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Fabian B, Foster C, Asher A, Hassan K, Paulsen I, Tetu S. Identifying the suite of genes central to swimming in the biocontrol bacterium Pseudomonas protegens Pf-5. Microb Genom 2024; 10:001212. [PMID: 38546328 PMCID: PMC11004494 DOI: 10.1099/mgen.0.001212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 02/20/2024] [Indexed: 04/12/2024] Open
Abstract
Swimming motility is a key bacterial trait, important to success in many niches. Biocontrol bacteria, such as Pseudomonas protegens Pf-5, are increasingly used in agriculture to control crop diseases, where motility is important for colonization of the plant rhizosphere. Swimming motility typically involves a suite of flagella and chemotaxis genes, but the specific gene set employed for both regulation and biogenesis can differ substantially between organisms. Here we used transposon-directed insertion site sequencing (TraDIS), a genome-wide approach, to identify 249 genes involved in P. protegens Pf-5 swimming motility. In addition to the expected flagella and chemotaxis, we also identified a suite of additional genes important for swimming, including genes related to peptidoglycan turnover, O-antigen biosynthesis, cell division, signal transduction, c-di-GMP turnover and phosphate transport, and 27 conserved hypothetical proteins. Gene knockout mutants and TraDIS data suggest that defects in the Pst phosphate transport system lead to enhanced swimming motility. Overall, this study expands our knowledge of pseudomonad motility and highlights the utility of a TraDIS-based approach for analysing the functions of thousands of genes. This work sets a foundation for understanding how swimming motility may be related to the inconsistency in biocontrol bacteria performance in the field.
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Affiliation(s)
- B.K. Fabian
- School of Natural Sciences, Macquarie University, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - C. Foster
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - A. Asher
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - K.A. Hassan
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
- School of Environmental and Life Sciences, University of Newcastle, Newcastle, Australia
| | - I.T. Paulsen
- School of Natural Sciences, Macquarie University, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - S.G. Tetu
- School of Natural Sciences, Macquarie University, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
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Silverio MP, Kraychete GB, Rosado AS, Bonelli RR. Pseudomonas fluorescens Complex and Its Intrinsic, Adaptive, and Acquired Antimicrobial Resistance Mechanisms in Pristine and Human-Impacted Sites. Antibiotics (Basel) 2022; 11:antibiotics11080985. [PMID: 35892375 PMCID: PMC9331890 DOI: 10.3390/antibiotics11080985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 12/16/2022] Open
Abstract
Pseudomonas spp. are ubiquitous microorganisms that exhibit intrinsic and acquired resistance to many antimicrobial agents. Pseudomonas aeruginosa is the most studied species of this genus due to its clinical importance. In contrast, the Pseudomonas fluorescens complex consists of environmental and, in some cases, pathogenic opportunistic microorganisms. The records of antimicrobial-resistant P. fluorescens are quite scattered, which hinders the recognition of patterns. This review compiles published data on antimicrobial resistance in species belonging to the P. fluorescens complex, which were identified through phylogenomic analyses. Additionally, we explored the occurrence of clinically relevant antimicrobial resistance genes in the genomes of the respective species available in the NCBI database. Isolates were organized into two categories: strains isolated from pristine sites and strains isolated from human-impacted or metal-polluted sites. Our review revealed that many reported resistant phenotypes in this complex might be related to intrinsic features, whereas some of them might be ascribed to adaptive mechanisms such as colistin resistance. Moreover, a few studies reported antimicrobial resistance genes (ARGs), mainly β-lactamases. In-silico analysis corroborated the low occurrence of transferable resistance mechanisms in this Pseudomonas complex. Both phenotypic and genotypic assays are necessary to gain insights into the evolutionary aspects of antimicrobial resistance in the P. fluorescens complex and the possible role of these ubiquitous species as reservoirs of clinically important and transmissible ARGs.
