Field-based evidence for copper contamination induced changes of antibiotic resistance in agricultural soils

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.

Food waste anaerobic biogas slurry as fertilizer: Potential salinization on different soil layer and effect on rhizobacteria community

Biogas slurry(BS) from food waste anaerobic fermentation coexisted a lot of salinity that could damage soil and crops health. So, this study was to explore the effect of the application of biogas slurry on soil salinization in 1 ∼ 4 cm, 4-6 cm and 6 ∼ 8 cm soil layers every 10 days, Chinese cabbage growth and rhizobacteria. The results indicated that ≤ 10% concentration of biogas slurry was uninjurious for soil and plant, the dry weight growth rate was 73.7% compared with CK, long term application should be further evaluated the potential risk of salinity on underground water and human health. As for high concentration of biogas slurry ≥ 10% concentration of biogas slurry could inhibit the seed germination and root elongation, and the germination percentage was declined from 87.6% to 2.4%, but 50% and 100% concentration of biogas slurry showed a promotion of crop growth because of sufficient nutrition. However, the potential accumulation of salinity could be seen in high concentration of biogas slurry for long term application especially in top1-4 cm soil. Correlation analysis showed that Cl^- was the main factor resulting high EC in all soil layers. 16S rRNA sequencing showed that UCG-004, Ketobacter, Sphingopyxis and RB41 could be regard as the indicators for determining the potential jeopardize on soil environmental by high salinity from biogas slurry.

Nanopore sequencing analysis of integron gene cassettes in sewages and soils

Integrons are genetic elements that can facilitate rapid spread of antibiotic resistance by insertion and removal of genes. However, knowledge about the diversity and distribution of gene cassettes embedded in class 1 integron is still limited. In this study, we sequenced integron gene cassettes using nanopore sequencing and quantified antibiotic resistance genes (ARGs) and integrase genes in the manured soils and sewages of a bioreactor. The results showed that class 1 integron integrase genes were the most abundant in soils and sewages compared with class 2 and class 3 integrase genes. Long-term manure application exacerbated the enrichment of total ARGs, integrase genes and antibiotic resistance-associated gene cassettes, while antibiotics and heavy metals showed no impact on the overall resistome profile. Sewage treatment could efficiently remove the absolute abundance of integrase genes (~3 orders of magnitude, copies/L) and antibiotic resistance gene cassettes. The resistance gene cassettes mainly carried the ARGs conferring resistance to aminoglycoside and beta-lactams in soils and sewages, some of which were persistent during the sewage treatment. This study underlined that soil and sewage were potential reservoirs for integron-mediated ARGs transfer, indicating that anthropogenic activity played a vital role in the prevalence and diversity of resistance gene cassettes in integrons.

Copper-based fungicide copper hydroxide accelerates the evolution of antibiotic resistance via gene mutations in Escherichia coli

The extensive use of copper-based fungicides in orchards, especially in vineyards, leads to the accumulation of copper, which has caused growing concern. However, data on the acquisition of antibiotic resistance in opportunistic pathogens under copper-based fungicides are scarce. In this study, we investigated the potential development of antibiotic resistance in Escherichia coli K12 under selective copper hydroxide pressure. The results indicated that copper hydroxide at concentrations of 100 mg/L and 200 mg/L evolved resistance against chloramphenicol and tolerance against tetracycline to 4-8 and 2.00-2.67 times than the initial minimal inhibitory concentrations (MICs), respectively. Whole-genome sequencing analysis showed that the obtained resistant strains carried gene mutations including AcrAB-TolC multidrug efflux pump (acrB and marR), outer membrane porin (evZ), and another indirect pathways. Furthermore, the expression of multidrug efflux pump genes and oxidative stress-related genes were significantly upregulated, whereas outer membrane porin genes were downregulated. Thus, our results could well explain the emergence of antibiotic resistance and resistance mechanisms selected by copper-based fungicide, and provide a basis for the management of copper-based fungicide in agriculture to avoid the spread of antibiotic resistance.

Potential threat of antibiotics resistance genes in bioleaching of heavy metals from sediment

Bioleaching is considered a promising technology for remediating heavy metals pollution in sediments. During bioleaching, the pressure from the metals bioleached is more likely to cause the spread of antibiotic resistance genes (ARGs). The changes in abundance of ARGs in two typical heavy metal bioleaching treatments using indigenous bacteria or functional bacteria agent were compared in this study. Results showed that both treatments successfully bioleached heavy metals, with a higher removal ratio of Cu with functional bacteria agent. The absolute abundances of most ARGs decreased by one log unit after bioleaching, particularly tetR (p = 0.02) and tetX (p = 0.04), and intI1 decreased from 10⁶ to 10⁴ copies/g. As for the relative abundance, ARGs in the non-agent treatment increased from 3.90 × 10^-4 to 1.67 × 10^-3 copies/16S rRNA gene copies (p = 0.01), and in the treatment with agent, it reached 6.65 × 10^-2 copies/16S rRNA gene copies, and intI1 relative abundance was maintained at 10^-3 copies/16S rRNA gene copies. The relative abundance of ARGs associated with efflux pump mechanism and ribosomal protection mechanism increased the most. The co-occurrence network indicated that Cu bioleached was the environmental factor determining the distribution of ARGs, Firmicutes might be the potential hosts of ARGs. Compared to bioleaching with indigenous bacteria, the addition of functional bacteria agent engendered a decrease in microbial alpha diversity and an increase in the amount of Cu bioleached, resulting in a higher relative abundance of ARGs. Heavy metal pollution can be effectively removed from sediments using the two bioleaching treatments, however, the risk of ARGs propagation posed by those procedures should be considered, especially the treatment with functional bacteria agents. In the future, an economical and efficient green technology that simultaneously reduces both the absolute abundance and relative abundance of ARGs should be developed.

Characteristics and mechanisms of ciprofloxacin degradation by black soldier fly larvae combined with associated intestinal microorganisms

Antibiotics are challenging to degrade and are excreted by livestock which results in environmental pollution. In this paper, we demonstrated that environmentally friendly manure bioremediation performed by black soldier fly larvae (BSFL) is a wise alternative, which could effectively degrade ciprofloxacin (CIP) by approached 85.48% in artificial diet and 84.22% in poultry manure within 12 days. They are up to 2.5-4.0 fold more than that achieved by natural fermentation. The five CIP-degrading strains were isolated from the larval gut, two of which, named by Klebsiella pneumoniae BSFLG-CIP1 and Proteus mirabilis BSFLG-CIP5, could degraded CIP by nearly 98.22% and 97.83% in vitro, respectively. When the intestinal isolates were re-inoculated to sterile BSFL system, the degradation level significantly increased up to 82.38%, comparing with the sterile BSFL system (21.76%). It is proved that the larvae intestinal microbiota might carry out this highly-efficient CIP-degradation. Furthermore, seven possible metabolites were identified for CIP-degradation in vitro, and they were referring three main potential degrading mechanisms of hydroxylize, piperazine ring substitute and cleavage, and quinoline ring cleavage. In conclusion, the present study may provide a strategy to reduce antibiotics pollution in animal waste through bioremediation with BSFL and adjusted intestinal microbes.

Attenuation of antibiotic resistance genes in livestock manure through vermicomposting via Protaetia brevitarsis and its fate in a soil-vegetable system

Scarab larvae (Protaetia brevitarsis) could transform large quantities of agricultural waste into compost, providing a promising bio-fertilizer for soil management. There is an urgent need to assess the risk of antibiotic resistance genes (ARGs) in soil-vegetable system with application of compost derived from P. brevitarsis larvae. We conducted a pot experiment to compare the changes of ARGs in the soil and lettuce by adding four types of manure, livestock manure (chicken and swine manure) and the corresponding larval frass. Significantly low numbers of ARGs and mobile genetic elements (MGEs) were detected in both larval frass compared with the corresponding livestock manure. Pot experiment showed that the detected numbers of ARGs and MGEs in bulk soil, rhizosphere soil, and root endophytes were significantly lower in the frass-amended treatments than the raw manure-amended treatments. Furthermore, the relative abundance of ARGs and MGEs with application of chicken-frass was significant lower in rhizosphere soil and leaf endophyte. Using non-metric multidimensional scaling analysis, the patterns of soil ARGs and MGEs with chicken-frass application were more close to those from the bulk soil in the control. Structural equation models indicated that livestock manure addition was the main driver shaping soil ARGs with raw manure application, while MGEs were the key drivers in frass-amended treatments. These findings demonstrated that application of livestock manure vermicomposting via scarab larvae (P. brevitarsis) may be at low risk in spreading manure-borne ARGs through soil-plant system, providing an alternative technique for reducing ARGs in organic waste.

