Effects of reductive soil disinfestation on potential pathogens and antibiotic resistance genes in soil.

Reductive soil disinfestation (RSD) is commonly employed for soil remediation in greenhouse cultivation. However, its influence on antibiotic resistance genes (ARGs) in soil remains uncertain. This study investigated the dynamic changes in soil communities, potential bacterial pathogens, and ARG profiles under various organic material treatments during RSD, including distillers' grains, potato peel, peanut vine, and peanut vine combined with charcoal. Results revealed that applying diverse organic materials in RSD significantly altered bacterial community composition and diminished the relative abundance of potential bacterial pathogens (P < 0.05). The relative abundance of high-risk ARGs decreased by 10.7%-30.6% after RSD treatments, the main decreased ARG subtypes were AAC(3)_Via, dfrA1, ErmB, lnuB, aadA. Actinobacteria was the primary host of ARGs and was suppressed by RSD. Soil physicochemical properties, such as total nitrogen, soil pH, total carbon, were crucial factors affecting ARG profiles. Our findings demonstrated that RSD treatment inhibited pathogenic bacteria and could be an option for reducing high-risk ARG proliferation in soil.

Antibiotics and Pesticides Enhancing the Transfer of Resistomes among Soil-Bayberry-Fruit Fly Food Chain in the Orchard Ecosystem.

While substantial amounts of antibiotics and pesticides are applied to maintain orchard yields, their influence on the dissemination and risk of antibiotic resisitome in the orchard food chain remains poorly understood. In this study, we characterized the bacterial and fungal communities and differentiated both antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in the soil, Chinese bayberry (matured and fallen), and fruit fly gut, collected from five geographic locations. Our results showed that fruit fly guts and soils exhibit a higher abundance of ARGs and VFGs compared with bayberry fruits. We identified 112 shared ARGs and 75 shared VFGs, with aminoglycoside and adherence factor genes being among the most abundant. The co-occurrence network revealed some shared microbes, such as Bacillus and Candida, as potential hosts of ARGs, highlighting the vector risks for both above- and below-ground parts of the orchard food chain. Notably, the elevated levels of antibiotics and pesticide residues in orchard soils increase ARGs, mobile genetic elements (MGEs), and VFGs in the soil-bayberry-fruit fly food chain. Our study highlighted that agricultural management, including the overuse of antibiotics and pesticides, could be the key factor in accumulating resistomes in the orchard food chain.

Biological Interactions Mediate Soil Functions by Altering Rare Microbial Communities.

Soil microbes, the main driving force of terrestrial biogeochemical cycles, facilitate soil organic matter turnover. However, the influence of the soil fauna on microbial communities remains poorly understood. We investigated soil microbiota dynamics by introducing competition and predation among fauna into two soil ecosystems with different fertilization histories. The interactions significantly affected rare microbial communities including bacteria and fungi. Predation enhanced the abundance of C/N cycle-related genes. Rare microbial communities are important drivers of soil functional gene enrichment. Key rare microbial taxa, including SM1A02, Gammaproteobacteria, and HSB_OF53-F07, were identified. Metabolomics analysis suggested that increased functional gene abundance may be due to specific microbial metabolic activity mediated by soil fauna interactions. Predation had a stronger effect on rare microbes, functional genes, and microbial metabolism compared to competition. Long-term organic fertilizer application increased the soil resistance to animal interactions. These findings provide a comprehensive understanding of microbial community dynamics under soil biological interactions, emphasizing the roles of competition and predation among soil fauna in terrestrial ecosystems.

The pH-specific response of soil resistome to triclocarban and arsenic co-contamination.

