Temporal effects of repeated application of biogas slurry on soil antibiotic resistance genes and their potential bacterial hosts

Anaerobic digestates in agricultural soils: A systematic review of their effects on antibiotic resistance genes

Tackling the dissemination of antibiotic resistance is one of the main global challenges. Manures from animal production are a recognized source of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) requiring appropriate treatment methods. One of the main approaches for manure treatment is anaerobic digestion (AD). Meta-analyses have demonstrated that AD can significantly reduce the load of ARGs. However, antibiotics, ARGs and MGEs still remain in the final product (digestate). A sustainable agricultural use of digestates under the One Health framework requires wide assessments of their effects in the soil resistome. The objective of this review was to present the state of the art of digestate effects on ARGs of agricultural soils, focusing exclusively on digestates from animal manures. A systematic review was conducted. The examination of the resulting literature indicated that although temporal decays are observed for a variety of ARGs in single-application and repeated-applications experiments, for certain ARGs the pre-treatment or control levels are not restored. However, the low number of studies and the heterogeneous experimental conditions preclude a clear understanding of the fate of ARGs in soil and their risk for agroecosystems. The inclusion of multiple MGEs and the assessment of the long-term influence of digestates on soil properties and microbial communities could be keystones for a better understanding of the risks associated with digestate-induced changes in the soil resistome.

Environmental risks in swine biogas slurry-irrigated soils: A comprehensive analysis of antibiotic residues, resistome, and bacterial pathogens

Simple anaerobic digestion is insufficient to completely remove residual parent antibiotics and antibiotic resistance genes (ARGs) from animal manure. ARG prevalence in swine biogas slurry-irrigated soils threatens human health. However, comprehensive analysis of antibiotic residues, high-resolution resistance gene profiles, and pathogenic microbiomes in biogas slurry-irrigated soils is very limited. Here, we comprehensively determined the antibiotics, resistome, and potential pathogens distribution in these soils, using high-performance liquid chromatography-tandem mass spectrometry, high-throughput quantitative PCR, and 16S rRNA gene sequencing. The results revealed a significant enrichment of tetracyclines and fluoroquinolones antibiotics and ARGs in soils with prolonged biogas slurry irrigation, with a total of 12 antibiotics, 175 unique ARGs, and 9 mobile genetic elements (MGEs) detected. Quantification of veterinary antibiotic residues (especially chlortetracycline) showed significant correlations with multiple ARGs. The abundance of ARGs and MGEs was highest in the biogas slurry-irrigated soils, denoting a tight link between the application of biogas slurry and the spread of antibiotic resistance. The presence of 50 potential pathogenic bacterial genera, including 13 with multidrug resistance, was identified. Variation partitioning, combined with hierarchical partitioning analysis, indicated that Firmicutes, MGEs, and tetracyclines were the key drivers shaping the ARG profiles in biogas slurry-irrigated soils. The findings offer insights into the mechanisms of antibiotic residue and ARGs spread from the agricultural practice of biogas slurry irrigation, underscoring the necessity of sustainable soil management to mitigate the spread of antibiotic resistance.

Investigation of high-risk antibiotic resistance bacteria and their associated antibiotic resistance genes in different agricultural soils with biogas slurry from China

High-risk antibiotic-resistant bacteria (ARB) and their accompanying antibiotic resistance genes (ARGs) seriously threaten public health. As a crucial medium for ARB and ARGs spread, soils with biogas slurry have been widely investigated. However, few studies focused on high-risk multi-drug resistant bacteria (MDRB) and their associated ARGs. This study examined ARB distribution in different agricultural soils with biogas slurry across 12 districts in China. It identified high-risk MDRB in various soil backgrounds, elucidating their resistance and spread mechanism. The findings revealed that diverse cultured ARB were enriched in soils with biogas slurry, especially soil ciprofloxacin ARB, which were enriched (>2.5 times) in 68.4 % of sampling sites. Four high-risk MDRB isolated from Hebei, Zhejiang, Shanxi, and Gansu districts were identified as severe or opportunistic pathogens, which carried abundant mobile genetic elements (MGEs) and 14 known high risk ARGs, including aac(3)-IId, aac(6')-Ib3, aph(6)-Id, aac(6')-Ib3, aadA1, blaOXA-10, blaTEM-1B, dfrA12, dfrA14, cmlA1, sul1, floR, tet(M) and tet(L). The antibiotics accumulation, diverse ARGs and MGEs enrichment, and proliferation of pathogenic bacteria could be potential driving factors of their occurrence and spread. Therefore, the coexistence of the high-risk MDRB and ARGs combined with the associated MGEs in soils with biogas slurry should be further investigated to develop technology and policy for reducing their negative influences on the effectiveness of clinical antibiotics.

