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Bertani I, Zampieri E, Bez C, Volante A, Venturi V, Monaco S. Isolation and Characterization of Pseudomonas chlororaphis Strain ST9; Rhizomicrobiota and in Planta Studies. PLANTS 2021; 10:plants10071466. [PMID: 34371669 PMCID: PMC8309335 DOI: 10.3390/plants10071466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/12/2021] [Accepted: 07/15/2021] [Indexed: 02/07/2023]
Abstract
The development of biotechnologies based on beneficial microorganisms for improving soil fertility and crop yields could help to address many current agriculture challenges, such as food security, climate change, pest control, soil depletion while decreasing the use of chemical fertilizers and pesticides. Plant growth-promoting (PGP) microbes can be used as probiotics in order to increase plant tolerance/resistance to abiotic/biotic stresses and in this context strains belonging to the Pseudomonas chlororaphis group have shown to have potential as PGP candidates. In this study a new P. chlororaphis isolate is reported and tested for (i) in vitro PGP features, (ii) whole-genome sequence analysis, and (iii) its effects on the rhizosphere microbiota composition, plant growth, and different plant genes expression levels in greenhouse experiments. Results showed that P. chlororaphis ST9 is an efficient rice root colonizer which integrates into the plant resident-microbiota and affects the expression of several plant genes. The potential use of this P. chlororaphis strain as a plant probiotic is discussed.
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Affiliation(s)
- Iris Bertani
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy; (I.B.); (C.B.)
| | - Elisa Zampieri
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, Italy; (E.Z.); (A.V.)
- Institute for Sustainable Plant Protection, National Research Council, Strada delle Cacce 73, 10135 Turin, Italy
| | - Cristina Bez
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy; (I.B.); (C.B.)
| | - Andrea Volante
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, Italy; (E.Z.); (A.V.)
- Council for Agricultural Research and Economics-Research Centre for Vegetable and Ornamental Crops, Corso Inglesi 508, 18038 Sanremo, Italy
| | - Vittorio Venturi
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy; (I.B.); (C.B.)
- Correspondence: (V.V.); (S.M.)
| | - Stefano Monaco
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, Italy; (E.Z.); (A.V.)
- Correspondence: (V.V.); (S.M.)
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Whole Genome Sequencing and Tn 5-Insertion Mutagenesis of Pseudomonas taiwanensis CMS to Probe Its Antagonistic Activity Against Rice Bacterial Blight Disease. Int J Mol Sci 2020; 21:ijms21228639. [PMID: 33207795 PMCID: PMC7696974 DOI: 10.3390/ijms21228639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 01/07/2023] Open
Abstract
The Gram-negative bacterium Pseudomonas taiwanensis is a novel bacterium that uses shrimp shell waste as its sole sources of carbon and nitrogen. It is a versatile bacterium with potential for use in biological control, with activities including toxicity toward insects, fungi, and the rice pathogen Xanthomonas oryzae pv.oryzae (Xoo). In this study, the complete 5.08-Mb genome sequence of P. taiwanensis CMS was determined by a combination of NGS/Sanger sequencing and optical mapping. Comparison of optical maps of seven Pseudomonas species showed that P. taiwanensis is most closely related to P. putida KT 2400. We screened a total of 11,646 individual Tn5-transponson tagged strains to identify genes that are involved in the production and regulation of the iron-chelator pyoverdine in P. taiwanensis, which is a key anti-Xoo factor. Our results indicated that the two-component system (TCS) EnvZ/OmpR plays a positive regulatory role in the production of pyoverdine, whereas the sigma factor RpoS functions as a repressor. The knowledge of the molecular basis of the regulation of pyoverdine by P. taiwanensis provided herein will be useful for its development for use in biological control, including as an anti-Xoo agent.
