Antibiotics in the Soil Environment-Degradation and Their Impact on Microbial Activity and Diversity

Short-Term Benzalkonium Chloride (C12) Exposure Induced the Occurrence of Wide-Spectrum Antibiotic Resistance in Agricultural Soils

Antibiotic resistance genes (ARGs) are global pollutants that pose a potential risk to human health. Benzalkonium chloride (C₁₂) (BC) disinfectants are thought to exert selection pressure on antibiotic resistance. However, evidence of BC-induced changes in antibiotic resistance in the soil environment is lacking. Here, we established short-term soil microcosms to investigate ARG profile dynamics in agricultural soils amended with sulfamethazine (SMZ, 10 mg kg^-1) and gradient concentrations of BC (0-100 mg kg^-1), using high-throughput quantitative PCR and Illumina sequencing. With the increase in BC concentration, the number of ARGs detected in the soil increased, but the normalized ARG abundance decreased. The added SMZ had a limited impact on ARG profiles. Compared to broad-spectrum fungicidal BC, the specificity of SMZ significantly affected the microbial community. Network analysis found that low-medium BC exposure concentrations resulted in the formation of small but strong ARG co-occurrence clusters in the soil, while high BC exposure concentration led to a higher incidence of ARGs. Variation partitioning analysis suggested that BC stress was the major driver shaping the ARG profile. Overall, this study highlighted the emergence and spread of BC-induced ARGs, potentially leading to the antimicrobial resistance problem in agricultural soils.

The enhanced degradation behavior of oxytetracycline by black soldier fly larvae with tetracycline resistance genes in the larval gut: Kinetic process and mechanism

Black soldier fly larvae (larvae) can digest organic wastes and degrade contaminants such as oxytetracycline (OTC). However, compared to the kinetic processes and enhanced mechanisms used in the traditional microbial degradation of OTC, those employed by larvae are largely uncharacterized. To obtain further details, a combined analysis of larval development, larval nutritional values (crude protein, crude fat and the composition of fatty acids) and the expression of tetracycline resistance genes (TRGs) in the larval gut was performed for the degradation of OTC added to substrates and for oxytetracycline bacterial residue (OBR). When the larvae were exposed to the substrates, the degradation processes were enhanced significantly (P < 0.01), with a 4.74-7.86-fold decrease in the degradation half-life (day^-1) and a 3.34-5.74-fold increase in the final degradation efficiencies. This result was attributed to the abundant TRGs (with a detection rate of 35.90%∼52.14%) in the larval gut. The TRGs presented the resistance mechanisms of cellular protection and efflux pumps, which ensured that the larvae could tolerate elevated OTC concentrations. Investigation of the TRGs indicated that enzymatic inactivation enhanced OTC degradation by larvae. These findings demonstrate that the larval degradation of antibiotic contaminants is an efficient method based on abundant TRGs in the larval gut, even though OTC degradation results in OBR. In addition, a more optimized system for higher reductions in antibiotic levels and the expansion of larval bioremediation to other fields is necessary.

Factors influencing the adsorption of antibiotics onto activated carbon in aqueous media

Widespread use of antibiotics for treating human and animal ailments has increased their discharge in the environment through excreta. Moreover, unscientific disposal of unused antibiotics has further increased their presence in the environmental matrices. Thus, occurrence of used and/or discarded antibiotics in water resources is becoming a growing concern across the globe. Antibiotics and their residues in the aquatic environment are emerging contaminants which pose a serious threat to the aquatic biota as well as human beings by enhancing antibiotic resistance. Various methods are being adopted for the removal of these contaminants. Adsorption over activated carbon is one such promising method which is environmentally friendly, cost-effective, and efficient. However, there are various factors which affect the overall process efficiency, such as, properties of activated carbon/antibiotics/reaction medium etc. In this article, emphasis has been laid down on evaluating these factors, so that the experimental procedures may be optimized to obtain the highest possible removal efficiency for antibiotics in the aqueous media.

Competitive adsorption and desorption of tetracycline and sulfadiazine in crop soils

In view of the environmental issues caused by antibiotics, this research studies competitive adsorption/desorption for tetracycline (TC) and sulfadiazine (SDZ) in agricultural soils. Competitive adsorption was studied in binary systems (adding equal concentrations of both antibiotics). In addition, it was compared with results from simple systems. In all cases, batch-type adsorption/desorption experiments were carried out. In the binary systems, for the highest antibiotic concentration added, adsorption percentages were always higher for TC (close to 100%) than for SDZ (10-90%). In these systems, TC desorption was lower than 5% for all soils, and generally <10% for SDZ. Comparing TC and SDZ adsorption for the different systems, SDZ was clearly affected by the presence of TC, with SDZ adsorption percentages being was much higher (with differences generally above 65%) in the binary than in the simple systems. On the contrary, comparing the results of TC adsorption in simple and binary systems, TC was not affected by the presence of SDZ, obtaining similar adsorption percentages in both systems. K_d and K_F values (in the Linear and Freundlich models), were higher in the simple systems in the case of TC, which could be due to competition with SDZ, while for SDZ K_d and K_F were higher in the binary systems, with a synergistic effect of TC favoring SDZ adsorption. Regarding desorption, it reached 100% for SDZ in some soils in simple systems, dropping to 10% in the presence of TC. TC desorption was <4%, not affected by SDZ. The results indicate that environmental risks would be higher for SDZ, showing differences when both antibiotics are present. This can be considered relevant as regards public health and environmental preservation, in view of direct toxicities and the promotion of resistance to antibiotics associated with the presence of these contaminants in the environment.

Non-corresponding contaminants in marine surface sediments as a factor of ARGs spread in the Sea of Azov

The present study aims to analyze the level and total toxicity of the most common pollutants in surface sediments and assess their impact on the occurrence of antibiotic resistance genes (ARGs) in the Sea of Azov. Biotesting using the whole-cell bacterial lux-biosensors showed high integral toxicity of surface sediments and the presence of genotoxicants and substances that cause oxidative stress and protein damage. Using cluster analysis, it was shown that the distribution of pollutants in the Sea of Azov depends on the type of surface sediments. The relative abundance and distribution of 14 ARGs in surface sediments were shown. Principle component analyses results suggest that non-corresponding contaminants do not exert direct influence on the ARGs abundance in the surface sediments of the Sea of Azov. Thus, the need to investigate the significance of non-corresponding pollutants in the selection and distribution of ARGs in the aquatic environment remains a pressing problem.

Effects of ciprofloxacin, trimethoprim, and amoxicillin on microbial structure and growth as emerging pollutants reaching crop soils

The presence of emerging pollutants, and specifically antibiotics, in agricultural soils has increased notably in recent decades, causing growing concern as regards potential environmental and health issues. With this in mind, the current study focuses on evaluating the toxicity exerted by three antibiotics (amoxicillin, trimethoprim, and ciprofloxacin) on the growth of soil bacterial communities, when these pollutants are present at different doses, and considered in the short, medium, and long terms (1, 8 and 42 days of incubation). Specifically, the research was carried out in 12 agricultural soils having different physicochemical characteristics and was performed by means of the leucine (³H) incorporation method. In addition, changes in the structure of soil microbial communities at 8 and 42 days were studied in four of these soils, using the phospholipids of fatty acids method for this. The main results indicate that the most toxic antibiotic was amoxicillin, followed by trimethoprim and ciprofloxacin. The results also show that the toxicity of amoxicillin decreases with time, with values of Log IC₅₀ ranging from 0.07 ± 0.05 to 3.43 ± 0.08 for day 1, from 0.95 ± 0.07 to 3.97 ± 0.15 for day 8, and from 2.05 ± 0.03 to 3.18 ± 0.04 for day 42, during the incubation period. Regarding trimethoprim, 3 different behaviors were observed: for some soils the growth of soil bacterial communities was not affected, for a second group of soils trimethoprim toxicity showed dose-response effects that remained persistent over time, and, finally, for a third group of soils the toxicity of trimethoprim increased over time, being greater for longer incubation times (42 days). As regards ciprofloxacin, this antibiotic did not show a toxicity effect on the growth of soil bacterial communities for any of the soils or incubation times studied. Furthermore, the principal component analysis performed with the phospholipids of fatty acids results demonstrated that the microbial community structure of these agricultural soils, which persisted after 42 days of incubation, depended mainly on soil characteristics and, to a lesser extent, on the dose and type of antibiotic (amoxicillin, trimethoprim or ciprofloxacin). In addition, it was found that, in this research, the application of the three antibiotics to soils usually favored the presence of fungi and Gram-positive bacteria.

