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Differential Genetic Strategies of Burkholderia vietnamiensis and Paraburkholderia kururiensis for Root Colonization of Oryza sativa subsp.
japonica
and O. sativa subsp.
indica
, as Revealed by Transposon Mutagenesis Sequencing. Appl Environ Microbiol 2022; 88:e0064222. [DOI: 10.1128/aem.00642-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Burkholderiaceae
are frequent and abundant colonizers of the rice rhizosphere and interesting candidates to investigate for growth promotion. Species of
Paraburkholderia
have repeatedly been described to stimulate plant growth.
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Marian M, Fujikawa T, Shimizu M. Genome analysis provides insights into the biocontrol ability of Mitsuaria sp. strain TWR114. Arch Microbiol 2021; 203:3373-3388. [PMID: 33880605 DOI: 10.1007/s00203-021-02327-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 12/31/2022]
Abstract
Mitsuaria sp. TWR114 is a biocontrol agent against tomato bacterial wilt (TBW). We aimed to gain genomic insights relevant to the biocontrol mechanisms and colonization ability of this strain. The draft genome size was found to be 5,632,523 bp, with a GC content of 69.5%, assembled into 1144 scaffolds. Genome annotation predicted a total of 4675 protein coding sequences (CDSs), 914 pseudogenes, 49 transfer RNAs, 3 noncoding RNAs, and 2 ribosomal RNAs. Genome analysis identified multiple CDSs associated with various pathways for the metabolism and transport of amino acids and carbohydrates, motility and chemotactic capacities, protection against stresses (oxidative, antibiotic, and phage), production of secondary metabolites, peptidases, quorum-quenching enzymes, and indole-3-acetic acid, as well as protein secretion systems and their related appendages. The genome resource will extend our understanding of the genomic features related to TWR114's biocontrol and colonization abilities and facilitate its development as a new biopesticide against TBW.
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Affiliation(s)
- Malek Marian
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan.,College of Agriculture, Ibaraki University, Ami, Inashiki, Ibaraki, 300-0393, Japan
| | - Takashi Fujikawa
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8605, Japan
| | - Masafumi Shimizu
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan.
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3
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Kim YC, Anderson AJ. Rhizosphere pseudomonads as probiotics improving plant health. MOLECULAR PLANT PATHOLOGY 2018; 19:2349-2359. [PMID: 29676842 PMCID: PMC6638116 DOI: 10.1111/mpp.12693] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 04/08/2018] [Accepted: 04/18/2018] [Indexed: 05/25/2023]
Abstract
Many root-colonizing microbes are multifaceted in traits that improve plant health. Although isolates designated as biological control agents directly reduce pathogen growth, many exert additional beneficial features that parallel changes induced in animal and other hosts by health-promoting microbes termed probiotics. Both animal and plant probiotics cause direct antagonism of pathogens and induce systemic immunity in the host to pathogens and other stresses. They also alter host development and improve host nutrition. The probiotic root-colonizing pseudomonads are generalists in terms of plant hosts, soil habitats and the array of stress responses that are ameliorated in the plant. This article illustrates how the probiotic pseudomonads, nurtured by the carbon (C) and nitrogen (N) sources released by the plant in root exudates, form protective biofilms on the root surface and produce the metabolites or enzymes to boost plant health. The findings reveal the multifunctional nature of many of the microbial metabolites in the plant-probiotic interplay. The beneficial effects of probiotics on plant function can contribute to sustainable yield and quality in agricultural production.
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Affiliation(s)
- Young Cheol Kim
- Department of Applied Biology, College of Agriculture and Life SciencesChonnam National UniversityGwangju 61186South Korea
| | - Anne J. Anderson
- Department of Biological EngineeringUtah State UniversityLoganUT 84322‐4105USA
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Etalo D, Jeon JS, Raaijmakers JM. Modulation of plant chemistry by beneficial root microbiota. Nat Prod Rep 2018; 35:398-409. [DOI: 10.1039/c7np00057j] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Beneficial root microbiota modulate plant chemistry and represent an untapped potential to discover new pathways involved in the biosynthesis of high value natural plant products.
