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Jung Y, Chhetri G, Kim I, So Y, Park S, Woo H, Lee KH, Seo T. Chryseobacterium edaphi sp. nov. and Chryseobacterium gilvum sp. nov., isolated from soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 37490399 DOI: 10.1099/ijsem.0.005989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023] Open
Abstract
Two Gram-stain-negative, aerobic, yellow and rod-shaped bacteria, designated as strains PBS4-4T and GMJ5T, were isolated from soil samples collected in Goyang-si and Paju-si, Gyeonggi-do, Republic of Korea. Strains PBS4-4T and GMJ5T were both positive for catalase and oxidase. Strain PBS4-4T grew at 15-37 °C and pH 5.0-12.0. Strain GMJ5T grew at 15-37 °C and pH 5.0-11.0. Neither strain required NaCl for growth. 16S rRNA sequence analysis revealed that strains PBS4-4T and GMJ5T form a closely related cluster with the genus Chryseobacterium. The average nucleotide identity and digital DNA-DNA hybridization values between strain PBS4-4T and its closely related strains were 79.4-84.5% and 23.2-28.7 %, respectively. For GMJ5T, the values were 78.3-79.3% and 22.0-22.6 %, respectively. The major fatty acids shared by both novel strains were iso-C15 : 0 and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c). Strain GMJ5T had one other major fatty acid: iso-C17 : 0 3OH. Based on phenotypic, genomic and phylogenetic results, strains PBS4-4T and GMJ5T represent novel species within the genus Chryseobacterium, and the names Chryseobacterium edaphi sp. nov. and Chryseobacterium gilvum sp. nov. are proposed, respectively. The type strain of C. edaphi is PBS4-4T (=KACC 22882T=TBRC 17052T) and the type strain of C. gilvum is GMJ5T (=KACC 22883T=TBRC 17053T).
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Affiliation(s)
- Yonghee Jung
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Sunho Park
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Haejin Woo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Ki-Ho Lee
- Department of Biochemistry and Molecular Biology, College of Medicine, Eulji University, Daejeon 34824, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
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Chryseobacterium paridis sp. nov., an endophytic bacterial species isolated from the root of Paris polyphylla Smith var. yunnanensis. Arch Microbiol 2021; 203:4777-4783. [PMID: 34345976 DOI: 10.1007/s00203-021-02504-2] [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: 05/14/2021] [Revised: 07/09/2021] [Accepted: 07/26/2021] [Indexed: 10/20/2022]
Abstract
A Gram-negative, yellow-pigmented, rod-shaped bacterial strain YIM B02567T was isolated from the root of Paris polyphylla Smith var. yunnanensis in China. Strain YIM B02567T grew optimally at 25-30 °C and at pH 7.0 in the absence of NaCl on nutrient agar. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain YIM B02567T belong to the genus Chryseobacterium, and was closely related to Chryseobacterium piperi CTMT and Chryseobacterium soli DSM 19298T. Whole genome sequencing indicated that the genome size was 4,774,612 bp and with a G + C content of 34.5 mol%. Values of the ANI and the dDDH between strain YIM B02567T and its closely related Chryseobacterium species were below 81.72% and 24.7%. Strain YIM B02567T contained menaquinone-6 as the sole isoprenoid quinone, anteiso-C15:0, iso-C17:1 ω9c and iso-C17:0 3-OH as major fatty acids and phosphatidylethanolamine as major polar lipid. Based on the polyphasic analyses, strain YIM B02567T could be differentiated genotypically and phenotypically from recognized species of the genus Chryseobacterium. The isolate, therefore, represents a novel species, for which the name Chryseobacterium paridis sp. nov. is proposed. The type strain is YIM B02567T (= CGMCC 1.18657T).
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Chhetri G, Kim J, Kim I, Kang M, Seo T. Chryseobacterium caseinilyticum sp. nov., a casein hydrolyzing bacterium isolated from rice plant and emended description of Chryseobacterium piscicola. Int J Syst Evol Microbiol 2021; 71. [PMID: 34232119 DOI: 10.1099/ijsem.0.004854] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, aerobic, asporogenous, catalase-positive and oxidase-negative, non-motile, golden-yellow pigmented, rod-shaped bacterium with casein-degrading ability, designated strain GCR10T, was isolated from roots of rice plants collected from a paddy field near Dongguk University, Republic of Korea. The results of subsequent 16S rRNA gene sequence analysis indicated that GCR10T shares the highest sequence identity with Chryseobacterium piscicola VQ-6316sT (98.3%). Strain GCR10T grew at 2-32 °C (optimum, 25 °C), at pH 6.0-8.0 (optimum, pH 7.0) and in the presence of 0-2.0% (w/v) NaCl (optimum in the absence of NaCl). The novel strain was able to produce carotenoid and flexirubin-type pigments. The predominant menaquinone was MK-6 and the major fatty acids were identified as iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 1ω9c. The polar lipids were phosphatidylethanolamine, four unidentified aminoglycolipids, two unidentified aminolipids and two unidentified glycolipids. The genome of GCR10T is 4.3 Mb in length with a DNA G+C content of 36.5 mol%. Average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values between GCR10T and Chryseobacterium piscicola VQ-6316sT were 82.1, 25.2 and 84.3 %, respectively, which clearly indicates that the novel strain is distinct from its closest relative. The demand for natural biodegradable pigments isolated frominsects, plants or microorganisms is increasing day by day because of their beneficial pharmacological properties. Here, we describe a novel strain that produces two types of pigment, carotenoid and flexirubin. On the basis of the results from phenotypic, genotypic and chemotaxonomic analyses, strain GCR10T represents a novel species of the genus Chryseobacterium, and the name Chryseobacterium caseinilyticum sp. nov. is proposed. The type strain is GCR10T (=KACC 21707T=NBRC 114715T).