Antibiotic resistance in the aquatic environment: Analytical techniques and interactive impact of emerging contaminants

Antibiotic pollution is becoming an increasingly severe threat globally. Antibiotics have emerged as a new class of environmental pollutants due to their expanding usage and indiscriminate application in animal husbandry as growth boosters. Contamination of aquatic ecosystems by antibiotics can have a variety of negative impacts on the microbial flora of these water bodies, as well as lead to the development and spread of antibiotic-resistant genes. Various strategies for removing antibiotics from aqueous systems and environments have been developed. Many of these approaches, however, are constrained by their high operating costs and the generation of secondary pollutants. This review aims to summarize research on the distribution and effects of antibiotics in aquatic environments, their interaction with other emerging contaminants, and their remediation strategy. The ecological risks associated with antibiotics in aquatic ecosystems and the need for more effective monitoring and detection system are also highlighted.

Determination of antimicrobial agents and their transformation products in an agricultural water-soil system modified with manure

Manure fertilization is the primary source of veterinary antimicrobials in the water-soil system. The research gap is the fate of antimicrobials after their release into the environment. This study aimed to provide a detailed and multi-faceted examination of fertilized cultivated fields using two types of manure (poultry and bovine) enriched with selected antimicrobials. The research focused on assessing the mobility and stability of antimicrobials in the water-soil system. Additionally, transformation products of antimicrobials in the environment were identified. The extraction (solid-phase extraction and/or solid-liquid extraction) and LC-MS/MS analysis procedures were developed to determine 14 antimicrobials in the soil and pore water samples. Ten out of fourteen antimicrobials were detected in manure-amended soil and pore water samples. The highest concentration in the soil was 109.1 ng g^-1 (doxycycline), while in pore water, it was 186.6 ng L^-1 (ciprofloxacin). Sixteen transformation products of antimicrobials were identified in the soil and soil-related pore water. The same transformation products were detected in both soil and soil pore water extracts, with significantly higher signal intensities observed in soil extracts than in water. Transformation products were formed in oxidation, carbonylation, and ring-opening reactions.

Impact of eight widely consumed antibiotics on the growth and physiological profile of natural soil microbial communities

Antibiotics' (ATBs) occurrence in soil ecosystems has a relevant effect in the structure and functionality of edaphic microbial communities, mainly because of their amendment with manure and biosolids that alter their key ecological functions. In this study, the impact of eight widely consumed ATBs on a natural soil microbial community, characterized through 16 S rRNA gene sequencing, was evaluated. Changes induced by the ATBs in the growth of the soil microbiota and in the community-level physiological profiling (CLPP), using Biolog EcoPlates™, were measured as endpoint. The eight assayed ATBs lead to a significant decrease in the growth of soil microbial communities in a dose-dependent way, ordered by its effect as follows: chloramphenicol > gentamycin > erythromycin > ampicillin > penicillin > amoxicillin > tetracycline > streptomycin. Chloramphenicol, gentamycin, and erythromycin adversely affected the physiological profile of the soil community, especially its ability to metabolize amino acids, carboxylic and ketonic acids and polymers. The analysis of the relationship between the physico-chemical properties of ATBs, as well as their mechanism of action, revealed that, except for the aminoglycosides, each ATB is influenced by a different physico-chemical parameters, even for ATBs of the same family. Significant effects were detected from 100 μg mL to 1, concentrations that can be found in digested sludge, biosolids and even in fertilized soils after repeated application of manure, so cumulative and long-term effects of these antibiotics on soil environment cannot be ruled out.

Effect of pesticides on nitrification activity and its interaction with chemical fertilizer and manure in long-term paddy soils

Effect of pesticides on nitrification activity and its interaction among heavy metal concentrations (HMCs), antibiotic resistance genes (ARGs), and ammonia monooxygenase (amoA) genes of long-term paddy soils is little known. The aim was to study the effect of pesticides on net nitrification rate (NR), potential nitrification rate (NP), HMCs, ARGs (sulI, sulII, tetO, and tetQ), and amoA (amoA-AOA, amoA-AOB, and amoA-NOB) genes in long-term treated paddy soils. NR and NP were significantly decreased (p < 0.05), whereas HMCs (Pb²⁺, Cu²⁺, Zn²⁺, and Fe³⁺) were a significantly increased (p < 0.05) in chemical fertilizer with pesticide treated paddy soils as compared with chemical fertilizer treated paddy soils. The scatter plot matrix indicated that total carbon (TC), soil organic carbon (SOC), total nitrogen (TN), and Fe were linearly correlated with NR and NP in long-term treated paddy soils. ARGs and amoA genes were significantly decreased (p < 0.05) in chemical fertilizer and manure with pesticide treated paddy soils. Overall, the result indicated the response of pesticide and their combination of manure with pesticide interaction present in long-term paddy soils, which will play a great role in the control uses of pesticides, manure, and chemical fertilizers in paddy soils and protect the nitrogen cycle as well as environment.

Rhodococcus strains as a good biotool for neutralizing pharmaceutical pollutants and obtaining therapeutically valuable products: Through the past into the future

Active pharmaceutical ingredients present a substantial risk when they reach the environment and drinking water sources. As a new type of dangerous pollutants with high chemical resistance and pronounced biological effects, they accumulate everywhere, often in significant concentrations (μg/L) in ecological environments, food chains, organs of farm animals and humans, and cause an intense response from the aquatic and soil microbiota. Rhodococcus spp. (Actinomycetia class), which occupy a dominant position in polluted ecosystems, stand out among other microorganisms with the greatest variety of degradable pollutants and participate in natural attenuation, are considered as active agents with high transforming and degrading impacts on pharmaceutical compounds. Many representatives of rhodococci are promising as unique sources of specific transforming enzymes, quorum quenching tools, natural products and novel antimicrobials, biosurfactants and nanostructures. The review presents the latest knowledge and current trends regarding the use of Rhodococcus spp. in the processes of pharmaceutical pollutants’ biodegradation, as well as in the fields of biocatalysis and biotechnology for the production of targeted pharmaceutical products. The current literature sources presented in the review can be helpful in future research programs aimed at promoting Rhodococcus spp. as potential biodegraders and biotransformers to control pharmaceutical pollution in the environment.

The evolution of spectrum in antibiotics and bacteriocins

A key property of many antibiotics is that they will kill or inhibit a diverse range of microbial species. This broad-spectrum of activity has its evolutionary roots in ecological competition, whereby bacteria and other microbes use antibiotics to suppress other strains and species. However, many bacteria also use narrow-spectrum toxins, such as bacteriocins, that principally target conspecifics. Why has such a diversity in spectrum evolved? Here, we develop an evolutionary model to understand antimicrobial spectrum. Our first model recapitulates the intuition that broad-spectrum is best, because it enables a microbe to kill a wider diversity of competitors. However, this model neglects an important property of antimicrobials: They are commonly bound, sequestered, or degraded by the cells they target. Incorporating this toxin loss reveals a major advantage to narrow-spectrum toxins: They target the strongest ecological competitor and avoid being used up on less important species. Why then would broad-spectrum toxins ever evolve? Our model predicts that broad-spectrum toxins will be favored by natural selection if a strain is highly abundant and can overpower both its key competitor and other species. We test this prediction by compiling and analyzing a database of the regulation and spectrum of toxins used in inter-bacterial competition. This analysis reveals a strong association between broad-spectrum toxins and density-dependent regulation, indicating that they are indeed used when strains are abundant. Our work provides a rationale for why bacteria commonly evolve narrow-spectrum toxins such as bacteriocins and suggests that the evolution of antibiotics proper is a signature of ecological dominance.

Visible-Light-Driven Photocatalytic Degradation of Tetracycline Using Heterostructured Cu2O-TiO2 Nanotubes, Kinetics, and Toxicity Evaluation of Degraded Products on Cell Lines

This study first reports on the tetracycline photodegradation with the synthesized heterostructured titanium oxide nanotubes coupled with cuprous oxide photocatalyst. The large surface area and more active sites on TiO₂ nanotubes with a reduced band gap (coupling of Cu₂O) provide faster photodegradation of tetracycline under visible light conditions. Cytotoxicity experiments performed on the RAW 264.7 (mouse macrophage) and THP-1 (human monocytes) cell lines of tetracycline and the photodegraded products of tetracycline as well as quenching experiments were also performed. The effects of different parameters like pH, photocatalyst loading concentration, cuprous oxide concentration, and tetracycline load on the photodegradation rate were investigated. With an enhanced surface area of nanotubes and a reduced band gap of 2.58 eV, 1.5 g/L concentration of 10% C-TAC showed the highest efficiency of visible-light-driven photodegradation (∼100% photodegradation rate in 60 min) of tetracycline at pH 5, 7, and 9. The photodegradation efficiency is not depleted up to five consecutive batch cycles. Quenching experiments confirmed that superoxide radicals and hydroxyl radicals are the most involved reactive species in the photodegradation of tetracycline, while valance band electrons are the least involved reactive species. The cytotoxicity percentage of tetracycline and its degraded products on RAW 264.7 (-0.932) as well as THP-1 (-0.931) showed a negative correlation with the degradation percentage with a p-value of 0.01. The toxicity-free effluent of photodegradation suggests the application of the synthesized photocatalyst in wastewater treatment.

