Resistance Genes In Soil Research Articles

Promotion effects and mechanisms of molybdenum disulfide on the propagation of antibiotic resistance genes in soil

The rapid development of nanotechnology has aroused considerable attentions toward understanding the effects of engineered nanomaterials (ENMs) on the propagation of antibiotic resistance. Molybdenum disulfide (MoS2) is an extensively used ENM and poses potential risks associated with environmental exposure; nevertheless, the role of MoS2 toward antibiotic resistance genes (ARGs) transfer remains largely unknown. Herein, it was discovered that MoS2 nanosheets accelerated the horizontal transfer of RP4 plasmid across Escherichia coli in a dose-dependent manner (0.5–10 mg/L), with the maximum transfer frequency 2.07-fold higher than that of the control. Integration of physiological, transcriptomics, and metabolomics analyses demonstrated that SOS response in bacteria was activated by MoS2 due to the elevation of oxidative damage, accompanied by cell membrane permeabilization. MoS2 promoted bacterial adhesion and intercellular contact via stimulating the secretion of extracellular polysaccharides. The ATP levels were maximally increased by 305.7 % upon exposure to MoS2, and the expression of plasmid transfer genes was up-regulated, contributing to the accelerated plasmid conjugation and increased ARG abundance in soil. Our findings highlight the roles of emerging ENMs (e.g., MoS2) in ARGs dissemination, which is significant for the safe applications and risk management of ENMs under the development scenarios of nanotechnology.

Bacterial community assembly and antibiotic resistance genes in soils exposed to antibiotics at environmentally relevant concentrations.

Understanding how bacterial community assembly and antibiotic resistance genes (ARGs) respond to antibiotic exposure is essential to deciphering the ecological risk of anthropogenic antibiotic pollution in soils. In this study, three loam soils with different land management (unmanured golf course, dairy-manured pasture, and swine-manured cornfield) were spiked with a mixture of 11 antibiotics at the initial concentration of 100 and 1000 μg kg-1 for each antibiotic and incubated over 132 days, mimicking a scenario of pulse disturbance and recovery in soils, with unspiked soil samples as the control treatment. The Infer Community Assembly Mechanisms by Phylogenetic-bin-based null model (iCAMP) analysis demonstrated that drift and dispersal limitation contributed to 57%-65% and 16%-25%, and homogeneous selection 12%-16% of soil bacterial community assembly. Interestingly, antibiotic exposure to 1000 μg kg-1 level significantly increased the contribution of drift to community assembly, largely due to the positive response from Acidobacteria-6 in the golf course and pasture soilsand from Chthoniobacteraceae in the cornfield soil to the antibiotic exposure. However, ARG abundance and diversity in the three soils exhibited antibiotics-independent temporal fluctuations, but were associated with the changes in soil bacterial communities over time. This study provides the first insight into the relative contributions of different bacterial community assembly processes in soils upon antibiotic exposure at environmentally relevant concentrations.

Transmission mechanisms of antibiotic resistance genes in arsenic-contaminated soil under sulfamethoxazole stress

Numerous studies have revealed the spread mechanism of antibiotic resistance genes (ARGs) in single antibiotic-contaminated soils. However, the comprehensive impacts of heavy metals and antibiotics on ARGs and the underlying mechanisms are still unknown. Here, high-throughput quantitative PCR and high-throughput sequencing were used to investigate changes in ARGs and bacterial communities under various sulfamethoxazole (SMX) regimes (0, 1, 10, 50 mg kg−1) in arsenic (As) contaminated soils. The study found that the abundances of ARGs, mobile genetic elements (MGEs), and heavy metal resistance genes (HMRGs) significantly increased in the soil fortified at 10 and 50 mg kg−1 SMX concentrations. The ARGs abundance increased with the increase in the MGEs abundance. Many significant positive correlations between various ARGs subtypes and HMRGs subtypes were found. These results indicate that the HMRGs and MGEs positively contributed to the enrichment of ARGs in As-contaminated soils under SMX stress. Meanwhile, the abundance of copiotrophic (Actinobacteriota) reduced and oligotrophic (Gemmatimonadota) increased, indicating that the life history strategy of the community changed. In addition, Gemmatimonadota was positively correlated to ARGs, HMRGs, and MGEs, suggesting that Gemmatimonadota, which can cope with As and SMX stress, was the host for resistance genes in the soil. Finally, the study found that MGEs play a determinant role in ARGs proliferation due to the direct utilization of HGT, and the indirect effect for ARGs spread under a co-selection mechanism of ARGs and HMRGs, while the bacterial community showed indirect influences by altering environmental factors to act on MGEs. Collectively, this study revealed new insights into the mechanisms of resistance gene transmission under combined SMX and As contamination in soil ecosystems.

