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Quezada-D’Angelo T, San Martín J, Ruiz B, Oyarzúa P, Vargas M, Fischer S, Cortés P, Astete P, Moya-Elizondo E. Use of Pseudomonas protegens to Control Root Rot Disease Caused by Boeremia exigua var. exigua in Industrial Chicory ( Cichorium intybus var. sativum Bisch.). PLANTS (BASEL, SWITZERLAND) 2024; 13:263. [PMID: 38256816 PMCID: PMC10818772 DOI: 10.3390/plants13020263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/16/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024]
Abstract
Boeremia exigua var. exigua is a recurrent pathogen causing root rot in industrial chicory. Currently, there is no chemical or varietal control for this disease, and thus, management strategies need to be developed. This study determined the biocontrol effect of strains of Pseudomonas protegens bacteria with antimicrobial compounds on the fungus B. exigua var. exigua under in vitro, in vivo, and field conditions. In addition, root colonization by these bacteria was estimated by the phlD-specific PCR-based dilution end point assay. Eighteen isolates of Pseudomonas spp were evaluated, and the strains that showed the greatest in vitro inhibition of fungal mycelial growth (mm), Ca10A and ChB7, were selected. Inoculation with the strain ChB7 showed less severity (necrotic area) under in vivo conditions (root trials) compared with the control inoculated with the pathogen (p ≤ 0.05). The molecular analysis revealed that the root colonization of plants grown in pots was equal to or greater than 70%. Similar levels were observed in the field trials conducted at the Selva Negra and Canteras experimental stations (2015-2016 season), with values ranging from 85.7 to 70.5% and from 75.0 to 79.5%, respectively. Regarding yield (ton ha-1), values were higher in the treatments inoculated with strains Ca10A and ChB7 (p ≤ 0.05) at both experimental sites, while a lower incidence and severity of root rot were observed at Selva Negra. These results suggest that the Chilean strains of P. protegens are a promising tool for the control of root diseases in industrial chicory.
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Affiliation(s)
- Tamara Quezada-D’Angelo
- Departamento de Producción Vegetal, Facultad de Agronomía, Universidad de Concepción, Chillán, Chile; (T.Q.-D.); (J.S.M.); (B.R.); (P.O.); (M.V.); (S.F.); (P.C.)
| | - Juan San Martín
- Departamento de Producción Vegetal, Facultad de Agronomía, Universidad de Concepción, Chillán, Chile; (T.Q.-D.); (J.S.M.); (B.R.); (P.O.); (M.V.); (S.F.); (P.C.)
| | - Braulio Ruiz
- Departamento de Producción Vegetal, Facultad de Agronomía, Universidad de Concepción, Chillán, Chile; (T.Q.-D.); (J.S.M.); (B.R.); (P.O.); (M.V.); (S.F.); (P.C.)
| | - Pía Oyarzúa
- Departamento de Producción Vegetal, Facultad de Agronomía, Universidad de Concepción, Chillán, Chile; (T.Q.-D.); (J.S.M.); (B.R.); (P.O.); (M.V.); (S.F.); (P.C.)
| | - Marisol Vargas
- Departamento de Producción Vegetal, Facultad de Agronomía, Universidad de Concepción, Chillán, Chile; (T.Q.-D.); (J.S.M.); (B.R.); (P.O.); (M.V.); (S.F.); (P.C.)
| | - Susana Fischer
- Departamento de Producción Vegetal, Facultad de Agronomía, Universidad de Concepción, Chillán, Chile; (T.Q.-D.); (J.S.M.); (B.R.); (P.O.); (M.V.); (S.F.); (P.C.)
| | - Pamela Cortés
- Departamento de Producción Vegetal, Facultad de Agronomía, Universidad de Concepción, Chillán, Chile; (T.Q.-D.); (J.S.M.); (B.R.); (P.O.); (M.V.); (S.F.); (P.C.)
| | - Patricio Astete
- Departamento de Investigación y Desarrollo, Orafti-Beneo S.A., Pemuco, Chile
| | - Ernesto Moya-Elizondo
- Departamento de Producción Vegetal, Facultad de Agronomía, Universidad de Concepción, Chillán, Chile; (T.Q.-D.); (J.S.M.); (B.R.); (P.O.); (M.V.); (S.F.); (P.C.)
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Lurthy T, Perot S, Gerin‐Eveillard F, Rey M, Wisniewski‐Dyé F, Vacheron J, Prigent‐Combaret C. Inhibition of broomrape germination by 2,4-diacetylphloroglucinol produced by environmental Pseudomonas. Microb Biotechnol 2023; 16:2313-2325. [PMID: 37897154 PMCID: PMC10686154 DOI: 10.1111/1751-7915.14336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 10/29/2023] Open
Abstract
Parasitic weeds such as broomrapes (Phelipanche ramosa and Orobanche cumana) cause severe damage to crops and their development must be controlled. Given that phloroglucinol compounds (PGCs) produced by environmental Pseudomonas could be toxic towards certain plants, we assessed the potential herbicidal effect of the bacterial model Pseudomonas ogarae F113, a PGCs-producing bacterium, on parasitic weed. By combining the use of a mutagenesis approach and of pure PGCs, we evaluated the in vitro effect of PGC-produced by P. ogarae F113 on broomrape germination and assessed the protective activity of a PGC-producing bacteria on oilseed rape (Brassica napus) against P. ramosa in non-sterile soils. We showed that the inhibition of the germination depends on the PGCs molecular structure and their concentrations as well as the broomrape species and pathovars. This inhibition caused by the PGCs is irreversible, causing a brown coloration of the broomrape seeds. The inoculation of PGCs-producing bacteria limited the broomrape infection of P. ramosa, without affecting the host growth. Moreover, elemental profiling analysis of oilseed rape revealed that neither F113 nor applied PGCs affected the nutrition capacity of the oilseed rape host. Our study expands the knowledge on plant-beneficial Pseudomonas as weed biocontrol agents and opens new avenues for the development of natural bioherbicides to enhance crop yield.
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Affiliation(s)
- Tristan Lurthy
- Ecologie MicrobienneUniversité Claude Bernard Lyon1, Université de Lyon, CNRS UMR‐5557, INRAe UMR‐1418, VetAgro SupVilleurbanneFrance
| | - Ségolène Perot
- Ecologie MicrobienneUniversité Claude Bernard Lyon1, Université de Lyon, CNRS UMR‐5557, INRAe UMR‐1418, VetAgro SupVilleurbanneFrance
| | - Florence Gerin‐Eveillard
- Ecologie MicrobienneUniversité Claude Bernard Lyon1, Université de Lyon, CNRS UMR‐5557, INRAe UMR‐1418, VetAgro SupVilleurbanneFrance
| | - Marjolaine Rey
- Ecologie MicrobienneUniversité Claude Bernard Lyon1, Université de Lyon, CNRS UMR‐5557, INRAe UMR‐1418, VetAgro SupVilleurbanneFrance
| | - Florence Wisniewski‐Dyé
- Ecologie MicrobienneUniversité Claude Bernard Lyon1, Université de Lyon, CNRS UMR‐5557, INRAe UMR‐1418, VetAgro SupVilleurbanneFrance
| | - Jordan Vacheron
- Department of Fundamental MicrobiologyUniversity of LausanneLausanneSwitzerland
| | - Claire Prigent‐Combaret
- Ecologie MicrobienneUniversité Claude Bernard Lyon1, Université de Lyon, CNRS UMR‐5557, INRAe UMR‐1418, VetAgro SupVilleurbanneFrance
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3
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Gruet C, Alaoui M, Gerin F, Prigent-Combaret C, Börner A, Muller D, Moënne-Loccoz Y. Genomic content of wheat has a higher influence than plant domestication status on the ability to interact with Pseudomonas plant growth-promoting rhizobacteria. PLANT, CELL & ENVIRONMENT 2023; 46:3933-3948. [PMID: 37614118 DOI: 10.1111/pce.14698] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/10/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023]
Abstract
Plant evolutionary history has had profound effects on belowground traits, which is likely to have impacted the ability to interact with microorganisms, but consequences on root colonization and gene expression by plant growth-promoting rhizobacteria (PGPR) remain poorly understood. Here, we tested the hypothesis that wheat genomic content and domestication are key factors determining the capacity for PGPR interaction. Thus, 331 wheat representatives from eight Triticum or Aegilops species were inoculated under standardized conditions with the generalist PGPR Pseudomonas ogarae F113, using an autofluorescent reporter system for monitoring F113 colonization and expression of phl genes coding for the auxinic inducing signal 2,4-diacetylphloroglucinol. The interaction with P. ogarae F113 was influenced by ploidy level, presence of genomes AA, BB, DD, and domestication. While root colonization was higher for hexaploid and tetraploid species, and phl expression level higher for hexaploid wheat, the diploid Ae. tauschii displayed higher phl induction rate (i.e., expression:colonisation ratio) on roots. However, a better potential of interaction with F113 (i.e., under non-stress gnotobiotic conditions) did not translate, after seed inoculation, into better performance of wheat landraces in non-sterile soil under drought. Overall, results showed that domestication and especially plant genomic content modulate the PGPR interaction potential of wheats.
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Affiliation(s)
- Cécile Gruet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Maroua Alaoui
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Florence Gerin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Claire Prigent-Combaret
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Andreas Börner
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, OT Gatersleben, Germany
| | - Daniel Muller
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
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Cheng L, Tao J, Qu Z, Lu P, Liang T, Meng L, Zhang W, Liu N, Zhang J, Cao P, Jin J. Carbon nanosol-induced assemblage of a plant-beneficial microbiome consortium. J Nanobiotechnology 2023; 21:436. [PMID: 37986003 PMCID: PMC10658824 DOI: 10.1186/s12951-023-02213-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/11/2023] [Indexed: 11/22/2023] Open
Abstract
Carbon nanosol (CNS) is a carbon-based nanomaterial that promotes plant growth; however, its functional mechanisms and effects on the microbiome are not fully understood. Here, we explored the effects of CNS on the relationship between the soil, endophytic microbiomes and plant productivity. CNS treatment increased the fresh biomass of tobacco (Nicotiana tabacum L.) plants by 27.4% ± 9.9%. Amplicon sequencing analysis showed that the CNS treatment significantly affected the composition and diversity of the microbial communities in multiple ecological niches associated with tobacco, especially the bulk soil and stem endophytic microbiome. Furthermore, the application of CNS resulted in enhanced network connectivity and stability of the microbial communities in different niches, particularly in the soil, implying a strengthening of certain microbial interactions. Certain potentially growth-promoting root endophytic bacteria were more abundant under the CNS treatment. In addition, CNS increased the abundance of some endophytic microbial functional genes known to enhance plant growth, such as those associated with nutrient metabolism and the plant hormone biosynthesis pathways. We isolated two bacterial strains (Sphingopyxis sp. and Novosphingobium sp.) that were enriched under CNS treatment, and they were confirmed to promote tobacco plant growth in vitro. These results suggested that CNS might, at least in part, promote plant growth by enriching beneficial bacteria in the microbiome.
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Affiliation(s)
- Lingtong Cheng
- Beijing Life Science Academy, Beijing, 102200, China
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Jiemeng Tao
- Beijing Life Science Academy, Beijing, 102200, China
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Zechao Qu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Peng Lu
- Beijing Life Science Academy, Beijing, 102200, China
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Taibo Liang
- Key Laboratory of Ecological Environment and Tobacco Quality, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Lijun Meng
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Wei Zhang
- China National Tobacco Quality Supervision and Test Center, Zhengzhou, 450003, China
| | - Nan Liu
- China National Tobacco Quality Supervision and Test Center, Zhengzhou, 450003, China
| | - Jianfeng Zhang
- Beijing Life Science Academy, Beijing, 102200, China
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Peijian Cao
- Beijing Life Science Academy, Beijing, 102200, China.
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Jingjing Jin
- Beijing Life Science Academy, Beijing, 102200, China.
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China.
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Valente J, Gerin F, Mini A, Richard R, Le Gouis J, Prigent-Combaret C, Moënne-Loccoz Y. Symbiotic Variations among Wheat Genotypes and Detection of Quantitative Trait Loci for Molecular Interaction with Auxin-Producing Azospirillum PGPR. Microorganisms 2023; 11:1615. [PMID: 37375117 DOI: 10.3390/microorganisms11061615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/13/2023] [Accepted: 06/17/2023] [Indexed: 06/29/2023] Open
Abstract
Crop varieties differ in their ability to interact with Plant Growth-Promoting Rhizobacteria (PGPR), but the genetic basis for these differences is unknown. This issue was addressed with the PGPR Azospirillum baldaniorum Sp245, using 187 wheat accessions. We screened the accessions based on the seedling colonization by the PGPR and the expression of the phenylpyruvate decarboxylase gene ppdC (for synthesis of the auxin indole-3-acetic acid), using gusA fusions. Then, the effects of the PGPR on the selected accessions stimulating Sp245 (or not) were compared in soil under stress. Finally, a genome-wide association approach was implemented to identify the quantitative trait loci (QTL) associated with PGPR interaction. Overall, the ancient genotypes were more effective than the modern genotypes for Azospirillum root colonization and ppdC expression. In non-sterile soil, A. baldaniorum Sp245 improved wheat performance for three of the four PGPR-stimulating genotypes and none of the four non-PGPR-stimulating genotypes. The genome-wide association did not identify any region for root colonization but revealed 22 regions spread on 11 wheat chromosomes for ppdC expression and/or ppdC induction rate. This is the first QTL study focusing on molecular interaction with PGPR bacteria. The molecular markers identified provide the possibility to improve the capacity of modern wheat genotypes to interact with Sp245, as well as, potentially, other Azospirillum strains.
