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

Induced antibiotic production against pathogenic Klebsiella pneumoniae by bacterial coculture

The world is running short of effective antibiotics due to rapid development of antibiotic resistance against currently available antibiotics. The frequency of new antibiotic discovery from conventional axenic cultures has decreased significantly. In current study, azithromycin and ciprofloxacin supplemented plates were used as selection filter for isolation of antibiotic-producing bacteria from Gomti river sediments. All bacterial isolates grown on antibiotic supplemented plates are antibiotic-resistant. Some of these, antibiotic-resistant isolates have ability to produce antibiotics of same scaffold for which they are resistant. Replica-plating technique have been successfully used to screen antibiotic producing among the antibiotic-resistant bacteria by modification of traditional resistance-guided approach. Seven antibiotic-producing bacterial isolates were isolated based on modified resistance-guided approach. All possible 21 two-membered combinations of these seven isolates were used to make bacterial consortia. Effectiveness of bacterial coculture has been evaluated based on antimicrobial potential of extracted antibiotics against pathogenic strains of Klebsiella pneumoniae by using well diffusion method. Significantly increased antibiotic production was observed in cocultures, namely RS2-RS6 and RS2-RS7. As azithromycin and ciprofloxacin were used as selection filter, the produced antibiotic will be either a macrolide or a fluoroquinolone. Highest antimicrobial activity was observed in RS2-RS6 coculture. Molecular characterization revealed that bacterial partners involved in RS2-RS6 coculture were strains of Bacillus cereus and K. pneumoniae which were shown significantly enhanced antibiotic production against pathogenic strains of Klebsiella pneumoniae. Presence of K. pneumoniae vbspurs6 in RS2-RS6 coculture indicates towards the possible use of pathogen related strains to induce antibiotic production against several other antibiotic resistance pathogens.

The response of microbial communities to environmental factors in bank soil and river sediment: A case study along the mainstream of the Yangtze River

Microbial communities, which are crucial for ecosystem function and sustainability, are under environmental pressure. Using phospholipid fatty acids (PLFAs) as a measure of microbial biomass and community structure, the responses of microorganisms to environmental drivers were studied in bank soil and sediment alongside the Yangtze River in China. Thirty-eight sites were investigated over a length of 5500 km, ranging from the plateau to the estuary. Redundancy analysis revealed that microbial community composition in the bank soil was affected by MP (7.8%), geography (19.2%), and physicochemical properties (23.1%), while in the sediment, relevant factors were MP additives (12.8%), metals (21.1%), and physicochemical properties (23.3%). Variations in climate conditions along the course of the river had no effect on the microbial communities in the two habitats. Linear discriminant analysis of the PLFAs profiles showed changes in microbial community composition due to land use (forest, grass, cropland and built land), site class (up-, mid- and downstream) and MPs pollution level in both bank soil and sediment. The increased Gram-positive to negative bacteria (g+/g-) ratio and decreased iso-to anteiso-fatty acid (i/a) ratio indicated greater stress, such as caused by MP pollution (g+/g-: 12.6 to 19.3; i/a: 1.9 to 1.6). In bank soil, total microbial biomass was influenced by urbanization rate and nutrient availability. Specifically, total carbon (TC), total phosphorus (TP), and ammonium nitrogen (NH4+-N) had a positive impact, while inorganic phosphorus (IP), total potassium (TK) and nitrate nitrogen (NO3--N) had a negative impact. In contrast, in sediment only TC had a negative effect on biomass. This study applied PLFA to explore microbial communities and structures responses to environmental drivers in riverine habitats, revealing that anthropogenic factors (e.g. MP pollution and nutrient enrichment) alter microbial communities with urbanization.

Systematic review and meta-analysis of antimicrobial resistant bacteria in free-ranging wild mammals

BACKGROUND

Bacterial antimicrobial resistance is a significant global threat to public health, closely linked to the misuse of antimicrobials in human and veterinary medicine, aquaculture, and agriculture. The consequences of antimicrobial resistance overcome species boundaries and require a holistic approach for mitigation actions. The study of antimicrobial resistance in wildlife is thus increasingly relevant to understand the spread of antimicrobial resistance in the environment and the animal community, as well as to investigate the role of wildlife either as a carrier, reservoir, spillover, or indicator of antimicrobial resistance. The aim of this study is to describe the prevalence and type of antimicrobial resistance in bacterial isolates from wild mammals through systematic review and meta-analysis of the available literature, following the Preferred Reporting Items for Systematic reviews and Meta-Analysis (PRISMA) guidelines.

RESULTS

Out of 5052 collected documents, 3795 were screened, and finally 139 studies on antimicrobial resistance in free-ranging wild mammals were included in the meta-analysis. The studies covered 37 countries, mostly European. The Enterobacterales Escherichia coli and Salmonella spp., as well as Campylobacter spp., were the most frequently targeted bacterial species, mainly in the Artiodactyla order and specifically in the Suidae and Cervidae families. Low to moderate prevalences of antimicrobial resistance were found in all the continents, countries, bacteria, host taxa, and antimicrobials included in the meta-analysis, even for critically important antimicrobials as defined by the World Health Organisation, with higher values in Africa and Asia, in carnivores, and in animal species with high adaptability to diverse habitats.

CONCLUSION

This meta-analysis showed that antimicrobial resistance in wild mammals is widespread and variable according to taxonomy, trophic source, and geographic location. The meta-analysis highlighted methodological gaps that need to be addressed to improve the interpretation and conclusions obtained from the data. Genetic analyses on antimicrobial resistance and population ecological data should be included in future analysis to achieve a standardised methodology and overcome current limitations. To date, wildlife appears to be an environmental indicator of antimicrobial resistance and should be included in antimicrobial resistance surveillance plans not only because this sentinel role but also to monitor potential spill-back to livestock and/or humans.

Unraveling fate of sulfonamide antibiotics in sandy loam soil and water of India and environmental risk assessment

Antibiotic resistance is an alarming issue nowadays due to the increased use of antibiotics in humans, veterinary, fisheries, etc. Sulfonamides are one group of highly used antibiotics frequently detected in the environmental matrices. So, in the present study, we evaluated the sorption and dissipation of two commonly detected sulfonamide antibiotics in water (sulfamethazine (SMZ) and sulfamethoxazole (SMXZ)) in sandy loam soil and irrigation waters in the tropical region. Soil samples were processed using modified QuEChERS and the residues were quantified using LC-MS/MS. Optimized sample processing methods gave recoveries in the range of 88-91% from soil and water. The sulfonamides persisted in soil and irrigation waters with an average half-life of 12-22 days for SMZ and 20-33 days for SMXZ in different moisture regimes in soil and 13 days (SMZ) and 9 days (SMXZ) in irrigation water. The sorption data fitted well to Freundlich isotherm and indicated hydrophobic partitioning as the major mechanism behind sorption. The antibiotics exhibited unfavorable sorption in sandy loam soil which led to their stronger potential to leach to groundwater as indicated by the Groundwater Ubiquity Scores (GUS) (2.19 for SMZ and 3.09 for SMXZ). The sorption was favored at acidic pH and the incorporation of compost in soil also favored the sorption process leading to high retention of these antibiotics onto the soil surface. The environmental risk assessment also indicates their tendency to develop antimicrobial resistance. So, these antibiotics should be used with proper measures to avoid adverse impacts on humans and the environment.

Spatial estimation of veterinary antibiotics from husbandry to soil to river with resistance risk assessment in urban agglomerations

The rapid development of husbandry has increased veterinary antibiotic pollution risks, making emission reduction essential for sustainable growth. This study presents a novel method to quantitively explore antibiotic pathways from livestock to soils and then to rivers at grid scale in the Shandong Peninsula urban agglomeration. Validation demonstrated the method can relatively precisely and accurately estimate the spatial distributions and transports of veterinary antibiotics compared to previous methods and observations. Random Forest model yielded robust livestock distribution estimates (R2 > 0.945 for internal cross-validation, R2 > 0.652 for external validation), with the concentration of bovine, swine, and poultry in the west of the study area. In addition, the spatial distributions of nighttime light index and cropland cover were significantly correlated to the livestock distribution. The spatial distribution of antibiotics in soils followed the livestock distribution pattern, mainly driven by poultry and bovine framing. The estimation of antibiotic loads to rivers, based on sand transport and surface runoff, demonstrated moderate to high accuracy with R2 = 0.377 for sulfadiazine (SDZ) and R2 = 0.602 for ciprofloxacin (CFX). Antibiotic loads to soils primarily determined its loads to rivers which accounted for only 1.24%-2.68% of total antibiotic loads. Fluoroquinolone levels were one to two orders of magnitude higher than sulfonamide levels. Resistance risks were in the moderate to high for CFX and enrofloxacin (EFX) in a few rivers, while SDZ and sulfamonomethoxine (SMM) had low risks for all rivers. This refined method provides valuable insights for managing livestock-related pollution and offers a scientific basis for regional pollution control, with potential applications in the regions facing similar challenges, such as data scarcity of the soil physicochemical properties.

Investigating the factors influencing antibiotic use practices and their association with antimicrobial resistance awareness among poultry farmers in Enugu State, Nigeria

Background

The irrational use of antibiotics in poultry production has far-reaching consequences and continues to impact the fight against antimicrobial resistance (AMR) in Africa. In Nigeria, antibiotics are available over-the-counter and are widely used in food animal production for various reasons, including prophylaxis and growth promotion. While this practice may support animal production, it also drives the spread of AMR, posing serious health challenges due to close human-livestock interactions and the country's high disease burden. This study examined poultry farmers' knowledge, attitudes, and practices (KAP) regarding antibiotic use and AMR, aiming to highlight the public health risks and challenges in combating AMR in Nigeria.