Combined use of digestate and inorganic fertilizer alleviates the burden of class 1 integrons in perennial ryegrass rhizosphere without compromising aerial biomass production

Antimicrobial resistance (AMR) is one of the main global health challenges. Anaerobic digestion (AD) can significantly reduce the burden of antibiotic resistance genes (ARGs) in animal manures. However, the reduction is often incomplete. The agronomic use of digestates requires assessments of their effects on soil ARGs. The objective of this study was to assess the effect of digestate on the abundance of ARGs and mobile genetic elements (MGEs) in the rhizosphere of ryegrass (Lolium perenne L.) and to determine whether half-dose replacement of digestate with urea (combined fertilizer) can be implemented as a safer approach while maintaining a similar biomass production. A greenhouse assay was conducted during 190 days under a completely randomized design with two experimental factors: fertilizer type (unfertilized control and fertilized treatments with equal N dose: digestate, urea and combined fertilizer) and sampling date (16 and 148 days after the last application). The results indicated that the digestate significantly increased the abundance of clinical class 1 integrons (intI1 gene) relative to the unfertilized control at both sampling dates (P < 0.05), while the combined fertilizer only increased them at the first sampling. Sixteen days after completing the fertilization scheme only the combined fertilizer and urea significantly increased the biomass production relative to the control (P < 0.05). Additionally, by the end of the assay, the combined fertilizer showed significantly lower levels of the macrolide-resistance gene ermB than digestate and a cumulative biomass similar to urea or digestate. Overall, the combined fertilizer can alleviate the burden of integrons and ermB while simultaneously improving biomass production.

Metagenomic insights into the impact of litter from poultry Concentrated Animal Feeding Operations (CAFOs) to adjacent soil and water microbial communities

In recent decades, human food consumption has led to an increased demand for animal-based foods, particularly chicken meat production. The state of Georgia, USA is one of the top broiler chicken producers in the United States, where animals are raised in Concentrated Animal Feeding Operations (CAFOs). Without proper management, CAFOs could negatively impact the environment and become a public health risk as a source of water and air pollution and/or by spreading antimicrobial resistance genes. In this study, we used metagenome sequencing to investigate the impact of the application of the CAFO's litter on adjacent soils and downstream creek waters in terms of microbial diversity and antimicrobial resistance profile changes. Our data indicate that while a few microbial groups increased in abundance within a short period of time after litter application, these populations subsequently decreased to levels similar to those found prior to the litter application or to below the detection limit of our metagenome sequencing effort. Microbial taxonomic composition analyses, relative abundance of Metagenome-Assembled Genomes (MAGs) and detection of Antimicrobial Resistance Genes (ARGs) allow us to conclude that this practice of litter application had a negligible effect on the microbiome or resistome profile of these soils and nearby waterways, likely due to its dilution in the field and/or outcompetition by indigenous microbes, revealing a minimal impact of these poultry facilities on the natural microbial communities.

Field-based evidence for the enrichment of intrinsic antibiotic resistome stimulated by plant-derived fertilizer in agricultural soil