NaCl salinity enhances tetracycline bioavailability to Escherichia coli on agar surfaces

Soil salinity is a worldwide problem and is damaging soil functions. Meanwhile, increasing amounts of anthropogenic antibiotics are discharged to agricultural soils. Little is known about how soil salinity (e.g., NaCl) could influence the bioavailability of antibiotics to bacteria. In this study, a tetracycline-responsive Escherichia coli bioreporter grew on the surfaces of agar microcosms at the same tetracycline concentration (200 μg/L), but various NaCl concentrations (0.5-19.2 g/L) with estimated osmotic potential of -0.18 to -1.80 MPa, and agar content (0.3%-5%) with estimated intrinsic permeability of 38 to 32,928 nm². These agar microcosms mimicked very fine textured soils with a range of NaCl salinity. Increasing agar content lowered the intrinsic permeability hence decreasing tetracycline bioavailability to E. coli, due likely to the reduced mass transfer of tetracycline via water flow. Intriguingly, tetracycline bioavailability increased with increasing NaCl concentration which caused the increase in osmotic stress. This is contradictory to the notion that osmotic stress reduces bacterial chemical uptake. Further analysis of E. coli membrane integrity demonstrated that the enhanced tetracycline bioavailability to bacteria could result from the compromised cell membranes and enhanced membrane permeability at higher NaCl salinity. Overall, this study suggests that high soil salinity (NaCl) may enhance the selection pressure exerted by antibiotics on bacteria.

Globally distributed mining-impacted environments are underexplored hotspots of multidrug resistance genes

Mining is among the human activities with widest environmental impacts, and mining-impacted environments are characterized by high levels of metals that can co-select for antibiotic resistance genes (ARGs) in microorganisms. However, ARGs in mining-impacted environments are still poorly understood. Here, we conducted a comprehensive study of ARGs in such environments worldwide, taking advantage of 272 metagenomes generated from a global-scale data collection and two national sampling efforts in China. The average total abundance of the ARGs in globally distributed studied mine sites was 1572 times per gigabase, being rivaling that of urban sewage but much higher than that of freshwater sediments. Multidrug resistance genes accounted for 40% of the total ARG abundance, tended to co-occur with multimetal resistance genes, and were highly mobile (e.g. on average 16% occurring on plasmids). Among the 1848 high-quality metagenome-assembled genomes (MAGs), 85% carried at least one multidrug resistance gene plus one multimetal resistance gene. These high-quality ARG-carrying MAGs considerably expanded the phylogenetic diversity of ARG hosts, providing the first representatives of ARG-carrying MAGs for the Archaea domain and three bacterial phyla. Moreover, 54 high-quality ARG-carrying MAGs were identified as potential pathogens. Our findings suggest that mining-impacted environments worldwide are underexplored hotspots of multidrug resistance genes.

Meta-analysis and machine learning to explore soil-water partitioning of common pharmaceuticals

The first meta-analysis and modelling from batch-sorption literature studies of the soil/water partitioning of pharmaceuticals is presented. Analysis of the experimental conditions reported in the literature demonstrated that though batch-sorption studies have value, they are limited in evaluating partitioning under environmentally-relevant conditions. Recommendations are made to utilise environmental relevant pharmaceutical concentrations, perform batch-sorption studies at temperatures other than 4, 20 and 25 °C to better reflect climate diversity, and utilise the Guideline 106 methodology as a benchmark to enable comparison between future studies (and support modelling and prediction). The meta-dataset comprised 82 data points, which were modelled using multivariate analysis; where K_d (soil/water partitioning coefficient) was the independent variable. The dependent variables fit into three categories: 1) pharmaceutical studied (including physical-chemical properties), 2) soil characteristics and 3) experimental conditions. The pharmaceutical solubility, the soil/liquid equilibration time (prior to adding the pharmaceutical), the soil organic carbon, the soil sterilisation method and the liquid phase were found to be significantly important variables for predicting K_d.

Migration and toxicity of toltrazuril and its main metabolites in the environment

Veterinary drugs heavily used in livestock are passed into the environment through different ways, resulting in risks to terrestrial environments and humans. The migration of toltrazuril (TOL), an important anticoccidial drug used intensively in livestock, and its main metabolites between the chicken manure compost, soil and vegetables was investigated, and then the impacts of TOL on the soil bacterial community and ARGs, soil enzyme activities and phytotoxicity were detected. In the process of aerobic composting for 80 days, except for toltrazuril sulfoxide (the degradation half-life was 59.74 d), TOL and ponazuril (PON) were not significantly degraded. However, TOL and its metabolites were significantly degraded in fertilized soil, and the degradation half-life was 28.17-346.50 d. Among the three drugs, only PON could migrate from soil to vegetables, and the residual concentrations of PON in lettuce and radish were 2.64-70.02 μg kg-1 and 0-2.80 μg kg-1, respectively. Moreover, TOL and its main metabolisms had no significant effect on the bacterial community structure and the abundance of antibiotic resistance genes during composting, but affected the microbial activity in the soil. The presence of TOL and its main metabolites reduced soil urease activity, increased catalase activity, and decreased alkaline phosphatase activity at the beginning and then increased slightly. They had negative effects on plant growth. Compared with the control group, the inhibition rates of TOL and its metabolites on lettuce and radish seed germination were 8.33% and 26.74% respectively, and the inhibition rates of root elongation length were 25.88% and 34.45% respectively. These results showed that TOL and its main metabolites were ineffectively removed by aerobic composting, and could be migrated from composting to soil and vegetables, which had adverse effects on soil enzyme activity and plant growth. Therefore, its environmental ecological risk and human health risk needs to be further evaluated.

Distribution and ecological risks of pharmaceuticals and personal care products with different anthropogenic stresses in a coastal watershed of China

The occurrences of pharmaceutical and personal care products (PPCPs) in both freshwater and sea have been widely reported. However, pollution control requires further information on riverine discharges with influence of land-based activities and associated risks to estuarine ecosystems. This study investigated the spatial occurrences and the relationship to sociodemographic parameters of 30 PPCPs in 67 rivers along the Bohai coastal region. The results showed that PPCPs were mainly deposited in aquatic phase, and the partitioning coefficient between water and sediment was highly determined by chemical properties. The levels of 30 PPCPs in rivers ranged from 8.33 to 894.48 ng/L, showing a large variance among regions. Caffeine, sulfamethoxazole, sulfamethazine, ofloxacin, anhydro-erythromycin, and trimethoprim were found to be the major pollutants. Multivariable analysis method was used to assess the correlation of PPCPs markers to socio-economic parameters. The results indicated that domestic emissions contributed most to the occurrences of PPCPs in the riverine water. Risk assessment result indicated that sulfamethoxazole, caffeine, tetracycline, and carbamazepine ranked top four with the highest risks to the most sensitive aquatic organisms. The results identified caffeine and carbamazepine with high detection frequency and concentration as the priority chemicals, while sulfamethoxazole and erythromycin should also be concerned due to their potential threats in specific rivers. This study provides valuable information for pollution control over PPCPs riverine discharges in estuarine regions.