Methods

A cross-sectional survey of 200 poultry farms in Enugu State, Southeast Nigeria, was conducted to evaluate farmers' KAP towards antibiotic usage and AMR. Using a validated, standardized, and self-administered questionnaire, data were collected from farmers responsible for key farm decisions, including input and feed management. The questionnaire comprised three sections: socio-demographic data, knowledge of AMR, and knowledge and practices regarding antibiotic use. Ethical approval was obtained, and participants gave oral consent based on their professional capacity.

Results

The evaluation of poultry's farmers KAP regarding antibiotic usage and AMR revealed that the majority of farmers (90.5%) reported using antibiotics, primarily for treating infections (80.5%) or for feed enhancement, growth promotion, and prophylaxis (61%). Ampicillin (75%), ciprofloxacin (71.5%), and doxycycline (71%) were the most commonly administered antibiotics. Monthly administration was the most common (48%), and 89% of respondents believed that antibiotics promote poultry growth. Interestingly, a substantial proportion of respondents (65%) were unaware of AMR, highlighting a significant knowledge gap, with only 16% recognizing the risk of AMR infections.

Conclusion

Our study revealed that the surveyed poultry farmers heavily rely on antibiotics, primarily for treating infections and, to a significant extent, for growth promotion, despite their limited awareness of AMR. Ampicillin was identified as the most commonly used antibiotic, raising concerns due to its potential link to beta-lactamase selection amid the country's carbapenem resistance issues. These findings underscore the urgent need for targeted education to address the AMR knowledge gap and reduce the misuse of antibiotics in poultry farming settings in Nigeria.

Microbial communities in biosolids-amended soils: A critical review of high-throughput sequencing approaches

Sustainable reuse of treated wastewater sludge or biosolids in agricultural production requires comprehensive understanding of their risks and benefits. Microbes are central mediators of many biosolids-associated risks and benefits, however understanding of their responses to biosolids remains minimal. Application of biosolids to soils amounts to a coalescence of two distinct microbial communities adapted to vastly different matrices. High-throughput DNA and RNA sequencing (HTS) approaches are required to accurately describe the compositional and functional outcomes of this process as they currently provide the highest possible resolution to deal with complex community-scale phenomena. Furthermore, linkage of HTS data to physicochemical and functional data can reveal biotic and abiotic drivers of coalescence, impacts of biosolids-borne contaminants and the collective downstream implications for soil and plant health. Here we review the current body of literature examining microbial communities in biosolids-amended soils using HTS of total community DNA and RNA. We provide a critical synthesis of soil microbial community composition and functional responses, the physical, chemical and biological drivers of these responses, and the influence of three major biosolids-borne anthropogenic contaminants of concern; antimicrobials and antimicrobial resistance genes, plastics, and per- and polyfluoroalkyl substances (PFAS). Finally, we identify methodological limitations and outstanding research questions precluding a holistic understanding of microbial responses in biosolids-amended soils and envision future research whereby sequence-based microbial ecology is integrated with soil, plant, and contaminant data to preserve soil health, support plant productivity, and remediate contaminants.

Current scenario of emerging pollutants in farmlands and water reservoirs: Prospects and challenges

Globally, roughly more than 400 million metric tons of plastics are produced annually. Similarly, the pharmaceuticals business is rising exponentially yearly, 5.8 %. It is expected to increase from USD 714 billion to USD 1454 billion by 2029. Beyond their intended uses, these substances are released into the environment as contaminants due to improper usage and management practices. Therefore, pharmaceuticals and microplastics (MPs) are classified as emerging pollutants (EPs), and their existence in agricultural ecosystems adversely affects soil and environmental health, ultimately impacting both ecological and human well-being. Pharmaceuticals and MP-loaded organic amendments (especially manure) are a primary cause of emerging soil pollutants. The increasing application of treated wastewater or biosolids as irrigation water or soil conditioners, mainly when derived from untreated sewage sludge, can introduce pharmaceuticals and MPs into the farmlands, merging these pollutants within the soil medium. The co-occurrence of MPs and pharmaceuticals leads to prolonged environmental presence and gradual bioaccumulation in organisms over time, contributing to persistent contamination and long-lasting effects on ecosystems. Moreover, these EPs have the potential to alter the composition of soil biogeochemistry and disrupt overall soil health and productivity. Numerous methods have been developed to address this emerging issue, including electrochemical degradation, advanced oxidation processes, photocatalytic degradation, biosurfactants, micro- and nano-bubble systems, ultrasonic cavitation, nanotechnology, constructed wetlands, and many hybrid approaches. This review explores the extent of EPs, their interactions, and management strategies in EPs-contaminated environments.

Freeze-thaw effect on adsorption and transport of two sulfonamides in soil: Batch and column studies

Freeze-thaw cycles (FTCs) have significant impacts on soil physicochemical properties, subsequently altering the fate of contaminants in soil. However, studies investigating the environmental behavior of antibiotics in soil subjected to FTCs are limited. This study investigated the effects of FTCs on the adsorption and transport of two commonly used sulfonamide antibiotics (SAs), sulfamethoxazole (SMX) and sulfapyridine (SPY), in soil. The results revealed that FTCs alter the adsorption behavior of SMX and SPY on the soil. Initially, after 1 FTC, the adsorption of both SMX and SPY decreased; however, subsequently, this adsorption gradually increased as the number of FTCs increased. This is because, during the FTCs, the increased soil pH hindered the adsorption of SAs by intensifying electrostatic repulsion between anionic SAs and soil particles. Subsequently, the increases in clay content, specific surface area (SA), small pores, and dissolved organic matter (DOM) provided more adsorption sites, overriding the initial pH effects and ultimately dominating the adsorption process. FTCs altered soil properties, which not only changed the adsorption of SAs but also induced the alteration of pore structure and the generation of preferential flow. During the vertical transport process, such changes in pore pathways played a dominant role, facilitating SMX and SPY transport in soil. The addition of heavy metals (Cd2+ and Cu2+) contributed to facilitating the transport of SMX and SPY in both unfrozen and freeze-thaw-treated soil columns. In the context of global climate change, this study offers valuable insights into the fate and environmental risks associated with pollutants in soil.

Four Decades of Bacillus Biofertilizers: Advances and Future Prospects in Agriculture

Over the past four decades, Bacillus biofertilizers, which are microbial formulations based on Bacillus species, have significantly contributed to sustainable agriculture by enhancing crop growth, improving soil health, and reducing the dependency on chemical fertilizers. Bacillus species, particularly known for their ability to promote plant growth, fix nitrogen, solubilize phosphorus, and produce growth-promoting substances such as phytohormones and antibiotics, have emerged as key players in the development of eco-friendly agricultural solutions. This research utilizes bibliometric analysis based on 3,242 documents sourced from the Web of Science database to map the development, key contributions, and innovation within the field from 1985 to 2023. This study identifies exponential growth in research output, particularly from 2003 onwards, indicating a robust interest and expanding research base predominantly in China, India, and the United States. We segmented the research timeline into three distinct phases, each marked by varying growth rates and research foci. This paper presents novel insights into the geographical and institutional distributions of research, highlighting the predominant role of developing countries in advancing Bacillus-based technologies. Key research hotspots have evolved from basic applications to complex interactions involving synthetic microbial communities and advanced multi-omics techniques. Our findings demonstrate a trend towards more strategic and technologically integrated approaches to developing Bacillus biofertilizers, reflecting broader shifts towards more sustainable agricultural systems. This study not only charts historical progress, but also proposes future research trajectories aimed at enhancing the application and effectiveness of microbial fertilizers across diverse ecosystems.

Identification of dissipation pathways for pharmaceuticals in soils - a modelling approach

Concentrations of pollutants like pharmaceuticals in soils typically decrease over time, though it often remains unclear whether this dissipation is caused by the transformation of the pollutant or a decreasing extractability. We developed a mathematical model that (1) explores the plausibility of different dissipation pathways, and (2) allows the quantification of concentration differences between aqueous soil extracts and soil solution. The model considers soil particles as uniform spheres, kinetic sorption towards an equilibrium (Freundlich model), and two dissipation pathways, i.e. irreversible transformation and mineralization (following 1st order kinetics) as well as the formation of non-extractable residues via intraparticle diffusion. Applying the model to 19 published datasets (eight pharmaceuticals, three soils) showed that intraparticle diffusion accounts for approximately two thirds of all simulated mass fluxes. Reversible formation of non-extractable residues could play a major role for dissipation, while irreversible transformation and mineralization cannot be excluded either based on the available datasets. The difference between concentrations in aqueous extracts and soil solution quantified by the model is below typical model and measurement uncertainties for most of the investigated pharmaceuticals. Larger differences might be linked to a positive ionic charge of the pollutant. The model helps in disentangling different dissipation pathways in soils and optimizing experiments elucidating the long-term fate of pollutants in soils.

