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Li XL, Lv XY, Ji JB, Wang WD, Wang J, Wang C, He HB, Ben AL, Liu TL. Complete genome sequence of Nguyenibacter sp. L1, a phosphate solubilizing bacterium isolated from Lespedeza bicolor rhizosphere. Front Microbiol 2023; 14:1257442. [PMID: 38152372 PMCID: PMC10752598 DOI: 10.3389/fmicb.2023.1257442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 11/27/2023] [Indexed: 12/29/2023] Open
Abstract
Phosphorus (P) deficiency is a predominant constraint on plant growth in acidified soils, largely due to the sequestration of P by toxic aluminum (Al) compounds. Indigenous phosphorus-solubilizing bacteria (PSBs) capable of mobilizing Al-P in these soils hold significant promise. A novel Al-P-solubilizing strain, Al-P Nguyenibacter sp. L1, was isolated from the rhizosphere soil of healthy Lespedeza bicolor plants indigenous to acidic terrains. However, our understanding of the genomic landscape of bacterial species within the genus Nguyenibacter remains in its infancy. To further explore its biotechnological potentialities, we sequenced the complete genome of this strain, employing an amalgamation of Oxford Nanopore ONT and Illumina sequencing platforms. The resultant genomic sequence of Nguyenibacter sp. L1 manifests as a singular, circular chromosome encompassing 4,294,433 nucleotides and displaying a GC content of 66.73%. The genome was found to host 3,820 protein-coding sequences, 12 rRNAs, and 55 tRNAs. Intriguingly, annotations derived from the eggNOG and KEGG databases indicate the presence of genes affiliated with phosphorus solubilization and nitrogen fixation, including iscU, glnA, and gltB/D associated with nitrogen fixation, and pqqBC associated with inorganic phosphate dissolution. Several bioactive secondary metabolite genes in the genome, including pqqCDE, phytoene synthase and squalene synthase predicted by antiSMASH. Moreover, we uncovered a complete metabolic pathway for ammonia, suggesting an ammonia-affinity property inherent to Nguyenibacter sp. L1. This study verifies the nitrogen-fixing and phosphate-dissolving abilities of Nguyenibacter sp. L1 at the molecular level through genetic screening and analysis. The insights gleaned from this study offer strategic guidance for future strain enhancement and establish a strong foundation for the potential incorporation of this bacterium into agricultural practices.
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Affiliation(s)
- Xiao Li Li
- School of Food Science, Nanjing Xiaozhuang University, Nanjing, China
| | - Xin Yang Lv
- School of Food Science, Nanjing Xiaozhuang University, Nanjing, China
| | - Jun Bin Ji
- School of Food Science, Nanjing Xiaozhuang University, Nanjing, China
| | - Wei Duo Wang
- School of Food Science, Nanjing Xiaozhuang University, Nanjing, China
| | - Ji Wang
- School of Food Science, Nanjing Xiaozhuang University, Nanjing, China
| | - Cong Wang
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Hai Bin He
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Ai Ling Ben
- School of Food Science, Nanjing Xiaozhuang University, Nanjing, China
| | - Ting Li Liu
- School of Food Science, Nanjing Xiaozhuang University, Nanjing, China
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Guardiola-Márquez CE, Santos-Ramírez MT, Figueroa-Montes ML, Valencia-de los Cobos EO, Stamatis-Félix IJ, Navarro-López DE, Jacobo-Velázquez DA. Identification and Characterization of Beneficial Soil Microbial Strains for the Formulation of Biofertilizers Based on Native Plant Growth-Promoting Microorganisms Isolated from Northern Mexico. PLANTS (BASEL, SWITZERLAND) 2023; 12:3262. [PMID: 37765426 PMCID: PMC10537599 DOI: 10.3390/plants12183262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/04/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
Plant growth-promoting microorganisms (PGPM) benefit plant health by enhancing plant nutrient-use efficiency and protecting plants against biotic and abiotic stresses. This study aimed to isolate and characterize autochthonous PGPM from important agri-food crops and nonagricultural plants to formulate biofertilizers. Native microorganisms were isolated and evaluated for PGP traits (K, P, and Zn solubilization, N2-fixation, NH3-, IAA and siderophore production, and antifungal activity against Fusarium oxysporum). Isolates were tested on radish and broccoli seedlings, evaluating 19 individual isolates and 12 microbial consortia. Potential bacteria were identified through DNA sequencing. In total, 798 bacteria and 209 fungi were isolated. Isolates showed higher mineral solubilization activity than other mechanisms; 399 bacteria and 156 fungi presented mineral solubilization. Bacteria were relevant for nitrogen fixation, siderophore, IAA (29-176 mg/L), and ammonia production, while fungi for Fusarium growth inhibition (40-69%). Twenty-four bacteria and eighteen fungi were selected for their PGP traits. Bacteria had significantly (ANOVA, p < 0.05) better effects on plants than fungi; treatments improved plant height (23.06-51.32%), leaf diameter (25.43-82.91%), and fresh weight (54.18-85.45%) in both crops. Most potential species belonged to Pseudomonas, Pantoea, Serratia, and Rahnella genera. This work validated a high-throughput approach to screening hundreds of rhizospheric microorganisms with PGP potential isolated from rhizospheric samples.