Exposure to cypermethrin pesticide disturbs the microbiome and disseminates antibiotic resistance genes in soil and the gut of Enchytraeus crypticus

Worldwide, pyrethroids, such as cypermethrin, are the second most applied group of insecticides, however, their effects on the soil microbiome and non-target soil fauna remain largely unknown. Herein, we assessed the change of bacterial communities and antibiotic resistance genes (ARGs) of soil and in the gut of the model soil species Enchytraeus crypticus using a combination of 16S rRNA gene amplicon sequencing, and high-throughput qPCR of ARGs. Results indicate that cypermethrin exposure enriches potential pathogens (e.g. Bacillus anthracis) in the soil and gut microbiome of E. crypticus, heavily disrupting the latter’s microbiome structure, and even disrupts activities of the E. crypticus immune system. The co-occurrence of potential pathogens (e.g. Acinetobacter baumannii), ARGs, and mobile genetic elements (MGEs) revealed the increased risk of pathogenicity as well as antibiotic resistance in potential pathogens. Moreover, structural equation modeling demonstrated that the dissemination of ARGs was not only promoted by MGEs, but also by the ratio of the core to non-core bacterial abundance. Collectively, these results provide an in-depth view of the previously unappreciated environmental risk of cypermethrin on the dissemination of ARGs in the soil and non-target soil fauna.

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.

Attenuation of tetracyclines and related resistance genes in soil when exposed to nanoscale zero-valent iron

Antibiotics pollution in soil poses increasing threats to human health due to stimulated proliferation and transmission of antibiotic resistance genes (ARGs). Nanoscale zero-valent iron (NZVI) is a promising material for the remediation of antibiotics, but how NZVI affects the diversity, abundance, and horizontal gene transfer potentials of ARGs remains unclear. Herein, the biotic and abiotic effects of NZVI at different concentrations on tetracyclines (TCs) and the associated ARGs were investigated. Results showed NZVI could effectively accelerate the degradation of TCs, which increased from 51.38% (without NZVI) to 57.96%− 71.66% (1–10 g NZVI/kg) in 20 days. Biotic degradation contributed to 66.10%− 76.30% of the total TCs removal. NZVI induced TCs biodegradation was probably due to alleviated toxicity of TCs on cells and increased microbial biomass and enzyme activities. Additionally, TCs-related ARGs were attenuated with decreased horizontal gene transfer potentials of intI1 and ISCR1, but opposite effects were observed for non TC-related ARGs, especially during excess exposure to NZVI. This study illustrated the possibility of remediating of antibiotic contaminated soil by NZVI and meanwhile reducing the potential risks of ARGs.

Heavy Metal Content and Resistance Gene Abundance and Related Properties in the Surface Soil around Qinghai Lake

Soil heavy metal pollution and the prevalence of resistance genes have been a global concern, and thus many studies have reported the content of heavy metals and resistance genes in soils; however, the contents of heavy metals and antibiotic resistance genes (ARGs) in the soil in highland areas is still unclear. In this study, the environmental residues and distribution of heavy metals and resistance genes in the soil in Qinghai were analyzed, and the relationship between the concentration of heavy metals and antibiotic resistance genes in the soil was explored. Among the soil samples, the content of heavy metal zinc was the highest ［mean: (50.27±19.88) mg·kg-1］, followed by the content of heavy metal cadmium ［mean: (30.27±9.45) mg·kg-1］, and the content of heavy metal mercury was the lowest ［mean: (0.027±0.019) mg·kg-1］. The subtypes of heavy metal resistance genes in soils were mainly czcA, merA, and merP, whose main function was to be responsible for developing mercury resistance. The relative abundance of β-lactamase resistance genes (0.1505) was the highest in soil, accounting for 47.54% of the total abundance of ARGs; tetracycline resistance genes accounted for 16.93% of the total abundance of ARGs, FCA accounted for approximately 14.56%, and MLSB accounted for approximately 8.77%. The diversity and relative abundance of movable genetic elements (MGEs) were low, and only the [STBX]tnpA01[STBZ] gene was detected; intl[STBX]1[STBZ] and intl[STBX]2[STBZ] were not detected. Correlation studies showed that Cu content (r=-0.533, P=0.006) and Hg (r=0.692, P=0.006) in soil were significantly negatively correlated with altitude, whereas other heavy metals were not significantly correlated with altitude. In addition, heavy metal content was significantly correlated with soil type (P<0.05). There was a significant positive correlation between heavy metal mercury content in soils and czcA (r=0.692, P=0.006), merA (r=0.816, P=0.007), and merP (r=0.594, P=0.02). The results of this study elucidated the occurrence and distribution of heavy metals and ARGs in the Tibetan Plateau region and found that the content of heavy metals in the soil was significantly related to resistance genes.

