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Chlebek D, Płociniczak T, Gobetti S, Kumor A, Hupert-Kocurek K, Pacwa-Płociniczak M. Analysis of the Genome of the Heavy Metal Resistant and Hydrocarbon-Degrading Rhizospheric Pseudomonas qingdaonensis ZCR6 Strain and Assessment of Its Plant-Growth-Promoting Traits. Int J Mol Sci 2021; 23:ijms23010214. [PMID: 35008639 PMCID: PMC8745256 DOI: 10.3390/ijms23010214] [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: 11/23/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 12/28/2022] Open
Abstract
The Pseudomonas qingdaonensis ZCR6 strain, isolated from the rhizosphere of Zea mays growing in soil co-contaminated with hydrocarbons and heavy metals, was investigated for its plant growth promotion, hydrocarbon degradation, and heavy metal resistance. In vitro bioassays confirmed all of the abovementioned properties. ZCR6 was able to produce indole acetic acid (IAA), siderophores, and ammonia, solubilized Ca3(PO4)2, and showed surface active properties and activity of cellulase and very high activity of 1-aminocyclopropane-1-carboxylic acid deaminase (297 nmol α-ketobutyrate mg−1 h−1). The strain degraded petroleum hydrocarbons (76.52% of the initial hydrocarbon content was degraded) and was resistant to Cd, Zn, and Cu (minimal inhibitory concentrations reached 5, 15, and 10 mM metal, respectively). The genome of the ZCR6 strain consisted of 5,507,067 bp, and a total of 5055 genes were annotated, of which 4943 were protein-coding sequences. Annotation revealed the presence of genes associated with nitrogen fixation, phosphate solubilization, sulfur metabolism, siderophore biosynthesis and uptake, synthesis of IAA, ethylene modulation, heavy metal resistance, exopolysaccharide biosynthesis, and organic compound degradation. Complete characteristics of the ZCR6 strain showed its potential multiway properties for enhancing the phytoremediation of co-contaminated soils. To our knowledge, this is the first analysis of the biotechnological potential of the species P. qingdaonensis.
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Effects of Pseudomonas alkylphenolica KL28 on immobilization of Hg in soil and accumulation of Hg in cultivated plant. Biotechnol Lett 2019; 41:1343-1354. [PMID: 31583497 DOI: 10.1007/s10529-019-02736-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/23/2019] [Indexed: 10/25/2022]
Abstract
OBJECTIVE The available content of mercury (Hg) in farmland soil is directly related to the safety of agricultural products. Meanwhile, humans may accumulate high concentrations of Hg through the food chain, resulting in health damage. Regarding the remediation technologies of Hg-contaminated soil, research and development is mainly concentrated on the immobilisation of Hg in soil and efficient extraction by accumulators. Therefore, in this work, the highly Hg-tolerant strain Pseudomonas alkylphenolica KL28 was used to study the removal effect of Hg in a solution, immobilization effect of Hg in soil, and its effect on growth, Hg accumulation and photosynthetic characteristics of Brassica campestris L. RESULTS KL28 could effectively remove Hg2+ in the solution, with the removal ratio of 96.0% at 24 h. This strain could reduce decreases in shoots' and roots' dry weights by 31% and 16%, respectively, at a Hg concentration of 20 mg/L. The available Hg in the soil decreased to 4.7-9.4% in 8 days treated with KL28 bacterial solution at a dosage of 100 L/hm2. Meanwhile, with increases in Hg concentrations, Fv/Fm, Y(II), Y(I) and Y(NPQ) in the leaves of B. campestris showed a downward trend while Y(ND) and Y(NO) displayed an upward trend. Under the stress of 20 mg/L Hg2+, KL28 could reduce the Fv/Fm from 11.2 to 6.1%. CONCLUSIONS KL28 could effectively remove Hg in the solution, immobilize Hg in soil, promote growth, decrease Hg accumulation and affect photosynthetic characteristics of B. campestris, indicating its potential use in Hg contaminated soils.
