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Belay WY, Getachew M, Tegegne BA, Teffera ZH, Dagne A, Zeleke TK, Abebe RB, Gedif AA, Fenta A, Yirdaw G, Tilahun A, Aschale Y. Mechanism of antibacterial resistance, strategies and next-generation antimicrobials to contain antimicrobial resistance: a review. Front Pharmacol 2024; 15:1444781. [PMID: 39221153 PMCID: PMC11362070 DOI: 10.3389/fphar.2024.1444781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024] Open
Abstract
Antibacterial drug resistance poses a significant challenge to modern healthcare systems, threatening our ability to effectively treat bacterial infections. This review aims to provide a comprehensive overview of the types and mechanisms of antibacterial drug resistance. To achieve this aim, a thorough literature search was conducted to identify key studies and reviews on antibacterial resistance mechanisms, strategies and next-generation antimicrobials to contain antimicrobial resistance. In this review, types of resistance and major mechanisms of antibacterial resistance with examples including target site modifications, decreased influx, increased efflux pumps, and enzymatic inactivation of antibacterials has been discussed. Moreover, biofilm formation, and horizontal gene transfer methods has also been included. Furthermore, measures (interventions) taken to control antimicrobial resistance and next-generation antimicrobials have been discussed in detail. Overall, this review provides valuable insights into the diverse mechanisms employed by bacteria to resist the effects of antibacterial drugs, with the aim of informing future research and guiding antimicrobial stewardship efforts.
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Affiliation(s)
- Wubetu Yihunie Belay
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Melese Getachew
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Bantayehu Addis Tegegne
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Zigale Hibstu Teffera
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Abebe Dagne
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Tirsit Ketsela Zeleke
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Rahel Belete Abebe
- Department of clinical pharmacy, College of medicine and health sciences, University of Gondar, Gondar, Ethiopia
| | - Abebaw Abie Gedif
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Abebe Fenta
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Getasew Yirdaw
- Department of environmental health science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Adane Tilahun
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Yibeltal Aschale
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
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Yang K, Wang L, Cao X, Gu Z, Zhao G, Ran M, Yan Y, Yan J, Xu L, Gao C, Yang M. The Origin, Function, Distribution, Quantification, and Research Advances of Extracellular DNA. Int J Mol Sci 2022; 23:13690. [PMID: 36430193 PMCID: PMC9698649 DOI: 10.3390/ijms232213690] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
In nature, DNA is ubiquitous, existing not only inside but also outside of the cells of organisms. Intracellular DNA (iDNA) plays an essential role in different stages of biological growth, and it is defined as the carrier of genetic information. In addition, extracellular DNA (eDNA) is not enclosed in living cells, accounting for a large proportion of total DNA in the environment. Both the lysis-dependent and lysis-independent pathways are involved in eDNA release, and the released DNA has diverse environmental functions. This review provides an insight into the origin as well as the multiple ecological functions of eDNA. Furthermore, the main research advancements of eDNA in the various ecological environments and the various model microorganisms are summarized. Furthermore, the major methods for eDNA extraction and quantification are evaluated.
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Affiliation(s)
- Kaixin Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Lishuang Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xinghong Cao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Zhaorui Gu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Guowei Zhao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Mengqu Ran
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yunjun Yan
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jinyong Yan
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Li Xu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Chunhui Gao
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Min Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
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3
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Schwaller C, Fokkens K, Helmreich B, Drewes JE. CFD simulations of flow fields during ultrafiltration: Effects of hydrodynamic strain rates with and without a particle cake layer on the permeation of mobile genetic elements. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2022.117606] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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4
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Cho KH, Wolny J, Kase JA, Unno T, Pachepsky Y. Interactions of E. coli with algae and aquatic vegetation in natural waters. WATER RESEARCH 2022; 209:117952. [PMID: 34965489 DOI: 10.1016/j.watres.2021.117952] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 11/27/2021] [Accepted: 12/05/2021] [Indexed: 06/14/2023]
Abstract
Both algae and bacteria are essential inhabitants of surface waters. Their presence is of ecological significance and sometimes of public health concern triggering various control actions. Interactions of microalgae, macroalgae, submerged aquatic vegetation, and bacteria appear to be important phenomena necessitating a deeper understanding by those involved in research and management of microbial water quality. Given the long-standing reliance on Escherichia coli as an indicator of the potential presence of pathogens in natural waters, understanding its biology in aquatic systems is necessary. The major effects of algae and aquatic vegetation on E. coli growth and survival, including changes in the nutrient supply, modification of water properties and constituents, impact on sunlight radiation penetration, survival as related to substrate attachment, algal mediation of secondary habitats, and survival inhibition due to the release of toxic substances and antibiotics, are discussed in this review. An examination of horizontal gene transfer and antibiotic resistance potential, strain-specific interactions, effects on the microbial, microalgae, and grazer community structure, and hydrodynamic controls is given. Outlooks due to existing and expected consequences of climate change and advances in observation technologies via high-resolution satellite imaging, unmanned aerial vehicles (drones), and mathematical modeling are additionally covered. The multiplicity of interactions among bacteria, algae, and aquatic vegetation as well as multifaceted impacts of these interactions, create a wide spectrum of research opportunities and technology developments.
