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Li G, Long TF, Zhou SY, Xia LJ, Gao A, Wan L, Diao XY, He YZ, Sun RY, Yang JT, Tang SQ, Ren H, Fang LX, Liao XP, Liu YH, Chen L, Sun J. CRISPR-AMRtracker: A novel toolkit to monitor the antimicrobial resistance gene transfer in fecal microbiota. Drug Resist Updat 2024; 77:101142. [PMID: 39214042 DOI: 10.1016/j.drup.2024.101142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 08/04/2024] [Accepted: 08/17/2024] [Indexed: 09/04/2024]
Abstract
The spread of antibiotic resistance genes (ARGs), particularly those carried on plasmids, poses a major risk to global health. However, the extent and frequency of ARGs transfer in microbial communities among human, animal, and environmental sectors is not well understood due to a lack of effective tracking tools. We have developed a novel fluorescent tracing tool, CRISPR-AMRtracker, to study ARG transfer. It combines CRISPR/Cas9 fluorescence tagging, fluorescence-activated cell sorting, 16S rRNA gene sequencing, and microbial community analysis. CRISPR-AMRtracker integrates a fluorescent tag immediately downstream of ARGs, enabling the tracking of ARG transfer without compromising the host cell's antibiotic susceptibility, fitness, conjugation, and transposition. Notably, our experiments demonstrate that sfGFP-tagged plasmid-borne mcr-1 can transfer across diverse bacterial species within fecal samples. This innovative approach holds the potential to illuminate the dynamics of ARG dissemination and provide valuable insights to shape effective strategies in mitigating the escalating threat of antibiotic resistance.
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Affiliation(s)
- Gong Li
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Teng-Fei Long
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Shi-Ying Zhou
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Li-Juan Xia
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Ang Gao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Lei Wan
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Xiao-Yuan Diao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Yu-Zhang He
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Ruan-Yang Sun
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Jin-Tao Yang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Sheng-Qiu Tang
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, PR China
| | - Hao Ren
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Liang-Xing Fang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Xiao-Ping Liao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Ya-Hong Liu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Liang Chen
- Department of Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214, United States.
| | - Jian Sun
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China.
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Schmidt SBI, Rodríguez-Rojas A, Rolff J, Schreiber F. Biocides used as material preservatives modify rates of de novo mutation and horizontal gene transfer in bacteria. JOURNAL OF HAZARDOUS MATERIALS 2022; 437:129280. [PMID: 35714537 DOI: 10.1016/j.jhazmat.2022.129280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 05/20/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Antimicrobial resistance (AMR) is a global health problem with the environment being an important compartment for the evolution and transmission of AMR. Previous studies showed that de-novo mutagenesis and horizontal gene transfer (HGT) by conjugation or transformation - important processes underlying resistance evolution and spread - are affected by antibiotics, metals and pesticides. However, natural microbial communities are also frequently exposed to biocides used as material preservatives, but it is unknown if these substances induce mutagenesis and HGT. Here, we show that active substances used in material preservatives can increase rates of mutation and conjugation in a species- and substance-dependent manner, while rates of transformation are not increased. The bisbiguanide chlorhexidine digluconate, the quaternary ammonium compound didecyldimethylammonium chloride, the metal copper, the pyrethroid-insecticide permethrin, and the azole-fungicide propiconazole increase mutation rates in Escherichia coli, whereas no increases were identified for Bacillus subtilis and Acinetobacter baylyi. Benzalkonium chloride, chlorhexidine and permethrin increased conjugation in E. coli. Moreover, our results show a connection between the RpoS-mediated general stress and the RecA-linked SOS response with increased rates of mutation and conjugation, but not for all biocides. Taken together, our data show the importance of assessing the contribution of material preservatives on AMR evolution and spread.
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Affiliation(s)
- Selina B I Schmidt
- Division of Biodeterioration and Reference Organisms (4.1), Department of Materials and the Environment, Federal Institute for Materials Research and Testing (BAM), Unter den Eichen 87, 12205 Berlin, Germany.
| | - Alexandro Rodríguez-Rojas
- Evolutionary Biology, Institute of Biology, Freie Universität Berlin, Königin-Luise-Straße 1-3, 14195 Berlin, Germany; Internal Medicine - Vetmeduni Vienna, Veterinärplatz 1, 1210 Vienna, Austria.
| | - Jens Rolff
- Evolutionary Biology, Institute of Biology, Freie Universität Berlin, Königin-Luise-Straße 1-3, 14195 Berlin, Germany.
| | - Frank Schreiber
- Division of Biodeterioration and Reference Organisms (4.1), Department of Materials and the Environment, Federal Institute for Materials Research and Testing (BAM), Unter den Eichen 87, 12205 Berlin, Germany.
