ARGs distribution and high-risk ARGs identification based on continuous application of manure in purple soil

Microplastics reduced the natural attenuation of antibiotic resistance genes in fertilized soils

The prolonged application of mulch and manure in agriculture has led to significant microplastic (MP) pollution in fertilized soils, raising global concerns about its potential impacts on soil health and ecosystem function. However, the effects of MP exposure on antibiotic resistance genes (ARGs) and microbial communities in fertilized soils are unknown. Therefore, we comprehensively explored the trends and drivers of ARGs during their natural abatement under the stress of conventional and biodegradable MP addition in fertilized soils using a soil microcosm experiment and metagenomic. The findings indicated that the presence of polybutylene succinate MPs (PBS-MPs) reduced the natural attenuation rate of ARGs in fertilized soils while increasing the fraction of high-risk ARGs in soils. Microbial communities and mobile genetic elements (MGEs) mainly drove the inhibitory effect of MPs on ARG abatement. Interestingly, most potential hosts for the coexistence of ARGs, metal resistance genes (MRGs), and MGEs were annotated as pathogens, such as Escherichia spp., Salmonella spp., and Klebsiella spp. In addition, MP stress in fertilized soil may lead to long-term contamination by highly virulent and antibiotic-resistant Escherichia coli. MPs influence the distribution of carbon sources, which in turn reduces the diversity and stability of soil microbial communities, while simultaneously promoting the colonization of crucial ARG hosts, like Dyella spp. This ultimately prolonged the high-risk state for ARG proliferation in the soil. This study highlights the significant risk posed by MPs to the persistence and spread of ARGs in fertilized soils. These results provide valuable insights for managing MP contamination in agricultural systems, emphasizing the need for sustainable practices to mitigate the long-term environmental risks associated with MP pollution.

Vertical Distribution and Drivers of Antibiotic Resistance Genes in Agricultural Soil Irrigated with Livestock Wastewater

Livestock wastewater reuse could be a potential source for the distribution of antibiotics, antibiotic resistance bacteria (ARB), and antibiotic resistance genes (ARGs) in agricultural soil. In this study, soil samples were collected from different depths (0-60 cm) of farmland that has been subjected to long-term application of livestock wastewater. The vertical distribution of antibiotics, bacterial communities, and ARGs were assessed to identify the driving factors that could potentially influence the distribution of ARB and ARGs. The results demonstrated distinguished distributions of antibiotics along the soil depths, with tetracyclines (TCs) mainly found in the top 10 cm of the soil (0.11-0.31 μg/kg), while quinolones (QNs), sulfonamides (SAs), and macrolides (MLs) were detected in all 60 cm of soil depth (0.01-0.22 μg/kg). The selection pressure of antibiotics to microorganisms led to the proliferation of ARB, especially tetracycline-resistant bacteria and erythromycin-resistant bacteria. In terms of the distribution/abundance of ARGs, novA and tetA (58) were relatively higher in 0-10 cm surface soil, while vanRM and vanRF were mainly detected in the deeper soil. Different ARGs may have the same host bacteria, which lead to the emergence of multidrug resistant bacteria, such as Ilumatobacter sp., Aggregatilinea sp., Rhabdothermincola sp., and Ornithinimicrobium sp. Soil pH, electrical conductivity (EC), and moisture content (MC) could affect the distribution and proliferation of ARB and were found negatively correlated with most of the ARGs except macB. Therefore, it is potentially possible to eliminate/inhibit the spread of ARGs by adjusting these soil parameters. These findings provide insights into the distribution and dissemination of antibiotics, ARB, and ARGs in agricultural practices of livestock wastewater irrigation and provide effective mitigation strategies to ensure the safe use of livestock wastewater in agriculture.

