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  • 1
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    Sphingomonas xanthus sp. nov., Isolated from Beach Soil
    Springer Science and Business Media LLC ; 2021
    In:  Current Microbiology Vol. 78, No. 1 ( 2021-01), p. 403-410
    Details
    In: Current Microbiology, Springer Science and Business Media LLC, Vol. 78, No. 1 ( 2021-01), p. 403-410
    Type of Medium: Online Resource
    ISSN: 0343-8651 , 1432-0991
    URL: Article
    DOI: 10.1007/s00284-020-02273-z
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 1458987-4
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  • 2
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    Hymenobacter setariae sp. nov., isolated from the ubiquitous weedy grass Setaria viridis
    Microbiology Society ; 2020
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 70, No. 6 ( 2020-06-01), p. 3724-3730
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 70, No. 6 ( 2020-06-01), p. 3724-3730
    Abstract: A Gram-stain-negative, short-rod, aerobic, non-motile, red to pink-pigmented bacterium, designated Fur1 T , was isolated from the dry spikelet clusters of a plant called Setaria viridis near Dongguk University. Phylogenetic analysis conducted based on 16S rRNA gene sequences indicated that strain Fur1 T belonged to the genus Hymenobacter of the family Hymenobacteraceae . The 16S rRNA gene of Fur1 T showed highest sequence similarity to those of Hymenobacter metalli KACC 17381 T (97.5 %) and Hymenobacter marinus KACC 19042 T (97.1 %). Growth occurred at 4–37 °C (optimum, 25–28 °C), up to 1.0 % NaCl (optimum, 0 %) and pH 5.5–9.0 (optimum, pH 6.0–7.5). The major fatty acids of strain Fur1 T were identified as iso-C 15 : 0 , C 16 : 1   ω5 c , anteiso-C 15 : 0 , summed feature 3 (comprising C 16 : 1   ω7 c and/or C 16 : 1   ω6 c ) and summed feature 4 (comprising anteiso-C 17 : 1 B and/or iso-C 17 : 1 I) as the major cellular fatty acids. The predominant respiratory quinone was identified as MK-7. The polar lipids were phosphatidylethanolamine, five unidentified aminophospholipids, two unidentified phospholipids, one unidentified glycolipid and one unidentified polar lipid. The genomic DNA G+C content based on the draft genome sequence was 58.7 mol%. DNA–DNA relatedness between strain Fur1 T and its closest relative was below 70 %. Characterization based on phylogenetic, chemotaxonomic and phenotypic analyses clearly indicated that strain Fur1 T represents a novel species of the genus Hymenobacter , for which the name Hymenobacter setariae sp. nov. is proposed. The type strain is Fur1 T (=KACC 19903 T =NBRC=113691 T ).
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.004226
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2020
    detail.hit.zdb_id: 215062-1
    detail.hit.zdb_id: 2056611-6
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  • 3
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    Adhaeribacter rhizoryzae sp. nov., a fibrillar matrix-producing bacterium isolated from the rhizosphere of rice plant
    Microbiology Society ; 2020
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 70, No. 10 ( 2020-10-01), p. 5382-5388
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 70, No. 10 ( 2020-10-01), p. 5382-5388
    Abstract: A novel fibrillar matrix-producing, rod-shaped, red–orange, asporogenous, aerobic bacterium, designated DK36 T , was isolated from roots of a rice plant in the Ilsan region near Dongguk University, South Korea. Cells of strain DK36 T were Gram-stain-negative and motile by means of gliding. The temperature and pH ranges for growth were 7–35 °C (optimum: 30 °C) and pH 5–10 (optimum: pH 7.0). The strain did not require NaCl for growth but tolerated up to 8 % (w/v) NaCl. Phylogenetic anlaysis of the 16S rRNA gene sequence revealed that DK36 T formed a monophyletic clade with Adhaeribacter aerophilus 6425 S-25 T , Adhaeribacter aerolatus 6515 J-31 T and Adhaeribacter swui 17mud1-7 T with sequence similarities of 96.3, 95.5 and 95.2%, respectively. The average nucleotide identity and in silico DNA–DNA hybridization values of strain DK36 T with the most closely related strains whose whole genomes are publicly available were 72.5–83.6% and 19–28 %, respectively. The strain showed the typical chemotaxonomic characteristics of the genus Adhaeribacter , with the presence of menaquinone MK-7 as the respiratory quinone, and C 16 : 1 ω5 c , iso-C 15 : 0 and summed feature 4 (composed of iso-C 17 : 1 I/anteiso-C 17 : 1 B) as the major fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, one unidentified aminophosphoglycolipid, one unidentified phospholipid, two unidentified aminolipids and five unidentified polar lipids. The genomic DNA G+C content based on the draft genome sequence was 43.4 mol%. The results of physiological and biochemical tests and 16S rRNA gene sequence analysis clearly revealed that strain DK36 T represents a novel species of the genus Adhaeribacter , for which the name Adhaeribacter rhizoryzae sp. nov. is proposed. The type strain is DK36 T (=KACC 19902 T =NBRC 113689 T ).