Animal manures have been demonstrated to enhance antibiotic resistance in agricultural soils. However, little is known about the effects of plant-derived fertilizer on soil antibiotic resistome. Herein, metagenomic sequencing was used to investigate the effects of a plant-derived fertilizer processed from sugarcane and beet on soil antibiotic resistance genes (ARGs) in a soybean field along crop growth stages. ARG profiles in the soils amended by plant-derived fertilizer were compared with those in the soils amended by chicken manure. The abundance and diversity of total ARGs in the soils amended by plant-derived fertilizer were significantly (P < 0.05) elevated at the sprout stage, to a level comparable to that in the manured soils. Whereas, unlike chicken manure mainly introducing manure-borne ARGs to soil, the plant-derived fertilizer was indicated to mainly enrich multidrug resistance genes in soil by nourishing indigenous bacteria. ARGs with abundances in amended soils significantly (P < 0.05) higher than in unamended soils at the sprout stage of soybean were considered as enriched ARGs. Decrease in the abundance of the enriched ARGs was observed in both the amended soils from the sprout to the harvest. Network analysis further identified Proteobacteria and Bacteroidetes as the primary bacterial taxa involved in the temporal variation of the enriched ARGs in the soils amended by plant-derived fertilizer, while in manured soils were Firmicutes and Actinobacteria. As revealed by multivariate statistical analyses, variation of the enriched ARGs in the soils amended by plant-derived fertilizer was majorly attributed to the response of co-occurred bacteria to depleting nutrients, which was different from the failed establishment of manure-borne bacteria in the manured soils. Our study provided field-based evidence that plant-derived fertilizer stimulated the intrinsic antibiotic resistome, and proposed attention to the un-perceived risk since some clinically relevant ARGs originate and evolve from natural resistome.

Swine-manure composts induce the enrichment of antibiotic-resistant bacteria but not antibiotic resistance genes in soils

Composting is a common and effective strategy for reducing antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) from animal manure. However, it is unclear whether the advantages of composting for the control of ARGs and ARB can be further increased in land application. This study investigated the fate of ARB and ARGs after land application of swine-manure composts (SMCs) to three different soil types (red soil, loess and black soil). The results showed that although the SMCs caused an increase in the abundance of total ARGs in the soil in the short period, they significantly reduced (p < 0.01) the abundance of total ARGs after 82 days compared to the control. The decay rate of ARGs reflected by the half-life times (t1/2) varied by soil type, with red soil being the longest. The SMCs mainly introduced ermF, tetG and tetX into the soils, while these ARGs quickly declined to the control level. Notably, SMCs increased the number of ARB in the soils, especially for cefotaxime-resistant bacteria. Although SMCs only affected the microbiome significantly during the early stage (p < 0.05), it took a much longer time for the microbiome to recover compared to the control. Statistical analysis indicated that changes in the microbial community contributed more to the fate of ARGs during SMCs land application than other factors. Overall, it is proposed that the advantages of ARGs control in the composting process for swine manure can be further increased in land application, but it can still bring some risks in regard to ARB.

Antibiotic resistance in soil-plant systems: A review of the source, dissemination, influence factors, and potential exposure risks

As an emerging environmental contaminant, the widespread of antibiotic resistance has caused a series of environmental issues and human health concerns. A load of antibiotic residues induced by agricultural practices have exerted selective pressure to bacterial communities in the soil-plant system, which facilitated the occurrence and dissemination of antibiotic resistance genes (ARGs) through horizontal gene transfer. As a result, the enrichment of ARGs within crops at harvest under the influence of food ingestion could lead to critical concerns of public health. In this review, the prevalence and dissemination of antibiotic resistance in the soil-plant system are highlighted. Moreover, different underlying mechanisms and detection methods for ARGs transfer between the soil environment and plant compartments are summarized and discussed. On the other hand, a wide range of influencing factors for the transfer and distribution of antibiotic resistance within the soil-plant system are also presented and discussed. In response to exposure of antibiotic residues and resistomes, corresponding hazard identification assessments have been summarized, which could provide beneficial guides of the toxicological tolerance for the general population. Finally, further research priorities for detection and management ARGs spread are also suggested.

The Source and Distribution of Tetracycline Antibiotics in China: A Review

In recent years, antibiotics have been listed as a new class of environmental pollutants. Tetracycline antibiotics (TCs) used in human medical treatment, animal husbandry and agricultural production are the most widely used antibiotics. Due to their wide range of activities and low cost, their annual consumption is increasing. TCs cannot be completely metabolized by humans and animals. They can be abused or overused, causing the continuous accumulation of TCs in the ecological environment and potential negative effects on non-target organisms. These TCs may spread into the food chain and pose a serious threat to human health and the ecology. Based on the Chinese environment, the residues of TCs in feces, sewage, sludge, soil and water were comprehensively summarized, as well as the potential transmission capacity of air. This paper collected the concentrations of TCs in different media in the Chinese environment, contributing to the collection of a TC pollutant database in China, and facilitating the monitoring and treatment of pollutants in the future.

