Development of antibiotic resistance genes in soils with ten successive treatments of chlortetracycline and ciprofloxacin

Tetracycline antibiotics in agricultural soil: Dissipation kinetics, transformation pathways, and structure-related toxicity

Tetracyclines (TCs) are the most common antibiotics in agricultural soil, due to their widespread usage and strong persistence. Biotic and abiotic degradation of TCs may generate toxic transformation products (TPs), further threatening soil ecological safety. Despite the increasing attention on the environmental behavior of TCs, a systematic review on the dissipation of TCs, evolution of TPs, and structure-toxicity relationship of TCs in agricultural soil remains lacking. This review aimed to provide a comprehensive overview of the environmental fate of TCs in agricultural soil. We first introduced the development history and structural features of different generations of TCs. Then, we comparatively evaluated the dissipation kinetics, transportation pathways, and ecological impacts of three representative TCs, namely tetracycline (TC), oxytetracycline (OTC), and chlortetracycline (CTC), in agricultural soil. The results showed that the dissipation kinetics of TCs generally followed the first-order kinetic model, with the median dissipation half-lives ranging from 20.0 to 38.8 days. Among the three TCs, OTC displayed the lowest dissipation rates due to its structural stability. The typical degradation pathways of TCs in soil included epimerization/isomerization, demethylation, and dehydration. Isomerization and dehydration reactions may lead to the formation of more toxic TPs, while demethylation was accompanied by the alteration of the minimal pharmacophore of TCs thus potentially reducing the toxicity. Toxicological experiments are urgently needed in future to comprehensively evaluate the ecological risks of TCs in agricultural soil.

Tetracycline and fluoroquinolone antibiotics contamination in agricultural soils fertilized long-term with chicken litter: Trends and ravages

We investigated the potential accumulation of tetracyclines (TCs) such as chlortetracycline (CTC), oxytetracycline (OTC) and doxycycline (DC), and fluoroquinolones (FQs) like enrofloxacin (ENR) and ciprofloxacin (CIP) in chicken litter and agricultural soils fertilized over short-term to long-term (<1-30 yrs) with chicken litter in a poultry hub for the first time from Tamil Nadu, India. CTC, OTC, DC, CIP, and ENR were detected in 46-92 % of the selected chicken litter samples, with mean levels ranging from 2.90 to 23.30 μg kg-1. Higher concentrations of TCs and FQs were observed in freshly collected chicken litter from poultry sheds than in those stockpiled in cultivated lands. CTC was the prevalent antibiotic in chicken litter. The overall occurrence, as well as the ecological risks of TCs and FQs, changed over a 30-yr period. The accumulation of veterinary antibiotics (VAs) (in μg kg-1) in short-term (>1 yr) to medium-term (1-3 yrs) chicken litter-fertilized soils reached a maximum of 11.60 for CTC, 6.50 for OTC, 0.80 for DC, 3.70 for CIP, and 3.60 for ENR, but decreased in long-term (10-30 yrs) fertilized soils. Ecological risk assessment revealed a Risk Quotient (RQ) of ≤0.10 for CTC, OTC, and DC in all soils, while an average risk (RQ >0.10-<1.0) was evident with CIP and ENR in short-term and medium-term fertilized soils. Antibiotic resistance genes (ARGs), including tetA, tetB, qnrA, qnrB and qnrS were detected in most of the chicken litter samples and litter-fertilized soils. Thus, it is critical to develop and adopt effective mitigation strategies before applying chicken litter in farmlands to decrease VAs and ARGs, reducing their associated risks to public health and ecosystems in India considering 'One Health' approach. Future investigations on the occurrence of other VAs and ARGs in soils fertilized with poultry litter at regional scale are required for effective risk mitigation of the widely used VAs.

Response of earthworm enzyme activity and gut microbial functional diversity to carbendazim in the manured soil