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Augsburger N, Zaouri N, Cheng H, Hong PY. The use of UV/H 2O 2 to facilitate removal of emerging contaminants in anaerobic membrane bioreactor effluents. ENVIRONMENTAL RESEARCH 2021; 198:110479. [PMID: 33212130 DOI: 10.1016/j.envres.2020.110479] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/21/2020] [Accepted: 11/11/2020] [Indexed: 06/11/2023]
Abstract
Effluent from anaerobic membrane bioreactor (AnMBR) contains ammonia and would require post-polishing treatment before it can be disinfected by chlorine. However, additional post-treatment steps to remove nutrients offset the energetic benefits derived from anaerobic fermentation. The use of chlorine or ozone also promotes concerns associated with disinfection byproducts. This study evaluates UV/H2O2 as a potential strategy suited for the removal of pharmaceutical compounds as well as antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) from AnMBR effluent. Our findings indicate that 10 mg/L H2O2 and 61.5 mJ/cm2 of UV fluence are able to achieve a 4-log removal of both Escherichia coli PI7 and Klebsiella pneumoniae L7. However, a higher fluence of 311 mJ/cm2 with the same amount of H2O2 would be required to achieve >90% removal of atenolol, carbamazepine and estrone. The removal of the pharmaceutical compounds was driven by the hydroxyl radicals generated from H2O2, while UV exposure governed the inactivation of ARB and ARGs. UV/H2O2 increased overall mutagenicity of the treated wastewater matrix but did not result in any changes to the natural transformation rates. Instead, UV significantly reduced natural transformation rates by means of DNA damage. Overall, UV/H2O2 could be the ideal final disinfection strategy for AnMBR effluent without requiring additional post-treatment prior disinfection.
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Affiliation(s)
- Nicolas Augsburger
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia; Center of Excellence for NEOM Research, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
| | - Noor Zaouri
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
| | - Hong Cheng
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia; Center of Excellence for NEOM Research, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
| | - Pei-Ying Hong
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia; Center of Excellence for NEOM Research, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia.
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Sivakumar K, Lehmann R, Rachmadi AT, Augsburger N, Zaouri N, Tegner J, Hong PY. Elucidating the Role of Virulence Traits in the Survival of Pathogenic E. coli PI-7 Following Disinfection. Front Bioeng Biotechnol 2021; 8:614186. [PMID: 33415102 PMCID: PMC7783314 DOI: 10.3389/fbioe.2020.614186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/03/2020] [Indexed: 11/13/2022] Open
Abstract
Reuse and discharge of treated wastewater can result in dissemination of microorganisms into the environment. Deployment of disinfection strategies is typically proposed as a last stage remediation effort to further inactivate viable microorganisms. In this study, we hypothesize that virulence traits, including biofilm formation, motility, siderophore, and curli production along with the capability to internalize into mammalian cells play a role in survival against disinfectants. Pathogenic E. coli PI-7 strain was used as a model bacterium that was exposed to diverse disinfection strategies such as chlorination, UV and solar irradiation. To this end, we used a random transposon mutagenesis library screening approach to generate 14 mutants that exhibited varying levels of virulence traits. In these 14 isolated mutants, we observed that an increase in virulence traits such as biofilm formation, motility, curli production, and internalization capability, increased the inactivation half-lives of mutants compared to wild-type E. coli PI-7. In addition, oxidative stress response and EPS production contributed to lengthening the lag phase duration (defined as the time required for exposure to disinfectant prior to decay). However, traits related to siderophore production did not help with survival against the tested disinfection strategies. Taken together, the findings suggested that selected virulence traits facilitate survival of pathogenic E. coli PI-7, which in turn could account for the selective enrichment of pathogens over the non-pathogenic ones after wastewater treatment. Further, the study also reflected on the effectiveness of UV as a more viable disinfection strategy for inactivation of pathogens.
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Affiliation(s)
- Krishnakumar Sivakumar
- Computational Bioscience Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Robert Lehmann
- Living Systems Laboratory, Environmental Epigenetic Program, Biological and Environmental Science and Engineering Division, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Andri Taruna Rachmadi
- Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Nicolas Augsburger
- Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Noor Zaouri
- Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Jesper Tegner
- Living Systems Laboratory, Environmental Epigenetic Program, Biological and Environmental Science and Engineering Division, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Pei-Ying Hong
- Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Jiang X, Palazzotto E, Wybraniec E, Munro LJ, Zhang H, Kell DB, Weber T, Lee SY. Automating Cloning by Natural Transformation. ACS Synth Biol 2020; 9:3228-3235. [PMID: 33231069 DOI: 10.1021/acssynbio.0c00240] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Affordable and automated cloning platforms are essential to many synthetic biology studies. However, the traditional E. coli-based cloning is a major bottleneck as it requires heat shock or electroporation implemented in the robotic workflows. To overcome this problem, we explored bacterial natural transformation for automatic DNA cloning and engineering. Recombinant plasmids are efficiently generated from Gibson or overlap extension PCR (OE-PCR) products by simply adding the DNA into Acinetobacter baylyi ADP1 cultures. No DNA purification, competence induction, or special equipment is required. Up to 10,000 colonies were obtained per microgram of DNA, while the number of false positive colonies was low. We cloned and engineered 21 biosynthetic gene clusters (BGCs) of various types, with length from 1.5 to 19 kb and GC content from 35% to 72%. One of them, a nucleoside BGC, showed antibacterial activity. Furthermore, the method was easily transferred to a low-cost benchtop robot with consistent cloning efficiency. Thus, this automatic natural transformation (ANT) cloning provides an easy, robust, and affordable platform for high throughput DNA engineering.