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Affiliation(s)
- Jordan Valente
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 Bd du 11 Novembre 1918, F-69622 Villeurbanne, France
| | - Florence Gerin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 Bd du 11 Novembre 1918, F-69622 Villeurbanne, France
| | - Agathe Mini
- GDEC, INRAE, UCA, F-63000 Clermont-Ferrand, France
| | | | | | - Claire Prigent-Combaret
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 Bd du 11 Novembre 1918, F-69622 Villeurbanne, France
| | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 Bd du 11 Novembre 1918, F-69622 Villeurbanne, France
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6
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Gruet C, Abrouk D, Börner A, Muller D, Moënne-Loccoz Y. Wheat genome architecture influences interactions with phytobeneficial microbial functional groups in the rhizosphere. PLANT, CELL & ENVIRONMENT 2023; 46:1018-1032. [PMID: 36494920 DOI: 10.1111/pce.14508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 11/29/2022] [Accepted: 12/04/2022] [Indexed: 06/17/2023]
Abstract
Wheat has undergone a complex evolutionary history, which led to allopolyploidization and the hexaploid bread wheat Triticum aestivum. However, the significance of wheat genomic architecture for beneficial plant-microbe interactions is poorly understood, especially from a functional standpoint. In this study, we tested the hypothesis that wheat genomic architecture was an overriding factor determining root recruitment of microorganisms with particular plant-beneficial traits. We chose five wheat species representing genomic profiles AA (Triticum urartu), BB {SS} (Aegilops speltoides), DD (Aegilops tauschii), AABB (Triticum dicoccon) and AABBDD (Triticum aestivum) and assessed by quantitative polymerase chain reaction their ability to interact with free-nitrogen fixers, 1-aminocyclopropane-1-carboxylate deaminase producers, 2,4-diacetylphloroglucinol producers and auxin producers via the phenylpyruvate decarboxylase pathway, in combination with Illumina MiSeq metabarcoding analysis of N fixers (and of the total bacterial community). We found that the abundance of the microbial functional groups could fluctuate according to wheat genomic profile, as did the total bacterial abundance. N fixer diversity and total bacterial diversity were also influenced significantly by wheat genomic profile. Often, rather similar results were obtained for genomes DD (Ae. tauschii) and AABBDD (T. aestivum), pointing for the first time that the D genome could be particularly important for wheat-bacteria interactions.
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Affiliation(s)
- Cécile Gruet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Danis Abrouk
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Andreas Börner
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Daniel Muller
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
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Morales Moreira ZP, Chen MY, Yanez Ortuno DL, Haney CH. Engineering plant microbiomes by integrating eco-evolutionary principles into current strategies. CURRENT OPINION IN PLANT BIOLOGY 2023; 71:102316. [PMID: 36442442 DOI: 10.1016/j.pbi.2022.102316] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Engineering plant microbiomes has the potential to improve plant health in a rapid and sustainable way. Rapidly changing climates and relatively long timelines for plant breeding make microbiome engineering an appealing approach to improving food security. However, approaches that have shown promise in the lab have not resulted in wide-scale implementation in the field. Here, we suggest the use of an integrated approach, combining mechanistic molecular and genetic knowledge, with ecological and evolutionary theory, to target knowledge gaps in plant microbiome engineering that may facilitate translatability of approaches into the field. We highlight examples where understanding microbial community ecology is essential for a holistic understanding of the efficacy and consequences of microbiome engineering. We also review examples where understanding plant-microbe evolution could facilitate the design of plants able to recruit specific microbial communities. Finally, we discuss possible trade-offs in plant-microbiome interactions that should be considered during microbiome engineering efforts so as not to introduce off-target negative effects. We include classic and emergent approaches, ranging from microbial inoculants to plant breeding to host-driven microbiome engineering, and address areas that would benefit from multidisciplinary approaches.
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Affiliation(s)
- Zayda P Morales Moreira
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Melissa Y Chen
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Daniela L Yanez Ortuno
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Cara H Haney
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.
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Afridi MS, Ali S, Salam A, César Terra W, Hafeez A, Ali B, S AlTami M, Ameen F, Ercisli S, Marc RA, Medeiros FHV, Karunakaran R. Plant Microbiome Engineering: Hopes or Hypes. BIOLOGY 2022; 11:biology11121782. [PMID: 36552290 PMCID: PMC9774975 DOI: 10.3390/biology11121782] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022]
Abstract
Rhizosphere microbiome is a dynamic and complex zone of microbial communities. This complex plant-associated microbial community, usually regarded as the plant's second genome, plays a crucial role in plant health. It is unquestioned that plant microbiome collectively contributes to plant growth and fitness. It also provides a safeguard from plant pathogens, and induces tolerance in the host against abiotic stressors. The revolution in omics, gene-editing and sequencing tools have somehow led to unravel the compositions and latent interactions between plants and microbes. Similarly, besides standard practices, many biotechnological, (bio)chemical and ecological methods have also been proposed. Such platforms have been solely dedicated to engineer the complex microbiome by untangling the potential barriers, and to achieve better agriculture output. Yet, several limitations, for example, the biological obstacles, abiotic constraints and molecular tools that capably impact plant microbiome engineering and functionality, remained unaddressed problems. In this review, we provide a holistic overview of plant microbiome composition, complexities, and major challenges in plant microbiome engineering. Then, we unearthed all inevitable abiotic factors that serve as bottlenecks by discouraging plant microbiome engineering and functionality. Lastly, by exploring the inherent role of micro/macrofauna, we propose economic and eco-friendly strategies that could be harnessed sustainably and biotechnologically for resilient plant microbiome engineering.
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Affiliation(s)
- Muhammad Siddique Afridi
- Department of Plant Pathology, Federal University of Lavras, (UFLA), Lavras 37200-900, MG, Brazil
| | - Sher Ali
- Department of Food Engineering, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Pirassununga 13635-900, SP, Brazil
| | - Abdul Salam
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Willian César Terra
- Department of Plant Pathology, Federal University of Lavras, (UFLA), Lavras 37200-900, MG, Brazil
| | - Aqsa Hafeez
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Baber Ali
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Mona S AlTami
- Biology Department, College of Science, Qassim University, Burydah 52571, Saudi Arabia
| | - Fuad Ameen
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Sezai Ercisli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, 25240 Erzurum, Turkey
| | - Romina Alina Marc
- Food Engineering Department, Faculty of Food Science and Technology, University of Agricultural Science and Veterinary Medicine Cluj-Napoca, 3-5 Calea Mănă ̧stur Street, 400372 Cluj-Napoca, Romania
| | - Flavio H V Medeiros
- Department of Plant Pathology, Federal University of Lavras, (UFLA), Lavras 37200-900, MG, Brazil
| | - Rohini Karunakaran
- Unit of Biochemistry, Centre of Excellence for Biomaterials Engineering, Faculty of Medicine, AIMST University, Semeling, Bedong 08100, Malaysia
- Department of Computational Biology, Institute of Bioinformatics, Saveetha School of Engineering (SSE), SIMATS, Thandalam, Chennai 602105, Tamil Nadu, India
- Centre of Excellence for Biomaterials Science, AIMST University, Semeling, Bedong 08100, Malaysia
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Dumack K, Feng K, Flues S, Sapp M, Schreiter S, Grosch R, Rose LE, Deng Y, Smalla K, Bonkowski M. What Drives the Assembly of Plant-associated Protist Microbiomes? Investigating the Effects of Crop Species, Soil Type and Bacterial Microbiomes. Protist 2022; 173:125913. [PMID: 36257252 DOI: 10.1016/j.protis.2022.125913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 08/24/2022] [Accepted: 09/22/2022] [Indexed: 12/30/2022]
Abstract
In a field experiment we investigated the influence of the environmental filters soil type (i.e. three contrasting soils) and plant species (i.e. lettuce and potato) identity on rhizosphere community assembly of Cercozoa, a dominant group of mostly bacterivorous soil protists. Plant species (14%) and rhizosphere origin (vs bulk soil) with 13%, together explained four times more variation in cercozoan beta diversity than the three soil types (7% explained variation). Our results clearly confirm the existence of plant species-specific protist communities. Network analyses of bacteria-Cercozoa rhizosphere communities identified scale-free small world topologies, indicating mechanisms of self-organization. While the assembly of rhizosphere bacterial communities is bottom-up controlled through the resource supply from root (secondary) metabolites, our results support the hypothesis that the net effect may depend on the strength of top-down control by protist grazers. Since grazing of protists has a strong impact on the composition and functioning of bacteria communities, protists expand the repertoire of plant genes by functional traits, and should be considered as 'protist microbiomes' in analogy to 'bacterial microbiomes'.
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Affiliation(s)
- Kenneth Dumack
- University of Cologne, Institute of Zoology, Terrestrial Ecology, Zülpicher Str. 47b, 50674 Köln, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Germany.
| | - Kai Feng
- University of Cologne, Institute of Zoology, Terrestrial Ecology, Zülpicher Str. 47b, 50674 Köln, Germany; CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Sebastian Flues
- University of Cologne, Institute of Zoology, Terrestrial Ecology, Zülpicher Str. 47b, 50674 Köln, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Germany
| | - Melanie Sapp
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Population Genetics, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Susanne Schreiter
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany; Helmholtz Centre for Environmental Research GmbH (UFZ), Deptartment Soil System Science, Theodor-Lieser-Str.4, 06120 Halle, Germany
| | - Rita Grosch
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Laura E Rose
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Population Genetics, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Kornelia Smalla
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Michael Bonkowski
- University of Cologne, Institute of Zoology, Terrestrial Ecology, Zülpicher Str. 47b, 50674 Köln, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Germany
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10
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Verma PK, Verma S, Pandey N. Root system architecture in rice: impacts of genes, phytohormones and root microbiota. 3 Biotech 2022; 12:239. [PMID: 36016841 PMCID: PMC9395555 DOI: 10.1007/s13205-022-03299-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 08/01/2022] [Indexed: 11/28/2022] Open
Abstract
To feed the continuously expanding world's population, new crop varieties have been generated, which significantly contribute to the world's food security. However, the growth of these improved plant varieties relies primarily on synthetic fertilizers, which negatively affect the environment and human health; therefore, continuous improvement is needed for sustainable agriculture. Several plants, including cereal crops, have the adaptive capability to combat adverse environmental changes by altering physiological and molecular mechanisms and modifying their root system to improve nutrient uptake efficiency. These plants operate distinct pathways at various developmental stages to optimally establish their root system. These processes include changes in the expression profile of genes, changes in phytohormone level, and microbiome-induced root system architecture (RSA) modification. Several studies have been performed to understand microbial colonization and their involvement in RSA improvement through changes in phytohormone and transcriptomic levels. This review highlights the impact of genes, phytohormones, and particularly root microbiota in influencing RSA and provides new insights resulting from recent studies on rice root as a model system and summarizes the current knowledge about biochemical and central molecular mechanisms.
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Affiliation(s)
- Pankaj Kumar Verma
- Department of Botany, University of Lucknow, Lucknow, India
- Present Address: French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
| | - Shikha Verma
- Present Address: French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
| | - Nalini Pandey
- Department of Botany, University of Lucknow, Lucknow, India
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11
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Mishra J, Mishra I, Arora NK. 2,4-Diacetylphloroglucinol producing Pseudomonas fluorescens JM-1 for management of ear rot disease caused by Fusarium moniliforme in Zea mays L. 3 Biotech 2022; 12:138. [PMID: 35646503 DOI: 10.1007/s13205-022-03201-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 03/05/2022] [Indexed: 11/27/2022] Open
Abstract
Maize (Zea mays L.) is a major cereal crop grown in a large number of countries. Loss in maize yield due to biotic stresses including fungal phytopathogens is a matter of immense concern. Control measures applied for eradication of fungal phytopathogens in maize are not up to the mark and more often involve harsh chemical(s)/pesticide(s) that cause deleterious effects both in humans and soil biota. Greener alternatives, such as the use of rhizosphere microbes in the form of bioinoculants, have proven to be very successful in terms of enhancing crop yield and suppressing fungal phytopathogens. In the present study, fluorescent pseudomonads were isolated from the maize rhizosphere and monitored for their plant growth-promoting (PGP) and biocontrol activities against Fusarium moniliforme. Based on various PGP traits and biocontrol potential, isolate JM-1 was found to be most effective and as per 16S rRNA gene sequencing analysis was identified as Pseudomonas fluorescens. Further experiments showed that the biocontrol potential of JM-1 against ear rot fungus involved the production of antifungal compound 2,4-diacetylphloroglucinol (DAPG). When examined for antagonistic interaction under scanning electron microscopy (SEM), structural abnormality, hyphal lysis, and deformity in fungal mycelium were observed. In the pot experiment, application of talc-based JM-1 containing bioformulation (in pot trials) showed significant enhancement in maize growth parameters (including the seed number and weight) in comparison to control even in presence of the phytopathogen. Ear fresh weight, dry weight, number of seeds per plant, and 100-grain weight were found to increase significantly by 34, 34, 52, and 18% respectively, in comparison to control. P. fluorescens JM-1 can therefore be used as a bioinoculant for ear rot disease control and sustainably enhancing maize yield. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03201-7.
