 7–209 h). The analysis of variance (ANOVA) was used to analyze the experimental results, which indicated good fit of the approximated to the experimental data (R² = 0.8901, R²_adj = 0.8168). The amendment of CaO₂ in optimal conditions (8 wt % of CaO_2, temperature 22 °C and contact time 108 h) caused a decrease in bacteria Escherichia coli (E. coli) in poultry manure from 8.7 log₁₀ CFU/g to the acceptable level of 3 log₁₀ CFU/g. The application of pretreated livestock waste on degraded soils and the studies on germination and growth of grass seed mixture (Lollum perenne—Naki, Lollum perenne—Grilla, Poa pratensis—Oxford, Festuca rubbra—Relevant, Festuca rubbra—Adio and Festuca trachypylla—Fornito) showed that a dose of 0.08 g of CaO₂ per 1 gram of poultry manure induced higher yield of grass plants. The calculated indicators for growth of roots (GFR) and shoots (GFS) in soils treated with poultry manure were 10–20% lower compared to soils with amended CaO₂. The evidence from this study suggests that CaO₂ could be used as an environmentally friendly oxidizer and microbiocidal agent for livestock waste.

Removal of antibiotic-resistant genes during drinking water treatment: A review

Once contaminate the drinking water source, antibiotic resistance genes (ARGs) will propagate in drinking water systems and pose a serious risk to human health. Therefore, the drinking water treatment processes (DWTPs) are critical to manage the risks posed by ARGs. This study summarizes the prevalence of ARGs in raw water sources and treated drinking water worldwide. In addition, the removal efficiency of ARGs and related mechanisms by different DWTPs are reviewed. Abiotic and biotic factors that affect ARGs elimination are also discussed. The data on presence of ARGs in drinking water help come to the conclusion that ARGs pollution is prevalent and deserves a high priority. Generally, DWTPs indeed achieve ARGs removal, but some biological treatment processes such as biological activated carbon filtration may promote antibiotic resistance due to the enrichment of ARGs in the biofilm. The finding that disinfection and membrane filtration are superior to other DWTPs adds weight to the advice that DWTPs should adopt multiple disinfection barriers, as well as keep sufficient chlorine residuals to inhibit re-growth of ARGs during subsequent distribution. Mechanistically, DWTPs obtain direct and inderect ARGs reduction through DNA damage and interception of host bacterias of ARGs. Thus, escaping of intracellular ARGs to extracellular environment, induced by DWTPs, should be advoided. This review provides the theoretical support for developping efficient reduction technologies of ARGs. Future study should focus on ARGs controlling in terms of transmissibility or persistence through DWTPs due to their biological related nature and ubiquitous presence of biofilm in the treatment unit.

Antibiotics and Antibiotic Resistance Genes in Animal Manure - Consequences of Its Application in Agriculture

Antibiotic resistance genes (ARGs) are a relatively new type of pollutant. The rise in antibiotic resistance observed recently is closely correlated with the uncontrolled and widespread use of antibiotics in agriculture and the treatment of humans and animals. Resistant bacteria have been identified in soil, animal feces, animal housing (e.g., pens, barns, or pastures), the areas around farms, manure storage facilities, and the guts of farm animals. The selection pressure caused by the irrational use of antibiotics in animal production sectors not only promotes the survival of existing antibiotic-resistant bacteria but also the development of new resistant forms. One of the most critical hot-spots related to the development and dissemination of ARGs is livestock and poultry production. Manure is widely used as a fertilizer thanks to its rich nutrient and organic matter content. However, research indicates that its application may pose a severe threat to human and animal health by facilitating the dissemination of ARGs to arable soil and edible crops. This review examines the pathogens, potentially pathogenic microorganisms and ARGs which may be found in animal manure, and evaluates their effect on human health through their exposure to soil and plant resistomes. It takes a broader view than previous studies of this topic, discussing recent data on antibiotic use in farm animals and the effect of these practices on the composition of animal manure; it also examines how fertilization with animal manure may alter soil and crop microbiomes, and proposes the drivers of such changes and their consequences for human health.