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Affiliation(s)
- Xinglin Jiang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Emilia Palazzotto
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Ewa Wybraniec
- Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Lachlan Jake Munro
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Haibo Zhang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P. R. China
| | - Douglas B. Kell
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Department of Biochemistry and Systems Biology,Institute of Systems, Molecular and Integrative Biology, Biosciences Building, University of Liverpool, LiverpoolL69 7ZB, UK
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Sang Yup Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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Augsburger N, Mantilla-Calderon D, Daffonchio D, Hong PY. Acquisition of Extracellular DNA by Acinetobacter baylyi ADP1 in Response to Solar and UV-C 254nm Disinfection. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:10312-10319. [PMID: 31386349 DOI: 10.1021/acs.est.9b01206] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Extracellular DNA (eDNA) cannot be effectively removed by most of the existing wastewater treatment technologies and can contribute to the gain of new functional traits when transformed into competent bacteria present in downstream environments. This study evaluates the contributions of solar and UV-C254nm irradiation to the transformation of eDNA in Acinetobacter baylyi ADP1. Solar irradiation was evaluated because it is a natural environmental stressor to which eDNA would be exposed during wastewater reuse. UV-C254nm was evaluated as an alternative to a chlorine-based disinfection strategy. Our findings showed that solar disinfection increased the natural transformation frequency by up to 2.0-fold after irradiance at 153 mJ/cm2. This was largely mediated by reactive oxygen species generation, which was correlated with an upregulation of both DNA repair (recA and ddrR) and competence (comA and pilX) genes. In contrast, even though UV-C254nm exposure was accompanied by the upregulation of DNA repair (recA, ddrR, and uvrB) genes and, hence, possibly higher integration rates of eDNA, we observed a concentration-dependent decrease in transformation rates. This decrease in transformation was likely due to the UV dimerization of eDNA, which resulted in the integration of damaged genes that cannot be transcribed into any functional gene products. These results imply that even though sunlight stimulates eDNA uptake and integration in the natural environment, UV disinfection implemented at a treatment plant can potentially minimize subsequent detrimental effects by damaging the extracellular genetic material and ensuring that there is no substantial expression of these transformed genes.
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Mantilla-Calderon D, Plewa MJ, Michoud G, Fodelianakis S, Daffonchio D, Hong PY. Water Disinfection Byproducts Increase Natural Transformation Rates of Environmental DNA in Acinetobacter baylyi ADP1. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:6520-6528. [PMID: 31050420 DOI: 10.1021/acs.est.9b00692] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The process of natural transformation allows for the stable uptake, integration, and functional expression of extracellular DNA. This mechanism of horizontal gene transfer has been widely linked to the acquisition of antibiotic resistance and virulence factors. Here, we demonstrate that bromoacetic acid (BAA)-a regulated drinking water disinfection byproduct (DBP)-can stimulate natural transformation rates in the model organism Acinetobacter baylyi ADP1. We demonstrate that transformation stimulation in response to BAA is concentration-dependent and is linked to the ability of this compound to generate DNA damage via oxidative stress. In presence of BAA, transcription of recA was upregulated 20-40% compared to the nontreated controls, indicating that this component of the DNA damage response could be associated with the increase in transformation. Other genes associated with DNA translocation across the cytoplasmic membrane (i.e., pilX, comA) did not exhibit increased transcription in the presence of BAA, indicating that the enhancement of transformation is not associated with increased translocation rates of environmental DNA. Overall, these results lead us to speculate that elevated recA transcription levels could lead to increased integration rates of foreign DNA within the recipient cell during DNA repair. Lastly, we show that an artificial DBP cocktail simulating the environmental concentrations of five water DBP classes stimulates natural transformation by almost 2-fold. The results of this study suggest that mutagens like DBPs may play an important role in enhancing the fixation rates of extracellular DNA in the environmental metagenome.
