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Zouagui R, Zouagui H, Aurag J, Ibrahimi A, Sbabou L. Functional analysis and comparative genomics of Rahnella perminowiae S11P1 and Variovorax sp. S12S4, two plant growth-promoting rhizobacteria isolated from Crocus sativus L. (saffron) rhizosphere. BMC Genomics 2024; 25:289. [PMID: 38500021 PMCID: PMC10946135 DOI: 10.1186/s12864-024-10088-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 02/03/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND Rahnella perminowiae S11P1 and Variovorax sp. S12S4 are two plant growth-promoting rhizobacteria that were previously isolated from the rhizosphere of Crocus sativus L. (saffron), and have demonstrated interesting PGP activities and promising results when used as inoculants in field trials. To further elucidate the molecular mechanisms underlying their beneficial effects on plant growth, comprehensive genome mining of S11P1 and S12S4 and comparative genomic analysis with closely related strains were conducted. RESULTS Functional annotation of the two strains predicted a large number of genes involved in auxin and siderophore production, nitrogen fixation, sulfur metabolism, organic acid biosynthesis, pyrroloquinoline quinone production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, volatile organic compounds production, and polyamine biosynthesis. In addition, numerous genes implicated in plant-bacteria interactions, such as those involved in chemotaxis and quorum sensing, were predicted. Moreover, the two strains carried genes involved in bacterial fitness under abiotic stress conditions. Comparative genomic analysis revealed an open pan-genomic structure for the two strains. COG annotation showed that higher fractions of core and accessory genes were involved in the metabolism and transport of carbohydrates and amino acids, suggesting the metabolic versatility of the two strains as effective rhizosphere colonizers. Furthermore, this study reports the first comparison of Multilocus sequence analysis (MLSA) and core-based phylogenies of the Rahnella and Variovorax genera. CONCLUSIONS The present study unveils the molecular mechanisms underlying plant growth promotion and biocontrol activity of S11P1 and S12S4, and provides a basis for their further biotechnological application in agriculture.
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Affiliation(s)
- Rahma Zouagui
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - Houda Zouagui
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
| | - Jamal Aurag
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - Azeddine Ibrahimi
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
| | - Laila Sbabou
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco.
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Bhagat N, Mansotra R, Patel K, Ambardar S, Vakhlu J. Molecular warfare between pathogenic Fusarium oxysporum R1 and host Crocus sativus L. unraveled by dual transcriptomics. PLANT CELL REPORTS 2024; 43:42. [PMID: 38246927 DOI: 10.1007/s00299-023-03101-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 09/25/2023] [Indexed: 01/23/2024]
Abstract
KEY MESSAGE Phenylpropanoid biosynthesis and plant-pathogen interaction pathways in saffron and cell wall degrading enzymes in Fusarium oxysporum R1 are key players involved in the interaction. Fusarium oxysporum causes corm rot in saffron (Crocus sativus L.), which is one of the most devastating fungal diseases impacting saffron yield globally. Though the corm rot agent and its symptoms are known widely, little is known about the defense mechanism of saffron in response to Fusarium oxysporum infection at molecular level. Therefore, the current study reports saffron-Fusarium oxysporum R1 (Fox R1) interaction at the molecular level using dual a transcriptomics approach. The results indicated the activation of various defense related pathways such as the mitogen activated protein kinase pathway (MAPK), plant-hormone signaling pathways, plant-pathogen interaction pathway, phenylpropanoid biosynthesis pathway and PR protein synthesis in the host during the interaction. The activation of pathways is involved in the hypersensitive response, production of various secondary metabolites, strengthening of the host cell wall, systemic acquired resistance etc. Concurrently, in the pathogen, 60 genes reported to be linked to pathogenicity and virulence has been identified during the invasion. The expression of genes encoding plant cell wall degrading enzymes, various transcription factors and effector proteins indicated the strong pathogenicity of Fusarium oxysporum R1. Based on the results obtained, the putative molecular mechanism of the saffron-Fox R1 interaction was identified. As saffron is a male sterile plant, and can only be improved by genetic manipulation, this work will serve as a foundation for identifying genes that can be used to create saffron varieties, resistant to Fusarium oxysporum infection.
