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Antoszewski M, Mierek-Adamska A, Dąbrowska GB. The Importance of Microorganisms for Sustainable Agriculture-A Review. Metabolites 2022; 12:1100. [PMID: 36422239 PMCID: PMC9694901 DOI: 10.3390/metabo12111100] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 08/27/2023] Open
Abstract
In the face of climate change, progressive degradation of the environment, including agricultural land negatively affecting plant growth and development, endangers plant productivity. Seeking efficient and sustainable agricultural techniques to replace agricultural chemicals is one of the most important challenges nowadays. The use of plant growth-promoting microorganisms is among the most promising approaches; however, molecular mechanisms underneath plant-microbe interactions are still poorly understood. In this review, we summarized the knowledge on plant-microbe interactions, highlighting the role of microbial and plant proteins and metabolites in the formation of symbiotic relationships. This review covers rhizosphere and phyllosphere microbiomes, the role of root exudates in plant-microorganism interactions, the functioning of the plant's immune system during the plant-microorganism interactions. We also emphasized the possible role of the stringent response and the evolutionarily conserved mechanism during the established interaction between plants and microorganisms. As a case study, we discussed fungi belonging to the genus Trichoderma. Our review aims to summarize the existing knowledge about plant-microorganism interactions and to highlight molecular pathways that need further investigation.
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Affiliation(s)
| | - Agnieszka Mierek-Adamska
- Department of Genetics, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland
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Job V, Gomez-Valero L, Renier A, Rusniok C, Bouillot S, Chenal-Francisque V, Gueguen E, Adrait A, Robert-Genthon M, Jeannot K, Panchev P, Elsen S, Fauvarque MO, Couté Y, Buchrieser C, Attrée I. Genomic erosion and horizontal gene transfer shape functional differences of the ExlA toxin in Pseudomonas spp. iScience 2022; 25:104596. [PMID: 35789842 PMCID: PMC9250014 DOI: 10.1016/j.isci.2022.104596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/15/2022] [Accepted: 06/08/2022] [Indexed: 12/31/2022] Open
Abstract
Two-partner secretion (TPS) is widespread in the bacterial world. The pore-forming TPS toxin ExlA of Pseudomonas aeruginosa is conserved in pathogenic and environmental Pseudomonas. While P. chlororaphis and P. entomophila displayed ExlA-dependent killing, P. putida did not cause damage to eukaryotic cells. ExlA proteins interacted with epithelial cell membranes; however, only ExlAPch induced the cleavage of the adhesive molecule E-cadherin. ExlA proteins participated in insecticidal activity toward the larvae of Galleria mellonella and the fly Drosophila melanogaster. Evolutionary analyses demonstrated that the differences in the C-terminal domains are partly due to horizontal movements of the operon within the genus Pseudomonas. Reconstruction of the evolutionary history revealed the complex horizontal acquisitions. Together, our results provide evidence that conserved TPS toxins in environmental Pseudomonas play a role in bacteria-insect interactions and discrete differences in CTDs may determine their specificity and mode of action toward eukaryotic cells. ExlA is a two-partner secreted toxin conserved across Pseudomonas spp. Environmental Pseudomonas strains encode ExlA with different cytotoxic activities ExlA of environmental Pseudomonas strains play a role in bacteria-insect interactions ExlBA operon shows a complex evolutionary history of horizontal gene transfer
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Affiliation(s)
- Viviana Job
- Université Grenoble Alpes, Institute of Structural Biology, Bacterial Pathogenesis and Cellular Responses Team, UMR5075 CNRS, IRIG, CEA, Grenoble, France
| | - Laura Gomez-Valero
- Institut Pasteur, Université de Paris, CNRS UMR 6047, Unité Biologie des Bactéries Intracellulaires, 75015 Paris, France
| | - Adèle Renier
- Université Grenoble Alpes, Institute of Structural Biology, Bacterial Pathogenesis and Cellular Responses Team, UMR5075 CNRS, IRIG, CEA, Grenoble, France
| | - Christophe Rusniok
- Institut Pasteur, Université de Paris, CNRS UMR 6047, Unité Biologie des Bactéries Intracellulaires, 75015 Paris, France
| | - Stephanie Bouillot
- Université Grenoble Alpes, Institute of Structural Biology, Bacterial Pathogenesis and Cellular Responses Team, UMR5075 CNRS, IRIG, CEA, Grenoble, France
| | - Viviane Chenal-Francisque
- Institut Pasteur, Université de Paris, CNRS UMR 6047, Unité Biologie des Bactéries Intracellulaires, 75015 Paris, France
| | - Erwan Gueguen
- University of Lyon, Université Lyon 1, INSA de Lyon, CNRS UMR 5240 Microbiologie Adaptation et Pathogénie, Lyon, France
| | - Annie Adrait
- Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, Grenoble, France
| | - Mylène Robert-Genthon
- Université Grenoble Alpes, Institute of Structural Biology, Bacterial Pathogenesis and Cellular Responses Team, UMR5075 CNRS, IRIG, CEA, Grenoble, France
| | - Katy Jeannot
- Centre National de Référence de la Résistance aux Antibiotiques, Laboratoire de Bactériologie, Centre Hospitalier Universitaire Jean Minjoz, UMR6249 CNRS, Université de Bourgogne-Franche Comté, Besançon, France
| | - Peter Panchev
- Université Grenoble Alpes, Institute of Structural Biology, Bacterial Pathogenesis and Cellular Responses Team, UMR5075 CNRS, IRIG, CEA, Grenoble, France
| | - Sylvie Elsen
- Université Grenoble Alpes, Institute of Structural Biology, Bacterial Pathogenesis and Cellular Responses Team, UMR5075 CNRS, IRIG, CEA, Grenoble, France
| | | | - Yohann Couté
- Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, Grenoble, France
- CNRS, CEA, FR2048, Grenoble, France
| | - Carmen Buchrieser
- Institut Pasteur, Université de Paris, CNRS UMR 6047, Unité Biologie des Bactéries Intracellulaires, 75015 Paris, France
- Corresponding author
| | - Ina Attrée
- Université Grenoble Alpes, Institute of Structural Biology, Bacterial Pathogenesis and Cellular Responses Team, UMR5075 CNRS, IRIG, CEA, Grenoble, France
- Corresponding author
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Lee JH, Anderson AJ, Kim YC. Root-Associated Bacteria Are Biocontrol Agents for Multiple Plant Pests. Microorganisms 2022; 10:microorganisms10051053. [PMID: 35630495 PMCID: PMC9146382 DOI: 10.3390/microorganisms10051053] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/15/2022] [Accepted: 05/16/2022] [Indexed: 02/01/2023] Open
Abstract
Biological control is an important process for sustainable plant production, and this trait is found in many plant-associated microbes. This study reviews microbes that could be formulated into pesticides active against various microbial plant pathogens as well as damaging insects or nematodes. The focus is on the beneficial microbes that colonize the rhizosphere where, through various mechanisms, they promote healthy plant growth. Although these microbes have adapted to cohabit root tissues without causing disease, they are pathogenic to plant pathogens, including microbes, insects, and nematodes. The cocktail of metabolites released from the beneficial strains inhibits the growth of certain bacterial and fungal plant pathogens and participates in insect and nematode toxicity. There is a reinforcement of plant health through the systemic induction of defenses against pathogen attack and abiotic stress in the plant; metabolites in the beneficial microbial cocktail function in triggering the plant defenses. The review discusses a wide range of metabolites involved in plant protection through biocontrol in the rhizosphere. The focus is on the beneficial firmicutes and pseudomonads, because of the extensive studies with these isolates. The review evaluates how culture conditions can be optimized to provide formulations containing the preformed active metabolites for rapid control, with or without viable microbial cells as plant inocula, to boost plant productivity in field situations.