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Fluorescence-Based Detection of Natural Transformation in Drug-Resistant Acinetobacter baumannii. J Bacteriol 2018; 200:JB.00181-18. [PMID: 30012729 PMCID: PMC6148472 DOI: 10.1128/jb.00181-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 06/27/2018] [Indexed: 01/05/2023] Open
Abstract
Acinetobacter baumannii is a nosocomial agent with a high propensity for developing resistance to antibiotics. This ability relies on horizontal gene transfer mechanisms occurring in the Acinetobacter genus, including natural transformation. To study natural transformation in bacteria, the most prevalent method uses selection for the acquisition of an antibiotic resistance marker in a target chromosomal locus by the recipient cell. Most clinical isolates of A. baumannii are resistant to multiple antibiotics, limiting the use of such selection-based methods. Here, we report the development of a phenotypic and selection-free method based on flow cytometry to detect transformation events in multidrug-resistant (MDR) clinical A. baumannii isolates. To this end, we engineered a translational fusion between the abundant and conserved A. baumannii nucleoprotein (HU) and the superfolder green fluorescent protein (sfGFP). The new method was benchmarked against the conventional antibiotic selection-based method. Using this new method, we investigated several parameters affecting transformation efficiencies and identified conditions of transformability one hundred times higher than those previously reported. Using optimized transformation conditions, we probed natural transformation in a set of MDR clinical and nonclinical animal A. baumannii isolates. Regardless of their origin, the majority of the isolates displayed natural transformability, indicative of a conserved trait in the species. Overall, this new method and optimized protocol will greatly facilitate the study of natural transformation in the opportunistic pathogen A. baumannii IMPORTANCE Antibiotic resistance is a pressing global health concern with the rise of multiple and panresistant pathogens. The rapid and unfailing resistance to multiple antibiotics of the nosocomial agent Acinetobacter baumannii, notably to carbapenems, prompt to understand the mechanisms behind acquisition of new antibiotic resistance genes. Natural transformation, one of the horizontal gene transfer mechanisms in bacteria, was only recently described in A. baumannii and could explain its ability to acquire resistance genes. We developed a reliable method to probe and study natural transformation mechanism in A. baumannii More broadly, this new method based on flow cytometry will allow experimental detection and quantification of horizontal gene transfer events in multidrug-resistant A. baumannii.
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de Santis B, Stockhofe N, Wal JM, Weesendorp E, Lallès JP, van Dijk J, Kok E, De Giacomo M, Einspanier R, Onori R, Brera C, Bikker P, van der Meulen J, Kleter G. Case studies on genetically modified organisms (GMOs): Potential risk scenarios and associated health indicators. Food Chem Toxicol 2018; 117:36-65. [DOI: 10.1016/j.fct.2017.08.033] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 07/03/2017] [Accepted: 08/22/2017] [Indexed: 01/07/2023]
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Identification of Major Rhizobacterial Taxa Affected by a Glyphosate-Tolerant Soybean Line via Shotgun Metagenomic Approach. Genes (Basel) 2018; 9:genes9040214. [PMID: 29659545 PMCID: PMC5924556 DOI: 10.3390/genes9040214] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/19/2018] [Accepted: 04/13/2018] [Indexed: 01/08/2023] Open
Abstract
The worldwide commercial cultivation of transgenic crops, including glyphosate-tolerant (GT) soybeans, has increased widely during the past 20 years. However, it is accompanied with a growing concern about potential effects of transgenic crops on the soil microbial communities, especially on rhizosphere bacterial communities. Our previous study found that the GT soybean line NZL06-698 (N698) significantly affected rhizosphere bacteria, including some unidentified taxa, through 16S rRNA gene (16S rDNA) V4 region amplicon deep sequencing via Illumina MiSeq. In this study, we performed 16S rDNA V5–V7 region amplicon deep sequencing via Illumina MiSeq and shotgun metagenomic approaches to identify those major taxa. Results of these processes revealed that the species richness and evenness increased in the rhizosphere bacterial communities of N698, the beta diversity of the rhizosphere bacterial communities of N698 was affected, and that certain dominant bacterial phyla and genera were related to N698 compared with its control cultivar Mengdou12. Consistent with our previous findings, this study showed that N698 affects the rhizosphere bacterial communities. In specific, N698 negatively affects Rahnella, Janthinobacterium, Stenotrophomonas, Sphingomonas and Luteibacter while positively affecting Arthrobacter, Bradyrhizobium, Ramlibacter and Nitrospira.
