Soil Antibiotic Resistance Research Articles

Metagenomic approach reveals the role of bioagents in the environmental dissemination risk of rhizosphere soil antibiotic resistance genes pollution

Antibiotic resistance genes (ARGs) have been identified as emerging contaminants, raising concerns around the world. As environmentally friendly bioagents (BA), plant growth-promoting rhizobacteria (PGPR) have been used in agricultural systems. The introduction of BA will lead to the turnover of the microbial communities structure. Nevertheless, it is still unclear how the colonization of the invaded microorganisms could affects the rhizosphere resistome. Consequently, 190 ARGs and 25 integrative and conjugative elements (ICEs) were annotated using the metagenomic approach in 18 samples from the Solanaceae crop rhizosphere soil under BA and conventional treatment (CK) groups. Our study found that, after 90 days of treatment, ARG abundance was lower in the CK group than in the BA group. The results showed that aminoglycoside antibiotic resistance (OprZ), phenicol antibiotic resistance (OprN), aminoglycoside antibiotic resistance (ceoA/B), aminocoumarin antibiotic resistance (mdtB) and phenicol antibiotic resistance (MexW) syntenic with ICEs. Moreover, in 11 sequences, OprN (phenicol antibiotic resistance) was observed to have synteny with ICEPaeLESB58-1, indicating that the ICEs could contribute to the spread of ARGs. Additionally, the binning result showed that the potential bacterial hosts of the ARGs were beneficial bacteria which could promote the nutrition cycle, such as Haliangium, Nitrospira, Sideroxydans, Burkholderia, etc, suggesting that bacterial hosts have a great influence on ARG profiles. According to the findings, considering the dissemination of ARGs, BA should be applied with caution, especially the use of beneficial bacteria in BA. In a nutshell, this study offers valuable insights into ARGs pollution control from the perspective of the development and application of BA, to make effective strategies for blocking pollution risk migration in the ecological environment.

Tomato bacterial wilt disease outbreaks are accompanied by an increase in soil antibiotic resistance

The presence of soil-borne disease obstacles and antibiotic resistance genes (ARGs) in soil leads to serious economic losses and health risks to humans. One area in need of attention is the evolution of ARGs as pathogenic soil gradually develops, which introduces uncertainty to the dynamic ability of conventional farming models to predict ARGs. Here, we investigated variations in tomato bacterial wilt disease accompanied by the resistome by metagenomic analysis in soils over 13 seasons of monoculture. The results showed that the abundance and diversity of ARGs and mobile genetic elements (MGEs) exhibited a significant and positive correlation with R. solanacearum. Furthermore, the binning approach indicated that fluoroquinolone (qepA), tetracycline (tetA), multidrug resistance genes (MDR, mdtA, acrB, mexB, mexE), and β-lactamases (ampC, blaGOB) carried by the pathogen itself were responsible for the increase in overall soil ARGs. The relationships between pathogens and related ARGs that might underlie the breakdown of soil ARGs were further studied in R. solanacearum invasion pot experiments. This study revealed the dynamics of soil ARGs as soil-borne diseases develop, indicating that these ecological trends can be anticipated. Overall, this study enhances our understanding of the factors driving ARGs in disease-causing soils.

Stimulating the biofilm formation of Bacillus populations to mitigate soil antibiotic resistome during insect fertilizer application

Antibiotic resistance in soil introduced by organic fertilizer application pose a globally recognized threat to human health. Insect organic fertilizer may be a promising alternative due to its low antibiotic resistance. However, it is not yet clear how to regulate soil microbes to reduce antibiotic resistance in organic fertilizer agricultural application. In this study, we investigated soil microbes and antibiotic resistome under black soldier fly organic fertilizer (BOF) application in pot and field systems. Our study shows that BOF could stimulate ARB (antibiotic resistant − bacteria) − suppressive Bacillaceae in the soil microbiome and reduce antibiotic resistome. The carbohydrate transport and metabolism pathway of soil Bacillaceae was strengthened, which accelerated the synthesis and transport of polysaccharides to form biofilm to antagonistic soil ARB, and thus reduced the antibiotic resistance. We further tested the ARB − suppressive Bacillus spp. in a microcosm assay, which resulted in a significant decrease in the presence of ARGs and ARB together with higher abundance in key biofilm formation gene (epsA). This knowledge might help to the development of more efficient bio-fertilizers aimed at mitigating soil antibiotic resistance and enhancing soil health, in particular, under the requirements of global “One Health”.