Surveillance of antimicrobial resistance using isothermal amplification: a review

The monitoring of antibiotic resistance genes (ARGs) is crucial for understanding the level of antimicrobial resistance and the associated health burden, which in turn is essential for the control and prevention of antimicrobial resistance (AMR). Isothermal amplification, an emerging molecular biology technology, has been widely used for drug resistance detection. Furthermore, its compatibility with a range of technologies enables high-specificity, high-throughput, and portable and integrated detection in drug resistance, particularly in resource-limited areas. However, to date, reviews involved in isothermal amplification all concentrate on its technological advancements and its application in nucleic acid point-of-care testing. Few reviews have been published that focus specifically on the application of isothermal amplification in the detection of drug resistance. This review summarizes the detection principles of different isothermal amplification techniques and discusses their strengths and weaknesses as well as the applicable scenarios for drug resistance detection. It also summarizes advances in the application, challenges and prospects of isothermal amplification technologies in conjunction with different methods such as base mismatch, CRISPR-Cas, lateral flow immunoassay, sensing and microfluidic technologies for improvement of specificity, throughput and integration for drug resistance detection. It is anticipated that this review will assist scientists in comprehending the evolution of isothermal amplification in the context of drug resistance detection and provide insights into the prospective applications of isothermal amplification for highly integrated and immediate on-site detection of drug resistance.

Assessing the Risks of Potential Pathogens and Antibiotic Resistance Genes Among Heterogeneous Habitats in a Temperate Estuary Wetland: a Meta-analysis

Temperate estuary wetlands act as natural filters for microbiological contamination and have a profound impact on "One Health." However, knowledge of microbiological ecology security across the different habitats in temperate estuarine wetlands remains limited. This study employed meta-analysis to explore the characteristics of bacterial communities, potential pathogens, and antibiotic resistance genes (ARGs) across three heterogeneous habitats (water, soil, and sediment) within the Liaohe Estuary landscape. The diversity and composition of the three bacterial communities differed with biogeography, temperature, and pH, with the highest α-diversity showing a significantly negative correlation along latitude in soil. Furthermore, aminoglycosides were significantly enriched in water and soil, while dihydrofolate was more likely to be enriched in soil. The potential pathogens, Pseudoalteromonas and Planococcus, were dominant in water and sediment, while Stenotrophomonas was the dominant bacterium in soil. The network topology parameter revealed interspecific interactions within the community. PLS-PM highlights the main direct factors affecting the abundance of potential pathogens and the spread of ARGs, while temperature and pH indirectly influence these potential pathogens. This study advances our understanding of bacterial communities in estuarine wetlands, while highlighting the need for effective monitoring to mitigate the risks associated with potential pathogens and ARGs in these ecosystems.

Manure application increases soil doxycycline and zinc levels and resistance gene abundance

Doxycycline (DOX) and zinc (Zn), are frequently detected in livestock manure. Untreated excrement carries a sizable load of DOX and Zn into the soil, exacerbating agricultural nonpoint source pollution. However, research on the effects of DOX and Zn on soil microbial diversity and the prevalence of resistance genes is limited. Through an 8-year field experiment coupled with 16S rRNA sequence analysis, we explored the dynamics of DOX and Zn contamination and their influence on soil microbial diversity and resistance gene expression. Our findings revealed a pronounced positive correlation between pig manure application and residual DOX and Zn levels in the soil, with the high pig manure) treatment resulting in increases of 16.42- and 1.14-fold in soil DOX and Zn levels, respectively, compared to those of the control. Soil DOX levels increased with pig and chicken manure application, whereas soil Zn levels showed divergent trends, increasing with pig manure application but decreasing with chicken manure application. As soil depth increased, the contamination risks from DOX and Zn in the soil decreased. Notably, soil DOX and Zn levels exhibited a significant positive correlation with Bacteroidota, Firmicutes, and Proteobacteria. The application of livestock and poultry manures amplified the abundance of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) in the soil, with higher ARG levels in pig manure-treated soil than in soil treated with chicken manure. Conversely, a greater abundance of MRGs was found in the soil treated with chicken manure than in the soil treated with pig manure. The results of this study on the DOX and Zn levels, microbial composition, and resistance genes with the continuous application of livestock and poultry manure in China will be highly valuable for the surveillance, maintenance, and biological removal of DOX and Zn composite pollution in manure.