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Circular pellicles formed by Pseudomonas alkylphenolica KL28 are a sophisticated architecture principally designed by matrix substance. J Microbiol 2018; 56:790-797. [PMID: 30353464 DOI: 10.1007/s12275-018-8252-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/23/2018] [Accepted: 07/26/2018] [Indexed: 10/28/2022]
Abstract
The colonization of liquid surfaces as floating biofilms or pellicles is a bacterial adaptation to optimally occupy the airliquid (A-L) niche. In aerobic heterotrophs, pellicle formation is beneficial for the utilization of O2 and nonpolar organic compounds. Pseudomonas alkylphenolica KL28, an alkylphenol degrader, forms flat circular pellicles that are 0.3-0.5 mm in diameter. In this study, we first monitored the pellicle developmental patterns of multicellular organization from the initial settlement stage. The pellicles developed by clonal growth and mutants for flagella and pilus formation established normal pellicles. In contrast, the mutants of an epm gene cluster for biosynthesis of alginate-like polymer were incompetent in cell alignment for initial two-dimensional (2D) pellicle growth, suggesting the role of the Epm polymer as a structural scaffold for pellicle biofilms. Microscopic observation revealed that the initial 2D growth transited to multilayers by an accumulated self-produced extracellular polymeric substance that may exert a constraint force. Electron microscopy and confocal laser scanning microscopy revealed that the fully matured pellicle structures were densly packed with matrix-encased cells displaying distinct arrangements. The cells on the surface of the pellicle were relatively flat, and those inside were longitudinally cross-packed. The extracellular polysaccharide stained by Congo red was denser on the pellicle rim and a thin film was observed in the open spaces, indicative of its role in pellicle flotation. Our results demonstrate that P. alkylphenolica KL28 coordinately dictates the cell arrangements of pellicle biofilms by the controlled growth of constituent cells that accumulate extracellular polymeric substances.
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Licciardello G, Caruso A, Bella P, Gheleri R, Strano CP, Anzalone A, Trantas EA, Sarris PF, Almeida NF, Catara V. The LuxR Regulators PcoR and RfiA Co-regulate Antimicrobial Peptide and Alginate Production in Pseudomonas corrugata. Front Microbiol 2018; 9:521. [PMID: 29662475 PMCID: PMC5890197 DOI: 10.3389/fmicb.2018.00521] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 03/08/2018] [Indexed: 02/02/2023] Open
Abstract
Cyclic lipopeptides (CLPs) are considered as some of the most important secondary metabolites in different plant-associated bacteria, thanks to their antimicrobial, cytotoxic, and surfactant properties. In this study, our aim was to investigate the role of the Quorum Sensing (QS) system, PcoI/PcoR, and the LuxR-type transcriptional regulator RfiA in CLP production in the phytopatogenic bacterium, Pseudomonas corrugata based on our previous work where we reported that the pcoR and rfiA mutants were devoid of the CLPs cormycin and corpeptin production. Due to the close genetic link between the QS system and the RfiA (rfiA is co-transcribed with pcoI), it was difficult to ascertain the specific regulatory role in the expression of target genes. A transcriptional approach was undertaken to identify the specific role of the PcoR and RfiA transcriptional regulators for the expression of genes involved in CLP production. The RNA-seq-based transcriptional analysis of the wild-type (WT) strain CFBP 5454 in comparison with GL2 (pcoR mutant) and GLRFIA (rfiA mutant) was performed in cultural conditions favoring CLP production. Differential gene expression revealed that 152 and 130 genes have significantly different levels of expression in the pcoR and rfiA mutants, respectively. Of these, the genes linked to the biosynthesis of CLPs and alginate were positively controlled by both PcoR and RfiA. Blast homology analysis showed that 19 genes in a large CLP biosynthetic cluster involved in the production of three antimicrobial peptides, which span approximately 3.5% of the genome, are strongly over-expressed in the WT strain. Thus, PcoR and RfiA function mainly as activators in the production of bioactive CLPs, in agreement with phenotype analysis of mutants. RNA-seq also revealed that almost all the genes in the structural/biosynthetic cluster of alginate exopolysaccharide (EPS) are under the control of the PcoR-RfiA regulon, as supported by the 10-fold reduction in total EPS yield isolated in both mutants in comparison to the parent strain. A total of 68 and 38 gene expressions was independently regulated by PcoR or RfiA proteins, respectively, but at low level. qPCR experiments suggest that growth medium and plant environment influence the expression of CLP and alginate genes.