Unraveling the determinants of antibiotic resistance evolution in farmland under fertilizations

Organic fertilization is a major driver potentiating soil antibiotic resistance in farmland. However, it remains unclear how bacterial antibiotic resistance evolves in fertilized soils and even spreads to crops. Compared with no fertilizer and commercial fertilizer treatments, organic fertilizers markedly increased the abundance of soil antibiotic resistance genes (ARGs) but the relatively weaker transfer of resistance genes from soil to crops. The introduction of organic fertilizers enriches the soil with nutrients, driving indigenous microorganisms towards a K-strategy. The pH, EC, and nutrients as key drivers influenced the ARGs abundance. The neutral (pH 7.2), low salt (TDS 1.4 %) and mesotrophic (carbon content 3.54 g/L) habitats similar to the soil environment conditioned by organic fertilizers. These environmental conditions clearly prolonged the persistence of resistant plasmids, and facilitated their dissemination to massive conjugators soil microbiome but not to plant endophytes. This suggested that organic fertilizers inhibited the spread of ARGs to crops. Moreover, the composition of conjugators showed differential selection of resistant plasmids by endophytes under these conditions. This study sheds light on the evolution and dissemination of antibiotic resistance in farmlands and can aid in the development of antimicrobial resistance control strategies in agriculture.

Suppressing Ralstonia solanacearum and Bacterial Antibiotic Resistance Genes in Tomato Rhizosphere Soil through Companion Planting with Basil or Cilantro

The effects of companion planting on soil antibiotic resistance genes (ARGs) and associated microbial composition have remained largely unclear until now. In this study, we assessed the changes in the soil microbiome and ARGs frequencies for tomato growing soils that were companion planted with basil (TB) or cilantro (TC) using a metagenome approach. The abundance of the phytopathogen Ralstonia solanacearum was significantly lower in the TC or TB treatments compared to the tomato monoculture soils (TT). A significant enrichment of Pseudomonas and Aquabacterium and a depletion of Nocardioides and Streptomyces were observed in the TC treatment. Interestingly, both TC and TB companion planting reduced the absolute abundance and the number of subtypes of ARGs. The TC soil showed the lowest numbers of unique ARG subtypes, especially the ARGs resistant to vancomycin and rifamycin, as well as those associated with multidrug resistance. Furthermore, network analysis further revealed that Nocardioides and Streptomyces were potential hosts of ARGs, whereas Flavobacterium negatively correlated with mdtG, suggesting a suppressive effect in reducing ARGs. Together, our results suggest that the companion planting of tomatoes with basil or cilantro can reduce the risk of ARG accumulation, making it a feasible farming management tool to promote soil and plant health in sustainable agriculture.

Body size: A hidden trait of the organisms that influences the distribution of antibiotic resistance genes in soil

Body size is a key life-history trait of organisms, which has important ecological functions. However, the relationship between soil antibiotic resistance gene (ARG) distribution and organisms' body size has not been systematically reported so far. Herein, the impact of organic fertilizer on the soil ARGs and organisms (bacteria, fungi, and nematode) at the aggregate level was analyzed. The results showed that the smaller the soil aggregate size, the greater the abundance of ARGs, and the larger the body size of bacteria and nematodes. Further analysis revealed significant positive correlations of ARG abundance with the body sizes of bacteria, fungi, and nematodes, respectively. Additionally, the structural equation model demonstrated that changes in soil fertility mainly regulate the ARG abundance by affecting bacterial body size. The random forest model revealed that total phosphorus was the primary soil fertility factor influencing the body size of organisms. Therefore, these findings proposed that excessive application of phosphate fertilizers could increase the risk of soil ARG transmission by increasing the body size of soil organisms. This study highlights the significance of organisms' body size in determining the distribution of soil ARGs and proposes a new disadvantage of excessive fertilization from the perspective of ARGs.