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Affiliation(s)
- Jitendra Mishra
- Department of Environmental Science, School of Earth and Environmental Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, UP 226025 India
| | - Isha Mishra
- Department of Environmental Science, School of Earth and Environmental Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, UP 226025 India
| | - Naveen Kumar Arora
- Department of Environmental Science, School of Earth and Environmental Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, UP 226025 India
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12
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Wheat Metabolite Interferences on Fluorescent Pseudomonas Physiology Modify Wheat Metabolome through an Ecological Feedback. Metabolites 2022; 12:metabo12030236. [PMID: 35323679 PMCID: PMC8955329 DOI: 10.3390/metabo12030236] [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: 02/05/2022] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 11/25/2022] Open
Abstract
Plant roots exude a wide variety of secondary metabolites able to attract and/or control a large diversity of microbial species. In return, among the root microbiota, some bacteria can promote plant development. Among these, Pseudomonas are known to produce a wide diversity of secondary metabolites that could have biological activity on the host plant and other soil microorganisms. We previously showed that wheat can interfere with Pseudomonas secondary metabolism production through its root metabolites. Interestingly, production of Pseudomonas bioactive metabolites, such as phloroglucinol, phenazines, pyrrolnitrin, or acyl homoserine lactones, are modified in the presence of wheat root extracts. A new cross metabolomic approach was then performed to evaluate if wheat metabolic interferences on Pseudomonas secondary metabolites production have consequences on wheat metabolome itself. Two different Pseudomonas strains were conditioned by wheat root extracts from two genotypes, leading to modification of bacterial secondary metabolites production. Bacterial cells were then inoculated on each wheat genotypes. Then, wheat root metabolomes were analyzed by untargeted metabolomic, and metabolites from the Adular genotype were characterized by molecular network. This allows us to evaluate if wheat differently recognizes the bacterial cells that have already been into contact with plants and highlights bioactive metabolites involved in wheat—Pseudomonas interaction.
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13
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Renoud S, Vacheron J, Abrouk D, Prigent-Combaret C, Legendre L, Muller D, Moënne-Loccoz Y. Field Site-Specific Effects of an Azospirillum Seed Inoculant on Key Microbial Functional Groups in the Rhizosphere. Front Microbiol 2022; 12:760512. [PMID: 35154023 PMCID: PMC8825484 DOI: 10.3389/fmicb.2021.760512] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/03/2021] [Indexed: 01/05/2023] Open
Abstract
The beneficial effects of plant growth–promoting Rhizobacteria (PGPR) entail several interaction mechanisms with the plant or with other root-associated microorganisms. These microbial functions are carried out by multiple taxa within functional groups and contribute to rhizosphere functioning. It is likely that the inoculation of additional PGPR cells will modify the ecology of these functional groups. We also hypothesized that the inoculation effects on functional groups are site specific, similarly as the PGPR phytostimulation effects themselves. To test this, we assessed in the rhizosphere of field-grown maize the effect of seed inoculation with the phytostimulatory PGPR Azospirillum lipoferum CRT1 on the size and/or diversity of selected microbial functional groups important for plant growth, using quantitative polymerase chain reaction and/or Illumina MiSeq metabarcoding. The functional groups included bacteria able to fix nitrogen (a key nutrient for plant growth), producers of 1-aminocyclopropane-1-carboxylate (ACC) deaminase (which modulate ethylene metabolism in plant and stimulate root growth), and producers of 2,4-diacetylphloroglucinol (an auxinic signal enhancing root branching). To test the hypothesis that such ecological effects were site-specific, the functional groups were monitored at three different field sites, with four sampling times over two consecutive years. Despite poor inoculant survival, inoculation enhanced maize growth. It also increased the size of functional groups in the three field sites, at the maize six-leaf and flowering stages for diazotrophs and only at flowering stage for ACC deaminase and 2,4-diacetylphloroglucinol producers. Sequencing done in the second year revealed that inoculation modified the composition of diazotrophs (and of the total bacterial community) and to a lesser extent of ACC deaminase producers. This study revealed an ecological impact that was field specific (even though a few taxa were impacted in all fields) and of unexpected magnitude with the phytostimulatory Azospirillum inoculant, when considering microbial functional groups. Further methodological developments are needed to monitor additional functional groups important for soil functioning and plant growth under optimal or stress conditions.
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Affiliation(s)
- Sébastien Renoud
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie Microbienne, Villeurbanne, France
| | - Jordan Vacheron
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie Microbienne, Villeurbanne, France
| | - Danis Abrouk
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie Microbienne, Villeurbanne, France
| | - Claire Prigent-Combaret
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie Microbienne, Villeurbanne, France
| | - Laurent Legendre
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie Microbienne, Villeurbanne, France.,Univ Lyon, Université de St Etienne, St Etienne, France
| | - Daniel Muller
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie Microbienne, Villeurbanne, France
| | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie Microbienne, Villeurbanne, France
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14
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Renoud S, Abrouk D, Prigent-Combaret C, Wisniewski-Dyé F, Legendre L, Moënne-Loccoz Y, Muller D. Effect of Inoculation Level on the Impact of the PGPR Azospirillum lipoferum CRT1 on Selected Microbial Functional Groups in the Rhizosphere of Field Maize. Microorganisms 2022; 10:microorganisms10020325. [PMID: 35208780 PMCID: PMC8877547 DOI: 10.3390/microorganisms10020325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 02/01/2023] Open
Abstract
The impact of inoculated plant growth-promoting rhizobacteria (PGPR) on its host physiology and nutrition depends on inoculum level. Whether the impact of the inoculated PGPR on the indigenous rhizosphere microbiota also varies with the PGPR inoculum level is unclear. Here, we tested this issue using the PGPR Azospirillum lipoferum CRT1—maize model system, where the initial seed inoculation is known to enhance maize growth and germination, and impacts the maize rhizomicrobiota, including microbial functional groups modulating plant growth. A. lipoferum CRT1 was added to the seeds at standard (105–6 cells.seed−1) or reduced (104–5 cells.seed−1) inoculation levels, in three fields. The effect of the two PGPR formulations was assessed on maize growth and on the nifH (nitrogen fixation), acdS (ACC deaminase activity) and phlD (2,4-diacetylphloroglucinol production) microbial functional groups. The size of the three functional groups was monitored by qPCR at the six-leaf stage and the flowering stage, and the diversity of the nifH and acdS functional groups (as well as the bacterial community) were estimated by MiSeq metabarcoding at the six-leaf stage. The results showed that the benefits of the reduced inoculant formulation were significant in two out of three fields, but different (often lower) than those of the standard formulation. The effects of formulations on the size of the three functional groups differed, and depended on field site and functional group. The reduced formulation had an impact on the diversity of nifH and acdS groups at one site, whereas the standard formulation had an impact at the two other sites. Inoculation significantly impacted the total bacterial community in the three fields, but only with the reduced formulation. In conclusion, the reduced inoculant formulation impacted the indigenous rhizosphere microbiota differently, but not less efficiently, than the standard formulation.
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Affiliation(s)
- Sébastien Renoud
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAe, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 Novembre 1918, F-69622 Villeurbanne, France; (S.R.); (D.A.); (C.P.-C.); (F.W.-D.); (L.L.); (Y.M.-L.)
| | - Danis Abrouk
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAe, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 Novembre 1918, F-69622 Villeurbanne, France; (S.R.); (D.A.); (C.P.-C.); (F.W.-D.); (L.L.); (Y.M.-L.)
| | - Claire Prigent-Combaret
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAe, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 Novembre 1918, F-69622 Villeurbanne, France; (S.R.); (D.A.); (C.P.-C.); (F.W.-D.); (L.L.); (Y.M.-L.)
| | - Florence Wisniewski-Dyé
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAe, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 Novembre 1918, F-69622 Villeurbanne, France; (S.R.); (D.A.); (C.P.-C.); (F.W.-D.); (L.L.); (Y.M.-L.)
| | - Laurent Legendre
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAe, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 Novembre 1918, F-69622 Villeurbanne, France; (S.R.); (D.A.); (C.P.-C.); (F.W.-D.); (L.L.); (Y.M.-L.)
- Département de Biologie Biochimie, Univ Lyon, Université Jean Monnet, UFR des Sciences et Techniques, F-42000 Saint-Etienne, France
| | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAe, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 Novembre 1918, F-69622 Villeurbanne, France; (S.R.); (D.A.); (C.P.-C.); (F.W.-D.); (L.L.); (Y.M.-L.)
| | - Daniel Muller
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAe, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 Novembre 1918, F-69622 Villeurbanne, France; (S.R.); (D.A.); (C.P.-C.); (F.W.-D.); (L.L.); (Y.M.-L.)
- Correspondence: ; Tel.: +33-4-72-43-27-14
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15
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Gruet C, Muller D, Moënne-Loccoz Y. Significance of the Diversification of Wheat Species for the Assembly and Functioning of the Root-Associated Microbiome. Front Microbiol 2022; 12:782135. [PMID: 35058901 PMCID: PMC8764353 DOI: 10.3389/fmicb.2021.782135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/30/2021] [Indexed: 12/15/2022] Open
Abstract
Wheat, one of the major crops in the world, has had a complex history that includes genomic hybridizations between Triticum and Aegilops species and several domestication events, which resulted in various wild and domesticated species (especially Triticum aestivum and Triticum durum), many of them still existing today. The large body of information available on wheat-microbe interactions, however, was mostly obtained without considering the importance of wheat evolutionary history and its consequences for wheat microbial ecology. This review addresses our current understanding of the microbiome of wheat root and rhizosphere in light of the information available on pre- and post-domestication wheat history, including differences between wild and domesticated wheats, ancient and modern types of cultivars as well as individual cultivars within a given wheat species. This analysis highlighted two major trends. First, most data deal with the taxonomic diversity rather than the microbial functioning of root-associated wheat microbiota, with so far a bias toward bacteria and mycorrhizal fungi that will progressively attenuate thanks to the inclusion of markers encompassing other micro-eukaryotes and archaea. Second, the comparison of wheat genotypes has mostly focused on the comparison of T. aestivum cultivars, sometimes with little consideration for their particular genetic and physiological traits. It is expected that the development of current sequencing technologies will enable to revisit the diversity of the wheat microbiome. This will provide a renewed opportunity to better understand the significance of wheat evolutionary history, and also to obtain the baseline information needed to develop microbiome-based breeding strategies for sustainable wheat farming.
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Affiliation(s)
| | | | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), VetAgro Sup, UMR 5557 Ecologie Microbienne, Villeurbanne, France
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16
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Nadarajah K, Abdul Rahman NSN. Plant-Microbe Interaction: Aboveground to Belowground, from the Good to the Bad. Int J Mol Sci 2021; 22:ijms221910388. [PMID: 34638728 PMCID: PMC8508622 DOI: 10.3390/ijms221910388] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/14/2021] [Accepted: 09/17/2021] [Indexed: 02/06/2023] Open
Abstract
Soil health and fertility issues are constantly addressed in the agricultural industry. Through the continuous and prolonged use of chemical heavy agricultural systems, most agricultural lands have been impacted, resulting in plateaued or reduced productivity. As such, to invigorate the agricultural industry, we would have to resort to alternative practices that will restore soil health and fertility. Therefore, in recent decades, studies have been directed towards taking a Magellan voyage of the soil rhizosphere region, to identify the diversity, density, and microbial population structure of the soil, and predict possible ways to restore soil health. Microbes that inhabit this region possess niche functions, such as the stimulation or promotion of plant growth, disease suppression, management of toxicity, and the cycling and utilization of nutrients. Therefore, studies should be conducted to identify microbes or groups of organisms that have assigned niche functions. Based on the above, this article reviews the aboveground and below-ground microbiomes, their roles in plant immunity, physiological functions, and challenges and tools available in studying these organisms. The information collected over the years may contribute toward future applications, and in designing sustainable agriculture.
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17
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Bargaz A, Elhaissoufi W, Khourchi S, Benmrid B, Borden KA, Rchiad Z. Benefits of phosphate solubilizing bacteria on belowground crop performance for improved crop acquisition of phosphorus. Microbiol Res 2021; 252:126842. [PMID: 34438221 DOI: 10.1016/j.micres.2021.126842] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/31/2021] [Accepted: 08/04/2021] [Indexed: 10/20/2022]
Abstract
Although research on plant growth promoting bacteria began in the 1950s, basic and applied research on bacteria improving use of phosphorus (P) continues to be a priority among many agricultural research institutions. Ultimately, identifying agriculturally beneficial microbes, notably P solubilizing bacteria (PSB), that enhance the efficient use of P supports more sustainable cropping systems and the judicious use of mineral nutrients. In parallel, there is more attention on improving crop root P acquisition of existing soil P pools as well as by increasing the proportion of fertilizer P that is taken up by crops. Today, new lines of research are emerging to investigate the co-optimization of PSB-fertilizer-crop root processes for improved P efficiency and agricultural performance. In this review, we compile and summarize available findings on the beneficial effects of PSB on crop production with a focus on crop P acquisition via root system responses at the structural, functional and transcriptional levels. We discuss the current state of knowledge on the mechanisms of PSB-mediated P availability, both soil- and root-associated, as well as crop uptake via P solubilization, mineralization and mobilization, mainly through the production of organic acids and P-hydrolyzing enzymes, and effects on phytohormone signaling for crop root developement. The systematic changes caused by PSB on crop roots are discussed and contextualized within promising functional trait-based frameworks. We also detail agronomic profitability of P (mineral and organic) and PSB co-application, in amended soils and inoculated crops, establishing the connection between the influence of PSB on agroecosystem production and the impact of P fertilization on microbial diversity and crop functional traits for P acquisition.