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Affiliation(s)
- Jang Hoon Lee
- Agricultural Solutions, BASF Korea Ltd., Seoul 04518, Korea;
| | - Anne J. Anderson
- Department of Biological Engineering, Utah State University, Logan, UT 84322, USA;
| | - Young Cheol Kim
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea
- Correspondence:
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Craig K, Johnson BR, Grunden A. Leveraging Pseudomonas Stress Response Mechanisms for Industrial Applications. Front Microbiol 2021; 12:660134. [PMID: 34040596 PMCID: PMC8141521 DOI: 10.3389/fmicb.2021.660134] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/12/2021] [Indexed: 12/25/2022] Open
Abstract
Members of the genus Pseudomonas are metabolically versatile and capable of adapting to a wide variety of environments. Stress physiology of Pseudomonas strains has been extensively studied because of their biotechnological potential in agriculture as well as their medical importance with regards to pathogenicity and antibiotic resistance. This versatility and scientific relevance led to a substantial amount of information regarding the stress response of a diverse set of species such as Pseudomonas chlororaphis, P. fluorescens, P. putida, P. aeruginosa, and P. syringae. In this review, environmental and industrial stressors including desiccation, heat, and cold stress, are cataloged along with their corresponding mechanisms of survival in Pseudomonas. Mechanisms of survival are grouped by the type of inducing stress with a focus on adaptations such as synthesis of protective substances, biofilm formation, entering a non-culturable state, enlisting chaperones, transcription and translation regulation, and altering membrane composition. The strategies Pseudomonas strains utilize for survival can be leveraged during the development of beneficial strains to increase viability and product efficacy.
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Affiliation(s)
- Kelly Craig
- AgBiome Inc., Research Triangle Park, NC, United States
| | | | - Amy Grunden
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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Ghergab A, Selin C, Tanner J, Brassinga AK, Dekievit T. Pseudomonas chlororaphis PA23 metabolites protect against protozoan grazing by the predator Acanthamoeba castellanii. PeerJ 2021; 9:e10756. [PMID: 33552738 PMCID: PMC7831366 DOI: 10.7717/peerj.10756] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/21/2020] [Indexed: 01/29/2023] Open
Abstract
Background Pseudomonas chlororaphis strain PA23 is a biocontrol agent that is able to protect canola against the pathogenic fungus Sclerotinia sclerotiorum. This bacterium secretes a number of metabolites that contribute to fungal antagonism, including pyrrolnitrin (PRN), phenazine (PHZ), hydrogen cyanide (HCN) and degradative enzymes. In order to be successful, a biocontrol agent must be able to persist in the environment and avoid the threat of grazing predators. The focus of the current study was to investigate whether PA23 is able to resist grazing by the protozoan predator Acanthamoeba castellanii (Ac) and to define the role of bacterial metabolites in the PA23-Ac interaction. Methods Ac was co-cultured with PA23 WT and a panel of derivative strains for a period of 15 days, and bacteria and amoebae were enumerated on days 1, 5, 10 and 15. Ac was subsequently incubated in the presence of purified PRN, PHZ, and KCN and viability was assessed at 24, 48 and 72 h. Chemotactic assays were conducted to assess whether PA23 compounds exhibit repellent or attractant properties towards Ac. Finally, PA23 grown in the presence and absence of amoebae was subject to phenotypic characterization and gene expression analyses. Results PRN, PHZ and HCN were found to contribute to PA23 toxicity towards Ac trophozoites, either by killing or inducing cyst formation. This is the first report of PHZ-mediated toxicity towards amoebae. In chemotaxis assays, amoebae preferentially migrated towards regulatory mutants devoid of extracellular metabolite production as well as a PRN mutant, indicating this antibiotic has repellent properties. Co-culturing of bacteria with amoebae led to elevated expression of the PA23 phzI/phzR quorum-sensing (QS) genes and phzA and prnA, which are under QS control. PHZ and PRN levels were similarly increased in Ac co-cultures, suggesting that PA23 can respond to predator cues and upregulate expression of toxins accordingly. Conclusions PA23 compounds including PRN, PHZ and HCN exhibited both toxic and repellent effects on Ac. Co-culturing of bacteria and amoebae lead to changes in bacterial gene expression and secondary metabolite production, suggesting that PA23 can sense the presence of these would-be predators and adjust its physiology in response.