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Affiliation(s)
- Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Minchung Kang
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
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Draft Genome Sequence of Phosphate-Solubilizing Chryseobacterium sp. Strain ISE14, a Biocontrol and Plant Growth-Promoting Rhizobacterium Isolated from Cucumber. GENOME ANNOUNCEMENTS 2018; 6:6/26/e00612-18. [PMID: 29954909 PMCID: PMC6025925 DOI: 10.1128/genomea.00612-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Chryseobacterium sp. strain ISE14 is a phosphate-solubilizing endophytic bacterium that exhibits plant growth promotion and biocontrol activities against Phytophthora blight and anthracnose on pepper. Chryseobacterium sp. strain ISE14 is a phosphate-solubilizing endophytic bacterium that exhibits plant growth promotion and biocontrol activities against Phytophthora blight and anthracnose on pepper. Here, we report the draft genome sequence of strain ISE14, which contains genes relating to phosphate solubilization, plant growth promotion, and biocontrol traits.
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Pérez-Sancho M, Vela AI, Kostrzewa M, Zamora L, Casamayor A, Domínguez L, Fernández-Garayzábal JF. First analysis by MALDI-TOF MS technique of Chryseobacterium species relevant to aquaculture. JOURNAL OF FISH DISEASES 2018; 41:389-393. [PMID: 29125187 DOI: 10.1111/jfd.12706] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 07/25/2017] [Accepted: 07/26/2017] [Indexed: 06/07/2023]
Affiliation(s)
- M Pérez-Sancho
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, Madrid, Spain
| | - A I Vela
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, Madrid, Spain
- Facultad de Veterinaria, Departamento de Sanidad Animal, Universidad Complutense, Madrid, Spain
| | | | - L Zamora
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, Madrid, Spain
| | - A Casamayor
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, Madrid, Spain
| | - L Domínguez
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, Madrid, Spain
- Facultad de Veterinaria, Departamento de Sanidad Animal, Universidad Complutense, Madrid, Spain
| | - J F Fernández-Garayzábal
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, Madrid, Spain
- Facultad de Veterinaria, Departamento de Sanidad Animal, Universidad Complutense, Madrid, Spain
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Draft Genome Sequence of
Chryseobacterium
sp. JV274 Isolated from Maize Rhizosphere. GENOME ANNOUNCEMENTS 2017; 5:5/15/e00122-17. [PMID: 28408666 PMCID: PMC5391404 DOI: 10.1128/genomea.00122-17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report the draft genome sequence of Chryseobacterium sp. JV274. This strain was isolated from the rhizosphere of maize during a greenhouse experiment. JV274 harbors genes involved in flexirubin production (darA and darB genes), bacterial competition (type VI secretion system), and gliding (bacterial motility; type IX secretion system).
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Jeong JJ, Lee DW, Park B, Sang MK, Choi IG, Kim KD. Chryseobacterium cucumeris sp. nov., an endophyte isolated from cucumber (Cucumis sativus L.) root, and emended description of Chryseobacterium arthrosphaerae. Int J Syst Evol Microbiol 2017; 67:610-616. [PMID: 27902284 DOI: 10.1099/ijsem.0.001670] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Gram-stain-negative, yellow-pigmented, rod-shaped bacterial strain GSE06T, isolated from the surface-sterilized root of a cucumber plant grown in a field in Gunsan, Korea, was characterized by not only cultural and morphological features but also physiological, biochemical and molecular analyses. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain GSE06T was most closely related to species of the genus Chryseobacterium. Furthermore, strain GSE06T exhibited the highest sequence similarities with the type strains Chryseobacterium indologenes ATCC 29897T (98.9 %), Chryseobacterium gleum ATCC 35910T (98.8 %), Chryseobacterium arthrosphaerae CC-VM-7T (98.7 %), Chryseobacterium contaminans C26T (98.5 %), Chryseobacterium artocarpi UTM-3T (98.3 %), and Chryseobacterium gallinarum 100T (97.9 %). Average nucleotide identity values between genome sequences of strain GSE06T and the above-mentioned reference strains ranged from 81.2 to 86.9 %, which were lower than the threshold of 95 % (corresponding to a DNA-DNA reassociation value of 70 %). The DNA G+C content of strain GSE06T was 36.1 mol%; the predominant respiratory quinone of the strain was MK-6. The major fatty acids were iso-C15 : 0, summed feature 9 (iso-C17 : 1ω9c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, three aminolipids, one aminophospholipid, four glycolipids and one unidentified lipid. These results of phenotypic and genotypic characteristics could differentiate strain GSE06T from closely related type strains belonging to the genus Chryseobacterium. Thus, strain GSE06T is proposed as a representative of a novel species in the genus Chryseobacterium, Chryseobacterium cucumeris sp. nov. The type strain is GSE06T (=KACC 18798T=JCM 31422T).