Antimicrobial Resistance and Its Drivers-A Review.

Antimicrobial resistance (AMR) is a critical issue in health care in terms of mortality, quality of services, and financial damage. In the battle against AMR, it is crucial to recognize the impacts of all four domains, namely, mankind, livestock, agriculture, and the ecosystem. Many sociocultural and financial practices that are widespread in the world have made resistance management extremely complicated. Several pathways, including hospital effluent, agricultural waste, and wastewater treatment facilities, have been identified as potential routes for the spread of resistant bacteria and their resistance genes in soil and surrounding ecosystems. The overuse of uncontrolled antibiotics and improper treatment and recycled wastewater are among the contributors to AMR. Health-care organizations have begun to address AMR, although they are currently in the early stages. In this review, we provide a brief overview of AMR development processes, the worldwide burden and drivers of AMR, current knowledge gaps, monitoring methodologies, and global mitigation measures in the development and spread of AMR in the environment.

The source, fate and prospect of antibiotic resistance genes in soil: A review

Antibiotic resistance genes (ARGs), environmental pollutants of emerging concern, have posed a potential threat to the public health. Soil is one of the huge reservoirs and propagation hotspot of ARGs. To alleviate the potential risk of ARGs, it is necessary to figure out the source and fate of ARGs in the soil. This paper mainly reviewed recent studies on the association of ARGs with the microbiome and the transmission mechanism of ARGs in soil. The compositions and abundance of ARGs can be changed by modulating microbiome, soil physicochemical properties, such as pH and moisture. The relationships of ARGs with antibiotics, heavy metals, polycyclic aromatic hydrocarbons and pesticides were discussed in this review. Among the various factors mentioned above, microbial community structure, mobile genetic elements, pH and heavy metals have a relatively more important impact on ARGs profiles. Moreover, human health could be impacted by soil ARGs through plants and animals. Understanding the dynamic changes of ARGs with influencing factors promotes us to develop strategies for mitigating the occurrence and dissemination of ARGs to reduce health risks.

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.

Plasmid-Mediated Transfer of Antibiotic Resistance Genes in Soil.

Due to selective pressure from the widespread use of antibiotics, antibiotic resistance genes (ARGs) are found in human hosts, plants, and animals and virtually all natural environments. Their migration and transmission in different environmental media are often more harmful than antibiotics themselves. ARGs mainly move between different microorganisms through a variety of mobile genetic elements (MGEs), such as plasmids and phages. The soil environment is regarded as the most microbially active biosphere on the Earth’s surface and is closely related to human activities. With the increase in human activity, soils are becoming increasingly contaminated with antibiotics and ARGs. Soil plasmids play an important role in this process. This paper reviews the current scenario of plasmid-mediated migration and transmission of ARGs in natural environments and under different antibiotic selection pressures, summarizes the current methods of plasmid extraction and analysis, and briefly introduces the mechanism of plasmid splice transfer using the F factor as an example. However, as the global spread of drug-resistant bacteria has increased and the knowledge of MGEs improves, the contribution of soil plasmids to resistance gene transmission needs to be further investigated. The prevalence of multidrug-resistant bacteria has also made the effective prevention of the transmission of resistance genes through the plasmid-bacteria pathway a major research priority.

The contribution of manure to antibiotic resistance and the spread of antibiotic resistance genes in soil: a review

The intensive use of antibiotics, worldwide, in animal husbandry, has led to the development and enrichment of different environments in antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs). Moreover, the subsequent application of manure contributes to the emergence of antimicrobial resistance (AMR) in soil. The spread of ARB and ARGs through trophic networks and potential human transmission indicate the need for innovative treatment approaches and strategies to reduce manure contaminants.

Dead but Not Forgotten: How Extracellular DNA, Moisture, and Space Modulate the Horizontal Transfer of Extracellular Antibiotic Resistance Genes in Soil.