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Affiliation(s)
- Kyung Hwa Cho
- Department of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Jennifer Wolny
- Division of Microbiology, Office of Regulatory Science, Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, USA
| | - Julie A Kase
- Division of Microbiology, Office of Regulatory Science, Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, USA
| | - Tatsui Unno
- College of Applied Life Science, Jeju National University, Republic of Korea
| | - Yakov Pachepsky
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, U.S. Department of Agriculture, USA.
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Aldeguer-Riquelme B, Ramos-Barbero MD, Santos F, Antón J. Environmental dissolved DNA harbours meaningful biological information on microbial community structure. Environ Microbiol 2021; 23:2669-2682. [PMID: 33817941 DOI: 10.1111/1462-2920.15510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 04/03/2021] [Indexed: 01/21/2023]
Abstract
Extracellular DNA (eDNA) comprises all the DNA molecules outside cells. This component of microbial ecosystems may serve as a source of nutrients and genetic information. Hypersaline environments harbour one of the highest concentrations of eDNA reported for natural systems, which has been attributed to the physicochemical preservative effect of salts and to high viral abundance. Here, we compared centrifugation and filtration protocols for the extraction of dissolved DNA (dDNA, as opposed to eDNA that also includes DNA from free viral particles) from a solar saltern crystallizer pond (CR30) water sample. The crystallizer dDNA fraction has been characterized, for the first time, and compared with cellular and viral metagenomes from the same location. High-speed centrifugation affected CR30 dDNA concentration and composition due to cell lysis, highlighting that protocol optimization should be the first step in dDNA studies. Crystallizer dDNA, which accounted for lower concentrations than those previously reported for hypersaline anoxic sediments, had a mixed viral and cellular origin, was enriched in archaeal DNA and had a distinctive taxonomic composition compared to that from the cellular assemblage of the same sample. Bioinformatic analyses indicated that nanohaloarchaeal viruses could be a cause for these differences.
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Affiliation(s)
- Borja Aldeguer-Riquelme
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, 03080, Spain
| | | | - Fernando Santos
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, 03080, Spain
| | - Josefa Antón
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, 03080, Spain.,Multidisciplinary Institute of Environmental Studies Ramón Margalef, University of Alicante, Alicante, 03080, Spain
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6
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Bien TLT, Thao NV, Kitamura SI, Obayashi Y, Suzuki S. Release and Constancy of an Antibiotic Resistance Gene in Seawater under Grazing Stress by Ciliates and Heterotrophic Nanoflagellates. Microbes Environ 2017; 32:174-179. [PMID: 28592722 PMCID: PMC5478541 DOI: 10.1264/jsme2.me17042] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Extracellular DNA (exDNA) is released from bacterial cells through various processes. The antibiotic resistance genes (ARGs) coded on exDNA may be horizontally transferred among bacterial communities by natural transformation. We quantitated the released/leaked tetracycline resistance gene, tet(M) over time under grazing stress by ciliates and heterotrophic nanoflagellates (HNFs), and found that extracellular tet(M) (ex-tetM) increased with bacterial grazing. Separate microcosms containing tet(M)-possessing bacteria with ciliates or HNFs were prepared. The copy number of ex-tetM in seawater in the ciliate microcosm rapidly increased until 3 d after the incubation, whereas that in the HNF microcosm showed a slower increase until 20 d. The copy number of ex-tetM was stable in both cases throughout the incubation period, suggesting that extracellular ARGs are preserved in the environment, even in the presence of grazers. Additionally, ARGs in bacterial cells were constant in the presence of grazers. These results suggest that ARGs are not rapidly extinguished in a marine environment under grazing stress.