Antibiotic resistance and resistome risks of inhalable bioaerosols at aeration tank of a full-scale wastewater treatment plant

Antibiotic resistome could be aerosolized under wastewater aeration processes, however, their seasonal variation, mobility, hosts, aerosolization behavior, and risk, are largely unknown. Herein, the antibiotic resistant pollution associated with fine particulate matter (PM2.5) from the actual aeration tank (AerT), was analyzed using metagenomic assembly. The antibiotic resistance of AerT-PM2.5 was characterized by significant seasonality. Antibiotic resistance genes (ARGs) in AerT-PM2.5, exhibited higher enrichment and mobility and were harbored more by pathogens than those in upwind-PM2.5, regardless of sampling season. Mobile ARGs were mainly flanked by transposase. Totally, 18 pathogenic antibiotic-resistant bacteria (PARB) carried more than one ARG, including 9 PARB with multiple ARG types. Although wastewater exerted a dominant source contribution for the airborne ARGs (47.31-55.56 %) and PARB (46.18-64.32 %), aeration endowed differential aerosolization capacity for various ARGs and PARB from wastewater. Airborne antibiotic resistome was mainly determined by bacterial community and indirectly influenced by meteorological conditions (i.e., relative humidity). Higher PM2.5-borne resistome risk was observed in AerT than upwind, and the most serious resistome risk of AerT-PM2.5 was found in winter. This study emphasizes the importance of wastewater aeration processes in emission of airborne antibiotic resistome and offers referenced information for mitigating air pollution in wastewater treatment plants.

Screening and Characterization of Probiotics Isolated from Traditional Fermented Products of Ethnic-Minorities in Northwest China and Evaluation Replacing Antibiotics Breeding Effect in Broiler

In this study, Lactobacillus fermentum DM7-6 (DM7-6), Lactobacillus plantarum DM9-7 (DM9-7), and Bacillus subtilis YF9-4 (YF9-4) were isolated from traditional fermented products. The survival rate of DM7-6, DM9-7, and YF9-4 in simulated intestinal gastric fluid reached 61.29%, 44.82%, and 55.26%, respectively. These strains had inhibition ability against common pathogens, and the inhibition zone diameters were more than 7 mm. Antioxidant tests showed these strains had good scavenging capacity for superoxide anion, hydroxyl radical and DPPH, and the total reduction capacity reached 65%. Then DM7-6, DM9-7 and YF9-4 were fed to broilers to study the effects on antioxidant capacity, immune response, biochemical indices, tissue morphology, and gut microbiota. 180 healthy broilers were allocated randomly into six experimental groups. SOD, GSH-Px, and T-AOC in broilers serum were detected, and the results showed probiotics significantly improve antioxidant capacity compared to CK group, while antibiotics showed the opposite result. Besides, IgA, IgM, IgG, TNF-α, and IL-2 indicated it could significantly improve immunity by adding probiotics in broilers diets. However, antibiotics reduced immunoglobulin levels and enhanced inflammation index. Biochemical indicators and tissue morphology showed probiotics had a protective effect on metabolic organs. Gut microbiota analysis proved antibiotics could significantly decrease microbial community diversity and increase the proportion of opportunistic pathogens, while probiotics could improve the diversity of gut microbiota and promote the colonization of beneficial microorganisms. In summary, probiotics DM7-6, DM9-7, and YF9-4 can improve the broiler's health by improving antioxidant capacity and immune function, regulating gut microbiota, and can be used as alternative probiotics for antibiotics-free breeding of broilers.