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Affiliation(s)
- Jin-Ju Jeong
- Laboratory of Plant Disease and Biocontrol, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Dong Wan Lee
- Department of Biosystems and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Byeonghyeok Park
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Mee Kyung Sang
- Present address: Division of Agricultural Microbiology, National Academy of Agricultural Science, Rural Development Administration, Jeonju 55365, Republic of Korea.,Laboratory of Plant Disease and Biocontrol, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - In-Geol Choi
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Ki Deok Kim
- Laboratory of Plant Disease and Biocontrol, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
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Zhao Z, Tu YQ, Shen X, Han SB, Zhang CY, Sun C, Wu M. Chryseobacterium lineare sp. nov., isolated from a limpid stream. Int J Syst Evol Microbiol 2016; 67:800-805. [PMID: 27902240 DOI: 10.1099/ijsem.0.001629] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, non-motile, rod-shaped, yellow-pigmented bacterial strain, XC0022T, isolated from freshwater of a limpid stream in Zhejiang, China, was studied using a polyphasic approach. The phylogenetic analysis based on 16S rRNA gene sequences clearly showed an allocation to the genus Chryseobacterium with the highest sequence similarities of 98.0 % to Chryseobacterium taeanense PHA3-4T, 97.2 % to Chryseobacterium taihuense THMBM1T, 97.1 % to Chryseobacterium rigui CJ16T and 97.1 % to Chryseobacteriumprofundimaris DY46T. 16S rRNA gene sequence similarities to all other species of the genus Chryseobacterium were below 97.0 % (92.3-96.8 %). DNA-DNA hybridization results showed that strain XC0022T was 55.3 %, 49.8 % and 31.1 % related to C. taeanense DSM 17071T, Chryseobacteriumtaichungense DSM 17453T and Chryseobacteriumgleum JCM 2410T, respectively. The quinone system was composed only of MK-6. Strain XC0022T possessed iso-C15 : 0, iso-C17 : 0 3-OH, C18 : 1ω9c and summed feature 3 (iso-C15 : 0 2-OH/C16 : 1ω7c) as the major fatty acids. The polar lipids profile consisted of one phosphatidylethanolamine, one unidentified glycolipid, four unidentified aminolipids and two unidentified lipids. The G+C content of the genomic DNA was 29.7 mol%. On the basis of phenotypic, phylogenetic and chemotaxonomic data, strain XC0022T (=KCTC 52364T=MCCC 1K02723T) represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium lineare sp. nov. is proposed.
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Affiliation(s)
- Zhe Zhao
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Yin-Qi Tu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Xia Shen
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Shuai-Bo Han
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Chong-Ya Zhang
- Ocean College, Zhejiang University, Hangzhou 310058, PR China
| | - Cong Sun
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Min Wu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
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Nishioka T, Elsharkawy MM, Suga H, Kageyama K, Hyakumachi M, Shimizu M. Development of Culture Medium for the Isolation of Flavobacterium and Chryseobacterium from Rhizosphere Soil. Microbes Environ 2016; 31:104-10. [PMID: 27098502 PMCID: PMC4912144 DOI: 10.1264/jsme2.me15144] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
An effective medium designated phosphate separately autoclaved Reasoner’s 2A supplemented with cycloheximide and tobramycin (PSR2A-C/T) has been developed for the isolation of Flavobacterium and Chryseobacterium strains from the plant rhizosphere. It consists of Reasoner’s 2A agar (R2A) prepared by autoclaving phosphate and agar separately and supplementing with 50 mg L−1 cycloheximide and 1 mg L−1 tobramycin. A comparison was made among the following nine media: PSR2A-C/T, PSR2A-C/T supplemented with NaCl, R2A agar, R2A agar supplemented with cycloheximide and tobramycin, 1/4-strength tryptic soy agar (TSA), 1/10-strength TSA, soil-extract agar, Schaedler anaerobe agar (SAA), and SAA supplemented with gramicidin, for the recovery of Flavobacterium and Chryseobacterium strains from the Welsh onion rhizosphere. Flavobacterium strains were only isolated on PSR2A-C/T, and the recovery rate of Chryseobacterium strains was higher from PSR2A-C/T than from the eight other media. In order to confirm the effectiveness of PSR2A-C/T, bacteria were isolated from onion rhizosphere soil with this medium. Flavobacterium and Chryseobacterium strains were successfully isolated from this sample at a similar rate to that from the Welsh onion rhizosphere.
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Affiliation(s)
- Tomoki Nishioka
- Graduate School of Applied Biological Sciences, Gifu University
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