Microbial community composition and antimicrobial resistance in agricultural soils fertilized with livestock manure from conventional farming in Northern Italy

Antimicrobials are commonly used in conventional livestock production and manure is widely applied to agricultural lands as fertilizer. This practice raises questions regarding the effects of fertilization on (i) soil microbiota composition and (ii) spread of antimicrobials and antimicrobial resistance (AMR) in the environment. This study was conducted in a high-density farming area of Northern Italy and aimed at assessing the impact of (dairy cattle, chickens and swine) manure application on soil microbiome, antimicrobial concentrations and antimicrobial resistance gene (ARG) abundance. We found the microbial community composition in manure to be different and less diverse than in soil, with manure application altering only marginally the soil microbiome. Exceptions were the phyla Firmicutes, Tenericutes and Cloacimonetes, which significantly enriched in fertilized soil. Of the antimicrobials investigated, only flumequine concentrations increased after manure application, albeit non-significantly. ARGs were more abundant in manure, with ermA, ermB, bla_OXA-1 and oqxA being significantly enriched in fertilized soil. Positive correlations between oqxA and qnrS abundances and flumequine concentrations were observed, together with the co-occurrence of some ARGs and microbial taxa (e.g. oqxA correlated with Acidobacteria and Gemmatimonadetes). This study showed that manure application has little effect on soil microbiome but may contribute to the dissemination of specific ARGs into the environment. Moreover, flumequine residues seem to enhance the emergence of oqxA and qnrS in soil.

Resilience of agricultural soils to antibiotic resistance genes introduced by agricultural management practices

Antimicrobial resistance (AR) represents a global threat in human and veterinary medicine. In that regard, AR proliferation and dissemination in agricultural soils after manure application raises concerns on the enrichment of endogenous soil bacterial population with allochthonous antibiotic resistance genes (ARGs). Natural resilience of agricultural soils and background concentrations of ARGs play key roles in the mitigation of AR propagation in natural environments. In the present study, we carried out a longitudinal sampling campaign for two crop vegetation periods to monitor spatial and temporal changes in the abundance of seven clinically relevant ARGs (sul1, ermB, vanA, aph(3')-IIa, aph(3')-IIIa, blaTEM-1 and tet(W)) and ribosomal 16S RNA. The absolute and relative abundances of the selected ARGs were quantified in total community DNA extracted from agricultural (manured and non-manured) and forest soils, fresh pig faeces and manure slurry. We observed that ARG concentrations return to background levels after manure-induced exposure within a crop growing season, highlighting the resilience capacity of soil. Naturally occurring high background concentrations of ARGs can be found in forest soil in due distance under low anthropogenic influences. It was observed that pesticide application increases the concentrations of three out of seven ARGs tested (ermB, aph(3')-IIIa and tet(W)). Moreover, we noticed that the absolute abundances of sul1, vanA, ermB and blaTEM-1 resistance genes show an increase by 100- to 10,000- fold, from maturation of fresh pig faeces to manure. Outcomes of our study suggest that agricultural soil environments show a strong capacity to alleviate externally induced disturbances in endogenous ARG concentrations. Naturally occurring high concentrations of ARGs are present also in low human impacted environments represented by the indigenous resistome.

Dissemination of blaNDM-5 via IncX3 plasmids in carbapenem-resistant Enterobacteriaceae among humans and in the environment in an intensive vegetable cultivation area in eastern China

The environment of a large-scale vegetable production area can be exposed to antibiotic residues and antibiotic-resistant bacteria (ARB) via animal manure and irrigation with contaminated water, which can facilitate the dissemination of ARB. However, the occurrence of ARB in plantation areas and their dissemination in this environment remain largely unexplored. In total, 382 samples including those from vegetable (n = 106), soil (n = 87), well water (n = 24), river water (n = 20), river sediments (n = 20), farmer feces (n = 58) and farmer hands (n = 67) were collected in 2019 from a large-scale cultivation area in Shandong, China. Selective agar plates were used to screen for carbapenem-resistant Enterobacteriaceae (CRE) and whole-genome sequencing and Southern blotting were used to characterise isolates and mobile genetic elements carrying carbapenem resistance determinants. A total of nine NDM-5-producing isolates of Escherichia coli, Klebsiella pneumoniae, and Citrobacter spp. were identified from environmental sources and human feces, all of which were multidrug-resistant. Single nucleotide polymorphism analysis suggested clonal transmission of carbapenem-resistant Citrobacter sedlakii within greenhouse soils in the area. Eight of the isolates carried closely related or identical IncX3 plasmids carrying blaNDM-5, which were shown to be conjugative via filter mating experiments, indicating the highly transmissible nature of this genetic element. Isolates of E. coli and Citrobacter freundii were detected in the feces of local farm workers and contained similar IncX3 plasmids with blaNDM-5 environmental isolates, suggesting a potential risk of CRE transfer from the work environment to the farm workers. Thus, further research is required to investigate the potential health risks associated with environmental exposure to CRE in vegetable cultivation areas.