Heavy metals as well as disinfectants affect the spread of antibiotic resistance genes (ARGs) in soil microbes, however, their cumulative impacts on the proliferation of ARGs are not well studied. In addition, both the chemical stability/availability and ARG profiles are affected by the soil pH, but it has never been considered in the systematic evaluation of soil resistome. In the present study, a microcosm experiment was conducted to study the combined effects of arsenic and triclocarban on the resistome in soil samples with variable pH (pH 4-7). The simultaneous additions of arsenic and triclocarban increase the ARG abundance at pH > 6, because of the intensive co-selective pressures triggered by the increase in concentrations of available arsenic and triclocarban. The occurrence of multidrug ARGs increases with the addition of arsenic and triclocarban, due to the preferred selection of their functional flexibility. The presence of arsenic and triclocarban is strongly related to the spread of MGEs affecting the soil resistome. Furthermore, pH alters the patterns of microbial inhabitants, increasing the relative abundance of Bacteroidota and Proteobacteria and contributing to the prevalence of tetracycline and sulfonamide ARGs at neutral pH. These findings have insight that the effects of arsenic and triclocarban co-contamination on the soil antibiotic resistome is pH dependent.

Effects of heavy metal and disinfectant on antibiotic resistance genes and virulence factor genes in the plastisphere from diverse soil ecosystems.

Antibiotic-resistance genes (ARGs) are world-wide contaminants posing potential health risks. Quaternary ammonium compounds (QACs) and heavy metals can apply selective pressure on antibiotic resistance. However, there is a lack of evidence regarding their coupled effect on changes in ARGs and virulence factor genes (VFGs) in various soil types and their plastispheres. Herein, we conducted a microcosm experiment to explore the abundances and profiles of ARGs and VFGs in soil plastispheres from three distinct types of soils amended with Cu and disinfectants. The plastispheres enriched the ARGs' abundance compared to soils and stimulated the coupling effect of combined pollutants on promoting the abundances of ARGs and VFGs. Horizontal gene transfer inevitably accelerates the propagation of ARGs and VFGs in plastispheres under pollutant stress. In plastispheres, combined exposure to disinfectants and Cu increased some potential pathogens' relative abundances. Moreover, the combined effect of disinfectants and Cu on ARGs and VFGs changed with soil type in plastispheres, emphasising the necessity to incorporate soil type considerations into health risk assessments for ARGs and VFGs. Overall, this study highlights the high health risks of ARGs under the selective pressure of combined pollutants in plastispheres and provides valuable insights for future risk assessments related to antibiotic resistance.

A new insight into the potential drivers of antibiotic resistance gene enrichment in the collembolan gut association with antibiotic and non-antibiotic agents.

Effects of non-antibiotic pharmaceuticals on antibiotic resistance genes (ARGs) in soil ecosystem are still unclear. In this study, we explored the microbial community and ARGs variations in the gut of the model soil collembolan Folsomia candida following soil antiepileptic drug carbamazepine (CBZ) contamination, while comparing with antibiotic erythromycin (ETM) exposure. Results showed that, CBZ and ETM all significantly influenced ARGs diversity and composition in the soil and collembolan gut, increasing the relative abundance of ARGs. However, unlike ETM, which influences ARGs via bacterial communities, exposure to CBZ may have primarily facilitated enrichment of ARGs in gut through mobile genetic elements (MGEs). Although soil CBZ contamination did not pose an effect on the gut fungal community of collembolans, it increased the relative abundance of animal fungal pathogens contained therein. Soil ETM and CBZ exposure both significantly increased the relative abundance of Gammaproteobacteria in the collembolan gut, which may be used to indicate soil contamination. Together, our results provide a fresh perspective for the potential drivers of non-antibiotic drugs on ARG changes based on the actual soil environment, revealing the potential ecological risk of CBZ on soil ecosystems involving ARGs dissemination and pathogens enrichment.

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Antibiotics have played an important role in the prevention and treatment of human and animal diseases as well as the improvement of animal products. However, the mass products and application of antibiotics, especially the abuse in animal industry and clinical medicine, led to the widespread of antibiotic resistance genes (ARGs) in the environment. They spread widely through conjugation, transposition, and transformation with the help of movable elements such as plasmid, transposon and integrons, resulting in the continuous enhancement of microbial medicinal properties and posing a serious threat to human health and ecological security. At present, great attention has been paid to the impacts of ARGs on human health, but limited research on the ecological risk of ARGs in the environment. Here, the status quo and ecological risks of ARGs pollution were summarized, and the future research priorities in this field were prospected. We hope it could pave the way for further studies and give references for the ecological control and prevention of ARGs pollution.