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Affiliation(s)
- Nancy Bhagat
- Metagenomic Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006, India
| | - Ritika Mansotra
- Metagenomic Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006, India
| | - Karan Patel
- DNA Xperts Private Limited, Noida, 201301, India
| | - Sheetal Ambardar
- Metagenomic Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006, India
| | - Jyoti Vakhlu
- Metagenomic Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006, India.
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Aguilera-Huertas J, Cuartero J, Ros M, Pascual JA, Parras-Alcántara L, González-Rosado M, Özbolat O, Zornoza R, Egea-Cortines M, Hurtado-Navarro M, Lozano-García B. How binomial (traditional rainfed olive grove-Crocus sativus) crops impact the soil bacterial community and enhance microbial capacities. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118572. [PMID: 37421720 DOI: 10.1016/j.jenvman.2023.118572] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/26/2023] [Accepted: 07/02/2023] [Indexed: 07/10/2023]
Abstract
Intercropping can favour the yield of the main crop. However, because of the potential competition among woody crops, this system is rarely used by farmers. To increase knowledge about the intercropping system, we have explored three different combinations of alley cropping in rainfed olive groves compared to conventional management (CP): (i) Crocus sativus (D-S); (ii) Vicia sativa/Avena sativa in annual rotation (D-O); and (iii) Lavandula x intermedia (D-L). Different soil chemical properties were analyzed to evaluate the effects of alley cropping, while 16S rRNA amplification and enzymatic activities were determined to study the changes that occurred in soil microbial communities and activity. In addition, the influence of intercropping on the potential functionality of the soil microbial community was measured. Data revealed that the intercropping systems highly affected the microbial community and soil properties. The D-S cropping system increased soil total organic carbon and total nitrogen that were correlated with the bacterial community, indicating that both parameters were the main drivers shaping the structure of the bacterial community. The D-S soil cropping system had significantly higher relative abundances of the phyla Bacteroidetes, Proteobacteria, and Patescibacteria compared to the other systems and the genera Adhaeribacter, Arthrobacter, Rubellimicrobium, and Ramlibacter, related to C and N functions. D-S soil was also related to the highest relative abundances of Pseudoarthrobacter and Haliangium, associated with the plant growth-promoting effect, antifungal activity, and a potential P solubilizer. A potentially increase of C fixation and N fixation in soils was also observed in the D-S cropping system. These positive changes were related to the cessation of tillage and the development of a spontaneous cover crop, which increased soil protection. Thus, management practices that contribute to increasing soil cover should be encouraged to improve soil functionality.
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Affiliation(s)
- Jesús Aguilera-Huertas
- SUMAS Research Group, Department of Agricultural Chemistry, Soil Science and Microbiology, Faculty of Science, Agrifood Campus of International Excellence - ceiA3, University of Cordoba, 14071, Cordoba, Spain
| | - Jessica Cuartero
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903, Birmensdorf, Switzerland; Grupo de Enzimología y Biorremediación de suelos y residuos Orgánicos. Centro de Edafología y Biología aplicada del Segura (CEBAS-CSIC), Campus Universitario de Espinardo, 30100, Murcia, Spain
| | - Margarita Ros
- Grupo de Enzimología y Biorremediación de suelos y residuos Orgánicos. Centro de Edafología y Biología aplicada del Segura (CEBAS-CSIC), Campus Universitario de Espinardo, 30100, Murcia, Spain
| | - Jose Antonio Pascual
- Grupo de Enzimología y Biorremediación de suelos y residuos Orgánicos. Centro de Edafología y Biología aplicada del Segura (CEBAS-CSIC), Campus Universitario de Espinardo, 30100, Murcia, Spain
| | - Luis Parras-Alcántara
- SUMAS Research Group, Department of Agricultural Chemistry, Soil Science and Microbiology, Faculty of Science, Agrifood Campus of International Excellence - ceiA3, University of Cordoba, 14071, Cordoba, Spain