Occurrence and antibacterial resistance of culturable antibiotic-resistant bacteria in the Fildes Peninsula, Antarctica

Quantifying the occurrence of Antarctic antibiotic-resistant bacteria (ARB) is essential for assessing the level of pollution and assessing the "baseline" or background level of ARB in human uninhabited environments. Animal feces, soil, and sediments were sampled from Fildes Peninsula. The abundance of sulfamethazine- and ciprofloxacin-resistance bacteria and antibotic resistance genes (ARGs) within ARB were investigated. The results showed Ciprofloxacin- and Sulfamethazine-resistant bacteria isolated from samples accounted for the highest abundances of 30 CFU/g and 79.8 CFU/g, respectively. The dominant genus of Sulfamethazine-and quinolone-resistance bacteria was Pseudomonas and Arthrobacter, respectively. 106 ARGs were detected from ARB. Strong positive correlations between mobile genetic elements (MGEs) and ARGs were found, what is relatively novel observation that the mechanism is confirmed to also occur in the Antarctic. This study reveals the compositional characteristics of ARGs of strains in Antarctic, providing support for the source of Antarctic antibiotic resistance and drug resistance mechanisms.

Sources of Antibiotic Resistant Bacteria (ARB) and Antibiotic Resistance Genes (ARGs) in the Soil: A Review of the Spreading Mechanism and Human Health Risks

Soil is an essential part of our ecosystem and plays a crucial role as a nutrient source, provides habitat for plants and other organisms. Overuse of antibiotics has accelerated the development and dissemination of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). ARB and ARGs are recognized as emerging environmental contaminants causing soil pollution and serious risks to public health. ARB and ARGs are discharged into soils through several pathways. Application of manure in agriculture is one of the primary sources of ARB and ARGs dissemination in the soil. Different sources of contamination by ARB and ARGs were reviewed and analyzed as well as dissemination mechanisms in the soil. The effects of ARB and ARGs on soil bacterial community were evaluated. Furthermore, the impact of different sources of manure on soil microbial diversity as well as the effect of antibiotics on the development of ARB and ARGs in soils was analyzed. Human health risk assessments associated with the spreading of ARB and ARGs in soils were investigated. Finally, recommendations and mitigation strategies were proposed.

The fate of antibiotic resistance genes in cow manure composting: shaped by temperature-controlled composting stages

Current work for animal manure processing is not up to the required standards and hence are not supposed to reflect the actual performance in antibiotic resistance control. As a result, this study carried out temperature-controlled aerobic composting, with sulfamethoxazole (SMX) as a typical antibiotic. The results of four different treatments demonstrated that temperature, water content, C/N ratio, EC, and pH showed no significant (p > 0.05) difference. Antibiotic resistance genes (ARGs) significantly decreased in the initial 10 days of the thermophilic phase, but the abundance of sul1 and sul2 increased greatly after 30 days. Moreover, ARGs were closely related with each other during the late stages of composting. A noteworthy effect of composting properties, especially temperature on bacterial community, which then had a positive effect on ARGs abundances. These findings provided evidence that the standard composting was still insufficient to control antibiotic resistance.