Insights into the Bacterial Diversity and Detection of Opportunistic Pathogens in Mexican Chili Powder

Chili powder is the most frequently consumed spice in Mexican diets. Thus, the dissemination of microorganisms associated with chili powder derived from Capsicum annuum L. is significant during microbial quality analysis, with special attention on detection of potential pathogens. The results presented here describe the initial characterization of bacterial community structure in commercial chili powder samples. Our results demonstrate that, within the domain Bacteria, the most abundant family was Bacillaceae, with a relative abundance of 99% in 71.4% of chili powder samples, while 28.6% of samples showed an average relative abundance of 60% for the Enterobacteriaceae family. Bacterial load for aerobic mesophilic bacteria (AMB) ranged from 10⁴ to 10⁶ cfu/g, while for sporulated mesophilic bacteria (SMB), the count ranged from 10² to 10⁵ cfu/g. Bacillus cereus sensu lato (s.l.) was observed at ca. ˂600 cfu/g, while the count for Enterobacteriaceae ranged from 10³ to 10⁶ cfu/g, Escherichia coli and Salmonella were not detected. Fungal and yeast counts ranged from 10² to 10⁵ cfu/g. Further analysis of the opportunistic pathogens isolated, such as B. cereus s.l. and Kosakonia cowanii, using antibiotic-resistance profiles and toxinogenic characteristics, revealed the presence of extended-spectrum β-lactamases (ESBLs) and Metallo-β-lactamases (MBLs) in these organisms. These results extend our knowledge of bacterial diversity and the presence of opportunistic pathogens associated with Mexican chili powder and highlight the potential health risks posed by its use through the spread of antibiotic-resistance and the production of various toxins. Our findings may be useful in developing procedures for microbial control during chili powder production.

Resistance towards Critically Important Antimicrobials among Enterococcus faecalis and E. faecium in Poultry Farm Environments in Selangor, Malaysia

Multidrug resistant (MDR) enterococci pose significant public health challenges. However, the extent of resistance in the environment is less explored. This study aimed to determine the antibiotic resistance in a poultry farm environment. Eighty enterococcal isolates recovered from the soil and effluent water of 28 poultry farms in Selangor state were included in the study for further bacterial identification and antibiotic susceptibility testing using a VITEK 2 system. Data were analyzed using Statistical Package for Social Science (SPSS) version 27. The resistance rate and MDR of enterococcal isolates were reported. Out of 80 isolates recovered, 72 (90%) exhibited resistance to at least one antibiotic, with 50 isolates (62.5%) being found to be MDR. All linezolid-resistant enterococci (LRE) exhibit MDR, which constituted 40% of resistance among all the isolates recovered from poultry environment. Since linezolid is listed as critically important antibiotics for clinical use by the World Health Organization (WHO), the higher resistance towards it and other critically important antibiotic for human use is a serious concern. Hence, relevant agencies need to investigate the use of clinically important antimicrobials in poultry farms paying special attention towards linezolid or any other antibiotics that can facilitate the development of LRE.

The formation of specific bacterial communities contributes to the enrichment of antibiotic resistance genes in the soil plastisphere

Soil serves as a major reservoir of both antibiotic resistance genes (ARGs) and microplastics. However, the characteristics of the antibiotic resistome in the soil plastisphere remain largely unknown. In this study, we used metagenomic approaches to reveal the changing patterns of ARGs and the bacterial community and their associations in response to three types of microplastics (light density polyethylene, LDPE; polypropylene, PP; polystyrene, PS) using particles 550 µm or 75 µm in diameter. The total ARG abundances significantly increased in the plastisphere and varied across plastic types. The LDPE plastisphere had the highest ARG total abundance and lowest Shannon diversity index, indicating that this plastic had the most severe negative impact on soil bacterial diversity. The PP plastisphere contained higher relative abundances of the pathogenic bacteria Acinetobacter johnsonii and Escherichia coli, demonstrating the higher pathogenic risk of the microbial communities enriched in the plastisphere. Specifically, multidrug resistance genes (ceoB and MuxB) co-existed with more than four microbial taxa, increasing the potential risk of ARG spread in pathogenic bacteria. These findings implied that the plastisphere acts as a hotspot for acquiring and spreading antibiotic resistance and may have long-term negative effects on the soil ecosystem and human health.

Occurrence of antibiotics in Lettuce (Lactuca sativa L.) and Radish (Raphanus sativus L.) following organic soil fertilisation under plot-scale conditions: Crop and human health implications

Recent studies have demonstrated the crop uptake of antibiotics (ABs) from soils treated with AB-carrying fertilisers. However, there is a lack of plot-scale studies linking their effects at the agronomic and metabolomic/transcriptomic level to their impact on human health. This paper assesses the plant uptake of 23 ABs following two productive cycles of lettuce and radish cropped with sewage sludge, pig slurry, the organic fraction of municipal solid waste, or chemical fertilisation under plot-scale conditions (32 plots spanning 3-10 m2 each). AB uptake by plants depended on both the vegetable and the AB class and was higher in radish than in lettuce edible parts. Levels ranged from undetectable to up to 76 ng/g (fresh weight). Repetitive organic fertilisation resulted in an increase in the concentration of ABs in lettuce leaves, but not in radish roots. Significant metabolomic and transcriptomic changes were observed following soil fertilisation. Nevertheless, a human health risk assessment indicates that the occurrence of ABs in lettuce or radish edible parts does not pose any risk. To our knowledge, this is the first holistic plot-scale study demonstrating that the use of organic fertilisers containing ABs is safe for crop security and human health.

Effects of litter from antimicrobial-fed broiler chickens on soil bacterial community structure and diversity

This study examined changes in soil bacterial community composition and diversity in response to fertilization with litter from chickens fed diet with no antibiotics, bambermycin, penicillin, bacitracin, salinomycin, and mix of salinomycin and bacitracin. Litter was applied to 24 agricultural-plots. Non-fertilized plots were used as a negative control. Soil samples collected from the studied plots were used to quantify Escherichia coli by plate counts, and Clostridium perfringens by qPCR. The 16S-rRNA gene sequencing was performed for microbiota analysis. Following litter application in December, the population size of E.coli was 5.4 log CFU/g, however, regardless of treatments the result revealed 5.2 and 1.4 log CFU/g of E.coli in soil sampled in January and March, respectively. Fertilization with antibiotic treated litter increased (P < 0.05) the relative abundance of Proteobacteria, Actinobacteria and Firmicutes in soil, but decreased Acidobacteria and Verrucomicrobia groups. The alpha-diversity parameters were higher (P < 0.05) in non-fertilized soil compared to the fertilized ones, suggesting that litter application was a major factor in shaping the soil bacterial communities. These results may help develop efficient litter management strategies like composting, autoclaving, or anaerobic digestion of poultry litter before application to land for preservation of soil health and crop productivity.

Excreted Antibiotics May Be Key to Emergence of Increasingly Efficient Antibiotic Resistance in Food Animal Production

At a time when antibiotic resistance is seemingly ubiquitous worldwide, understanding the mechanisms responsible for successful emergence of new resistance genes may provide insights into the persistence and pathways of dissemination for antibiotic-resistant organisms in general. For example, Escherichia coli strains harboring a class A β-lactamase-encoding gene (bla_CTX-M-15) appear to be displacing strains that harbor a class C β-lactamase gene (bla_CMY-2) in Washington State dairy cattle. We cloned these genes with native promoters into low-copy-number plasmids that were then transformed into isogenic strains of E. coli, and growth curves were generated for two commonly administered antibiotics (ampicillin and ceftiofur). Both strains met the definition of resistance for ampicillin (≥32 μg/mL) and ceftiofur (≥16 μg/mL). Growth of the CMY-2-producing strain was compromised at 1,000 μg/mL ampicillin, whereas the CTX-M-15-producing strain was not inhibited in the presence of 3,000 μg/mL ampicillin or with most concentrations of ceftiofur, although there were mixed outcomes with ceftiofur metabolites. Consequently, in the absence of competing genes, E. coli harboring either gene would experience a selective advantage if exposed to these antibiotics. Successful emergence of CTX-M-15-producing strains where CMY-2-producing strains are already established, however, requires high concentrations of antibiotics that can only be found in the urine of treated animals (e.g., >2,000 μg/mL for ampicillin, based on literature). This ex vivo selection pressure may be important for the emergence of new and more efficient antibiotic resistance genes and likely for persistence of antibiotic-resistant bacteria in food animal populations. IMPORTANCE We studied the relative fitness benefits of a cephalosporin resistance enzyme (CTX-M-15) that is displacing a similar enzyme (CMY-2), which is extant in E. coli from dairy cattle in Washington State. In vitro experiments demonstrated that CTX-M-15 provides a significant fitness advantage, but only in the presence of very high concentrations of antibiotic that are only found when the antibiotic ampicillin, and to a lesser extent ceftiofur, is excreted in urine from treated animals. As such, the increasing prevalence of bacteria with bla_CTX-M-15 is likely occurring ex vivo. Interventions should focus on controlling waste from treated animals and, when possible, selecting antibiotics that are less likely to impact the proximal environment of treated animals.