Spread of antibiotic-resistant actinobacteria in soils exposed to various types of anthropogenic impact

The work investigated the spectra of resistance to a certain set of antibiotics and the frequency of occurrence of resistant strains among typical soil bacteria – actinomycetes. Equal samples of isolates from sod-podzolic soil were used, selected at sites typifying various types of economic activity, namely: the production areas of a plywood factory and a chemical plant, the territory of a medical institution, and a solid waste collection and storage site. A total of 58 isolates with features characteristic of actinomycetes of the genus Streptomyces of the sections Cinereus, Helvolo-Flavus and Albus were obtained. It has been established that various types of economic activity lead to specific changes in the antibiotic resistance, which characterizes the soil of a natural grass-grass meadow (back-ground). Isolates with resistance to nalidixic acid, amoxicillin and ceftriaxone were found in the sample taken on the territory of the chemical plant more often than in the soil of the background site. The proportion of strains resistant to nalidixic acid, lincomycin and azithromycin was significantly (P<0.05) higher in the soil samples taken at the MSW collection site and the territory of the medical institution, while those resistant to nalidixic acid and amoxicillin were in the sample from the plywood factory Groups of antibiotics (quinolones – nalidixic acid, and β-lactams – amoxicillin and ceftriaxone) were identified, the resistance to which in streptomyces isolates from soils involved in economic activity was significantly higher than in soil isolates from the background territory. The data obtained in the work indicate the need to monitor the spread of antibiotic resistance in soils that are not only at risk of accumulation of residual concentrations of antibiotics, but also other consequences of anthropogenic influences.

Distribution, source apportionment, and ecological risk assessment of soil antibiotic resistance genes in urban green spaces

Urban green spaces play a crucial role in cities by providing near-natural environments that greatly impacts the health of residents. However, these green spaces have recently been scrutinized as potential reservoirs of antibiotic resistance genes (ARGs), posing significant ecological risks. Despite this concern, our understanding of the distribution, sources, and ecological risks associated with ARGs remains limited. In this study, we investigated the spatial distribution of soil ARGs using spatial interpolation and auto-correlation analysis. To apportion the source of soil ARGs in urban green spaces of Tianjin, Geo-detector method (GDM) was employed. Furthermore, we evaluated the ecological risk posed by ARGs employing risk quotients (RQ). The results of our study showed a significantly higher abundance of Quinolone resistance genes in the soil of urban green spaces in Tianjin. These genes were mainly found in the northwest, central, and eastern regions of the city. Our investigation identified three main factors contributing to the presence of soil ARGs: antibiotic production, precipitation, livestock breeding, and hospital. The results of ecological risk in RQ value showed a high risk associated with Quinolone resistance genes, followed by Aminoglycoside, Tetracycline, Multidrug, MLSB, Beta Lactam, Sulfonamide, and Chloramphenicol. Mantel-test and correlation analysis revealed that the ecological risk of ARGs was greatly influenced by soil properties and heavy metals. This study provides a new perspective on source apportionment and the ecological risk assessment of soil ARGs in urban green spaces.

Impact of biochar on the antibiotic resistome and associated microbial functions in rhizosphere and bulk soil in water-saving and flooding irrigated paddy fields

The addition of biochar in paddies under the condition of water-saving irrigation can simultaneously achieve soil improvement and water conservation, but little is known about the role of these two regulations in mediating the fate of antibiotic resistome in paddy soils. Here, metagenomic analysis was conducted to investigate the effects and intrinsic mechanisms of biochar application and irrigation patterns on propagation of antibiotic resistance genes (ARGs) in paddy soils. The addition of biochar in paddy soil resulted in a reduction of approximately 1.32%–8.01% in the total absolute abundance of ARGs and 0.60%–22.09% in the numbers of ARG subtype. Compared with flooding irrigation, the numbers of detected ARG subtype were reduced by 1.60%–22.90%, but the total absolute abundance of ARGs increased by 0.06%–5.79% in water-saving irrigation paddy soils. Moreover, the combined treatments of flooding irrigation and biochar could significantly reduce the abundance of ARGs in paddy soils. The incremental antibiotic resistance in soil induced by water-saving irrigation was likewise mitigated by the addition of biochar. Correlation analyses indicated that, the differences in soil physicochemical properties under biochar addition or irrigation treatments contributed to the corresponding changes in the abundance of ARGs. Moreover, the variations of microbial community diversity, multidrug efflux abundance and transport system-related genes in paddy soil were also important for mediating the corresponding differences in the abundance of ARGs under the conditions of biochar addition or irrigation treatments. The findings of this study demonstrated the effectiveness of biochar application in mitigating antibiotic resistance in paddy soils. However, it also highlighted a potential concern relating to the elevated antibiotic resistance associated with water-saving irrigation in paddy fields. Consequently, these results contribute to a deeper comprehension of the environmental risks posed by ARGs in paddy soils.