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Affiliation(s)
- Thi Lan Thanh Bien
- Center for Marine Environmental Studies, Ehime University.,The United Graduate School of Agricultural Sciences, Ehime University.,Department of Biotechnology, Nong Lam University
| | - Ngo Vy Thao
- Center for Marine Environmental Studies, Ehime University.,Faculty of Environment and Resources, Nong Lam University
| | | | | | - Satoru Suzuki
- Center for Marine Environmental Studies, Ehime University
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Hufton J, Harding JH, Romero-González ME. The role of extracellular DNA in uranium precipitation and biomineralisation. Phys Chem Chem Phys 2016; 18:29101-29112. [DOI: 10.1039/c6cp03239g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The reaction mechanism for the formation of uranyl–eDNA precipitates was determined as a phosphate mediated process.
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Affiliation(s)
- Joseph Hufton
- Department of Geography
- The University of Sheffield
- Sheffield
- UK
| | - John H. Harding
- Department of Materials Science and Engineering
- Sir Robert Hadfield Building
- University of Sheffield
- Sheffield
- UK
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8
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Torti A, Lever MA, Jørgensen BB. Origin, dynamics, and implications of extracellular DNA pools in marine sediments. Mar Genomics 2015; 24 Pt 3:185-96. [DOI: 10.1016/j.margen.2015.08.007] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 08/29/2015] [Indexed: 12/17/2022]
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9
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Antimicrobial resistance in the food chain: a review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2013; 10:2643-69. [PMID: 23812024 PMCID: PMC3734448 DOI: 10.3390/ijerph10072643] [Citation(s) in RCA: 319] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 06/14/2013] [Accepted: 06/17/2013] [Indexed: 11/17/2022]
Abstract
Antimicrobial resistant zoonotic pathogens present on food constitute a direct risk to public health. Antimicrobial resistance genes in commensal or pathogenic strains form an indirect risk to public health, as they increase the gene pool from which pathogenic bacteria can pick up resistance traits. Food can be contaminated with antimicrobial resistant bacteria and/or antimicrobial resistance genes in several ways. A first way is the presence of antibiotic resistant bacteria on food selected by the use of antibiotics during agricultural production. A second route is the possible presence of resistance genes in bacteria that are intentionally added during the processing of food (starter cultures, probiotics, bioconserving microorganisms and bacteriophages). A last way is through cross-contamination with antimicrobial resistant bacteria during food processing. Raw food products can be consumed without having undergone prior processing or preservation and therefore hold a substantial risk for transfer of antimicrobial resistance to humans, as the eventually present resistant bacteria are not killed. As a consequence, transfer of antimicrobial resistance genes between bacteria after ingestion by humans may occur. Under minimal processing or preservation treatment conditions, sublethally damaged or stressed cells can be maintained in the food, inducing antimicrobial resistance build-up and enhancing the risk of resistance transfer. Food processes that kill bacteria in food products, decrease the risk of transmission of antimicrobial resistance.
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Matsui K, Ishii N, Kawabata Z. Microbial interactions affecting the natural transformation of Bacillus subtilis in a model aquatic ecosystem. FEMS Microbiol Ecol 2012; 45:211-8. [PMID: 19719590 DOI: 10.1016/s0168-6496(03)00148-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
The involvement of microbial interactions in natural transformation of bacteria was evaluated using an aquatic model system. For this purpose, the naturally transformable Bacillus subtilis was used as the model bacterium which was co-cultivated with the protist Tetrahymena thermophila (a consumer) and/or the photosynthetic alga Euglena gracilis (a producer). Co-cultivation with as few as 10(2) individuals ml(-1) of T. thermophila lowered the number of transformants to less than the detectable level (<1x10(0) ml(-1)), while co-cultivation with E. gracilis did not. Metabolites from co-cultures of T. thermophila and B. subtilis also decreased the number of transformants to less than the detectable level, while metabolites from co-culture of T. thermophila and B. subtilis with E. gracilis did not. Thus, the introduction of transformation inhibitory factor(s) by the grazing of T. thermophila and the attenuation of this inhibitory factor(s) by E. gracilis is indicated. These observations suggest that biological components do affect the natural transformation of B. subtilis. The study described is the first to suggest that ecological interactions are responsible not only for the carbon and energy cycles, but also for the processes governing horizontal transfer of genes, in microbial ecosystems.