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Duca DR, Glick BR. Indole-3-acetic acid biosynthesis and its regulation in plant-associated bacteria. Appl Microbiol Biotechnol 2020; 104:8607-8619. [PMID: 32875364 DOI: 10.1007/s00253-020-10869-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 08/19/2020] [Accepted: 08/26/2020] [Indexed: 11/28/2022]
Abstract
Numerous studies have reported the stimulation of plant growth following inoculation with an IAA-producing PGPB. However, the specific mode of IAA production by the PGPB is rarely elucidated. In part, this is due to the overwhelming complexity of IAA biosynthesis and regulation. The promiscuity of the enzymes implicated in IAA biosynthesis adds another element of complexity when attempting to decipher their role in IAA biosynthesis. To date, the majority of research on IAA biosynthesis describes three separate pathways classified in terms of their intermediates-indole acetonitrile (IAN), indole acetamide (IAM), and indole pyruvic acid (IPA). Each of these pathways is mediated by a set of enzymes, many of which are traditionally assumed to exist for that specific catalytic role. This lends the possibility of missing other, novel, enzymes that may also incidentally serve that function. Some of these pathways are constitutively expressed, while others are inducible. Some enzymes involved in IAA biosynthesis are known to be regulated by IAA or by IAA precursors, as well as by a multitude of environmental cues. This review aims to provide an update to our current understanding of the biosynthesis and regulation of IAA in bacteria. KEY POINTS: • IAA produced by PGPB improves bacterial stress tolerance and promotes plant growth. • Bacterial IAA biosynthesis is convoluted; multiple interdependent pathways. • Biosynthesis of IAA is regulated by IAA, IAA-precursors, and environmental factors.
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Affiliation(s)
- Daiana R Duca
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
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Wu X, Chi X, Wang Y, Zhang K, Kai L, He Q, Tang J, Wang K, Sun L, Hao X, Xie W, Ge Y. vfr, A Global Regulatory Gene, is Required for Pyrrolnitrin but not for Phenazine-1-carboxylic Acid Biosynthesis in Pseudomonas chlororaphis G05. THE PLANT PATHOLOGY JOURNAL 2019; 35:351-361. [PMID: 31481858 PMCID: PMC6706016 DOI: 10.5423/ppj.oa.01.2019.0011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/07/2019] [Accepted: 04/09/2019] [Indexed: 06/10/2023]
Abstract
In our previous study, pyrrolnitrin produced in Pseudomonas chlororaphis G05 plays more critical role in suppression of mycelial growth of some fungal pathogens that cause plant diseases in agriculture. Although some regulators for pyrrolnitrin biosynthesis were identified, the pyrrolnitrin regulation pathway was not fully constructed. During our screening novel regulator candidates, we obtained a white conjugant G05W02 while transposon mutagenesis was carried out between a fusion mutant G05ΔphzΔprn::lacZ and E. coli S17-1 (pUT/mini-Tn5Kan). By cloning and sequencing of the transposon-flanking DNA fragment, we found that a vfr gene in the conjugant G05W02 was disrupted with mini-Tn5Kan. In one other previous study on P. fluorescens, however, it was reported that the deletion of the vfr caused increased production of pyrrolnitrin and other antifungal metabolites. To confirm its regulatory function, we constructed the vfr-knockout mutant G05Δvfr and G05ΔphzΔprn::lacZΔvfr. By quantifying β-galactosidase activities, we found that deletion of the vfr decreased the prn operon expression dramatically. Meanwhile, by quantifying pyrrolnitrin production in the mutant G05Δvfr, we found that deficiency of the Vfr caused decreased pyrrolnitrin production. However, production of phenazine-1-carboxylic acid was same to that in the wild-type strain G05. Taken together, Vfr is required for pyrrolnitrin but not for phenazine-1-carboxylic acid biosynthesis in P. chlororaphis G05.
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Affiliation(s)
- Xia Wu
- Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai 264025,
China
| | - Xiaoyan Chi
- Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai 264025,
China
| | - Yanhua Wang
- Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai 264025,
China
| | - Kailu Zhang
- Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai 264025,
China
| | - Le Kai
- Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai 264025,
China
| | - Qiuning He
- Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai 264025,
China
| | - Jinxiu Tang
- Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai 264025,
China
| | - Kewen Wang
- Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai 264025,
China
| | - Longshuo Sun
- Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai 264025,
China
| | - Xiuying Hao
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830001,
China
| | - Weihai Xie
- Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai 264025,
China
| | - Yihe Ge
- Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai 264025,
China