Influence of the Antibiotic Oxytetracycline on the Morphometric Characteristics and Endophytic Bacterial Community of Lettuce (Lactuca sativa L.).

Antibiotics enter the soil with compost prepared from livestock manures and other sources. There is concern that they may influence plant growth and cause antibiotic resistance in soil and plant endospheric microbiomes. In the present work, lettuce plants were cultivated in soil and hydroponics spiked with oxytetracycline (0, 15, and 300 mg × kg-1 and 0, 15, and 50 mg × L-1, respectively) during a 28-day greenhouse experiment. It was revealed that the antibiotic reduced the chlorophyll content, the biomass, and the length of the roots and stems by 1.4-4.7, 1.8-39, 2.5-3.2, and 1.8-6.3 times in soil and in hydroponics. The copy numbers of the tet(A) and tet(X) genes were revealed to be 4.51 × 103-1.58 × 105 and 8.36 × 106-1.07 × 108 copies × g-1, respectively, suggesting the potential migration of these genes from soil/hydroponics to plant roots and leaves. According to a non-metric multidimensional scaling (NMDS) analysis of the 16S rRNA amplicon sequencing data, endospheric bacterial communities were similar in leaves and roots independent of the growing substrate and antibiotic concentration. While soil bacterial communities were unaffected by the presence of antibiotics, hydroponic communities exhibited dependency, likely attributable to the absence of the mitigating effect of soil particle absorption.

Response of soil antibiotic resistance genes and bacterial communities to fresh cattle manure and organic fertilizer application

Livestock manure use in agriculture contributes to pollutants like antibiotic resistance genes (ARGs) and resistant bacteria. This practice could potentially facilitate ARGs development in soil ecosystems. Our study aimed to explore ARGs and bacterial communities in cattle manure from Ningxia beef cattle farms with varying breeding periods. We also assessed the impact of different application rates of cattle manure compost, created by mixing manure with different growing periods, on soil's physicochemical and heavy metal properties. High-throughput PCR and sequencing were used to analyze ARGs and bacterial communities. We aimed to understand ARGs dynamics in cattle manure during breeding stages and the impact of different fertilizer application rates on soil bacteria and resistance genes. We found 212 ARGs from cattle manure, spanning tetracycline, aminoglycoside, multidrug, and MLSB categories. Relative ARGs abundance was presented across breeding stages: lactation (C1), breeding (C3), pre-fattening (C4), calving (C2), and late fattening (C5). pH, total nitrogen (TN), electrical conductivity (EC), arsenic (As) and cadmium (Cd) presence significantly impacted ARGs quantity and microbial community structure in manure. Mobile genetic elements (MGEs) were the primary factor altering ARGs in manure (65.56%). Heavy metals contributed to 18.60% of ARGs changes. Manure application changed soil ARGs abundance, notably in soils with high application rates, primarily associated with aminoglycoside, multidrug and sulfonamide resistance. Soils with higher manure rates had elevated MGEs, positively correlated with most ARGs, suggesting MGEs' role in ARGs dissemination. Soil microbial community structure was influenced by fertilization, particularly with the highest application rate. Heavy metals (specifically Cd, contributing to 23.12%), microbial community changes (17.42%), and MGEs (17.38%) were the main factors affecting soil antibiotic resistance. Our study establishes a framework for understanding ARGs emergence in manure and treated soils. This informs strategies to mitigate environmental ARGs transmission and guides diverse livestock manure application and management.