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Affiliation(s)
- Adnane Bargaz
- Mohammed VI Polytechnic University, Agrobiosciences Program, Plant & Soil Microbiome Subprogram, Bengurir, 43150, Morocco.
| | - Wissal Elhaissoufi
- Mohammed VI Polytechnic University, Agrobiosciences Program, Plant & Soil Microbiome Subprogram, Bengurir, 43150, Morocco; Cadi Ayyad University, Faculty of Sciences and Techniques, Biology Dep., Marrakech, Morocco
| | - Said Khourchi
- Mohammed VI Polytechnic University, Agrobiosciences Program, Plant & Soil Microbiome Subprogram, Bengurir, 43150, Morocco; University of Liège, Gembloux Agro-Bio Tech, Liège, Belgium
| | - Bouchra Benmrid
- Mohammed VI Polytechnic University, Agrobiosciences Program, Plant & Soil Microbiome Subprogram, Bengurir, 43150, Morocco
| | - Kira A Borden
- University of British Columbia, Faculty of Land and Food Systems, Vancouver, V6T 1Z4, Canada
| | - Zineb Rchiad
- Mohammed VI Polytechnic University, Agrobiosciences Program, Plant & Soil Microbiome Subprogram, Bengurir, 43150, Morocco
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18
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Rose MM, Scheer D, Hou Y, Hotter VS, Komor AJ, Aiyar P, Scherlach K, Vergara F, Yan Q, Loper JE, Jakob T, van Dam NM, Hertweck C, Mittag M, Sasso S. The bacterium Pseudomonas protegens antagonizes the microalga Chlamydomonas reinhardtii using a blend of toxins. Environ Microbiol 2021; 23:5525-5540. [PMID: 34347373 DOI: 10.1111/1462-2920.15700] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/24/2021] [Accepted: 07/31/2021] [Indexed: 11/27/2022]
Abstract
The unicellular alga Chlamydomonas reinhardtii and the bacterium Pseudomonas protegens serve as a model to study the interactions between photosynthetic and heterotrophic microorganisms. P. protegens secretes the cyclic lipopeptide orfamide A that interferes with cytosolic Ca2+ homeostasis in C. reinhardtii resulting in deflagellation of the algal cells. Here, we studied the roles of additional secondary metabolites secreted by P. protegens using individual compounds and co-cultivation of algae with bacterial mutants. Rhizoxin S2, pyrrolnitrin, pyoluteorin, 2,4-diacetylphloroglucinol (DAPG) and orfamide A all induce changes in cell morphology and inhibit the growth of C. reinhardtii. Rhizoxin S2 exerts the strongest growth inhibition, and its action depends on the spatial structure of the environment (agar versus liquid culture). Algal motility is unaffected by rhizoxin S2 and is most potently inhibited by orfamide A (IC50 = 4.1 μM). Pyrrolnitrin and pyoluteorin both interfere with algal cytosolic Ca2+ homeostasis and motility whereas high concentrations of DAPG immobilize C. reinhardtii without deflagellation or disturbance of Ca2+ homeostasis. Co-cultivation with a regulatory mutant of bacterial secondary metabolism (ΔgacA) promotes algal growth under spatially structured conditions. Our results reveal how a single soil bacterium uses an arsenal of secreted antialgal compounds with complementary and partially overlapping activities.
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Affiliation(s)
- Magdalena M Rose
- Institute of Biology, Leipzig University, Leipzig, Germany.,Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena, Germany
| | - Daniel Scheer
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena, Germany
| | - Yu Hou
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena, Germany
| | - Vivien S Hotter
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena, Germany
| | - Anna J Komor
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Prasad Aiyar
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena, Germany
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Fredd Vergara
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Qing Yan
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana, USA
| | - Joyce E Loper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Torsten Jakob
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Nicole M van Dam
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | - Maria Mittag
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena, Germany
| | - Severin Sasso
- Institute of Biology, Leipzig University, Leipzig, Germany.,Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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19
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Li E, de Jonge R, Liu C, Jiang H, Friman VP, Pieterse CMJ, Bakker PAHM, Jousset A. Rapid evolution of bacterial mutualism in the plant rhizosphere. Nat Commun 2021; 12:3829. [PMID: 34158504 PMCID: PMC8219802 DOI: 10.1038/s41467-021-24005-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 05/24/2021] [Indexed: 02/07/2023] Open
Abstract
While beneficial plant-microbe interactions are common in nature, direct evidence for the evolution of bacterial mutualism is scarce. Here we use experimental evolution to causally show that initially plant-antagonistic Pseudomonas protegens bacteria evolve into mutualists in the rhizosphere of Arabidopsis thaliana within six plant growth cycles (6 months). This evolutionary transition is accompanied with increased mutualist fitness via two mechanisms: (i) improved competitiveness for root exudates and (ii) enhanced tolerance to the plant-secreted antimicrobial scopoletin whose production is regulated by transcription factor MYB72. Crucially, these mutualistic adaptations are coupled with reduced phytotoxicity, enhanced transcription of MYB72 in roots, and a positive effect on plant growth. Genetically, mutualism is associated with diverse mutations in the GacS/GacA two-component regulator system, which confers high fitness benefits only in the presence of plants. Together, our results show that rhizosphere bacteria can rapidly evolve along the parasitism-mutualism continuum at an agriculturally relevant evolutionary timescale.
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Affiliation(s)
- Erqin Li
- grid.5477.10000000120346234Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands ,grid.14095.390000 0000 9116 4836Freie Universität Berlin, Institut für Biologie, Berlin, Germany ,grid.452299.1Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Ronnie de Jonge
- grid.5477.10000000120346234Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands ,grid.11486.3a0000000104788040VIB Center for Plant Systems Biology, Ghent, Belgium ,grid.5342.00000 0001 2069 7798Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
| | - Chen Liu
- grid.5477.10000000120346234Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Henan Jiang
- grid.5477.10000000120346234Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Ville-Petri Friman
- grid.5685.e0000 0004 1936 9668University of York, Department of Biology, York, UK
| | - Corné M. J. Pieterse
- grid.5477.10000000120346234Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Peter A. H. M. Bakker
- grid.5477.10000000120346234Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Alexandre Jousset
- grid.5477.10000000120346234Utrecht University, Department of Biology, Ecology and Biodiversity, Utrecht, The Netherlands
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20
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Li E, de Jonge R, Liu C, Jiang H, Friman VP, Pieterse CMJ, Bakker PAHM, Jousset A. Rapid evolution of bacterial mutualism in the plant rhizosphere. Nat Commun 2021. [PMID: 34158504 DOI: 10.1038/s41467-012-24005-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
While beneficial plant-microbe interactions are common in nature, direct evidence for the evolution of bacterial mutualism is scarce. Here we use experimental evolution to causally show that initially plant-antagonistic Pseudomonas protegens bacteria evolve into mutualists in the rhizosphere of Arabidopsis thaliana within six plant growth cycles (6 months). This evolutionary transition is accompanied with increased mutualist fitness via two mechanisms: (i) improved competitiveness for root exudates and (ii) enhanced tolerance to the plant-secreted antimicrobial scopoletin whose production is regulated by transcription factor MYB72. Crucially, these mutualistic adaptations are coupled with reduced phytotoxicity, enhanced transcription of MYB72 in roots, and a positive effect on plant growth. Genetically, mutualism is associated with diverse mutations in the GacS/GacA two-component regulator system, which confers high fitness benefits only in the presence of plants. Together, our results show that rhizosphere bacteria can rapidly evolve along the parasitism-mutualism continuum at an agriculturally relevant evolutionary timescale.
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Affiliation(s)
- Erqin Li
- Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
- Freie Universität Berlin, Institut für Biologie, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Ronnie de Jonge
- Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium.
| | - Chen Liu
- Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Henan Jiang
- Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | | | - Corné M J Pieterse
- Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Peter A H M Bakker
- Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Alexandre Jousset
- Utrecht University, Department of Biology, Ecology and Biodiversity, Utrecht, The Netherlands.
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21
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Garrido-Sanz D, Redondo-Nieto M, Martin M, Rivilla R. Comparative genomics of the Pseudomonas corrugata subgroup reveals high species diversity and allows the description of Pseudomonas ogarae sp. nov. Microb Genom 2021; 7:000593. [PMID: 34184980 PMCID: PMC8461476 DOI: 10.1099/mgen.0.000593] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/26/2021] [Indexed: 12/29/2022] Open
Abstract
Pseudomonas corrugata constitute one of the phylogenomic subgroups within the Pseudomonas fluorescens species complex and include both plant growth-promoting rhizobacteria (PGPR) and plant pathogenic bacteria. Previous studies suggest that the species diversity of this group remains largely unexplored together with frequent misclassification of strains. Using more than 1800 sequenced Pseudomonas genomes we identified 121 genomes belonging to the P. corrugata subgroup. Intergenomic distances obtained using the genome-to-genome blast distance (GBDP) algorithm and the determination of digital DNA-DNA hybridization values were further used for phylogenomic and clustering analyses, which revealed 29 putative species clusters, of which only five correspond to currently named species within the subgroup. Comparative and functional genome-scale analyses also support the species status of these clusters. The search for PGPR and plant pathogenic determinants showed that approximately half of the genomes analysed could have a pathogenic behaviour based on the presence of a pathogenicity genetic island, while all analysed genomes possess PGPR traits. Finally, this information together with the characterization of phenotypic traits, allows the reclassification proposal of Pseudomonas fluorescens F113 as Pseudomonas ogarae sp. nov., nom rev., type strain F113T (=DSM 112162T=CECT 30235T), which is substantiated by genomic, functional genomics and phenotypic differences with their closest type strains.
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Affiliation(s)
- Daniel Garrido-Sanz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
- Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Miguel Redondo-Nieto
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
| | - Marta Martin
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
| | - Rafael Rivilla
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
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22
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Biessy A, Filion M. Phloroglucinol Derivatives in Plant-Beneficial Pseudomonas spp.: Biosynthesis, Regulation, and Functions. Metabolites 2021; 11:metabo11030182. [PMID: 33804595 PMCID: PMC8003664 DOI: 10.3390/metabo11030182] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/12/2021] [Accepted: 03/17/2021] [Indexed: 11/16/2022] Open
Abstract
Plant-beneficial Pseudomonas spp. aggressively colonize the rhizosphere and produce numerous secondary metabolites, such as 2,4-diacetylphloroglucinol (DAPG). DAPG is a phloroglucinol derivative that contributes to disease suppression, thanks to its broad-spectrum antimicrobial activity. A famous example of this biocontrol activity has been previously described in the context of wheat monoculture where a decline in take-all disease (caused by the ascomycete Gaeumannomyces tritici) has been shown to be associated with rhizosphere colonization by DAPG-producing Pseudomonas spp. In this review, we discuss the biosynthesis and regulation of phloroglucinol derivatives in the genus Pseudomonas, as well as investigate the role played by DAPG-producing Pseudomonas spp. in natural soil suppressiveness. We also tackle the mode of action of phloroglucinol derivatives, which can act as antibiotics, signalling molecules and, in some cases, even as pathogenicity factors. Finally, we discuss the genetic and genomic diversity of DAPG-producing Pseudomonas spp. as well as its importance for improving the biocontrol of plant pathogens.
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23
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Rieusset L, Rey M, Gerin F, Wisniewski-Dyé F, Prigent-Combaret C, Comte G. A Cross-Metabolomic Approach Shows that Wheat Interferes with Fluorescent Pseudomonas Physiology through Its Root Metabolites. Metabolites 2021; 11:84. [PMID: 33572622 PMCID: PMC7911646 DOI: 10.3390/metabo11020084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 12/13/2022] Open
Abstract
Roots contain a wide variety of secondary metabolites. Some of them are exudated in the rhizosphere, where they are able to attract and/or control a large diversity of microbial species. In return, the rhizomicrobiota can promote plant health and development. Some rhizobacteria belonging to the Pseudomonas genus are known to produce a wide diversity of secondary metabolites that can exert a biological activity on the host plant and on other soil microorganisms. Nevertheless, the impact of the host plant on the production of bioactive metabolites by Pseudomonas is still poorly understood. To characterize the impact of plants on the secondary metabolism of Pseudomonas, a cross-metabolomic approach has been developed. Five different fluorescent Pseudomonas strains were thus cultivated in the presence of a low concentration of wheat root extracts recovered from three wheat genotypes. Analysis of our metabolomic workflow revealed that the production of several Pseudomonas secondary metabolites was significantly modulated when bacteria were cultivated with root extracts, including metabolites involved in plant-beneficial properties.
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Affiliation(s)
| | | | | | | | | | - Gilles Comte
- Ecologie Microbienne, Université Claude Bernard Lyon1, Université de Lyon, CNRS UMR-5557, INRAe UMR-1418, VetAgroSup, 43 Boulevard du 11 novembre 1918, 69622 Villeurbanne, France; (L.R.); (M.R.); (F.G.); (F.W.-D.); (C.P.-C.)