The effect of pesticide pollution on environmental microorganisms in soil has become the focus of widespread concern in society today. The response of earthworm gut and surrounding soil microbial functional diversity and enzyme activity to carbendazim (CBD) was studied in a soil-earthworm ecosystem amended with manure. In the experiment, CBD was added to the manured soil (MS). Meanwhile, the pesticide treatment without manure and the control treatment without pesticides were also set up. The activities of catalase (CAT) and acetylcholinesterase (AChE) were measured to evaluate the toxicity of CBD. The Biolog method was used to assess the functional diversity of the microbial community. In the 2 mg/kg CBD treatment, earthworm AChE activity decreased significantly in the MS after 14 d, which occurred earlier than in the un-manured soil (NS). The changes of earthworm CAT activity in the pesticide treatments showed a trend of initially increasing and then maintaining at a high activity level. However, the CAT activities at 28 d in the manured soils were clearly lower than that at 7 d for both the CBD treatments, while they remained stable in the control treatments. The carbon source utilization, Simpson index, Shannon index, and McIntosh index of soil microorganisms in the MS treatments were significantly higher than those in the NS treatments. The overall activity of earthworm gut microorganisms in the MS treated with 2 mg/kg CBD was higher than that in the control. Also, CBD treatment (2 mg/kg) increased significantly the Simpson index and McIntosh index of earthworm gut microorganisms. The results indicated that the enzyme activities in the manured soils increased before 7 d for the pesticide treatments. Furthermore, exposure to CBD at a high concentration in the MS not only led to the earlier inhibition of earthworm enzyme activity but also significantly improved the overall activity of earthworm gut microorganisms and microbial functional diversity. This study revealed the ecotoxicological effects of earthworms in response to pesticide stress following the use of organic fertilizers under facility environmental conditions, which can provide a theoretical basis for the remediation of pesticide pollution in soil in the future.

Characteristics of tetracycline antibiotic resistance gene enrichment and migration in soil-plant system

Tetracycline Resistance Genes (TRGs) have received widespread attention in recent years, as they are a novel environmental pollutant that can rapidly accumulate and migrate in soil plant systems through horizontal gene transfer (HGT), posing a potential threat to food safety and public health. This article systematically reviews the pollution sources, enrichment, and migration characteristics of TRGs in soil. The main sources of TRGs include livestock manure and contaminated wastewater, especially in intensive farming environments where TRGs pollution is more severe. In soil, TRGs diffuse horizontally between bacteria and migrate to plant tissues through mechanisms such as plasmid conjugation, integron mediation, and phage transduction. The migration of TRGs is not limited to the soil interior, and increasing evidence suggests that they can also enter the plant system through plant root absorption and the HGT pathway of endophytic bacteria, ultimately accumulating in plant roots, stems, leaves, fruits, and other parts. This process has a direct impact on human health, especially when TRGs are found in crops such as vegetables, which may be transmitted to the human body through the food chain. In addition, this article also deeply analyzed various factors that affect the migration of TRGs, including the residual level of tetracycline in soil, the type and concentration of microorganisms, heavy metal pollution, and the presence of new pollutants such as microplastics. These factors significantly affect the enrichment rate and migration mode of TRGs in soil. In addition, two technologies that can effectively eliminate TRGs in livestock breeding environments were introduced, providing reference for healthy agricultural production. The article concludes by summarizing the shortcomings of current research on TRGs, particularly the limited understanding of TRG migration pathways and their impact mechanisms. Future research should focus on revealing the migration mechanisms of TRGs in soil plant systems and developing effective control and governance measures to reduce the environmental transmission risks of TRGs and ensure the safety of ecosystems and human health.

Chlorinated organophosphorus flame retardants induce the propagation of antibiotic resistance genes in sludge fermentation systems: Insight of chromosomal mutation and microbial traits

Waste activated sludge (WAS) is a critical reservoir for antibiotic resistance genes (ARGs) due to the prevalent misuse of antibiotics. Horizontal gene transfer (HGT) is the primary mechanism for ARGs spread through mobile genetic elements (MGEs). However, the role of non-antibiotic organophosphorus flame retardants (Cl-OFRs) in ARG transmission in the WAS fermentation system remains unclear. This study examines the effects of tris(2-chloroethyl) phosphate (TCEP), a representative Cl-OFR, on ARG dynamics in WAS fermentation using molecular docking and metagenomic analysis. The results showed a 33.4 % increase in ARG abundance in the presence of TCEP. Interestingly, HGT did not appear to be the primary mechanism of ARG dissemination under TCEP stress, as evidenced by a 2.51 % decrease in MGE abundance. TCEP binds to sludge through hydrogen bonds with a binding energy of - 3.6 kJ/mol, leading to microbial damage and an increase in the proportion of non-viable cells. This interaction prompts a microbial shift toward Firmicutes with thick cell walls, which are significant ARG carriers. Additionally, TCEP induces chromosomal mutations through oxidative stress and the SOS response, contributing to ARG formation. Microorganisms also develop multidrug resistance mechanisms to expel TCEP and mitigate its toxicity. This study provides a comprehensive understanding of Cl-OFRs effects on the ARGs fates in WAS fermentation system and offers guidance for the safe and efficient treatment of Cl-OFRs and WAS.