Influence of soil type on bacterial growth and tolerance to experimentally added human antibiotics

The human antibiotics cefuroxime (CXM) and azithromycin (AZI) are among the most commonly prescribed. A significant portion of both are excreted and has been detected in sewage treatment plant effluents. The increasing use of such effluents in crops for irrigation and as fertilisers poses a threat to soil microbiota because of the presence of antibiotics. The lack of studies on CXM and AZI in soils hinders our understanding of their potential toxic effects on soil bacterial communities and ecosystem services. This study significantly contributes to the literature by quantifying the toxicity of CXM and AZI at varying concentrations in 12 different crop soils and tracking their evolution over time. The study also examined whether antibiotic pressure led to the development of more tolerant bacterial communities. The results of this study are the values of the logarithm of the antibiotic concentration at which 50 % of bacterial growth is inhibited (Log IC50) and indicate that both antibiotics are toxic to soil bacteria. The direct toxicity of CXM (1 day after contamination) was higher (Log IC50: 0.9 = 7.9 mg kg-1) than that of AZI (Log IC50: 3.4 = 2362 mg kg-1). However, bacterial growth was less affected by CXM over time, whereas AZI remained toxic in some soils until day 42 (Log IC50: 3.2 = 1533 mg kg-1 and 3.4 = 2291 mg kg-1, respectively). The overall results indicate that selective pressure exerted by antibiotics generates antibiotic tolerance in soils, even at the lowest antibiotic concentration studied (7.8 mg kg-1). The general trend was to increase tolerance to higher antibiotic concentrations up to the highest concentration studied (2000 mg kg-1). However, the degree of tolerance developed was highly dependent on soil type. More studies should be conducted to quantitatively assess the toxic and tolerance-developing effects of antibiotics in soils. Such information will be valuable for identifying which antibiotics pose a threat to the soil microbiota and consequently to human health.

Plasma Optimization as a Novel Tool to Explore Plant-Microbe Interactions in Climate Smart Agriculture

Plasma treatment has emerged as a promising tool for manipulating plant microbiomes and metabolites. This review explores the diverse applications and effects of plasma on these biological systems. It is hypothesized that plasma treatment will not induce substantial changes in the composition of plant microbiomes or the concentration of plant metabolites. We delve into the mechanisms by which plasma can regulate microbial communities, enhance antimicrobial activity, and recruit beneficial microbes to mitigate stress. Furthermore, we discuss the optimization of plasma parameters for effective microbiome interaction and the role of plasmids in plant-microbe interactions. By characterizing plasmidome responses to plasma exposure and investigating transcriptional and metabolomic shifts, we provide insights into the potential of plasma as a tool for engineering beneficial plant-microbe interactions. The review presented herein demonstrates that plasma treatment induces substantial changes in both microbial community composition and metabolite levels, thereby refuting our initial hypothesis. Finally, we integrate plasmidome, transcriptome, and metabolome data to develop a comprehensive understanding of plasma's effects on plant biology and explore future perspectives for agricultural applications.

Exacerbation of virulence of multi-drug resistant Escherichia coli O104:H4 by subinhibitory concentrations of ampicillin

Little is known about how subinhibitory concentrations of antibiotics to which bacteria are resistant affect bacterial virulence. In this study, the effect of subinhibitory concentrations of ampicillin on the virulence of E. coli O104:H4 was analyzed. Bacteria were pre-exposed to 0.1, 0.3, or 0.5 mg/mL of ampicillin in LB media and incubated for 4 h at 37 °C. Transformation capacity (using plasmids and PCR-amplified DNA sequences), swarming motility, biofilm production, curli formation, and virulence gene expression were determined. Ampicillin increased the transformation of E. coli O104:H4, with the highest number of transformants (>104 CFU/ng DNA; p ≤ 0.05) detected after exposure to DNA sequences of spectinomycin. In addition, bacteria pre-treated with 0.5 mg/mL of ampicillin exhibited higher swarming motility (7.6 cm, vs 6.0 cm for control; p ≤ 0.05) and biofilm production (up to 1.9-fold; p ≤ 0.05) when subsequently exposed to 0.1 and 0.3 mg/mL of antibiotic compared with the control. Also, significant overexpression of the virulence-related genes flhC (≤16.1-fold), fliA (≤22.1-fold), csgA (≤3.6-fold), csgD (≤9.1-fold), stx2a (≤32.2-fold), and the antibiotic resistance gene blaTEM-1 (≤5.5-fold) was observed. In conclusion, ampicillin-resistant E. coli O104:H4 increased the expression of its virulence factors when exposed to most subinhibitory concentrations of ampicillin analyzed in this study.

Human and Veterinary Medicine Collaboration: Synergistic Approach to Address Antimicrobial Resistance Through the Lens of Planetary Health

Antimicrobial resistance (AMR) represents a critical threat to human, animal, and environmental health, challenging global efforts to maintain sustainable ecosystems and public health systems. In this review, the complex, cross-disciplinary issues of AMR are explored within the framework of planetary health, emphasizing the interconnectedness of human and veterinary medicine with broader environmental and social systems. Specifically, it addresses the social, economic, environmental, and health dimensions of AMR under the planetary health framework. The social aspects consider how public awareness, education, and healthcare practices shape antimicrobial use (AMU) and resistance patterns. The economic impact evaluates the cost burdens of AMR, including healthcare costs, loss of productivity, and the implications for the livestock and food production industries. The environmental dimension highlights the role of pharmaceutical waste, agricultural runoff, and industrial pollution in contributing to the spread of antimicrobials and resistant pathogens in ecosystems. To illustrate these challenges, a comprehensive literature review using the PubMed and Web of Science databases was conducted, identifying 91 relevant articles on planetary health and AMR. In this review, the knowledge from these studies and additional references is integrated to provide a holistic overview of the AMR crisis. By applying the four pillars of planetary health-social, economic, environmental, and health knowledge-in this manuscript, the necessity is underscored of collaborative strategies across human and veterinary medicine to combat AMR. Ultimately, this synergistic approach aims to shape the policies and practices that safeguard public health, protect ecosystems, and promote a sustainable future by implementing antimicrobial stewardship programs and encouraging prudent AMU.

Temporal dynamic of soil microbial communities and antibiotic resistance markers exposed to increasing concentrations of sulfamethoxazole

The reuse of treated wastewater (TWW) for irrigation is widely applied to alleviate pressure on freshwater resources. However, TWW contains antibiotics that once in soils, can exert selective pressure, promoting the emergence and spread of antimicrobial resistance (AMR) in the environment. Current environmental risk assessments for antibiotic residues rely on indicators such as Predicted No Effect Concentrations (PNECs), usually determined in liquid media. These PNECs aim to predict antibiotic concentrations that may promote resistance in the environment. Given the complexity of soil matrices, few studies have established PNEC values for soil, which likely differ significantly from aquatic environments. To address this gap, we developed a simplified experimental model using soil microcosms irrigated with TWW and the antibiotic sulfamethoxazole (SMX) to estimate threshold concentrations favouring resistance transfer or/and emergence within the soil microbiome. We identified SMX concentrations between 0.01 and 0.1 mg/kgdry soil that likely increased the abundance of sulfonamide resistance genes in soil. A time window of 1-7 days post-exposure showed a temporary rise in sul1 and intl1 gene abundance (over 1 log/soil 16S rDNA), the appearance of SMX transformation products, and an increase in some Rhodocyclaceae. After 1.5 months of incubation and complete SMX transformation, the relative abundance of sul1 and intl1 remained about 0.5 log higher than in SMX-free controls and soils with SMX levels below 0.1 mg/kg dry soil. A persistent transformation product, 4-N-glucuronide-SMX, was also observed. Here, the estimated PNEC for SMX in soil, between 0.01 and 0.1 mg/kg, exceeds typical SMX concentrations found in soils exposed to TWW. This may suggest low impact on resistance selection for this compound in the context of TWW exposure. However further studies on other soils, water, and antibiotics need to be conducted to expand our knowledge on soil PNECs.

Entry, fate and impact of antibiotics in rice agroecosystem: a comprehensive review

Antibiotics are extensively used to manage human, animal and plant ailments caused by microbial infections. However, rampant use of antibiotics has led to the development of antibiotic resistance, which is a public health concern. The development of antibiotic resistance is significantly influenced by agro-ecosystems. Rice agroecosystem receives high levels of antibiotics from direct applications, and sources like manure and irrigation water. Consequently, uptake of antibiotic residues by rice (Oryza sativa L.) is resulting in accumulation of antibiotics in plant parts. Accumulation of these antibiotics can be toxic to plant, and can be partitioned to rice grain and straw, and reach the human and animal food chain leading to the development of antibiotic resistance. Moreover, the antibiotics can alter soil microbes, which would result in loss of production. This study compiles information from existing literature on global antibiotic usage and explores how antibiotics enter the rice ecosystem through contaminated wastewater, manure, sewage sludge, and through direct application. A detailed discussion on the persistence and movement of antibiotics in different environment compartments is provided. The review also highlights the impacts of antibiotics on plants and natural microbiota, as well as issues pertaining to antimicrobial resistance in public health sectors. For sustainable mitigation of the issues of antibiotic residues in rice ecosystem, we suggest application of decontaminated manure, microbial bioremediation, optimization of the use of plant-based alternatives, enhancing regulations, and fostering global collaboration. We advocate integrated disease management approaches which can significantly reduce the antibiotic use in rice agroecosystem.

Comparison of Oxytetracycline and Sulfamethazine Effects Over Root Elongation in Selected Wild and Crop Plants Commonly Present in the Mediterranean Cropland and Pasture Scenarios

Fertilization with animal manure and sewage sludge, and the use of sewage water for irrigation, can lead to high antimicrobial concentrations in agricultural soils. Once in soil, antimicrobials can exert direct and indirect toxic effects on plants by misbalancing plant-microbe symbiotic relationships. We performed germination tests to determine the optimum germination conditions of 24 plant species (10 crop and 14 wild species). Subsequently, we analyzed the differences in oxytetracycline and sulfamethazine phytotoxicity in 19 plant species for which optimum germination conditions could be established. The root elongation of the majority of wild species was inhibited in the presence of oxytetracycline and sulfamethazine, whereas crops were mainly affected by oxytetracycline. There were no differences in sensitivity to oxytetracycline between crop and wild plant species, whereas wild plants were significantly more susceptible to sulfamethazine than crop species. Thus, to cover both productivity and biodiversity protection goals, we recommend pharmaceuticals' predicted no-effect concentration (PNEC) values based on crop and wild plant species phytotoxicity data.