An assessment of resistome and mobilome in wastewater treatment plants through temporal and spatial metagenomic analysis

Wastewater treatment plants (WWTPs) are regarded as critical points in disseminating antibiotic resistance genes (ARGs). In particular, the discharging effluents from WWTPs generally bring downstream catchment areas exogenous ARGs and resistant bacteria. However, there lacks a sufficient assessment of the resistome and mobilome in effluents. In this study, a consecutive monthly sampling was conducted over 13 months in three Hong Kong (HK) WWTPs for metagenomic sequencing. Prevalence information of ARGs and mobile genetic elements (MGEs) was compared with counterparts in effluents from cities of North America, South America, Europe, and Asia. Moreover, a publicly accessible platform integrating the exposure ranking scheme, which was based on the global archive of ARG abundance, and a readily implementable online pipeline was developed to benefit communication in academia and government consultancy. Results demonstrated HK WWTPs were featured high ARG removal efficiency of 2.34-2.43 log reduction rate, and effluents were ranked in moderate levels of Level 2 and Level 3 in the exposure prioritizing scheme based on total ARG abundance. Moreover, absolute quantification of temporal variations of effluent resistome disclosed distinct changes over time among varied ARG types which were associated with prevalently used antibiotics, including quinolone and sulfonamide. This reinforces the need for real-time management of WWTP systems. Notably, ARGs of anthropogenic prevalence, high mobility, and potential pathogenicity were found to be present in HK effluents, drawing attention to the necessity for improved risk management. In addition, source tracking of effluent resistome and structural equation model analysis was conducted to explore the disparity in ARG abundance and diversity in different samples. The discovery of this study and the recommendation of a comprehensive exposure assessment will facilitate decision-making in resistome management in WWTPs to reduce the ARG and antibiotic resistant bacteria (ARB) contamination in the receiving environments.

Fumigation practice combined with organic fertilizer increase antibiotic resistance in watermelon rhizosphere soil

Chemical fumigants and organic fertilizer are commonly used in facility agriculture to control soil-borne diseases and promote soil health. However, there is a lack of evidence for the effect of non-antibiotic fumigants on the distribution of antibiotic resistance genes (ARGs) in plant rhizosphere soils. Here, the response of a wide spectrum of ARGs and mobile genetic elements (MGEs) to dazomet fumigation practice in the rhizosphere soil of watermelon was investigated along its branching, flowering and fruiting growth stages in plastic shelters using high-throughput quantitative PCR approach. Our results indicated that soil fumigation combined with organic fertilizer application significantly increased the relative abundance of ARGs and MGEs in the rhizosphere soil of watermelon plant. The positive correlations between the relative abundance of ARGs and MGEs suggested that soil fumigation might increase the horizontal gene transfer (HGT) potential of ARGs. This result was further confirmed by the enhanced associations between ARG and MGE subtypes in the networks of fumigation treatments. Moreover, bipartite associations between ARGs/MGEs and microbial communities (bacteria and fungi) revealed a higher percentage of linkage between MGEs and microbial taxa in the fumigated soils. Structural equation model analysis further suggested that the increases in antibiotic resistance after fumigation and organic fertilizer application were mainly driven by MGEs and fungal community. Together, our results provide vital evidence that dazomet fumigation process combined with organic fertilizer in plastic shelters has the great potential to promote ARGs' dissemination in the rhizosphere, and raise cautions of the acquired resistance by soil-borne fungal pathogen and the potential spreading of ARGs along soil-plant continuum.

The Formation of Antibiotic Resistance Genes in Bacterial Communities During Garlic Powder Processing

Chinese garlic powder (GP) is exported to all countries in the world, but the excess of microorganisms is a serious problem that affects export. The number of microorganisms has a serious impact on the pricing of GP. It is very important to detect and control the microorganism in GP. The purpose of this study was to investigate the contamination and drug resistance of microorganisms during the processing of GP. We used metagenomics and Illumina sequencing to study the composition and dynamic distribution of antibiotic resistance genes (ARGs), but also the microbial community in three kinds of garlic products from factory processing. The results showed that a total of 126 ARG genes were detected in all the samples, which belonged to 11 ARG species. With the processing of GP, the expression of ARGs showed a trend to increase at first and then to decrease. Network analysis was used to study the co-occurrence patterns among ARG subtypes and bacterial communities and ARGs.

Profiling the antibiotic resistome in soils between pristine and human-affected sites on the Tibetan Plateau

With increasing pressure from anthropogenic activity in pristine environments, the comprehensive profiling of antibiotic resistance genes (ARGs) is essential to evaluate the potential risks from human-induced antibiotic resistance in these under-studied places. Here, we characterized the microbial resistome in relatively pristine soil samples collected from four distinct habitats on the Tibetan Plateau, using a Smart chip based high-throughput qPCR approach. We compared these to soils from the same habitats that had been subjected to various anthropogenic activities, including residential sewage discharge, animal farming, atmospheric deposition, and tourism activity. Compared to pristine samples, an average of 23.7% more ARGs were detected in the human-affected soils, and the ARGs enriched in these soils mainly encoded resistances to aminoglycoside and beta-lactam. Of the four habitats studied, soils subjected to animal farming showed the highest risks of ARG enrichment and dissemination. As shown, the number of ARGs enriched (a total of 42), their fold changes (17.6 fold on average), and the co-occurrence complexity between ARGs and mobile genetic elements were all the highest in fecal-polluted soils. As well as antibiotics themselves, heavy metals also influenced ARG distributional patterns in Tibetan environments. However, compared to urban areas, the Tibetan Plateau had a low potential for ARG selection and exhibited low carriage of ARGs by mobile genetic elements, even in environments impacted by humans, suggesting that these ARGs have a limited capacity to disseminate. The present study examined the effects of multiple anthropogenic activities on the soil resistomes in relatively pristine environments.

Influence of tetracycline on arsenic mobilization and biotransformation in flooded soils

This study examined the effect of tetracycline addition on arsenic (As) mobilization and biotransformation in two contrasting soils (upland soil and paddy soil) under flooded conditions. The soils with added tetracycline (0-50 mg kg^-1) were incubated for 30 days, and soil properties and microbial functional genes over time were quantified. Tetracycline significantly promoted As reduction and As release into porewater in both soils. The enhancement had resulted from an increase in the concentration of dissolved organic carbon and a decrease in soil redox potential. Tetracycline also increased the abundances of As-reducing genes (arsC and arrA) and the relative abundances of As-reducing bacteria Streptomyces, Bacillus, Burkholderia, Clostridium and Rhodococcus, all of which have been found resistant to tetracycline. These genera play a key part in stimulating As reduction in the presence of tetracycline. The study indicated the significance of tetracycline in the biochemical behavior of As in flooded soils and provided new insights into the potential effects of tetracycline on the quality and safety of agricultural products in the future.

Response of heavy metal and antibiotic resistance genes and related microorganisms to different heavy metals in activated sludge

With the recent growing interest of antibiotic resistance genes (ARGs) and their co-selection with heavy metal resistance genes (HMRGs), their relationship to heavy metals needs further analysis. This study examined the response of heavy metal resistant microorganisms (HMRMs) and antibiotic resistant microorganisms (ARMs) and their resistance genes (HMRGs and ARGs) to Cu and Cr stresses using metagenome. Results showed that Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, and Nitrospirae are the dominant HMRMs and ARMs, with majority of HMRMs taxa presenting changes similar to ARMs under heavy metal stresses. Types of HMRGs and ARGs changed (increased or decreased) under Cu and Cr stresses, and a significant relationship was noted between HMRGs and ARGs and their related microbe (p < 0.05). Network analysis revealed synergistic relationships between majority of HMRGs and ARGs; however, negative correlations were also noted between them. Co-occurrence of HMRGs and ARGs was mainly observed in chromosomes, and plasmids were found to provide limited opportunities for heavy metals to promote antibiotic resistance through co-selection. These findings imply that the response of HMRMs and ARMs is induced by heavy metals, and that the changes in these microbial communities are the main factor driving the diversity and abundance of HMRGs and ARGs.