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Affiliation(s)
- Grazia Licciardello
- Parco Scientifico e Tecnologico della Sicilia, Catania, Italy
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi di Catania, Catania, Italy
| | - Andrea Caruso
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi di Catania, Catania, Italy
| | - Patrizia Bella
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Rodolpho Gheleri
- School of Computing, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
| | - Cinzia P. Strano
- Dipartimento di Agraria, Università degli Studi “Mediterranea” di Reggio Calabria, Reggio Calabria, Italy
| | - Alice Anzalone
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi di Catania, Catania, Italy
| | - Emmanouil A. Trantas
- Department of Agriculture, School of Agriculture, Food and Nutrition, Technological Educational Institute of Crete, Heraklion, Greece
| | - Panagiotis F. Sarris
- Department of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology – Hellas, Heraklion, Greece
| | - Nalvo F. Almeida
- School of Computing, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
| | - Vittoria Catara
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi di Catania, Catania, Italy
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Lee K, Ha GS, Veeranagouda Y, Seo YS, Hwang I. A CHASE3/GAF sensor hybrid histidine kinase BmsA modulates biofilm formation and motility in Pseudomonas alkylphenolica. MICROBIOLOGY-SGM 2016; 162:1945-1954. [PMID: 27655385 DOI: 10.1099/mic.0.000373] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Pseudomonas alkylphenolica is an important strain in the biodegradation of toxic alkylphenols and mass production of bioactive polymannuronate polymers. This strain forms a diverse, 3D biofilm architecture, including mushroom-like aerial structures, circular pellicles and surface spreading, depending on culture conditions. A mutagenesis and complementation study showed that a predicted transmembrane kinase, PSAKL28_21690 (1164 aa), harbouring a periplasmic CHASE3 domain flanked by two transmembrane helices in addition to its cytoplasmic GAF, histidine kinase and three CheY-like response regulator domains, plays a positive role in the formation of the special biofilm architecture and a negative role in swimming activity. In addition, the gene, named here as bmsA, is co-transcribed with three genes encoding proteins with CheR (PSAKL28_21700) and CheB (PSAKL28_21710) domains and response regulator and histidine kinase domains (PSAKL28_21720). This gene cluster is thus named bmsABCD and is found widely distributed in pseudomonads and other bacteria. Deletion of the genes in the cluster, except forbmsA, did not result in changes in biofilm-related phenotypes. The RNA-seq analysis showed that the expression of genes coding for flagellar synthesis was increased when bmsA was mutated. In addition, the expression of rsmZ, which is one of final targets of the Gac regulon, was not significantly altered in the bmsA mutant, and overexpression of bmsA in the gacA mutant did not produce the WT phenotype. These results indicate that the sensory Bms regulon does not affect the upper cascade of the Gac signal transduction pathway for the biofilm-related phenotypes in P. alkylphenolica.