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Affiliation(s)
- Akrm Ghergab
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Carrie Selin
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jennifer Tanner
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Ann Karen Brassinga
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Teresa Dekievit
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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Mohanan N, Gislason A, Sharma PK, Ghergab A, Plouffe J, Levin DB, de Kievit T. Quorum sensing and the anaerobic regulator (ANR) control polyhydroxyalkanoate (PHA) production in Pseudomonas chlororaphis PA23. FEMS Microbiol Lett 2020; 366:5613363. [PMID: 31688920 DOI: 10.1093/femsle/fnz223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/31/2019] [Indexed: 11/14/2022] Open
Abstract
Pseudomonas chlororaphis PA23 is a biocontrol agent that, in addition to producing antifungal compounds, synthesizes polyhydroxyalkanoate (PHA) polymers as a carbon and energy sink. Quorum sensing (QS) and the anaerobic regulator (ANR) are required for PA23-mediated fungal suppression; however, the role of these regulators in PHA production is unknown. Strains lacking either QS or ANR accumulated less PHA polymers when propagated on Ramsay's minimal medium (RMM) with glucose or octanoate as the carbon source. In the acyl-homoserine lactone (AHL)-deficient background, all six of the genes in the pha locus (phaC1, phaC2, phaZ, phaD, phaF, phaI) showed reduced expression in RMM glucose, and all except phaC2 were repressed in RMM octanoate. Although changes in gene activity were observed in the anr mutant, they were less pronounced. Analysis of the promoter regions for QS- and ANR-binding consensus sequences revealed putative phzboxes upstream of phaZ and phaI, but no anr boxes were identified. Our findings indicate that altered pha gene expression likely contributes to the lower PHA accumulation in the QS- and ANR-deficient strains, which may be in part indirectly mediated. This study is the first to show that mcl-PHA production is under QS and ANR control.
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Affiliation(s)
- Nisha Mohanan
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - April Gislason
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - Parveen K Sharma
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - Akrm Ghergab
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - Jocelyn Plouffe
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - David B Levin
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - Teresa de Kievit
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
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Anderson AJ, Kim YC. Insights into plant-beneficial traits of probiotic Pseudomonas chlororaphis isolates. J Med Microbiol 2020; 69:361-371. [DOI: 10.1099/jmm.0.001157] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pseudomonas chlororaphisisolates have been studied intensively for their beneficial traits.P. chlororaphisspecies function as probiotics in plants and fish, offering plants protection against microbes, nematodes and insects. In this review, we discuss the classification ofP. chlororaphisisolates within four subspecies; the shared traits include the production of coloured antimicrobial phenazines, high sequence identity between housekeeping genes and similar cellular fatty acid composition. The direct antimicrobial, insecticidal and nematocidal effects ofP. chlororaphisisolates are correlated with known metabolites. Other metabolites prime the plants for stress tolerance and participate in microbial cell signalling events and biofilm formation among other things. Formulations ofP. chlororaphisisolates and their metabolites are currently being commercialized for agricultural use.
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Affiliation(s)
- Anne J. Anderson
- Department of Biological Engineering, Utah State University, Logan UT84322, USA
| | - Young Cheol Kim
- Department of Applied Biology, Chonnam National University, Gwangju 61186, Republic of Korea
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Shah N, Gislason AS, Becker M, Belmonte MF, Fernando WGD, de Kievit TR. Investigation of the quorum-sensing regulon of the biocontrol bacterium Pseudomonas chlororaphis strain PA23. PLoS One 2020; 15:e0226232. [PMID: 32109244 PMCID: PMC7048289 DOI: 10.1371/journal.pone.0226232] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/12/2020] [Indexed: 12/15/2022] Open
Abstract
Pseudomonas chlororaphis strain PA23 is a biocontrol agent capable of protecting canola from stem rot disease caused by the fungal pathogen Sclerotinia sclerotiorum. PA23 produces several inhibitory compounds that are under control of a complex regulatory network. Included in this cascade is the PhzRI quorum sensing (QS) system, which plays an essential role in PA23 biocontrol, as well as CsaRI and AurRI, which have not yet been characterized in PA23. The focus of the current study was to employ RNA sequencing to explore the spectrum of PA23 genes under QS control. In this work, we investigated genes under the control of the main QS transcriptional regulator, PhzR, as well as those differentially expressed in an AHL-deficient strain, PA23-6863, which constitutively expresses an AiiA lactonase, rendering the strain QS defective. Transcriptomic profiling revealed 545 differentially expressed genes (365 downregulated; 180 upregulated) in the phzR mutant and 534 genes (382 downregulated; 152 upregulated) in the AHL-deficient PA23-6863. In both strains, decreased expression of phenazine, pyrrolnitrin, and exoprotease biosynthetic genes was observed. We have previously reported that QS activates expression of these genes and their encoded products. In addition, elevated siderophore and decreased chitinase gene expression was observed in the QS-deficient stains, which was confirmed by phenotypic analysis. Inspection of the promoter regions revealed the presence of "phz-box" sequences in only 58 of the 807 differentially expressed genes, suggesting that much of the QS regulon is indirectly regulated. Consistent with this notion, 41 transcriptional regulators displayed altered expression in one or both of the QS-deficient strains. Collectively, our findings indicate that QS governs expression of approximately 13% of the PA23 genome affecting diverse functions ranging from secondary metabolite production to general metabolism.
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Affiliation(s)
- Nidhi Shah
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - April S. Gislason
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Michael Becker
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Mark F. Belmonte
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Teresa R. de Kievit
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- * E-mail:
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Wu L, Wang Z, Guan Y, Huang X, Shi H, Liu Y, Zhang X. The (p)ppGpp-mediated stringent response regulatory system globally inhibits primary metabolism and activates secondary metabolism in Pseudomonas protegens H78. Appl Microbiol Biotechnol 2020; 104:3061-3079. [PMID: 32009198 DOI: 10.1007/s00253-020-10421-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/18/2020] [Accepted: 01/26/2020] [Indexed: 01/08/2023]
Abstract
Pseudomonas protegens H78 produces multiple secondary metabolites, including antibiotics and iron carriers. The guanosine pentaphosphate or tetraphosphate ((p)ppGpp)-mediated stringent response is utilized by bacteria to survive during nutritional starvation and other stresses. RelA/SpoT homologues are responsible for the biosynthesis and degradation of the alarmone (p)ppGpp. Here, we investigated the global effect of relA/spoT dual deletion on the transcriptomic profiles, physiology, and metabolism of P. protegens H78 grown to mid- to late log phase. Transcriptomic profiling revealed that relA/spoT deletion globally upregulated the expression of genes involved in DNA replication, transcription, and translation; amino acid metabolism; carbohydrate and energy metabolism; ion transport and metabolism; and secretion systems. Bacterial growth was partially increased, while the cell survival rate was significantly reduced by relA/spoT deletion in H78. The utilization of some nutritional elements (C, P, S, and N) was downregulated due to relA/spoT deletion. In contrast, relA/spoT mutation globally inhibited the expression of secondary metabolic gene clusters (plt, phl, prn, ofa, fit, pch, pvd, and has). Correspondingly, antibiotic and iron carrier biosynthesis, iron utilization, and antibiotic resistance were significantly downregulated by the relA/spoT mutation. This work highlights that the (p)ppGpp-mediated stringent response regulatory system plays an important role in inhibiting primary metabolism and activating secondary metabolism in P. protegens.