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.004422
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2020
    detail.hit.zdb_id: 215062-1
    detail.hit.zdb_id: 2056611-6
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  • 4
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    Cohnella terricola sp. nov., isolated from soil
    Microbiology Society ; 2021
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 71, No. 6 ( 2021-06-23)
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 71, No. 6 ( 2021-06-23)
    Abstract: A Gram-positive, aerobic, flagellated, endospore-forming, rod-shaped strain, designated as G13 T , was isolated from soil. The results of 16S rRNA gene sequence analysis led to the conclusion that strain G13 T was phylogenetically related to Cohnella boryungensis BR29 T (97.5 %) and Cohnella phaseoli CECT 7287 T (96.9 %) with digital DNA–DNA hybridization values of 21.0 and 21.4 %, and distantly related to Cohnella thermotolerans CCUG 47242 T (94.8 %), type species of the genus Cohnella , at 19.0 %. The genome size of strain G13 T was 5 387 258 bp, with 51.3 mol% G+C content. The predominant fatty acids were summed feature 9 (iso-C 17 : 1  ω 9 c and/or C 16 : 0 10-methyl), anteiso-C 17 : 0 , iso-C 17 : 0 and iso-C 15 : 0 . The predominant quinone was menaquinone-7 and the major polar lipids were diphosphatidyglycerol, phosphatidylethanolamine, phosphatidylglycerol, lysylphosphatidylglycerol, three aminophospholipids, two phosphoglycolipids, three aminolipids and two unidentified lipids. Based on the data from phenotypic tests and the genotypic differences between strain G13 T and its close phylogenetic relatives, strain G13 T represents a new species belonging to the genus Cohnella , for which the name Cohnella terricola sp. nov. (=KACC 19905 T =NBRC 113748 T ) is proposed.
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.004835
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2021
    detail.hit.zdb_id: 215062-1
    detail.hit.zdb_id: 2056611-6
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  • 5
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    Chryseobacterium edaphi sp. nov. and Chryseobacterium gilvum sp. nov., isolated from soil
    Microbiology Society ; 2023
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 73, No. 7 ( 2023-07-25)
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 73, No. 7 ( 2023-07-25)
    Abstract: Two Gram-stain-negative, aerobic, yellow and rod-shaped bacteria, designated as strains PBS4-4 T and GMJ5 T , were isolated from soil samples collected in Goyang-si and Paju-si, Gyeonggi-do, Republic of Korea. Strains PBS4-4 T and GMJ5 T were both positive for catalase and oxidase. Strain PBS4-4 T grew at 15–37 °C and pH 5.0–12.0. Strain GMJ5 T grew at 15–37 °C and pH 5.0–11.0. Neither strain required NaCl for growth. 16S rRNA sequence analysis revealed that strains PBS4-4 T and GMJ5 T form a closely related cluster with the genus Chryseobacterium . The average nucleotide identity and digital DNA–DNA hybridization values between strain PBS4-4 T and its closely related strains were 79.4–84.5% and 23.2–28.7 %, respectively. For GMJ5 T , the values were 78.3–79.3% and 22.0–22.6 %, respectively. The major fatty acids shared by both novel strains were iso-C 15 : 0 and summed feature 3 (C 16 : 1 ω 7 c /C 16 : 1 ω 6 c ). Strain GMJ5 T had one other major fatty acid: iso-C 17 : 0 3OH. Based on phenotypic, genomic and phylogenetic results, strains PBS4-4 T and GMJ5 T 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 PBS4-4 T (=KACC 22882 T =TBRC 17052 T ) and the type strain of C. gilvum is GMJ5 T (=KACC 22883 T =TBRC 17053 T ).