Controlling pathogenic risks of water treatment biotechnologies at the source by genetic editing means

Antimicrobial-resistant pathogens in the environment and wastewater treatment systems, many of which are also important pollutant degraders and are difficult to control by traditional disinfection approaches, have become an unprecedented treat to ecological security and human health. Here, we propose the adoption of genetic editing techniques as a highly targeted, efficient and simple tool to control the risks of environmental pathogens at the source. An 'all-in-one' plasmid system was constructed in Aeromonas hydrophila to accurately identify and selectively inactivate multiple key virulence factor genes and antibiotic resistance genes via base editing, enabling significantly suppressed bacterial virulence and resistance without impairing their normal phenotype and pollutant-degradation functions. Its safe application for bioaugmented treatment of synthetic textile wastewater was also demonstrated. This genetic-editing technique may offer a promising solution to control the health risks of environmental microorganisms via targeted gene inactivation, thereby facilitating safer application of water treatment biotechnologies.

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.

Combined pollution of arsenic and Polymyxin B enhanced arsenic toxicity and enriched ARG abundance in soil and earthworm gut microbiotas

Polymyxin B (PMB) is considered as the last line of antibiotic defense available to humans. The environmental effects of the combined pollution with PMB and heavy metals and their interaction mechanisms are unclear. We explored the effects of the combined pollution with PMB and arsenic (As) on the microbial composition of the soil and in the earthworm gut, as well as the spread and transmission of antibiotic resistance genes (ARGs). The results showed that, compared with As alone, the combined addition of PMB and As could significantly increase the bioaccumulation factor and toxicity of As in earthworm tissues by 12.1% and 16.0%, respectively. PMB treatment could significantly increase the abundance of Actinobacteria in the earthworm gut (from 35.6% to 45.2%), and As stress could significantly increase the abundance of Proteobacteria (from 19.8% to 56.9%). PMB and As stress both could significantly increase the abundance of ARGs and mobile genetic elements (MGEs), which were positively correlated, indicating that ARGs might be horizontally transferred. The inactivation of antibiotics was the main resistance mechanism that microbes use to resist PMB and As stress. Network analysis showed that PMB and As might have antagonistic effects through competition with multi-drug resistant ARGs. The combined pollution by PMB and As significantly promoted the relative abundance of microbes carrying multi-drug resistant ARGs and MGEs, thereby increasing the risk of transmission of ARGs. This research advances the understanding of the interaction mechanism between antibiotics and heavy metals and provides new theoretical guidance for the environmental risk assessment and combined pollution management.

Exposure to heavy metal and antibiotic enriches antibiotic resistant genes on the tire particles in soil

The widespread occurrence of tire particles (TPs) in soils has attracted considerable attention due to their potential threats. The assemblage of bacteria and associated antibiotic resistant genes (ARGs) on TPs is yet largely unknown, especially under the stress of soil pollutants. In the present study, TPs were incubated in soils with or without the stress of heavy metal (Cu²⁺) or/and antibiotic (tetracycline), and bacterial community and ARG profile on TPs and in soils were explored using high-throughput sequencing and high-throughput quantitative PCR. Results indicated that bacterial community structure on TPs was significantly different from the surrounding soils, with a lower diversity, and significantly shifted by heavy metal and antibiotic exposure. Additionally, a diverse set of ARGs were detected on TPs, and their abundances were significantly increased under the stress of heavy metal and antibiotic, revealing a strong synergistic effect. Moreover, a good fit was observed for the correlation between bacterial community and ARG profile on TPs. Taken together, this study, for the first time, demonstrates that TPs can provide a novel niche for soil bacteria and soil resistome, and heavy metal and antibiotic exposure may potentially increase the abundance of ARGs on TPs, threatening soil ecosystems and human health.

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.

Magnesium Oxide Nanomaterial, an Alternative for Commercial Copper Bactericides: Field-Scale Tomato Bacterial Spot Disease Management and Total and Bioavailable Metal Accumulation in Soil

Copper (Cu) is the most extensively used bactericide worldwide in many agricultural production systems. However, intensive application of Cu bactericide have increased the selection pressure toward Cu-tolerant pathogens, including Xanthomonas perforans, the causal agent of tomato bacterial spot. However, alternatives for Cu bactericides are limited and have many drawbacks including plant damage and inconsistent effectiveness under field conditions. Also, potential ecological risk on nontarget organisms exposed to field runoff containing Cu is high. However, due to lack of alternatives for Cu, it is still widely used in tomato and other crops around the world in both conventional and organic production systems. In this study, a Cu-tolerant X. perforans strain GEV485, which can tolerate eight tested commercial Cu bactericides, was used in all the field trials to evaluate the efficacy of MgO nanomaterial. Four field experiments were conducted to evaluate the impact of intensive application of MgO nanomaterial on tomato bacterial spot disease severity, and one field experiment was conducted to study the impact of soil accumulation of total and bioavailable Cu, Mg, Mn, and Zn. In the first two field experiments, twice-weekly applications of 200 μg/mL MgO significantly reduced disease severity by 29-38% less in comparison to a conventional Cu bactericide Kocide 3000 and 19-30% less in comparison to the water control applied at the same frequency (p = 0.05). The disease severity on MgO twice-weekly was 12-32% less than Kocide 3000 + Mancozeb treatment. Single weekly applications of MgO had 13-19% higher disease severity than twice weekly application of MgO. In the second set of two field trials, twice-weekly applications of MgO at 1000 μg/mL significantly reduced disease severity by 32-40% in comparison to water control applied at the same frequency (p = 0.05). There was no negative yield impact in any of the trials. The third field experiment demonstrated that application of MgO did not result in significant accumulation of total and bioavailable Mg, Mn, Cu, or Zn in the root-associated soil and in soil farther away from the production bed compared to the water control. However, Cu bactericide contributed to significantly higher Mn, Cu, and Zn accumulation in the soil compared to water control (p = 0.05). This study demonstrates that MgO nanomaterial could be an alternative for Cu bactericide and have potential in reducing risks associated with development of tolerant strains and for reducing Cu load in the environment.

Impact of biochar-induced vertical mobilization of dissolved organic matter, sulfamethazine and antibiotic resistance genes variation in a soil-plant system

The migration risk of antibiotic and antibiotic resistance genes (ARGs) have attracted lots of attentions due to their potential threaten to public health. Strategies to reduce their vertical mobilization risk are urgently required for groundwater safety and human health. Biochar enjoys numerous interests due to its excellent sorption affinity. However, little was known about the efficacy of biochar amendment in impeding the vertical mobilization of antibiotic and ARGs. To fill this gap, a column study was carried out to investigate biochar-induced variations in the leaching behavior of dissolved organic matter (DOM), sulfamethazine (SMZ) and ARGs. Results showed that biochar addition enhanced DOM export from soil, changed its composition and impeded the vertical transport of SMZ. Biochar amendment could effectively decrease the occurrence of extracellular and intracellular sul2 in soil and impede its vertical transportation, however, it did not work out with sul1 gene. Structural equation modeling analysis demonstrated that the abundance of sul2 was significantly controlled by SMZ concentration, while the primary drivers of sul1 were SMZ concentration and DOM content. These results indicated the failure in inhibiting the vertical transfer of sul1 under biochar amendment and highlighted the important role of DOM in the leaching of soil ARGs.