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Affiliation(s)
- Lingyu Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zheng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yejun Guan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xianqing Huang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Huimin Shi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yujie Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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Freimoser FM, Rueda-Mejia MP, Tilocca B, Migheli Q. Biocontrol yeasts: mechanisms and applications. World J Microbiol Biotechnol 2019; 35:154. [PMID: 31576429 PMCID: PMC6773674 DOI: 10.1007/s11274-019-2728-4] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/17/2019] [Indexed: 01/10/2023]
Abstract
Yeasts occur in all environments and have been described as potent antagonists of various plant pathogens. Due to their antagonistic ability, undemanding cultivation requirements, and limited biosafety concerns, many of these unicellular fungi have been considered for biocontrol applications. Here, we review the fundamental research on the mechanisms (e.g., competition, enzyme secretion, toxin production, volatiles, mycoparasitism, induction of resistance) by which biocontrol yeasts exert their activity as plant protection agents. In a second part, we focus on five yeast species (Candida oleophila, Aureobasidium pullulans, Metschnikowia fructicola, Cryptococcus albidus, Saccharomyces cerevisiae) that are or have been registered for the application as biocontrol products. These examples demonstrate the potential of yeasts for commercial biocontrol usage, but this review also highlights the scarcity of fundamental studies on yeast biocontrol mechanisms and of registered yeast-based biocontrol products. Yeast biocontrol mechanisms thus represent a largely unexplored field of research and plentiful opportunities for the development of commercial, yeast-based applications for plant protection exist.
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Affiliation(s)
- Florian M Freimoser
- Agroscope, Research Division Plant Protection, Müller-Thurgau-Strasse 29, 8820, Wädenswil, Switzerland.
| | - Maria Paula Rueda-Mejia
- Agroscope, Research Division Plant Protection, Müller-Thurgau-Strasse 29, 8820, Wädenswil, Switzerland
| | - Bruno Tilocca
- Dipartimento di Agraria, Università degli Studi di Sassari, Viale Italia 39, 07100, Sassari, Italy
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, Viale Europa, 88100, Catanzaro, Italy
| | - Quirico Migheli
- Dipartimento di Agraria, Università degli Studi di Sassari, Viale Italia 39, 07100, Sassari, Italy
- Istituto Nazionale di Biostrutture e Biosistemi and NRD - Nucleo di Ricerca sulla Desertificazione, Università degli Studi di Sassari, Viale Italia 39, 07100, Sassari, Italy
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Polyhydroxyalkanoate (PHA) Polymer Accumulation and pha Gene Expression in Phenazine (phz⁻) and Pyrrolnitrin (prn⁻) Defective Mutants of Pseudomonas chlororaphis PA23. Polymers (Basel) 2018; 10:polym10111203. [PMID: 30961128 PMCID: PMC6290614 DOI: 10.3390/polym10111203] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/19/2018] [Accepted: 10/25/2018] [Indexed: 11/16/2022] Open
Abstract
Pseudomonas chlororaphis PA23 was isolated from the rhizosphere of soybeans and identified as a biocontrol bacterium against Sclerotinia sclerotiorum, a fungal plant pathogen. This bacterium produces a number of secondary metabolites, including phenazine-1-carboxylic acid, 2-hydroxyphenazine, pyrrolnitrin (PRN), hydrogen cyanide, proteases, lipases and siderophores. It also synthesizes and accumulates polyhydroxyalkanoate (PHA) polymers as carbon and energy storage compounds under nutrient-limited conditions. Pseudomonads like P. chlororaphis metabolize glucose via the Entner-Doudoroff and Pentose Phosphate pathways, which provide precursors for phenazine production. Mutants defective in phenazine (PHZ; PA23-63), PRN (PA23-8), or both (PA23-63-1) accumulated higher concentrations of PHAs than the wild-type strain (PA23) when cultured in Ramsay’s Minimal Medium with glucose or octanoic acid as the carbon source. Expression levels of six pha genes, phaC1, phaZ, phaC2, phaD, phaF, and phaI, were compared with wild type PA23 by quantitative real time polymerase chain reaction (qPCR). The qPCR studies indicated that there was no change in levels of transcription of the PHA synthase genes phaC1 and phaC2 in the phz- (PA23-63) and phz-prn- (PA23-63-1) mutants in glucose medium. There was a significant increase in expression of phaC2 in octanoate medium. Transcription of phaD, phaF and phaI increased significantly in the phz-prn- (PA23-63-1) mutant. Mutations in regulatory genes like gacS, rpoS, and relA/spoT, which affect PHZ and PRN production, also resulted in altered gene expression. The expression of phaC1, phaC2, phaF, and phaI genes was down-regulated significantly in gacS and rpoS mutants. Thus, it appears that PHZ, PRN, and PHA production is regulated by common mechanisms. Higher PHA production in the phz- (PA23-63), prn- (PA23-8), and phz-prn- (PA23-63-1) mutants in octanoic medium could be correlated with higher expression of phaC2. Further, the greater PHA production observed in the phz- and prn- mutants was not due to increased transcription of PHA synthase genes in glucose medium, but due to more accessibility of carbon substrates and reducing power, which were otherwise used for the synthesis of PHZ and PRN.