Biochar immobilized hydrolase degrades PET microplastics and alleviates the disturbance of soil microbial function via modulating nitrogen and phosphorus cycles

Microplastics (MPs) pose an emerging threat to soil ecological function, yet effective solutions remain limited. This study introduces a novel approach using magnetic biochar immobilized PET hydrolase (MB-LCC-FDS) to degrade soil polyethylene terephthalate microplastics (PET-MPs). MB-LCC-FDS exhibited a 1.68-fold increase in relative activity in aquatic solutions and maintained 58.5 % residual activity after five consecutive cycles. Soil microcosm experiment amended with MB-LCC-FDS observed a 29.6 % weight loss of PET-MPs, converting PET into mono(2-hydroxyethyl) terephthalate (MHET). The generated MHET can subsequently be metabolized by soil microbiota to release terephthalic acid. The introduction of MB-LCC-FDS shifted the functional composition of soil microbiota, increasing the relative abundances of Microbacteriaceae and Skermanella while reducing Arthobacter and Vicinamibacteraceae. Metagenomic analysis revealed that MB-LCC-FDS enhanced nitrogen fixation, P-uptake and transport, and organic-P mineralization in PET-MPs contaminated soil, while weakening the denitrification and nitrification. Structural equation model indicated that changes in soil total carbon and Simpson index, induced by MB-LCC-FDS, were the driving factors for soil carbon and nitrogen transformation. Overall, this study highlights the synergistic role of magnetic biochar-immobilized PET hydrolase and soil microbiota in degrading soil PET-MPs, and enhances our understanding of the microbiome and functional gene responses to PET-MPs and MB-LCC-FDS in soil systems.

Effect of polyethylene microplastics on antibiotic resistance genes: A comparison based on different soil types and plant types

Microplastics (MPs) and antibiotic resistance genes (ARGs) are two types of contaminants that are widely present in the soil environment. MPs can act as carriers of microbes, facilitating the colonization and spread of ARGs and thus posing potential hazards to ecosystem safety and human health. In the present study, we explored the microbial networks and ARG distribution characteristics in different soil types (heavy metal (HM)-contaminated soil and agricultural soil planted with different plants: Bidens pilosa L., Ipomoea aquatica F., and Brassica chinensis L.) after the application of MPs and evaluated environmental factors, potential microbial hosts, and ARGs. The microbial communities in the three rhizosphere soils were closely related to each other, and the modularity of the microbial networks was greater than 0.4. Moreover, the core taxa in the microbial networks, including Actinobacteriota, Proteobacteria, and Myxococcota, were important for resisting environmental stress. The ARG resistance mechanisms were dominated by antibiotic efflux in all three rhizosphere soils. Based on the annotation results, the MP treatments induced changes in the relative abundance of microbes carrying ARGs, and the G1-5 treatment significantly increased the abundance of MuxB in Verrucomicrobia, Elusimicrobia, Actinobacteria, Planctomycetes, and Acidobacteria. Path analysis showed that changes in MP particle size and dosage may indirectly affect soil enzyme activities by changing pH, which affects microbes and ARGs. We suggest that MPs may provide surfaces for ARG accumulation, leading to ARG enrichment in plants. In conclusion, our results demonstrate that MPs, as potentially persistent pollutants, can affect different types of soil environments and that the presence of ARGs may cause substantial environmental risks.

The resistome of the food chain: A One Health perspective

Antimicrobial resistance (AMR) represents a significant global health problem which challenges Sustainable Development Goal 3 of the United Nations, with growing concerns about the possibility of AMR transmission through the food chain. The indiscriminate use of antimicrobials for the treatment of food production animals and for agricultural crop improvement, in addition to the direct discharge of livestock farm residues to sewage and the use of animal manure in agriculture, are among the factors that can facilitate the selection and transmission of AMR throughout the food chain. The study of food microbiomes has been boosted by the advent of next-generation sequencing techniques, which have enabled gaining in-depth understanding of the diversity of antimicrobial resistance genes present in food and associated environments (the so-called resistome). The aim of this review is to provide an accurate and comprehensive overview of the knowledge currently available on the resistome of the most frequently consumed foods worldwide, from a One Health perspective. To this end, the different metagenomic studies which have been conducted to characterize the resistome of foods are compiled and critically discussed.