Antibiotic-resistant bacteria and the spread of antibiotic resistance genes (ARGs) pose a serious risk to human and veterinary health. While many studies focus on the movement of live antibiotic-resistant bacteria to the environment, it is unclear whether extracellular ARGs (eARGs) from dead cells can transfer to live bacteria to facilitate the evolution of antibiotic resistance in nature. Here, we use eARGs from dead, antibiotic-resistant Pseudomonas stutzeri cells to track the movement of eARGs to live P. stutzeri cells via natural transformation, a mechanism of horizontal gene transfer involving the genomic integration of eARGs. In sterile, antibiotic-free agricultural soil, we manipulated the eARG concentration, soil moisture, and proximity to eARGs. We found that transformation occurred in soils inoculated with just 0.25 μg of eDNA g-1 soil, indicating that even low concentrations of soil eDNA can facilitate transformation (previous estimates suggested ∼2 to 40 μg eDNA g-1 soil). When eDNA was increased to 5 μg g-1 soil, there was a 5-fold increase in the number of antibiotic-resistant P. stutzeri cells. We found that eARGs were transformed under soil moistures typical of terrestrial systems (5 to 30% gravimetric water content) but inhibited at very high soil moistures (>30%). Overall, this work demonstrates that dead bacteria and their eARGs are an overlooked path to antibiotic resistance. More generally, the spread of eARGs in antibiotic-free soil suggests that transformation allows genetic variants to establish in the absence of antibiotic selection and that the soil environment plays a critical role in regulating transformation. IMPORTANCE Bacterial death can release eARGs into the environment. Agricultural soils can contain upwards of 109 ARGs g-1 soil, which may facilitate the movement of eARGs from dead to live bacteria through a mechanism of horizontal gene transfer called natural transformation. Here, we track the spread of eARGs from dead, antibiotic-resistant Pseudomonas stutzeri cells to live antibiotic-susceptible P. stutzeri cells in sterile agricultural soil. Transformation increased with the abundance of eARGs and occurred in soils ranging from 5 to 40% gravimetric soil moisture but was lowest in wet soils (>30%). Transformants appeared in soil after 24 h and persisted for up to 15 days even when eDNA concentrations were only a fraction of those found in field soils. Overall, our results show that natural transformation allows eARGs to spread and persist in antibiotic-free soils and that the biological activity of eDNA after bacterial death makes environmental eARGs a public health concern.

Restriction of biosolids returning to land: Fate of antibiotic resistance genes in soils after long-term biosolids application

Although the utilization of biosolids in agricultural lands is widely considered as an effective way to improve resource reuse, the presence of antibiotic resistance genes (ARGs) severely restricts biosolids returning to fields. A 12-year long-term experiment with different biosolids application rates (from 0 to 36 t ha−1 yr−1) was conducted to study the effect of biosolids application on shaping ARGs in soil. Biosolids application significantly increased ARGs abundance in the soil, except for MBS treatment (9 t ha−1 yr−1 biosolids application). The abundance of ARGs in soil did not increase linearly with the dose of biosolids applied, but they were significantly (P < 0.05) positively correlated. A total of 173 subtypes were detected, among them mobile genetic elements (MGEs), aminoglycoside, and multidrug resistance genes were the most dominant types. Except for MBS treatment, most of the ARGs detected were enriched in amended soils after long-term continuous biosolids application. Specifically, tetPA, sul1, mefA, and IS6100 were highly enriched in all amended soils. In addition, biosolids application increased soil nutrients and heavy metals, and changed the soil microbial community, all of which affected ARGs formation. But MGEs may be a greater factor for shaping ARGs profiles than soil properties. Overall, controlling the rate of biosolid application is the key to reducing the accumulation and horizontal transfer of ARGs in soils.

Impact of fertilization with pig or calf slurry on antibiotic residues and resistance genes in the soil

Antibiotic residues and antibiotic resistance genes can enter the environment via fertilization with calf and pig manure. In a longitudinal study, nine antibiotic resistance genes (tet(B), tet(L), tet(M), tet(O), tet(Q), tet(W), erm(B), erm(F) and sul2) and 56 antibiotic residues were investigated in 288 soil samples and 8 corresponding slurry samples from 6 pig farms and 2 veal farms using qPCR and LC-MS/MS, respectively. A significant increase in gene copy number of tet(M), erm(B), erm(F) and sul2 was observed in all the soil layers between sampling times prior to (T1) and 2–3 weeks after fertilization (T3). Tet(B), tet(Q) and tet(L) were least abundant in the soil among the genes tested. From 7 classes of antibiotics, 20 residues were detected in soil and slurry using an optimized and validated extraction method. Flumequine was detected in all soil samples in concentrations below 100 μg/kg despite being detected in only half of the corresponding slurry samples. Doxycycline, oxytetracycline, lincomycin and sulfadiazine were also frequently detected in concentrations ranging from 0.1 μg/kg to 500 μg/kg and from 2 μg/kg and 9480 μg/kg in soil and slurry, respectively. Furthermore a positive association between the presence of antibiotic residues (total antibiotic load) and antibiotic resistance genes in soil was found. One possible explanation for this is a simultaneous introduction of antibiotic residues and resistance genes upon application of animal slurry.