High-generation tetracyclines shifted microbial community composition and induced the emergence of antibiotic resistant bacteria in soil

Tetracyclines (TCs) have been widely detected in agricultural soil due to their widespread use in animal husbandry. The impact of low-generation TCs, i.e., the first- and second- generations, on soil ecosystem has attracted widespread attention. However, the dynamic response of soil microbial community to high-generation TCs, i.e., the third- and fourth- generations, remains largely unknown. Herein, we characterized the variations in the composition, diversity and succession of microbial community and the proliferation of antibiotic resistance genes (ARGs) under the stress of four generations of TCs in brown soil and red soil. The results demonstrated that the exposure of low- and high- generation TCs consistently decreased the alpha diversity and stimulated the succession rate of microbial community in soil. High-generation TCs strongly shifted microbial community composition by reducing community resilience. The complexity of microbial networks and cross-module associations were strengthened to cope with the stress of high-generation TCs in soil. The abundance of ARGs was exacerbated by 1.75 times in response to the fourth-generation TCs compared to control in brown soil. The potential bacterial hosts of ARGs were more diverse in brown soil exposed to high-generation TCs, but the dominant hosts were not changed. These results highlight the potential ecological risk of the newly developed antibiotics, which is helpful for a comprehensive risk assessment of emerging contaminants.

Combined effects of bacteria and antibiotics on surface properties and transport of nanoplastics in porous media

Currently, research on the individual effects of bacteria and antibiotics on the transport of nanoplastics (NPs) in porous media is in its infancy, while research on their combined effect is absent. It is well known that bacteria and antibiotics also interact with each other, so this synergistic transport of bacteria, antibiotics, and NPs in porous media must be very interesting. For exploring this aspect, we investigated the individual and combined effects of bacteria and antibiotics on the transport of polystyrene NPs (PS-NPs) in saturated porous media. Hydrophobicity, roughness, and the Derjaguin-Landau-Verwey-Overbeek (DLVO) interaction energy were measured and calculated. The PS-NPs' transport in porous media was fitted using a mathematical model. Enhanced roughness and size of PS-NPs with increased bacterial concentration dominated and inhibited the PS-NPs' transport in porous media, although the hydrophilicity of PS-NPs and the energy barrier between PS-NPs and porous media were also increased. An increase in antibiotic concentration reduced the energy barrier between PS-NPs and porous media, thereby decreasing the PS-NPs' transport. Combined effects of bacteria and antibiotics on the PS-NPs' transport were complex and distinct from individual effects, but the mechanisms were clear. Roughness and hydrophilicity of PS-NPs and the DLVO interaction energy between PS-NPs and porous media together influenced this process. In the presence of bacteria, antibiotics could alter the bacterial surface roughness by altering bacterial extracellular polymeric substances, and thus alter the PS-NPs' surface roughness, thereby affecting the PS-NPs' transport in porous media. When antibiotics were present, enhanced bacterial concentration increased the PS-NPs' hydrophilicity and the energy barrier between PS-NPs and porous media, thus promoting the PS-NPs' transport. The findings of this study provided a theoretical basis for clarifying the transport of NPs in porous media under complex environments, facilitating a reduction in environmental pollution of NPs.

Key taxa and mobilome-mediated responses co-reshape the soil antibiotic resistome under dazomet fumigation stress

Agrochemicals are emergingly being implicated in the widespread dissemination of antibiotic resistance genes (ARGs) in agroecosystems. However, minimal research exists on the disturbance of fumigant on soil ARGs. Focusing on a typical fumigant dazomet in a simulated soil microcosm, we characterized the dazomet-triggered timely response and longstanding dynamic of ARGs at one-fold and two-fold field recommended doses using metagenome and quantitative PCR. Dazomet treatments reduced 13.17%-69.98% of absolute abundance of 16S rRNA gene and targeted ARGs, but, awfully, boosted diversity and relative abundance of ARGs up to 1.33-1.60 and 1.62-1.90 folds, respectively. Approximately 77.28% of changes in relative abundance of ARGs could be explained by bacterial community and mobile genetic elements (MGEs). Mechanistically, primary hosts of ARGs shifted from Proteobacteria (control) to Firmicutes and Actinobacteria (treatments) accompanied with corresponding changes in their abundance by combining community analysis, host tracking analysis and antibiotic resistant bacteria assay. Meanwhile, dazomet exposure significantly increased the incidence of MGEs and stimulated the conjugation of antibiotic-resistant plasmid. In addition, absolute abundance of targeted ARGs gradually recovered in the post-fumigation stage. Collectively, our results elucidate the dazomet-triggered emergence and spread of soil ARGs and highlight the importance of navigating toward rational use of fumigant in agricultural fields.