Flushing control strategies to improve the stability of a biogas slurry drip irrigation system: Behavioral characteristics and mechanisms

Biogas slurry drip irrigation can mitigate environmental pollution and reduce the use of chemical fertilizers to enable sustainable development. However, the stability of the biogas slurry drip irrigation system (BSDIS) is disrupted by emitter clogging; hence, it is essential to explore the flushing control strategy of BSDIS. By means of combining actual measurement and simulation, this study investigates the BSDIS stability based on the three technical parameters of the flushing control strategy. Appropriate flushing control strategies can improve system stability and cause spatial differences on the drip irrigation tape. Under various flushing control strategies, the system stability primarily undergoes delays, sensitivity, and ineffectiveness of flushing with time. Compared with the without flushing and emitter outlet downward-oriented treatment, the optimal flushing combination (the high frequency flushing + emitter outlet upward-oriented treatment) reduces the emitter clogging content by approximately 70.97% and increases system stability by 189.1%. In the internal hydrodynamics, the laying direction of emitters does not change the movement characteristics of water flow, although the clogging particles do not completely follow the water flow, with some particles settling owing to gravity, thereby clotting the emitters. When clogging occurs, the increase in flushing speed is conducive to the increase in turbulent kinetic energy on the inlet surface of the emitter, which facilitate the flushing of clogged substances. This study proposes optimal flushing strategy parameters along with a new management mode for the waste liquid represented by biogas slurry.

Effects of functional modules and bacterial clusters response on transmission performance of antibiotic resistance genes under antibiotic stress during anaerobic digestion of livestock wastewater

The formation and transmission of antibiotic resistance genes (ARGs) have attracted increasing attention. It is unclear whether the internal mechanisms by which antibiotics affect horizontal gene transfer (HGT) of ARGs during anaerobic digestion (AD) were influenced by dose and type. We investigated the effects of two major antibiotics (oxytetracycline, OTC, and sulfamethoxazole, SMX) on ARGs during AD according to antibiotic concentration in livestock wastewater influent. The low-dose antibiotic (0.5 mg/L) increased ROS and SOS responses, promoting the formation of ARGs. Meanwhile, low-dose antibiotics could also promote the spread of ARGs by promoting pili, communication responses, and the type IV secretion system (T4SS). However, different types and doses of antibiotics would lead to changes in the above functional modules and then affect the enrichment of ARGs. With the increasing dose of SMX, the advantages of pili and communication responses would gradually change. In the OTC system, low-dose has the strongest promoting ability in both pili and communication responses. Similarly, an increase in the dose of SMX would change T4SS from facilitation to inhibition, while OTC completely inhibits T4SS. Microbial and network analysis also revealed that low-dose antibiotics were more favorable for the growth of host bacteria.

The role of the biogas slurry microbial communities in suppressing fusarium wilt of cucumber

The clarification of the suppressive effect of biogas slurries (BSs) on soil-borne plant pathogens is needed for their large-scale use as a biocontrol tool in potting soil in order to understand the mechanisms of suppression. In this study, pig manure biogas slurry (PS) and vinasse biogas slurry (VS) were used to conduct assays of pathogen mycelial growth suppression and pot experiment to evaluate their effects on the growth of Fusarium. oxysporum f. sp. cucumerinum (FOC) mycelia and cucumber fusarium wilt. The microbial communities of the PS and VS were deeply analyzed to explore the key taxa and potential mechanisms. Results showed that the PS and VS have similar suppression on FOC mycelia and on the control efficiency, while they were significantly weakened when the PS and VS were used after sterilization. The microbial parameters of the two BSs were obviously different, and functional microbial taxa for disease resistance were observed in the two BSs. Spearman correlation showed that genera of the Pseudomonas, Ochrobactrum, Papiliotrema, etc., were the suppression-related taxa in the PS, while Leucobacter, unclassified_Microbacteriaceae, etc. in the VS. Overall, various key taxa in the PS and VS produced similar suppression on cucumber fusarium wilt.