Variations in antibiotic resistomes associated with archaeal, bacterial, and viral communities affected by integrated rice-fish farming in the paddy field ecosystem

Antibiotic resistance genes (ARGs) serving as a newly recognized pollutant that poses potential risks to global human health, which in the paddy soil can be potentially altered by different agricultural production patterns. To elucidate the impacts and mechanisms of the widely used and sustainable agricultural production pattern, namely integrated rice-fish farming, on the antibiotic resistomes, we applied metagenomic sequencing to assess ARGs, mobile genetic elements (MGEs), bacteria, archaea, and viruses in paddy soil. There were 20 types and 359 subtypes of ARGs identified in paddy soil. The integrated rice-fish farming reduced the ARG and MGE diversities and the abundances of dominant ARGs and MGEs. Significantly decreased ARGs were mainly antibiotic deactivation and regulator types and primarily ranked level IV based on their potential threat to human health. The integrated rice-fish farming decreased the alpha diversities and altered microbial community compositions. MGEs, bacteria, archaea, and virus exhibited significant correlations with ARGs, while integrated rice-fish farming effectively changed their interrelationships. Viruses, bacteria, and MGEs played crucial roles in affecting the ARGs by the integrated rice-fish farming. The most crucial pathway by which integrated rice-fish farming affected ARGs was through the modulation of viral communities, thereby directly or indirectly influencing ARG abundance. Our research contributed to the control and restoration of ARGs pollution from a new perspective and providing theoretical support for the development of clean and sustainable agricultural production.

From organic fertilizer to the soils: What happens to the microplastics? A critical review

In recent, soil microplastic pollution arising from organic fertilizers has been of a great increasing concern. In response to this concern, this review presents a comprehensive analysis of the occurrence and evolution of microplastics in organic fertilizers, their ingress into the soil, and the subsequent impacts. Organic fertilizers are primarily derived from solid organic waste generated by anthropocentric activities including urban (daily-life, municipal wastes and sludge), agricultural (manure, straw), and industrial (like food industrial waste etc.) processes. In order to produce organic fertilizer, the organic solid wastes are generally treated by aerobic composting or anaerobic digestion. Currently, microplastics have been widely detected in the raw materials and products of organic fertilizer. During the process of converting organic solid waste materials into fertilizer, intense oxidation, hydrolysis, and microbial actions significantly alter the physical, chemical, and surface biofilm properties of the plastics. After the organic fertilizer application, the abundances of microplastics significantly increased in the soil. Additionally, the degradation of these microplastics often promotes the adsorption of organic pollutants and affects their retention time in the soil. These microplastics, covered by biofilms, also significantly alter soil ecology due to the unique properties of the biofilm. Furthermore, the biofilms also play a role in the degradation of microplastics in the soil environment. This review offers a new perspective on the soil environmental processes involving microplastics from organic fertilizer sources and highlights the challenges associated with further research on organic fertilizers and microplastics.

Effect of reactor operation modes on mitigating antibiotic resistance genes (ARGs) and methane production from hydrothermally-pretreated pig manure