Effect of copper and zinc as sulfate or nitrate salts on soil microbiome dynamics and blaVIM-positive Pseudomonas aeruginosa survival

The exposure of soil to metals and to antibiotic resistant bacteria may lead to the progressive deterioration of soil quality. The persistence of antibiotic resistant bacteria or antibiotic resistance genes in soil can be influenced by the microbial community or by soil amendments with metal salts. This work assessed the effect of soil amendment with copper and zinc, as sulfate or nitrate salts, on the fate of a carbapenem-resistant (bla_VIM⁺) hospital effluent isolate of Pseudomonas aeruginosa (strain H1FC49) and on the variations of the microbial community composition. Microcosms with soil aged or not with copper and zinc salts (20 mM), and inoculated with P. aeruginosa H1FC49 were monitored at 0, 7, 14 and/or 30 days, for community composition (16S rRNA gene amplicon) and strain H1FC49 persistence. Data on culturable P. aeruginosa, quantitative PCR of the housekeeping gene ecf, and the presumably acquired genes bla_VIM⁺ and integrase (intI1), and community composition were interpreted based on descriptive statistics and multivariate analysis. P. aeruginosa and the presumably acquired genes, were quantifiable in soil for up to one month, in both metal-amended and non-amended soil. Metal amendments were associated with a significant decrease of bacterial community diversity and richness. The persistence of P. aeruginosa and acquired genes in soils, combined with the adverse effect of metals on the bacterial community, highlight the vulnerability of soil to both types of exogenous contamination.

Diversity and abundance of antibiotic resistance genes in rhizosphere soil and endophytes of leafy vegetables: Focusing on the effect of the vegetable species

Antibiotic resistance genes (ARGs) in the endophytes of vegetables represent a potential route of human exposure to the soil resistome. However, the effect of vegetable species on the endophytic ARG profiles is unclear, hampering our understanding of how ARGs migrate into the soil-vegetable system and their potential health risks. Here, we planted four leafy vegetables (cilantro, endive, lettuce, and pak choi), which are commonly eaten raw, and analyzed the resistomes and microbiomes in three sample types (rhizosphere soil, root, and leaf endophytes). A total of 150 ARG subtypes were detected using high-throughput quantitative PCR. Vegetable species had a significant effect on ARG diversity and abundance, and pak choi accumulated more ARGs in its associated microbiome than the other three vegetables. The bacterial community was the primary factor shaping ARG profiles and was significantly correlated with ARG subtypes. We identified aadE, tet(34), and vanSB as shared ARGs among leaves of the four vegetables; the bacterial families correlated with tet(34) and vanSB were also shared across the vegetables and belonged to Proteobacteria. This study deepens our understanding of how endophytic ARG profiles vary among different vegetables and highlights the potential health risk associated with consuming these vegetables raw.

Mercury and Antibiotic Resistance Co-Selection in Bacillus sp. Isolates from the Almadén Mining District

Antibiotic resistance (AR) in the environment is of great global concern and a threat to public health. Soil bacteria, including Bacillus spp., could act as recipients and reservoirs of AR genes of clinical, livestock, or agricultural origin. These genes can be shared between bacteria, some of which could be potentially human pathogens. This process can be favored in conditions of abiotic stress, such as heavy metal contamination. The Almadén mining district (Ciudad Real, Spain) is one of the environments with the highest mercury (Hg) contamination worldwide. The link between heavy metal contamination and increased AR in environmental bacteria seems clear, due to co-resistance and co-selection phenomena. In the present study, 53 strains were isolated from rhizospheric and bulk soil samples in Almadén. AR was tested using Vitek^® 2 and minimum inhibitory concentration (MIC) values were obtained and interpreted based on the criteria of the Clinical and Laboratory Standards Institute (CLSI) guidelines. Based on the resistance profiles, five different antibiotypes were established. The Hg minimum bactericidal concentration (MBC) of each strain was obtained using the plating method with increasing concentrations of HgCl2. A total of 72% of Bacillus spp. showed resistance to two or more commonly used antibiotics. A total of 38 isolates expressed AR to cephalosporins. Finally, the environmental co-selection of AR to cephalosporins and tetracyclines by selective pressure of Hg has been statistically demonstrated.

Comparison of the dynamic responses of different anammox granules to copper nanoparticle stress: Antibiotic exposure history made a difference

Two types of anaerobic ammonium oxidation (anammox) seed sludge were selected to evaluate their responses to copper nanoparticles (CuNPs) exposure. Antibiotic-exposed anammox granules (R₁) were more likely to be inhibited by 5.0 mg L^-1 CuNPs than the normal anammox granules (C₁). The nitrogen removal efficiency (NRE) of C₁ decreased by 9.00% after two weeks of exposure to CuNPs, whereas that of R₁ decreased by 20.32%. Simultaneously, the abundance of Candidatus. Kuenenia decreased by 27.65% and 36.02% in C₁ and R₁ under CuNPs stress conditions, respectively. Generally, R₁ was more susceptible to CuNPs than C₁. The correlation analysis indicated that the horizontal transfer of antibiotic resistance genes and copA triggered by intI1 facilitated the generation of multiresistance in the anammox process. Moreover, the potential multiresistance mechanism of anammox bacteria was hypothesized based on previous results. The results will generate new ideas for the treatment of complex wastewater using the anammox process.

Distribution of the microbial community and antibiotic resistance genes in farmland surrounding gold tailings: A metagenomics approach

Metal mining has caused the accumulation of waste mine tailing dumps from abandoned mines. The pollution of farmlands surrounding metal tailings by heavy metals has been a long-recognized problem. However, the distribution of antibiotic resistance genes (ARGs) in tailings and the main factors influencing this distribution have rarely been reported. In this study, a metagenomics approach was used to investigate the microbial community and ARGs present in farmland surrounding gold tailings in northern China. The results showed that the main pollutants in the farmland were As, Pb, and Cd. Proteobacteria and Actinobacteria were the dominant phyla of microbes in farmlands surrounding gold tailings. A total of 75 ARGs with 327 ARG subtypes were detected in soil samples. Macrolide-, lincosaminide-, and streptogramin B resistant genes accounted for the majority of ARGs in this study, and Actinobacteria, Proteobacteria, and Acidobacteria were the hosts of most ARGs. Partial least squares path modeling revealed that the microbial community was the most influential driver moderating the distribution of soil ARGs near tailings, and heavy metals have direct and partially indirect effects on these ARGs. In contrast to previous analyses of ARGs, our study found that mobile gene elements had a minimal impact on ARGs. Overall, this study presents a complete ARG survey that sheds light on the distribution and fate of ARGs under heavy metal contamination in farmland around gold tailings.

The Interactions Between Antibiotic Resistance Genes and Heavy Metal Pollution Under Co-Selective Pressure Influenced the Bio-Enzyme Activity

The spread of antibiotic resistance genes (ARGs) has brought potential risks to public health. However, the interactions between heavy metals and ARGs, as well as their potential effect on bio-enzyme activity under the pressure of co-selectivity in soil still remain poorly understood. In this work, the distribution characteristics and the co-selective relationship of 28 ARGs and eight heavy metals in soil in a dairy farm were visualized via the geographic information system (GIS) technique. Eight kinds of heavy metals were detected by an atomic fluorescence spectrometer and atomic absorption spectrophotometer, which were further evaluated via the single factor pollution index value. The GIS analysis showed that arsenic (As) was the key element responsible for soil pollution, which was found to be positively related to soil depths. The top three comprehensive scores of ARGs ranked the orders of sul2 > tetX > blaTEM, indicating the high potential of risk caused by these genes in the soil environment. In addition, the functional predications performed with the 16 SrDNA sequencing data based on the KEGG database indicated that the sulfonamides in soil involved multiple pathways, especially the metabolism, transport and catabolism, and membrane transport processes. This suggested that most bio-enzymes were found to be expressed in low activities in different pathways. Significant correlations were observed between the heavy metals and ARGs (p < 0.05), particularly between the ARGs and As, Cu, Ni, Pb, and Zn (p < 0.01). This study offers deep insights into the potential interactions between heavy metals and ARGs in soil and provides guidance for the fabrication of enzyme-based smart materials for soil remediation in dairy farms.