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Affiliation(s)
- Kazuaki Matsui
- Center for Ecological Research, Kyoto University, Kamitanakami Hirano-cho 509-3, Otsu 520-2113, Japan.
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Drudge CN, Warren LA. Prokaryotic Horizontal Gene Transfer in Freshwater Lakes: Implications of Dynamic Biogeochemical Zonation. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/jep.2012.312181] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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12
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Environment–KHV–carp–human linkage as a model for environmental diseases. Ecol Res 2011. [DOI: 10.1007/s11284-011-0881-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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13
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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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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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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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Miki T, Ueki M, Kawabata Z, Yamamura N. Long-term dynamics of catabolic plasmids introduced to a microbial community in a polluted environment: a mathematical model. FEMS Microbiol Ecol 2007; 62:211-21. [PMID: 17627781 DOI: 10.1111/j.1574-6941.2007.00357.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The long-term dynamics of mobile plasmids in natural environments are unclear. This is the first study of the long-term dynamics of introduced plasmids with xenobiotic degradation abilities using a mathematical model that describes the horizontal gene transfer (HGT) of plasmids into indigenous bacteria via conjugation. We focussed on negative feedback between the spread of plasmids and their selective advantage, i.e. the severe competition between plasmid-bearing and plasmid-free bacteria resulting from a decrease in xenobiotic concentration caused by the gene expression of plasmids, favoring plasmid-free bacteria. Two types of HGT enhanced the persistence of plasmids and the degradation of the xenobiotic in different conditions: a relatively low rate of 'intergeneric HGT' from introduced to indigenous bacteria and a high rate of 'intraindigenous HGT' from indigenous to indigenous bacteria. In addition, when the indigenous resource supply rate was high and when the cost of bearing plasmids was low, both types of HGT made large contributions to xenobiotic degradation compared to the contribution of vertical transfer via plasmid replication within the introduced host population. Initial conditions were also important; a higher initial density of introduced plasmid-bearing bacteria led to a lower degradation rate over a long time scale.
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Affiliation(s)
- Takeshi Miki
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan.
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Ray JL, Andersen HK, Young S, Nielsen KM, O'Callaghan M. An assessment of the potential of herbivorous insect gut bacteria to develop competence for natural transformation. ACTA ACUST UNITED AC 2007; 6:135-47. [PMID: 17961487 DOI: 10.1051/ebr:2007032] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Whereas the capability of DNA uptake has been well established for numerous species and strains of bacteria grown in vitro, the broader distribution of natural transformability within bacterial communities remains largely unexplored. Here, we investigate the ability of bacterial isolates from the gut of grass grub larvae (Costelytra zealandica (White); Coleoptera: Scarabaeidae) to develop natural genetic competence in vitro. A total of 37 mostly species-divergent strains isolated from the gut of grass grub larvae were selected for spontaneous rifampicin-resistance. Genomic DNA was subsequently isolated from the resistant strains and exposed to sensitive strains grown individually using established filter transformation protocols. DNA isolated from wild-type strains was used as a control. None of the 37 isolates tested exhibited a frequency of conversion to rifampicin-resistance in the presence of DNA at rates that were significantly higher than the rate of spontaneous mutation to rifampicin-resistance in the presence of wild-type DNA (the limit of detection was approximately < 1 culturable transformant per 10(9) exposed bacteria). To further examine if conditions were conducive to bacterial DNA uptake in the grass grubs gut, we employed the competent bacterium Acinetobacter baylyi strain BD413 as a recipient species for in vivo studies. However, no transformants could be detected above the detection limit of 1 transformant per 10(3) cells, possibly due to low population density and limited growth of A. baylyi cells in grass grub guts. PCR analysis indicated that chromosomal Acinetobacter DNA remains detectable by PCR for up to 3 days after direct inoculation into the alimentary tract of grass grub larvae. Nevertheless, neither transforming activity of the DNA recovered from the alimentary tract of grass grubs larvae nor competence of bacterial cells recovered from inoculated larvae could be shown.
