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Mankoti M, Pandit NK, Meena SS, Mohanty A. Investigating the genomic and metabolic abilities of PGPR Pseudomonas fluorescens in promoting plant growth and fire blight management. Mol Genet Genomics 2024; 299:110. [PMID: 39601883 DOI: 10.1007/s00438-024-02198-3] [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: 06/30/2024] [Accepted: 10/26/2024] [Indexed: 11/29/2024]
Abstract
Pseudomonas fluorescens is commonly found in diverse environments and is well known for its metabolic and antagonistic properties. Despite its remarkable attributes, its potential role in promoting plant growth remains unexplored. This study examines these traits across 14 strains residing in diverse rhizosphere environments through pangenome and comparative genome analysis, alongside molecular docking studies against Erwinia amylovora to combat fire blight. Whole genome analysis revealed circular chromosome (6.01-7.07 Mb) with GC content averaging 59.95-63.39%. Predicted genes included 16S rRNA and protein-coding genes ranging from 4435 to 6393 bp and 1527 to 1541 bp, respectively. Pangenome analysis unveiled an open pangenome, shedding light on genetic factors influencing plant growth promotion and biocontrol, including nitrogen fixation, phosphorus solubilization, siderophore production, stress tolerance, flagella biosynthesis, and induced systemic resistance. Furthermore, pyrrolnitrin, phenazine-1-carboxylic acid, pyoluteorin, lokisin, 2,4-diacetylpholoroglucinol and pseudomonic acid were identified. Molecular docking against key proteins of E. amylovora highlighted the high binding affinities of 2,4-diacetylphloroglucinol, pseudomonic acid, and lokisin. These findings underscore the multifaceted role of P. fluorescens in plant growth promotion and biocontrol, with key biomolecules showing promising applications in plant growth and defense against pathogens.
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Affiliation(s)
- Megha Mankoti
- Department of Biotechnology, Dr B R Ambedkar National Institute of Technology Jalandhar, Punjab, India
| | - Nisha Kumari Pandit
- Department of Biotechnology, Dr B R Ambedkar National Institute of Technology Jalandhar, Punjab, India
| | - Sumer Singh Meena
- Department of Biotechnology, Dr B R Ambedkar National Institute of Technology Jalandhar, Punjab, India.
| | - Anee Mohanty
- Department of Biotechnology, Dr B R Ambedkar National Institute of Technology Jalandhar, Punjab, India.
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Kumari K, Aggarwal Y, Singh RP. Molecular characterization and in-depth genomic analysis to unravel the pathogenic features of an environmental isolate Enterobacter sp. S-33. Int Microbiol 2024; 27:1095-1110. [PMID: 38044418 DOI: 10.1007/s10123-023-00461-y] [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: 08/17/2023] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 12/05/2023]
Abstract
Enterobacter species represent widely distributed opportunistic pathogens, commonly associated with plants and humans. In the present study, we performed a detailed molecular characterization as well as genomic study of a type VI secretion system (T6SS) bacterium belonging to member of the family Enterobacteriaceae and named Enterobacter sp. S-33. The comparative sequence analysis of the 16S rRNA gene showed that the strain was closely related to other Enterobacter species. The complete genome of the strain with a genome size of 4.6 Mbp and GC-content of 55.63% was obtained through high-quality sequencing. The genomic analysis with online tools unravelled the various genes belonging to the bacterial secretion system, antibiotic resistance, virulence, efflux pumps, etc. The isolate showed the motility behavior that contributes to Enterobacter persistence in a stressed environment and further supports infections. PCR amplification and further sequencing confirmed the presence of drug-efflux genes acrA, acrB, and outer membrane genes, viz. OmpA, OmpC, and OmpF. The cell surface hydrophobicity and co-aggregation assay against different bacterial strains illustrated its putative pathogenic nature. Genome mining identified various biosynthetic gene clusters (BGCs) corresponding to non-ribosomal proteins (NRPS), siderophore, and arylpolyene production. Briefly, genome sequencing and detailed characterization of environmental Enterobacter isolate will assist in understanding the epidemiology of Enterobacter species, and the further prevention and treatment of infectious diseases caused by these broad-host range species.
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Affiliation(s)
- Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Yogender Aggarwal
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Rajnish Prakash Singh
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India.