Escherichia coli: An arduous voyage from commensal to Antibiotic-resistance

Escherichia coli (E. coli), a normal intestinal microbiota is one of the most common pathogen known for infecting urinary tract, wound, lungs, bone marrow, blood system and brain. Irrational and overuse of commercially available antibiotics is the most imperative reason behind the emergence of the life threatening infections caused due to antibiotic resistant pathogens. The World Health Organization (WHO) identified antimicrobial resistance (AMR) as one of the 10 biggest public health threats of our time. This harmless commensal can acquire a range of mobile genetic elements harbouring genes coding for virulence factors becoming highly versatile human pathogens causing severe intestinal and extra intestinal diseases. Although, E. coli has been the most widely studied micro-organism, it never ceases to astound us with its ability to open up new research avenues and reveal cutting-edge survival mechanisms in diverse environments that impact human and surrounding environment. This review aims to summarize and highlight persistent research gaps in the field, including: (i) the transfer of resistant genes among bacterial species in diverse environments, such as those associated with humans and animals; (ii) the development of resistance mechanisms against various classes of antibiotics, including quinolones, tetracyclines, etc., in addition to β-lactams; and (iii) the relationship between resistance and virulence factors for understanding how virulence factors and resistance interact to gain a better grasp of how resistance mechanisms impact an organism's capacity to spread illness and interact with the host's defences. Moreover, this review aims to offer a thorough overview, exploring the history and factors contributing to antimicrobial resistance (AMR), the different reported pathotypes, and their links to virulence in both humans and animals. It will also examine their prevalence in various contexts, including food, environmental, and clinical settings. The objective is to deliver a more informative and current analysis, highlighting the evolution from microbiota (historical context) to sophisticated diseases caused by highly successful pathogens. Developing more potent tactics to counteract antibiotic resistance in E. coli requires filling in these gaps. By bridging these gaps, we can strengthen our capacity to manage and prevent resistance, which will eventually enhance public health and patient outcomes.

Prevalence of antibiotic resistance genes in mining-impacted farmland environments

Mining activities produce large quantities of tailings and acid mine drainage, which contain varieties of heavy metals, thereby affecting the downstream farmland soils and crops. Heavy metals could induce antibiotic resistance through co-selection pressure. However, the profiles of antibiotic resistance genes (ARGs) in the mining-affected farmland soils and crops are still unclear. Here we investigated contents of heavy metals, ARG abundances, mobile genetic elements (MGEs), and microbial community in mining-affected farmland soils and vegetables from Shangba village (SB), in comparison to a nearby reference village Taiping (TP). Results showed that in SB group, except for Cr, other metals were all above the Chinese Standards. When compared with the reference group, higher ARG abundances were detected in mining-affected farmland soils and vegetables, with great proportions of genes resistant to sulfonamides, chloramphenicols and tetracyclines. In addition, positive correlations were found between the above three ARG classes and heavy metals concentrations (especially Cu, Pb and Zn). Spearman's correlations revealed that there were positive correlations between sul1 and total nitrogen, as well as tetB/P and pH. Additionally, the Shannon index values were different for the samples from two villages (p < 0.05). Proteobacteria and Actinobacteria were dominant phyla in soil samples. Network analysis suggested that multiple genera (belonging to Proteobacteria and Actinobacteria) were positively associated with many ARGs (p < 0.05), implying they might be potential hosts for ARGs. To sum up, this study provided clear evidence that mining activities caused severe heavy metals pollution to the farmland, thus posing co-selection pressure on the persistence of ARGs in the affected farmland environments.

Removing high strength lincomycin in pharmaceutical wastewater by a bacteria microalgae consortium co-immobilized filter

Lincomycin (LIN) in pharmaceutical wastewater would enter municipal wastewater treatment plants and decrease their performance, leading to residual LIN enter the natural environment and pose serious eco-risk. In this study, a bacterium-microalgae consortium co-immobilized filter (BMCCF) was established and used to remove LIN in artificial pharmaceutical wastewater treatment plants effluents (PWWTPE). LIN removal mechanisms and degradation products' eco-toxicity was studied, and the abundance change of class 1 integrase gene (intI1) and antibiotic resistance genes (ARGs) was monitored. As a result, 98.54% of 82 mg L-1 LIN was removed within 7 days, LIN removal was mainly attributed to bio-degradation by the Bacillus subtilis strain, and LIN degradation products were less toxic than their substrate. Therefore, the BMCCF established in this study provides a promising alternative for the bio-treatment of pharmaceutical wastewater containing high concentration of LIN.

Effects of glyphosate on antibiotic resistance in soil bacteria and its potential significance: A review

The evolution and spread of antibiotic resistance are problems with important consequences for bacterial disease treatment. Antibiotic use in animal production and the subsequent export of antibiotic resistance elements in animal manure to soil is a concern. Recent reports suggest that exposure of pathogenic bacteria to glyphosate increases antibiotic resistance. We review these reports and identify soil processes likely to affect the persistence of glyphosate, antibiotic resistance elements, and their interactions. The herbicide molecular target of glyphosate is not shared by antibiotics, indicating that target-site cross-resistance cannot account for increased antibiotic resistance. The mechanisms of bacterial resistance to glyphosate and antibiotics differ, and bacterial tolerance or resistance to glyphosate does not coincide with increased resistance to antibiotics. Glyphosate in the presence of antibiotics can increase the activity of efflux pumps, which confer tolerance to glyphosate, allowing for an increased frequency of mutation for antibiotic resistance. Such effects are not unique to glyphosate, as other herbicides and chemical pollutants can have the same effect, although glyphosate is used in much larger quantities on agricultural soils than most other chemicals. Most evidence indicates that glyphosate is not mutagenic in bacteria. Some studies suggest that glyphosate enhances genetic exchange of antibiotic-resistance elements through effects on membrane permeability. Glyphosate and antibiotics are often present together in manure-treated soil for at least part of the crop-growing season, and initial studies indicate that glyphosate may increase abundance of antibiotic resistance genes in soil, but longer term investigations under realistic field conditions are needed. Although there are demonstratable interactions among glyphosate, bacteria, and antibiotic resistance, there is limited evidence that normal use of glyphosate poses a substantial risk for increased occurrence of antibiotic-resistant, bacterial pathogens. Longer term field studies using environmentally relevant concentrations of glyphosate and antibiotics are needed.

Toxic effects of tetracycline on non-target lichen Evernia prunastri

Tetracycline (TC) antibiotics are one of the class of drugs widely used in clinical practice but also constitute a significant environmental concern. However, the adverse effects of TC on non-target organisms have not been well studied. The aim of this study was to examine the influence of exposure to high levels of TC on thalli of lichens to determine the impact on (1) physiological parameters including integrity of cell membranes, photosynthetic efficiency and viability, (2) oxidative stress response such as membrane lipid peroxidation, and (3) enzymatic antioxidant activities as catalase (CAT), superoxide dismutase (SOD), ascorbate peroxidase (APX), and glutathione reductase (GR). Data demonstrated that exposure to tetracycline did not markedly affect the lichen membrane damage as indicated by no change in conductivity. This antibiotic diminished the potential photosystem II efficiency (FV/FM) indicating enhanced susceptibility as evidenced by lower chlorophyll fluorescence and chlorophyll content. The viability of lichens exposed to high concentrations of tetracycline was significantly reduced. The concentrations of thiobarbituric acid reactive substances were markedly elevated with increasing concentrations of antibiotics. At higher TC concentrations, 500 mg/L SOD activity was significantly elevated. In the case of CAT, APX and GR, TC at higher concentrations significantly decreased these enzymic activities. The findings of this study contribute to the knowledge that TC antibiotics exert adverse ecotoxicological effects on lichens at high concentrations and provided a better understanding of the mechanisms underlying toxicity. Data also indicates that lichens may serve as an effective biomonitoring species for TC antibiotic exposure.

Response surface methodology and Box-Behnken design optimization of Sulfaquinoxaline removal efficiency and degradation mechanisms by Bacillus sp. strain DLY-11

Antibiotic pollution, particularly the persistence of Sulfaquinoxaline (SQ) residues in livestock and poultry farming environments, has emerged as a pressing environmental concern. Despite this, there remains a limited understanding of the optimized conditions and mechanisms for the efficient degradation of SQ by microorganisms. To address this knowledge gap, we isolated Bacillus sp. strain DLY-11 from aerobically composted manure, which exhibits exceptional SQ degradation capability. Using response surface methodology and Box-Behnken design, we optimized the conditions: 5 % inoculum, 60 °C, pH 8.02, and 0.5 g/L MgSO4. Strain DLY-11 achieved 95.5 % SQ degradation in 2 d. We identified 12 degradation products, including one newly reported, and proposed four degradation pathways involving S-N and C-N bond cleavage, hydroxylation, SO2 release, deamination, oxidation, acetylation, and formylation. One of the proposed pathways is entirely new and has not been previously reported in the literature. This work closes important information gaps in the bacterial degradation pathways of SQ by optimizing the degradation conditions and introducing a useful microbial resource for the effective breakdown of SQ. It also provides a solid theoretical foundation for tackling the problem of antibiotic contamination in livestock and poultry production.