Protistan predation selects for antibiotic resistance in soil bacterial communities

Understanding how antibiotic resistance emerges and evolves in natural habitats is critical for predicting and mitigating antibiotic resistance in the context of global change. Bacteria have evolved antibiotic production as a strategy to fight competitors, predators and other stressors, but how predation pressure of their most important consumers (i.e., protists) affects soil antibiotic resistance genes (ARGs) profiles is still poorly understood. To address this gap, we investigated responses of soil resistome to varying levels of protistan predation by inoculating low, medium and high concentrations of indigenous soil protist suspensions in soil microcosms. We found that an increase in protistan predation pressure was strongly associated with higher abundance and diversity of soil ARGs. High protist concentrations significantly enhanced the abundances of ARGs encoding multidrug (oprJ and ttgB genes) and tetracycline (tetV) efflux pump by 608%, 724% and 3052%, respectively. Additionally, we observed an increase in the abundance of numerous bacterial genera under high protistan pressure. Our findings provide empirical evidence that protistan predation significantly promotes antibiotic resistance in soil bacterial communities and advances our understanding of the biological driving forces behind the evolution and development of environmental antibiotic resistance.

Large mulch film residues are more unfavourable to the reduction of soil antibiotic resistance genes induced by organic fertilisation than small mulch film residues

Plastic film mulching and organic fertilisation result in the coexistence of mulch film residues of multiple sizes and antibiotic resistance genes (ARGs) in farmlands. However, the differential effects of large and small low-density polyethylene mulch film (LDPEM) and biodegradable mulch film (BDM) residues on ARGs have not yet been studied. In this study, we investigated the dynamic variations in soil ARGs induced by organic fertiliser application under treatments with different LDPEM and BDM residue sizes. The results indicated that the target ARGs could be divided into six clusters according to their variation characteristics with sampling time. The reduction rates of most target ARGs, including ermC, aadA-01, qacEdelta1-01, sul1, sul2, tetM-01, tetM-02 and tetPA in treatments with large mulch film residues were lower than those with small mulch film residues for both LDPEM and BDM, which resulted from the higher average degree and positive correlation ratio in the networks between the soil bacterial community and ARGs. The results of structural equation modelling indicated that soil bacterial communities directly affected soil ARGs, with a path coefficient of −0.6428. Soil physicochemical properties and soil enzyme activities affected soil ARGs through the soil bacterial community with path coefficients of 0.24 and 0.28, respectively. The results of the present study emphasise that the environmental impact of large mulch film residues should not be ignored.

Distribution and Driving Mechanisms of Antibiotic Resistance Genes in Desert-Oasis Continuum

The oasis agro-ecosystem is a complex ecosystem with intensive human activities in arid areas. Microbial antibiotic resistance is posing threats to human health and ecological balance. It is of great importance to investigate the diversity, distribution profiles, and driving factors of soil antibiotic resistance genes under different land use patterns in a desert-oasis continuum, especially for assessing soil environmental and human health risks in arid regions. In this study, high throughput sequencing combined with high throughput quantitative PCR were used to investigate the microbial community structure and patterns of antibiotic resistance genes in a desert-oasis continuum, aiming to explore the distribution characteristics and driving mechanisms of soil resistance genes. The results showed that the diversity and abundance of antibiotic resistance increased significantly from the edge of desert to the central oasis, along with Dest, Cotn, Maiz, Reed, and Sedt, consecutively, implying that farmland soil was an important reservoir of resistance genes, which was closely related to land use and land cover change. Soil microbial communities were significantly correlated with antibiotic resistance genes. Thiobacillus, Pontibacter, Nocardioides, Salinimicrobium, Solirubrobacter, and Streptomyces were important potential hosts of various resistance genes. The patterns of antibiotic resistance genes were shaped by heavy metal elements, MGEs, and microbial communities in arid soil, which accumulatively accounted for 70% of the variations in resistance genes alone or together and therefore drove the occurrence, enrichment, and evolution of resistance genes in agricultural soil of the desert-oasis continuum.