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Xiong L, Yu H, Zeng K, Li Y, Wei Y, Li H, Ji X. Whole genome analysis of Pseudomonas mandelii SW-3 and the insights into low-temperature adaptation. Folia Microbiol (Praha) 2024; 69:775-787. [PMID: 38051419 DOI: 10.1007/s12223-023-01117-0] [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: 04/14/2023] [Accepted: 11/14/2023] [Indexed: 12/07/2023]
Abstract
Pseudomonas mandelii SW-3, isolated from the Napahai plateau wetland, can survive in cold environments. The mechanisms underlying the survival of bacteria in low temperatures and high altitudes are not yet fully understood. In this study, the whole genome of SW-3 was sequenced to identify the genomic features that may contribute to survival in cold environments. The results showed that the genome size of strain SW-3 was 6,538,059 bp with a GC content of 59%. A total of 67 tRNAs, a 34,110 bp prophage sequence, and a large number of metabolic genes were found. Based on 16S rRNA gene phylogeny and average nucleotide identity analysis among P. mandelii, SW-3 was identified as a strain belonging to P. mandelii. In addition, we clarified the mechanisms by which SW-3 survived in a cold environment, providing a basis for further investigation of host-phage interaction. P. mandelii SW-3 showed stress resistance mechanisms, including glycogen and trehalose metabolic pathways, and antisense transcriptional silencing. Furthermore, cold shock proteins and glucose 6-phosphate dehydrogenase may play pivotal roles in facilitating adaptation to cold environmental conditions. The genome-wide analysis provided us with a deeper understanding of the cold-adapted bacterium.
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Affiliation(s)
- Lingling Xiong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Hang Yu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Kun Zeng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Yanmei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Yunlin Wei
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Haiyan Li
- Medical School, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Xiuling Ji
- Medical School, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China.
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Sáez LP, Rodríguez-Caballero G, Olaya-Abril A, Cabello P, Moreno-Vivián C, Roldán MD, Luque-Almagro VM. Genomic Insights into Cyanide Biodegradation in the Pseudomonas Genus. Int J Mol Sci 2024; 25:4456. [PMID: 38674043 PMCID: PMC11049912 DOI: 10.3390/ijms25084456] [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: 03/15/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Molecular studies about cyanide biodegradation have been mainly focused on the hydrolytic pathways catalyzed by the cyanide dihydratase CynD or the nitrilase NitC. In some Pseudomonas strains, the assimilation of cyanide has been linked to NitC, such as the cyanotrophic model strain Pseudomonas pseudoalcaligenes CECT 5344, which has been recently reclassified as Pseudomonas oleovorans CECT 5344. In this work, a phylogenomic approach established a more precise taxonomic position of the strain CECT 5344 within the species P. oleovorans. Furthermore, a pan-genomic analysis of P. oleovorans and other species with cyanotrophic strains, such as P. fluorescens and P. monteilii, allowed for the comparison and identification of the cioAB and mqoAB genes involved in cyanide resistance, and the nitC and cynS genes required for the assimilation of cyanide or cyanate, respectively. While cyanide resistance genes presented a high frequency among the analyzed genomes, genes responsible for cyanide or cyanate assimilation were identified in a considerably lower proportion. According to the results obtained in this work, an in silico approach based on a comparative genomic approach can be considered as an agile strategy for the bioprospection of putative cyanotrophic bacteria and for the identification of new genes putatively involved in cyanide biodegradation.
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Affiliation(s)
- Lara P. Sáez
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, 14071 Córdoba, Spain; (L.P.S.); (G.R.-C.); (A.O.-A.); (C.M.-V.); (M.D.R.)
| | - Gema Rodríguez-Caballero
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, 14071 Córdoba, Spain; (L.P.S.); (G.R.-C.); (A.O.-A.); (C.M.-V.); (M.D.R.)
| | - Alfonso Olaya-Abril
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, 14071 Córdoba, Spain; (L.P.S.); (G.R.-C.); (A.O.-A.); (C.M.-V.); (M.D.R.)
| | - Purificación Cabello
- Departamento de Botánica, Ecología y Fisiología Vegetal, Edificio Celestino Mutis, Campus de Rabanales, Universidad de Córdoba, 14071 Córdoba, Spain;
| | - Conrado Moreno-Vivián
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, 14071 Córdoba, Spain; (L.P.S.); (G.R.-C.); (A.O.-A.); (C.M.-V.); (M.D.R.)
| | - María Dolores Roldán
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, 14071 Córdoba, Spain; (L.P.S.); (G.R.-C.); (A.O.-A.); (C.M.-V.); (M.D.R.)
| | - Víctor M. Luque-Almagro
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, 14071 Córdoba, Spain; (L.P.S.); (G.R.-C.); (A.O.-A.); (C.M.-V.); (M.D.R.)
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