Profile of Bacterial Community and Antibiotic Resistance Genes in Typical Vegetable Greenhouse Soil

The use of vegetable greenhouse production systems has increased rapidly because of the increasing demand for food materials. The vegetable greenhouse production industry is confronted with serious environmental problems, due to their high agrochemical inputs and intensive utilization. Besides this, antibiotic-resistant bacteria, carrying antibiotic-resistance genes (ARGs), may enter into a vegetable greenhouse with the application of animal manure. Bacterial communities and ARGs were investigated in two typical vegetable-greenhouse-using counties with long histories of vegetable cultivation. The results showed that Proteobacteria, Firmicutes, Acidobacteria, Chloroflexi, and Gemmatimonadetes were the dominant phyla, while aadA, tetL, sul1, and sul2 were the most common ARGs in greenhouse vegetable soil. Heatmap and principal coordinate analysis (PCoA) demonstrated that the differences between two counties were more significant than those among soils with different cultivation histories in the same county, suggesting that more effects on bacterial communities and ARGs were caused by soil type and manure type than by the accumulation of cultivation years. The positive correlation between the abundance of the intI gene with specific ARGs highlights the horizontal transfer potential of these ARGs. A total of 11 phyla were identified as the potential hosts of specific ARGs. Based on redundancy analysis (RDA), Ni and pH were the most potent factors determining the bacterial communities, and Cr was the top factor affecting the relative abundance of the ARGs. These results might be helpful in drawing more attention to the risk of manure recycling in the vegetable greenhouse, and further developing a strategy for practical manure application and sustainable production of vegetable greenhouses.

Characterization of labyrinth emitter-clogging substances in biogas slurry drip irrigation systems

Drip irrigation is important for efficiently returning biogas slurry to fields. Elucidating the characteristics and components of clogging substances produced by labyrinth emitters in biogas slurry drip irrigation systems will help to develop various clogging substance-remediation strategies. However, previous studies were unable to characterize the clogging substances in emitters. Thus, we aimed to characterize and quantify the substances clogging emitters in a biogas slurry drip irrigation system and determine the micromorphology and dominance of microbial communities. Here, emitter discharge changes and the micromorphologies, phase compositions, and biological communities of clogging substances were studied via hydraulic performance tests, scanning electron microscopy-energy depressive spectra (SEM-EDS), and high-throughput sequencing. The degree of emitter-clogging increased over time (first quickly, then slowly) and was deeper at the end of the drip irrigation tape than at the head. The clogging substances were viscous agglomerations primarily comprising 0.3-1.5-μm particles. Their formation was affected by settlement with gravity, water pressure adhesion, and mobile biological adhesion. The dominant microbial communities in the clogging substances included Firmicutes (29.7%) and Proteobacteria (19%); the emitter-clogging substances primarily comprised water (85%) and composite dry matter. The water, dry matter, and extracellular polymer substance (EPS) weights in the clogging substances increased over time, but their relative proportions remained stable. In the composite dry matter, typical physical (organic carbon, Al₂O₃, and SiO₂), chemical (CaCO₃ and MgCO₃), and biological (EPS) clogging substances accounted for >50, 9, and 5.62% of the total dry matter mass, respectively. This study provides a good foundation and reference idea and will be very helpful to propose targeted solutions for solving the clogging of biogas slurry drip irrigation system.

Characteristics of antibiotic resistance genes in full-scale anaerobic digesters of food waste and the effects of application of biogas slurry on soil antibiotic resistance genes