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.005989
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2023
    detail.hit.zdb_id: 215062-1
    detail.hit.zdb_id: 2056611-6
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  • 6
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    Limnohabitans radicicola sp. nov., a slow-growing bacterium isolated from rhizosphere of rice plant and emended description of the genus Limnohabitans
    Microbiology Society ; 2021
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 71, No. 8 ( 2021-08-17)
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 71, No. 8 ( 2021-08-17)
    Abstract: In the present study, in an attempt to explore the diversity of bacteria in the roots of rice plants, a Gram-stain-negative, motile, facultatively anaerobic, non-pigmented, catalase-positive, oxidase-negative and rod-shaped bacterium with polar flagella was isolated. Phylogenetic analysis based on 16S rRNA gene sequences revealed highest sequence similarity to Limnohabitans parvus KCTC 42859 T (98.2%) followed by Limnohabitans curvus KCTC 42562 T (98%), Limnohabitans planktonicicus II-D5 T (97.9%) and Limnohabitans australis MWH-BRAZ-DAM2D T (97.4%). Growth of strain JUR4 T occurred at 10–37 °C (optimum, 30 °C), at pH 5.5–8.0 (optimum, 6.5–7) and in the presence of 0–0.2% NaCl (optimum, 0%, w/v). The genome size of strain JUR4 T was found to be 3.34 Mb containing 3139 predicted protein-coding genes with a DNA G+C content of 61.5 mol%. The digital DNA–DNA hybridization and average nucleotide identity values between the genome sequence of strain JUR4 T and closely related reference strains were 21.0–24.8% and 74.7–81.4%, respectively. Strain JUR4 T contained diphosphatidylglycerol, phoshatidylethanolamine, one unidentified phosphoglycolipid, one unidentified aminophosphoglycolipid, one unidentified phospholipid and seven unidentified glycolipids. The major fatty acids were C 16:0 and summed feature 3 (comprising C 16:1 ω 7 c and/or C 16:1 ω 6 c ), and ubiquinone Q-8 was the sole isoprenoid quinone. So far, all species belonging to the genus Limnohabitans have been described as non-motile and devoid of flagella. All species were isolated from freshwater and are therefore denoted as planktonic bacteria. This present study introduces a novel motile member of Limnohabitans isolated from the root of rice plant, and introduces the genes associated with motility and methyl-accepting chemotaxis proteins. Phylogenetic, phenotypic, chemotaxonomic and genotypic data clearly indicates that strain JUR4 T represents a novel species of the genus Limnohabitans for which the name Limnohabitans radicicola sp. nov. is proposed. The type strain is JUR4 T (=KACC 21745 T =NBRC 114484 T ).
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.004957
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2021
    detail.hit.zdb_id: 215062-1
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  • 7
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    Nocardioides baculatus sp. nov., a novel actinomycete isolated from the rhizosphere of Tagetes patula
    Microbiology Society ; 2021
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 71, No. 9 ( 2021-09-20)
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 71, No. 9 ( 2021-09-20)
    Abstract: An aerobic, Gram-stain-positive, non-motile, dull-yellow, short rod-shaped actinomycete strain, designated G10 T , was isolated from Tagetes patula (marigold) roots collected from Goyang in the Republic of Korea. The isolate showed best growth on Reasoner's 2A agar at 25 °C, pH 6.5.0 and with 0% NaCl (w/v). The strain was negative for oxidase activity and positive for catalase activity. On the basis of 16S RNA gene sequence similarity, strain G10 T was affiliated to the genus Nocardioides and the closest species were Nocardioides glacieisoli HLT3-15 T (98.8 %), Nocardioides zhouii HLT2-9 T (98.8 %), Nocardioides ganghwensis JC2055 T (98.7 %), Nocardioides cavernae YIM A1136 T (98.6 %), Nocardioides flavus Y4 T (98.5 %), Nocardioides oleivorans DSM 16090 T (98.3 %), Nocardioides alpinus Cr7-14 T (98.2 %), Nocardioides exalbidus DSM 22017 T (98.1 %) and Nocardioides hwasunensis KCTC 19197 T (98.1 %). Strain G10 T formed a monophyletic cluster with N. glacieisoli HLT3-15 T , N. zhouii HLT2-9 T and N. hwasunensis KCTC 19197 T in all phylogenetic trees. The cell-wall peptidoglycan of strain G10 T contained ll -diaminopimelic acid as the diagnostic amino acid. The predominant fatty acids were iso-C 16 : 0 and C 17 : 1  ω 8 c . MK-8(H 4 ) was the major isoprenoid quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. Average nucleotide identity and digital DNA–DNA hybridization values were 78.6–88.7 % and 21.5–36.2 %, respectively, with the type strains of related species of the genus Nocardioides , suggesting that strain G10 T represents a novel species. The genome of strain G10 T is 4 231 000 bp long with a DNA G+C content of 71.5 mol% and encodes 4071 predicted proteins, six rRNAs and 46 tRNAs. The genome of strain G10 T comprises the biosynthetic gene cluster for T3PKS, terpene, NRPS-like fragment and RRE-containing element as secondary metabolites. The results of taxonomic, phylogenetic, biochemical, chemotaxonomic and genomic analysis clearly supported that strain G10 T represent a novel species within the genus Nocardioides , for which the name Nocardioides baculatus sp. nov is proposed and the type strain is G10 T (=KCTC 49626 T =NBRC 114801 T ).