Numerous efforts have been made to enhance the performance of anaerobic digestion (AD) for accelerating renewable energy generation, however, it remains unclear whether the intensified measures could enhance the proliferation and transmissions of antibiotic resistance genes (ARGs) in the system. This study assessed the impact of an innovative pig manure AD process, which includes hydrothermal pretreatment (HTP) and a two-stage configuration with separated acidogenic and methanogenic phases, on biomethane (CH4) production and ARGs dynamics. Results showed that HTP significantly increase CH4 production from 0.65 to 0.75 L/L/d in conventional single-stage AD to 0.82 and 0.91 L/L/d in two-stage AD. This improvement correlated with a rise in the relative abundance of Methanosarcina, a key methanogenesis microorganism. In the two-stage AD, the methanogenic stage offered an ideal environment for methanogens growth, resulting in substantially faster and higher CH4 production by about 10% compared to single-stage AD. Overall, the combined use of HTP and the two-stage AD configuration enhanced CH4 production by 40% compared to traditional single-stage AD. The abundance and diversity of ARGs were significantly reduced in the acidogenic reactors after HTP. However, the ARGs levels increased by about two times in the following methanogenesis stage and reached similar or higher levels than in single stage AD. The erm(F), erm(G), ant(6)-Ia, tet(W), mef(A) and erm(B) were the six main ARGs with significant differences in relative abundances in various treatments. The two-stage AD mode could better remove sul2, but it also had a rebound which elevated the risk of ARGs to the environment and human health. Network analysis identified pH and TVFAs as critical factors driving microbial communities and ARG proliferation in the new AD process. With the results, this study offers valuable insights into the trade-offs between AD performance enhancement and ARG-related risks, pinpointing essential areas for future research and practical improvements.

Tracing the transfer characteristics of antibiotic resistance genes from swine manure to biogas residue and then to soil

Based on laboratory simulation experiments and metagenomic analysis, this study tracked the transmission of antibiotic resistance genes (ARGs) from swine manure (SM) to biogas residue and then to soil (biogas residue as organic fertilizer (OF) application). ARGs were abundant in SM and they were assigned to 11 categories of antibiotics. Among the 383 ARG subtypes in SM, 43 % ARG subtypes were absent after anaerobic digestion (AD), which avoided the transfer of these ARGs from SM to soil. Furthermore, 9 % of the ARG subtypes in SM were introduced into soil after amendment with OF. Moreover, 43 % of the ARG subtypes in SM were present in OF and soil, and their abundances increased slightly in the soil amended with OF. The bacterial community in the soil treated with OF was restored to its original state within 60 to 90 days, probably because the abundances of ARGs were elevated but not significantly in the soil. Network analysis identified 31 potential co-host bacteria of ARGs based on the relationships between the bacteria community members, where they mainly belonged to Firmicutes, followed by Bacteroidetes, Actinobacteria, and Proteobacteria. This study provides a basis for objectively evaluating pollution by ARGs in livestock manure for agricultural use.

A review on the effects of discharging conventionally treated livestock waste to the environmental resistome

Globally, animal production has developed rapidly as a consequence of the ongoing population growth, to support food security. This has consequently led to an extensive use of antibiotics to promote growth and prevent diseases in animals. However, most antibiotics are not fully metabolized by these animals, leading to their excretion within urine and faeces, thus making these wastes a major reservoir of antibiotics residues, antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) in the environment. Farmers normally depend on conventional treatment methods to mitigate the environmental impact of animal waste; however, these methods are not fully efficient to remove the environmental resistome. The present study reviewed the variability of residual antibiotics, ARB, as well as ARGs in the conventionally treated waste and assessed how discharging it could increase resistome in the receiving environments. Wherein, considering the efficiency and environmental safety, an addition of pre-treatments steps with these conventional treatment methods could enhance the removal of antibiotic resistance agents from livestock waste.

Effects of soil habitat changes on antibiotic resistance genes and related microbiomes in paddy fields

