Degradation and deactivation of a plasmid-encoded extracellular antibiotic resistance gene during separate and combined exposures to UV254 and radicals

Nihemaiti, Maolida; Yoon, Younggun; He, Huan; Dodd, Michael C.; Croué, Jean-Philippe; Lee, Yunho

doi:10.1016/j.watres.2020.115921

Cited by 63 publications

(47 citation statements)

References 55 publications

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“…The data analysis and visualization process involved in this study were conducted by Microsoft Excel 2016, GraphPad Prism 8.0.1 and R (RStudio 3.6.1) [45]. Histograms, line charts, box plots, absolute gene copies were plotted with GraphPad Prism, while UpSet-Venn diagrams, heatmap were visualized using ggplot2 UpSetR of R (Supplementary Information).…”

Section: Discussionmentioning

confidence: 99%

“…S11). According to the previous studies [45][46][47][48], especially in oligotrophic and pollutedstress, microorganisms could passively or actively release eDNA through plasmid and chromosome DNA sections of living cells, phage infection, or pyrolysis of dead cells.Meanwhile, natural competent microorganisms could integrate and express free or bonded eDNA fragments through natural transformation, which was a parasexual mechanism of microbes forsurviving environmental stress andfor generating diversity and adaptation [37,[45][46]48].Therefore, gene exchanges within e-iDNA factions could enhance the process of natural transformation, and play a vital role in microorganism responses to environmental stress [46,48]. Furthermore, in this study, the proportion of copresence gene interactions in the co-occurrence networks of low-and high-OCP-induced soil groups was signi cantly higher than that in the clean soil (Fig.…”

Section: S21-25)mentioning

confidence: 99%

“…Keystone genes exchange under exposure to p-NCB-stress to the above metagenomic analysis, nine KGs (i.e., livH, yfcG, gst, parB, ssuD, coxA, accC, nuoD and fadA) and nine non-KGs (i.e., prkC, fusA, livK, uvrA, asnB, yfbK, dnaE, ftsH and topA) were separately inserted into Plasmid pUC19 for transformation tests using E. coli DH5α as the recipient bacteria (Table . S4) [45]. Brie y, 5 μL of E. coli (OD 600 = 2.40) were added into 5 mL of LB medium with gradient p-NCB pesticide concentrations (i.e., 0, 10 and 100 mg L -1 ) and then shaken (250 rpm, 37℃) for 10 min.…”

Section: Metagenomic Sequencing and Bioinformatic Analysismentioning

confidence: 99%

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Keystone Genes from Extracellular DNA Facilitate Microbial Adaptation in Organochlorine Pesticide-Contaminated Soil

Zhang

Adams

et al. 2022

Preprint

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Background: Keystone genes exert great influence on maintaining microbiome stability and functional recovery irrespective of their environmental abundance. Elucidating the effects of environmental stresses on their variation is vital for identifying the recovery potential of ecosystems and regulating microbial adaptation within. Extracellular and intracellular gene transfer under pesticide-induced selection is convenient for studying keystone genes shifts and their role in ecosystem recovery potential. Results: Metagenomic analysis revealed that increased stress induced by organochlorine pesticides (OCPs) decreased soil bacterial diversity, and enriched abundance of functional genes associated with metabolism and gene transfer potential, both in extracellular and intracellular DNA. Increased OCP concentrations also significantly enhanced intercellular gene associations, which facilitated the abundance of keystone genes associated with metabolic functions by a factor of 2.14 times. Keystone genes devoted their niche specificity in microbiome co-occurrence networks, enhancing microbial survival under OCP stress where they had been taken up and incorporated by intercellular transfer. This was verified by culturing on media containing OCP (e.g., p-nitrochlorobenzene). Furthermore, in a 100-day field observation of ten different OCP-contaminated sites, China, keystone genes genes ssuD, livH, yfcG, coxA and gst, showed significant variations in abundance in response to the recovery of OCP-induced ecosystems and their intercellular transfer was promoted by 0~1.50 orders of magnitude. Conclusion: Under OCP-induced stress, the microbial community composition, community structure and certain transferable keystone genes all participate in the adaptive response to the environmental stresses. The observed gene transfers within the extracellular and intracellular DNA fractions emphasize the pivotal influence of keystone genes in maintaining ecosystem stability and resilience.

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Section: Discussionmentioning

confidence: 99%

Section: S21-25)mentioning

confidence: 99%

Section: Metagenomic Sequencing and Bioinformatic Analysismentioning

confidence: 99%

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Keystone Genes from Extracellular DNA Facilitate Microbial Adaptation in Organochlorine Pesticide-Contaminated Soil

Zhang

Adams

et al. 2022

Preprint

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“…Oxidative gases (i.e., O 3 and NO x ) can degrade proteins/polypeptides to form amino acids − and induce bacterial lysis, , leading to the release of free DNA to the extracellular environment. Free ARGs may thus be influenced by oxidative gases and ultraviolet radiation, which can act in a manner similar to disinfection techniques. , Phage-associated ARGs are generated in metabolically active hosts during a viral infection and assemble to transfer ARGs among hosts . Relative humidity (RH) is an important factor in modulating the survival and/or infectivity of viruses, , which may have implications for phage-associated ARGs.…”

Section: Introductionmentioning

confidence: 99%

Intracellular and Extracellular Antibiotic Resistance Genes in Airborne PM_2.5 for Respiratory Exposure in Urban Areas

Liu

Xie

et al. 2021

Environ. Sci. Technol. Lett.