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Santala V, Karp M, Santala S. Bioluminescence-based system for rapid detection of natural transformation. FEMS Microbiol Lett 2016; 363:fnw125. [DOI: 10.1093/femsle/fnw125] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2016] [Indexed: 11/13/2022] Open
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12
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Raneri M, Sciandrone B, Briani F. A whole-cell assay for specific inhibitors of translation initiation in bacteria. ACTA ACUST UNITED AC 2015; 20:627-33. [PMID: 25586496 DOI: 10.1177/1087057114566376] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 12/05/2014] [Indexed: 11/15/2022]
Abstract
The bacterial translational apparatus is an ideal target for the search of new antibiotics. In fact, it performs an essential process carried out by a large number of potential subtargets for antibiotic action. Moreover, it is sufficiently different in several molecular details from the apparatus of Eukarya and Archaea to generally ensure specificity for the bacterial domain. This applies in particular to translation initiation, which is the most different step in the process. In bacteria, the 30S ribosomal subunit directly binds to the translation initiation region, a site within the messenger RNA (mRNA) 5'-untranslated region (5'-UTR). 30S binding is mediated by the interaction of both the 16S ribosomal RNA and the ribosomal protein S1 with specific regions of the mRNA 5'-UTR. An alternative, S1-independent pathway is enjoyed by leaderless mRNAs (i.e., transcripts devoid of a 5'-UTR). We have developed a simple fluorescence-based whole-cell assay in Escherichia coli to find inhibitors of the canonical S1-dependent translation initiation pathway. The assay has been set up both in a common E. coli laboratory strain and in a strain with an outer membrane permeability defect. Compared with other whole-cell assays for antibacterials, the major advantages of the screen described here are high sensitivity and specificity.
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Affiliation(s)
- Matteo Raneri
- Dipartimento di Bioscienze, Università degli Studi di Milano, Italy
| | | | - Federica Briani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Italy
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Delvillani F, Sciandrone B, Peano C, Petiti L, Berens C, Georgi C, Ferrara S, Bertoni G, Pasini ME, Dehò G, Briani F. Tet-Trap, a genetic approach to the identification of bacterial RNA thermometers: application to Pseudomonas aeruginosa. RNA (NEW YORK, N.Y.) 2014; 20:1963-1976. [PMID: 25336583 PMCID: PMC4238360 DOI: 10.1261/rna.044354.114] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 09/10/2014] [Indexed: 06/04/2023]
Abstract
Modulation of mRNA translatability either by trans-acting factors (proteins or sRNAs) or by in cis-acting riboregulators is widespread in bacteria and controls relevant phenotypic traits. Unfortunately, global identification of post-transcriptionally regulated genes is complicated by poor structural and functional conservation of regulatory elements and by the limitations of proteomic approaches in protein quantification. We devised a genetic system for the identification of post-transcriptionally regulated genes and we applied this system to search for Pseudomonas aeruginosa RNA thermometers, a class of regulatory RNA that modulates gene translation in response to temperature changes. As P. aeruginosa is able to thrive in a broad range of environmental conditions, genes differentially expressed at 37 °C versus lower temperatures may be involved in infection and survival in the human host. We prepared a plasmid vector library with translational fusions of P. aeruginosa DNA fragments (PaDNA) inserted upstream of TIP2, a short peptide able to inactivate the Tet repressor (TetR) upon expression. The library was assayed in a streptomycin-resistant merodiploid rpsL(+)/rpsL31 Escherichia coli strain in which the dominant rpsL(+) allele, which confers streptomycin sensitivity, was repressed by TetR. PaDNA fragments conferring thermosensitive streptomycin resistance (i.e., expressing PaDNA-TIP2 fusions at 37°C, but not at 28°C) were sequenced. We identified four new putative thermosensors. Two of them were validated with conventional reporter systems in E. coli and P. aeruginosa. Interestingly, one regulates the expression of ptxS, a gene implicated in P. aeruginosa pathogenesis.
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Affiliation(s)
- Francesco Delvillani
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Barbara Sciandrone
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Clelia Peano
- Istituto di Tecnologie Biomediche, CNR, 20090 Segrate, Italy
| | - Luca Petiti
- Istituto di Tecnologie Biomediche, CNR, 20090 Segrate, Italy Doctoral Program of Molecular and Translational Medicine, Università degli Studi di Milano, 20133 Milano, Italy
| | - Christian Berens
- Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Christiane Georgi
- Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Silvia Ferrara
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Giovanni Bertoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Maria Enrica Pasini
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Gianni Dehò
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Federica Briani
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
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Disruption of putrescine biosynthesis in Shewanella oneidensis enhances biofilm cohesiveness and performance in Cr(VI) immobilization. Appl Environ Microbiol 2013; 80:1498-506. [PMID: 24362428 DOI: 10.1128/aem.03461-13] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although biofilm-based bioprocesses have been increasingly used in various applications, the long-term robust and efficient biofilm performance remains one of the main bottlenecks. In this study, we demonstrated that biofilm cohesiveness and performance of Shewanella oneidensis can be enhanced through disrupting putrescine biosynthesis. Through random transposon mutagenesis library screening, one hyperadherent mutant strain, CP2-1-S1, exhibiting an enhanced capability in biofilm formation, was obtained. Comparative analysis of the performance of biofilms formed by S. oneidensis MR-1 wild type (WT) and CP2-1-S1 in removing dichromate (Cr2O7(2-)), i.e., Cr(VI), from the aqueous phase showed that, compared with the WT biofilms, CP2-1-S1 biofilms displayed a substantially lower rate of cell detachment upon exposure to Cr(VI), suggesting a higher cohesiveness of the mutant biofilms. In addition, the amount of Cr(III) immobilized by CP2-1-S1 biofilms was much larger, indicating an enhanced performance in Cr(VI) bioremediation. We further showed that speF, a putrescine biosynthesis gene, was disrupted in CP2-1-S1 and that the biofilm phenotypes could be restored by both genetic and chemical complementations. Our results also demonstrated an important role of putrescine in mediating matrix disassembly in S. oneidensis biofilms.