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Jagmann N, Philipp B. SpoT-Mediated Regulation and Amino Acid Prototrophy Are Essential for Pyocyanin Production During Parasitic Growth of Pseudomonas aeruginosa in a Co-culture Model System With Aeromonas hydrophila. Front Microbiol 2018; 9:761. [PMID: 29720972 PMCID: PMC5915560 DOI: 10.3389/fmicb.2018.00761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 04/04/2018] [Indexed: 11/17/2022] Open
Abstract
The opportunistic pathogen Pseudomonas aeruginosa employs its complex quorum sensing (QS) network to regulate the expression of virulence factors such as pyocyanin. Besides cell density, QS in this bacterium is co-regulated by environmental cues. In this study, we employed a previously established co-culture model system to identify metabolic influences that are involved in the regulation of pyocyanin production in P. aeruginosa. In this co-culture consisting of P. aeruginosa and the chitinolytic bacterium Aeromonas hydrophila, parasitic growth of P. aeruginosa is strictly dependent on the production of pyocyanin. We could show that in this co-culture, pyocyanin production is likely induced by the stringent response mediated by SpoT in response to nutrient limitation. Pyocyanin production by stringent response mutants in the co-culture could not be complemented by overexpression of PqsE. Via transposon mutagenesis, several amino acid auxotrophic mutants were identified that were also unable to produce pyocyanin when PqsE was overexpressed or when complementing amino acids were present. The inability to produce pyocyanin even though PqsE was overexpressed was likely a general effect of amino acid auxotrophy. These results show the value of the co-culture approach to identify both extra- and intracellular metabolic influences on QS that might be important in infection processes as well.
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Affiliation(s)
- Nina Jagmann
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
| | - Bodo Philipp
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
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Pletzer D, Wolfmeier H, Bains M, Hancock REW. Synthetic Peptides to Target Stringent Response-Controlled Virulence in a Pseudomonas aeruginosa Murine Cutaneous Infection Model. Front Microbiol 2017; 8:1867. [PMID: 29021784 PMCID: PMC5623667 DOI: 10.3389/fmicb.2017.01867] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/13/2017] [Indexed: 02/05/2023] Open
Abstract
Microorganisms continuously monitor their surroundings and adaptively respond to environmental cues. One way to cope with various stress-related situations is through the activation of the stringent stress response pathway. In Pseudomonas aeruginosa this pathway is controlled and coordinated by the activity of the RelA and SpoT enzymes that metabolize the small nucleotide secondary messenger molecule (p)ppGpp. Intracellular ppGpp concentrations are crucial in mediating adaptive responses and virulence. Targeting this cellular stress response has recently been the focus of an alternative approach to fight antibiotic resistant bacteria. Here, we examined the role of the stringent response in the virulence of P. aeruginosa PAO1 and the Liverpool epidemic strain LESB58. A ΔrelA/ΔspoT double mutant showed decreased cytotoxicity toward human epithelial cells, exhibited reduced hemolytic activity, and caused down-regulation of the expression of the alkaline protease aprA gene in stringent response mutants grown on blood agar plates. Promoter fusions of relA or spoT to a bioluminescence reporter gene revealed that both genes were expressed during the formation of cutaneous abscesses in mice. Intriguingly, virulence was attenuated in vivo by the ΔrelA/ΔspoT double mutant, but not the relA mutant nor the ΔrelA/ΔspoT complemented with either gene. Treatment of a cutaneous P. aeruginosa PAO1 infection with anti-biofilm peptides increased animal welfare, decreased dermonecrotic lesion sizes, and reduced bacterial numbers recovered from abscesses, resembling the phenotype of the ΔrelA/ΔspoT infection. It was previously demonstrated by our lab that ppGpp could be targeted by synthetic peptides; here we demonstrated that spoT promoter activity was suppressed during cutaneous abscess formation by treatment with peptides DJK-5 and 1018, and that a peptide-treated relA complemented stringent response double mutant strain exhibited reduced peptide susceptibility. Overall these data strongly indicated that synthetic peptides target the P. aeruginosa stringent response in vivo and thus offer a promising novel therapeutic approach.
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Affiliation(s)
- Daniel Pletzer
- Department of Microbiology and Immunology, Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Heidi Wolfmeier
- Department of Microbiology and Immunology, Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Manjeet Bains
- Department of Microbiology and Immunology, Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Robert E W Hancock
- Department of Microbiology and Immunology, Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
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Nandi M, Selin C, Brawerman G, Fernando WGD, de Kievit TR. The global regulator ANR is essential for Pseudomonas chlororaphis strain PA23 biocontrol. MICROBIOLOGY-SGM 2017; 162:2159-2169. [PMID: 27998371 DOI: 10.1099/mic.0.000391] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Pseudomonas chlororaphis PA23 is a biocontrol agent capable of protecting canola from stem rot disease caused by the fungus Sclerotinia sclerotiorum. The focus of the current study was to elucidate the role of the transcriptional regulator ANR in the biocontrol capabilities of this bacterium. An anr mutant was created, PA23anr, that was devoid antifungal activity. In other pseudomonads, ANR is essential for regulating HCN production. Characterization of PA23anr revealed that, in addition to HCN, ANR controls phenazine (PHZ), pyrrolnitrin (PRN), protease and autoinducer (AHL) signal molecule production. In gene expression studies, hcnA, phzA, prnA and phzI were found to be downregulated, consistent with our endproduct analysis. Because the phenotype of PA23anr closely resembles that of quorum sensing (QS)-deficient strains, we explored whether there is a connection between ANR and the PhzRI QS system. Both phzI and phzR are positively regulated by ANR, whereas PhzR represses anr transcription. Complementation of PA23anr with pUCP-phzR, C6-HSL or both yielded no change in phenotype. Conversely, PA23phzR harbouring pUCP23-anr exhibited partial-to-full restoration of antifungal activity, HCN, PRN and AHL production together with hcnA, prnA, phzI and rpoS expression. PHZ and protease production remained unchanged indicating that ANR can complement the QS-deficient phenotype with respect to some but not all traits. Our experiments were conducted at atmospheric O2 levels underscoring the fact that ANR has a profound effect on PA23 physiology under aerobic conditions.