Induced development of oxytetracycline tolerance in bacterial communities from soil amended with well-aged cow manure

The use of animal manure as organic fertilizer is a common agricultural practice that can improve soil health and crop yield. However, antibiotics and their metabolites are often present in animal manure and, hence, in manure-amended soil. The aim of this study was to assess the induced development of oxytetracycline (OTC) tolerance in soil bacterial communities as a result of the addition of OTC to soil amended with well-aged cow manure. To this purpose, soil amended with well-aged cow manure was repeatedly - three times - spiked with different OTC concentrations (0, 2, 20, 60, 150, and 500 mg OTC kg^-1 dry weight soil, each time) according to a pollution-induced community tolerance (PICT) assay. The PICT detection phase was conducted in Biolog EcoPlates^TM in the presence of the following OTC concentration gradient in the wells: 0, 5, 20, 40, 60, and 100 mg L^-1. For all treatments, the application of OTC in the PICT selection phase resulted in lower values of bacterial metabolic activity (i.e., lower values of average well color development) in the PICT detection phase. A significant increase in OTC tolerance was observed in soil bacterial communities that had been exposed three times to ≥ 20 mg OTC kg^-1 DW soil during the PICT selection phase. In general, higher levels of OTC exposure during the PICT selection phase resulted in bacterial tolerance to higher OTC concentrations during the PICT detection phase, pointing to a dose-dependent induced tolerance. It is important to (i) rationalize the amount of antibiotics administered to livestock, and (ii) treat properly the antibiotic-containing manure before its application to agricultural soil as fertilizer.

Effect of graphene and graphene oxide on antibiotic resistance genes during copper-contained swine manure anaerobic digestion

Copper is an important selectors for antibiotic resistance genes (ARGs) transfer because of metal-antibiotic cross-resistance and/or coresistance. Due to carbon-based materials' good adsorption capacity for heavy metals, graphene and graphene oxide have great potential to reduce ARGs abundance in the environment with copper pollution. To figure out the mechanics, this study investigated the effects of graphene and graphene oxide on the succession of ARGs, mobile genetic elements (MGEs), heavy metal resistance genes (HMRGs), and bacterial communities during copper-contained swine manure anaerobic digestion. Results showed that graphene and graphene oxide could reduce ARGs abundance in varying degrees with the anaerobic reactors that contained a higher concentration of copper. Nevertheless, graphene decreased the abundance of ARGs more effectively than graphene oxide. Phylum-level bacteria such as Firmicutes, Bacteroidetes, Spirochaetes, and Verrucomicrobiaat were significantly positively correlated with most ARGs. Network and redundancy analyses demonstrated that alterations in the bacterial community are one of the main factors leading to the changes in ARGs. Firmicutes, Bacteroidetes, and Spirochaetes were enriched lower in graphene reactor than graphene oxide in anaerobic digestion products, which may be the main reason that graphene is superior to graphene oxide in reduced ARGs abundance. Additionally, ARGs were close to HMRGs than MGEs in the treatments with graphene, the opposite in graphene oxide reactors. Therefore, we speculate that the reduction of HMRGs in graphene may contribute to the result that graphene is superior to graphene oxide in reduced ARGs abundance in anaerobic digestion.

Enhanced removal of tetracycline from synthetic wastewater using an optimal ratio of co-culture of Desmodesmus sp. and Klebsiella pneumoniae

A sustainable approach of Desmodesmus sp. GIEC-179: Klebsiella pneumoniae (DUT-XJR-t-1.2) co-culture ratios were optimized to remove tetracycline (TET) from synthetic wastewater. To enhance the tetracycline removal performance, the effect of microalgae-bacterial co-culture ratio, maximum TET concentration, effective inoculum amount, growth temperature and pH were studied. The optimized ratio 1:2 of Desmodesmus sp.: K. pneumoniae showed the optimal removal percentage at the temperature of 25 °C, pH 7 and 10% inoculum amount; and the removal of TET was recorded as 95%. Moreover, this study explored the Desmodesmus sp.: K. pneumoniae (1:2) nutrient (COD, NH₄⁺ and PO₄^3-) exchange relationship and their interaction of TET removal to better understand their fundamental mechanism. According to the results of this study, Desmodesmus sp.: K. pneumoniae co-culture could be a green option for bio-removal of tetracycline from wastewater.