Genomic Analysis of Talaromyces verruculosus SJ9: An Efficient Tetracycline-, Enrofloxacin-, and Tylosin-Degrading Fungus

BACKGROUND/OBJECTIVES

Many fungi related to Talaromyces verruculosus can degrade a wide range of pollutants and are widely distributed globally. T. verruculosus SJ9 was enriched from fresh strawberry inter-root soil to yield fungi capable of degrading tetracycline, enrofloxacin, and tylosin.

METHODS

T. verruculosus SJ9 genome was sequenced, assembled, and annotated in this study utilizing bioinformatics software, PacBio, and the Illumina NovaSeq PE150 technology.

RESULTS

The genome size is 40.6 Mb, the N50 scaffold size is 4,534,389 bp, and the predicted number of coding genes is 8171. The T. verruculosus TS63-9 genome has the highest resemblance to the T. verruculosus SJ9 genome, according to a comparative genomic analysis of seven species. In addition, we annotated many genes encoding antibiotic-degrading enzymes in T. verruculosus SJ9 through genomic databases, which also provided strong evidence for its ability to degrade antibiotics.

CONCLUSIONS

Through the correlation analysis of the whole-genome data of T. verruculosus SJ9, we identified a number of genes capable of encoding antibiotic-degrading enzymes in its gene function annotation database. These antibiotic-related enzymes provide some evidence that T. verruculosus SJ9 can degrade fluoroquinolone antibiotics, tetracycline antibiotics, and macrolide antibiotics. In summary, the complete genome sequence of T. verruculosus SJ9 has now been published, and this resource constitutes a significant dataset that will inform forthcoming transcriptomic, proteomic, and metabolic investigations of this fungal species. In addition, genomic studies of other filamentous fungi can utilize it as a reference. Thanks to the discoveries made in this study, the future application of this fungus in industrial production will be more rapid.

Opportunities and challenges of using human excreta-derived fertilizers in agriculture: A review of suitability, environmental impact and societal acceptance

Human excreta-derived fertilizers (HEDFs) are organic fertilizers made from human excreta sources such as urine and feces. HEDFs can contribute to a sustainable and circular agriculture by reuse of valuable nutrients that would otherwise be discarded. However, HEDFs may contain contaminants such as pharmaceuticals, persistent organic compounds, heavy metals and pathogens which can negatively affect plant, water and soil quality. Moreover, consumer prejudice, farmer hesitance and strict regulations can discourage utilization of HEDFs. Here, we conducted a thorough review of published literature to explore the opportunities and challenges of using HEDFs in agricultural systems by evaluating the suitability of human excreta as a nutrient source, their typical contaminant composition, how they affect the quality of crops, soils and water and their societal impact and acceptance. We found that HEDFs are suitable nutrient-rich fertilizers, but may contain contaminants. Processing treatments increase the fertilizer quality by reducing these contaminants, but they do not remove all contaminants completely. Regarding the environmental impacts of these fertilizers, we found overall positive effects on crop yield, soil nutrients, plant-soil-microbe interactions and plant pathogen suppression. The use of HEDFs reduces water contamination from sewage waste dumping, but nutrient leaching dependent on soil type may still affect water quality. We found no increased risks with human pathogens compared to inorganic fertilizers but identified processing treatment as well as crop and soil type significantly affect these risks. Lastly, we found that public acceptance is possible with clear regulations and outreach to inform consumers and farmers of their multi-faceted benefits and safe usage after processing treatments. In summary, this review emphasizes the great potential of HEDFs and its positive impacts on society, especially in regions where conventional fertilizers are scarce, while also stressing the need for adaptation to specific soils and crops.

Antibiotic resistance in urban soils: Dynamics and mitigation strategies

Antibiotic resistance (AR) is a critical global health issue with significant clinical and economic implications. AR occurs when microorganisms develop mechanisms to withstand the effects of antibiotics, reducing treatment efficacy and increasing the risk of mortality and healthcare costs. While the connection between antibiotic use in clinical and agricultural settings and the emergence of AR is well-established, the role of urban soils as reservoirs and spreaders of AR is underexplored. This review examines the complex dynamics of AR in urban soils, highlighting the various sources of antibiotics, including domestic wastewater, industrial effluents, urban agricultural practices, but also microplastics and domestic animal excrements. The selective pressure exerted by these anthropogenic sources promotes the proliferation of antibiotic-resistant bacteria, particularly through horizontal gene transfer, which facilitates the transmission of resistance genes among soil microorganisms in urban environments. About that, the presence of antibiotics in urban soils poses a significant threat to public health by potentially transferring resistance genes to human pathogens through multiple pathways, including direct contact, food consumption, and water ingestion. Furthermore, AR in urban soils disrupts microbial community dynamics, impacting soil fertility, plant growth, and overall environmental quality. Therefore, this review aims to address gaps in understanding AR in urban soils, offering insights into its implications for human health and ecosystem integrity. By identifying these gaps and suggesting evidence-based strategies, this review proposes valid and sustainable solutions to mitigate and counteract the spread of AR in urban environments.

Cross-environmental cycling of antimicrobial resistance in agricultural areas fertilized with poultry litter: A one health approach

Poultry litter, commonly used as an organic fertilizer, can contain antimicrobial residues, resistant bacteria, and/or antimicrobial resistance genes. After application to soil, these contaminants can reach crops and be transported to aquatic systems through leaching and runoff. Once in water bodies, they can return to soil and crops through irrigation, establishing a cycle that promotes the selection, spread and persistence of antimicrobial resistance. To investigate the hypothesis of a cyclical event, samples of poultry litter, cultivable soil fertilized with this organic residue, rhizosphere soil from Sechium edule (chayote), water, and sediments from irrigation ponds were collected across two agricultural and poultry-producing areas during the dry and rainy seasons. Clinically significant bacteria, especially bacteria belonging to the Enterobacteriaceae family, were isolated. Fifty-three strains exhibited one or more antimicrobial resistance genes, as detected by PCR amplification, including those conferring resistance to sulfonamides (sul1 and sul2), fluoroquinolones (qnrB, qnrA, and qnrS), and β-lactams (blaGES, blaTEM, blaSHV, blaCTX-M-1/2,blaCTX-M-8, and blaCTX-M-14). Genes encoding integrases related to class-1 and 2 integrons (intI1 and intI2) were also observed. A rare occurrence of the blaGES gene was observed in Stenotrophomonas sp. and Brevundimonas sp. Strains of Escherichia sp. were multidrug resistant. Sequencing of the 16S rRNA encoding gene indicated unique operational taxonomic units (OTUs) originating from poultry litter and found in the soil, rhizosphere, water, and sediment, highlighting the dissemination of this material across agricultural substrates. These findings strongly suggest the spread of antimicrobial-resistant bacteria in agricultural environments, posing potential risks to both human and animal health.

Tetracycline but not sulfamethazine inhibits early root growth of wild grassland species, while seed germination is hardly affected by either antibiotic

Seed germination and early growth of grassland species might be influenced by veterinary antibiotics that are extensively released into agricultural habitats. Therefore, we tested impacts of the commonly used antibiotics tetracycline and sulfamethazine, single and in mixture, on seed germination and seedling root growth of six typical species of temperate European grasslands (Carum carvi, Centaurea jacea, Galium mollugo, Plantago lanceolata, Silene latifolia, Dactylis glomerata). In standardised germination experiments, we assessed three germination variables (germination percentage, mean germination time, synchrony of germination) and one post-germination variable (seedling root length) under different environmentally realistic antibiotic concentrations (0.1, 1, 10 mg l-1 and a water control). While the germination variables were only irregularly and weakly affected by both antibiotics, seedling root length was strongly reduced by tetracycline, but not by sulfamethazine. Among the test species, D. glomerata was most sensitive to tetracycline with the average root length reduced up to 81 % in the 10 mg l-1 treatment. Its germination behaviour, however, was almost insensitive to the two antibiotics. Mixture effects were only shown in relation to the germination of single species, where the binary mixture produced effects but not the two single antibiotics or, conversely, effects of single antibiotics were lost in the mixture. These findings highlight the potential threat of plant regeneration from seed by veterinary antibiotics, particularly affecting early root growth and potentially influencing plant population growth in natural habitats.

Fate of fluoroquinolones associated with antimicrobial resistance in circular periurban agriculture

Animal antibiotic use contributes to antimicrobial resistance (AMR) in humans. While animal manure benefits soil fertility, it also acts as hotspot for antibiotic residues, antibiotic-resistant bacteria, and their genes. Amending soils with poultry litter is recognized as "magic" among horticulture farmers and it remains a common practice globally. However, this poses a risk especially in countries where prophylactic use of antibiotics is allowed. In Argentina, fluoroquinolones are used in this way besides being listed as essential medicines and classified as "watch" by the World Health Organization. Antibiotic selective pressure can favour AMR in the environment but the fate of antibiotic residues and AMR dissemination from these practices remains poorly understood. Our research addresses this gap with a biological model tracing fluoroquinolones from poultry to soil to lettuce and tracking anthropogenic AMR with the proposed biomarker genes sul1 and intI1. Fresh poultry litter was stored for six months before application in a horticulture field experiment. The experiment included control and manured plots where lettuce was cultivated till harvest. Enrofloxacin concentration was 7.3 μg/kg in fresh poultry litter, while its metabolite ciprofloxacin was 39.22 μg/kg after storage. Although no fluoroquinolones were detected in soils, lettuce from manured plots contained enrofloxacin and ciprofloxacin at 14.97 and 9.77 μg/kg, respectively, providing evidence of fluoroquinolone bioaccumulation in plants. Abundance of sul1 and intI1 in poultry litter was not affected by storage. Manured soils showed better soil quality than controls, but sul1 gene abundance was 1.6 times higher, reaching 7.61 Log sul1/g soil. A less sensitive, but significant effect was registered for intI1. These findings show that static storage is insufficient to stop the transmission of antibiotics and AMR biomarkers from poultry to horticulture. Amending soil with industrial poultry litter contributes to pollution with these emergent contaminants and risks human antibiotic exposure through fresh vegetables.