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The current research paradigm for the environmental dissemination of antibiotic resistance genes (ARGs) focuses on those harbored within bacteria (i.e., intracellular fraction). Understanding both intracellular and extracellular ARGs has particular implications for the flux and fate of ARGs that are airborne via fine particulate matter (PM 2.5 ) from the ambient atmosphere to the human airway. In this study, we developed an operationally defined protocol for urban PM 2.5 to quantify the abundance of ARGs occurring in free and phage-associated DNA, in addition to their counterparts commonly analyzed within bacterial cells. The results demonstrated that the extracellular fraction comprises a significant proportion of total ARGs in PM 2.5 , with subtype-specific dominance in either free or phage-associated DNA. A comparison between temperate and subtropical cities revealed geographical disparities of PM 2.5 -associated intracellular and extracellular ARGs due to the influences of regional meteorological factors and oxidative gases. Considering the potential for horizontal gene transfers and the efficiency of respiratory deposition, the extracellular fraction could represent >60% of the modeled inhalational intake of most of the analyzed ARGs in some cities. This study highlights the importance of the dynamics of ARGs in airborne PM 2.5 and their health implications across climate zones and pollution gradients.

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“…Copper ions (Cu 2+ ) promote the horizontal transfer of plasmid-mediated ARGs in freshwater microcosms (Wang et al, 2020). HGT includes conjugation (mediated by cell-to-cell contact), transformation (mediated by extracellular DNA), and transduction (bacteriophage mediated) (Partridge et al, 2018;McInnes et al, 2020;Nihemaiti et al, 2020). The conjugation between the donor and the recipient mostly mediates the transfer of plasmids and integrative and conjugative elements (ICEs) (Hastings et al, 2004;Redondo-Salvo et al, 2020;Rodriguez-Beltran et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Copper Ions Facilitate the Conjugative Transfer of SXT/R391 Integrative and Conjugative Element Across Bacterial Genera

Song

Zuo

et al. 2021

Front. Microbiol.

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Copper can persist stably in the environment for prolonged periods. Except for inducing antibiotic resistance in bacteria, copper ions (Cu2+) can facilitate the horizontal transfer of plasmid DNA. However, whether and how Cu2+ can accelerate the conjugative transfer of SXT/R391 integrative and conjugative element (ICE) is still largely unknown. In this study, Proteus mirabilis ChSC1905, harboring an SXT/R391 ICE that carried 21 antibiotic resistance genes (ARGs), was used as a donor, and Escherichia coli EC600 was used as a recipient. Cu2+, at subinhibitory and environmentally relevant concentrations (1–10 μmol/L), significantly accelerated the conjugative transfer of SXT/R391 ICE across bacterial genera (from P. mirabilis to E. coli) (p < 0.05). The combined analyses of phenotypic tests and genome-wide sequencing indicated that reactive oxygen species (ROS) production and cell membrane permeability were critical in the enhanced conjugative transfer of SXT/R391 ICE. Furthermore, the expression of genes related to cell adhesion and ATP synthesis was also significantly upregulated on exposure to Cu2+ at a concentration of 5 μmol/L. This study clarified the potential mechanisms of Cu2+ to promote the conjugative transfer of SXT/R391 ICE, revealing the potential risk imposed by Cu2+ on the horizontal transfer of SXT/R391 ICE-mediated ARGs.

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Degradation and deactivation of a plasmid-encoded extracellular antibiotic resistance gene during separate and combined exposures to UV254 and radicals

Cited by 63 publications

References 55 publications

Keystone Genes from Extracellular DNA Facilitate Microbial Adaptation in Organochlorine Pesticide-Contaminated Soil

Keystone Genes from Extracellular DNA Facilitate Microbial Adaptation in Organochlorine Pesticide-Contaminated Soil

Intracellular and Extracellular Antibiotic Resistance Genes in Airborne PM_2.5 for Respiratory Exposure in Urban Areas

Copper Ions Facilitate the Conjugative Transfer of SXT/R391 Integrative and Conjugative Element Across Bacterial Genera

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Degradation and deactivation of a plasmid-encoded extracellular antibiotic resistance gene during separate and combined exposures to UV254 and radicals

Cited by 63 publications

References 55 publications

Keystone Genes from Extracellular DNA Facilitate Microbial Adaptation in Organochlorine Pesticide-Contaminated Soil

Keystone Genes from Extracellular DNA Facilitate Microbial Adaptation in Organochlorine Pesticide-Contaminated Soil

Intracellular and Extracellular Antibiotic Resistance Genes in Airborne PM2.5 for Respiratory Exposure in Urban Areas

Copper Ions Facilitate the Conjugative Transfer of SXT/R391 Integrative and Conjugative Element Across Bacterial Genera

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Product

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Intracellular and Extracellular Antibiotic Resistance Genes in Airborne PM_2.5 for Respiratory Exposure in Urban Areas