An Overview of Antibiotic Resistance and Abiotic Stresses Affecting Antimicrobial Resistance in Agricultural Soils

Excessive use of antibiotics in the healthcare sector and livestock farming has amplified antimicrobial resistance (AMR) as a major environmental threat in recent years. Abiotic stresses, including soil salinity and water pollutants, can affect AMR in soils, which in turn reduces the yield and quality of agricultural products. The objective of this study was to investigate the effects of antibiotic resistance and abiotic stresses on antimicrobial resistance in agricultural soils. A systematic review of the peer-reviewed published literature showed that soil contaminants derived from organic and chemical fertilizers, heavy metals, hydrocarbons, and untreated sewage sludge can significantly develop AMR through increasing the abundance of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARBs) in agricultural soils. Among effective technologies developed to minimize AMR's negative effects, salinity and heat were found to be more influential in lowering ARGs and subsequently AMR. Several strategies to mitigate AMR in agricultural soils and future directions for research on AMR have been discussed, including integrated control of antibiotic usage and primary sources of ARGs. Knowledge of the factors affecting AMR has the potential to develop effective policies and technologies to minimize its adverse impacts.

Time-course evolution of bacterial community tolerance to tetracycline antibiotics in agricultural soils: A laboratory experiment

The presence of antibiotics in soils may increase the selection pressure on soil bacterial communities and cause tolerance to these pollutants. The temporal evolution of bacterial community tolerance to different concentrations of tetracycline (TC), oxytetracycline (OTC) and chlortetracycline (CTC) was evaluated in two soils. The results showed an increase of soil bacterial community tolerance to TC, CTC and OTC only in samples polluted with the highest antibiotic concentrations tested (2000 mg kg^-1). The magnitude of those increases was higher in the soil with the lower organic carbon content (1.6%) than in the soil with an organic carbon content reaching 3.4%. In the soil with low organic carbon content, the time-course evolution showed a maximum increase in the tolerance of bacterial communities to tetracycline antibiotics between 45 and 100 incubation days, while for longer incubation times (360 days) the tolerance decreased. In the soil with high organic carbon content, a similar behavior was found for OTC. However, for CTC and TC, slightly increases and decreases (respectively) were found in the bacterial community tolerance at intermediate incubation times, followed by values close to zero for TC after 360 days of incubation, while for CTC they remained higher than in the control. In conclusion, soil pollution due to tetracyclines may cause bacterial community tolerance to these antibiotics when present at high concentrations. In addition, the risk is higher in soils with low organic matter content, and it decreases with time.

Efficient biodegradation of chlortetracycline in high concentration from strong-acidity pharmaceutical residue with degrading fungi

Chlortetracycline (CTC) pharmaceutical residue with strong acidity and in high CTC concentration is a hazardous solid waste. There is a huge attention but few studies on whether and how the CTC raw residue (CRR) can be degraded in microbiological way. In this study, three self-screened fungi, LJ245, LJ302 and LJ318, were used and thoroughly investigated to remove CTC, strong acidity and biotoxicity in CRR. The result disclosed that the concentration of CTC decreased rapidly in the first seven days and declined slowly subsequently, and the decreasing curve was similar to "L" shape. the corresponding degradation ratios of three strains were 95.73%, 98.53% and 98.07%, respectively. Meanwhile, numerous intermediates in degradation appeared in early days and gradually reduced, and eventually disappeared once the degradation time was long enough, among which eleven intermediates from CTC were identified. Moreover, the strong acidity of CRR declined dramatically using this biological method along with the CTC being metabolized, the pH value increased from 2.30 to 8.32 in the first 7 days. The toxicity of CRR was significantly reduced by LJ302 with inhibition rate from 96.02% to no inhibition effect to Micrococcus luteus. Therefore, CTC, strong acidity and biotoxicity of CRR could be effectively removed simultaneously through a biodegradation process driven with proposed strains.

Cosorption of Zn(II) and chlortetracycline onto montmorillonite: pH effects and molecular investigations

Ionic antibiotics and metals generally coexist, and their interaction can affect their sorption behaviors onto soil minerals, therefore determining their environmental hazards. This study investigated the sorption and cosorption of Zn(II) and chlortetracycline (CTC) onto montmorillonite at different solution pH (3-10) using batch experiments and extended X-ray absorption fine structure (EXAFS) analysis. The Langmuir model could reproduce well the sorption isotherms of Zn(II) and CTC. The presence of CTC/Zn(II) could promote the maximum sorption capacity (Q_m) of Zn(II)/CTC, based on site energy distribution (SED) theory. Generally, Zn(II) sorption increased with pH increasing. Comparatively, CTC sorption decreased as pH increased till approximately pH 5.0, then increased continuously with pH increasing. Both CTC and Zn(II) co-existence enhanced their individual sorption in both acidic and neutral environments. The processes behind CTC and Zn(II) sorption mainly included cation exchange and surface complexation. The EXAFS data evidenced that the presence of CTC could alter the species of Zn(II) on montmorillonite via surface complexation at pH 4.5 and 7.5, with Zn-CTC complexes being the predominant species on montmorillonite at pH 7.5. At pH 9.5, Zn(II) may exist onto montmorillonite in precipitated form similar to Zn-Al hydrotalcite-like compound (HTlc) regardless of CTC presence.