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Affiliation(s)
- Kyoung Lee
- Department of Bio Health Science, Changwon National University, Changwon-si, Kyongnam 51140, Republic of Korea
| | - Gwang Su Ha
- Department of Bio Health Science, Changwon National University, Changwon-si, Kyongnam 51140, Republic of Korea
| | - Yaligara Veeranagouda
- Department of Bio Health Science, Changwon National University, Changwon-si, Kyongnam 51140, Republic of Korea
| | - Young-Su Seo
- Department of Microbiology, Pusan National University, Busan 46241, Republic of Korea
| | - Ingyu Hwang
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
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Mulet M, Sánchez D, Lalucat J, Lee K, García-Valdés E. Pseudomonas alkylphenolica sp. nov., a bacterial species able to form special aerial structures when grown on p-cresol. Int J Syst Evol Microbiol 2015; 65:4013-4018. [DOI: 10.1099/ijsem.0.000529] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas sp. KL28T is an aerobic, rod-shaped bacterium that was isolated from the soil of Changwon, South Korea, based on its ability to grow in the presence of linear alkylphenols (C1–C5). Despite several studies on strain KL28T, it could not be assigned to any known species in the genus Pseudomonas. The name ‘Pseudomonas alkylphenolia’ was proposed for KL28T, but the strain had not until now been characterized taxonomically and the name currently has no standing in the bacterial nomenclature. A 16S rRNA gene sequence based phylogenetic analysis suggested an affiliation of strain KL28T with the Pseudomonas putida group, with Pseudomonas vranovensis DSM 16006T as the most closely related type strain (99.1 % similarity). A multilocus phylogenetic sequence analysis performed by concatenating 16S rRNA, gyrB, rpoD and rpoB partial gene sequences showed that isolate KL28T could be differentiated from P. vranovensis DSM 16006T (sequence similarity 93.7 %). Genomic comparisons of strain KL28T with the type strains of the species in the P. putida group using average nucleotide index based on blast (ANIb) and genome-to genome distances (GGDC) revealed 87.06 % and 32.20 % similarities with P. vranovensis DSM 16006T, respectively, as the closest type strain. Both values are far from the thresholds established for species differentiation. These results, together with differences in phenotypic features and chemotaxonomic analyses [fatty acids and whole-cell matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS], support the proposal of strain KL28T ( = JCM 16553T = KCTC 22206T) as the type strain of a novel species, for which the formerly proposed name, ‘P. alkylphenolia’, is correctly latinized as Pseudomonas alkylphenolica sp. nov.
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Affiliation(s)
- Magdalena Mulet
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Crtra. Valldemossa km 7.5, Campus UIB, 07122 Palma de Mallorca, Spain
| | - David Sánchez
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Crtra. Valldemossa km 7.5, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Jorge Lalucat
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Crtra. Valldemossa km 7.5, Campus UIB, 07122 Palma de Mallorca, Spain
- Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain
| | - Kyoung Lee
- Department of Bio Health Science, Changwon National University, Changwon-si, Kyongnam 641-773, Republic of Korea
| | - Elena García-Valdés
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Crtra. Valldemossa km 7.5, Campus UIB, 07122 Palma de Mallorca, Spain
- Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain
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Zhurina MV, Gannesen AV, Zdorovenko EL, Plakunov VK. Composition and functions of the extracellular polymer matrix of bacterial biofilms. Microbiology (Reading) 2014. [DOI: 10.1134/s002626171406023x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Bilcu M, Grumezescu AM, Oprea AE, Popescu RC, Mogoșanu GD, Hristu R, Stanciu GA, Mihailescu DF, Lazar V, Bezirtzoglou E, Chifiriuc MC. Efficiency of vanilla, patchouli and ylang ylang essential oils stabilized by iron oxide@C14 nanostructures against bacterial adherence and biofilms formed by Staphylococcus aureus and Klebsiella pneumoniae clinical strains. Molecules 2014; 19:17943-56. [PMID: 25375335 PMCID: PMC6271200 DOI: 10.3390/molecules191117943] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 10/22/2014] [Accepted: 10/29/2014] [Indexed: 12/11/2022] Open
Abstract
Biofilms formed by bacterial cells are associated with drastically enhanced resistance against most antimicrobial agents, contributing to the persistence and chronicization of the microbial infections and to therapy failure. The purpose of this study was to combine the unique properties of magnetic nanoparticles with the antimicrobial activity of three essential oils to obtain novel nanobiosystems that could be used as coatings for catheter pieces with an improved resistance to Staphylococcus aureus and Klebsiella pneumoniae clinical strains adherence and biofilm development. The essential oils of ylang ylang, patchouli and vanilla were stabilized by the interaction with iron oxide@C14 nanoparticles to be further used as coating agents for medical surfaces. Iron oxide@C14 was prepared by co-precipitation of Fe+2 and Fe+3 and myristic acid (C14) in basic medium. Vanilla essential oil loaded nanoparticles pelliculised on the catheter samples surface strongly inhibited both the initial adherence of S. aureus cells (quantified at 24 h) and the development of the mature biofilm quantified at 48 h. Patchouli and ylang-ylang essential oils inhibited mostly the initial adherence phase of S. aureus biofilm development. In the case of K. pneumoniae, all tested nanosystems exhibited similar efficiency, being active mostly against the adherence K. pneumoniae cells to the tested catheter specimens. The new nanobiosystems based on vanilla, patchouli and ylang-ylang essential oils could be of a great interest for the biomedical field, opening new directions for the design of film-coated surfaces with anti-adherence and anti-biofilm properties.