Effect of Biochar Modification by Vitamin C, Hydrogen Peroxide or Silver Nanoparticles on Its Physicochemistry and Tetracycline Removal

Chemical modification of biochars can improve their adsorption capacity relative to antibiotics, posing a serious threat to the environment. Therefore, this research is aimed at the treatment of sunflower husk biochar (BC) by vitamin C, hydrogen peroxide or silver nanoparticles and the impact of this procedure on the biochar porosity, surface chemistry, and ability to remove tetracycline (TC). During the study, BC was produced by pyrolysis of sunflower husks at 650 °C. All solids were characterized using potentiometric titration, nitrogen adsorption/desorption, Fourier transform infrared spectroscopy, etc. The experimental adsorption data was described by kinetics equations: pseudo-first order, pseudo-second order, and particle internal diffusion (IPD) models as well as by isotherms of Langmuir, Langmuir-Freundlich, and Redlich-Peterson. The obtained results indicated that the biochar upgraded by vitamin C (BCV) had the highest ability to attract antibiotic molecules and, as a result, the TC adsorption on its surface was the largest. Furthermore, the TC desorption from this material was minimal. The measured TC adsorbed amounts for the modified BCs were as follows: 47.75% (7.47 mg/g) for BCV, 37.35% (8.41 mg/g)-for biochar treated by hydrogen peroxide (BCH), and 42.04% (9.55 mg/g) for biochar modified by silver nanoparticles (BCA). The lowest adsorption level was noted for non-modified biochar, i.e., 34.17% (6.83 mg/g). Based on the presented results it can be stated that the upgraded biochars had a good potential to improve the tetracycline removal from aqueous media, e.g., groundwater.

Identifying the spatiotemporal vulnerability of soils to antimicrobial contamination through land application of animal manure in Minnesota, United States

Antimicrobials may reach the soil environment from a variety of sources and pathways, including land application of human biosolids and animal manure. Once in soil, antimicrobials can affect the abundance and activity of soil microorganisms and exert selection pressures that enhance the emergence and spread of antimicrobial resistance (AMR). To mitigate the spread of AMR it is important to understand the spatial and temporal interactions between antimicrobials and soil. The goal of this study was to assess the vulnerability of Minnesota (U.S.) soil to contamination with specific antimicrobial compounds at temperatures experienced throughout the year. Soil contamination potential was estimated based upon specific antimicrobial drug binding and permanence, and average monthly temperature. Minnesota soil vulnerability was estimated by incorporating spatially explicit soil contamination potential, land cover type, and livestock density. Assessment of antimicrobials used in livestock production showed that soils are most vulnerable to antimicrobial contamination in southwestern Minnesota, to enrofloxacin, chlortetracycline, and oxytetracycline, and in the months of April and October. While the assessment herein was not based on actual on-farm antimicrobial use data and subsequent excretion of antimicrobial metabolites into the environment, this study provides an overview of the spatial and temporal potential for Minnesota soil to be contaminated by several antimicrobial drugs and demonstrates how specific vulnerability assessments might be conducted for geographic areas with known exposure (e.g., cropland fertilized with livestock manure and/or human biosolids). Such assessments might be used to identify best practices for mitigating antimicrobial exposure to soils and guide additional research to understand the role of environmental antimicrobial contamination in the problem of AMR.

Synthetic organic antibiotics residues as emerging contaminants waste-to-resources processing for a circular economy in China: Challenges and perspective

Synthetic antibiotics have been known for years to combat bacterial antibiotics. But their overuse and resistance have become a concern recently. The antibiotics reach the environment, including soil from the manufacturing process and undigested excretion by cattle and humans. It leads to overburden and contamination of the environment. These organic antibiotics remain in the environment for a very long period. During this period, antibiotics come in contact with various flora and fauna. The ill manufacturing practices and inadequate wastewater treatment cause a severe problem to the water bodies. After pretreatment from pharmaceutical industries, the effluents are released to the water bodies such as rivers. Even after pretreatment, effluents contain a significant number of antibiotic residues, which affect the living organisms living in the water bodies. Ultimately, river contaminated water reaches the ocean, spreading the contamination to a vast environment. This review paper discusses the impact of synthetic organic contamination on the environment and its hazardous effect on health. In addition, it analyzes and suggests the biotechnological strategies to tackle organic antibiotic residue proliferation. Moreover, the degradation of organic antibiotic residues by biocatalyst and biochar is analyzed. The circular economy approach for waste-to-resource technology for organic antibiotic residue in China is analyzed for a sustainable solution. Overall, the significant challenges related to synthetic antibiotic residues and future aspects are analyzed in this review paper.

Degrading Characterization of the Newly Isolated Nocardioides sp. N39 for 3-Amino-5-methyl-isoxazole and the Related Genomic Information

3-amino-5-methyl-isoxazole (3A5MI) is a persistent and harmful intermediate in the degradation of antibiotic sulfamethoxazole. It was accumulated in the environments day by day and has caused great environmental risks due to its refractory characteristic. Microbial degradation is economic and environmentally friendly and a promising method to eliminate this pollutant. In this study, a bacterial strain, Nocardioides sp. N39, was isolated. N39 can grow on 3A5MI as the sole carbon, nitrogen and energy resource. The effect of different factors on 3A5MI degradation by N39 was explored, including initial 3A5MI concentration, temperature, pH value, dissolved oxygen and additional carbon or nitrogen source. The degradation ability of N39 to various 3A5MI analogs was also explored. Nevertheless, the degrading ability of N39 for 3A5MI is not permanent, and long-term storage would lead to the loss of this ability. This may result from the mobile genetic elements in the bacterium according to the genomic comparison of N39 and its degrading ability-lost strain, N40. Despite this, N39 could support a lot of useful information about the degradation of 3A5MI and highlight the importance of studies about the environmental effects and potential degradation mechanism.

Transformation products of sulfonamides in aquatic systems: Lessons learned from available environmental fate and behaviour data

Sulfonamides (SUAs) and their transformation products (TPs) contribute to environmental pollution. Importance of research on TPs' properties has been emphasised, e.g. allowing a comprehensive environmental risk assessment of their parent compounds. However, TPs' properties have been discussed in reviews on SUAs only marginally, if at all. For the first time, a scientific literature review aims to discuss the current state of knowledge on SUA-TPs including research gaps, and commonalities of SUA-TPs and TPs in general. Literature on SUA-TPs was consulted systematically to collect data on occurrence, physicochemical properties, degradability, and (eco)toxicity. TPs of 14 SUAs were reviewed, and aspects applicable for TPs in general were identified to guide future handling of TPs as a complex category of compounds. The data of sulfamethoxazole (SMX), the main representative, was analysed in more detail to discuss insights on a chemical level. Literature search resulted in 607 SUA-TPs reported in 222 publications. Only for 4%, 31%, and 35% of these TPs, data on occurrence in aquatic systems, on degradation, and (eco)toxicity, respectively, was found. Several mixtures of SUA-TPs were more ecotoxic than their parent compounds, e.g. 10 of 15 mixtures of SMX-TPs. Only few TPs were tested as single substance. Although several TPs could be eliminated experimentally, their mineralisation rate remained often unknown. Thus, further transformation to persistent TPs could not be ruled out. Standardised biodegradability tests of individual TPs would monitor their mineralisation rate, but are almost completely lacking. Reasons are likely poor availability of TPs, but also the focus on abiotic water treatment. Data assessment demonstrated that data of high significance according to standard methods, e.g. OECD methods for chronic (eco)toxicity and ready biodegradability, is needed to assess environmental risks of prioritised TPs, but also to redesign their parent pharmaceutical for complete environmental mineralisation in a long-term (Benign by Design).

Dynamics of the Gut Microbiome and Transcriptome in Korea Native Ricefish (Oryzias latipes) during Chronic Antibiotic Exposure

Antibiotics have been widely used to inhibit microbial growth and to control bacterial infection; however, they can trigger an imbalance in the gut flora of the host and dysregulate the host gene regulatory system when discharged into the aquatic environment. We investigated the effects of chronic exposure to a low concentration of erythromycin and ampicillin, focusing on gut microbiome and global gene expression profiles from Korea native ricefish (Oryzias latipes). The proportion of Proteobacteria (especially the opportunistic pathogen Aeromonas veronii) was significantly increased in the ricefish under the chronic exposure to erythromycin and ampicillin, whereas that of other bacterial phyla (i.e., Fusobacteria) decreased. In addition, the expression of genes involved in immune responses such as chemokines and immunocyte chemotaxis was significantly influenced in ricefish in the aquatic environment with antibiotics present. These results show that the internal microbial flora and the host gene expression are susceptible even at a low concentration of chronic antibiotics in the environment, supporting the importance of the appropriate use of antibiotic dose to maintain the sustainable and healthy aquaculture industry and water ecosystem.