Contribution of enrofloxacin and Cu2+ to the antibiotic resistance of bacterial community in a river biofilm

Pollutants discharged from wastewater are the main cause of the spread of antibiotic resistance in river biofilms. There is controversy regarding the primary contribution of environmental selectors such as antibiotics and heavy metals to the development of antibiotic resistance in bacterial communities. Here, this study compared the effect of environmental safety concentration Cu²⁺ and enrofloxacin (ENR) on the evolution of antibiotic resistance by examining phenotypic characteristics and genotypic profiles of bacterial communities in a river biofilm, and then distinguished the major determinants from a comprehensive perspective. The pollution induced community tolerance in ENR-treated group was significantly higher than that in Cu²⁺-treated group (at concentration levels of 100 and 1000 μg/L). Metagenomic sequencing results showed that ENR significantly increased the number and total abundance of antibiotic resistance genes (ARGs), but there was no significant change in the Cu²⁺- treated group. Compared with Cu²⁺, ENR was the major selective agent in driving the change of taxonomic composition because the taxonomic composition in ENR was the most different from the original biofilm. Comparing and analyzing the prokaryotic composition, the phylum of Proteobacteria was enriched in both ENR and Cu²⁺ treated groups. Among them, Acidovorax and Bosea showed resistance to both pollutants. Linking taxonomic composition to ARGs revealed that the main potential hosts of fluoroquinolone resistance genes were Comamonas, Sphingopyxis, Bradyrhizobium, Afipia, Rhodopseudomonas, Luteimonas and Hoeflea. The co-occurrence of ARGs and metal resistance genes (MRGs) showed that the multidrug efflux pump was the key mechanism connecting MRGs and ARGs. Network analysis also revealed that the reason of Cu²⁺ selected for fluoroquinolones resistant bacterial communities was the coexistence of multidrug efflux gene and MRGs. Our research emphasizes the importance of antibiotics in promoting the development of antibiotic resistant bacterial communities from the perspective of changes in community structure and resistome in river biofilms.

Burkholderiaceae and Multidrug Resistance Genes Are Key Players in Resistome Development in a Germfree Soil Model

Assembly of a resistome in parallel with the establishment of a microbial community is not well understood. Germfree models can reveal microbiota interactions and shed light on bacterial colonization and resistance development under antibiotic pressure. In this study, we exposed germfree soil (GS), GS with diluted nontreated soil (DS), and nontreated soil (NS) to various concentrations of tetracycline (TET) in a nongermfree environment for 10 weeks, followed by 2 weeks of exposure to water. High-throughput sequencing was used to profile bacterial communities and antibiotic resistance genes (ARGs) in the soils. The initial bacterial loads were found to shape the profiles of bacterial communities and the resistomes. GS and DS treated with TET and the same soils left untreated had similar profiles, whereas NS showed different profiles. Soils with the same initial bacterial loads had their profiles shifted by TET treatment. Multidrug resistance (MDR) genes were the most abundant ARG types in all soils, with multidrug efflux pump genes being the discriminatory ARGs in GS regardless of different TET treatments and in GS, DS, and NS after TET. Furthermore, MDR genes were significantly enriched by TET treatment. In contrast, tetracycline resistance genes were either absent or low in relative abundance. The family Burkholderiaceae was predominant in all soils (except in NS treated with water) and was positively selected for by TET treatment. Most importantly, Burkholderiaceae were the primary carrier of ARGs, including MDR genes. IMPORTANCE This is the first study to examine how resistomes develop and evolve using GS. GS can be used to study the colonization and establishment of bacterial communities under antibiotic selection. Surprisingly, MDR genes were the main ARGs detected in GS, and TET treatments did not positively select for specific tetracycline resistance genes. Additionally, Burkholderiaceae were the key bacterial hosts for MDR genes in the current GS model under the conditions investigated. These results show that the family Burkholderiaceae underpins the development of resistome and serves as a source of ARGs. The ease of establishment of Burkholderiaceae and MDR genes in soils has serious implications for human health, since these bacteria are versatile and ubiquitous in the environment.