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Affiliation(s)
- Maxim Bilcu
- Microbiology Department, Faculty of Biology, Research Institute of the University of Bucharest, University of Bucharest, Aleea Portocalelor No. 1-3, 060101 Bucharest, Romania.
| | - Alexandru Mihai Grumezescu
- Department of Science and Engineering of Oxide Materials and Nanomaterials, Faculty of Applied Chemistry and Materials Science, University Politehnica of Bucharest, Polizu Street No. 1-7, 011061 Bucharest, Romania.
| | - Alexandra Elena Oprea
- Department of Science and Engineering of Oxide Materials and Nanomaterials, Faculty of Applied Chemistry and Materials Science, University Politehnica of Bucharest, Polizu Street No. 1-7, 011061 Bucharest, Romania.
| | - Roxana Cristina Popescu
- Department of Science and Engineering of Oxide Materials and Nanomaterials, Faculty of Applied Chemistry and Materials Science, University Politehnica of Bucharest, Polizu Street No. 1-7, 011061 Bucharest, Romania.
| | - George Dan Mogoșanu
- Department of Pharmacognosy & Phytotherapy, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania.
| | - Radu Hristu
- Center for Microscopy-Microanalysis and Information Processing, University Politehnica of Bucharest, 313 Splaiul Independentei, 060042 Bucharest, Romania.
| | - George A Stanciu
- Center for Microscopy-Microanalysis and Information Processing, University Politehnica of Bucharest, 313 Splaiul Independentei, 060042 Bucharest, Romania.
| | - Dan Florin Mihailescu
- Microbiology Department, Faculty of Biology, Research Institute of the University of Bucharest, University of Bucharest, Aleea Portocalelor No. 1-3, 060101 Bucharest, Romania.
| | - Veronica Lazar
- Microbiology Department, Faculty of Biology, Research Institute of the University of Bucharest, University of Bucharest, Aleea Portocalelor No. 1-3, 060101 Bucharest, Romania.
| | - Eugenia Bezirtzoglou
- Laboratory of Microbiology, Biotechnology and Hygiene, Department of Food Science and Technology, Faculty of Agricultural Development, Democritus University of Thrace, 68200 Orestiada, Greece.
| | - Mariana Carmen Chifiriuc
- Microbiology Department, Faculty of Biology, Research Institute of the University of Bucharest, University of Bucharest, Aleea Portocalelor No. 1-3, 060101 Bucharest, Romania.
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Lim JY, Lee K, Hwang I. Complete genome sequence of the mushroom-like aerial structure-forming Pseudomonas alkylphenolia, a platform bacterium for mass production of poly-β-d-mannuronates. J Biotechnol 2014; 192 Pt A:20-1. [PMID: 25300744 DOI: 10.1016/j.jbiotec.2014.09.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 09/17/2014] [Indexed: 10/24/2022]
Abstract
Pseudomonas alkylphenolia (KCTC 22206, JCM 16553) metabolizes phenols with an alkyl chain (C1-C5) at the para position. This strain forms mushroom-like aerial structures under p-cresol vapor, and its mutants are exploited to augment the production of poly-β-d-mannuronate and its derivatives. In this study, we report the 5.7Mbp complete genome sequence of P. alkylphenolia, which will provide a basis for biotechnological applications of this strain.
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Affiliation(s)
- Jae Yun Lim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea
| | - Kyoung Lee
- Department of Microbiology, Changwon National University, Changwon-si 641-773, Republic of Korea.
| | - Ingyu Hwang
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea.
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