Poultry litter as potential source of pathogens and other contaminants in groundwater and surface water proximal to large-scale confined poultry feeding operations

Manure from livestock production has been associated with the contamination of water resources. To date, research has primarily focused on runoff of these contaminants from animal operations into surface water, and the introduction of poultry-derived pathogenic zoonoses and other contaminants into groundwater is under-investigated. We characterized pathogens and other microbial and chemical contaminants in poultry litter, groundwater, and surface water near confined poultry feeding operations (chicken layer, turkey) at 9 locations in Iowa and one in Wisconsin from May and June 2016. Results indicate that poultry litter from large-scale poultry confined feeding operations is a likely source of environmental contamination and that groundwater is also susceptible to such poultry-derived contamination. Poultry litter, groundwater, and surface water samples had detections of viable bacteria growth (Salmonella spp., enterococci, staphylococci, lactobacilli), multi-drug resistant Salmonella DT104 flo_st and int genes, F⁺ RNA coliphage (group I and IV), antibiotic resistance genes (ARGs; bla_DHA, bla_OXA-48, bla_TEM, bla_CMY-2, tetM), phytoestrogens (biochanin A, daidzein, formononetin), and a progestin (progesterone). In addition, mcr-1 (a colistin ARG), was detected in a groundwater sample and in another groundwater sample, antibiotic resistant isolates were positive for Brevibacterium spp., a potential signature of poultry in the environment. Detectable estrogenicity was not measured in poultry litter, but was observed in 67% of the surface water samples and 22% were above the U.S. Environmental Protection Agency trigger level of 1 ng/L. The transport of microbial pathogens to groundwater was significantly greater (p < 0.001) than the transport of trace organic contaminants to groundwater in this study. In addition to viable pathogens, several clinically important ARGs were detected in litter, groundwater, and surface water, highlighting the need for additional research on sources of these contaminants in livestock dominated areas.

Shifts in microbial community, pathogenicity-related genes and antibiotic resistance genes during dairy manure piled up

The uncomposted faeces of dairy cow are usually stacked on cow breeding farms, dried under natural conditions and then used as cow bedding material or they may be continuously piled up. However, no information is available to evaluate variations in the human and animal pathogen genes and antibiotic resistance during the accumulation of fresh faeces of dairy cow to manure. Here, we present the metagenomic analysis of fresh faeces and manure from a dairy farm in Ning Xia, showing a unique enrichment of human and animal pathogen genes and antibiotic resistance genes (ARGs) in manure. We found that manure accumulation could significantly increase the diversity and abundance of the pathogenic constituents. Furthermore, pathogens from manure could spread to the plant environment and enphytotic pathogens could affect the yield and quality of crops during the use of manure as a fertilizer. Levels of virulence genes and ARGs increased with the enrichment of microbes and pathogens when faeces accumulated to manure. Accumulated manure was also the transfer station of ARGs to enrich the ARGs in the environment, indicating the ubiquitous presence of environmental antibiotic resistance genes. Our results demonstrate that manure accumulation and usage without effective manure management is an unreasonable approach that could enrich pathogenic microorganisms and ARGs in the environment. The manure metagenome structure allows us to appreciate the overall influence and interaction of animal waste on water, soil and other areas impacted by faecal accumulation and the factors that influence pathogen occurrence in products from dairy cows.

The role of stereochemistry of antibiotic agents in the development of antibiotic resistance in the environment

Antibiotic resistance (ABR) is now recognised as a serious global health and economic threat that is most efficiently managed via a 'one health' approach incorporating environmental risk assessment. Although the environmental dimension of ABR has been largely overlooked, recent studies have underlined the importance of non-clinical settings in the emergence and spread of resistant strains. Despite this, several research gaps remain in regard to the development of a robust and fit-for-purpose environmental risk assessment for ABR drivers such as antibiotics (ABs). Here we explore the role the environment plays in the dissemination of ABR within the context of stereochemistry and its particular form, enantiomerism. Taking chloramphenicol as a proof of principle, we argue that stereoisomerism of ABs impacts on biological properties and the mechanisms of resistance and we discuss more broadly the importance of stereochemistry (enantiomerism in particular) with respect to antimicrobial potency and range of action.

