Long-lasting effect of mercury contamination on the soil microbiota and its co-selection of antibiotic resistance

Construction of protein-protein interaction network in sulfate-reducing bacteria: Unveiling of global response to Hg

Sulfate-reducing bacteria (SRB) play pivotal roles in the biotransformation of mercury (Hg). However, unrevealed global responses of SRB to Hg have restricted our understanding of details of Hg biotransformation processes. The absence of protein-protein interaction (PPI) network under Hg stimuli has been a bottleneck of proteomic analysis for molecular mechanisms of Hg transformation. This study constructed the first comprehensive PPI network of SRB in response to Hg, encompassing 67 connected nodes, 26 independent nodes, and 121 edges, covering 93% of differentially expressed proteins from both previous studies and this study. The network suggested that proteomic changes of SRB in response to Hg occurred globally, including microbial metabolism in diverse environments, carbon metabolism, nucleic acid metabolism and translation, nucleic acid repair, transport systems, nitrogen metabolism, and methyltransferase activity, partial of which could cover the known knowledge. Antibiotic resistance was the original response revealed by this network, providing insights into of Hg biotransformation mechanisms. This study firstly provided the foundational network for a comprehensive understanding of SRB's responses to Hg, convenient for exploration of potential targets for Hg biotransformation. Furthermore, the network indicated that Hg enhances the metabolic activities and modification pathways of SRB to maintain cellular activities, shedding light on the influences of Hg on the carbon, nitrogen, and sulfur cycles at the cellular level.

Design and Validation of Primer Sets for the Detection and Quantification of Antibiotic Resistance Genes in Environmental Samples by Quantitative PCR

The high prevalence of antibiotic resistant bacteria (ARB) in several environments is a great concern threatening human health. Particularly, wastewater treatment plants (WWTP) become important contributors to the dissemination of ARB to receiving water bodies, due to the inefficient management or treatment of highly antibiotic-concentrated wastewaters. Hence, it is vital to develop molecular tools that allow proper monitoring of the genes encoding resistances to these important therapeutic compounds (antibiotic resistant genes, ARGs). For an accurate quantification of ARGs, there is a need for sensitive and robust qPCR assays supported by a good design of primers and validated protocols. In this study, eleven relevant ARGs were selected as targets, including aadA and aadB (conferring resistance to aminoglycosides); ampC, blaTEM, blaSHV, and mecA (resistance to beta-lactams); dfrA1 (resistance to trimethoprim); ermB (resistance to macrolides); fosA (resistance to fosfomycin); qnrS (resistance to quinolones); and tetA(A) (resistance to tetracyclines). The in silico design of the new primer sets was performed based on the alignment of all the sequences of the target ARGs (orthology grade > 70%) deposited in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, allowing higher coverages of the ARGs' biodiversity than those of several primers described to date. The adequate design and performance of the new molecular tools were validated in six samples, retrieved from both natural and engineered environments related to wastewater treatment. The hallmarks of the optimized qPCR assays were high amplification efficiency (> 90%), good linearity of the standard curve (R2 > 0.980), repeatability and reproducibility across experiments, and a wide linear dynamic range. The new primer sets and methodology described here are valuable tools to upgrade the monitorization of the abundance and emergence of the targeted ARGs by qPCR in WWTPs and related environments.

Key taxa and mobilome-mediated responses co-reshape the soil antibiotic resistome under dazomet fumigation stress

Agrochemicals are emergingly being implicated in the widespread dissemination of antibiotic resistance genes (ARGs) in agroecosystems. However, minimal research exists on the disturbance of fumigant on soil ARGs. Focusing on a typical fumigant dazomet in a simulated soil microcosm, we characterized the dazomet-triggered timely response and longstanding dynamic of ARGs at one-fold and two-fold field recommended doses using metagenome and quantitative PCR. Dazomet treatments reduced 13.17%-69.98% of absolute abundance of 16S rRNA gene and targeted ARGs, but, awfully, boosted diversity and relative abundance of ARGs up to 1.33-1.60 and 1.62-1.90 folds, respectively. Approximately 77.28% of changes in relative abundance of ARGs could be explained by bacterial community and mobile genetic elements (MGEs). Mechanistically, primary hosts of ARGs shifted from Proteobacteria (control) to Firmicutes and Actinobacteria (treatments) accompanied with corresponding changes in their abundance by combining community analysis, host tracking analysis and antibiotic resistant bacteria assay. Meanwhile, dazomet exposure significantly increased the incidence of MGEs and stimulated the conjugation of antibiotic-resistant plasmid. In addition, absolute abundance of targeted ARGs gradually recovered in the post-fumigation stage. Collectively, our results elucidate the dazomet-triggered emergence and spread of soil ARGs and highlight the importance of navigating toward rational use of fumigant in agricultural fields.