Long-term application of swine manure and sewage sludge differently impacts antibiotic resistance genes in soil and phyllosphere

Field application of organic fertilizers may promote the spread of antibiotic resistance genes (ARGs) in farmland ecosystems, which represents a major threat to public health. However, impacts of multi-year organic fertilization on the spread of soil and phyllosphere ARGs and the possible transmission pathways remain elusive. Here, we investigated the patterns of ARGs and structures of bacterial and fungal communities in soil and wheat crop phyllosphere, under long-term fertilization of swine manure or sewage sludge using high-throughput quantitative PCR and amplicon sequencing. It was found that application of swine manure and sewage sludge had more influence on the prevalence of ARGs in phyllosphere than in soil. SourceTracker analysis revealed that a few bacterial taxa from swine manure and sewage sludge could survive in soil, but hardly in phyllosphere. Mantel test and variation partitioning analysis further revealed that shift in the microbial community compositions was an important factor affecting soil ARGs, while horizontal gene transfer mediated by mobile genetic elements might contribute to the spread of phyllosphere ARGs. Overall, these results demonstrated that long-term application of swine manure and sewage sludge differently impacts the ARGs in soil and phyllosphere, which have implications for sustainable agricultural management.

Application of the hydrothermally treated oxytetracycline fermentation residue in agriculture: concentrations of antibiotic and resistance genes in soil and plant

Application of the hydrothermally treated oxytetracycline fermentation residue in agriculture: concentrations of antibiotic and resistance genes in soil and plant

Microplastic Alleviating the Effect of Biochar on the Removal of Antibiotic Resistance Genes in Soil

Microplastic Alleviating the Effect of Biochar on the Removal of Antibiotic Resistance Genes in Soil

Varying characteristics and driving mechanisms of antibiotic resistance genes in farmland soil amended with high-density polyethylene microplastics

The differential effects of microplastics and phthalates released from microplastics on antibiotic resistance genes in soil remain unknown. This study aims to analyze the varying characteristics and driving mechanisms of antibiotic resistance genes in soils amended with high-density polyethylene microplastics (with and without phthalates) through a 60-day microcosm experiment. The results indicate that the amended high-density polyethylene microplastics (containing phthalates) enhanced the abundance of antibiotic resistance genes in the soil, a phenomenon that markedly increased with the amendment period. Nevertheless, the addition of high-density polyethylene microplastics (without phthalates) mitigated the abundance of antibiotic resistance genes, which was less significant with increasing amendment period. Furthermore, addition of high-density polyethylene microplastics altered the soil properties, especially porosity. The phthalates released from high-density polyethylene microplastics and the changes in the soil properties transformed soil bacterial communities, resulting in increased abundance of bacterial hosts harboring antibiotic resistance genes (Calditrichaeota, Candidate division CPR1, Candidatus Delongbacteria, Candidatus Kapabacteria, Candidatus Spechtbacteria, Candidatus Wildermuthbacteria, and Ignavibacteriae), thereby enhancing the abundance of antibiotic resistance genes. These findings suggest that compared to microplastics, the phthalates released from microplastics considerably affect the antibiotic resistance genes in soils, thereby promoting the propagation of antibiotic resistance genes in agricultural environments.

Viral Community and Virus-Associated Antibiotic Resistance Genes in Soils Amended with Organic Fertilizers

Antibiotic resistance is a global health concern. Long-term organic fertilization can influence the antibiotic resistome of agricultural soils, posing potential risks to human health. However, little is known about the contribution of viruses to the dissemination of antibiotic resistance genes (ARGs) in this context. Here, we profiled the viral communities and virus-associated ARGs in a long-term (over 10 years) organic fertilized field by viral metagenomic analysis. A total of 61,520 viral populations (viral operational taxonomic units, vOTUs) were retrieved, of which 21,308 were assigned at the family level. The viral community structures were significantly correlated with the bacterial community structures (P < 0.001) and the dosage of applied sewage sludge (r2 = 0.782). A total of 16 unique ARGs were detected in soil viromes, and the number of virus-associated ARG subtypes was higher in sewage sludge treatments (except for 1 SS) than others. The network analysis showed that the application of the organic fertilizer increased the bacteria-virus interactions, suggesting that the chances of ARG exchange between viruses and their hosts may increase. Overall, our results provide a novel understanding about virus-associated ARGs and factors affecting the profile of viral community in fertilized soil.