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Affiliation(s)
- Jessica L Ray
- Department of Pharmacy, University of Tromsø, 9037, Tromsø, Norway
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Nielsen KM, Johnsen PJ, Bensasson D, Daffonchio D. Release and persistence of extracellular DNA in the environment. ACTA ACUST UNITED AC 2007; 6:37-53. [DOI: 10.1051/ebr:2007031] [Citation(s) in RCA: 366] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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19
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Ishii N, Sakashita T, Takeda H, Kubota Y, Fuma S, Doi M, Takahashi S. Impact of gamma irradiation on the transformation efficiency for extracellular plasmid DNA. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2007; 97:159-67. [PMID: 17544184 DOI: 10.1016/j.jenvrad.2007.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2006] [Revised: 04/06/2007] [Accepted: 04/13/2007] [Indexed: 05/15/2023]
Abstract
Extracellular DNA is omnipresent in aquatic environments and is thought to be a genetic material for horizontal gene transformation between microorganisms. We studied the impact of gamma irradiation on the transformation efficiency (transformants number per ng of DNA per ml) of extracellular DNA. Plasmid pEGFP as a model extracellular DNA was irradiated by gamma rays. The transformation efficiency decreased with the increase in radiation dose. A total dose of 10Gy is normally not lethal for microorganisms but certainly affects the transformation efficiency of extracellular DNA. The decrease in the efficiency would be induced by strand breaks of extracellular DNA because the yield of both single-strand breaks (SSBs) and double-strand breaks (DSBs) increased with the increase in radiation dose. The relative transformation efficiency of SSBs and DSBs to that of covalently closed circles (CCCs) was 30.3% and 0.2%, respectively. This impact on natural transformation suggests an inability of microorganisms to acquire new characteristics which should be normally acquired.
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Affiliation(s)
- Nobuyoshi Ishii
- Environmental and Toxicological Sciences Research Group, National Institute of Radiological Sciences, Anagawa 4-9-1, Chiba 263-8555, Japan.
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Ishii N, Uchida S. Removal of technetium from solution by algal flagellate Euglena gracilis. JOURNAL OF ENVIRONMENTAL QUALITY 2006; 35:2017-20. [PMID: 17071870 DOI: 10.2134/jeq2006.0045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Based on limited data for the removal of radioactive (99)Tc by freshwater phytoplankton, it has been thought that phytoplankton are unsuitable for remediation of (99)Tc-contaminated waters. This work sought to verify the validity of this assumption by studying the removal of (99)TcO(4)(-) by freshwater and brackish water phytoplankton. The phytoplankton used were Euglena gracilis, Chlamydomonas pulsatilla, Chlorella vulgaris, and Spirulina platensis. Each of them was incubated for 63 d, and the removal of (99)Tc from solution was periodically determined. Significant removal of (99)Tc was observed only for E. gracilis, and the maximum removal was 70% of the total (99)Tc added. The killed cells of E. gracilis, however, removed hardly any (99)Tc. When E. gracilis cells were washed with fresh culture medium, only 13% of the total (99)Tc was desorbed. These results suggested that intracellular uptake of (99)Tc by E. gracilis occurred. These results are the first documented example of significant removal of (99)Tc by planktonic microalgae.
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Affiliation(s)
- Nobuyoshi Ishii
- Office of Biospheric Assessment for Waste Disposal, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba-shi, 263-8555 Japan.
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Affiliation(s)
- Douglas H Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093-0202, USA.