Complex interactions between diverse mobile genetic elements drive the evolution of metal-resistant bacterial genomes

In this study, we compared the genomes of three metal-resistant bacteria isolated from mercury-contaminated soil. We identified diverse and novel MGEs with evidence of multiple LGT events shaping their genomic structure and heavy metal resistance. Among the three metal-resistant strains, Sphingobium sp SA2 and Sphingopyxis sp SE2 were resistant to multiple metals including mercury, cadmium, copper, zinc and lead. Pseudoxanthomonas sp SE1 showed resistance to mercury only. Whole genome sequencing by Illumina and Oxford Nanopore technologies was undertaken to obtain comprehensive genomic data. The Sphingobium and Sphingopyxis strains contained multiple chromosomes and plasmids, whereas the Pseudoxanthomonas strain contained one circular chromosome. Consistent with their metal resistance profiles, the strains of Sphingobium and Sphingopyxis contained a higher quantity of diverse metal resistance genes across their chromosomes and plasmids compared to the single-metal resistant Pseudoxanthomonas SE1. In all three strains, metal resistance genes were principally associated with various novel MGEs including genomic islands (GIs), integrative conjugative elements (ICEs), transposons, insertion sequences (IS), recombinase in trio (RIT) elements and group II introns, indicating their importance in facilitating metal resistance adaptation in a contaminated environment. In the Pseudoxanthomonas strain, metal resistance regions were largely situated on a GI. The chromosomes of the strains of Sphingobium and Sphingopyxis contained multiple metal resistance regions, which were likely acquired by several GIs, ICEs, numerous IS elements, several Tn3 family transposons and RIT elements. Two of the plasmids of Sphingobium were impacted by Tn3 family transposons and ISs likely integrating metal resistance genes. The two plasmids of Sphingopyxis harboured transposons, IS elements, an RIT element and a group II intron. This study provides a comprehensive annotation of complex genomic regions of metal resistance associated with novel MGEs. It highlights the critical importance of LGT in the evolution of metal resistance of bacteria in contaminated environments.

Toxicity of Heavy Metals and Recent Advances in Their Removal: A Review

Natural and anthropogenic sources of metals in the ecosystem are perpetually increasing; consequently, heavy metal (HM) accumulation has become a major environmental concern. Human exposure to HMs has increased dramatically due to the industrial activities of the 20th century. Mercury, arsenic lead, chrome, and cadmium have been the most prevalent HMs that have caused human toxicity. Poisonings can be acute or chronic following exposure via water, air, or food. The bioaccumulation of these HMs results in a variety of toxic effects on various tissues and organs. Comparing the mechanisms of action reveals that these metals induce toxicity via similar pathways, including the production of reactive oxygen species, the inactivation of enzymes, and oxidative stress. The conventional techniques employed for the elimination of HMs are deemed inadequate when the HM concentration is less than 100 mg/L. In addition, these methods exhibit certain limitations, including the production of secondary pollutants, a high demand for energy and chemicals, and reduced cost-effectiveness. As a result, the employment of microbial bioremediation for the purpose of HM detoxification has emerged as a viable solution, given that microorganisms, including fungi and bacteria, exhibit superior biosorption and bio-accumulation capabilities. This review deals with HM uptake and toxicity mechanisms associated with HMs, and will increase our knowledge on their toxic effects on the body organs, leading to better management of metal poisoning. This review aims to enhance comprehension and offer sources for the judicious selection of microbial remediation technology for the detoxification of HMs. Microbial-based solutions that are sustainable could potentially offer crucial and cost-effective methods for reducing the toxicity of HMs.