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Affiliation(s)
- Myllena Pereira Silverio
- Laboratório de Ecologia Molecular Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil
- Laboratório de Investigação em Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil
| | - Gabriela Bergiante Kraychete
- Laboratório de Investigação em Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil
| | - Alexandre Soares Rosado
- Laboratório de Ecologia Molecular Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Raquel Regina Bonelli
- Laboratório de Investigação em Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil
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Henderson PJF, Maher C, Elbourne LDH, Eijkelkamp BA, Paulsen IT, Hassan KA. Physiological Functions of Bacterial "Multidrug" Efflux Pumps. Chem Rev 2021; 121:5417-5478. [PMID: 33761243 DOI: 10.1021/acs.chemrev.0c01226] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacterial multidrug efflux pumps have come to prominence in human and veterinary pathogenesis because they help bacteria protect themselves against the antimicrobials used to overcome their infections. However, it is increasingly realized that many, probably most, such pumps have physiological roles that are distinct from protection of bacteria against antimicrobials administered by humans. Here we undertake a broad survey of the proteins involved, allied to detailed examples of their evolution, energetics, structures, chemical recognition, and molecular mechanisms, together with the experimental strategies that enable rapid and economical progress in understanding their true physiological roles. Once these roles are established, the knowledge can be harnessed to design more effective drugs, improve existing microbial production of drugs for clinical practice and of feedstocks for commercial exploitation, and even develop more sustainable biological processes that avoid, for example, utilization of petroleum.
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Affiliation(s)
- Peter J F Henderson
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Claire Maher
- School of Environmental and Life Sciences, University of Newcastle, Callaghan 2308, New South Wales, Australia
| | - Liam D H Elbourne
- Department of Biomolecular Sciences, Macquarie University, Sydney 2109, New South Wales, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney 2019, New South Wales, Australia
| | - Bart A Eijkelkamp
- College of Science and Engineering, Flinders University, Bedford Park 5042, South Australia, Australia
| | - Ian T Paulsen
- Department of Biomolecular Sciences, Macquarie University, Sydney 2109, New South Wales, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney 2019, New South Wales, Australia
| | - Karl A Hassan
- School of Environmental and Life Sciences, University of Newcastle, Callaghan 2308, New South Wales, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney 2019, New South Wales, Australia
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Michavila G, Adler C, De Gregorio PR, Lami MJ, Caram Di Santo MC, Zenoff AM, de Cristobal RE, Vincent PA. Pseudomonas protegens CS1 from the lemon phyllosphere as a candidate for citrus canker biocontrol agent. PLANT BIOLOGY (STUTTGART, GERMANY) 2017; 19:608-617. [PMID: 28194866 DOI: 10.1111/plb.12556] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 02/08/2017] [Indexed: 06/06/2023]
Abstract
Citrus canker is a worldwide-distributed disease caused by Xanthomonas citri subsp. citri. One of the most used strategies to control the disease is centred on copper-based compounds that cause environmental problems. Therefore, it is of interest to develop new strategies to manage the disease. Previously, we reported the ability of the siderophore pyochelin, produced by the opportunistic human pathogen Pseudomonas aeruginosa, to inhibit in vitro several bacterial species, including X. citri subsp. citri. The action mechanism, addressed with the model bacterium Escherichia coli, was connected to the generation of reactive oxygen species (ROS). This work aimed to find a non-pathogenic strain from the lemon phyllosphere that would produce pyochelin and therefore serve in canker biocontrol. An isolate that retained its capacity to colonise the lemon phyllosphere and inhibit X. citri subsp. citri was selected and characterised as Pseudomonas protegens CS1. From a liquid culture of this strain, the active compound was purified and identified as the pyochelin enantiomer, enantio-pyochelin. Using the producing strain and the pure compound, both in vitro and in vivo, we determined that the action mechanism of X. citri subsp. citri inhibition also involved the generation of ROS. Finally, the potential application of P. protegens CS1 was evaluated by spraying the bacterium in a model that mimics the natural X. citri subsp. citri infection. The ability of P. protegens CS1 to reduce canker formation makes this strain an interesting candidate as a biocontrol agent.