Co-effect of cadmium and iron oxide nanoparticles on plasmid-mediated conjugative transfer of antibiotic resistance genes

Conjunctive transfer of antibiotic resistance genes (ARGs) among bacteria driven by plasmids facilitated the evolution and spread of antibiotic resistance. Heavy metal exposure accelerated the plasmid-mediated conjunctive transfer of ARGs. Nanomaterials are well-known adsorbents for heavy metals removal, with the capability of combatting resistant bacteria/facilitating conjunctive transfer of ARGs. However, co-effect of heavy metals and nanomaterials on plasmid-mediated conjunctive transfer of ARGs was still unknown. In this study, we investigated the effect of the simultaneous exposure of Cd²⁺ and nano Fe₂O₃ on conjugative transfer of plasmid RP4 from Pseudomonas putida KT2442 to water microbial community. The permeability of bacterial cell membranes, antioxidant enzyme activities and conjugation gene expression were also investigated. The results suggested that the combination of Cd²⁺ and high concentration nano Fe₂O₃ (10 mg/L and 100 mg/L) significantly increased conjugative transfer frequencies of RP4 plasmid (p < 0.05). The most transconjugants were detected in the treatment of co-exposure to Cd²⁺ and nano Fe₂O₃, the majority of which were identified to be human pathogens. The mechanisms of the exacerbated conjugative transfer of ARGs were involved in the enhancement of cell membrane permeability, antioxidant enzyme activities, and mRNA expression levels of the conjugation genes by the co-effect of Cd²⁺ and nano Fe₂O₃. This study confirmed that the simultaneous exposure to Cd²⁺and nano Fe₂O₃ exerted a synergetic co-effect on plasmid-mediated conjunctive transfer of ARGs, emphasizing that the co-effect of nanomaterials and heavy metals should be prudently evaluated when combating antibiotic resistance.

Co-occurrence and patterns of phosphate solubilizing, salt and metal tolerant and antibiotic-resistant bacteria in diverse soils

Soil is a treasure chest for beneficial bacteria with applications in diverse fields, which include agriculture, rhizoremediation, and medicine. Metagenomic analysis of four soil samples identified Proteobacteria as the dominant phylum (32-52%) followed by the phylum Acidobacteria (11-21% in three out of four soils). Bacteria that were prevalent at the highest level belong to the genus Kaistobacter (8-19%). PICRUSt analysis predicted KEGG functional pathways associated with the metagenomes of the four soils. The identified pathways could be attributed to metal tolerance, antibiotic resistance and plant growth promotion. The prevalence of phosphate solubilizing bacteria (PSB) was investigated in four soil samples, ranging from 26 to 59% of the total culturable bacteria. The abundance of salt-tolerant and metal-tolerant bacteria showed considerable variation ranging from 1 to 62% and 4-69%, respectively. In comparison, the soil with the maximum prevalence of temperature-tolerant and antibiotic-resistant bacteria was close 30%. In this study, the common pattern observed was that PSB were the most abundant in all types of soils compared to other traits. Conversely, most of the isolates, which are salt-tolerant, copper-tolerant, and ampicillin-resistant, showed phosphate solubilization activity. The sequencing of the partial 16S-rRNA gene revealed that PSB belonged to Bacillus genera.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02904-7.

Termite mound formation reduces the abundance and diversity of soil resistomes

Termites are pivotal ecosystem engineers in tropical and subtropical habitats, where they construct massive nests ('mounds') that substantially modify soil properties and promote nutrient cycling. Yet, little is known about the roles of termite nesting activity in regulating the spread of antimicrobial resistance (AMR), one of the major Global Health challenges. Here, we conducted a large-scale (> 1500 km) investigation in northern Australia and found distinct resistome profiles in termite mounds and bulk soils. By profiling a wide spectrum of ARGs, we found that the abundance and diversity of antibiotic resistance genes (ARGs) were significantly lower in termite mounds than in bulk soils (P < 0.001). The proportion of efflux pump ARGs was significantly lower in termite mound resistome than in bulk soil resistome (P < 0.001). The differences in resistome profiles between termite mounds and bulk soils may result from the changes in microbial interactions owing to the substantial increase in pH and nutrient availability induced by termite nesting activities. These findings advance our understanding of the profile of ARGs in termite mounds, which is a crucial step to evaluate the roles of soil faunal activity in regulating soil resistome under global environmental change.

Heavy metal could drive co-selection of antibiotic resistance in terrestrial subsurface soils

Terrestrial surface ecosystems are important sinks for antibiotic resistance genes (ARGs) due to the continuous discharge of contaminants from human-impacted ecosystems. However, the abundance and resistance types of ARGs and their influencing factors in terrestrial subsurface soils are not well known. In this study, we investigated the abundance and diversity of ARGs, and their correlations with metal resistance genes (MRGs), mobile genetic elements (MGEs), bacteria, and heavy metals in subsurface soils using high throughput quantitative PCR and metagenomic sequencing approaches. Abundant and diverse ARGs were detected with high spatial heterogeneity among sampling sites. Vertically, there was no significant difference in ARG profiles between the aquifer and non-aquifer soils. Heavy metals were key factors shaping ARG profiles in soils with high heavy metal contents, while they showed no significant effect in low contents. Moreover, heavy metals could trigger the proliferation of antibiotic resistance by increasing MGE abundance or influencing bacterial communities. Metagenomic analysis also revealed the widespread co-occurrence of ARGs and MRGs, with heavy metals possibly enhancing the co-selection of ARGs and MRGs in soils with high heavy metal contents. This study highlighted the heavy metal-driven co-selection of ARGs and revealed the occurrence of ARG pollution in terrestrial subsurface soils.

Seasonal change is a major driver of soil resistomes at a watershed scale

Soils harbor the most diverse naturally evolved antibiotic resistomes on Earth that threaten human health, ecosystem processes, and food security. Yet the importance of spatial and temporal variability in shaping the distribution of soil resistomes is not well explored. Here, a total of 319 topsoil samples were collected at a watershed scale during four seasons (spring to winter) and high-throughput quantitative PCR (HT-qPCR) was used to characterize the profiles of soil antibiotic resistance genes (ARGs). A significant and negative correlation was observed between soil ARG profiles and seasonal dissimilarity, which along with seasonally dependent distance-decay relationships highlight the importance of seasonal variability in shaping soil antibiotic resistomes. Significant, though weak, distance-decay relationships were identified in spring, summer and winter, for ARG similarities with geographic distances. There were also strong interactions between specific soil ARGs and Actinobacteria, Firmicutes and Proteobacteria. Moreover, we found that the relative abundance of soil Actinobacteria, Firmicutes and Proteobacteria correlated significantly with annual mean temperature and annual mean precipitation at a watershed scale. A random forest model showed that seasonal change rather than spatial variation was the most important predictor of the composition of soil ARGs. Together, these results constitute an advance in our understanding of the relative importance of spatial and temporal variability in shaping soil ARG profiles, which will provide novel insights allowing us to forecast their distribution under a changing environment.

Agricultural Soils Amended With Thermally-Dried Anaerobically-Digested Sewage Sludge Showed Increased Risk of Antibiotic Resistance Dissemination

The application of sewage sludge (SS) to agricultural soil can help meet crop nutrient requirements and enhance soil properties, while reusing an organic by-product. However, SS can be a source of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), resulting in an increased risk of antibiotic resistance dissemination. We studied the effect of the application of thermally-dried anaerobically-digested SS on (i) soil physicochemical and microbial properties, and (ii) the relative abundance of 85 ARGs and 10 MGE-genes in soil. Soil samples were taken from a variety of SS-amended agricultural fields differing in three factors: dose of application, dosage of application, and elapsed time after the last application. The relative abundance of both ARGs and MGE-genes was higher in SS-amended soils, compared to non-amended soils, particularly in those with a more recent SS application. Some physicochemical parameters (i.e., cation exchange capacity, copper concentration, phosphorus content) were positively correlated with the relative abundance of ARGs and MGE-genes. Sewage sludge application was the key factor to explain the distribution pattern of ARGs and MGE-genes. The 30 most abundant families within the soil prokaryotic community accounted for 66% of the total variation of ARG and MGE-gene relative abundances. Soil prokaryotic α-diversity was negatively correlated with the relative abundance of ARGs and MGE-genes. We concluded that agricultural soils amended with thermally-dried anaerobically-digested sewage sludge showed increased risk of antibiotic resistance dissemination.