Novel and simple analytical method for simultaneous determination of sulfonamide, quinolone, tetracycline, macrolide, and chloramphenicol antibiotics in soil

The multiclass determination of antibiotic residues in the soil is challenging because of its complex physicochemical properties. In this study, a simple analytical method was developed to simultaneously extract and determine 58 antibiotics from the soil. A novel acidity-regulated extraction-partition-concentration protocol was established for the simultaneous extraction of five classes (23 sulfonamides, 18 quinolones, five tetracyclines, eight macrolides, and four chloramphenicols) of antibiotics from the soil. Compared to traditional methods, the sample preparation efficiency was significantly improved by four times (45 min vs. 230 min) by optimizing the extraction method and omitting the time-consuming solid-phase extraction (SPE) procedure. The ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method was optimized to determine the 58 antibiotics in a single run by applying positive/negative switching acquisition mode in less than 10 min with the baseline separation of sulfameter and sulfamethoxypyridazine. Suitable recoveries, ranging between 60 and 120%, were obtained for most antibiotics, with RSD <20%. The limits of quantification (LOQ) of the method were 2 μg/kg and 5 μg/kg. Thus, this study provides a simple, reliable, and economical method for accurately and rapidly determining a multiclass of antibiotics in the soil.

Impact of Antibiotics as Waste, Physical, Chemical, and Enzymatical Degradation: Use of Laccases

The first traces of Tetracycline (TE) were detected in human skeletons from Sudan and Egypt, finding that it may be related to the diet of the time, the use of some dyes, and the use of soils loaded with microorganisms, such as Streptomyces spp., among other microorganisms capable of producing antibiotics. However, most people only recognise authors dating between 1904 and 1940, such as Ehrlich, Domagk, and Fleming. Antibiotics are the therapeutic option for countless infections treatment; unfortunately, they are the second most common group of drugs in wastewaters worldwide due to failures in industrial waste treatments (pharmaceutics, hospitals, senior residences) and their irrational use in humans and animals. The main antibiotics problem lies in delivered and non-prescribed human use, use in livestock as growth promoters, and crop cultivation as biocides (regulated activities that have not complied in some places). This practice has led to the toxicity of the environment as antibiotics generate eutrophication, water pollution, nutrient imbalance, and press antibiotic resistance. In addition, the removal of antibiotics is not a required process in global wastewater treatment standards. This review aims to raise awareness of the negative impact of antibiotics as residues and physical, chemical, and biological treatments for their degradation. We discuss the high cost of physical and chemical treatments, the risk of using chemicals that worsen the situation, and the fact that each antibiotic class can be transformed differently with each of these treatments and generate new compounds that could be more toxic than the original ones; also, we discuss the use of enzymes for antibiotic degradation, with emphasis on laccases.

Occurrence of antibiotics and bacterial resistance genes in wastewater: resistance mechanisms and antimicrobial resistance control approaches

Antimicrobial pharmaceuticals are classified as emergent micropollutants of concern, implying that even at low concentrations, long-term exposure to the environment can have significant eco-toxicological effects. There is a lack of a standardized regulatory framework governing the permissible antibiotic content for monitoring environmental water quality standards. Therefore, indiscriminate discharge of antimicrobials at potentially active concentrations into urban wastewater treatment facilities is rampant. Antimicrobials may exert selective pressure on bacteria, leading to resistance development and eventual health consequences. The emergence of clinically important multiple antibiotic-resistant bacteria in untreated hospital effluents and wastewater treatment plants (WWTPs) has been linked to the continuous exposure of bacteria to antimicrobials. The levels of environmental exposure to antibiotics and their correlation to the evolution and spread of resistant bacteria need to be elucidated to help in the formulation of mitigation measures. This review explores frequently detected antimicrobials in wastewater and gives a comprehensive coverage of bacterial resistance mechanisms to different antibiotic classes through the expression of a wide variety of antibiotic resistance genes either inherent and/or exchanged among bacteria or acquired from the reservoir of antibiotic resistance genes (ARGs) in wastewater systems. To complement the removal of antibiotics and ARGs from WWTPs, upscaling the implementation of prospective interventions such as vaccines, phage therapy, and natural compounds as alternatives to widespread antibiotic use provides a multifaceted approach to minimize the spread of antimicrobial resistance.

The Role of Grass Compost and Zea Mays in Alleviating Toxic Effects of Tetracycline on the Soil Bacteria Community

Given their common use for disease treatment in humans, and particularly in animals, antibiotics pose an exceptionally serious threat to the soil environment. This study aimed to determine the response of soil bacteria and oxidoreductases to a tetracycline (Tc) contamination, and to establish the usability of grass compost (G) and Zea mays (Zm) in mitigating adverse Tc effects on selected microbial properties of the soil. The scope of microbiological analyses included determinations of bacteria with the conventional culture method and new-generation sequencing method (NGS). Activities of soil dehydrogenases and catalase were determined as well. Tc was found to reduce counts of organotrophic bacteria and actinobacteria in the soils as well as the activity of soil oxidoreductases. Soil fertilization with grass compost (G) and Zea mays (Zm) cultivation was found to alleviate the adverse effects of tetracycline on the mentioned group of bacteria and activity of oxidoreductases. The metagenomic analysis demonstrated that the bacteria belonging to Acidiobacteria and Proteobacteria phyla were found to prevail in the soil samples. The study results recommend soil fertilization with G and Zm cultivation as successful measures in the bioremediation of tetracycline-contaminated soils and indicate the usability of the so-called core bacteria in the bioaugmentation of such soils.

Antimicrobial Resistance in New Zealand-A One Health Perspective

Antimicrobial resistance (AMR) is an increasing global threat that affects human, animal and, often less acknowledged, environmental health. This complex issue requires a multisectoral One Health approach to address the interconnectedness of humans, animals and the natural environment. The prevalence of AMR in these reservoirs varies widely among countries and thus often requires a country-specific approach. In New Zealand (NZ), AMR and antimicrobial usage in humans are relatively well-monitored and -understood, with high human use of antimicrobials and the frequency of resistant pathogens increasing in hospitals and the community. In contrast, on average, NZ is a low user of antimicrobials in animal husbandry systems with low rates of AMR in food-producing animals. AMR in New Zealand’s environment is little understood, and the role of the natural environment in AMR transmission is unclear. Here, we aimed to provide a summary of the current knowledge on AMR in NZ, addressing all three components of the One Health triad with a particular focus on environmental AMR. We aimed to identify knowledge gaps to help develop research strategies, especially towards mitigating AMR in the environment, the often-neglected part of the One Health triad.

Impact of fertilization with pig or calf slurry on antibiotic residues and resistance genes in the soil

Antibiotic residues and antibiotic resistance genes can enter the environment via fertilization with calf and pig manure. In a longitudinal study, nine antibiotic resistance genes (tet(B), tet(L), tet(M), tet(O), tet(Q), tet(W), erm(B), erm(F) and sul2) and 56 antibiotic residues were investigated in 288 soil samples and 8 corresponding slurry samples from 6 pig farms and 2 veal farms using qPCR and LC-MS/MS, respectively. A significant increase in gene copy number of tet(M), erm(B), erm(F) and sul2 was observed in all the soil layers between sampling times prior to (T1) and 2-3 weeks after fertilization (T3). Tet(B), tet(Q) and tet(L) were least abundant in the soil among the genes tested. From 7 classes of antibiotics, 20 residues were detected in soil and slurry using an optimized and validated extraction method. Flumequine was detected in all soil samples in concentrations below 100 μg/kg despite being detected in only half of the corresponding slurry samples. Doxycycline, oxytetracycline, lincomycin and sulfadiazine were also frequently detected in concentrations ranging from 0.1 μg/kg to 500 μg/kg and from 2 μg/kg and 9480 μg/kg in soil and slurry, respectively. Furthermore a positive association between the presence of antibiotic residues (total antibiotic load) and antibiotic resistance genes in soil was found. One possible explanation for this is a simultaneous introduction of antibiotic residues and resistance genes upon application of animal slurry.