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Affiliation(s)
- G Michavila
- Facultad de Bioquímica, Química y Farmacia, UNT, Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica "Dr. Bernabé Bloj", San Miguel de Tucumán, Argentina
| | - C Adler
- Facultad de Bioquímica, Química y Farmacia, UNT, Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica "Dr. Bernabé Bloj", San Miguel de Tucumán, Argentina
| | - P R De Gregorio
- Facultad de Bioquímica, Química y Farmacia, UNT, Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica "Dr. Bernabé Bloj", San Miguel de Tucumán, Argentina
| | - M J Lami
- Facultad de Bioquímica, Química y Farmacia, UNT, Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica "Dr. Bernabé Bloj", San Miguel de Tucumán, Argentina
| | - M C Caram Di Santo
- Facultad de Bioquímica, Química y Farmacia, UNT, Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica "Dr. Bernabé Bloj", San Miguel de Tucumán, Argentina
| | - A M Zenoff
- Facultad de Bioquímica, Química y Farmacia, UNT, Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica "Dr. Bernabé Bloj", San Miguel de Tucumán, Argentina
| | - R E de Cristobal
- Facultad de Bioquímica, Química y Farmacia, UNT, Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica "Dr. Bernabé Bloj", San Miguel de Tucumán, Argentina
| | - P A Vincent
- Facultad de Bioquímica, Química y Farmacia, UNT, Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica "Dr. Bernabé Bloj", San Miguel de Tucumán, Argentina
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Ong KS, Aw YK, Lee LH, Yule CM, Cheow YL, Lee SM. Burkholderia paludis sp. nov., an Antibiotic-Siderophore Producing Novel Burkholderia cepacia Complex Species, Isolated from Malaysian Tropical Peat Swamp Soil. Front Microbiol 2016; 7:2046. [PMID: 28066367 PMCID: PMC5174137 DOI: 10.3389/fmicb.2016.02046] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 12/06/2016] [Indexed: 11/25/2022] Open
Abstract
A novel Gram negative rod-shaped bacterium, designated strain MSh1T, was isolated from Southeast Pahang tropical peat swamp forest soil in Malaysia and characterized using a polyphasic taxonomy approach. The predominant cellular fatty acids (>10.0%) were C16:0 (31.7%), C17:0 cyclo (26.6%), and C19:0 cyclo ω8c (16.1%). The polar lipids detected were phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol. The predominant ubiquinone was Q-8. This revealed that strain MSh1T belongs to the genus Burkholderia. The type strain MSh1T can be differentiated from other Burkholderia cepacia complex (Bcc) species by phylogenetic analysis of 16S rRNA gene sequence, multilocus sequence analysis (MLSA), average nucleotide identity (ANI) and biochemical tests. DNA-DNA relatedness values between strain MSh1T and closely related type strains were below the 70% threshold value. Based on this polyphasic study of MSh1T, it can be concluded that this strain represents a novel species within the Bcc, for which the name Burkholderia paludis sp. nov. is proposed. The type strain is MSh1T (= DSM 100703T = MCCC 1K01245T). The dichloromethane extract of MSh1T exhibited antimicrobial activity against four Gram positive bacteria (Enterococcus faecalis ATCC 29212, E. faecalis ATCC 700802, Staphylococcus aureus ATCC 29213, S. aureus ATCC 700699) and a Gram negative bacteria (Escherichia coli ATCC 25922). Further purification work has led to the isolation of Compound 1, pyochelin. Pyochelin demonstrated antimicrobial activity against four S. aureus strains and three E. faecalis strains with MIC-values of 3.13 μg/ml and 6.26 μg/ml, respectively. SEM analysis showed that the cellular morphology of E. faecalis ATCC 700802 was not affected by pyochelin; suggesting that it might target the intracellular components. Pyochelin, a siderophore with antimicrobial activity might be useful in treating bacterial infections caused by S. aureus and E. faecalis, however further work has to be done.
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Affiliation(s)
- Kuan Shion Ong
- School of Science, Monash University MalaysiaBandar Sunway, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University MalaysiaBandar Sunway, Malaysia
| | - Yoong Kit Aw
- School of Science, Monash University MalaysiaBandar Sunway, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University MalaysiaBandar Sunway, Malaysia
| | - Learn Han Lee
- Novel Bacteria and Drug Discovery Research Group, School of Pharmacy, Monash University MalaysiaBandar Sunway, Malaysia
- Center of Health Outcomes Research and Therapeutic Safety (Cohorts), School of Pharmaceutical Sciences, University PhayaoPhayao, Thailand
| | - Catherine M. Yule
- School of Science, Monash University MalaysiaBandar Sunway, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University MalaysiaBandar Sunway, Malaysia
| | - Yuen Lin Cheow
- School of Science, Monash University MalaysiaBandar Sunway, Malaysia
| | - Sui Mae Lee
- School of Science, Monash University MalaysiaBandar Sunway, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University MalaysiaBandar Sunway, Malaysia
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