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Affiliation(s)
- Munmun Nandi
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Carrie Selin
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Gabriel Brawerman
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Teresa R de Kievit
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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15
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Shah N, Klaponski N, Selin C, Rudney R, Fernando WGD, Belmonte MF, de Kievit TR. PtrA Is Functionally Intertwined with GacS in Regulating the Biocontrol Activity of Pseudomonas chlororaphis PA23. Front Microbiol 2016; 7:1512. [PMID: 27713742 PMCID: PMC5031690 DOI: 10.3389/fmicb.2016.01512] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 09/09/2016] [Indexed: 11/13/2022] Open
Abstract
In vitro inhibition of the fungal pathogen Sclerotinia sclerotiorum by Pseudomonas chlororaphis PA23 is reliant upon a LysR-type transcriptional regulator (LTTR) called PtrA. In the current study, we show that Sclerotinia stem rot and leaf infection are significantly increased in canola plants inoculated with the ptrA-mutant compared to the wild type, establishing PtrA as an essential regulator of PA23 biocontrol. LTTRs typically regulate targets that are upstream of and divergently transcribed from the LTTR locus. We identified a short chain dehydrogenase (scd) gene immediately upstream of ptrA. Characterization of a scd mutant revealed that it is phenotypically identical to the wild type. Moreover, scd transcript abundance was unchanged in the ptrA mutant. These findings indicate that PtrA regulation does not involve scd, rather this LTTR controls genes located elsewhere on the chromosome. Employing a combination of complementation and transcriptional analysis we investigated whether connections exist between PtrA and other regulators of biocontrol. Besides ptrA, gacS was the only gene able to partially rescue the wild-type phenotype, establishing a connection between PtrA and the sensor kinase GacS. Transcriptomic analysis revealed decreased expression of biosynthetic (phzA, prnA) and regulatory genes (phzI, phzR, rpoS, gacA, rsmX, rsmZ, retS) in the ptrA mutant; conversely, rsmE, and rsmY were markedly upregulated. The transcript abundance of ptrA was nine-fold higher in the mutant background indicating that this LTTR negatively autoregulates itself. In summary, PtrA is an essential regulator of genes required for PA23 biocontrol that is functionally intertwined with GacS.
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Affiliation(s)
- Nidhi Shah
- Department of Microbiology, University of Manitoba Winnipeg, MB, Canada
| | - Natasha Klaponski
- Department of Microbiology, University of Manitoba Winnipeg, MB, Canada
| | - Carrie Selin
- Department of Plant Science, University of Manitoba Winnipeg, MB, Canada
| | - Rachel Rudney
- Department of Microbiology, University of Manitoba Winnipeg, MB, Canada
| | | | - Mark F Belmonte
- Department of Biological Science, University of Manitoba Winnipeg, MB, Canada
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16
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Matilla MA, Leeper FJ, Salmond GPC. Biosynthesis of the antifungal haterumalide, oocydin A, in Serratia, and its regulation by quorum sensing, RpoS and Hfq. Environ Microbiol 2015; 17:2993-3008. [PMID: 25753587 PMCID: PMC4552970 DOI: 10.1111/1462-2920.12839] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/27/2015] [Accepted: 03/02/2015] [Indexed: 02/02/2023]
Abstract
Polyketides represent an important class of bioactive natural products with a broad range of biological activities. We identified recently a large trans-acyltransferase (AT) polyketide synthase gene cluster responsible for the biosynthesis of the antifungal, anti-oomycete and antitumor haterumalide, oocydin A (ooc). Using genome sequencing and comparative genomics, we show that the ooc gene cluster is widespread within biocontrol and phytopathogenic strains of the enterobacteria, Serratia and Dickeya. The analysis of in frame deletion mutants confirmed the role of a hydroxymethylglutaryl-coenzyme A synthase cassette, three flavin-dependent tailoring enzymes, a free-standing acyl carrier protein and two hypothetical proteins in oocydin A biosynthesis. The requirement of the three trans-acting AT domains for the biosynthesis of the macrolide was also demonstrated. Expression of the ooc gene cluster was shown to be positively regulated by an N-acyl-L-homoserine lactone-based quorum sensing system, but operating in a strain-dependent manner. At a post-transcriptional level, the RNA chaperone, Hfq, plays a key role in oocydin A biosynthesis. The Hfq-dependent regulation is partially mediated by the stationary phase sigma factor, RpoS, which was also shown to positively regulate the synthesis of the macrolide. Our results reveal differential regulation of the divergently transcribed ooc transcriptional units, highlighting the complexity of oocydin A production.
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Affiliation(s)
- Miguel A Matilla
- Department of Biochemistry, University of CambridgeTennis Court Road, Cambridge, CB2 1QW, UK
| | - Finian J Leeper
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW, UK
| | - George P C Salmond
- Department of Biochemistry, University of CambridgeTennis Court Road, Cambridge, CB2 1QW, UK,*For correspondence. E-mail ; Tel. +44 (0)1223 333650; Fax +44 (0)1223 766108
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17
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Chapelle E, Mendes R, Bakker PAHM, Raaijmakers JM. Fungal invasion of the rhizosphere microbiome. ISME JOURNAL 2015; 10:265-8. [PMID: 26023875 DOI: 10.1038/ismej.2015.82] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 04/10/2015] [Accepted: 04/16/2015] [Indexed: 11/09/2022]
Abstract
The rhizosphere is the infection court where soil-borne pathogens establish a parasitic relationship with the plant. To infect root tissue, pathogens have to compete with members of the rhizosphere microbiome for available nutrients and microsites. In disease-suppressive soils, pathogens are strongly restricted in growth by the activities of specific rhizosphere microorganisms. Here, we sequenced metagenomic DNA and RNA of the rhizosphere microbiome of sugar beet seedlings grown in a soil suppressive to the fungal pathogen Rhizoctonia solani. rRNA-based analyses showed that Oxalobacteraceae, Burkholderiaceae, Sphingobacteriaceae and Sphingomonadaceae were significantly more abundant in the rhizosphere upon fungal invasion. Metatranscriptomics revealed that stress-related genes (ppGpp metabolism and oxidative stress) were upregulated in these bacterial families. We postulate that the invading pathogenic fungus induces, directly or via the plant, stress responses in the rhizobacterial community that lead to shifts in microbiome composition and to activation of antagonistic traits that restrict pathogen infection.