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Rizzo L, Manaia C, Merlin C, Schwartz T, Dagot C, Ploy MC, Michael I, Fatta-Kassinos D. Urban wastewater treatment plants as hotspots for antibiotic resistant bacteria and genes spread into the environment: a review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2013; 447:345-60. [PMID: 23396083 DOI: 10.1016/j.scitotenv.2013.01.032] [Citation(s) in RCA: 1259] [Impact Index Per Article: 114.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 01/08/2013] [Accepted: 01/08/2013] [Indexed: 05/20/2023]
Abstract
Urban wastewater treatment plants (UWTPs) are among the main sources of antibiotics' release into the environment. The occurrence of antibiotics may promote the selection of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB), which shade health risks to humans and animals. In this paper the fate of ARB and ARGs in UWTPs, focusing on different processes/technologies (i.e., biological processes, advanced treatment technologies and disinfection), was critically reviewed. The mechanisms by which biological processes influence the development/selection of ARB and ARGs transfer are still poorly understood. Advanced treatment technologies and disinfection process are regarded as a major tool to control the spread of ARB into the environment. In spite of intense efforts made over the last years to bring solutions to control antibiotic resistance spread in the environment, there are still important gaps to fill in. In particular, it is important to: (i) improve risk assessment studies in order to allow accurate estimates about the maximal abundance of ARB in UWTPs effluents that would not pose risks for human and environmental health; (ii) understand the factors and mechanisms that drive antibiotic resistance maintenance and selection in wastewater habitats. The final objective is to implement wastewater treatment technologies capable of assuring the production of UWTPs effluents with an acceptable level of ARB.
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Affiliation(s)
- L Rizzo
- Department of Civil Engineering, University of Salerno, 84084, Fisciano (SA), Italy.
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Scientific Opinion on an application from Pioneer Hi‐Bred International and Dow AgroSciences LLC (EFSA‐GMO‐NL‐2005‐23) for placing on the market of genetically modified maize 59122 for food and feed uses, import, processing and cultivation under Regulation (EC) No 1829/2003. EFSA J 2013. [DOI: 10.2903/j.efsa.2013.3135] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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18
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Scientific Opinion on an application (EFSA-GMO-NL-2009-70) for the placing on the market of genetically modified drought tolerant maize MON 87460 for food and feed uses, import and processing under Regulation (EC) No 1829/2003 from Monsanto. EFSA J 2012. [DOI: 10.2903/j.efsa.2012.2936] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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19
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Scientific Opinion on an application (EFSA‐GMO‐NL‐2005‐24) for the placing on the market of the herbicide tolerant genetically modified soybean 40‐3‐2 for cultivation under Regulation (EC) No 1829/2003 from Monsanto. EFSA J 2012. [DOI: 10.2903/j.efsa.2012.2753] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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20
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Rizzi A, Raddadi N, Sorlini C, Nordgrd L, Nielsen KM, Daffonchio D. The Stability and Degradation of Dietary DNA in the Gastrointestinal Tract of Mammals: Implications for Horizontal Gene Transfer and the Biosafety of GMOs. Crit Rev Food Sci Nutr 2012; 52:142-61. [DOI: 10.1080/10408398.2010.499480] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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21
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Scientific Opinion on application (EFSA-GMO-UK-2008-60) for placing on the market of genetically modified herbicide tolerant maize GA21 for food and feed uses, import, processing and cultivation under Regulation (EC) No 1829/2003 from Syngenta Seeds. EFSA J 2011. [DOI: 10.2903/j.efsa.2011.2480] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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22
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Scientific Opinion on application (EFSA-GMO-CZ-2008-54) for placing on the market of genetically modified insect resistant and herbicide tolerant maize MON 88017 for cultivation under Regulation (EC) No 1829/2003 from Monsanto. EFSA J 2011. [DOI: 10.2903/j.efsa.2011.2428] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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23
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Elliott KT, Neidle EL. Acinetobacter baylyi ADP1: Transforming the choice of model organism. IUBMB Life 2011; 63:1075-80. [DOI: 10.1002/iub.530] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 06/09/2011] [Indexed: 11/12/2022]
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24