Ecological influences of sulfadiazine on rhizosphere soil microbial communities in ryegrass (Lolium perenne L.)-soil potting systems: Perspectives on diversity, co-occurrence networks, and assembly processes

Microorganisms in the soil are crucial constituents of land ecosystems, significantly influencing their structure and functionality. However, the accumulation of antibiotics in agricultural practices may negatively affect these microbial communities. The objective of this study was to explore the ecological effects of the sulfonamide drug sulfadiazine (SDZ) on the rhizosphere soil microbial communities of ryegrass (Lolium perenne L.). A potting system experiment was constructed by exposing for 45 days after treatments with different initial concentrations of SDZ (0, 1, 10, and 30 mg/kg) to assess the effects of SDZ on soil microbial diversity, bacterial-fungal co-occurrence networks, and community assembly processes. The findings indicated that SDZ treatment significantly altered the community composition, especially for bacteria in the phylum Proteobacteria and Gemmatimonadota and fungi in the phylum Mortierellomycota and Aphelidiomycota. Network analysis revealed that SDZ stress caused alterations in microbial interaction patterns, especially at high treatment concentrations, and reduced network connectivity. In addition, SDZ significantly affected microbial community assembly processes, where stochastic processes were enhanced in bacterial communities, while fungal communities showed a balance of stochastic and deterministic processes. Analysis of environmental variables revealed that the presence of SDZ may disrupt the link between soil microorganisms and soil nitrogen compounds. The results provide new perspectives for understanding the ecological impacts of antibiotic residues in agroecosystems and provide a scientific basis for soil health management.

Microplastic and associated emerging contaminants in marine fish from the South China Sea: Exposure and human risks

Microplastics can act as vectors of chemical contaminants in aquatic environments, but the extent to which this phenomenon contributes to chemical exposure in marine organisms remains poorly understood. We investigated the occurrence of microplastics and emerging contaminants (ECs), including antibiotics and per- and polyfluoroalkyl substances (PFAS) in 14 marine fish species. Microplastics were detected in all marine fish species, mainly in the gastrointestinal tract. Fluoroquinolones and tetracyclines were the dominant antibiotics in fish muscles with maximum concentrations of 24.84 and 26.95 ng g-1 ww, while perfluorooctanesulfonic acid (PFOS, 0.039-0.95 ng g-1 ww) was the dominant component in the PFAS profile. Fish with more microplastics had significantly higher concentrations of fluoroquinolones and perfluoroalkyl acids than fish with less microplastics (p < 0.05), but the correlation was not observed in other chemicals. Structural equation modeling revealed the contribution of microplastics in fish on the level of ECs contamination. The health quotient value indicated the low health risk of single compounds via fish consumption to humans; however, the combined risk of microplastics and ECs still needs to be considered. This work highlights the link between microplastics with associated ECs ingested by aquatic organisms and the human health risk of consuming polluted seafood.

Nano-enabled strategies in sustainable agriculture for enhanced crop productivity: A comprehensive review

The global food demand is increasing with the world population, burdening agriculture with unprecedented challenges. Agricultural techniques that ushered in the green revolution are now unsustainable, owing to population growth and climate change. The agri-tech revolution that promises a robust, efficient, and sustainable agricultural system while enhancing food security is expected to be greatly aided by advancements in nanotechnology, which have been reviewed here. Nanofertilizers and nanoinsecticides can benefit agricultural practices economically without major environment impact. Owing to their unique size and features, nano-agrochemicals provide enhanced delivery of active ingredients and increased bioavailability, and posing lesser environment hazard. Nano-agrochemicals should be improved for increased efficiency in the future. In this context, nanocomposites have drawn considerable interest with regard to food security. Nanocomposites can overcome the drawbacks of chemical fertilizers and improve plant output and nutrient bioavailability. Similarly, metallic and polymeric nanoparticles (NPs) can potentially improve sustainable agriculture via better plant development, increased nutrient uptake, and soil healing. Hence, they can be employed as nanofertilizers, nanopesticides, and nanoherbicides. Nanotechnology is also being used to enhance crop production via genetic modification of traits for efficient use of soil nutrients and higher yields. Furthermore, NPs can help plants overcome salinity stress-induced oxidative damage. We also review the fate of NPs in the soil system, plants, animals, and humans, highlight the shortcomings of previous research, and offer suggestions for toxicity studies that would aid regulatory bodies and benefit the agrochemical sector, consequently promoting efficient and sustainable use of nano-agrochemicals.

Comparison of antimicrobial resistant Enterobacterales isolates from the dairy production environment in low and high zinc containing regions

Heavy metals occur naturally in the environment, and their concentration varies in soil across different regions. However, the presence of heavy metals may influence the antimicrobial resistance (AMR) in bacterial populations. Therefore, the objective of this study was to investigate and characterise the antimicrobial resistance profiles of Enterobacterales in soil and bovine milk filters from high and low zinc-containing regions in Ireland. In total, 50 soil samples and 29 milk filters were collected from two geographic locations with varying soil zinc concentrations. Samples were cultured for the enumeration and detection of Enterobacterales. Specifically, extended-spectrum beta-lactamase-producing Enterobacterales, carbapenem-resistant Enterobacterales and ciprofloxacin-resistant Enterobacterales were isolated using selective media. Species identification was performed using MALDI-TOF. The phenotypic resistance profiles of selected Enterobacterales were determined by disk diffusion testing, following EUCAST and CLSI criteria; while, the genotypic resistance profiles of the same isolates were determined by whole genome sequencing (WGS). Heavy metal concentrations were also measured for all soil samples. A total of 40 antimicrobial resistant Enterobacterales were identified in soil (n = 31) and milk filters (n = 9). The predominant species detected in the high zinc-containing region was Escherichia coli in both sample types (soil n = 10, milk filters n = 2), while in the low zinc-containing region Serratia fonticola was predominant in soil samples (n = 8) and E. coli in milk filters (n = 4). Ten E. coli isolates identified from soil samples in the high zinc-containing region were multidrug resistant, showing resistance to all the antimicrobials tested, except for carbapenems. The WGS findings confirmed the phenotypic resistance results. Moreover, zinc resistance-associated genes and genes encoding for efflux pumps were identified. The current study revealed distinct phenotypic resistance profiles of Enterobacterales in low and high zinc-containing regions, and highlighted the benefit of utilising milk filters for AMR surveillance in dairy production.

Antibiotic resistant bacteria and antibiotic resistance genes as contaminants of emerging concern: Occurrences, impacts, mitigations and future guidelines

Antibiotic resistance, driven by the proliferation of antibiotic resistance genes (ARGs) and antibiotic resistance bacteria (ARBs), has emerged as a pressing global health concern. Antimicrobial resistance is exacerbated by the widespread use of antibiotics in agriculture, aquaculture, and human medicine, leading to their accumulation in various environmental compartments such as soil, water, and sediments. The presence of ARGs in the environment, particularly in municipal water, animal husbandry, and hospital environments, poses significant risks to human health, as they can be transferred to potential human pathogens. Current remediation strategies, including the use of pyroligneous acid, coagulants, advanced oxidation, and bioelectrochemical systems, have shown promising results in reducing ARGs and ARBs from soil and water. However, these methods come with their own set of challenges, such as the need for elevated base levels in UV-activated persulfate and the long residence period required for photocatalysts. The future of combating antibiotic resistance lies in the development of standardized monitoring techniques, global collaboration, and the exploration of innovative remediation methods. Emphasis on combination therapies, advanced oxidation processes, and monitoring horizontal gene transfer can pave the way for a comprehensive approach to mitigate the spread of antibiotic resistance in the environment.

Combined effects of polyamide microplastic and sulfamethoxazole in modulating the growth and transcriptome profile of hydroponically grown rice (Oryza sativa L.)

The use of reclaimed water from wastewater treatment plants for irrigation has a risk of introducing micropollutants such as microplastics (MPs) and antimicrobials (AMs) into the agroecosystem. This study was conducted to investigate the effects of single and combined treatment of 0.1 % polyamide (PA ∼15 μm), and varying sulfamethoxazole (SMX) levels 0, 10, 50, and 150 mg/L on rice seedlings (Oryza sativa L.) for 12 days. The study aimed to assess the impact of these contaminants on the morphological, physiological, and biochemical parameters of the rice plants. The findings revealed that rice seedlings were not sensitive to PA alone. However, SMX alone or in combination with PA, significantly inhibited shoot and root growth, total biomass, and affected photosynthetic pigments. Higher concentrations of SMX increased antioxidant enzyme activity, indicating oxidative stress. The roots had a higher SMX content than the shoots, and the concentration of minerals such as iron, copper, and magnesium were reduced in roots treated with SMX. RNA-seq analysis showed changes in the expression of genes related to stress, metabolism, and transport in response to the micropollutants. Overall, this study provides valuable insights on the combined impacts of MPs and AMs on food crops, the environment, and human health in future risk assessments and management strategies in using reclaimed water.