Reforestation substantially changed the soil antibiotic resistome and its relationships with metal resistance genes, mobile genetic elements, and pathogens

Revealing the effects of reforestation on soil antibiotic resistome is essential for assessing ecosystem health, yet related studies remain scarce. Here, to determine the responses of the soil antibiotic resistome to reforestation, 30 pairs of cropland and forest soil samples were collected from southwestern China, a region with high environmental heterogeneity. All the forests had been derived from croplands more than one decade ago. The diversity and abundance of soil antibiotic resistance genes (ARGs), metal resistance genes (MRGs), mobile genetic elements (MGEs), and pathogens were determined by metagenomic sequencing and real-time PCR. The results showed that reforestation significantly increased soil microbial abundance and the contents of Cu, total carbon, total nitrogen, total organic carbon, and ammonium nitrogen. Nevertheless, it decreased the contents of soil Zn, Ba, nitrate nitrogen, and available phosphorus. The main soil ARGs identified in this region were vancomycin, multidrug, and bacitracin resistance genes. Reforestation significantly increased the soil ARG abundance by 62.58%, while it decreased the ARG richness by 16.50%. Reforestation exerted no significant effects on the abundance of heavy metal resistance genes and pathogens, but it doubled the abundance of MGEs. Additionally, reforestation substantially decreased the co-occurrence frequencies of ARGs with MRGs and pathogens. In contrast, the correlation between ARGs and MGEs was greatly enhanced by reforestation. Similarly, the correlations between soil ARG abundance and environmental factors were also strengthened by reforestation. These findings suggest that reforestation can substantially affect the soil antibiotic resistome and exerts overall positive effects on soil health by decreasing ARG richness, providing critical information for assessing the effects of “grain for green” project on soil health.

Elucidating the role of two types of essential oils in regulating antibiotic resistance in soil

Although several approaches for reducing antibiotic resistance genes (ARGs) in soil have been proposed, the application of environmentally friendly approaches is now attracting much more attention. In the present study, two types of essential oils (EOs), namely lavender essential oil (LEO) and oregano essential oil (OEO), were selected to investigate their roles in regulating ARGs in soil. In a 28-day microcosm experiment, it was found that the different types and doses of EOs significantly changed the composition of microbial communities. The LEO treatments enriched more taxa belonging to Actinobacteria than the control, whereas the low dose of OEO reduced Actinobacteria enrichment. Besides, the control and the treatments with a high dose of LEO and OEO all significantly enriched the functional pathways related to Human Diseases, which were positively associated with ARGs. However, the low dose of these EOs helped to reduce the pathways. Because of inhibition of the functional pathways and ARG hosts, the low dose of OEO reduce the ARGs related to antibiotic efflux by 71.8% and the resistance genes to multidrug by 56.4%, but these roles did not occur in LEO treatments. These outcomes provide practical and theoretical support for the application of EOs in remediating ARG-contaminated soils.

Effects of freeze-thaw dynamics and microplastics on the distribution of antibiotic resistance genes in soil aggregates

This is the first study investigating the effects of freeze-thaw (FT) and microplastics (MPs) on the distribution of antibiotic resistance genes (ARGs) in soil aggregates (i.e., soil basic constituent and functional unit) via microcosm experiments. The results showed that FT significantly increased the total relative abundance of target ARGs in different aggregates due to the increase in intI1 and ARG host bacteria. However, polyethylene MPs (PE-MPs) hindered the increase in ARG abundance caused by FT. The host bacteria carrying ARGs and intI1 varied with aggregate size, and the highest number of hosts was observed in micro-aggregates (<0.25 mm). FT and MPs altered host bacteria abundance by affecting aggregate physicochemical properties and bacterial community and enhanced multiple antibiotic resistance via vertical gene transfer. Although the dominant factors affecting ARGs varied with aggregate size, intI1 was a co-dominant factor in various-sized aggregates. Furthermore, other than ARGs, FT, PE-MPs, and their integration promoted the proliferation of human pathogenic bacteria in aggregates. These findings suggested that FT and its integration with MPs significantly affected ARG distribution in soil aggregates. They amplified antibiotic resistance environmental risks, contributing to a profound understanding of soil antibiotic resistance in the boreal region.