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Demanèche S, Monier JM, Dugat-Bony E, Simonet P. Exploration of horizontal gene transfer between transplastomic tobacco and plant-associated bacteria. FEMS Microbiol Ecol 2011; 78:129-36. [PMID: 21564143 DOI: 10.1111/j.1574-6941.2011.01126.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The likelihood of gene transfer from transgenic plants to bacteria is dependent on the transgene copy number and on the presence of homologous sequences for recombination. The large number of chloroplast genomes in a plant cell as well as the prokaryotic origin of the transgene may thus significantly increase the likelihood of gene transfer from transplastomic plants to bacteria. In order to assess the probability of such a transfer, bacterial isolates, screened for their ability to colonize decaying tobacco plant tissue and possessing DNA sequence similarity to the chloroplastic genes accD and rbcL flanking the transgene (aadA), were tested for their ability to take up extracellular DNA (broad host-range pBBR1MCS-3-derived plasmid, transplastomic plant DNA and PCR products containing the genes accD-aadA-rbcL) by natural or electrotransformation. The results showed that among the 16 bacterial isolates tested, six were able to accept foreign DNA and acquire the spectinomycin resistance conferred by the aadA gene on plasmid, but none of them managed to integrate transgenic DNA in their chromosome. Our results provide no indication that the theoretical gene transfer-enhancing properties of transplastomic plants cause horizontal gene transfer at rates above those found in other studies with nuclear transgenes.
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Affiliation(s)
- Sandrine Demanèche
- Environmental Microbial Genomics Group, Laboratoire AMPERE, UMR CNRS 5005, Ecole Centrale de Lyon, Université de Lyon, Ecully, France.
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25
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Development of a new tool to improve gene transfer frequency calculations. J Microbiol Methods 2011; 86:255-7. [DOI: 10.1016/j.mimet.2011.05.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 05/20/2011] [Accepted: 05/20/2011] [Indexed: 11/21/2022]
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26
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Phenotypic and physiological changes in Acinetobacter sp. strain DR1 with exogenous plasmid. Curr Microbiol 2010; 62:249-54. [PMID: 20607540 DOI: 10.1007/s00284-010-9698-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Accepted: 06/10/2010] [Indexed: 10/19/2022]
Abstract
The genus Acinetobacter has been recognized to take up exogenous DNA from the environment. In this study, we conducted natural transformation with a novel diesel-degrading Acinetobacter sp. strain, designated strain DR1, using the broad host range plasmid pRK415. Many factors, including temperature, quantities of DNA, and aeration have proven critically important for efficient natural transformation. Interestingly, the Acinetobacter sp. strain DR1 (pRK415) differed both phenotypically and physiologically from the wild-type strain in several regards, including motility, biofilm formation ability, and responses to oxidative stress: the transformed cells were rendered more sensitive to hydrogen peroxide and cumene hydroperoxide, and their motilities and biofilm formation activity were also attenuated. Our data demonstrated that caution should be exercised when conducting genetic manipulation with plasmids, due to the possibility that phenotypic and physiological changes in the host might occur along with the uptake of plasmids.
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Brigulla M, Wackernagel W. Molecular aspects of gene transfer and foreign DNA acquisition in prokaryotes with regard to safety issues. Appl Microbiol Biotechnol 2010; 86:1027-41. [DOI: 10.1007/s00253-010-2489-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 12/18/2009] [Accepted: 01/31/2010] [Indexed: 11/30/2022]
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28
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Tani K, Nasu M. Roles of Extracellular DNA in Bacterial Ecosystem. NUCLEIC ACIDS AND MOLECULAR BIOLOGY 2010. [DOI: 10.1007/978-3-642-12617-8_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Pontiroli A, Rizzi A, Simonet P, Daffonchio D, Vogel TM, Monier JM. Visual evidence of horizontal gene transfer between plants and bacteria in the phytosphere of transplastomic tobacco. Appl Environ Microbiol 2009; 75:3314-22. [PMID: 19329660 PMCID: PMC2681637 DOI: 10.1128/aem.02632-08] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Accepted: 03/20/2009] [Indexed: 12/29/2022] Open
Abstract
Plant surfaces, colonized by numerous and diverse bacterial species, are often considered hot spots for horizontal gene transfer (HGT) between plants and bacteria. Plant DNA released during the degradation of plant tissues can persist and remain biologically active for significant periods of time, suggesting that soil or plant-associated bacteria could be in direct contact with plant DNA. In addition, nutrients released during the decaying process may provide a copiotrophic environment conducive for opportunistic microbial growth. Using Acinetobacter baylyi strain BD413 and transplastomic tobacco plants harboring the aadA gene as models, the objective of this study was to determine whether specific niches could be shown to foster bacterial growth on intact or decaying plant tissues, to develop a competence state, and to possibly acquire exogenous plant DNA by natural transformation. Visualization of HGT in situ was performed using A. baylyi strain BD413(rbcL-DeltaPaadA::gfp) carrying a promoterless aadA::gfp fusion. Both antibiotic resistance and green fluorescence phenotypes were restored in recombinant bacterial cells after homologous recombination with transgenic plant DNA. Opportunistic growth occurred on decaying plant tissues, and a significant proportion of the bacteria developed a competence state. Quantification of transformants clearly supported the idea that the phytosphere constitutes a hot spot for HGT between plants and bacteria. The nondisruptive approach used to visualize transformants in situ provides new insights into environmental factors influencing HGT for plant tissues.