Distribution and migration of antibiotic resistance genes, as well as their correlation with microbial communities in swine farm and its surrounding environments

The prevalence and correlation of antibiotic resistance genes (ARGs) in pig farm wastewater treatment plants (WWTPs) and surrounding environment were investigated using metagenomics and real time quantitative PCR (q-PCR). The hosts of ARGs were also studied in this study. The abundance of ARGs decreased significantly in the anoxic/oxic (A/O) process and disinfection tank of WWTPs. New ARGs emerged in wastewater that passed though the anaerobic reactor. The abundances of ARGs in the soils and water near pig farm were 10- and 35-fold higher than those in the control, respectively. The abundance of ARGs in wells near pig farm were an order of magnitude higher than that in the control. Similarly, a high abundance of ARGs was detected in swine manure. After composting, most of the ARGs were eliminated, but sul1 increased 10.5-fold. A high-throughput analysis revealed that the pig farm altered the microbial community structure in the surrounding environment, with 52% and 37% of the operational taxonomic units (OTUs) endemic to the soil and water samples near pig farm in comparison with these data in the control, respectively. The phyla Proteobacteria, Choroflexi, and Actinobacteriota dominated the water and soil samples. In addition, three pathogenic genera were found in the surrounding soil and water samples. A metagenomic analysis identified 14 types of ARGs (>1%), with the highest proportion of multidrug ARGs at 47%. A total of 28 subtypes of ARGs were detected (>1%), with macB the most prevalent. The correlation analysis revealed that several key phyla, including Proteobacteria, Actinobacteria and Acidobacteria, were the main potential hosts and posed a positive correlation with the ARGs. Efflux pumps (60-66%) were the primary resistance mechanism, and each resistance mechanism was distributed in similar proportions in the microbial community.

Plasmid Genomes Reveal the Distribution, Abundance, and Organization of Mercury-Related Genes and Their Co-Distribution with Antibiotic Resistant Genes in Gammaproteobacteria

Mercury (Hg) pollution poses human health and environmental risks worldwide, as it can have toxic effects and causes selective pressure that facilitates the spread of antibiotic resistant genes (ARGs) among microbes. More and more studies have revealed that numerous Hg-related genes (HRGs) can help to resist and transform Hg. In the present study, we systematically analyzed the HRG distribution, abundance, organization, and their co-distribution with ARGs, using 18,731 publicly available plasmid genomes isolated from a Gammaproteobacteria host. Our results revealed that there were many Hg-resistant (mer) operon genes but they were not extensively distributed across plasmids, with only 9.20% of plasmids harboring HRGs. Additionally, no hgcAB genes (which methylate Hg to create methylmercury) were identified in any of the analyzed plasmids. The host source significantly influenced the number of HRGs harbored by plasmids; plasmids isolated from humans and animals harbored a significantly smaller number of HRGs than plasmids isolated from the wastewater and sludge. HRG clusters displayed an extremely high organizational diversity (88 HRG cluster types), though incidences of more than half of the HRG cluster types was <5. This indicates the frequent rearrangement among HRGs in plasmids. The 1368 plasmids harboring both HRGs and ARGs, were dominated by Klebsiella, followed by Escherichia, Salmonella, and Enterobacter. The tightness of the HRG and ARG co-distribution in plasmids was affected by the host sources but not by pathogenicity. HRGs were more likely to co-occur with specific ARG classes (sulfonamide, macrolide-lincosamide-streptogramin, and aminoglycoside resistance genes). Collectively, our results reveal the distribution characteristics of HRGs in plasmids, and they have important implications for further understanding the environmental risks caused by the spread of ARGs through the plasmid-mediated co-transfer of ARGs and HRGs.

Long-term mercury contamination does not affect the microbial gene potential for C and N cycling in soils but enhances detoxification gene abundance

Soil microorganisms are key transformers of mercury (Hg), a toxic and widespread pollutant. It remains uncertain, however, how long-term exposure to Hg affects crucial microbial functions, such as litter decomposition and nitrogen cycling. Here, we used a metagenomic approach to investigate the state of soil functions in an agricultural floodplain contaminated with Hg for more than 80 years. We sampled soils along a gradient of Hg contamination (high, moderate, low). Hg concentrations at the highly contaminated site (36 mg kg–1 dry soil on average) were approximately 10 times higher than at the moderately contaminated site (3 mg kg–1 dry soil) and more than 100 times higher than at the site with low contamination (0.25 mg kg–1 dry soil; corresponding to the natural background concentration in Switzerland). The analysis of the CAZy and NCyc databases showed that carbon and nitrogen cycling was not strongly affected with high Hg concentrations, although a significant change in the beta-diversity of the predicted genes was observed. The only functional classes from the CAZy database that were significantly positively overrepresented under higher Hg concentrations were genes involved in pectin degradation, and from the NCyc database dissimilatory nitrate reduction and N-fixation. When comparing between low and high Hg concentrations the genes of the EggNOG functional category of inorganic ion transport and metabolism, two genes encoding Hg transport proteins and one gene involved in heavy metal transport detoxification were among those that were highly significantly overrepresented. A look at genes specifically involved in detoxification of Hg species, such as the mer and hgc genes, showed a significant overrepresentation when Hg contamination was increased. Normalized counts of these genes revealed a dominant role for the phylum Proteobacteria. In particular, most counts for almost all mer genes were found in Betaproteobacteria. In contrast, hgc genes were most abundant in Desulfuromonadales. Overall, we conclude from this metagenomic analysis that long-term exposure to high Hg triggers shifts in the functional beta-diversity of the predicted microbial genes, but we do not see a dramatic change or breakdown in functional capabilities, but rather functional redundancy.