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24
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Vishwakarma K, Kumar N, Shandilya C, Mohapatra S, Bhayana S, Varma A. Revisiting Plant-Microbe Interactions and Microbial Consortia Application for Enhancing Sustainable Agriculture: A Review. Front Microbiol 2020; 11:560406. [PMID: 33408698 PMCID: PMC7779480 DOI: 10.3389/fmicb.2020.560406] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 11/23/2020] [Indexed: 12/20/2022] Open
Abstract
The present scenario of agricultural sector is dependent hugely on the use of chemical-based fertilizers and pesticides that impact the nutritional quality, health status, and productivity of the crops. Moreover, continuous release of these chemical inputs causes toxic compounds such as metals to accumulate in the soil and move to the plants with prolonged exposure, which ultimately impact the human health. Hence, it becomes necessary to bring out the alternatives to chemical pesticides/fertilizers for improvement of agricultural outputs. The rhizosphere of plant is an important niche with abundant microorganisms residing in it. They possess the properties of plant growth promotion, disease suppression, removal of toxic compounds, and assimilating nutrients to plants. Utilizing such beneficial microbes for crop productivity presents an efficient way to modulate the crop yield and productivity by maintaining healthy status and quality of the plants through bioformulations. To understand these microbial formulation compositions, it becomes essential to understand the processes going on in the rhizosphere as well as their concrete identification for better utilization of the microbial diversity such as plant growth–promoting bacteria and arbuscular mycorrhizal fungi. Hence, with this background, the present review article highlights the plant microbiome aboveground and belowground, importance of microbial inoculants in various plant species, and their subsequent interactive mechanisms for sustainable agriculture.
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Affiliation(s)
| | - Nitin Kumar
- Department of Biotechnology, Periyar Maniammai Institute of Science and Technology, Thanjavur, India
| | | | - Swati Mohapatra
- Amity Institute of Microbial Technology, Amity University, Noida, India
| | - Sahil Bhayana
- Amity Institute of Microbial Technology, Amity University, Noida, India
| | - Ajit Varma
- Amity Institute of Microbial Technology, Amity University, Noida, India
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25
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Rieusset L, Rey M, Muller D, Vacheron J, Gerin F, Dubost A, Comte G, Prigent-Combaret C. Secondary metabolites from plant-associated Pseudomonas are overproduced in biofilm. Microb Biotechnol 2020; 13:1562-1580. [PMID: 33000552 PMCID: PMC7415375 DOI: 10.1111/1751-7915.13598] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 02/06/2023] Open
Abstract
Plant rhizosphere soil houses complex microbial communities in which microorganisms are often involved in intraspecies as well as interspecies and inter-kingdom signalling networks. Some members of these networks can improve plant health thanks to an important diversity of bioactive secondary metabolites. In this competitive environment, the ability to form biofilms may provide major advantages to microorganisms. With the aim of highlighting the impact of bacterial lifestyle on secondary metabolites production, we performed a metabolomic analysis on four fluorescent Pseudomonas strains cultivated in planktonic and biofilm colony conditions. The untargeted metabolomic analysis led to the detection of hundreds of secondary metabolites in culture extracts. Comparison between biofilm and planktonic conditions showed that bacterial lifestyle is a key factor influencing Pseudomonas metabolome. More than 50% of the detected metabolites were differentially produced according to planktonic or biofilm lifestyles, with the four Pseudomonas strains overproducing several secondary metabolites in biofilm conditions. In parallel, metabolomic analysis associated with genomic prediction and a molecular networking approach enabled us to evaluate the impact of bacterial lifestyle on chemically identified secondary metabolites, more precisely involved in microbial interactions and plant-growth promotion. Notably, this work highlights the major effect of biofilm lifestyle on acyl-homoserine lactone and phenazine production in P. chlororaphis strains.
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Affiliation(s)
- Laura Rieusset
- CNRS UMR-5557, INRAe UMR-1418, Ecologie Microbienne, VetAgroSup, Université de Lyon, Université Claude Bernard Lyon1, 43 Boulevard du 11 novembre 1918, Villeurbanne, 69622, France
| | - Marjolaine Rey
- CNRS UMR-5557, INRAe UMR-1418, Ecologie Microbienne, VetAgroSup, Université de Lyon, Université Claude Bernard Lyon1, 43 Boulevard du 11 novembre 1918, Villeurbanne, 69622, France
| | - Daniel Muller
- CNRS UMR-5557, INRAe UMR-1418, Ecologie Microbienne, VetAgroSup, Université de Lyon, Université Claude Bernard Lyon1, 43 Boulevard du 11 novembre 1918, Villeurbanne, 69622, France
| | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, 1015, Switzerland
| | - Florence Gerin
- CNRS UMR-5557, INRAe UMR-1418, Ecologie Microbienne, VetAgroSup, Université de Lyon, Université Claude Bernard Lyon1, 43 Boulevard du 11 novembre 1918, Villeurbanne, 69622, France
| | - Audrey Dubost
- CNRS UMR-5557, INRAe UMR-1418, Ecologie Microbienne, VetAgroSup, Université de Lyon, Université Claude Bernard Lyon1, 43 Boulevard du 11 novembre 1918, Villeurbanne, 69622, France
| | - Gilles Comte
- CNRS UMR-5557, INRAe UMR-1418, Ecologie Microbienne, VetAgroSup, Université de Lyon, Université Claude Bernard Lyon1, 43 Boulevard du 11 novembre 1918, Villeurbanne, 69622, France
| | - Claire Prigent-Combaret
- CNRS UMR-5557, INRAe UMR-1418, Ecologie Microbienne, VetAgroSup, Université de Lyon, Université Claude Bernard Lyon1, 43 Boulevard du 11 novembre 1918, Villeurbanne, 69622, France
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26
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Chae DH, Kim DR, Cho G, Moon S, Kwak YS. Genome-Wide Investigation of 2,4-Diacetylphloroglucinol Protection Genes in Arabidopsis thaliana. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:1072-1079. [PMID: 32370644 DOI: 10.1094/mpmi-04-20-0084-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The compound 2,4-diacetylphloroglucinol (DAPG) is a well-known secondary metabolite produced by Pseudomonas spp. that are used as biocontrol agents. DAPG displays a remarkably broad spectrum of toxic activity against pathogens of plants. Yet high concentrations of DAPG may also have negative effect on plants, but the phytotoxicity of DAPG is not clearly understood. Here, we used genome-wide activation, tagging Arabidopsis plants as the model plant to investigate the plant response to DAPG. A total of 15 lines were selected as DAPG-tolerant plants from among 62,000 lines investigated. The DAPG-responsible genes were then identified via thermal asymmetric interlaced PCR and quantitative reverse transcription PCR, and the gene ontology analysis showed the distribution of these genes having different biological processes, cellular regulations, and molecular functional properties. Collectively, these findings suggest that plants may rely on several pathways to prevent DAPG phytotoxicity.
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Affiliation(s)
- Dae-Han Chae
- Division of Applied Life Science (BK21Plus), Gyeongsang National University, Jinju 52828, Korea
| | - Da-Ran Kim
- Department of Plant Medicine, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Gyeongjun Cho
- Division of Applied Life Science (BK21Plus), Gyeongsang National University, Jinju 52828, Korea
| | - Suhyeon Moon
- Department of Plant Medicine, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Youn-Sig Kwak
- Division of Applied Life Science (BK21Plus), Gyeongsang National University, Jinju 52828, Korea
- Department of Plant Medicine, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Korea
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27
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Chae DH, Kim DR, Cheong MS, Lee YB, Kwak YS. Investigating the Induced Systemic Resistance Mechanism of 2,4-Diacetylphloroglucinol (DAPG) using DAPG Hydrolase-Transgenic Arabidopsis. THE PLANT PATHOLOGY JOURNAL 2020; 36:255-266. [PMID: 32547341 PMCID: PMC7272852 DOI: 10.5423/ppj.oa.02.2020.0031] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/09/2020] [Accepted: 03/06/2020] [Indexed: 05/29/2023]
Abstract
Plant immune responses can be triggered by chemicals, microbes, pathogens, insects, or abiotic stresses. In particular, induced systemic resistance (ISR) refers to the activation of the immune system due to a plant's interaction with beneficial microorganisms. The phenolic compound, 2,4-diacetylphloroglucinol (DAPG), which is produced by beneficial Pseudomonas spp., acts as an ISR elicitor, yet DAPG's mechanism in ISR remains unclear. In this study, transgenic Arabidopsis thaliana plants overexpressing the DAPG hydrolase gene (phlG) were generated to investigate the functioning of DAPG in ISR. DAPG was applied onto 3-week-old A. thaliana Col-0 and these primed plants showed resistance to the pathogens Botrytis cinerea and Pseudomonas syringae pv. tomato DC3000. However, in the phlG transgenic A. thaliana, the ISR was not triggered against these pathogens. The DAPG-mediated ISR phenotype was impaired in transgenic A. thaliana plants overexpressing phlG, thus showing similar disease severity when compared to untreated control plants. Furthermore, the DAPG-treated A. thaliana Col-0 showed an increase in their gene expression levels of PDF1.2 and WRKY70 but this failed to occur in the phlG transgenic lines. Collectively, these experimental results indicate that jasmonic acid/ethylene signal-based defense system is effectively disabled in phlG transgenic A. thaliana lines.
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Affiliation(s)
- Dae-Han Chae
- Division of Applied Life Science (BK21Plus) and Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Da-Ran Kim
- Department of Plant Medicine, Gyeongsang National University, Jinju 52828, Korea
| | - Mi Sun Cheong
- Division of Applied Life Science (BK21Plus) and Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Yong Bok Lee
- Division of Applied Life Science (BK21Plus) and Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Youn-Sig Kwak
- Division of Applied Life Science (BK21Plus) and Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Korea
- Department of Plant Medicine, Gyeongsang National University, Jinju 52828, Korea
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28
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Bukhat S, Imran A, Javaid S, Shahid M, Majeed A, Naqqash T. Communication of plants with microbial world: Exploring the regulatory networks for PGPR mediated defense signaling. Microbiol Res 2020; 238:126486. [PMID: 32464574 DOI: 10.1016/j.micres.2020.126486] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/20/2020] [Accepted: 03/28/2020] [Indexed: 02/01/2023]
Abstract
Agricultural manipulation of potentially beneficial rhizosphere microbes is increasing rapidly due to their multi-functional plant-protective and growth related benefits. Plant growth promoting rhizobacteria (PGPR) are mostly non-pathogenic microbes which exert direct benefits on plants while there are rhizosphere bacteria which indirectly help plant by ameliorating the biotic and/or abiotic stress or induction of defense response in plant. Regulation of these direct or indirect effect takes place via highly specialized communication system induced at multiple levels of interaction i.e., inter-species, intra-species, and inter-kingdom. Studies have provided insights into the functioning of signaling molecules involved in communication and induction of defense responses. Activation of host immune responses upon bacterial infection or rhizobacteria perception requires comprehensive and precise gene expression reprogramming and communication between hosts and microbes. Majority of studies have focused on signaling of host pattern recognition receptors (PRR) and nod-like receptor (NLR) and microbial effector proteins under mining the role of other components such as mitogen activated protein kinase (MAPK), microRNA, histone deacytylases. The later ones are important regulators of gene expression reprogramming in plant immune responses, pathogen virulence and communications in plant-microbe interactions. During the past decade, inoculation of PGPR has emerged as potential strategy to induce biotic and abiotic stress tolerance in plants; hence, it is imperative to expose the basis of these interactions. This review discusses microbes and plants derived signaling molecules for their communication, regulatory and signaling networks of PGPR and their different products that are involved in inducing resistance and tolerance in plants against environmental stresses and the effect of defense signaling on root microbiome. We expect that it will lead to the development and exploitation of beneficial microbes as source of crop biofertilizers in climate changing scenario enabling more sustainable agriculture.
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Affiliation(s)
- Sherien Bukhat
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, 60800 Multan, Pakistan.
| | - Asma Imran
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Jhang Road, Faisalabad, Pakistan.
| | - Shaista Javaid
- Institute of Molecular Biology and Biotechnology, University of Lahore Main Campus, Defense road, Lahore, Pakistan.
| | - Muhammad Shahid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad 38000, Pakistan.
| | - Afshan Majeed
- Department of Soil and Environmental Sciences, The University of Poonch, Rawalakot, Azad Jammu and Kashmir, Pakistan.
| | - Tahir Naqqash
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, 60800 Multan, Pakistan.
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29
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Yang M, Mavrodi DV, Mavrodi OV, Thomashow LS, Weller DM. Exploring the Pathogenicity of Pseudomonas brassicacearum Q8r1-96 and Other Strains of the Pseudomonas fluorescens Complex on Tomato. PLANT DISEASE 2020; 104:1026-1031. [PMID: 31994984 PMCID: PMC7163159 DOI: 10.1094/pdis-09-19-1989-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Pseudomonas brassicacearum and related species of the P. fluorescens complex have long been studied as biocontrol and growth-promoting rhizobacteria involved in suppression of soilborne pathogens. We report here that P. brassicacearum Q8r1-96 and other 2,4-diacetylphloroglucinol (DAPG)-producing fluorescent pseudomonads involved in take-all decline of wheat in the Pacific Northwest of the United States can also be pathogenic to other plant hosts. Strain Q8r1-96 caused necrosis when injected into tomato stems and immature tomato fruits, either attached or removed from the plant, but lesion development was dose dependent, with a minimum of 106 CFU ml-1 required to cause visible tissue damage. We explored the relative contribution of several known plant-microbe interaction traits to the pathogenicity of strain Q8r1-96. Type III secretion system (T3SS) mutants of Q8r1-96, injected at a concentration of 108 CFU ml-1, were significantly less virulent, but not consistently, as compared with the wild-type strain. However, a DAPG-deficient phlD mutant of Q8r1-96 was significantly and consistently less virulent as compared with the wild type. Strain Q8r1-96acc, engineered to over express ACC deaminase, caused a similar amount of necrosis as the wild type. Cell-free culture filtrates of strain Q8r1-96 and pure DAPG also cause necrosis in tomato fruits. Our results suggest that DAPG plays a significant role in the ability of Q8r1-96 to cause necrosis of tomato tissue, but other factors also contribute to the pathogenic properties of this organism.