Effects of the C/N ratio and moisture content on the survival of ESBL-producing Escherichia coli during chicken manure composting

Antibiotic-resistant bacteria are a threat to human and animal health. In recent years, the presence of extended-spectrum-β-lactamase (ESBL)-producing Escherichia (E.) coli in chicken manure, which is used as organic fertilizer, is a concern. The aim of the present study was to determine the effects of the carbon/nitrogen (C/N) ratio and moisture content (MC) on the survival of ESBL-producing E. coli during laboratory-scale composting of chicken manure. Nine different compost mixtures were enriched with an ESBL-producing E. coli strain to an initial concentration of 7 log₁₀ CFU/g, and the number of E. coli, temperature, and chemical conditions during composting were determined. The fastest decrease in E. coli occurred for all mixtures with a C/N ratio of 10:1. Additionally, dry mixtures with an MC of 20% and a C/N ratio of either 10:1 or 40:1 exhibited faster reductions in E. coli than the moist mixtures did, despite having lower maximum temperatures within the bioreactors. The decimal reduction times ranged from 0.27 days in a mixture with a C/N ratio of 10:1 and 40% MC to 4.82 days in a mixture with a C/N ratio of 40:1 and 40% MC. Both the C/N ratio and MC had a significant effect on the number of ESBL-producing E. coli and on temperature development; the C/N ratio additionally affected the pH value and content of ammoniacal nitrogen during chicken manure composting. The results of this study demonstrate a considerable range of mechanisms involved in the inactivation of E. coli during chicken manure composting.

Profiles of antibiotic resistome with animal manure application in black soils of northeast China

Black soils (Mollisols) are important soil resources for crop production and maintain food safety in China. For keeping soil fertility, the application of animal manure is commonly practiced in black soils. However, the impact of this application on abundance and diversity of antibiotic resistance genes (ARGs) in black soils of China remains unclear. Here, we surveyed the profiles of ARGs in 72 soil samples collected from four long-term experimental stations with different fertilization regimes and from open farmlands in two sites across northeast China using high-throughput quantitative PCR. Results showed that a total of 178 ARGs including mobile genetic elements (MGEs) were detected, and the diversity and abundance of ARGs were significantly increased with manure application. Additionally, the finding of a significant positive correlation between relative abundance of ARGs and MGEs (P <  0.0001), suggesting that horizontal gene transfer may potentially impact the transmission of ARGs. Furthermore, two genes aadA-1-01 and mexF, encoding resistance to aminoglycoside and multidrug, respectively, were recognized as indicators to estimate the abundance of other co-occurring ARGs. These findings provided insights into the soil resistome in black soils of northeast China and also highlighted the environmental risks caused by manure application should not be ignored.

Distribution characteristics of antibiotic resistant bacteria and genes in fresh and composted manures of livestock farms

Livestock manure is a major reservoir of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). This study investigated the distribution characteristics of ARB, ARGs in fresh and composted manures of traditional breading industry in rural areas in China. Samples collected were naturally piled without professional composting, and will be applied to farmland. The real-time quantitative polymerase chain reaction (qPCR) results showed the presence of ten target ARGs and two mobile genetic elements (MGEs) in the tested manure samples. The relative abundance of tetracycline and sulfonamide resistance genes (TRGs and SRGs) was generally higher than that of macrolide resistance genes (MRGs), followed by quinolone resistance genes (QRGs). There were significant positive correlations between the abundance of sul1, sul2, tetW and MGEs (intl1, intl2). In addition, the distribution of target ARGs was associated with the residual concentrations of doxycycline (DOX), sulfamethazine (SM2), enrofloxacin (ENR) and tylosin (TYL). Overall, a total of 24 bacterial genera were identified. The resistance rates of ARB were 17.79%-83.70% for SM2, followed 0.40%-63.77% for TYL, 0.36%-43.90% for DOX and 0.00%-13.36% for ENR, which showed a significant dose-effect. This study also demonstrated that the abundance of clinically relevant ARB and ARGs in chicken, swine and cow fresh manures significantly greater than that in composted manures, and chicken and swine manures had higher proportion of ARB and higher abundance of ARGs than that in cow manures.

Sludge bio-drying followed by land application could control the spread of antibiotic resistance genes

The process of sludge bio-drying has been adopted in response to the increasing amount of residual sewage sludge. It has been demonstrated that sludge bio-drying effectively reduces both antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), whereas ermF, tetX, and sulII become enriched in response to the dynamic development of the microbial community. The present study further demonstrated that the land application of sludge bio-drying products under current application rate did not cause an increase in the abundance of quantified ARGs in the soil but the persistence of ARB should be paid attention. Although land application introduced ermF, tetX, and tetG into the soil, these soon decreased to control levels. Furthermore, the decay rate varied between soil types, with red soil being the most persistent based on kinetics modeling. The fate of ARGs could also be attributed to the dynamics of the microbial community during land application, and the genus Parasegetibacter, which can degrade extracellular DNA, might play a key role in the control of ARGs. In summary, sludge bio-drying following land application could constitute an effective means of controlling the spread of ARGs, and microbial community changes contributed the most to the fate of the ARGs during the entire treatment chain (residual sewage sludge → bio-drying process → land application).