Profiles of antibiotic- and heavy metal-related resistance genes in animal manure revealed using a metagenomic analysis

Farmed animals produce excrement containing excessive amounts of toxic heavy metals as a result of consuming compound feed as well as receiving medical treatments, and the presence of these heavy metals may aggravate the risk of spreading drug-resistance genes through co-selection during manure treatment and application processes. However, research on the association between heavy metals and antimicrobial resistance is still lacking. In this study, metagenomic sequencing was used to explore the effects of the co-selection of environmentally toxic heavy metals on the resistome in manure. A relevance network analysis showed that metal-resistance genes (MRGs), especially for copper (Cu) and zinc (Zn), were positively correlated with multiple types of antibiotic-resistance genes (ARGs) and formed a complex network. Most bacteria that co-occurred with both MRGs and ARGs simultaneously are members of Proteobacteria and accounted for 54.7% of the total microbial species in the relevance network. The remaining bacteria belonged to Firmicutes, Bacteroidetes and Actinobacteria. Among the four phyla, Cu- and Zn-resistance genes had more complex correlations with ARGs than other MRG types, reflecting the occurrence of ARG co-selection under the selective pressure of high Cu and Zn levels. In addition, approximately 64.8%, 59.1% and 68.4% of MRGs that correlated with the presence of plasmids, viruses and prophages, respectively, are Cu- or Zn-resistant, and they co-occurred with various ARGs, indicating that mobile genetic elements participate in mediating ARG co-selection in response to Cu and Zn pressure. The results indicated that the use of heavy-metal additives in feed induces the increases of drug resistance genes in manure through co-selection, aggravating the risk of antimicrobial resistance diffusion from animal farm to manure land applications.

The impact of silver nanoparticles on microbial communities and antibiotic resistance determinants in the environment

Nanosilver (NAg) is currently one of the major alternative antimicrobials to control microorganisms. With its broad-spectrum efficacy and lucrative commercial values, NAg has been used in medical devices and increasingly, in consumer products and appliances. This widespread use has inevitably led to the release and accumulation of the nanoparticle in water and sediment, in soil and even, wastewater treatment plants (WWTPs). This Article describes the physical and chemical transformations of NAg as well as the impact of the nanoparticle on microbial communities in different environmental settings; how the nanoparticle shifts not only the diversity and abundance of microbes, including those that are important in nitrogen cycles and decomposition of organic matters, but also their associated genes and in turn, the key metabolic processes. Current findings on the microbiological activity of the leached soluble silver, solid silver particulates and their respective transformed products, which underpin the mechanism of the nanoparticle toxicity in environmental microbes, is critically discussed. The Article also addresses the emerging evidence of silver-driven co-selection of antibiotic resistance determinants. The mechanism has been linked to the increasing pools of many antibiotic resistance genes already detected in samples from different environmental settings, which could ultimately find their ways to animals and human. The realized ecological impact of NAg calls for more judicial use of the nanoparticle. The generated knowledge can inform strategies for a better 'risks versus benefits' assessment of NAg applications, including the disposal stage.

Occurrence of antibiotic resistome in farmland soils near phosphorus chemical industrial area

Heavy metal pollution of soil surrounding phosphorus chemical industry has been a long-concerned problem; however, the occurrence of antibiotic resistance genes (ARGs) in farmland soils in its vicinity remains unexplored. In this study, variations of heavy metals, ARGs, mobile genetic elements (MGEs), and microbiome in surface soils of farmland along the prevailing downwind direction of a phosphorus chemical industrial zone were investigated. Cadmium (Cd) contents in soils close to the industrial zone (≤ 500 m away) were statistically higher than those at greater distances (1000 to 4000 m). A comparable ARG diversity was observed across soils, while the relative abundance of ARGs decreased markedly with increasing distance in the range of 1000 m. The soil in closest proximity to the industrial zone (20 m away) exhibited divergent compositions of ARGs, MGEs, and bacterial community from the other soils at farther locations (500 to 4000 m away). Variation partitioning analysis revealed that Cd and MGEs levels were the primary factors controlling ARG distribution. Structural equation modeling further indicated that the direct effect of Cd on ARG abundance was stronger than its indirect effect via affecting MGEs and microbiome. The observed prevalence of ARGs in farmland soils highlights the necessity of including resistome in the framework for environmental risk assessment of phosphorus chemical manufacturing.