Effects of sulfamethazine and tetracycline at molecular, cellular and tissue levels in Eisenia fetida earthworms

Soil contamination by antibiotics is a global issue of great concern that contributes to the rise of bacterial antibiotic resistance and can have toxic effects on non-target organisms. This study evaluated the variations of molecular, cellular, and histological parameters in Eisenia fetida earthworms exposed to sulfamethazine (SMZ) and tetracycline (TC), two antibiotics commonly found in agricultural soils. The earthworms were exposed for 14 days to a series of concentrations (0, 10, 100, and 1000 mg/kg) of both antibiotics. SMZ and TC did not affect the survival of E. fetida, however, other effects at different levels of biological complexity were detected. The two highest concentrations of SMZ reduced the viability of coelomocytes. At the highest TC concentration, there was a noticeable decline in cell viability, acetylcholinesterase activity (neurotoxicity), and the relative presence of mucopolysaccharides in the epidermis (mucous production). Glutathione S-transferase activity decreased in all TC treatments and at the highest SMZ concentration. However, levels of malondialdehyde and protein carbonyls did not change, suggesting an absence of oxidative stress. Tetracycline was neurotoxic to E. fetida and changed the integrity of the epidermis. Both antibiotics altered the intestinal microbiota of E. fetida, leading to a reduction in the relative abundance of bacteria from the phyla Proteobacteria and Bacteroidetes, while causing an increase in the phylum Actinobacteroidota. All observed changes indicate that both SMZ and TC can disrupt the earthworms' immune system and gut microbiome, while fostering the growth of bacteria that harbour antibiotic resistance genes. Finally, both antibiotics exerted additional metabolic and physiological effects that increased the vulnerability of E. fetida to pathogens.

Effects of sulfamethoxazole and copper on the natural microbial community from a fertilized soil

Cattle manure or its digestate, which often contains antibiotic residues, can be used as an organic fertilizer and copper (Cu) as a fungicide in agriculture. Consequently, both antibiotics and Cu are considered soil contaminants. In this work, microcosms were performed with soil amended with either manure or digestate with Cu and an antibiotic (sulfamethoxazole, SMX) co-presence and the planting of Lactuca sativa. After the addition of the organic amendments, a prompt increase in the microbial activity and at the same time of the sul1 and intI1 genes was observed, although ARGs generally decreased over time. In the amended and spiked microcosms, the microbial community was able to remove more than 99% of SMX in 36 days and the antibiotic did not bioaccumulate in the lettuce. Interestingly, where Cu and SMX were co-present, ARGs (particularly sul2) increased, showing how copper had a strong effect on resistance persistence in the soil. Copper also had a detrimental effect on the plant-microbiome system, affecting plant biomass and microbial activity in all conditions except in a digestate presence. When adding digestate microbial activity, biodiversity and lettuce biomass increased, with or without copper present. Not only did the microbial community favour plant growth, but lettuce also positively influenced its composition by increasing bacterial diversity and classes (e.g., Alphaproteobacteria) and genera (e.g., Bacillus), thus indicating a good-quality soil. KEY POINTS: • Cattle digestate promoted the highest microbial activity, diversity, and plant growth • Cattle digestate counteracted detrimental contaminant effects • Cu presence promoted antibiotic cross-resistance in soil.

Selective increase of antibiotic-resistant denitrifiers drives N2O production in ciprofloxacin-contaminated soils

Agricultural systems significantly contribute to global N2O emissions, which is intensified by excessive fertilization and antibiotic residues, attracting global concerns. However, the dynamics and pathways of antibiotics-induced soil N2O production coupled with microbial metabolism remain controversial. Here, we explored the pathways of N2O production in agricultural soils exposed to ciprofloxacin (CIP), and revealed the underlying mechanisms of CIP degradation and the associated microbial metabolisms using 15N-isotope labeling and molecular techniques. CIP exposure significantly increases the total soil N2O production rate. This is attributed to an unexpected shift from heterotrophic and autotrophic nitrification to denitrification and an increased abundance of denitrifiers Methylobacillus members under CIP exposure. The most striking strain M. flagellatus KT is further discovered to harbor N2O-producing genes but lacks a N2O-reducing gene, thereby stimulating denitrification-based N2O production. Moreover, this denitrifying strain is probably capable of utilizing the byproducts of CIP as carbon sources, evidenced by genes associated with CIP resistance and degradation. Molecular docking further shows that CIP is well ordered in the catalytic active site of CotA laccase, thus affirming the potential for this strain to degrade CIP. These findings advance the mechanistic insights into N2O production within terrestrial ecosystems coupled with the organic contaminants degradation.

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.

Influence of combined application of tetracycline and streptomycin on microbial diversity and function in rice soil

A microcosm experiment was performed to quantify the residues of antibiotics [tetracycline (TC), streptomycin (STR), and streptocycline (STC; a mixture of TC and STR)] in rice soil and to assess their impact on microbial community structure and function using Illumina-MiSeq metagenomic analysis. Antibiotics were applied at half the recommended dose (0.5RD), recommended dose (RD), and double the recommended dose (2RD). At RD, TC was degraded in soil within 9 days of its application, whereas it took 21 days for STR and STC to degrade below limit of quantification (LOQ) level. The residue data were fitted in decay models, and half-lives (DT50) were 46.5-53.3 h and 177.6-198 h for TC and STR, respectively. Soil enzyme activities (dehydrogenase, β-glucosidase, fluorescein diacetate hydrolase, acid phosphatase, alkaline phosphatase) were negatively affected in the antibiotic-treated soil. Targeted metagenomic analysis showed that the major bacterial phyla such as Chloroflexi, Actinobacteria, Planctomycetes, Crenarchaeota, and Gemmatimonadetes were suppressed by antibiotic treatments as compared to control. Shannon, Simpson, ACE, and Chao1 diversity indices showed that bacterial diversity decreased with the application of antibiotics, and decrease in bacterial diversity was more prominent in case of STC as compared to TC and STR. Overall, the combination of antibiotics negatively affected the soil microbial community structure and function in comparison to their individual application.

Sorption and desorption behavior and mechanism of oxytetracycline on soil aggregates organic matter separated from soils and sediments in the Yellow River Delta

Soil aggregates organic matter (SAOM) is composed of free particulate organic matter (fPOM), intra-aggregate particulate organic matter (iPOM), and mineral-associated organic matter (mSOM), which are major antibiotic sorbents that play a significant role in the soil organic matter (SOM) turnover process. To date, the oxytetracycline (OTC) sorption and desorption behavior and mechanisms on SAOM have not been contrastively analyzed. SAOM organic components have been used to study scientific problems and to determine their influence on the fate and migration of OTC among the SOM turnover process. Results demonstrated that SAOM had great OTC sorption capacity ranging from approximately 12100-513,000 mg kg-1 and the desorption proportion was no more than 33.60%. The slow organic carbon pool (mSOM) had greater OTC accumulation capacity than the intermediate active pool (iPOM) and the active pool (fPOM), while OTC was more likely to reside in the active pool in wetlands (fPOM-w) and oil waste land (fPOM-o) than the organic carbon pool (mSOM-f) in farmland with human activity interference. The hysteresis was affected by SAOM's physical surface characteristics when the OTC initial equilibrium sorption concentration was higher than 200 mg L-1. When it was lower than that, it was affected by the organic carbon composition. Hydrogen bonds, electrostatic interactions, and π-π interactions dominated the SAOM-OTC interactions. The results of this study will be useful for evaluating the long-term behavior and migration of antibiotics in SOM turnover processes and could refine risk assessments of antibiotics contamination in soil environmental systems.

Ecological consequences of antimicrobial residues and bioactive chemicals on antimicrobial resistance in agroecosystems

BACKGROUND

The widespread use of antimicrobials in agriculture, coupled with bioactive chemicals like pesticides and growth-promoting agents, has accelerated the global crisis of antimicrobial resistance (AMR). Agroecosystems provides a platform in the evolution and dissemination of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs), which pose significant threats to both environmental and public health.

AIM OF REVIEW

This review explores the ecological consequences of antimicrobial residues and bioactive chemicals in agroecosystems, with a focus on their role in shaping AMR. It delves into the mechanisms by which these substances enter agricultural environments, their interactions with soil microbiomes, and the subsequent impacts on microbial community structure.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Evidence indicates that the accumulation of antimicrobials promotes resistance gene transfer among microorganisms, potentially compromising ecosystem health and agricultural productivity. By synthesizing current research, we identify critical gaps in knowledge and propose strategies for mitigating the ecological risks associated with antimicrobial residues. Moreover, this review highlights the urgent need for integrated management approaches to preserve ecosystem health and combat the spread of AMR in agricultural settings.

Advancements in enzymatic reaction-mediated microbial transformation

Enzymatic reaction-mediated microbial transformation has emerged as a promising technology with significant potential in various industries. These technologies offer the ability to produce enzymes on a large scale, optimize their functionality, and enable sustainable production processes. By utilizing microbial hosts and manipulating their genetic makeup, enzymes can be synthesized efficiently and tailored to meet specific industrial requirements. This leads to enhanced enzyme performance and selectivity, facilitating the development of novel processes and the production of valuable compounds. Moreover, microbial transformation and biosynthesis offer sustainable alternatives to traditional chemical methods, reducing environmental impact and promoting greener production practices. Microbial transformations enrich drug candidate diversity and enhance active ingredient potency, benefiting the pharmaceutical industry. Continued advancements in genetic engineering and bioprocess optimization drive further innovation and application development in Enzymatic reaction-mediated microbial transformation. The integration of AI for predicting enzymatic reactions and optimizing pathways marks a promising direction for future research. In summary, these technologies have the potential to revolutionize several industries by providing cost-effective, sustainable solutions.