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Affiliation(s)
- Mingming Yang
- Corresponding authors: Mingming Yang: ; David M. Weller:
| | - Dmitri V. Mavrodi
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Olga V. Mavrodi
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Linda S. Thomashow
- U. S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA 99164-6430, USA
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30
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Chu TN, Bui LV, Hoang MTT. Pseudomonas PS01 Isolated from Maize Rhizosphere Alters Root System Architecture and Promotes Plant Growth. Microorganisms 2020; 8:E471. [PMID: 32224990 PMCID: PMC7232511 DOI: 10.3390/microorganisms8040471] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/14/2020] [Accepted: 03/23/2020] [Indexed: 01/09/2023] Open
Abstract
The objectives of this study were to evaluate the plant growth promoting effects on Arabidopsis by Pseudomonas sp. strains associated with rhizosphere of crop plants grown in Mekong Delta, Vietnam. Out of all the screened isolates, Pseudomonas PS01 isolated from maize rhizosphere showed the most prominent plant growth promoting effects on Arabidopsis and maize (Zea mays). We also found that PS01 altered root system architecture (RSA). The full genome of PS01 was resolved using high-throughput sequencing. Phylogenetic analysis identified PS01 as a member of the Pseudomonas putida subclade, which is closely related to Pseudomonas taiwanensis.. PS01 genome size is 5.3 Mb, assembled in 71 scaffolds comprising of 4820 putative coding sequence. PS01 encodes genes for the indole-3-acetic acid (IAA), acetoin and 2,3-butanediol biosynthesis pathways. PS01 promoted the growth of Arabidopsis and altered the root system architecture by inhibiting primary root elongation and promoting lateral root and root hair formation. By employing gene expression analysis, genetic screening and pharmacological approaches, we suggested that the plant-growth promoting effects of PS01 and the alteration of RSA might be independent of bacterial auxin and could be caused by a combination of different diffusible compounds and volatile organic compounds (VOCs). Taken together, our results suggest that PS01 is a potential candidate to be used as bio-fertilizer agent for enhancing plant growth.
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Affiliation(s)
- Thanh Nguyen Chu
- Faculty of Biology and Biotechnology, University of Science-Ho Chi Minh City, Ho Chi Minh City 700000, Vietnam;
- Laboratory of Molecular Biotechnology, Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Le Van Bui
- Faculty of Biology and Biotechnology, University of Science-Ho Chi Minh City, Ho Chi Minh City 700000, Vietnam;
- Laboratory of Molecular Biotechnology, Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Minh Thi Thanh Hoang
- Faculty of Biology and Biotechnology, University of Science-Ho Chi Minh City, Ho Chi Minh City 700000, Vietnam;
- Laboratory of Molecular Biotechnology, Vietnam National University, Ho Chi Minh City 700000, Vietnam
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Valente J, Gerin F, Le Gouis J, Moënne-Loccoz Y, Prigent-Combaret C. Ancient wheat varieties have a higher ability to interact with plant growth-promoting rhizobacteria. PLANT, CELL & ENVIRONMENT 2020; 43:246-260. [PMID: 31509886 DOI: 10.1111/pce.13652] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 05/27/2023]
Abstract
Plant interactions with plant growth-promoting rhizobacteria (PGPR) are highly dependent on plant genotype. Modern plant breeding has largely sought to improve crop performance but with little focus on the optimization of plant × PGPR interactions. The interactions of the model PGPR strain Pseudomonas kilonensis F113 were therefore compared in 199 ancient and modern wheat genotypes. A reporter system, in which F113 colonization and expression of 2,4-diacetylphloroglucinol biosynthetic genes (phl) were measured on roots was used to quantify F113 × wheat interactions under gnotobiotic conditions. Thereafter, eight wheat accessions that differed in their ability to interact with F113 were inoculated with F113 and grown in greenhouse in the absence or presence of stress. F113 colonization was linked to improved stress tolerance. Moreover, F113 colonization and phl expression were higher overall on ancient genotypes than modern genotypes. F113 colonization improved wheat performance in the four genotypes that showed the highest level of phl expression compared with the four genotypes in which phl expression was lowest. Taken together, these data suggest that recent wheat breeding strategies have had a negative impact on the ability of the plants to interact with PGPR.
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Affiliation(s)
- Jordan Valente
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Florence Gerin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, F-69622 Villeurbanne, France
| | | | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Claire Prigent-Combaret
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, F-69622 Villeurbanne, France
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Lucke M, Correa MG, Levy A. The Role of Secretion Systems, Effectors, and Secondary Metabolites of Beneficial Rhizobacteria in Interactions With Plants and Microbes. FRONTIERS IN PLANT SCIENCE 2020; 11:589416. [PMID: 33240304 PMCID: PMC7680756 DOI: 10.3389/fpls.2020.589416] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/14/2020] [Indexed: 05/05/2023]
Abstract
Beneficial rhizobacteria dwell in plant roots and promote plant growth, development, and resistance to various stress types. In recent years there have been large-scale efforts to culture root-associated bacteria and sequence their genomes to uncover novel beneficial microbes. However, only a few strains of rhizobacteria from the large pool of soil microbes have been studied at the molecular level. This review focuses on the molecular basis underlying the phenotypes of three beneficial microbe groups; (1) plant-growth promoting rhizobacteria (PGPR), (2) root nodulating bacteria (RNB), and (3) biocontrol agents (BCAs). We focus on bacterial proteins and secondary metabolites that mediate known phenotypes within and around plants, and the mechanisms used to secrete these. We highlight the necessity for a better understanding of bacterial genes responsible for beneficial plant traits, which can be used for targeted gene-centered and molecule-centered discovery and deployment of novel beneficial rhizobacteria.
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Cupriavidus sp. HN-2, a Novel Quorum Quenching Bacterial Isolate, is a Potent Biocontrol Agent Against Xanthomonas campestris pv. campestris. Microorganisms 2019; 8:microorganisms8010045. [PMID: 31881662 PMCID: PMC7022395 DOI: 10.3390/microorganisms8010045] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 12/21/2019] [Accepted: 12/22/2019] [Indexed: 11/17/2022] Open
Abstract
Diffusible signal factor (DSF) represents a family of widely conserved quorum sensing (QS) signals involved in the regulation of virulence factor production in many Gram-negative bacterial pathogens. Quorum quenching, which disrupts QS either by degradation of QS signals or interference of signal generation or perception, is a promising strategy for prevention and control of QS-mediated bacterial infections. In this study, a novel DSF-degrading strain, HN-2, was isolated from contaminated soil and identified as Cupriavidus sp. The isolate exhibited superior DSF degradation activity and completely degraded 2 mmol·L–1 of DSF within 24 h. Analysis of the degradation products of DSF by gas chromatography–mass spectrometry led to the identification of trans-2-decenoic acid methyl ester as the main intermediate product, suggesting that DSF could be degraded by oxidation and hydroxylation. Moreover, this study presents for the first time, evidence that Cupriavidus sp. can reduce the black rot disease caused by Xanthomonas campestris pv. campestris (Xcc). Application of the HN-2 strain as a biocontrol agent could substantially reduce the disease severity. These findings reveal the biochemical basis of a highly efficient DSF-degrading bacterial isolate and present a useful agent for controlling infectious diseases caused by DSF-dependent bacterial pathogens.
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Silencing of Phytopathogen Communication by the Halotolerant PGPR Staphylococcus equorum Strain EN21. Microorganisms 2019; 8:microorganisms8010042. [PMID: 31878301 PMCID: PMC7022284 DOI: 10.3390/microorganisms8010042] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 12/20/2019] [Accepted: 12/22/2019] [Indexed: 12/16/2022] Open
Abstract
Increasing world food demand together with soil erosion and indiscriminate use of chemical fertilization highlight the need to adopt sustainable crop production strategies. In this context, a combination of plant growth-promoting rhizobacteria (PGPR) and pathogen management represents a sustainable and efficient alternative. Though little studied, halophilic and halotolerant PGPR could be a beneficial plant growth promotion strategy for saline and non-saline soils. The virulence of many bacterial phytopathogens is regulated by quorum sensing (QS) systems. Quorum quenching (QQ) involves the enzymatic degradation of phytopathogen-generated signal molecules, mainly N-acyl homoserine lactones (AHLs). In this study, we investigate plant growth-promoting (PGP) activity and the capacity of the halotolerant bacterium Staphylococcus equorum strain EN21 to attenuate phytopathogens virulence through QQ. We used biopriming and in vivo tomato plant experiments to analyse the PGP activity of strain EN21. AHL inactivation was observed to reduce Pseudomonas syringae pv. tomato infections in tomato and Arabidopsis plants. Our study of Dickeya solani, Pectobacterium carotovorum subsp. carotovorum and Erwinia amylovora bacteria in potato tubers, carrots and pears, respectively, also demonstrated the effectiveness of QS interruption by EN21. Overall, this study highlights the potential of strain S. equorum EN21 in plant growth promotion and QQ-driven bacterial phytopathogen biocontrol.
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Kępczyńska E, Karczyński P. Medicago truncatula root developmental changes by growth-promoting microbes isolated from Fabaceae, growing on organic farms, involve cell cycle changes and WOX5 gene expression. PLANTA 2019; 251:25. [PMID: 31784832 DOI: 10.1007/s00425-019-03300-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 10/11/2019] [Indexed: 06/10/2023]
Abstract
Both root nodules and the rhizosphere of Fabaceae plants grown on organic farms are a rich source of bacteria, mainly from the families Enterobacteriaceae and Pseudomonadaceae. The enhanced root system growth in M. truncatula after inoculation with selected bacteria includes an increase of nuclei in the cell cycle S phase and a reduction in phase G2 as well as an enhanced expression of the WOX5 gene. Synthetic fertilizers and pesticides are commonly used to improve plant quality and health. However, it is necessary to look for other efficient and also environmentally safe methods. One such method involves the use of bacteria known as plant growth-promoting bacteria (PGPB). Seventy-two bacterial isolates from the rhizospheric soil and root nodule samples of legumes, including bean, alfalfa, lupine and barrel medic, grown on an organic farm in Western Pomerania (Poland) were screened for their growth-promoting capacities and 38 selected isolates were identified based on 16S rRNA gene sequencing. The analysis showed the isolates to represent 17 strains assigned to 6 families: Enterobacteriaceae, Pseudomonadaceae, Xanthomonadaceae, Rhizobiaceae, Bacillaceae and Alcaligenaceae. Pot experiments showed that 13 strains, capable of producing indole compounds from tryptophan in vitro, could significantly enhance the root and shoot weight of 10-week-old Medicago truncatula seedlings. Compared to non-inoculated seedlings, the root system of inoculated ones was more branched; in addition, the root length, surface area and, especially, the root volume were higher. The 24-h root inoculation with the three selected strains increased the nuclei population in the G1 and S phases, decreased it in the G2 phase and enhanced the WUSCHEL-related Homeobox5 (WOX5) gene expression in root tips and lateral zones. The "arrest" of nuclei in the S phase and the enhancement of the WOX5 gene expression were observed to gradually disappear once the bacterial suspension was rinsed off the seedling roots and the roots were transferred to water for further growth. This study shows that the nodules and rhizosphere of legumes grown on organic farms are a rich source of different PGPB species and provides new data on the ability of these bacteria to interfere with cell cycle and gene expression during the root development.
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Affiliation(s)
- Ewa Kępczyńska
- Department of Plant Biotechnology, Faculty of Biology, University of Szczecin, Wąska 13, 71-413, Szczecin, Poland.
| | - Piotr Karczyński
- Department of Plant Biotechnology, Faculty of Biology, University of Szczecin, Wąska 13, 71-413, Szczecin, Poland
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Huang P, Xu J, Kloepper JW. Plant-microbe-soil fertility interaction impacts performance of a Bacillus-containing bioproduct on bell pepper. J Basic Microbiol 2019; 60:27-36. [PMID: 31617947 DOI: 10.1002/jobm.201900435] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/10/2019] [Accepted: 09/21/2019] [Indexed: 01/01/2023]
Abstract
Limited information is available on the performance of plant growth-promoting inoculants or bioproducts under different soil nutritional or fertility conditions. Consequently, the objective of this study was to evaluate the effects of a commercially available Bacillus-containing bioproduct, Microlife Abundance, at concentrations of 5.5 and 6.5 log cfu/ml on early growth, fertilizer use-efficiency, and fruit yield of bell pepper (Capsicum annuum L.) under two different soil fertility conditions (25% and 100% recommended N rates). Two pot experiments were conducted with bell pepper: (a) a 4-week-long early growth test with inoculant treatments applied once at transplanting; and (b) a 13-week-long yield test with inoculant treatments applied at transplanting and again at first blossom-set. Results from the early growth test indicated that at both N fertilization levels, applying Abundance once at transplanting at 6.5 log cfu/ml rather than 5.5 log cfu/ml significantly increased root dry weight, total root length, root volume, root surface area, and total length of very fine roots compared with the noninoculated control by 20%, 13%, 17%, 15%, and 12%, respectively. In contrast to the early growth, results from the yield test showed that only at the 100% recommended N rate, applying Abundance twice at both concentrations significantly enhanced N fertilizer use-efficiency and marketable yield of bell pepper over the noninoculated control by 34% (5.5 log cfu/ml) and 30% (6.5 log cfu/ml). Therefore, the efficacy of the Bacillus-containing bioproduct Abundance in enhancing fertilizer use-efficiency and marketable yield of bell pepper varied between soil nutritional conditions, but the early growth promotion effect of Abundance did not. Our results also demonstrate that selected microbial-based bioproducts, like Abundance, can be compatible with chemical fertilizers to enhance fertilizer use-efficiency and crop yields, but cannot be used as complete substitutes for chemical fertilizers.