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Affiliation(s)
- Emilie Chapelle
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Rodrigo Mendes
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands.,Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, Embrapa Environment, Jaguariuna, Brazil
| | - Peter A H M Bakker
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Jos M Raaijmakers
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands.,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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18
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Nandi M, Selin C, Brassinga AKC, Belmonte MF, Fernando WGD, Loewen PC, de Kievit TR. Pyrrolnitrin and Hydrogen Cyanide Production by Pseudomonas chlororaphis Strain PA23 Exhibits Nematicidal and Repellent Activity against Caenorhabditis elegans. PLoS One 2015; 10:e0123184. [PMID: 25901993 PMCID: PMC4406715 DOI: 10.1371/journal.pone.0123184] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 03/02/2015] [Indexed: 11/19/2022] Open
Abstract
Pseudomonas chlororaphis strain PA23 is a biocontrol agent able to suppress growth of the fungal pathogen Sclerotinia sclerotiorum. This bacterium produces an arsenal of exometabolites including pyrrolnitrin (PRN), phenazine (PHZ), hydrogen cyanide (HCN), and degradative enzymes. Production of these compounds is controlled at both the transcriptional and posttranscriptional levels by the Gac-Rsm system, RpoS, PsrA, and the Phz quorum-sensing system. Beyond pathogen-suppression, the success of a biocontrol agent is dependent upon its ability to establish itself in the environment where predation by bacterivorous organisms, including nematodes, may threaten persistence. The focus of this study was to investigate whether PA23 is able to resist grazing by Caenorhabditis elegans and to define the role played by exoproducts in the bacterial-nematode interaction. We discovered that both PRN and HCN contribute to fast- and slow-killing of C. elegans. HCN is well-established as having lethal effects on C. elegans; however, PRN has not been reported to be nematicidal. Exposure of L4 stage nematodes to purified PRN reduced nematode viability in a dose-dependent fashion and led to reduced hatching of eggs laid by gravid adults. Because bacterial metabolites can act as chemoattractants or repellents, we analyzed whether PA23 exhibited attractant or repulsive properties towards C. elegans. Both PRN and HCN were found to be potent repellents. Next we investigated whether the presence of C. elegans would elicit changes in PA23 gene activity. Co-culturing the two organisms increased expression of a number of genes associated with biocontrol, including phzA, hcnA, phzR, phzI, rpoS and gacS. Exoproduct analysis showed that PHZ and autoinducer signals were upregulated, consistent with the gene expression profiles. Collectively, these findings indicate that PA23 is able to sense the presence of C. elegans and it is able to both repel and kill the nematodes, which should facilitate environmental persistence and ultimately biocontrol.
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Affiliation(s)
- Munmun Nandi
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Carrie Selin
- Department of Plant Science University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Mark F. Belmonte
- Department of Biological Sciences University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Peter C. Loewen
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Teresa R. de Kievit
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- * E-mail:
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Draft Genome Sequence of Rice Isolate Pseudomonas chlororaphis EA105. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01342-14. [PMID: 25540352 PMCID: PMC4276830 DOI: 10.1128/genomea.01342-14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Pseudomonas chlororaphis EA105, a strain isolated from rice rhizosphere, has shown antagonistic activities against a rice fungal pathogen, and could be important in defense against rice blast. We report the draft genome sequence of EA105, which is an estimated size of 6.6 Mb.
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Abstract
Pseudomonas chlororaphis strain PA23 is a plant-beneficial bacterium that is able to suppress disease caused by the fungal pathogen Sclerotinia sclerotiorum through a process known as biological control. Here we present a 7.1-Mb assembly of the PA23 genome.
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The requirement for the LysR-type regulator PtrA for Pseudomonas chlororaphis PA23 biocontrol revealed through proteomic and phenotypic analysis. BMC Microbiol 2014; 14:94. [PMID: 24739259 PMCID: PMC3997438 DOI: 10.1186/1471-2180-14-94] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 04/09/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pseudomonas chlororaphis strain PA23 is a biocontrol agent capable of suppressing the fungal pathogen Sclerotinia sclerotiorum. This bacterium produces the antibiotics phenazine and pyrrolnitrin together with other metabolites believed to contribute to biocontrol. A mutant no longer capable of inhibiting fungal growth was identified harboring a transposon insertion in a gene encoding a LysR-type transcriptional regulator (LTTR), designated ptrA (Pseudomonas transcriptional regulator). Isobaric tag for relative and absolute quantitation (iTRAQ) based protein analysis was used to reveal changes in protein expression patterns in the ptrA mutant compared to the PA23 wild type. RESULTS Relative abundance profiles showed 59 differentially-expressed proteins in the ptrA mutant, which could be classified into 16 clusters of orthologous groups (COGs) based on their predicted functions. The largest COG category was the unknown function group, suggesting that many yet-to-be identified proteins are involved in the loss of fungal activity. In the secondary metabolite biosynthesis, transport and catabolism COG, seven proteins associated with phenazine biosynthesis and chitinase production were downregulated in the mutant. Phenotypic assays confirmed the loss of phenazines and chitinase activity. Upregulated proteins included a lipoprotein involved in iron transport, a flagellin and hook-associated protein and four proteins categorized into the translation, ribosome structure and biogenesis COG. Phenotypic analysis revealed that the mutant exhibited increased siderophore production and flagellar motility and an altered growth profile, supporting the proteomic findings. CONCLUSION PtrA is a novel LTTR that is essential for PA23 fungal antagonism. Differential protein expression was observed across 16 COG categories suggesting PtrA is functioning as a global transcriptional regulator. Changes in protein expression were confirmed by phenotypic assays that showed reduced phenazine and chitinase expression, elevated flagellar motility and siderophore production, as well as early entrance into log phase growth.
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Xu J, Deng P, Showmaker KC, Wang H, Baird SM, Lu SE. The pqqC gene is essential for antifungal activity of Pseudomonas kilonensis JX22 against Fusarium oxysporum f. sp. lycopersici. FEMS Microbiol Lett 2014; 353:98-105. [PMID: 24588744 DOI: 10.1111/1574-6968.12411] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 02/13/2014] [Accepted: 02/25/2014] [Indexed: 11/29/2022] Open
Abstract
Strain JX22, exhibiting a broad range of antimicrobial activities to fungal pathogens, was isolated and classified as representing Pseudomonas kilonensis. In this study, the mutant JX22MT1 was obtained by the EZ-Tn5 transposon mutation and showed no antifungal activity against Fusarium oxysporum f. sp. lycopersici as compared with wild-type strain JX22. The pqqC gene was disrupted in the mutant. Antifungal activity at the wild-type level was restored from the mutant JX22MT1 with the introduction of the functional pqqC gene, which encodes pyrroloquinoline-quinone synthesis protein C. The results suggest that pqqC is essential for antifungal activity of P. kilonensis JX22 against F. oxysporum f. sp. lycopersici.