Phenotypic and Phylogenetic Characterization of Cu Homeostasis among Xylella fastidiosa Strains

Xylella fastidiosa is a bacterial pathogen causing severe diseases and asymptomatic colonization in more than 600 plants worldwide. Copper (Cu) is a widely used antimicrobial treatment for various plant diseases, including those affecting X. fastidiosa hosts. Cu homeostasis among X. fastidiosa strains from different geographical locations and host species has not been characterized. Here, we assessed minimum inhibitory concentration (MIC) of Cu for 54 X. fastidiosa strains. We observed strain-level variation in MIC values within each subspecies. We hypothesized that these differences could be explained by sequence variation in Cu homeostasis genes. Phylogenies based on copA, copB, copL, and cutC were created using 74 genomes (including 43 strains used in vitro) of X. fastidiosa, showing that the phylogenetic clustering of Cu homeostasis associated with clustering was based on core genome phylogenies, rather than on pattern of MIC. No association was found among Cu MIC, subspecies classification, and host and location of isolation, probably due to uneven and limited group of strains whose genomes are available. Further analysis focused on a subgroup of isolates from Georgia’s vineyards that shared similar Cu-related phenotypes. Further research is needed to better understand the distribution of Cu homeostasis for this pathogen.

Selective enrichment of antibiotic resistance genes and pathogens on polystyrene microplastics in landfill leachate

Landfill leachate is an important reservoir of antibiotic resistance genes (ARGs) and microplastics (MPs). However, the enrichment characteristics of ARGs on MPs and the effect of MPs' presence on ARGs in surrounding leachates are little studied. Therefore, we investigated the differences of ARGs, mobile genetic elements (MGEs), bacterial communities and pathogens on polystyrene MPs, in MPs-surrounding leachate and in control (leachate with the absence of MPs). The results revealed that ARGs were selectively enriched on MPs, which was similar in three types of leachate environments. The genes strB and bla_TEM were maximally enriched and mefA, ermB, tetM and tetQ were slightly enriched on MPs, and the degree of ARGs enrichment increased with time during the 60 days of the experiment. Furthermore, compared to the leachate, MPs were observed to have the higher abundances of MGEs and distinct bacterial communities, both of which were closely associated with ARGs on MPs. Pathogens were distinct and more abundant on MPs compared to that in leachate, and 11 pathogens were identified as potential hosts for ARGs on MPs. Additionally, the presence of MPs (500 mg/L) induced few changes in ARGs' abundances, MGEs' abundances and bacterial communities in MP-surrounding leachate within 60 days. Overall, this study suggested that MPs could selectively enrich ARGs and pathogens from the surrounding environments, which promoted the understanding of the combined pollution properties of MPs and ARGs.

The composition of antibiotic resistance genes is not affected by grazing but is determined by microorganisms in grassland soils

Grazing is expected to exert a substantial influence on antibiotic resistance genes (ARGs) in grassland ecosystems. However, the precise effects of grazing on the composition of ARGs in grassland soils remain unclear. This is especially the case for grassland soils subject to long-term grazing. Here, we investigated ARGs and bacterial community composition in soils subject to long-term historic grazing (13-39 years) and corresponding ungrazed samples. Using a combination of shotgun metagenomics, amplicon analyses and associated soil physicochemical data, we provide novel insights regarding the structure of ARGs in grassland soils. Interestingly, our analysis revealed that long-term historic grazing had no impacts on the composition of ARGs in grassland soils. An average of 378 ARGs, conferring resistance to 14 major categories of antibiotics (80%), were identified in both grazing and ungrazed sites. Actinobacteria, Proteobacteria and Acidobacteria were the most prevalent predicted hosts in these soils and were also shown to harbour genetic capacity for multiple-resistant ARGs. Our results suggested that positive effects of bacterial community composition on ARGs could potentially be controlled by affecting MGEs. Soil properties had direct effects on the composition of ARGs through affecting the frequency of horizontal gene transfer among bacteria. Twelve novel ARGs were found in S. grandis steppe grasslands, indicating that different vegetation types might induce shifts in soil ARGs. Collectively, these findings suggest that soil properties, plants and microorganisms play critical roles in shaping ARG patterns in grasslands. Together, these data establish a solid baseline for understanding environmental antibiotic resistance in grasslands.

A Synergic Potential of Antimicrobial Peptides against Pseudomonas syringae pv. actinidiae

Pseudomonas syringae pv. actinidiae (Psa) is the pathogenic agent responsible for the bacterial canker of kiwifruit (BCK) leading to major losses in kiwifruit productions. No effective treatments and measures have yet been found to control this disease. Despite antimicrobial peptides (AMPs) having been successfully used for the control of several pathogenic bacteria, few studies have focused on the use of AMPs against Psa. In this study, the potential of six AMPs (BP100, RW-BP100, CA-M, 3.1, D4E1, and Dhvar-5) to control Psa was investigated. The minimal inhibitory and bactericidal concentrations (MIC and MBC) were determined and membrane damaging capacity was evaluated by flow cytometry analysis. Among the tested AMPs, the higher inhibitory and bactericidal capacity was observed for BP100 and CA-M with MIC of 3.4 and 3.4-6.2 µM, respectively and MBC 3.4-10 µM for both. Flow cytometry assays suggested a faster membrane permeation for peptide 3.1, in comparison with the other AMPs studied. Peptide mixtures were also tested, disclosing the high efficiency of BP100:3.1 at low concentration to reduce Psa viability. These results highlight the potential interest of AMP mixtures against Psa, and 3.1 as an antimicrobial molecule that can improve other treatments in synergic action.

Response of ammonia-oxidizing archaea and bacteria to sulfadiazine and copper and their interaction in black soils

The large-scale development of animal husbandry and the wide agricultural application of livestock manure lead to more and more serious co-pollution of heavy metals and antibiotics in soil. In this study, two common feed additives, copper (Cu) and sulfadiazine (SDZ), were selected as target pollutants to evaluate the toxicity and interaction of antibiotics and heavy metals on ammonia oxidizers diversity, potential nitrification rate (PNR), and enzymatic activity in black soils. The results showed that soil enzyme activity was significantly inhibited by single Cu pollution, but the toxicity could be reduced by introducing low-concentration SDZ (5 mg · kg^-1), which showed an antagonistic effect between Cu and SDZ (5 mg · kg^-1), while the combined toxicity of high-concentration SDZ (10 mg · kg^-1) and Cu were strengthened compared with the single Cu contamination on soil enzymes. In contrast, soil PNR was more sensitive to single Cu pollution and its combined pollution with SDZ than the enzyme activity. Real-time fluorescence quota PCR and Illumina Hiseq/Miseq sequencing results showed that ammonia-oxidizing archaea (AOA) was decreased in C2 (200 mg · kg^-1 Cu treatment) and ammonia-oxidizing bacteria (AOB) was obviously stimulated in soil contaminated in C2, while in S5 (5 mg · kg^-1 SDZ treatment), AOB was decreased; both AOA and AOB were significantly decreased at gene level in soils with combined pollutants (C2S5, 200 mg · kg^-1 Cu combined with 5 mg · kg^-1 SDZ). So, it can be concluded that combined pollution can cause more serious toxicity on the enzymatic activity, PNR, and ammonia-oxidizing microorganisms in soil through the synergistic effect between heavy metals and antibiotics pollutants.