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.005012
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2021
    detail.hit.zdb_id: 215062-1
    detail.hit.zdb_id: 2056611-6
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  • 8
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    Nocardioides donggukensis sp. nov. and Hyunsoonleella aquatilis sp. nov., isolated from Jeongbang Waterfall on Jeju Island
    Microbiology Society ; 2021
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 71, No. 12 ( 2021-12-20)
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 71, No. 12 ( 2021-12-20)
    Abstract: Two bacterial strains, designated MJB4 T and SJ7 T , were isolated from water samples collected from Jeongbang Falls on Jeju Island, Republic of Korea. Phylogenetic analysis of 16S rRNA gene sequences indicated that the two strains belonged to the genera Nocardioides and Hyunsoonleella , owing to their high similarities to Nocardioides jensenii DSM 29641 T (97.5 %) and Hyunsoonleella rubra FA042 T (96.3 %), respectively. These values are much lower than the gold standard for bacterial species (98.7 %). The average nucleotide identity values between strains MJB4 T , SJ7 T and the reference strains, Nocardioides jensenii DSM 29641 T , Nocardioides daejeonensis MJ31 T and Hyunsoonleella flava T58 T were 77.2, 75.9 and 75.4 %, respectively. Strains MJB4 T and SJ7 T and the type strains of the species involved in system incidence have average nucleotide identity and average amino acid threshold values of 60.1–82.6 % for the species boundary (95–96 %), which confirms that strains MJB4 T and SJ7 T represent two new species of genus Nocardioides and Hyunsoonleella , respectively. Based on phylogenetic and phenotypic data, strains MJB4 T and SJ7 T are considered to represent novel species of the genus Nocardioides and Hyunsoonleella , respectively, for which the names Nocardioides donggukensis sp. nov. (type strain MJB4 T =KACC 21724 T =NBRC 114402 T ) and Hyunsoonleella aquatilis sp. nov., (type strain SJ7 T =KACC 21715 T =NBRC 114486 T ) have been proposed.
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.005176
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2021
    detail.hit.zdb_id: 215062-1
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  • 9
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    Roseateles albus sp. nov., Roseateles koreensis sp. nov. and Janthinobacterium fluminis sp. nov., isolated from freshwater at Jucheon River, and emended description of Roseateles aquaticus comb. nov.
    Microbiology Society ; 2023
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 73, No. 9 ( 2023-09-26)
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 73, No. 9 ( 2023-09-26)
    Abstract: Three Gram-stain-negative, facultatively anaerobic, rod-shaped, catalase-positive, oxidase-negative bacterial strains were designated as hw1 T , hw8 T and hw3 T . Strains hw1 T , hw8 T and hw3 T grew at 15–28 °C (optimum, 25 °C), 15–35 °C (optimum, 30 °C) and 4–28 °C (optimum, 20 °C), respectively, and at pH 7.0–12.0 (optimum, pH 9.0), pH 6.0–11.0 (optimum, pH 9.0) and 5.0–12.0 (optimum, pH 7.0), respectively. Additionally, strains hw1 T and hw8 T only grew when the NaCl concentration was 0 %, while strain hw3 T grew at between 0 and 0.5 % (w/v; optimum, 0 %). The average nucleotide identity (ANI) values between strains hw1 T , hw8 T and the Roseateles type strains ranged from 73.8 to 84.2 %, while the digital DNA–DNA hybridization (dDDH) values ranged from 19.7 to 27.5 %. The ANI values between strain hw3 T and the Janthinobacterium type strains ranged from 78.7 to 80.7 %, while dDDH values ranged from 22.3 to 23.0 %. The draft genomes of strains hw1 T , hw8 T and hw3 T consisted of 5.5, 4.4 and 5.9 Mbp, with DNA G+C contents of 61.7, 61.8 and 66.0 mol%, respectively. The results of the dDDH, ANI, phylogenetic, biochemical and physiological analyses indicated that the novel strains were distinct from other members of their genera. Thus, we proposed the names Roseateles albus sp. nov. (type strain hw1 T = KACC 22887 T = TBRC 16613 T ), Roseateles koreensis sp. nov. (type strain hw8 T = KACC 22885 T = TBRC 16614 T ) and Janthinobacterium fluminis sp. nov. (type strain hw3 T = KACC 22886 T = TBRC 16615 T ).
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.006043
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2023
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  • 10
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    Sphingopyxis lutea sp. nov., a novel moderately halotolerant bacterium isolated from pebbles
    Springer Science and Business Media LLC ; 2022
    In:  Archives of Microbiology Vol. 204, No. 7 ( 2022-07)
    Details
    In: Archives of Microbiology, Springer Science and Business Media LLC, Vol. 204, No. 7 ( 2022-07)
    Type of Medium: Online Resource
    ISSN: 0302-8933 , 1432-072X
    URL: Article
    DOI: 10.1007/s00203-022-03042-1
    RVK:
    WA 15000
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 1458451-7
    detail.hit.zdb_id: 477-7
    detail.hit.zdb_id: 124824-8
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