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Affiliation(s)
- Carlos Esteban Guardiola-Márquez
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. General Ramon Corona 2514, Zapopan 45138, Jalisco, Mexico; (C.E.G.-M.)
| | - María Teresa Santos-Ramírez
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. General Ramon Corona 2514, Zapopan 45138, Jalisco, Mexico; (C.E.G.-M.)
| | - Melina Lizeth Figueroa-Montes
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. General Ramon Corona 2514, Zapopan 45138, Jalisco, Mexico; (C.E.G.-M.)
| | | | - Iván Jesús Stamatis-Félix
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. General Ramon Corona 2514, Zapopan 45138, Jalisco, Mexico; (C.E.G.-M.)
| | - Diego E. Navarro-López
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. General Ramon Corona 2514, Zapopan 45138, Jalisco, Mexico; (C.E.G.-M.)
| | - Daniel A. Jacobo-Velázquez
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. General Ramon Corona 2514, Zapopan 45138, Jalisco, Mexico; (C.E.G.-M.)
- Tecnologico de Monterrey, Institute for Obesity Research, Av. General Ramon Corona 2514, Zapopan 45201, Jalisco, Mexico
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Wang B, Jin H, Xu Y, Sun Z. Isolation, Characterization, and Genomic Analysis of Multidrug-Resistant Rahnella aquatilis from Fruits in China. Curr Microbiol 2023; 80:321. [PMID: 37587316 DOI: 10.1007/s00284-023-03436-4] [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: 04/12/2023] [Accepted: 07/31/2023] [Indexed: 08/18/2023]
Abstract
Many fruits are consumed raw and act as vehicles for spreading antibiotic-resistant bacteria to consumers; hence, preventing foodborne diseases and ensuring food safety of fresh fruits are challenging. In this study, we aimed to analyze contamination in fruits and characterize antibiotic resistance genes in pathogenic microorganisms isolated from fruits. Sixty fruit samples were collected and screened for pathogenic microorganisms. The strains were identified, and the minimum inhibitory concentration for various antibiotics was determined. Antibiotic-resistant strains were analyzed by whole-genome sequencing. We isolated strain L46 from lemon samples and identified it as Rahnella aquatilis using MALDI-TOF MS and 16S rRNA sequencing. The whole genome of R. aquatilis L46 was 4.94 Mb and contained 291 putative antibiotic resistance genes (6.53%), including the gene coding for β-lactamase RAHN-1 CTX-M-2 and conferring resistance to ampicillin, polymyxin B, nitrofurantoin, imipenem, aztreonam, and cefotaxime. Thus, fruits can pose a potential hazard to human health and require greater surveillance and attention, as they may contain pathogenic and multidrug-resistant bacteria.
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Affiliation(s)
- Bing Wang
- Department of Infectious Disease Control and Prevention, Hangzhou Center of Disease Control and Prevention, Hangzhou, China.