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Affiliation(s)
- Ping Huang
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama
| | - Jia Xu
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama
| | - Joseph W Kloepper
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama
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Gao Z, Karlsson I, Geisen S, Kowalchuk G, Jousset A. Protists: Puppet Masters of the Rhizosphere Microbiome. TRENDS IN PLANT SCIENCE 2019; 24:165-176. [PMID: 30446306 DOI: 10.1016/j.tplants.2018.10.011] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 10/15/2018] [Accepted: 10/18/2018] [Indexed: 05/18/2023]
Abstract
The rhizosphere microbiome is a central determinant of plant performance. Microbiome assembly has traditionally been investigated from a bottom-up perspective, assessing how resources such as root exudates drive microbiome assembly. However, the importance of predation as a driver of microbiome structure has to date largely remained overlooked. Here we review the importance of protists, a paraphyletic group of unicellular eukaryotes, as a key regulator of microbiome assembly. Protists can promote plant-beneficial functions within the microbiome, accelerate nutrient cycling, and remove pathogens. We conclude that protists form an essential component of the rhizosphere microbiome and that accounting for predator-prey interactions would greatly improve our ability to predict and manage microbiome function at the service of plant growth and health.
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Affiliation(s)
- Zhilei Gao
- Institute of Environmental Biology, Ecology & Biodiversity, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; These authors contributed equally
| | - Ida Karlsson
- Institute of Environmental Biology, Ecology & Biodiversity, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Dept. of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 75007 Uppsala, Sweden; These authors contributed equally
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands
| | - George Kowalchuk
- Institute of Environmental Biology, Ecology & Biodiversity, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Alexandre Jousset
- Institute of Environmental Biology, Ecology & Biodiversity, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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Yang M, Mavrodi DV, Thomashow LS, Weller DM. Differential Response of Wheat Cultivars to Pseudomonas brassicacearum and Take-All Decline Soil. PHYTOPATHOLOGY 2018; 108:1363-1372. [PMID: 29905506 PMCID: PMC6483097 DOI: 10.1094/phyto-01-18-0024-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
2,4-Diacetylphloroglucinol (DAPG)-producing Pseudomonas spp. in the P. fluorescens complex are primarily responsible for a natural suppression of take-all of wheat known as take-all decline (TAD) in many fields in the United States. P. brassicacearum, the most common DAPG producer found in TAD soils in the Pacific Northwest (PNW) of the United States, has biological control, growth promoting and phytotoxic activities. In this study, we explored how the wheat cultivar affects the level of take-all suppression when grown in a TAD soil, and how cultivars respond to colonization by P. brassicacearum. Three cultivars (Tara, Finley, and Buchanan) supported similar rhizosphere population sizes of P. brassicacearum when grown in a TAD soil, however they developed significantly different amounts of take-all. Cultivars Tara and Buchanan developed the least and most take-all, respectively, and Finley showed an intermediate amount of disease. However, when grown in TAD soil that was pasteurized to eliminate both DAPG producers and take-all suppression, all three cultivars were equally susceptible to take-all. The three cultivars also responded differently to the colonization and phytotoxicity of P. brassicacearum strains Q8r1-96 and L5.1-96, which are characteristic of DAPG producers in PNW TAD soils. Compared with cultivar Tara, cultivar Buchanan showed significantly reduced seedling emergence and root growth when colonized by P. brassicacearum, and the response of Finley was intermediate. However, all cultivars emerged equally when treated with a DAPG-deficient mutant of Q8r1-96. Our results indicate that wheat cultivars grown in a TAD soil modulate both the robustness of take-all suppression and the potential phytotoxicity of the antibiotic DAPG.
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Affiliation(s)
| | - Dmitri V. Mavrodi
- Department of Cell and Molecular Biology, The University of Southern Mississippi, Hattiesburg 39406
| | - Linda S. Thomashow
- U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA 99164-6430
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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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Besset-Manzoni Y, Rieusset L, Joly P, Comte G, Prigent-Combaret C. Exploiting rhizosphere microbial cooperation for developing sustainable agriculture strategies. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:29953-29970. [PMID: 29313197 DOI: 10.1007/s11356-017-1152-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 12/26/2017] [Indexed: 05/23/2023]
Abstract
The rhizosphere hosts a considerable microbial community. Among that community, bacteria called plant growth-promoting rhizobacteria (PGPR) can promote plant growth and defense against diseases using diverse distinct plant-beneficial functions. Crop inoculation with PGPR could allow to reduce the use of pesticides and fertilizers in agrosystems. However, microbial crop protection and growth stimulation would be more efficient if cooperation between rhizosphere bacterial populations was taken into account when developing biocontrol agents and biostimulants. Rhizospheric bacteria live in multi-species biofilms formed all along the root surface or sometimes inside the plants (i.e., endophyte). PGPR cooperate with their host plants and also with other microbial populations inside biofilms. These interactions are mediated by a large diversity of microbial metabolites and physical signals that trigger cell-cell communication and appropriate responses. A better understanding of bacterial behavior and microbial cooperation in the rhizosphere could allow for a more successful use of bacteria in sustainable agriculture. This review presents an ecological view of microbial cooperation in agrosystems and lays the emphasis on the main microbial metabolites involved in microbial cooperation, plant health protection, and plant growth stimulation. Eco-friendly inoculant consortia that will foster microbe-microbe and microbe-plant cooperation can be developed to promote crop growth and restore biodiversity and functions lost in agrosystems.
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Affiliation(s)
- Yoann Besset-Manzoni
- UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, 43 bd du 11 Novembre 1918, F-69622, Villeurbanne cedex, France
- Biovitis, 15 400, Saint Etienne-de-Chomeil, France
| | - Laura Rieusset
- UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, 43 bd du 11 Novembre 1918, F-69622, Villeurbanne cedex, France
| | - Pierre Joly
- Biovitis, 15 400, Saint Etienne-de-Chomeil, France
| | - Gilles Comte
- UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, 43 bd du 11 Novembre 1918, F-69622, Villeurbanne cedex, France
| | - Claire Prigent-Combaret
- UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, 43 bd du 11 Novembre 1918, F-69622, Villeurbanne cedex, France.
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Vacheron J, Desbrosses G, Renoud S, Padilla R, Walker V, Muller D, Prigent-Combaret C. Differential Contribution of Plant-Beneficial Functions from Pseudomonas kilonensis F113 to Root System Architecture Alterations in Arabidopsis thaliana and Zea mays. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:212-223. [PMID: 28971723 DOI: 10.1094/mpmi-07-17-0185-r] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Fluorescent pseudomonads are playing key roles in plant-bacteria symbiotic interactions due to the multiple plant-beneficial functions (PBFs) they are harboring. The relative contributions of PBFs to plant-stimulatory effects of the well-known plant growth-promoting rhizobacteria Pseudomonas kilonensis F113 (formerly P. fluorescens F113) were investigated using a genetic approach. To this end, several deletion mutants were constructed, simple mutants ΔphlD (impaired in the biosynthesis of 2,4-diacetylphloroglucinol [DAPG]), ΔacdS (deficient in 1-aminocyclopropane-1-carboxylate deaminase activity), Δgcd (glucose dehydrogenase deficient, impaired in phosphate solubilization), and ΔnirS (nitrite reductase deficient), and a quadruple mutant (deficient in the four PBFs mentioned above). Every PBF activity was quantified in the wild-type strain and the five deletion mutants. This approach revealed few functional interactions between PBFs in vitro. In particular, biosynthesis of glucose dehydrogenase severely reduced the production of DAPG. Contrariwise, the DAPG production impacted positively, but to a lesser extent, phosphate solubilization. Inoculation of the F113 wild-type strain on Arabidopsis thaliana Col-0 and maize seedlings modified the root architecture of both plants. Mutant strain inoculations revealed that the relative contribution of each PBF differed according to the measured plant traits and that F113 plant-stimulatory effects did not correspond to the sum of each PBF relative contribution. Indeed, two PBF genes (ΔacdS and ΔnirS) had a significant impact on root-system architecture from both model plants, in in vitro and in vivo conditions. The current work underscored that few F113 PBFs seem to interact between each other in the free-living bacterial cells, whereas they control in concert Arabidopsis thaliana and maize growth and development.
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Affiliation(s)
- Jordan Vacheron
- 1 UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, 43 bd du 11 Novembre, F-69622 Villeurbanne, France; and
| | - Guilhem Desbrosses
- 2 CNRS, INRA, UMR5004, Biochimie & Physiologie Moléculaire des Plantes, Montpellier, France
| | - Sébastien Renoud
- 1 UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, 43 bd du 11 Novembre, F-69622 Villeurbanne, France; and
| | - Rosa Padilla
- 1 UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, 43 bd du 11 Novembre, F-69622 Villeurbanne, France; and
| | - Vincent Walker
- 1 UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, 43 bd du 11 Novembre, F-69622 Villeurbanne, France; and
| | - Daniel Muller
- 1 UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, 43 bd du 11 Novembre, F-69622 Villeurbanne, France; and
| | - Claire Prigent-Combaret
- 1 UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, 43 bd du 11 Novembre, F-69622 Villeurbanne, France; and
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Towards a better greener future - an alternative strategy using biofertilizers. I: Plant growth promoting bacteria. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2017.07.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Pseudomonas aestus sp. nov., a plant growth-promoting bacterium isolated from mangrove sediments. Arch Microbiol 2017; 199:1223-1229. [PMID: 28702688 DOI: 10.1007/s00203-017-1410-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 06/13/2017] [Accepted: 07/04/2017] [Indexed: 10/19/2022]
Abstract
Strain CMAA 1215T, a Gram-reaction-negative, aerobic, catalase positive, polarly flagellated, motile, rod-shaped (0.5-0.8 × 1.3-1.9 µm) bacterium, was isolated from mangrove sediments, Cananéia Island, Brazil. Analysis of the 16S rRNA gene sequences showed that strain CMAA 1215T forms a distinct phyletic line within the Pseudomonas putida subclade, being closely related to P. plecoglossicida ATCC 700383T, P. monteilii NBRC 103158T, and P. taiwanensis BCRC 17751T of sequence similarity of 98.86, 98.73, and 98.71%, respectively. Genomic comparisons of the strain CMAA 1215T with its closest phylogenetic type strains using average nucleotide index (ANI) and DNA:DNA relatedness approaches revealed 84.3-85.3% and 56.0-63.0%, respectively. A multilocus sequence analysis (MLSA) performed concatenating 16S rRNA, gyrB and rpoB gene sequences from the novel species was related with Pseudomonas putida subcluster and formed a new phylogenetic lineage. The phenotypic, physiological, biochemical, and genetic characteristics support the assignment of CMAA 1215T to the genus Pseudomonas, representing a novel species. The name Pseudomonas aestus sp.nov. is proposed, with CMAA 1215T (=NRRL B-653100T = CBMAI 1962T) as the type strain.
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Almario J, Bruto M, Vacheron J, Prigent-Combaret C, Moënne-Loccoz Y, Muller D. Distribution of 2,4-Diacetylphloroglucinol Biosynthetic Genes among the Pseudomonas spp. Reveals Unexpected Polyphyletism. Front Microbiol 2017; 8:1218. [PMID: 28713346 PMCID: PMC5491608 DOI: 10.3389/fmicb.2017.01218] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 06/15/2017] [Indexed: 11/13/2022] Open
Abstract
Fluorescent pseudomonads protecting plant roots from phytopathogens by producing 2,4-diacetylphloroglucinol (DAPG) are considered to form a monophyletic lineage comprised of DAPG+Pseudomonas strains in the "P. corrugata" and "P. protegens" subgroups of the "Pseudomonas fluorescens" group. However, DAPG production ability has not been investigated for many species of these two subgroups, and whether or not the DAPG+Pseudomonas are truly monophyletic remained to be verified. Thus, the distribution of the DAPG biosynthetic operon (phlACBD genes) in the Pseudomonas spp. was investigated in sequenced genomes and type strains. Results showed that the DAPG+Pseudomonas include species of the "P. fluorescens" group, i.e., P. protegens, P. brassicacearum, P. kilonensis, and P. thivervalensis, as expected, as well as P. gingeri in which it had not been documented. Surprisingly, they also include bacteria outside the "P. fluorescens" group, as exemplified by Pseudomonas sp. OT69, and even two Betaproteobacteria genera. The phl operon-based phylogenetic tree was substantially congruent with the one inferred from concatenated housekeeping genes rpoB, gyrB, and rrs. Contrariwise to current supposition, ancestral character reconstructions favored multiple independent acquisitions rather that one ancestral event followed by vertical inheritance. Indeed, based on synteny analyses, these acquisitions appeared to vary according to the Pseudomonas subgroup and even the phylogenetic groups within the subgroups. In conclusion, our study shows that the phl+Pseudomonas populations form a polyphyletic group and suggests that DAPG biosynthesis might not be restricted to this genus. This is important to consider when assessing the ecological significance of phl+ bacterial populations in rhizosphere ecosystems.