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Affiliation(s)
- Desalegn W. Etalo
- Netherlands Institute of Ecology NIOO-KNAW
- Department of Microbial Ecology
- Wageningen
- Netherlands
| | - Je-Seung Jeon
- Netherlands Institute of Ecology NIOO-KNAW
- Department of Microbial Ecology
- Wageningen
- Netherlands
- Institute of Biology
| | - Jos M. Raaijmakers
- Netherlands Institute of Ecology NIOO-KNAW
- Department of Microbial Ecology
- Wageningen
- Netherlands
- Institute of Biology
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Cheng X, Etalo DW, van de Mortel JE, Dekkers E, Nguyen L, Medema MH, Raaijmakers JM. Genome-wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens. Environ Microbiol 2017; 19:4638-4656. [PMID: 28892231 DOI: 10.1111/1462-2920.13927] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 09/04/2017] [Indexed: 11/28/2022]
Abstract
Pseudomonas fluorescens strain SS101 (Pf.SS101) promotes growth of Arabidopsis thaliana, enhances greening and lateral root formation, and induces systemic resistance (ISR) against the bacterial pathogen Pseudomonas syringae pv. tomato (Pst). Here, targeted and untargeted approaches were adopted to identify bacterial determinants and underlying mechanisms involved in plant growth promotion and ISR by Pf.SS101. Based on targeted analyses, no evidence was found for volatiles, lipopeptides and siderophores in plant growth promotion by Pf.SS101. Untargeted, genome-wide analyses of 7488 random transposon mutants of Pf.SS101 led to the identification of 21 mutants defective in both plant growth promotion and ISR. Many of these mutants, however, were auxotrophic and impaired in root colonization. Genetic analysis of three mutants followed by site-directed mutagenesis, genetic complementation and plant bioassays revealed the involvement of the phosphogluconate dehydratase gene edd, the response regulator gene colR and the adenylsulfate reductase gene cysH in both plant growth promotion and ISR. Subsequent comparative plant transcriptomics analyses strongly suggest that modulation of sulfur assimilation, auxin biosynthesis and transport, steroid biosynthesis and carbohydrate metabolism in Arabidopsis are key mechanisms linked to growth promotion and ISR by Pf.SS101.
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Affiliation(s)
- Xu Cheng
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands.,Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands
| | - Desalegn W Etalo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen 6708 PB, The Netherlands
| | - Judith E van de Mortel
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands.,HAS University of Applied Sciences, Spoorstraat 61, Venlo 5911 KJ, The Netherlands
| | - Ester Dekkers
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands
| | - Linh Nguyen
- Bioinformatics Group Wageningen University, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group Wageningen University, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen 6708 PB, The Netherlands.,Institute of Biology (IBL) Leiden University, Sylviusweg 72, Leiden 2333 BE, The Netherlands
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Gill SK, Hui K, Farne H, Garnett JP, Baines DL, Moore LS, Holmes AH, Filloux A, Tregoning JS. Increased airway glucose increases airway bacterial load in hyperglycaemia. Sci Rep 2016; 6:27636. [PMID: 27273266 PMCID: PMC4897689 DOI: 10.1038/srep27636] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 05/19/2016] [Indexed: 01/15/2023] Open
Abstract
Diabetes is associated with increased frequency of hospitalization due to bacterial lung infection. We hypothesize that increased airway glucose caused by hyperglycaemia leads to increased bacterial loads. In critical care patients, we observed that respiratory tract bacterial colonisation is significantly more likely when blood glucose is high. We engineered mutants in genes affecting glucose uptake and metabolism (oprB, gltK, gtrS and glk) in Pseudomonas aeruginosa, strain PAO1. These mutants displayed attenuated growth in minimal medium supplemented with glucose as the sole carbon source. The effect of glucose on growth in vivo was tested using streptozocin-induced, hyperglycaemic mice, which have significantly greater airway glucose. Bacterial burden in hyperglycaemic animals was greater than control animals when infected with wild type but not mutant PAO1. Metformin pre-treatment of hyperglycaemic animals reduced both airway glucose and bacterial load. These data support airway glucose as a critical determinant of increased bacterial load during diabetes.
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Affiliation(s)
- Simren K. Gill
- Mucosal Infection & Immunity Group, Section of Virology, Imperial College London, St Mary’s Campus, London, W2 1PG, UK
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Kailyn Hui
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Hugo Farne
- Airway Disease Infection Section, National Heart & Lung Institute, Imperial College London, London, W2 1PG, UK
| | - James P. Garnett
- Institute for Infection and Immunity, St George’s, University of London, London SW17 0RE, UK
| | - Deborah L. Baines
- Institute for Infection and Immunity, St George’s, University of London, London SW17 0RE, UK
| | - Luke S.P. Moore
- Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance, Imperial College London, Hammersmith Campus, London W12 0HS, UK
| | - Alison H. Holmes
- Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance, Imperial College London, Hammersmith Campus, London W12 0HS, UK
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - John S. Tregoning
- Mucosal Infection & Immunity Group, Section of Virology, Imperial College London, St Mary’s Campus, London, W2 1PG, UK
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