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RpoS differentially affects the general stress response and biofilm formation in the endophytic Serratia plymuthica G3. Res Microbiol 2016; 167:168-77. [DOI: 10.1016/j.resmic.2015.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 11/17/2015] [Accepted: 11/23/2015] [Indexed: 11/22/2022]
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Gade A, Adams J, Britt DW, Shen FA, McLean JE, Jacobson A, Kim YC, Anderson AJ. Ag nanoparticles generated using bio-reduction and -coating cause microbial killing without cell lysis. Biometals 2016; 29:211-23. [DOI: 10.1007/s10534-015-9906-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 12/17/2015] [Indexed: 12/11/2022]
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Kim JS, Kim YH, Anderson AJ, Kim YC. The Sensor Kinase GacS Negatively Regulates Flagellar Formation and Motility in a Biocontrol Bacterium, Pseudomonas chlororaphis O6. THE PLANT PATHOLOGY JOURNAL 2014; 30:215-9. [PMID: 25289006 PMCID: PMC4174843 DOI: 10.5423/ppj.nt.11.2013.0109] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 01/03/2014] [Accepted: 01/24/2014] [Indexed: 05/24/2023]
Abstract
The GacS/GacA two component system regulates various traits related to the biocontrol potential of plant-associated pseudomonads. The role of the sensor kinase, GacS, differs between strains in regulation of motility. In this study, we determined how a gacS mutation changed cell morphology and motility in Pseudomonas chlororaphis O6. The gacS mutant cells were elongated in stationary-phase compared to the wild type and the complemented gacS mutant, but cells did not differ in length in logarithmic phase. The gacS mutant had a two-fold increase in the number of flagella compared with the wild type strain; flagella number was restored to that of the wild type in the complemented gacS mutant. The more highly flagellated gacS mutant cells had greater swimming motilities than that of the wild type strain. Enhanced flagella formation in the gacS mutant correlated with increased expression of three genes, fleQ, fliQ and flhF, involved in flagellar formation. Expression of these genes in the complemented gacS mutant was similar to that of the wild type. These findings show that this root-colonizing pseudomonad adjusts flagella formation and cell morphology in stationary-phase using GacS as a major regulator.
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Affiliation(s)
- Ji Soo Kim
- Institute of Environmentally-Friendly Agriculture, Chonnam National University, Gwangju 500-757, Korea
| | - Yong Hwan Kim
- Korea Institute of Planning & Evaluation for Technology on Food, Agriculture, Forestry & Fisheries, Anyang 431-060, Korea
| | - Anne J Anderson
- Department of Biology, Utah State University, Logan, UT, USA
| | - Young Cheol Kim
- Institute of Environmentally-Friendly Agriculture, Chonnam National University, Gwangju 500-757, Korea
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Kim CH, Kim YH, Anderson AJ, Kim YC. Proteomic Analysis of a Global Regulator GacS Sensor Kinase in the Rhizobacterium, Pseudomonas chlororaphis O6. THE PLANT PATHOLOGY JOURNAL 2014; 30:220-7. [PMID: 25289007 PMCID: PMC4174846 DOI: 10.5423/ppj.nt.02.2014.0012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/26/2014] [Accepted: 03/27/2014] [Indexed: 05/09/2023]
Abstract
The GacS/GacA system in the root colonizer Pseudomonas chlororaphis O6 is a key regulator of many traits relevant to the biocontrol function of this bacterium. Proteomic analysis revealed 12 proteins were down-regulated in a gacS mutant of P. chlororaphis O6. These GacS-regulated proteins functioned in combating oxidative stress, cell signaling, biosynthesis of secondary metabolism, and secretion. The extent of regulation was shown by real-time RT-PCR to vary between the genes. Mutants of P. chlororaphis O6 were generated in two GacS-regulated genes, trpE, encoding a protein involved in tryptophan synthesis, and prnA, required for conversion of tryptophan to the antimicrobial compound, pyrrolitrin. Failure of the trpE mutant to induce systemic resistance in tobacco against a foliar pathogen causing soft rot, Pectobacterium carotovorum SCCI, correlated with reduced colonization of root surfaces implying an inadequate supply of tryptophan to support growth. Although colonization was not affected by mutation in the prnA gene, induction of systemic resistance was reduced, suggesting that pyrrolnitrin was an activator of plant resistance as well as an antifungal agent. Study of mutants in the other GacS-regulated proteins will indicate further the features required for biocontrol-activity in this rhizobacterium.
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Affiliation(s)
- Chul Hong Kim
- Department of Floriculture, Chunnam Techno University, Jeonnam 516-911, Korea
| | - Yong Hwan Kim
- Korea Institute of Planning & Evaluation for Technology on Food, Agriculture, Forestry & Fisheries, Anyang 431-060, Korea
| | - Anne J. Anderson
- Department of Biology, Utah State University, Logan, Utah 843220-5305, USA
| | - Young Cheol Kim
- Institute of Environmentally-Friendly Agriculture, Chonnam National University, Gwangju 500-757, Korea
- Corresponding author. Phone) +82-62-530-2071, FAX) +82-62-530-2079, E-mail)
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