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Steinberger RE, Holden PA. Extracellular DNA in single- and multiple-species unsaturated biofilms. Appl Environ Microbiol 2005; 71:5404-10. [PMID: 16151131 PMCID: PMC1214645 DOI: 10.1128/aem.71.9.5404-5410.2005] [Citation(s) in RCA: 224] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The extracellular polymeric substances (EPS) of bacterial biofilms form a hydrated barrier between cells and their external environment. Better characterization of EPS could be useful in understanding biofilm physiology. The EPS are chemically complex, changing with both bacterial strain and culture conditions. Previously, we reported that Pseudomonas aeruginosa unsaturated biofilm EPS contains large amounts of extracellular DNA (eDNA) (R. E. Steinberger, A. R. Allen, H. G. Hansma, and P. A. Holden, Microb. Ecol. 43:416-423, 2002). Here, we investigated the compositional similarity of eDNA to cellular DNA, the relative quantity of eDNA, and the terminal restriction fragment length polymorphism (TRFLP) community profile of eDNA in multiple-species biofilms. By randomly amplified polymorphic DNA analysis, cellular DNA and eDNA appear identical for P. aeruginosa biofilms. Significantly more eDNA was produced in P. aeruginosa and Pseudomonas putida biofilms than in Rhodococcus erythropolis or Variovorax paradoxus biofilms. While the amount of eDNA in dual-species biofilms was of the same order of magnitude as that of of single-species biofilms, the amounts were not predictable from single-strain measurements. By the Shannon diversity index and principle components analysis of TRFLP profiles generated from 16S rRNA genes, eDNA of four-species biofilms differed significantly from either cellular or total DNA of the same biofilm. However, total DNA- and cellular DNA-based TRFLP analyses of this biofilm community yielded identical results. We conclude that extracellular DNA production in unsaturated biofilms is species dependent and that the phylogenetic information contained in this DNA pool is quantifiable and distinct from either total or cellular DNA.
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Affiliation(s)
- R E Steinberger
- Donald Bren School of Environmental Science and Management, University of California-Santa Barbara, Bren Hall, Santa Barbara, CA 93106-5131, USA
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Jasso-Chávez R, García-Cano I, Marín-Hernández A, Mendoza-Cózatl D, Rendón JL, Moreno-Sánchez R. The bacterial-like lactate shuttle components from heterotrophic Euglena gracilis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2005; 1709:181-90. [PMID: 16112076 DOI: 10.1016/j.bbabio.2005.07.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2005] [Revised: 07/22/2005] [Accepted: 07/25/2005] [Indexed: 10/25/2022]
Abstract
The structural and kinetic analyses of the components of the lactate shuttle from heterotrophic Euglena gracilis were carried out. Mitochondrial membrane-bound, NAD(+)-independent d-lactate dehydrogenase (d-iLDH) was purified by solubilization with CHAPS and heat treatment. The active enzyme was a 62-kDa monomer containing non-covalently bound FAD as cofactor. d-iLDH was specific for d-lactate and it was able to reduce quinones of different redox potential values. Oxalate and l-lactate were mixed-type inhibitors of d-iLDH. Mitochondrial l-iLDH also catalyzed the reduction of quinones, but it was inactivated during the extraction with detergents. Both l-iLDH and d-iLDH were inhibited by the specific flavoprotein-inhibitor diphenyleneiodonium, suggesting that l-iLDH was also a flavoprotein. Affinity chromatography revealed that the E. gracilis cytosolic fraction contained two types of NAD(+)-dependent LDH specific for the generation of d- and l-lactate (d-nLDH and l-nLDH, respectively). These two enzymes were tetramers of 126-132 kDa and showed an ordered bi-bi kinetic mechanism. Kinetic properties were different in both enzymes. Pyruvate reduction by d-nLDH was inhibited by its two products; the d-lactate oxidation was 40-fold lower than forward reaction. l-lactate oxidation by l-nLDH was not detected, whereas pyruvate reduction was activated by fructose-1, 6-bisphosphate, K(+) or NH(4)(+). Interestingly, membrane-bound l- and d-lactate dehydrogenases with quinone reductase activity have been only detected in bacteria, whereas the activity of soluble d-nLDH has been identified in bacteria and some yeast. Also, FBP-activated l-nLDH has been found solely in lactic bacteria. Based on their similar kinetic and structural characteristics, a possible common origin among bacterial and E. gracilis lactic dehydrogenase enzymes is discussed.
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Affiliation(s)
- Ricardo Jasso-Chávez
- Departamento de Bioquímica, Instituto Nacional de Cardiología, Juan Badiano #1, Col. Sección XVI, Tlalpan, México, D. F. 14080, México.
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