Chryseobacterium cucumeris sp. nov., an endophyte isolated from cucumber (Cucumis sativus L.) root, and emended description of Chryseobacterium arthrosphaerae

Jin Ju Jeong, Dong Wan Lee, Byeonghyeok Park, Mee Kyung Sang, In-Geol Choi, Ki Deok Kim

Research output: Contribution to journalComment/debate

6 Citations (Scopus)

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).

Original languageEnglish
Article number001670
Pages (from-to)610-616
Number of pages7
JournalInternational Journal of Systematic and Evolutionary Microbiology
Volume67
Issue number3
DOIs
Publication statusPublished - 2017 Apr 1

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aprepitant
Chryseobacterium
Endophytes
Cucumis sativus
endophyte
endophytes
cucumbers
DNA
new species
lipid
fatty acid
genome
phylogenetics
gene
Chryseobacterium gleum
Chryseobacterium indologenes
Lipids
Genes
Glycolipids
Base Composition

Keywords

  • Average nucleotide identity
  • Biocontrol agent
  • Chryseobacterium cucumeris
  • Chryseobacterium strain GSE06
  • Endophytic bacterium

ASJC Scopus subject areas

  • Microbiology
  • Ecology, Evolution, Behavior and Systematics

Cite this

Chryseobacterium cucumeris sp. nov., an endophyte isolated from cucumber (Cucumis sativus L.) root, and emended description of Chryseobacterium arthrosphaerae. / Jeong, Jin Ju; Lee, Dong Wan; Park, Byeonghyeok; Sang, Mee Kyung; Choi, In-Geol; Kim, Ki Deok.

In: International Journal of Systematic and Evolutionary Microbiology, Vol. 67, No. 3, 001670, 01.04.2017, p. 610-616.

Research output: Contribution to journalComment/debate

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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).",
keywords = "Average nucleotide identity, Biocontrol agent, Chryseobacterium cucumeris, Chryseobacterium strain GSE06, Endophytic bacterium",
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AU - Lee, Dong Wan

AU - Park, Byeonghyeok

AU - Sang, Mee Kyung

AU - Choi, In-Geol

AU - Kim, Ki Deok

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N2 - 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).

AB - 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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