The fate of antibiotic resistance genes (ARGs) in full-scale anaerobic digestion (AD) of food waste (FW) and in the soil applied with biogas slurry has not been fully understood. In this study, 12 targeted ARGs and intI1 in FW, intermediate product, and biogas slurry from three full-scale AD were analyzed. The results showed that subcritical water pretreatment was an effective method for ARG attenuation, by which the absolute abundance of total targeted ARGs was removed by 99.69%. The predominant ARGs (ermB, tetM, and tetW) in FW were removed more than 99% after subcritical water pretreatment. The result of field experiments with biogas slurry as fertilizer showed that the absolute abundance of several ARGs (sul2, tetM, blaOXA-1, blaTEM) and intI1 accumulated significantly compared to the control group (CK) during three consecutive growth stages of the rice. The detected abundance of ARGs in paddy field soil increased from 190.50 (CK) to 8.87 × 10⁴ copies/g (wet weight) (soil) during tillering stage, and increased from 4102.65 (CK) to 4.38 × 10⁴ copies/g (wet weight) (soil) during heading time. Biogas slurry improved the soil nutrients (TN, AN, TP, and AP); meanwhile, the concentrations of total salt and Cl^- increased. Network analysis indicated that 28 genera were the possible hosts of ARGs; variation partitioning analysis (VPA) indicated that microbial communities (contribution 59.30%) were the main factors that affected the fate of ARGs and intI1.

A sustainable and economic strategy to reduce risk antibiotic resistance genes during poultry manure bioconversion by black soldier fly Hermetia illucens larvae: Larval density adjustment

Black soldier fly (Hermetia illucens) larvae (BSFL) are common insects that are known for bioconversion of organic waste into a sustainable utilization resource. However, a strategy to increase antibiotic resistance gene (ARG) elimination in sustainable and economic ways through BSFL is lacking. In the present study, different larval densities were employed to assess the mcr-1 and tetX elimination abilities, and potential mechanisms were investigated. The application and economic value of each larval density were also analyzed. The results showed that the 100 larvae cultured in 100 g of manure group had the best density because the comprehensive disadvantage evaluation ratio was the lowest (14.97%, good bioconversion manure quality, low ARG deposition risk and reasonable larvae input cost). Further investigation showed that mcr-1 could be significantly decreased by BSFL bioconversion (4.42 ×10⁷ copies/g reduced to 4.79 ×10⁶-2.14 ×10⁵ copies/g)(P＜0.05); however, mcr-1 was increasingly deposited in the larval gut with increasing larval density. The tetX abundance was stabilized by BSFL bioconversion, except that the abundance at the lowest larval density increased (1.22 ×10¹⁰ copies/g increase, 34-fold). Escherichia was the host of mcr-1 and tetX in all samples, especially in fresh manure; Alcaligenes was the host of tetX in bioconversion manure; and the abundance of Alcaligenes was highly correlated with the pH of bioconversion manure. The pH of bioconversion manure was extremely correlated with the density of larvae. Klebsiella and Providencia were both hosts of tetX in the BSF larval gut, and Providencia was also the host of mcr-1 in the BSF larval gut. The density of larvae influenced the bioconversion manure quality and caused the ARG host abundance to change to control the abundance of ARGs, suggesting that larval density adjustment was a useful strategy to manage the ARG risk during BSFL manure bioconversion.

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

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

From gut to mud: dissemination of antimicrobial resistance between animal and agricultural niches

With increasing reports on antimicrobial resistance (AMR) in humans, animals and the environment, we are at risk of returning to a pre-antibiotic era. Therefore, AMR is recognized as one of the major global health threats of this century. Antibiotics are used extensively in farming systems to treat and prevent infections in food animals or to increase their growth. Besides the risk of a transfer of AMR between the human and the animal sector, there is another yet largely overlooked sector in the One Health triad. Human-dominated ecosystems such as agricultural soils are a major sink for antibiotics and AMR originating from livestock farming. This review summarizes current knowledge on the prevalence of AMR at the interface of animal and agricultural production and discusses the potential implications for human health. Soil resistomes are augmented by the application of manure from treated livestock. Subsequent transfer of AMR into plant microbiomes may likely play a critical role in human exposure to antibiotic resistance in the environment. Based on the knowledge that is currently available we advocate that more attention should be paid to the role of environmental resistomes in the AMR crisis.

Effects of bentonite on antibiotic resistance genes in biogas slurry and residue from thermophilic and mesophilic anaerobic digestion of food waste

Anaerobic digestion (AD) processes of food waste (FW) have potential risk on environments due to the prevalence and dissemination of antibiotic resistance genes (ARGs). This study investigated the effect of bentonite on methane production and the abundance of ARGs in biogas slurry and residue during AD of FW. Results showed that methane production increased by 68.52% and 56.79% with 3 g/L and 5 g/L of bentonite in mesophilic and thermophilic digestion, respectively. Adding 5 g/L of bentonite effectively reduced the genes of ermB, ermF, tetQ, tetX, sul1, sul2 and intI1 with a range of 80.82% - 100.00% in biogas residue under mesophilic reactor. The abundance of ARGs and intI1 in biogas residue were lower than in slurry under both temperatures with 5 g/L of bentonite. Statistical analysis indicated that bentonite and temperature were main driver factors which could impact ARGs by influencing the abundance and structure of microbial communities.