RESISTANCE TO ANTIBIOTICS AND THEIR UTILIZATION BY MICROORGANISMS

With the development of antibiotics application, their spread in the natural environment increases dramatically. The presence of antibiotics in the environment changes microorganism and other living beings ratio and composition, which causes a negative impact on biochemical processes that take place in the environment. The spread of antibiotic resistance genes in environmental microorganisms is a growing problem of environmental safety and human health. Aim. The objective of the work was to analyze the adaptation mechanisms of microorganisms to the influence of antibiotics and methods for antibiotics utilization. Results. The mechanisms of microorganisms’ adaptation to antibiotics are shown. The conditions for utilization of different antibiotics classes by microorganisms are provided. Conclusions. Methods of antibiotics destruction depend on its structure and physicochemical properties. Physico-chemical methods are used for local waste purification and are not suitable for antibiotics disposal in the natural environment. The decomposition products can also have a negative effect on the microorganisms’ cells. Depending on the class of antibiotics, their biodegradation occurs by different types of microorganisms. It has been shown that sulfonamides and amphinecoles are easily destroyed by many heterotrophic bacteria; biodegradation of aminoglycosides occurs by a strain of Pseudomonas spp.; tetracyclines - mushrooms; β-lactams - through the microorganisms’ association including: Burkholderiales, Pseudomonadales, Enterobacteriales, Actinomycetales, Rhizobiales, Sphingobacteriales. A consortium of destructors must be created to dispose of a specific classes of antibiotics.

Enhancement of chlortetracycline biodegradation with Trichoderma harzianum LJ245 and its spore-producing mutants using co-metabolism

Chlortetracycline (CTC) has been widely used in veterinary medicine in recent years, which has resulted in severe environmental issues due to its low degradation rate and high risk to induce antibiotic resistance bacteria and genes. In previous studies, CTC could be efficiently degraded by Trichoderma harzianum LJ245. Nevertheless, the strain itself suffers from relatively poor adaptability due to the limited number of spores produced. In this paper, ultraviolet (UV) mutagenesis was conducted on LJ245, and various mutants with high sporulation rate were generated to expand the environmental adaptability and enhance CTC degradation. An OmniLog-based method, where 95 types of carbon sources were applied, was first proposed to acquire the carbon metabolic profile of the strains. Several controlled experiments were performed to evaluate the impact of co-substrate metabolism on strain growth, CTC biodegradation, and metabolites biotoxicity removal. The result shows that produced mutants could significantly broaden the carbon metabolic profile and expand the environmental adaptability compared to the original LJ245, where the mutants obtained remarkable increase in total number of usable carbon sources. Meanwhile, as the sole carbon source, CTC could not be fully degraded by the strains. However, the use of co-metabolism could considerably enhance CTC degradation and completely remove CTC degradation products biotoxicity by all strains. Specifically, amino acids and carboxylic acids had the best performance on both strain growth and CTC degradation among all carbon source categories. The results can be applied to the biodegradation treatment of CTC in solid residue, waste water and other environments.

Detection and Profiling of Antibiotic Resistance among Culturable Bacterial Isolates in Vended Food and Soil Samples

The emergence and persistence of antibiotic resistance remain formidable health challenges. This study aimed at detecting and profiling antibiotic resistance of bacterial contaminants in vended food and the environment. Seventy antibiotic-resistant bacterial isolates were isolated from fried fish, African sausages, roasted meat, smokies, samosa, chips (potato fries), vegetable salads, and soil samples collected from Embu Town and Kangaru Market in Embu County, Kenya. The antibiotic susceptibility test, morphological and biochemical characterization, antibiosis assay, polymerase chain reaction-based detection of antibiotic resistance genes, and sequencing of the 16S rRNA gene were done. Analysis of variance on all measured data was done, and Tukey's honest test was used to compare and separate mean diameters of zones inhibition. Resistance of bacterial isolates to antibiotics was chloramphenicol (90%), cefotaxime (84.29%), nalidixic acid (81.43%), tetracycline (77.14%), amoxicillin (72.86%), gentamycin (48.57%), streptomycin (32.86%), and trimethoprim + sulphamethoxazole (30%). Isolate KMP337, Salmonella spp., exhibited highly significant antibiosis against S. aureus recording a mean inhibition diameter and standard error (SE) of 16.33 ± 0.88 mm, respectively, at P=0.001. The 70 bacterial isolates belonged to Bacillus, Paraclostridium, Lysinibacillus, Virgibacillus, and Serratia genera. The study isolated Bacillus wiedmannii (KC75) which is a risk group 2 as well as Serratia marcescens (KMP95) and Bacillus anthracis (KS606) which are risk group 3 organisms. The presence of antibiotic resistance genes Tet A, ^BlaTEM, StrB, Dfr A, Amp, and FloR genes was confirmed by a polymerase chain reaction. Samples from Kangaru Market recorded a higher (88.57%) proportion of resistant isolates as compared to isolates from Embu Town (11.43%). The study confirmed the presence of antibiotic-resistant bacteria in vended fast food and the soil in Embu Town and Kangaru Market. This study calls for continuous monitoring of bacterial status and hygienic handling of vended food.