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Affiliation(s)
- Alessandra Pontiroli
- Environmental Microbial Genomics Group, Laboratoire Ampère, Ecole Centrale de Lyon, Université de Lyon, Ecully, France
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Abstract
Horizontal gene transfer (HGT) is the stable transfer of genetic material from one organism to another without reproduction or human intervention. Transfer occurs by the passage of donor genetic material across cellular boundaries, followed by heritable incorporation to the genome of the recipient organism. In addition to conjugation, transformation and transduction, other diverse mechanisms of DNA and RNA uptake occur in nature. The genome of almost every organism reveals the footprint of many ancient HGT events. Most commonly, HGT involves the transmission of genes on viruses or mobile genetic elements. HGT first became an issue of public concern in the 1970s through the natural spread of antibiotic resistance genes amongst pathogenic bacteria, and more recently with commercial production of genetically modified (GM) crops. However, the frequency of HGT from plants to other eukaryotes or prokaryotes is extremely low. The frequency of HGT to viruses is potentially greater, but is restricted by stringent selection pressures. In most cases the occurrence of HGT from GM crops to other organisms is expected to be lower than background rates. Therefore, HGT from GM plants poses negligible risks to human health or the environment.
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Affiliation(s)
- Paul Keese
- Office of the Gene Technology Regulator, GPO Box 9848 Canberra, ACT 2601 [corrected] Australia.
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31
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Borin S, Crotti E, Mapelli F, Tamagnini I, Corselli C, Daffonchio D. DNA is preserved and maintains transforming potential after contact with brines of the deep anoxic hypersaline lakes of the Eastern Mediterranean Sea. SALINE SYSTEMS 2008; 4:10. [PMID: 18681968 PMCID: PMC2531117 DOI: 10.1186/1746-1448-4-10] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Accepted: 08/05/2008] [Indexed: 11/25/2022]
Abstract
Background Extracellular dissolved DNA has been demonstrated to be present in many terrestrial and aquatic environments, actively secreted, or released by decaying cells. Free DNA has the genetic potential to be acquired by living competent cells by horizontal gene transfer mediated by natural transformation. The aim of this work is to study the persistence of extracellular DNA and its biological transforming activity in extreme environments like the deep hypersaline anoxic lakes of the Mediterranean Sea. The brine lakes are separated from the upper seawater by a steep chemocline inhabited by stratified prokaryotic networks, where cells sinking through the depth profile encounter increasing salinity values and osmotic stress. Results Seven strains belonging to different taxonomic groups isolated from the seawater-brine interface of four hypersaline lakes were grown at medium salinity and then incubated in the brines. The osmotic stress induced the death of all the inoculated cells in variable time periods, between 2 hours and 144 days, depending on the type of brine rather than the taxonomic group of the strains, i.e. Bacillaceae or gamma-proteobacteria. The Discovery lake confirmed to be the most aggressive environment toward living cells. In all the brines and in deep seawater dissolved plasmid DNA was substantially preserved for a period of 32 days in axenic conditions. L'Atalante and Bannock brines induced a decrease of the supercoiled form up to 70 and 40% respectively; in the other brines only minor changes in plasmid conformation were observed. Plasmid DNA after incubation in the brines maintained the capacity to transform naturally competent cells of Acinetobacter baylii strain BD413. Conclusion Free dissolved DNA is likely to be released by the lysis of cells induced by osmotic stress in the deep hypersaline anoxic lakes. Naked DNA was demonstrated to be preserved and biologically active in these extreme environments, and hence could constitute a genetic reservoir of traits acquirable by horizontal gene transfer.
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Affiliation(s)
- Sara Borin
- University of Milan, Department of Food Science and Microbiology, Milan, Italy.
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