The changes of paddy soil habitat profoundly affect the structure and function of soil microorganisms, but how this process drives the growth and spread of manure- derived antibiotic resistance genes (ARGs) after entering the soil is unclear. Herein, this study explored the environmental fate and behavior of various ARGs in the paddy soil during rice growth period. Results showed that most ARG abundances in flooded soil was lower than that in non-flooded soil during rice growth (decreased by 33.4 %). And soil dry-wet alternation altered microbial community structure in paddy field (P < 0.05), showing that Actinobacteria and Firmicutes increased in proportion under non-flooded conditions, and Chloroflexi, Proteobacteria and Acidobacteria evolved into the dominant groups in flooded soil. Meanwhile, the correlation between ARGs and bacterial communities was stronger than that with mobile genetic elements (MGEs) in both flooded and non-flooded paddy soils. Furthermore, soil properties, especially oxidation reduction potential (ORP), were proved to be an essential factor in regulating the variability of ARGs in the whole rice growth stage by structural equation model, with a direct influence (λ = 0.38, P < 0.05), following by similar effects of bacterial communities and MGEs (λ = 0.36, P < 0.05; λ = 0.29, P < 0.05). This study demonstrated that soil dry-wet alternation effectively reduced the proliferation and dissemination of most ARGs in paddy fields, providing a novel agronomic measure for pollution control of antibiotic resistance in farmland ecosystem.

Long-term impacts of conservation pasture management in manuresheds on system-level microbiome and antibiotic resistance genes

Animal manure improves soil fertility and organic carbon, but long-term deposition may contribute to antibiotic resistance genes (ARGs) entering the soil-water environment. Additionally, long-term impacts of applying animal manure to soil on the soil-water microbiome, a crucial factor in soil health and fertility, are not well understood. The aim of this study is to assess: (1) impacts of long-term conservation practices on the distribution of ARGs and microbial dynamics in soil, and runoff; and (2) associations between bacterial taxa, heavy metals, soil health indicators, and ARGs in manures, soils, and surface runoff in a study following 15 years of continuous management. This management strategy consists of two conventional and three conservation systems, all receiving annual poultry litter. High throughput sequencing of the 16S ribosomal RNA was carried out on samples of cattle manure, poultry litter, soil, and runoff collected from each manureshed. In addition, four representative ARGs (intl1, sul1, ermB, and blactx-m-32) were quantified from manures, soil, and runoff using quantitative PCR. Results revealed that conventional practice increased soil ARGs, and microbial diversity compared to conservation systems. Further, ARGs were strongly correlated with each other in cattle manure and soil, but not in runoff. After 15-years of conservation practices, relationships existed between heavy metals and ARGs. In the soil, Cu, Fe and Mn were positively linked to intl1, sul1, and ermB, but trends varied in runoff. These findings were further supported by network analyses that indicated complex co-occurrence patterns between bacteria taxa, ARGs, and physicochemical parameters. Overall, this study provides system-level linkages of microbial communities, ARGs, and physicochemical conditions based on long-term conservation practices at the soil-water-animal nexus.

Emerging soil contamination of antibiotics resistance bacteria (ARB) carrying genes (ARGs): New challenges for soil remediation and conservation

Soil plays a vital role as a nutrient source for microflora and plants in ecosystems. The accumulation and proliferation of antibiotics resistance bacteria (ARB) and antibiotics resistance genes (ARGs) causes emerging soil contamination and pollution, posing new challenges for soil remediation, recovery, and conservation. Fertilizer application in agriculture is one of the most important sources of ARB and ARGs contamination in soils. The recent existing techniques for the remediation of soil polluted with ARB and ARGs are very limited in terms of ARB and ARGs removal in soil. Bioelectrochemical remediation using bioelectrochemical systems such as microbial fuel cells and microbial electrolysis cells are promising technologies for the removal of ARB and ARGs in soil. Herein, diverse sources of ARB and ARGs in soil have been reviewed, their effects on soil microbial diversity have been analyzed, and the causes of ARB and ARGs rapid proliferation in soil are explained. Bioelectrochemical systems used for the remediation of soil contaminated with ARB and ARGs is still in its infancy stage and presents serious disadvantage and limits, therefore it needs to be well understood and implemented. In general, merging soil contamination of ARB and ARGs is an increasing concern threatening the soil ecosystem while the remediation technologies are still challenging. Efforts need to be made to develop new, effective, and efficient technologies for soil remediation and conservation to tackle the spread of ARB and ARGs and overcome the new challenges posed by ARB and ARGs contamination in soil.