Fertilizing drug resistance: Dissemination of antibiotic resistance genes in soil and plant bacteria under bovine and swine slurry fertilization

The increasing global demand for food production emphasizes the use of organic animal fertilizers, such as manure and slurry, to support sustainable agricultural practices. However, recent studies highlight concerns about antibiotic resistance determinants in animal excrements, posing a potential risk of spreading antibiotic resistance genes (ARGs) in agricultural soil and, consequently, in food products. This study examines the dissemination of ARGs within the soil and plant-associated microbiomes in cherry radish following the application of swine and bovine slurry. In a 45-day pot experiment, slurry-amended soil, rhizospheric bacteria, and endophytic bacteria in radish roots and leaves were sampled and analyzed for 21 ARGs belonging to 7 Antibiotic Resistance Phenotypes (ARPs). The study also assessed slurry's impact on soil microbiome functional diversity, enzymatic activity, physicochemical soil parameters, and the concentration of 22 selected antimicrobials in soil and plant tissues. Tetracyclines and β-lactams were the most frequently identified ARGs in bovine and swine slurry, aligning with similar studies worldwide. Swine slurry showed a higher prevalence of ARGs in soil and plant-associated bacteria, particularly TET genes, reflecting pig antibiotic treatments. The persistent dominance of TET genes across slurry, soil, and plant microbiomes highlights significant influence of slurry application on gene occurrence in plant bacteria. The presence of ARGs in edible plant parts underscores health risks associated with raw vegetable consumption. Time-dependent dynamics of ARG occurrence highlighted their persistent presence throughout the experiment duration, influenced by the environmental factors and antibiotic residuals. Notably, ciprofloxacin, which was the only one antimicrobial detected in fertilized soil, significantly impacted bovine-amended variants. Soil salinity modifications induced by slurry application correlated with changes in ARG occurrence. Overall, the research underscores the complex relationships between agricultural practices, microbial activity, and antibiotic resistance dissemination, emphasizing the need for a more sustainable and health-conscious farming approaches.

Global hierarchical meta-analysis to identify the factors for controlling effects of antibiotics on soil microbiota

It is widely known that antibiotics can affect the structure and function of soil microbial communities, but the specific degree of impact and controlled factors on different indicators remain inconclusive. We conducted a multiple hierarchical mixed effects meta-analysis on 2564 observations that were extracted from 60 publications, to comprehensively assess the impact of antibiotics on soil microbiota. The results showed that antibiotics had significant negative effects on soil microbial biomass, α-diversity and soil enzyme activity. Under neutral initial soil, when soil was derived from agricultural land or had a fine-textured, the negative impacts of antibiotics on soil microbial community were exacerbated. Both single and mixed additions of antibiotics had significant inhibitory effects on soil microbial enzyme activities. The Random Forest model predicted the following key moderators involved in the effects of antibiotics on the soil microbiome, and antibiotics type, soil texture were key moderators on the severity of soil microbial biomass changes. Soil texture, temperature and single or combined application constitute of antibiotics were the main drivers of effects on soil enzyme activities. The reported results can be helpful to assess the ecological risk of antibiotics in a soil environment and provides a scientific basis for the rational of antibiotics use in the soil environment.

How Pharmaceutical Residues Occur, Behave, and Affect the Soil Environment

Many pharmaceuticals (PhMs), compounds for the treatment or prevention of diseases in humans and animals, have been identified as pollutants of emerging concern (PECs) due to their wide environmental distribution and potential adverse impact on nontarget organisms and populations. They are often found at significant levels in soils due to the continuous release of effluent and sludge from wastewater treatment plants (WWTPs), the release of which occurs much faster than the removal of PhMs. Although they are generally present at low environmental concentrations, conventional wastewater treatment cannot successfully remove PhMs from influent streams or biosolids. In addition, the soil application of animal manure can result in the pollution of soil, surface water, and groundwater with PhMs through surface runoff and leaching. In arid and semiarid regions, irrigation with reclaimed wastewater and the soil application of biosolids are usual agricultural practices, resulting in the distribution of a wide number of PhMs in agricultural soils. The ability to accurately study the fate of PhMs in soils is critical for careful risk evaluation associated with wastewater reuse or biosolid return to the environment. The behavior and fate of PhMs in soils are determined by a number of processes, including adsorption/desorption (accumulation) to soil colloids, biotic (biodegradation) and abiotic (chemical and photochemical degradation) degradation, and transfer (movement) through the soil profile. The sorption/desorption of PhMs in soils is the main determinant of the amount of organic chemicals taken up by plant roots. The magnitude of this process depends on several factors, such as crop type, the physicochemical properties of the compound, environmental properties, and soil-plant characteristics. PhMs are assumed to be readily bioavailable in soil solutions for uptake by plants, and such solutions act as carriers to transport PhMs into plants. Determining microbial responses under exposure conditions can assist in elucidating the impact of PhMs on soil microbial activity and community size. For all of the above reasons, soil remediation is critical when soil pollutants threaten the environment.

Antibiotics pollutants in agricultural soil: Kinetic, sorption, and thermodynamic of ciprofloxacin

The entry of antibiotics, as pollutants, into the environment has created great concerns. Environmental dynamics of antibiotics based on soil chemical properties need to be a better understanding of their chemical behavior. This research is focused on studying the adsorption behavior and kinetic mechanisms of ciprofloxacin (CIP) in an agricultural soil. For this purpose, a batch experiment was conducted at different times (5 min-24 h), and using initial concentrations of CIP (0-1 mmol L-1) in the soil. The adsorption processes as affected by pH and ionic strength were assessed based on the modeling with response surface methodology (RSM). According to the results, the sorption equilibrium was found within 240 min, and the pseudo second-order model was the best for describing the data. Increasing the initial CIP concentration increased CIP adsorption, but increases in ionic strength and pH had an inverse effect. Based on RSM modeling, the CIP adsorption was 7.31 and 7.03 (mg g-1) in the presence of NaCl and CaCl2 electrolytes, respectively, in the optimized conditions (pH 6.5 and ionic strength 0.01 mol L-1). The spontaneous nature of CIP adsorption was determined based on thermodynamic calculations (ΔG° = -10.8 to -12.4 kJ mol-1). The interaction of pH and ionic strength was described with the quadratic model. The obtained results contribute to understanding the CIP fate in the soil environment and facilitate decisions regarding entry and controlling soil contamination due to this antibiotic.

Effects of 3-year organic farming management on soil antibiotic resistant genes and virulence factors in a double rice cropping system

Investigating the antibiotic resistance genes (ARGs) and virulence factors (VFs) within soil microbial communities is crucial for understanding microbial ecology and the evolution of antibiotic resistance. However, the study of ARGs, VFs, and their predominant microbial hosts in soils under varying rice production management practices remains largely underexplored. To this end, a three-year field experiment was conducted under organic management within a double rice cropping system in South China. The study revealed that, in contrast to conventional management (CK), organic farming practices did not significantly alter the total reads of ARGs and VFs. However, there was a notable alteration in the ARGs abundance at the antibiotic class level, such as an increase (P < 0.05) in the abundance of Multidrug ARGs (by 1.7 %) and a decrease (P < 0.05) in Rifamycin (by 17.5 %) and Fosfomycin ARGs (by 15.3 %). Furthermore, a significant shift in VFs was observed under organic farming compared to CK, characterized by an increase (P < 0.05) in offensive VFs and a decrease (P < 0.05) in nonspecific VFs and the regulation of virulence-associated genes. Key microbial taxa identified as influencing ARGs and VFs in the tested soil samples, e.g., Proteobacteria. The findings highlight the need for more detailed attention to soil ecology within organic rice production systems in South China, particularly concerning the significant alterations observed in ARGs and VFs.

Microbial degradation of contaminants of emerging concern: metabolic, genetic and omics insights for enhanced bioremediation

The perpetual release of natural/synthetic pollutants into the environment poses major risks to ecological balance and human health. Amongst these, contaminants of emerging concern (CECs) are characterized by their recent introduction/detection in various niches, thereby causing significant hazards and necessitating their removal. Pharmaceuticals, plasticizers, cyanotoxins and emerging pesticides are major groups of CECs that are highly toxic and found to occur in various compartments of the biosphere. The sources of these compounds can be multipartite including industrial discharge, improper disposal, excretion of unmetabolized residues, eutrophication etc., while their fate and persistence are determined by factors such as physico-chemical properties, environmental conditions, biodegradability and hydrological factors. The resultant exposure of these compounds to microbiota has imposed a selection pressure and resulted in evolution of metabolic pathways for their biotransformation and/or utilization as sole source of carbon and energy. Such microbial degradation phenotype can be exploited to clean-up CECs from the environment, offering a cost-effective and eco-friendly alternative to abiotic methods of removal, thereby mitigating their toxicity. However, efficient bioprocess development for bioremediation strategies requires extensive understanding of individual components such as pathway gene clusters, proteins/enzymes, metabolites and associated regulatory mechanisms. "Omics" and "Meta-omics" techniques aid in providing crucial insights into the complex interactions and functions of these components as well as microbial community, enabling more effective and targeted bioremediation. Aside from natural isolates, metabolic engineering approaches employ the application of genetic engineering to enhance metabolic diversity and degradation rates. The integration of omics data will further aid in developing systemic-level bioremediation and metabolic engineering strategies, thereby optimising the clean-up process. This review describes bacterial catabolic pathways, genetics, and application of omics and metabolic engineering for bioremediation of four major groups of CECs: pharmaceuticals, plasticizers, cyanotoxins, and emerging pesticides.