Enterobacteriaceae predominate in the endophytic microbiome and contribute to the resistome of strawberry

Antibiotic resistance genes (ARGs) harbored by plant microbiomes have been implicated as a potential risk to public health via food chain, especially directly edible fruits and vegetables. Here, we investigated the microbiome and antibiotic resistome in soil-strawberry ecosystem using shotgun metagenomic sequencing. The results showed that the enterobacterial population dominated the endophytes of strawberry fruits. Moreover, 85 subtypes of ARGs, including several clinically important ARGs, were detected in the strawberry fruit metagenomes. Additionally, host tracking analysis in combination with antibiotic-resistant bacterial isolate screening suggested that fruit-borne ARGs were mainly carried by members of the Enterobacteriaceae family. Unexpectedly, most of fruit-borne isolates were found to be resistant to several clinically important antimicrobials, e.g., erythromycin and cephalexin. Our findings provide broad insights into endophytic antibiotic resistomes of direct edible strawberry fruits and their potential hosts, and highlight the potential exposure risks of plant microbiomes to the human food chain.

Insights into degradation pathways and toxicity changes during electro-catalytic degradation of tetracycline hydrochloride

The removal of antibiotics has attracted much attention due to their extremely high adverse impacts on the environment. However, the potential risks of degradation intermediates are seldom reported. In this work, the influence of different factors on the electro-catalytic degradation efficiency of tetracycline hydrochloride (TCH) by the prepared carbon nanotubes/agarose/indium tin oxide (CNTs/AG/ITO) electrode was investigated. Under optimal conditions (10 wt% CNTs dosage, pH = 7), the maximum degradation efficiency for TCH (10 mg L^-1) reached up to 96% within 30 min treatment with 4 V potential. Superoxide anions (•O₂^-) played an important role in the electro-catalytic degradation. Totally 10 degradation intermediates were identified using HPLC-MS/MS, and the degradation pathway was proposed. Toxicities of the parent antibiotic and the identified intermediates were calculated using the ECOSAR (Ecological Structure Activity Relationship) program in EPISuite, and results showed that more toxic intermediates were generated. The maximal chronic toxicity for green algae of the intermediate increased 1439.92 times. Furthermore, antimicrobial activity was further verified by disk agar biocidal tests with Escherichia coli ATCC25922 and higher biotoxicity intermediates compared with parent compounds were confirmed to be formed. Therefore, more attention should be paid on the potential risk of degradation intermediates in the treatment of wastewater containing antibiotics.

Azoxystrobin dissipation and its effect on soil microbial community structure and function in the presence of chlorothalonil, chlortetracycline and ciprofloxacin

The residual characteristics and the adsorption-desorption behaviors of azoxystrobin (AZO) as well as the soil ecological effects in the individual repeated treatments of AZO and its combination with chlorothalonil (CTL), chlortetracycline (CTC) and ciprofloxacin (CIP) were systematically studied in organic manure (OM)-amended soil under laboratory conditions. The presence of CTL, CTC, and CIP, both individually and combined, decreased the sorption affinity of AZO with the Freundlich adsorption and desorption coefficient decreasing by 0.3-24.2%, and CTC and CIP exhibited greater adverse effects than CTL. AZO dissipated slowly and the residues significantly accumulated during ten repeated treatments. The dissipation of AZO was inhibited to different degrees in the combined treatments. Biolog analysis revealed that the soil microbial functional diversity in the OM-soil + AZO and OM-soil + AZO + CTL treatments was higher than that in the OM-soil treatment during the former three repeated treatments, but which was inhibited during the latter seven repeated treatments. The soil microbial functional diversity in the OM-soil + AZO + CTC, OM-soil + AZO + CIP and OM-soil + AZO + CTL + CTC + CIP treatments was inhibited during the ten repeated treatments compared with OM-soil treatment. Metagenomic results showed that all repeated treatments significantly increased the relative abundance of Actinobacteria, but significantly decreased that of Proteobacteria and Firmicutes during the ten repeated treatments. Furthermore, the relative abundance of soil dominant bacterial genera Rhodococcus, Mycobacterium and Arthrobacter in all the repeated treatments significantly increased by 1.5-1283.9% compared with the OM-soil treatment. It is concluded that coexistence of CTL, CTC and CIP, both individually and combined, with AZO can inhibit the dissipation of AZO, reduce the adsorption affinity of AZO on soil, and alter the soil microbial community structure and functional diversity.