In situ analysis of antibiotic resistance genes in anaerobically digested dairy manure and its subsequent disposal facilities

The metagenomic and quantitative polymerase chain reaction approaches were combined to evaluate the profiles of ARGs and plasmids in anaerobically digested dairy manure in situ and reveal the persistence and elevation of typical ARGs and plasmids in its subsequent disposal facilities in CAFOs, respectively. Our results indicated that the typical ARGs and plasimd were mainly sul2, mefa, tetm-01, tetm-02, tetw, aph3iiia, and clostridioides difficile strain 12,038 plasmid unnamed in CAFOs, some of which greatly enriched in AD residue after its storage, especially sul1 and sul2. Meantime, the AD slurry recycling introduced the bacteria carrying ARGs into soil, especially Romboutsia genus, which greatly enriched sul2, tetm-01, tetm-02, aphiiia, and mefa. In the present study, ARGs occurrence, persistence and distribution were understood through in situ analysis of their profiles during dairy manure AD treatment and subsequent disposals in CAFOs, which are helpful for controlling the potential environmental risks from dairy manure recycling.

Effect of Digestate and Straw Combined Application on Maintaining Rice Production and Paddy Environment

Few studies have focused on the combined application of digestate and straw and its feasibility in rice production. Therefore, we conducted a two-year field experiment, including six treatments: without nutrients and straw (Control), digestate (D), digestate + fertilizer (DF), digestate + straw (DS), digestate + fertilizer + straw (DFS) and conventional fertilizer + straw (CS), to clarify the responses of rice growth and paddy soil nutrients to different straw and fertilizer combinations. Our results showed that digestate and straw combined application (i.e., treatment DFS) increased rice yield by 2.71 t ha⁻¹ compared with the Control, and digestate combined with straw addition could distribute more nitrogen (N) to rice grains. Our results also showed that the straw decomposition rate at 0 cm depth under DS was 5% to 102% higher than that under CS. Activities of catalase, urease, sucrase and phosphatase at maturity under DS were all higher than that under both Control and CS. In addition, soil organic matter (SOM) and total nitrogen (TN) under DS and DFS were 20~26% and 11~12% higher than that under B and DF respectively, suggesting straw addition could benefit paddy soil quality. Moreover, coupling straw and digestate would contribute to decrease the N content in soil surface water. Overall, our results demonstrated that digestate and straw combined application could maintain rice production and have potential positive paddy environmental effects.

Manure Microbial Communities and Resistance Profiles Reconfigure after Transition to Manure Pits and Differ from Those in Fertilized Field Soil

In agricultural settings, microbes and antimicrobial resistance genes (ARGs) have the potential to be transferred across diverse environments and ecosystems. The consequences of these microbial transfers are unclear and understudied. On dairy farms, the storage of cow manure in manure pits and subsequent application to field soil as a fertilizer may facilitate the spread of the mammalian gut microbiome and its associated ARGs to the environment. To determine the extent of both taxonomic and resistance similarity during these transitions, we collected fresh manure, manure from pits, and field soil across 15 different dairy farms for three consecutive seasons. We used a combination of shotgun metagenomic sequencing and functional metagenomics to quantitatively interrogate taxonomic and ARG compositional variation on farms. We found that as the microbiome transitions from fresh dairy cow manure to manure pits, microbial taxonomic compositions and resistance profiles experience distinct restructuring, including decreases in alpha diversity and shifts in specific ARG abundances that potentially correspond to fresh manure going from a gut-structured community to an environment-structured community. Further, we did not find evidence of shared microbial community or a transfer of ARGs between manure and field soil microbiomes. Our results suggest that fresh manure experiences a compositional change in manure pits during storage and that the storage of manure in manure pits does not result in a depletion of ARGs. We did not find evidence of taxonomic or ARG restructuring of soil microbiota with the application of manure to field soils, as soil communities remained resilient to manure-induced perturbation.