Antibiotic Resistance in Agricultural Soil and Crops Associated to the Application of Cow Manure-Derived Amendments From Conventional and Organic Livestock Farms

The application of organic amendments to agricultural soil can enhance crop yield, while improving the physicochemical and biological properties of the recipient soils. However, the use of manure-derived amendments as fertilizers entails environmental risks, such as the contamination of soil and crops with antibiotic residues, antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). In order to delve into these risks, we applied dairy cow manure-derived amendments (slurry, fresh manure, aged manure), obtained from a conventional and an organic farm, to soil. Subsequently, lettuce and wheat plants were grown in the amended soils. After harvest, the abundance of 95 ARGs and MGE-genes from the amended soils and plants were determined by high-throughput qPCR. The structure of soil prokaryotic communities was determined by 16S rRNA amplicon sequencing and qPCR. The absolute abundance of ARGs and MGE-genes differed between treatments (amended vs. unamended), origins of amendment (conventional vs. organic), and types of amendment (slurry vs. fresh manure vs. aged manure). Regarding ARG-absolute abundances in the amendments themselves, higher values were usually found in slurry vs. fresh or aged manure. These abundances were generally higher in soil than in plant samples, and higher in wheat grain than in lettuce plants. Lettuce plants fertilized with conventional amendments showed higher absolute abundances of tetracycline resistance genes, compared to those amended with organic amendments. No single treatment could be identified as the best or worst treatment regarding the risk of antibiotic resistance in soil and plant samples. Within the same treatment, the resistome risk differed between the amendment, the amended soil and, finally, the crop. In other words, according to our data, the resistome risk in manure-amended crops cannot be directly inferred from the analysis of the amendments themselves. We concluded that, depending on the specific question under study, the analysis of the resistome risk should specifically focus on the amendment, the amended soil or the crop.

Metallic Nanoparticles-Friends or Foes in the Battle against Antibiotic-Resistant Bacteria?

The rapid spread of antibiotic resistances among bacteria demands novel strategies for infection control, and metallic nanoparticles appear as promising tools because of their unique size and tunable properties that allow their antibacterial effects to be maximized. Furthermore, their diverse mechanisms of action towards multiple cell components have suggested that bacteria could not easily develop resistance against nanoparticles. However, research published over the last decade has proven that bacteria can indeed evolve stable resistance mechanisms upon continuous exposure to metallic nanoparticles. In this review, we summarize the currently known individual and collective strategies employed by bacteria to cope with metallic nanoparticles. Importantly, we also discuss the adverse side effects that bacterial exposure to nanoparticles may have on antibiotic resistance dissemination and that might constitute a challenge for the implementation of nanoparticles as antibacterial agents. Overall, studies discussed in this review point out that careful management of these very promising antimicrobials is necessary to preserve their efficacy for infection control.

Large-scale biogeographical patterns of antibiotic resistome in the forest soils across China

Soil is a reservoir of environmental resistomes. Information about their distribution, profiles, and driving forces in undisturbed environments is essential for understanding and managing modern antibiotic resistance genes (ARGs) in human disturbed environments. However, knowledge about the resistomes in pristine soils is limited, particularly at national scale. Here, we conducted a national-scale investigation of soil resistomes in pristine forests across China. Although the antibiotics content was low and ranged from below limit of detection (LOD) to 0.290 μg/kg, numerous detected ARGs conferring resistance to major classes of modern antibiotics were identified and indicated forest soils as a potential source of resistance traits. ARGs ranged from 6.20 × 10^-7 to 2.52 × 10^-3 copies/16S-rRNA and were predominated by those resisting aminoglycoside and encoding deactivation mechanisms. Low abundance of mobile genetic elements (MGEs) and its scarcely positive connections with ARGs suggest the low potential of horizontal gene transfer. The geographic patterns of ARGs and ARG-hosts in pristine forest soils were mainly driven by soil physiochemical variables and followed a distance-decay relationship. This work focusing on pristine soils can provide valuably new information for our understanding of the ARGs in human disturbed environments.

A Smart and Sustainable Future for Viticulture Is Rooted in Soil: How to Face Cu Toxicity

In recent decades, agriculture has faced the fundamental challenge of needing to increase food production and quality in order to meet the requirements of a growing global population. Similarly, viticulture has also been undergoing change. Several countries are reducing their vineyard areas, and several others are increasing them. In addition, viticulture is moving towards higher altitudes and latitudes due to climate change. Furthermore, global warming is also exacerbating the incidence of fungal diseases in vineyards, forcing farmers to apply agrochemicals to preserve production yields and quality. The repeated application of copper (Cu)-based fungicides in conventional and organic farming has caused a stepwise accumulation of Cu in vineyard soils, posing environmental and toxicological threats. High Cu concentrations in soils can have multiple impacts on agricultural systems. In fact, it can (i) alter the chemical-physical properties of soils, thus compromising their fertility; (ii) induce toxicity phenomena in plants, producing detrimental effects on growth and productivity; and (iii) affect the microbial biodiversity of soils, thereby influencing some microbial-driven soil processes. However, several indirect (e.g., management of rhizosphere processes through intercropping and/or fertilization strategies) and direct (e.g., exploitation of vine resistant genotypes) strategies have been proposed to restrain Cu accumulation in soils. Furthermore, the application of precision and smart viticulture paradigms and their related technologies could allow a timely, localized and balanced distribution of agrochemicals to achieve the required goals. The present review highlights the necessity of applying multidisciplinary approaches to meet the requisites of sustainability demanded of modern viticulture.

Cadmium enhances conjugative plasmid transfer to a fresh water microbial community

Co-selection of antibiotic resistance genes (ARGs) by heavy metals might facilitate the spread of ARGs in the environments. Cadmium contamination is ubiquitous, while, it remains unknown the extent to which cadmium (Cd²⁺) impact plasmid-mediated transfer of ARGs in aquatic bacterial communities. In the present study, we found that Cd²⁺ amendment at sub-inhibitory concentration significantly increased conjugation frequency of RP4 plasmid from Pseudomonas putida KT2442 to a fresh water microbial community by liquid mating method. Cd²⁺ treatment (1-100 mg/L) significantly increased the cell membrane permeability and antioxidant activities of conjugation mixtures. Amendments of 10 and 100 mg/L Cd²⁺ significantly enhanced the mRNA expression levels of mating pair formation gene (trbBp) and the DNA transfer and replication gene (trfAp) due to the repression of regulatory genes (korA, korB and trbA). Phylogenetic analysis of transconjugants indicated that Proteobacteria was the dominant recipients and high concentration of Cd²⁺ treatment resulted in expanded recipient taxa. This study suggested that sub-inhibitory Cd²⁺ contamination would facilitate plasmid conjugation and contributed to the maintenance and spread of plasmid associated ARGs, and highlighted the urgent need for effective remediation of Cd²⁺ in aquatic environments.

Selection of antibiotic resistance by metals in a riverine bacterial community

Antibiotic resistance is a health challenge across human, animal and environmental settings. In the environment, metals may contribute to antibiotic resistance selection. This study aimed to investigate the role of copper and zinc in the selection of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in a riverine bacterial community. Using a microcosm approach, bacteria in water samples were exposed to 50 μg L^-1 and 100 μg L^-1 of copper and zinc, for 20 days. The prevalence of ARB was determined from colony forming units counts in media with and without antibiotics. A significant increase in the prevalence of cefotaxime-resistant (from 2.3% in control to 9.5% in Cu50 and 16.8% in Cu100) and tetracycline-resistant bacteria (from 0.03% to 0.23% in Cu100) was observed in communities exposed to copper. Zinc exposure resulted in an increase in the prevalence of cefotaxime-resistant bacteria (from 24.6% to 91.3% in Zn50 and 72.4% in Zn100) and of kanamycin-resistant bacteria (from 6.1% to 24.1% in Zn50 and 43% in Zn100). Cefotaxime- and kanamycin-resistant bacteria belonged to genera intrinsically resistant to these compounds. DGGE profiling confirmed that metal exposure altered the structure and diversity of bacterial communities. Changes in the abundance of genes usually associated with mobile genetic elements (bla_CTX-M, bla_TEM, tet(A) and intI1) were not detected after exposure. Results demonstrated the selection of bacteria intrinsically resistant to antibiotics imposed by copper and zinc exposure, suggesting an important role played by cross-resistance mechanisms.