| | - Manuel González-Rosado
- SUMAS Research Group, Department of Agricultural Chemistry, Soil Science and Microbiology, Faculty of Science, Agrifood Campus of International Excellence - ceiA3, University of Cordoba, 14071, Cordoba, Spain; Department of Agricultural Science, Universidad Politécnica de Cartagena, Paseo Alfonso XIII 48, 30203, Cartagena, Spain
| | - Onurcan Özbolat
- Department of Agricultural Science, Universidad Politécnica de Cartagena, Paseo Alfonso XIII 48, 30203, Cartagena, Spain; Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, Plaza del Hospital s/n, 30202, Cartagena, Spain
| | - Raúl Zornoza
- Department of Agricultural Science, Universidad Politécnica de Cartagena, Paseo Alfonso XIII 48, 30203, Cartagena, Spain; Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, Plaza del Hospital s/n, 30202, Cartagena, Spain
| | - Marcos Egea-Cortines
- Department of Agricultural Science, Universidad Politécnica de Cartagena, Paseo Alfonso XIII 48, 30203, Cartagena, Spain; Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, Plaza del Hospital s/n, 30202, Cartagena, Spain
| | - María Hurtado-Navarro
- Grupo de Enzimología y Biorremediación de suelos y residuos Orgánicos. Centro de Edafología y Biología aplicada del Segura (CEBAS-CSIC), Campus Universitario de Espinardo, 30100, Murcia, Spain
| | - Beatriz Lozano-García
- SUMAS Research Group, Department of Agricultural Chemistry, Soil Science and Microbiology, Faculty of Science, Agrifood Campus of International Excellence - ceiA3, University of Cordoba, 14071, Cordoba, Spain.
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Bhagat N, Magotra S, Gupta R, Sharma S, Verma S, Verma PK, Ali T, Shree A, Vakhlu J. Invasion and Colonization of Pathogenic Fusarium oxysporum R1 in Crocus sativus L. during Corm Rot Disease Progression. J Fungi (Basel) 2022; 8:jof8121246. [PMID: 36547579 PMCID: PMC9784501 DOI: 10.3390/jof8121246] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/03/2022] [Accepted: 10/12/2022] [Indexed: 11/29/2022] Open
Abstract
The corm rot of saffron caused by Fusarium oxysporum (Fox) has been reported to be the most destructive fungal disease of the herb globally. The pathogen, Fusarium oxysporum R1 (Fox R1) isolated by our group from Kashmir, India, was found to be different from Fusarium oxysporum f.sp. gladioli commonly reported corm rot agent of saffron. In the present study, Fox R1 was further characterized using housekeeping genes and pathogenicity tests, as Fusarium oxysporum R1 f.sp. iridacearum race 4. Though Fox R1 invaded the saffron plant through both corm and roots, the corm was found to be the preferred site of infection. In addition, the route of pathogen movement wastracked by monitoring visual symptoms, semi-quantitative PCR, quantitative-PCR (q-PCR), real-time imaging of egfp-tagged Fusarium oxysporum R1, and Fox R1 load quantification. This study is the first study of its kind on the bidirectional pathogenesis from corm to roots and vice-versa, as the literature only reports unidirectional upward movement from roots to other parts of the plant. In addition, the colonization pattern of Fox R1 in saffron corms and roots was studied. The present study involved a systematic elucidation of the mode and mechanism of pathogenesis in the saffron Fusarium oxysporum strain R1 pathosystem.
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Affiliation(s)
- Nancy Bhagat
- Metagenomic Laboratory, School of Biotechnology, University of Jammu, Jammu 180006, India
| | - Shanu Magotra
- Metagenomic Laboratory, School of Biotechnology, University of Jammu, Jammu 180006, India
- University Institute of Biotechnology, Chandigarh University, Ajitgarh 140413, India
| | - Rikita Gupta
- Metagenomic Laboratory, School of Biotechnology, University of Jammu, Jammu 180006, India
| | - Shikha Sharma
- Metagenomic Laboratory, School of Biotechnology, University of Jammu, Jammu 180006, India
| | - Sandhya Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Praveen Kumar Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Tahir Ali
- Metagenomic Laboratory, School of Biotechnology, University of Jammu, Jammu 180006, India
| | - Ankita Shree
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Jyoti Vakhlu
- Metagenomic Laboratory, School of Biotechnology, University of Jammu, Jammu 180006, India
- Correspondence:
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