Influence of Legacy Mercury on Antibiotic Resistomes: Evidence from Agricultural Soils with Different Cropping Systems

Agricultural soils are important reservoirs for antibiotic resistance genes (ARGs), which have close linkage to human health via crop production. Metal stress in environments may function as a selection pressure for antibiotic resistomes. However, there is still a lack of field studies focusing on the effect of historical mercury (Hg) contamination on antibiotic resistomes in agricultural soils. Here, we explored the ARG profile in soils with different cropping systems (paddy and upland) and linked them to legacy Hg exposure. We found that ARG profiles were significantly different between paddy and upland soils. However, both paddy and upland soils with long-term field Hg contamination harbored higher diversity and abundance of ARGs than non-polluted soils. The co-occurrence network reveals significant associations among Hg, Hg resistance genes, mobile genetic elements (MGEs), and ARGs. Together with path analysis showing legacy Hg possibly affecting soil resistomes through the shifts of soil microbiota, Hg resistance genes, and MGEs, we suggest that legacy Hg-induced potential co-selection might elevate the ARG level. Redundancy analysis further supports that legacy Hg pollution had a significant association with ARG variations in the paddy and upland soils (P < 0.01). Collectively, our results highlight the underappreciated role of legacy Hg as a potential persistent selecting agent in contributing to soil ARGs in agroecosystems.

Effects of coexistence of tetracycline, copper and microplastics on the fate of antibiotic resistance genes in manured soil

The coexistence of antibiotics, heavy metals and microplastics is becoming commonplace and may affect antibiotic resistance in manured soil. The current understanding of the role of microplastics in soil with combined pollution of antibiotics, heavy metals and antibiotic resistance genes (ARGs) is limited. Here, the effects of the coexistence of tetracycline (TC), Cu and environmental microplastics (EM) on the fate of nine ARGs and three heavy metal resistance genes in agricultural soil were investigated by batch and microcosm experiments. EM were obtained by exposing virgin microplastics to soil environments for 80 days, which exhibited higher adsorption affinity for Cu and TC than soil particles and virgin microplastics. 1% EM in soil increased bioavailable concentrations of TC and Cu by 79-138% and 88-135%, respectively, and decreased TC dissipation from 11.79 mg kg^-1 to 3.08 mg kg^-1. Correspondingly, the total relative abundances of target ARGs increased by 219-348%. The significant correlations of tetG, tetB, tetQ, sul2, sul1 and intl1 with bioavailable fractions of TC and Cu in soil environments were revealed by network analysis. Moreover, scanning electron micrographs showed the special plastisphere around EM. Attributed to the biofilm generation and higher pollutant accumulation in the plastisphere, EM could be the source of antibiotic-resistant bacteria and ARGs in soil environments. Structure equation models further identified that indirect effects of EM acted a major role in the propagation of ARGs by altering soil properties, soil microbial diversity and intl1 abundance. This study revealed that EM could increase the stimulative effects of Cu and TC on antibiotic resistance and magnify the environmental risk of manure application in soil environments.

Tracking antibiotic resistance genes (ARGs) during earthworm conversion of cow dung in northern China

Using cow dung to breed earthworms poses a risk of environmental transmission of antibiotic resistance genes (ARGs). The purpose of this study was to address the occurrence, persistence and environmental fate of ARGs during earthworm conversion of cow dung. The results showed that ARGs persisted through the whole process. Notably, earthworm conversion effectively reduced some ARGs in cow dung, but a definite concentration of ARGs still remained in earthworms and vermicompost (up to 10^-1 and 10^-2 copies/16S copies, respectively). We found that tet-ARGs were the most abundant in 15 earthworm farms (10^-6~10^-1 copies/16S copies) and some high-risk ARGs (i.e., bla_ampC, bla_OXA-1 and bla_TEM-1) were even prevalent in these farms. Interestingly, although ARGs differ widely in cow dung (10^-10~10^-1 copies/16S copies), the ARGs levels were comparable in vermicompost samples from different farms (10^-8~10^-2 copies/16S copies). Notably, earthworm conversion effectively reduced some ARGs in cow dung, but significant level of ARGs still remained in earthworms and vermicompost (up to 10^-1 and 10^-2 copies/16S copies, respectively). Nevertheless, the concentrations of some heavy metals (Cu, Zn and Ni), the abundance of mobile genetic elements (MGEs) and total nitrogen content were confirmed to be correlated to the enrichment of some ARGs. Overall, this study demonstrated the high prevalence of ARGs contamination in earthworm farms, and also highlighted the dissemination risk of ARGs during the earthworm conversion of cow dung.