Application of nematicide avermectin enriched antibiotic-resistant bacteria and antibiotic resistance genes in farmland soil

The extensive use of antibiotics in medicine and agriculture has resulted in the accumulation of antibiotic-resistant microorganisms and antibiotic resistance genes (ARGs) in environments, which threaten human health and contaminate environment. Nematicide avermectin is widely applied to control root-knot nematodes. The effect of five-years application of avermectin on rhizosphere microbiome and resistome of sick tobacco plants in farmland were investigated in present study. The environmental risks of avermectin was assessed adequately. Metagenomic method was used to analyze antibiotic-resistant bacteria and antibiotic resistance genes in the avermectin-treated soil. The abundance and distribution of antibiotic-resistant bacteria and their antibiotic resistance genes were affected by avermectin application. The antibiotic resistant Proteobacteria occupied the highest percentage (36%) in rhizosphere soil and carried 530 ARGs. Opportunistic human pathogens carrying antibiotic resistance genes were enriched in the avermectin-treated soil. Avermectin application increased the counts of many types of antibiotic resistance genes. The relative abundances of genes adeF, BahA, fusH, ileS, and tlrB in the avermectin-treated soil were significantly greater than in the untreated control soil. Different resistance mechanisms were revealed in the avermectin-treated soil. The efflux of antibiotic (670 ARGs), inactivation of antibiotic (475 ARGs), and alteration of antibiotic target (267 ARGs) were the main resistance mechanisms. Rigid control the avermectin dose and use frequency and other pesticides can decrease soil antibiotic resistance genes and protect agricultural products’ safety and public health. Overall, application of nematicide avermectin enriched antibiotic-resistant bacteria and antibiotic resistance genes in farmland soil, which should be on the alert for environment protection.

Exploring the interaction between agronomic practices and soil characteristics on the presence of antibiotic resistance genes in soil

In this study, field-scale experiments were carried out to analyze the coupling effects of typical agronomic measures and soil types on soil antibiotic resistance genes (ARGs) using high-throughput fluorescence quantitative PCR. The results indicated that agronomic measures enhanced ARG abundance in different soil types. For the same soil type, the enhancement of ARG abundance in response to agronomic measures could be ordered as follows: livestock manure application (257.6–131.7 %) > sewage irrigation (57.6–35.0 %) > plastic film mulching (21.2–5.0 %). Under the same agronomic measures, enhancement of ARG abundance according to soil type was: clay (257.6–21.2 %) > loam (147.8–15.9 %) > sandy (131.7–5.0 %). Furthermore, the contributions of environmental factors in determining ARG abundance in different soil types differed in response to the application of different agronomic measures. Phthalates had the most and least pronounced effects on ARG abundance in sandy and loam soils, respectively. Effects of moisture on ARG abundance were minor in loam soil, but greater in clay and sandy soils. These findings provide new insights into the dissemination of soil ARGs promoted by the adoption of agronomic measures.

Does increasing the organic fertilizer application rate always boost the antibiotic resistance level in agricultural soils?

The amendment of organic fertilizer derived from livestock manure or biosolids is a significant driver of increasing antibiotic resistance in agricultural soils; however, it remains unclear whether increasing organic fertilizer application rates consistently enhances soil antibiotic resistance levels. Herein, we collected soils with long-term amendment with three types of organic fertilizers at four application rates (15, 30, 45, and 60 t/ha/y) and found that the higher the fertilization rate, the higher the antibiotic resistance gene (ARG) abundance. However, when the fertilization rate exceeded 45 t/ha/y, the ARG abundance ceased to significantly increase. Moreover, the soil ARG abundance was positively correlated with total nitrogen (TN) content and bacterial abundance, especially Firmicutes, and negatively affected by pH and bacterial diversity. Soil TN/bacterial abundance and pH/bacterial diversity reached maximum and minimum values at the 45 t/ha/y fertilization rate, respectively. Meanwhile, at this fertilization rate, Firmicutes enrichment peaked. Therefore, an organic fertilization rate of 45 t/ha/y appeared to represent the threshold for soil antibiotic resistance in this study. The underlying mechanism for this threshold was closely related to soil TN, pH, bacterial abundance, and diversity. Taken together, the findings of this study advance the current understanding regarding the soil resistome under different fertilization rates, while also providing novel insights into organic fertilizer management in agricultural practices.