Analysis of the occurrence and molecular characteristics of drug-resistant strains of Enterococcus faecalis isolated from the gastrointestinal tract of insectivorous bat species in Poland: A possible essential impact on the spread of drug resistance?

Bats are poorly understood as a reservoir of multidrug-resistant strains; therefore, the aim of this study was to determine molecular characterization of multidrug-resistant Enterococcus strains isolated from bat species from Poland. A multi-stage analysis based on targeted isolation of drug-resistant strains (selective media with tetracycline, chloramphenicol, gentamicin, streptomycin, and vancomycin), determination of the phenotypic profile of drug-susceptibility using the disc diffusion method, and amplification of DNA fragments surrounding rare restriction sites (ADSRRS-fingerprinting) was used for the isolation and differentiation of strains. The applied strategy finally allowed identification of E. faecalis resistant to at least one antimicrobial in 47.2% of the single-animal group and in 46.9% of the pooled samples of bat's guano. Out of the 36 distinct isolates, 69% met the criteria of multi-drug resistance, with a dominant combination of resistance to tetracycline, erythromycin, and rifampicin. Simultaneously, 41.6% of the strains were high-level aminoglycoside resistant (HLAR). In most strains, phenotypic resistance was reflected in the presence of at least one gene encoding resistance to a given drug. Moreover, our research results show that some genes were detected simultaneously in the same strain statistically significantly more frequently. This may confirm that the spread of some genes (tetM and ermB or aph (3')-IIIa as well as gelE and aac (6')-Ie-aph (2″)-Ia or ant (6)-Ia) is associated with their common occurrence on the same mobile genetic element. To our knowledge, this is the first analysis of multidrug-resistance among E. faecalis isolated from bats. Our research demonstrates that the One Health concept is not associated exclusively with food-producing animals and humans, but other species of wildlife animals should be covered by monitoring programs as well. We confirmed for the first time that bats are an important reservoir of multi-resistant E. faecalis strains and could have a great impact on environmental resistance.

Changes and distributions of antibiotic resistance genes in liquid and solid fractions in mesophilic and thermophilic anaerobic digestion of dairy manure

This study mainly explored the changes and distributions of antibiotic resistance genes (ARGs) in liquid fraction (L_F) and solid fraction (S_F) in anaerobic digestion (AD) of dairy manure. After mesophilic and thermophilic AD, the copy numbers of ARGs in L_F decreased by 0.06-1.80 logs while those in S_F increased by 0.08-7.85 logs, suggesting the enrichment of ARGs in S_F. Statistical analysis elucidated that high total solids promoted the enrichment of ARGs in S_F. The increased abundances of genera such as Ruminofilibacter, Treponema and Sphaerochaeta in S_F were responsible for the enrichment of most ARGs. These insights demonstrated the digested solid had the potential risks to promote the spread of ARGs in the environment, and the digested solid of livestock manure should be post-treated before the application.

Manure as a Potential Hotspot for Antibiotic Resistance Dissemination by Horizontal Gene Transfer Events

The increasing demand for animal-derived foods has led to intensive and large-scale livestock production with the consequent formation of large amounts of manure. Livestock manure is widely used in agricultural practices as soil fertilizer worldwide. However, several antibiotic residues, antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria are frequently detected in manure and manure-amended soils. This review explores the role of manure in the persistence and dissemination of ARGs in the environment, analyzes the procedures used to decrease antimicrobial resistance in manure and the potential impact of manure application in public health. We highlight that manure shows unique features as a hotspot for antimicrobial gene dissemination by horizontal transfer events: richness in nutrients, a high abundance and diversity of bacteria populations and antibiotic residues that may exert a selective pressure on bacteria and trigger gene mobilization; reduction methodologies are able to reduce the concentrations of some, but not all, antimicrobials and microorganisms. Conjugation events are often seen in the manure environment, even after composting. Antibiotic resistance is considered a growing threat to human, animal and environmental health. Therefore, it is crucial to reduce the amount of antimicrobials and the load of antimicrobial resistant bacteria that end up in soil.