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Affiliation(s)
- Juliana Almario
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université de Lyon, Université Claude Bernard Lyon1, VetAgro Sup, UMR Ecologie MicrobienneVilleurbanne, France
| | - Maxime Bruto
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université de Lyon, Université Claude Bernard Lyon1, VetAgro Sup, UMR Ecologie MicrobienneVilleurbanne, France
| | - Jordan Vacheron
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université de Lyon, Université Claude Bernard Lyon1, VetAgro Sup, UMR Ecologie MicrobienneVilleurbanne, France
| | - Claire Prigent-Combaret
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université de Lyon, Université Claude Bernard Lyon1, VetAgro Sup, UMR Ecologie MicrobienneVilleurbanne, France
| | - Yvan Moënne-Loccoz
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université de Lyon, Université Claude Bernard Lyon1, VetAgro Sup, UMR Ecologie MicrobienneVilleurbanne, France
| | - Daniel Muller
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université de Lyon, Université Claude Bernard Lyon1, VetAgro Sup, UMR Ecologie MicrobienneVilleurbanne, France
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Almario J, Bruto M, Vacheron J, Prigent-Combaret C, Moënne-Loccoz Y, Muller D. Distribution of 2,4-Diacetylphloroglucinol Biosynthetic Genes among the Pseudomonas spp. Reveals Unexpected Polyphyletism. Front Microbiol 2017; 8:1218. [PMID: 28713346 DOI: 10.3389/fmibc.2017.01218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 06/15/2017] [Indexed: 05/26/2023] Open
Abstract
Fluorescent pseudomonads protecting plant roots from phytopathogens by producing 2,4-diacetylphloroglucinol (DAPG) are considered to form a monophyletic lineage comprised of DAPG+Pseudomonas strains in the "P. corrugata" and "P. protegens" subgroups of the "Pseudomonas fluorescens" group. However, DAPG production ability has not been investigated for many species of these two subgroups, and whether or not the DAPG+Pseudomonas are truly monophyletic remained to be verified. Thus, the distribution of the DAPG biosynthetic operon (phlACBD genes) in the Pseudomonas spp. was investigated in sequenced genomes and type strains. Results showed that the DAPG+Pseudomonas include species of the "P. fluorescens" group, i.e., P. protegens, P. brassicacearum, P. kilonensis, and P. thivervalensis, as expected, as well as P. gingeri in which it had not been documented. Surprisingly, they also include bacteria outside the "P. fluorescens" group, as exemplified by Pseudomonas sp. OT69, and even two Betaproteobacteria genera. The phl operon-based phylogenetic tree was substantially congruent with the one inferred from concatenated housekeeping genes rpoB, gyrB, and rrs. Contrariwise to current supposition, ancestral character reconstructions favored multiple independent acquisitions rather that one ancestral event followed by vertical inheritance. Indeed, based on synteny analyses, these acquisitions appeared to vary according to the Pseudomonas subgroup and even the phylogenetic groups within the subgroups. In conclusion, our study shows that the phl+Pseudomonas populations form a polyphyletic group and suggests that DAPG biosynthesis might not be restricted to this genus. This is important to consider when assessing the ecological significance of phl+ bacterial populations in rhizosphere ecosystems.
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Affiliation(s)
- Juliana Almario
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université de Lyon, Université Claude Bernard Lyon1, VetAgro Sup, UMR Ecologie MicrobienneVilleurbanne, France
| | - Maxime Bruto
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université de Lyon, Université Claude Bernard Lyon1, VetAgro Sup, UMR Ecologie MicrobienneVilleurbanne, France
| | - Jordan Vacheron
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université de Lyon, Université Claude Bernard Lyon1, VetAgro Sup, UMR Ecologie MicrobienneVilleurbanne, France
| | - Claire Prigent-Combaret
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université de Lyon, Université Claude Bernard Lyon1, VetAgro Sup, UMR Ecologie MicrobienneVilleurbanne, France
| | - Yvan Moënne-Loccoz
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université de Lyon, Université Claude Bernard Lyon1, VetAgro Sup, UMR Ecologie MicrobienneVilleurbanne, France
| | - Daniel Muller
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université de Lyon, Université Claude Bernard Lyon1, VetAgro Sup, UMR Ecologie MicrobienneVilleurbanne, France
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Interaction between 2,4-Diacetylphloroglucinol- and Hydrogen Cyanide-Producing Pseudomonas brassicacearum LBUM300 and Clavibacter michiganensis subsp. michiganensis in the Tomato Rhizosphere. Appl Environ Microbiol 2017; 83:AEM.00073-17. [PMID: 28432096 DOI: 10.1128/aem.00073-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 04/07/2017] [Indexed: 11/20/2022] Open
Abstract
We have previously demonstrated that inoculation of tomato plants with 2,4-diacetylphloroglucinol (DAPG)- and hydrogen cyanide (HCN)-producing Pseudomonas brassicacearum LBUM300 could significantly reduce bacterial canker symptoms caused by Clavibacter michiganensis subsp. michiganensis In this study, in order to better characterize the population dynamics of LBUM300 in the rhizosphere of tomato plants, we characterized the role played by DAPG and HCN production by LBUM300 on rhizosphere colonization of healthy and C. michiganensis subsp. michiganensis-infected tomato plants. The impact of C. michiganensis subsp. michiganensis presence on the expression of DAPG and HCN biosynthetic genes in the rhizosphere was also examined. In planta assays were performed using combinations of C. michiganensis subsp. michiganensis and wild-type LBUM300 or DAPG (LBUM300ΔphlD) or HCN (LBUM300ΔhcnC) isogenic mutant strains. Populations of LBUM300 and phlD and hcnC gene expression levels were quantified in rhizosphere soil at several time points up to 264 h postinoculation using culture-independent quantitative PCR (qPCR) and reverse transcriptase quantitative PCR (RT-qPCR) TaqMan assays, respectively. The presence of C. michiganensis subsp. michiganensis significantly increased rhizospheric populations of LBUM300. In C. michiganensis subsp. michiganensis-infected tomato rhizospheres, the populations of wild-type LBUM300 and strain LBUM300ΔhcnC, both producing DAPG, were significantly higher than the population of strain LBUM300ΔphlD A significant upregulation of phlD expression was observed in the presence of C. michiganensis subsp. michiganensis, while hcnC expression was only slightly increased in the mutant strain LBUM300ΔphlD when C. michiganensis subsp. michiganensis was present. Additionally, biofilm production was found to be significantly reduced in strain LBUM300ΔphlD compared to the wild-type and LBUM300ΔhcnC strains.IMPORTANCE The results of this study suggest that C. michiganensis subsp. michiganensis infection of tomato plants contributes to increasing rhizospheric populations of LBUM300, a biocontrol agent, as well as the overexpression of the DAPG biosynthetic operon in this bacterium. The increasing rhizospheric populations of LBUM300 represent one of the key factors in controlling C. michiganensis subsp. michiganensis in tomato plants, as DAPG-producing bacteria have shown the ability to decrease bacterial canker symptoms in tomato plants.
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Zhang R, Vivanco JM, Shen Q. The unseen rhizosphere root-soil-microbe interactions for crop production. Curr Opin Microbiol 2017; 37:8-14. [PMID: 28433932 DOI: 10.1016/j.mib.2017.03.008] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/22/2017] [Indexed: 02/03/2023]
Abstract
The underground root-soil-microbe interactions are extremely complex, but vitally important for aboveground plant growth, health and fitness. The pressure to reduce our reliance on agrochemicals, and sustainable efforts to develop agriculture makes rhizosphere interactions' research a hotspot. Recent advances provide new insights about the signals, pathways, functions and mechanisms of these interactions. In this review, we provide an overview about recent progress in rhizosphere interaction networks in crops. We also discuss a holistic view of the root-soil-rhizomicrobiome interactions achieved through the advances of omics and bioinformatics technologies, and the potential strategies to manage the complex rhizosphere interactions for enhancing crop production.
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Affiliation(s)
- Ruifu Zhang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China; Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Jorge M Vivanco
- Department of Horticulture and Landscape Architecture and Center for Rhizosphere Biology, Colorado State University, Fort Collins, CO 80523, United States
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China.
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Garge SS, Nerurkar AS. Evaluation of quorum quenching Bacillus spp. for their biocontrol traits against Pectobacterium carotovorum subsp. carotovorum causing soft rot. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2017. [DOI: 10.1016/j.bcab.2016.11.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Kim IS, Yang SY, Park SK, Kim YC. Quorum sensing is a key regulator for the antifungal and biocontrol activity of chitinase-producing Chromobacterium sp. C61. MOLECULAR PLANT PATHOLOGY 2017; 18:134-140. [PMID: 26833901 PMCID: PMC6638307 DOI: 10.1111/mpp.12379] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 01/14/2016] [Accepted: 01/29/2016] [Indexed: 06/05/2023]
Abstract
Chromobacterium sp. strain C61 has strong biocontrol activity; however, the genetic and biochemical determinants of its plant disease suppression activity are not well understood. Here, we report the identification and characterization of two new determinants of its biocontrol activity. Transposon mutagenesis was used to identify mutants that were deficient in fungal suppression. One of these mutants had an insertion in a homologue of depD, a structural gene in the dep operon, that encodes a protein involved in non-ribosomal peptide synthesis. In the second mutant, the insertion was in a homologue of the luxI gene, which encodes a homoserine lactone synthase. The luxI- and depD- mutants had no antifungal activity in vitro and a dramatically reduced capacity to suppress various plant diseases in planta. Antifungal production and biocontrol were restored by complementation of the luxI- mutant. Other phenotypes associated with effective biological control, including motility and lytic enzyme secretion, were also affected by the luxI mutation. Biochemical analysis of ethyl acetate extracts of culture filtrates of the mutant and wild-type strains showed that a key antifungal compound, chromobactomycin, was produced by wild-type C61 and the complemented luxI- mutant, but not by the luxI- or depD- mutant. These data suggest that multiple biocontrol-related phenotypes are regulated by homoserine lactones in C61. Thus, quorum sensing plays an essential role in the biological control potential of diverse bacterial lineages.
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Affiliation(s)
- In Seon Kim
- Institute of Environmentally‐Friendly AgricultureCollege of Agriculture and Life Sciences, Chonnam National UniversityGwangju61186South Korea
| | - Si Young Yang
- Institute of Environmentally‐Friendly AgricultureCollege of Agriculture and Life Sciences, Chonnam National UniversityGwangju61186South Korea
| | - Seur Kee Park
- Department of Agricultural BiologySunchon National UniversitySuncheon 57922South Korea
| | - Young Cheol Kim
- Institute of Environmentally‐Friendly AgricultureCollege of Agriculture and Life Sciences, Chonnam National UniversityGwangju61186South Korea
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Canchignia H, Altimira F, Montes C, Sánchez E, Tapia E, Miccono M, Espinoza D, Aguirre C, Seeger M, Prieto H. Candidate nematicidal proteins in a new Pseudomonas veronii isolate identified by its antagonistic properties against Xiphinema index. J GEN APPL MICROBIOL 2016; 63:11-21. [PMID: 27989999 DOI: 10.2323/jgam.2016.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The nematode Xiphinema index affects grape vines and transmits important viruses associated with fanleaf degeneration. Pseudomonas spp. are an extensive bacterial group in which important biodegradation and/or biocontrol properties can occur for several strains in the group. The aim of this study was to identify new Pseudomonas isolates with antagonist activity against X. index. Forty bacterial isolates were obtained from soil and root samples from Chilean vineyards. Thirteen new fluorescent pseudomonads were found and assessed for their antagonistic capability. The nematicide Pseudomonas protegens CHA0 was used as a control. Challenges of nematode individuals in King's B semi-solid agar Petri dishes facilitated the identification of the Pseudomonas veronii isolate R4, as determined by a 16S rRNA sequence comparison. This isolate was as effective as CHA0 as an antagonist of X. index, although it had a different lethality kinetic. Milk-induced R4 cultures exhibited protease and lipase activities in cell supernatants using both gelatin/tributyrin Petri dish assays and zymograms. Three proteins with these activities were isolated and subjected to mass spectrometry. Amino acid partial sequences enabled the identification of a 49-kDa protease similar to metalloprotease AprA and two lipases of 50 kDa and 69 kDa similar to LipA and ExoU, respectively. Electron microscopy analyses of challenged nematodes revealed degraded cuticle after R4 supernatant treatment. These results represent a new and unexplored property in this species associated with the presence of secretable lipases and protease, similar to characterized enzymes present in biocontrol pseudomonads.
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Affiliation(s)
- Hayron Canchignia
- Biotechnology Doctoral Program, Universidad Técnica Federico Santa María-Pontificia Universidad Católica de Valparaíso
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