| | - Hui Jin
- Department of Infectious Disease Control and Prevention, Hangzhou Center of Disease Control and Prevention, Hangzhou, China
| | - Yongjie Xu
- Department of Infectious Disease Control and Prevention, Hangzhou Center of Disease Control and Prevention, Hangzhou, China
| | - Zhou Sun
- Department of Infectious Disease Control and Prevention, Hangzhou Center of Disease Control and Prevention, Hangzhou, China
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Wang X, Wu Z, Xiang H, He Y, Zhu S, Zhang Z, Li X, Wang J. Whole genome analysis of Enterobacter cloacae Rs-2 and screening of genes related to plant-growth promotion. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:21548-21564. [PMID: 36272007 DOI: 10.1007/s11356-022-23564-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
The genus Enterobacter is widely recognized for its biotechnology potential in improving soil environment and crop growth promotion. To further explore these biotechnological potentials, we sequenced and analyzed the whole genome of Enterobacter cloacae Rs-2. The analysis showed that the total length of the Rs-2 genome was 6,965,070,514 bp, and GC content was 55.80%; the annotation results of GO and COG databases showed that the genome contains a variety of growth-promoting genes, such as iscU, glnA, glnB (nitrogen fixation); iucABCD (siderophore synthesis) and fepA, fcuA, fhuA, and pfeA, etc. (siderophore transport); ipdC (secreted IAA) and gcd, pqqBCDEF (dissolved phosphorus), etc. No pathogenic factors such as virulence genes were found. The application of Rs-2 as a soil inoculant in pot experiments showed great potential for growth promotion. This study proved the plant growth-promoting ability of Rs-2 at the molecular level through genetic screening and analysis, which provided guidance for the further improvement of the strain and laid a foundation for its application in agricultural production.
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Affiliation(s)
- Xiaobo Wang
- Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, School of Environmental and Chemical Engineering, Xi'an Polytechnic University, Xi'an, 710048, People's Republic of China
| | - Zhansheng Wu
- Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, School of Environmental and Chemical Engineering, Xi'an Polytechnic University, Xi'an, 710048, People's Republic of China.
| | - Huichun Xiang
- Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, School of Environmental and Chemical Engineering, Xi'an Polytechnic University, Xi'an, 710048, People's Republic of China
| | - Yanhui He
- Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, School of Environmental and Chemical Engineering, Xi'an Polytechnic University, Xi'an, 710048, People's Republic of China
| | - Shuangxi Zhu
- Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, School of Environmental and Chemical Engineering, Xi'an Polytechnic University, Xi'an, 710048, People's Republic of China
| | - Ziyan Zhang
- Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, School of Environmental and Chemical Engineering, Xi'an Polytechnic University, Xi'an, 710048, People's Republic of China
| | - Xueping Li
- Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, School of Environmental and Chemical Engineering, Xi'an Polytechnic University, Xi'an, 710048, People's Republic of China
| | - Jianwen Wang
- Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, School of Environmental and Chemical Engineering, Xi'an Polytechnic University, Xi'an, 710048, People's Republic of China
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Xu S, Zhang Z, Xie X, Shi Y, Chai A, Fan T, Li B, Li L. Comparative genomics provides insights into the potential biocontrol mechanism of two Lysobacter enzymogenes strains with distinct antagonistic activities. Front Microbiol 2022; 13:966986. [PMID: 36033849 PMCID: PMC9410377 DOI: 10.3389/fmicb.2022.966986] [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: 06/12/2022] [Accepted: 07/27/2022] [Indexed: 11/29/2022] Open
Abstract
Lysobacter enzymogenes has been applied as an abundant beneficial microorganism to control plant disease; however, most L. enzymogenes strains have been mainly reported to control fungal diseases, not bacterial diseases. In this study, two L. enzymogenes strains were characterized, of which CX03 displayed a broad spectrum of antagonistic activities toward multiple bacteria, while CX06 exhibited a broad spectrum of antagonistic activities toward diverse fungi and oomycete, and the whole genomes of the two strains were sequenced and compared. The genome annotation showed that the CX03 genome comprised a 5,947,018 bp circular chromosome, while strain CX06 comprised a circular 6,206,196 bp chromosome. Phylogenetic analysis revealed that CX03 had a closer genetic relationship with L. enzymogenes ATCC29487T and M497-1, while CX06 was highly similar to L. enzymogenes C3. Functional gene annotation analyses of the two L. enzymogenes strains showed that many genes or gene clusters associated with the biosynthesis of different secondary metabolites were found in strains CX03 and CX06, which may be responsible for the different antagonistic activities against diverse plant pathogens. Moreover, comparative genomic analysis revealed the difference in bacterial secretory systems between L. enzymogenes strains CX03 and CX06. In addition, numerous conserved genes related to siderophore biosynthesis, quorum sensing, two-component systems, flagellar biosynthesis and chemotaxis were also identified in the genomes of strains CX03 and CX06. Most reported L. enzymogenes strains were proven mainly to suppress fungi, while CX03 exhibited direct inhibitory activities toward plant bacterial pathogens and showed an obvious role in managing bacterial disease. This study provides a novel understanding of the biocontrol mechanisms of L. enzymogenes, and reveals great potential for its application in plant disease control.
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