Unveiling the Gut Microbiota and Resistome of Wild Cotton Mice, Peromyscus gossypinus, from Heavy Metal- and Radionuclide-Contaminated Sites in the Southeastern United States

The prevalence of antibiotic resistance genes (ARGs) can be driven by direct selection from antibiotic use and indirect selection from substances such as heavy metals (HMs). While significant progress has been made to characterize the influence of HMs on the enrichment and dissemination of ARGs in the environment, there is still much we do not know. To fill this knowledge gap, we present a comprehensive analysis of gut bacteria associated with wild cotton mice (Peromyscus gossypinus) trapped from several areas affected by legacies of HM and radionuclide contamination. We explore how these contaminants affect gut microbial community (GMC) composition and diversity and the enrichment of antibiotic, biocide, and metal resistance genes. Although we were able to identify that a myriad of co-occurring antimicrobial and HM resistance genes appear in mice from all areas, including those without a history of contamination, the proportions of co-occurring ARGs and metal resistance genes (MRGs) are higher in sites with radionuclide contamination. These results support those from several previous studies and enhance our understanding of the coselection process, while providing new insights into the ubiquity of antimicrobial resistance in the resistome of wild animals. IMPORTANCE Antimicrobial resistance is a serious global public health concern because of its prevalence and ubiquitous distribution. The rapid dissemination of antibiotic resistance genes is thought to be the result of the massive overuse of antibiotics in agriculture and therapeutics. However, previous studies have demonstrated that the spread of antibiotic resistance genes can also be influenced by heavy metal contamination. This coselection phenomenon, whereby different resistance determinants are genetically linked on the same genetic element (coresistance) or a single genetic element provides resistance to multiple antimicrobial agents (cross-resistance), has profound clinical and environmental implications. In contrast to antibiotics, heavy metals can persist in the environment as a selection pressure for long periods of time. Thus, it is important to understand how antibiotic resistance genes are distributed in the environment and to what extent heavy metal contaminants may be driving their selection, which we have done in one environmental setting.

The Role of Agriculture in the Dissemination of Class 1 Integrons, Antimicrobial Resistance, and Diversity of Their Gene Cassettes in Southern China

Integrons are hot spots for acquiring gene cassettes from the environment and play a major role in the bacterial evolution and dissemination of antimicrobial resistance (AMR), thus posing a serious threat. There are currently studies on integrons and antibiotic resistance genes; however, the presence and association of integrons in different agricultural crops and their subsequent dissemination and role in AMR have not been reported previously. This study examines the abundance of integrons, their gene cassette diversity in various crop soils, and their role in the dissemination of AMR in the southern region of China. Samples from different agri-crop soil, such as rice (R.S), sugarcane (S.S), citrus (C.S), banana (B.S), agricultural runoff (the point where the runoff of all sites meet (R.O)), and wild (non-agricultural) soil (W.S), were collected. Quantitative PCR was used to determine the abundance of integrons, and clone libraries were constructed to examine the gene cassette arrays. All the tested samples were found positive for Class-I (CL1) integrons and revealed a higher concentration and higher relative abundance of R.S than the others, with the least found at the W.S site. The W.S CL1 cassette arrays were found empty, and no putative conserved domains were found. The R.O was found to contain a high number of gene cassettes with various functions, while the smallest number of gene cassettes was found in the S.S among the crop soils. Most of the gene cassettes presented by the R.O were primarily shared with other sites, and the antibiotic-resistant genes were consistently observed to be dominant. The constructed clone libraries represented a diverse gene cassette array with 16% novel gene cassettes that play a vital role in pathogenesis, transportation, biosynthesis, and AMR. Most resistance-related gene cassettes were associated with the genes encoding resistance to quaternary ammonium compound (QAC) and aminoglycosides. This study highlights the significant differences in the abundance of integrons among various agricultural soils and offers deep insight into the pools of gene cassettes that play a key role in the dissemination of integrons and AMR.