The fate of erythromycin in soils and its effect on soil microbial community structure

Erythromycin is one of the most commonly used macrolide antibiotics. However, little is known currently about the environmental behavior and fate of erythromycin in soils. Here erythromycin was ¹⁴C-labeled to investigate its degradation, mineralization and bound residues (BRs) in three typical agricultural soils. Results indicated the fate of ¹⁴C-erythromycin in soils varied greatly with soils types. Erythromycin was rapidly mineralized in black soil (BS) and fluvo-aquic soil (FS), whereas it rapidly formed large amounts of BRs in red soil (RS) with slow mineralization. At 120 d, about 90% of the introduced ¹⁴C-erythromycin was mineralized as ¹⁴CO₂ in BS and FS, but only 30% in RS. There was still a certain proportion of BRs in all soils, especially in RS, up to 50%. Erythromycin residues (ERs) may be underestimated if its residues are only assessed by extractable residues. We recommend to include a practical silylation procedure to quantify Type I BRs in regular erythromycin residue monitoring, which can be used as signal of the need to initiate further laboratory BRs experiments. The degradation of erythromycin was mainly attributed to soil microorganisms, which promote erythromycin mineralization and lead to the re-release of BRs. Microbial analysis showed that erythromycin persisted longer in soils with lower microbial diversity and richness. Erythromycin at 2.5 mg kg^-1 showed no significant impact on soil microbial diversity in all treatments, but caused changes in soil community composition. This study provides a reference for scientific evaluation and pollution remediation of erythromycin in soils.

Following the route of veterinary antibiotics tiamulin and tilmicosin from livestock farms to agricultural soils

Veterinary antibiotics (VAs) are not completely metabolized in the animal body. Hence, when animal excretes are used as soil manures, VA residues are dispersed with potential implications for environmental quality and human health. We studied the persistence of tiamulin (TIA) and tilmicosin (TLM) along their route from pig administration to fecal excretion and to agricultural soils. TLM was detected in feces at levels folds higher (4.27-749.6 μg g^-1) than TIA (0.55-5.99 μg g^-1). Different administration regimes (feed or water) showed different excretion patterns and residual levels for TIA and TLM, respectively. TIA and TLM (0.5, 5 and 50 μg g^-1) dissipated gradually from feces when stored at ambient conditions (DT₅₀ 5.85-35.9 and 23.5-49.8 days respectively), while they persisted longer during anaerobic digestion (DT₉₀ >365 days) with biomethanation being adversely affected at VA levels > 5 μg g^-1. When applied directly in soils, TLM was more persistent than TIA with soil fumigation extending their persistence suggesting microbial degradation, while soil application through feces increased their persistence, probably due to increased sorption to the fecal organic matter. The use of TIA- and TLM-contaminated feces as manures is expected to lead to VAs dispersal with unexplored consequences for the environment and human health.

Assessing the inhibitory activity of culture supernatants against foodborne pathogens of two psychrotrophic bacteria isolated from river trout

There is a need for new natural products with antimicrobial activity to treat multidrug resistant bacteria that can cause human illness. Some of them are foodborne pathogens. Two different Gram-negative psychrotrophic strains were isolated from healthy trout river samples (Salmotrutta). Based on phenotypic characterization, proteomics, genotyping and phylogenetic analyses of 16 rRNA gene, strains TCPS12 and TCPS13 were identified as Shewanellabaltica and Pseudomonasfragi, respectively. Both of them produced an exopolysaccharide that showed antimicrobial activity against four foodborne pathogens. P. fragi supernatant (AS13) showed higher antimicrobial activity than S. baltica supernatant (AS12) against all tested pathogens. The stability of the antimicrobial activity of AS13 was assessed against Enterococcus faecalis ATCC 29212 under different conditions. This solution was stable when exposed for 30 min to temperatures ranging from 40 to 100 °C. In addition, it retained its activity within a pH range of 2–8 during 2 h of incubation, showing higher activity at pH 6. Serine proteases and α-amylase inactivated significantly the antimicrobial activity of AS13, suggesting that the active molecule could most likely be a glycoprotein. These products are interesting for their possible application as biopreservatives in the food industry.

Microbial community and antimicrobial resistance in fecal samples from wild and domestic ruminants in Maiella National Park, Italy

This study aimed to provide new insights about antimicrobial resistance genes abundance and microbial communities of wild and domestic ruminants in wildlife-livestock interface. In total, 88 fecal samples were recovered from Apennine chamois, red deer, goat, cattle and sheep, and were collected in pools. The populations under study were selected based on ecological data useful to define sympatric and non-sympatric populations. Samples were screened for commonly used in farms under study or critically important antimicrobial resistance genes (aadA2, TetA, TetB, TetK, TetM, mcr-1). The microbial community composition was found to be different based on the species and land use of animals under study. Indeed, it was mostly characterized by phyla Firmicutes in bovine, Bacteroidota in chamois and Proteobacteria in red deer. Additionally, positive correlations between antibiotic resistance genes and microbial taxa (e.g., Tet genes correlated with Firmicutes and Patescibacteria) were described. Of the antimicrobials investigated, the abundance of mcr-1 gene suggests the importance of monitoring the wildlife in order to detect the emerging resistance genes contamination in environment. This study provides new data that highlight the importance of multidisciplinary and uncultured study in order to describe the spreading of antimicrobial resistance and related contamination in the environment.

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Multidisciplinary approach including ecological data, real time PCRs and 16S rRNA analysis

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Microbial communities composition of rare species as Apennine chamois

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Evaluation of antibiotic resistance genes abundance in feces of wild and domestic ruminants

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Detection of mcr-1 resistance gene relevant for Public Health

The impact of newly synthesized sulfonamides on soil microbial population and respiration in rhizospheric soil of wheat (Triticum aestivum L.)

Antibiotics released into agricultural fields through the manure of grazing animals could exert harmful impacts on soil microbes and plants. Antibiotics exert high impacts on environment than other pharmaceuticals due to their higher biological activity. However, little is known about their impacts on plants, despite indications that antibiotics exert negative effects on soil microorganisms, which ultimately harm the plants. It has been demonstrated that beneficial microorganisms promote plant growth and development under various stresses. This study evaluated the toxicity of four newly derived sulfonamides (SAs), i.e., 2-(phenylsulfonyl) hydrazine carbothioamide (TSBS-1), N, 2-bis phenyl hydrazine carbothioamide (TSBS-2), aminocarbonyl benzene sulfonamide (UBS-1), and N, N’-carbonyl dibenzene sulfonamide (UBS-2) on bacterial growth and soil microbial respiration. Each SA was tested at four different concentrations (i.e., 2.25, 2.5, 3, 4 mg/ml) against five rhizospheric bacterial strains, including AC (Actinobacteria sp.), RS-3a (Bacillus sp.), RS-7a (Bacillus subtilis), RS-4a (Enterobacter sp.), and RS-5a (Enterobacter sp.). Antimicrobial activity was checked by disc diffusion method, which showed that inhibition zone increased with increasing concentration of SAs. The UBS-1 resulted in the highest inhibition zone (11.47 ± 0.90 mm) against RS-4a with the highest concentration (4 mg/ml). Except TSBS-1, all sulfonamide derivatives reduced CO₂ respiration rates in soil. Soil respiration values significantly increased till 6^th day; however, exposure of sulfonamide derivatives suppressed microbial respiration after 6^th day. On the 20^th day, poor respiration activity was noted at 0.23, 0.2, and 0.4 (CO₂ mg/g dry soil) for TSBS-1, UBS-1, and UBS-2, respectively. Our results demonstrate that sulfonamides, even in small concentrations, significantly affect soil microbial population and respiration. Soil microbial respiration changes mediated by sulfonamides were dependent on length of exposure and concentration. It is recommended that antibiotics should be carefully watched and their impact on plant growth should be tested in the future studies.

Mutational meltdown of putative microbial altruists in Streptomyces coelicolor colonies

In colonies of the filamentous multicellular bacterium Streptomyces coelicolor, a subpopulation of cells arises that hyperproduces metabolically costly antibiotics, resulting in a division of labor that increases colony fitness. Because these cells contain large genomic deletions that cause massive reductions to individual fitness, their behavior is similar to altruistic worker castes in social insects or somatic cells in multicellular organisms. To understand these mutant cells’ reproductive and genomic fate after their emergence, we use experimental evolution by serially transferring populations via spore-to-spore transfer for 25 cycles, reflective of the natural mode of bottlenecked transmission for these spore-forming bacteria. We show that in contrast to wild-type cells, putatively altruistic mutant cells continue to decline in fitness during transfer while they lose more fragments from their chromosome ends. In addition, the base-substitution rate in mutants increases roughly 10-fold, possibly due to mutations in genes for DNA replication and repair. Ecological damage, caused by reduced sporulation, coupled with DNA damage due to point mutations and deletions, leads to an inevitable and irreversible type of mutational meltdown in these cells. Taken together, these results suggest the cells arising in the S. coelicolor division of labor are analogous to altruistic reproductively sterile castes of social insects.