Characterizing the soil microbiome and quantifying antibiotic resistance gene dynamics in agricultural soil following swine CAFO manure application

As agriculture industrializes, concentrated animal feeding operations (CAFOs) are becoming more common. Feces from CAFOs is often used as fertilizer on fields. However, little is known about the effects manure has on the soil microbiome, which is an important aspect of soil health and fertility. In addition, due to the subtherapeutic levels of antibiotics necessary to keep the animals healthy, CAFO manure has elevated levels of antibiotic resistant bacteria. Using 16s rRNA high-throughput sequencing and qPCR, this study sought to determine the impact of swine CAFO manure application on both the soil microbiome and abundance of select antibiotic resistance genes (ARGs) and mobile element genes (erm(B), erm(C), sul1, str(B), intI1, IncW repA) in agricultural soil over the fall and spring seasons. We found the manure community to be distinct from the soil community, with a majority of bacteria belonging to Bacteroidetes and Firmicutes. The soil samples had more diverse communities dominated by Acidobacteria, Actinobacteria, Proteobacteria, Verrucomicrobia, and unclassified bacteria. We observed significant differences in the soil microbiome between all time points, except between the spring samples. However, by tracking manure associated taxa, we found the addition of the manure microbiome to be a minor driver of the shift. Of the measured genes, manure application only significantly increased the abundance of erm(B) and erm(C) which remained elevated in the spring. These results suggest bacteria in the manure do not survive well in soil and that ARG dynamics in soil following manure application vary by resistance gene.

Field-based evidence for enrichment of antibiotic resistance genes and mobile genetic elements in manure-amended vegetable soils

The increasing prevalence of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) in the soil environment represents a serious threat to public health. In this study, the diversity and abundance of ARGs and mobile genetic elements (MGEs) in different years of manure-amended vegetable soils were investigated. A total of eight genes, including four tetracycline resistance genes: tetW, tetM, tetO and tetT; two sulfonamide resistance genes: sul1 and sul2; and two MGEs: intI1 and intI2; were quantified in ten vegetable soils. The relative abundance of ARGs in soils amended with manure was significantly higher than that in soils without manure application. The relative abundance of the intI1 and intI2 genes had significantly positive correlations with the relative abundance of the tetW, tetO, sul1 and sul2 genes. Under different concentrations of antibiotics, the resistant bacteria rates of manure-amended soil were much higher than the control soil. Bacillus and Chryseobacterium, more likely to be multi-drug-resistant bacteria, were detected in both two antibiotics. Moreover, the significant correlation was found between the concentrations of Cu and Zn and the ARGs. Our findings provide empirical evidence that the dissemination risk of ARGs and ARB in long-term manure-amended vegetable soils, which might promote to the development of effective strategies to reduce the spread of ARGs in agro-ecosystems.

Review: Environmental impact of livestock farming and Precision Livestock Farming as a mitigation strategy

This paper reviews the environmental impact of current livestock practices and discusses the advantages offered by Precision Livestock Farming (PLF), as a potential strategy to mitigate environmental risks. PLF is defined as: "the application of process engineering principles and techniques to livestock farming to automatically monitor, model and manage animal production". The primary goal of PLF is to make livestock farming more economically, socially and environmentally sustainable and this can be obtained through the observation, interpretation of behaviours and, if possible, individual control of animals. Furthermore, adopting PLF to support management strategies, may lead to the reduction of the environmental impact of farms. Currently, few studies reported PLF efficacy in reducing the environmental impact, however further studies are necessary to better analyze the actual potential of PLF as a mitigation strategy. Literature shows the potentiality of the application of PLF, as the introduction of PLF in farms can lead to a reduction of Greenhouse gases (GHG) and ammonia (NH3) emission in air, nitrates and antibiotics pollution in water bodies, phosphorus, antibiotics and heavy metals in the soil.

'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.