High frequency of antibiotic tolerance in deep subsurface heterotrophic cultivable bacteria from the Rozália Gold Mine, Slovakia

The Rozália Mine, with its long mining history, could represent an environmental threat connected with metal contamination and associated antibiotic tolerance. Metal and antibiotic tolerance profiles of heterotrophic, cultivable bacteria isolated from the Rozália Gold Mine in Hodruša-Hámre, Slovakia, and the surrounding area were analysed. Subsurface samples were collected from different mine levels or an ore storage dump. As expected, heterotrophic cultivable bacteria showed high minimum inhibitory concentrations for metals (up to 1000 mg/l for zinc and nickel, 2000 mg/l for lead and 500 mg/l for copper). Surprisingly, very high minimum inhibitory concentrations of selected antibiotics were observed, e.g. > 10,000 μg/ml for ampicillin, up to 4800 μg/ml for kanamycin, 800 μg/ml for chloramphenicol and 50 μg/ml for tetracycline. Correlation analysis revealed a linkage between increased tolerance to the antibiotics ampicillin and chloramphenicol and metal tolerance to nickel and copper. A correlation was also observed between tetracycline-kanamycin tolerance and zinc-lead tolerance. Our data indicate that high levels of antibiotic tolerance occur in deep subsurface microbiota, which is probably connected with the increased level of metal concentrations in the mine environment.

Critical Review: Propensity of Premise Plumbing Pipe Materials to Enhance or Diminish Growth of Legionella and Other Opportunistic Pathogens

Growth of Legionella pneumophila and other opportunistic pathogens (OPs) in drinking water premise plumbing poses an increasing public health concern. Premise plumbing is constructed of a variety of materials, creating complex environments that vary chemically, microbiologically, spatially, and temporally in a manner likely to influence survival and growth of OPs. Here we systematically review the literature to critically examine the varied effects of common metallic (copper, iron) and plastic (PVC, cross-linked polyethylene (PEX)) pipe materials on factors influencing OP growth in drinking water, including nutrient availability, disinfectant levels, and the composition of the broader microbiome. Plastic pipes can leach organic carbon, but demonstrate a lower disinfectant demand and fewer water chemistry interactions. Iron pipes may provide OPs with nutrients directly or indirectly, exhibiting a high disinfectant demand and potential to form scales with high surface areas suitable for biofilm colonization. While copper pipes are known for their antimicrobial properties, evidence of their efficacy for OP control is inconsistent. Under some circumstances, copper's interactions with premise plumbing water chemistry and resident microbes can encourage growth of OPs. Plumbing design, configuration, and operation can be manipulated to control such interactions and health outcomes. Influences of pipe materials on OP physiology should also be considered, including the possibility of influencing virulence and antibiotic resistance. In conclusion, all known pipe materials have a potential to either stimulate or inhibit OP growth, depending on the circumstances. This review delineates some of these circumstances and informs future research and guidance towards effective deployment of pipe materials for control of OPs.

The formation mechanism of antibiotic-resistance genes associated with bacterial communities during biological decomposition of household garbage

Food wastes are significant reservoir of antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) available for exchange with clinical pathogens. However, food wastes-related changes of antibiotic resistance in long-period decomposition have been overlooked. Here, we evaluated the comprehensive ARG profile and its association with microbial communities, explained how this might vary with household garbage decomposition. Average of 128, 150 and 91 ARGs were detected in meat, vegetable and fruit wastes, respectively, with multidrug and tetracycline as the predominant ARG types. ARG abundance significantly increased at initial stage of waste fermentation and then decreased. High abundance of Eubacterium-coprostanoligenes, Sporanaerobacter, Peptoniphilus, Peptostreptococcus might be explained for the high relative abundance of ARGs in meat, while high abundance of Advenella, Prevotella, Solobacterium was attributed to the high diversity of ARGs in vegetables. Significant correlations were observed among volatile organic compounds, mobile genetic elements and ARGs, implying that they might contribute to transfer and transport of ARGs. Network analysis revealed that aph(2')-Id-01, acrA-05, tetO-1 were potential ARG indicators, while Hathewaya, Paraclostridium and Prevotellaceae were possible hosts of ARGs. Our work might unveil underlining mechanism of the effects of food wastes decomposition on development and spread of ARGs in environment and also clues to ARG mitigation.

Distribution of antibiotic and metal resistance genes in two glaciers of North Sikkim, India

Glacier studies as of late have ruffled many eyeballs, exploring this frigid ecology to understand the impact of climate change. Mapquesting the glaciers led to the discovery of concealed world of "psychrophiles" harboring in it. In the present study, the antibiotic resistance genes (ARGs) and heavy metal resistance genes (MRGs) were evaluated through both the culture-dependent and culture-independent methods. Samples were collected from two different glaciers, i.e., debris-covered glacier (Changme Khangpu) and debris-free glacier (Changme Khang). Functional metagenomics of both the glacier samples, provided evidence of presence of resistant genes against various antibiotic groups. Bacitracin resistant gene (bacA) was the predominant ARG in both the glaciers. MRGs in both the glacier samples were diversified as the genes detected were resistant against various heavy metals such as arsenic, tungsten, mercury, zinc, chromium, copper, cobalt, and iron. Unique MRGs identified from Changme Khangpu glacier were resistant to copper (cutA, cutE, cutC, cutF, cueR, copC, and copB) and chromium (yelf, ruvB, nfsA, chrR, and chrA) whereas, from Changme Khang glacier they showed resistance against cobalt (mgtA, dmef, corD, corC, corB, and cnrA), and iron (yefD, yefC, yefB, and yefA) heavy metals. ARGs aligned maximum identity with Gram-negative psychrotolerant bacteria. The cultured bacterial isolates showed tolerance to high concentrations of tested heavy metal solutions. Interestingly, some of the antibiotic resistant bacterial isolates also showed tolerance towards the higher concentrations of heavy metals. Thus, an introspection of the hypothesis of co-occurrence and/co-selection of ARGs and MRGs in such environments has been highlighted here.

Prevalence, virulence genes, and antimicrobial resistance of Vibrio species isolated from diseased marine fish in South China

Here, 70 potential Vibrio pathogens belonging to nine species, dominated by Vibrio harveyi, were isolated and identified from diseased aquacultured marine fish in South China. Subsequently, the prevalence of 11 virulence genes and the resistance to 15 antibiotics in these strains were determined. Most strains possessed atypical virulence genes in addition to typical virulence genes. Notably, hflk and chiA originating from V. harveyi, and flaC associated with V. anguillarum were detected in more than 40% of atypical host strains. Multidrug resistance was widespread: 64.29% strains were resistant to more than three antibiotics, and the multi-antibiotic resistance index ranged from 0.00 to 0.60. The proportions of strains resistant to the antibiotics vancomycin, amoxicillin, midecamycin, and furazolidone all exceeded 50%; nevertheless, all strains were sensitive to florfenicol, norfloxacin, and ciprofloxacin. Furthermore, both virulence genes and antibiotic resistance were more prevalent in Hainan than in Guangdong, owing to the warmer climate and longer annual farming time in Hainan. These results therefore suggest that warming temperatures and overuse of antibiotics are probably enhancing antibiotic resistance and bacterial infection. This study reveals that pathogenic Vibrio spp. with multi-antibiotic resistance are highly prevalent among marine fish in South China and thus warrant further attention. The results will provide helpful guidance for ecological regulation and local antibiotic use in the control of marine fish farming’ Vibrio diseases in South China, facilitating the implementation of national green and healthful aquaculture.

Genetic Determinants for Metal Tolerance and Antimicrobial Resistance Detected in Bacteria Isolated from Soils of Olive Tree Farms

Copper-derived compounds are often used in olive tree farms. In a previous study, a collection of bacterial strains isolated from olive tree farms were identified and tested for phenotypic antimicrobial resistance and heavy metal tolerance. The aim of this work was to study the genetic determinants of resistance and to evaluate the co-occurrence of metal tolerance and antibiotic resistance genes. Both metal tolerance and antibiotic resistance genes (including beta-lactamase genes) were detected in the bacterial strains from Cu-treated soils. A high percentage of the strains positive for metal tolerance genes also carried antibiotic resistance genes, especially for genes involved in resistances to beta-lactams and tetracycline. Significant associations were detected between genes involved in copper tolerance and genes coding for beta-lactamases or tetracycline resistance mechanisms. A significant association was also detected between zntA (coding for a Zn(II)-translocating P-type ATPase) and tetC genes. In conclusion, bacteria from soils of Cu-treated olive farms may carry both metal tolerance and antibiotic resistance genes. The positive associations detected between metal tolerance genes and antibiotic resistance genes suggests co-selection of such genetic traits by exposure to metals.