In Streptomyces coelicolor, a subpopulation of cells can arise that produce metabolically costly antibiotics and a division of labor that maximizes colony fitness. This study uses experimental evolution to understand the reproductive and genomic fate of these mutant cells, showing that the arising altruistic cells are analogous to the reproductively sterile castes of social insects.

Plants Mitigate Nitrous Oxide Emissions from Antibiotic-Contaminated Agricultural Soils

Vegetable production systems are hotspots of nitrous oxide (N₂O) emissions and antibiotic pollution. However, little is known about the interconnections among N₂O emissions, vegetable growth, and antibiotic contamination. To understand how plants regulate N₂O emissions from enrofloxacin (ENR)-contaminated soils, in situ N₂O emissions were measured in pot experiments with cherry radish and pakchoi. Gross N₂O production and consumption processes were discriminated based on an acetylene inhibition experiment. Results indicated that vegetable growth decreased the cumulative N₂O flux from 0.71 to -0.29 kg ha^-1 and mitigated the ENR-induced increase in N₂O emissions. Radish displayed better mitigation of N₂O emissions than pakchoi. By combining the analysis of N₂O flux with soil physicochemical and microbiological properties, we demonstrated that growing vegetables could either promote gross N₂O consumption or decrease gross N₂O production, primarily by interacting with soil nitrate, clade II nosZ (nosZII)-carrying bacteria, and Deinococcus-Thermus. ENR inhibited N₂O consumption more than N₂O production, with the nosZII-carrying bacteria, represented by Gemmatimonadetes, as the main inhibition target. However, increasing nosZII-carrying bacteria by growing radish offsets the inhibitory effect of ENR. These findings provide new insights into N₂O emissions and antibiotic pollution in vegetable-soil ecosystems and broaden the options for mitigating N₂O emissions.

Pharmaceutical residues in digested sewage sludge: Occurrence, seasonal variation and risk assessment for soil

The occurrences, temporal variations and ecotoxicological risks of 38 selected pharmaceuticals from 7 therapeutic classes (i.e. antibiotics, analgesics, anti-inflammatories, beta-blockers, lipid regulators, anticancer agents, and psychiatric drugs) have been observed in the anaerobically treated sludge of the urban wastewater treatment plant (WWTP) in Konya, Turkey. Sampling was carried out to assess the seasonal variations in one year. The total daily wastewater flow rate of the WWTP was approximately 200,000 m³/day, and 140 tons/day of treated sludge were produced. The total concentrations of all pharmaceutical compounds ranged from 280 to 4898 μg/kg of dry matter (dm). The dominant therapeutic class was analgesics and anti-inflammatories (49%), which was followed by antibiotics (31%). Clarithromycin and azithromycin were the most abundant compounds, with concentrations of 1496 μg/kg dm. The total daily pharmaceutical load in the treated sludge was as high as 1.002 kg/day in the winter season, while the annual pharmaceutical mass load that was discharged into the environment was estimated to be approximately 71.6 kg. The use of treated sludge as fertilizer in agricultural lands causes continuous contamination of the terrestrial environment by pharmaceuticals. Five antibiotics (i.e., azithromycin, clarithromycin, erythromycin, sulfamethoxazole, and doxycycline), one analgesic (acetylsalicylic acid) and one beta-blocker (atenolol) in the digested sludge pose acute and short chronic high risks to environment. The highest short chronic risk in the digested sludge-amended soils was determined for azithromycin (RQ: 54.9). To reduce the potential environmental impact of pharmaceuticals, digested sludge should be monitored in terms of the pharmaceutical contents before being applied to soil.

Emerging frontiers in microbe-mediated pesticide remediation: Unveiling role of omics and In silico approaches in engineered environment

The overuse of pesticides for augmenting agriculture productivity always comes at the cost of environment, biodiversity, and human health and has put the land, water, and environmental footprints under severe threat throughout the globe. Underpinning and maximizing the microbiome functions in pesticide-contaminated environments has become a prerequisite for a sustainable environment and resilient agriculture. It is imperative to elucidate the metabolic network of the microbial communities and environmental variables at the contaminated site to predict the best strategy for remediation and soil microbe-pesticide interactions. High throughput next-generation sequencing and in silico analysis allow us to identify and discern the members and characteristics of core microbiomes at the contaminated site. Integration of modern high throughput multi-omics investigations and informatics pipelines provide novel approaches and pathways to capitalize on the core microbiomes for enhancing environmental functioning and mitigation. The role of eco-genomics tools in visualising the microbial network, taxonomy, functional potential, and environmental variables in contaminated habitats is discussed in this review. The integrated role of the potential microbe identification as individual or consortia, mechanistic approach for pesticide degradation, identification of responsible enzymes/genes, and in silico approach is emphasized for the prospects of the area.

Advances on tailored biochar for bioremediation of antibiotics, pesticides and polycyclic aromatic hydrocarbon pollutants from aqueous and solid phases

Biochar is gaining incredible importance for remediation applications due to their attractive removal properties. Moreover, it is becoming ecofriendly, cost-effective and sustainable bioadsorbents towards replacing expensive activated carbons. Studies reveal biochar effectiveness for removal of important and potentially severe organic pollutants such as antibiotics and pesticides. Recent research advancements on biochar modification (physical, chemical and biological) opens greater opportunity to form tailored biochar with improved surface properties than their native forms for offering better removal efficiencies. Further attentions paid towards emergent new modification methods to cover broad-spectrum pollutants using tailored biochar. Current review aims to summarize recent updates upon biochar tailoring, comparative account of tailored biochars removal efficiencies with respect to their native forms and to provide in-depth discussion covering specific interactions of tailored biochars with antibiotics, polycyclic aromatic hydrocarbons (PAHs) and pesticides for their effective removals and degradation from polluted environments. Application of inducer compounds e.g., peroxymonosulfate and sodium percarbonate further improved the biochar role towards degradation of toxic organic pollutants into their less or nontoxic forms. Biochar engineered with specific metals enable them for the same role without inducer compounds. Moreover, microbial interactions with biochar not only improve the bioremediation level further but also degrade the pollutants from the environment and open up better environmental and socio-economic prospects. Application of green, cost-effective and sustainable biochar for remediation of environmentally potential organic pollutants offers economical treatment methods as well as safe environment. These benefits are inline with global trends towards developing a sustainable process for biocircular economy.

Hiding in plain sight - Wildlife as a neglected reservoir and pathway for the spread of antimicrobial resistance: A narrative review

Antimicrobial resistance represents a global health problem, with infections due to pathogenic antimicrobial resistant bacteria (ARB) predicted to be the most frequent cause of human mortality by 2050. The phenomenon of antimicrobial resistance has spread to and across all ecological niches, and particularly in livestock used for food production with antimicrobials consumed in high volumes. Similarly, hospitals and other healthcare facilities are recognized as significant “hotspots” of ARB and antimicrobial resistance genes (ARGs); however, over the past decade, new and previously overlooked ecological niches are emerging as hidden reservoirs of ARB/ARGs. Increasingly extensive and intensive industrial activities, degradation of natural environments, burgeoning food requirements, urbanization, and global climatic change have all dramatically affected the evolution and proliferation of ARB/ARGs, which now stand at extremely concerning ecological levels. While antimicrobial resistant bacteria and genes as they originate and emanate from livestock and human hosts have been extensively studied over the past 30 years, numerous ecological niches have received considerably less attention. In the current descriptive review, the authors have sought to highlight the importance of wildlife as sources/reservoirs, pathways and receptors of ARB/ARGs in the environment, thus paving the way for future primary research in these areas.

Bacterial Glycocalyx Integrity Impacts Tolerance of Myxococcus xanthus to Antibiotics and Oxidative-Stress Agents

The presence of an exopolysaccharide (EPS) layer surrounding bacterial cells, termed a "glycocalyx", confers protection against toxic molecules. However, the effect of glycocalyx integrity on the tolerance to such agents is poorly understood. Using a modified disc-diffusion assay, we tested the susceptibility to a panel of antibiotics and oxidative stress-inducing compounds of various mutant strains of the social predatory Gram-negative soil bacterium Myxococcus xanthus; the selected mutants were those that manifest different physical states of their respective EPS glycocalyces. While the overall presence of an EPS layer was indeed beneficial for tolerance, the integrity of this layer was also found to affect the susceptibility of the bacterium to killing; however, this finding was not universal, and instead was dependent on the specific compound tested. Thus, the integrity of the cell-surface EPS glycocalyx plays an important role in the tolerance of M. xanthus to harmful compounds.