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Affiliation(s)
- Jianhong Xu
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture/Jiangsu Academy of Agricultural Sciences, Nanjing, China; Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
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Oh SA, Kim JS, Han SH, Park JY, Dimkpa C, Edlund C, Anderson AJ, Kim YC. The GacS-regulated sigma factor RpoS governs production of several factors involved in biocontrol activity of the rhizobacterium Pseudomonas chlororaphis O6. Can J Microbiol 2013; 59:556-62. [DOI: 10.1139/cjm-2013-0062] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Pseudomonas chlororaphis O6 possesses many beneficial traits involved in biocontrol of plant diseases. In this paper, we examined the effect of a mutation in rpoS encoding a stress-related alternative sigma factor to better understand the regulation of these traits. Biochemical studies indicated that production of acyl homoserine lactones was altered and phenazine was increased in the P. chlororaphis O6 rpoS mutant. The rpoS mutation reduced hydrogen cyanide levels, but the rpoS mutant still displayed a level of in vitro antifungal activity against Fusarium graminearum and Alternaria alternata. Tomato root colonization by the rpoS mutant was lower than that by the wild type at 5, 7, and 13 days after inoculation. The rpoS mutant was less effective than the wild type in induction of systemic resistance to two foliar pathogens after root inoculation of the tomato plants. Our findings demonstrate that the stationary-phase sigma factor RpoS regulates production of several key factors involved in the biocontrol potential of P. chlororaphis O6, some independently of the global regulator GacS.
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Affiliation(s)
- Sang A. Oh
- Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, South Korea
| | - Ji Soo Kim
- Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, South Korea
| | - Song Hee Han
- Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, South Korea
| | - Ju Yeon Park
- Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, South Korea
| | | | - Chet Edlund
- Department of Biology, Utah State University, Logan, Utah, USA
| | | | - Young Cheol Kim
- Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, South Korea
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Xie K, Peng H, Hu H, Wang W, Zhang X. OxyR, an important oxidative stress regulator to phenazines production and hydrogen peroxide resistance in Pseudomonas chlororaphis GP72. Microbiol Res 2013; 168:646-53. [PMID: 23778235 DOI: 10.1016/j.micres.2013.05.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 05/19/2013] [Indexed: 12/21/2022]
Abstract
Pseudomonas chlororaphis GP72 is an important plant growth-promoting rhizobacteria (PGPR) with a wide-spectrum antibiotic activity toward several soil-borne pathogens. The adaption of this strain to different environmental oxidative stress and redox phenazine pigment by the predicted regulator OxyR were investigated. The deletion of oxyR led to a significant reduction of the viability, production of three phenazine derivatives and resistance to hydrogen peroxide and paraquat on the KB agar plates. However, the mutant ΔoxyR grew better with shorter delay. In addition, the mutant ΔoxyR showed an increased resistance to hydrogen peroxide, which occurred at the concentration varying from 1.0mM to 5.0mM in the KB broth, as compared with the wild type. In addition, the biofilm formation ability was obviously enhanced and influenced by the different oxidants in the mutant. Quantitative RT-PCR experiments indicated that the expression of katG, ahpC, ahpD and phzE were increased in the oxyR mutant background in response to hydrogen peroxide. katG was mainly responsible for the enhanced resistance to hydrogen peroxide. The loss of oxyR is suggested to benefit the hydrogen peroxide inducible gene expression. Thus, OxyR is an important global regulator that regulates multiple pathways to enhance the survival of P. chlororaphis GP72 exposed to different oxidative stresses.
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Affiliation(s)
- Kan Xie
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
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Fighting Plant Diseases Through the Application of Bacillus and Pseudomonas Strains. SOIL BIOLOGY 2013. [DOI: 10.1007/978-3-642-39317-4_9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Selin C, Fernando WGD, de Kievit T. The PhzI/PhzR quorum-sensing system is required for pyrrolnitrin and phenazine production, and exhibits cross-regulation with RpoS in Pseudomonas chlororaphis PA23. MICROBIOLOGY-SGM 2012; 158:896-907. [PMID: 22262095 DOI: 10.1099/mic.0.054254-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The aim of the current study was to determine how quorum sensing (QS) affects the production of secondary metabolites in Pseudomonas chlororaphis strain PA23. A phzR mutant (PA23phzR) and an N-acylhomoserine lactone (AHL)-deficient strain (PA23-6863) were generated that no longer inhibited the fungal pathogen Sclerotinia sclerotiorum in vitro. Both strains exhibited reduced pyrrolnitrin (PRN), phenazine (PHZ) and protease production. Moreover, phzA-lacZ and prnA-lacZ transcription was significantly reduced in PA23phzR and PA23-6863. As the majority of secondary metabolites are produced at the onset of stationary phase, we investigated whether cross-regulation occurs between QS and RpoS. Analysis of transcriptional fusions revealed that RpoS has a positive and negative effect on phzI and phzR, respectively. In a reciprocal manner, RpoS is positively regulated by QS. Characterization of a phzRrpoS double mutant showed reduced antifungal activity as well as PRN and PHZ production, similar to the QS-deficient strains. Furthermore, phzR but not rpoS was able to complement the phzRrpoS double mutant for the aforementioned traits, indicating that the Phz QS system is a central regulator of PA23-mediated antagonism. Finally, we discovered that QS and RpoS have opposing effects on PA23 biofilm formation. While both QS-deficient strains produced little biofilm, the rpoS mutant showed enhanced biofilm production compared with PA23. Collectively, our findings indicate that QS controls diverse aspects of PA23 physiology, including secondary metabolism, RpoS and biofilm formation. As such, QS is expected to play a crucial role in PA23 biocontrol and persistence in the environment.
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Affiliation(s)
- Carrie Selin
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | | | - Teresa de Kievit
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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