Cohnella abietis sp. nov., isolated from Korean fir (Abies koreana) rhizospheric soil of Halla mountain

Jiang, Lingmin; Pheng, Sophea; Lee, Keun Chul; Kang, Se Won; Jeong, Jae Cheol; Kim, Cha Young; Park, Hyeong Cheol; Kim, Dae-Hyuk; Kim, Suk Weon; Kim, Song‐Gun; Lee, Ji-Young

doi:10.1007/s12275-019-9136-1

“…Considering that the proposed and generally accepted species boundaries are 95-96 % (ANI and AAI) and 70 % (dDDH), respectively [34,35], strain MFER-1 T was supposed to be a novel taxon clearly distinguishable from those species. Data from: *Jiang et al [42]; †Jiang et al [41]; ‡Kim et al [45]; §Lee et al [43]; ¶Meng et al [9]; **Caiet al [40]; † †Flores-Félix et al [8]; ‡ ‡Garcia-Fraileet al [3].…”

Section: Genomic Featuresmentioning

confidence: 99%

Cohnella herbarum sp. nov., isolated from wild grass fermentation broth

Won

¹

,

Lee

²

,

Hong

³

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

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A novel strictly aerobic, Gram-stain-positive, rod-shaped, motile, endospore-forming, white-coloured bacterium, designated strain MFER-1T, was isolated from a fermented liquor of wild grasses sampled in the Republic of Korea. The respiratory quinone of strain MFER-1T was menaquinone-7 and its major cellular fatty acids were anteiso-C15 : 0 (55.3 %), iso-C16 : 0 (17.5 %) and C16 : 0 (12.1 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unidentified aminophospholipids and an unidentified phospholipid. The 16S rRNA gene sequence of strain MFER-1T showed similarity of 98.1 % to ‘Cohnella cholangitidis’ 1 605-214T and below 98.0 % sequence similarity to the other Cohnella species. The phylogenomic tree indicated that strain MFER-1T formed a reliable cluster with several Cohnella species. The estimated genome size of strain MFER-1T was 8.52 Mb. Genomic DNA G+C content was 50.7mol%. The orthologous average nucleotide identity, digital DNA–DNA hybridization and amino acid identity values of strain MFER-1T with the most closely related species ‘Cohnella cholangitidis’ 1 605-214T were 78.7, 23.0 and 79.6 %, respectively. Based on the phenotypic, chemotaxonomic and phylogenetic results, strain MFER-1T should represent a novel species of the genus Cohnella , for which the name Cohnella herbarum sp. nov. is proposed, with strain MFER-1T (=KACC 21 257T=NBRC 114 628T) as the type strain.

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“…To determine the optimal pH for the growth, marine broth was adjusted in a pH range of pH 4.5–10.0 with a buffer system to a final concentration of 20 mM (at intervals of 0.5 pH units), phosphate buffer for pH 4.5–8.0 and carbonate buffer for pH 8.5–10.0. Growth was measured by taking OD at 600 nm using a DU 700 UV-visible spectrophotometer (Beckman Coulter) [38]. Catalase activity was determined by the production of oxygen bubbles when fresh cells were added to 3 % (v/v) H 2 O 2 [39].…”

Section: Physiological Characterization and Taxonomymentioning

confidence: 99%

Flavobacterium litorale sp. nov., isolated from red alga

Muhammad

¹

,

Han

²

,

Lee

³

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

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A Gram-stain-negative and rod-shaped bacterial strain (WSW3-B6T) was isolated from red alga collected from the West Sea, Republic of Korea. Cells of strain WSW3-B6T were non-motile, aerobic and produced slightly yellow and mucoid colonies on marine agar. The strain grew optimally at 23–30 °C, with 0.5–4 % NaCl (w/v) and at pH 6.5–8.5. A phylogenetic analysis of the 16S rRNA gene revealed that strain WSW3-B6T belongs to the genus Flavobacterium within the family Flavobacteriaceae , having the highest sequence similarity to Flavobacterium arcticum SM1502T (96.7%), followed by Flavobacterium salilacus subsp. altitudinum LaA7.5T (96.2%) and Flavobacterium salilacus subsp. salilacus SaA2.12T (96.2%). The complete sequence of a circular chromosome of strain WSW3-B6T determined by combination of Oxford Nanopore and Illumina platforms comprised a total 2 725 095 bp with G+C content of 37.1 mol%. A comparative analysis based on the whole genome also showed the distinctiveness of strain WSW3-B6T. The average nucleotide identity (ANI) values between strain WSW3-B6T and the closest strains F. arcticum SM1502T, F. salilacus subsp. altitudinum LaA7.5T and F. salilacus subsp. salilacus SaA2.12T were 78.3, 77.8 and 77.7 %, respectively, while the digital DNA–DNA hybridization (dDDH) values between strain WSW3-B6T and the above closely related strains were 21.0, 20.4 and 20.3 %, respectively. Both the ANI and dDDH values supported the creation of a new species in the genus Flavobacterium . The major fatty acids (>10 %) were iso-C15 : 0 (19.3 %), C16 : 0 (14.0 %), iso-C17 : 0 3-OH (13.1 %) and C18 : 0 (10.7 %). The polar lipids of strain WSW3-B6T included phosphatidylethanolamine, three unidentified aminolipids and three unidentified lipids. Moreover, MK-6 was the only respiratory quinone. A comparison of the phylogenetic distinctiveness and the unique phenotypic and chemotaxonomic characteristics among strain WSW3-B6T and closely related type strains supported that strain WSW3-B6T (=KCTC 82708T=GDMCC 1.2627T) represents a novel species of the genus Flavobacterium , for which the name Flavobacterium litorale sp. nov. is proposed.

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“…Gram reaction was tested by the Gram Stain Solution kit (Difco) according to the manufacturer's instructions. Motility was determined by diffusion growing in TSB supplemented with 0.4 % agar [32]. Anaerobic growth was determined after incubation on TSA for 7 days at 25 °C in an anaerobic chamber (Coy Scientific) with 86 % N 2 , 7 % CO 2 and 7 % H 2 atmosphere.…”

Section: Physiology and Chemotaxonomymentioning

confidence: 99%

Pedobacter endophyticus sp. nov., an endophytic bacterium isolated from Carex pumila

Peng

¹

,

Jiang

²

,

Seo

³

et al. 2021

International Journal of Systematic and Evolutionary Microbiology

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An aerobic, Gram-stain-negative, weak-motile, short-rod-shaped bacterial strain, designated JBR3-12T, was isolated from halophyte Carex pumila plants, and its taxonomic position was investigated by using a polyphasic taxonomic approach. The strain produced a pink pigment on tryptic soy agar and grew optimally at 25 °C, pH 8 and in the presence of 3 % (w/v) NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strain JBR3-12T formed a lineage within the genus Pedobacter and was most closely related to Pedobacter sandarakinus DS-27T (98.0 %) and Pedobacter agri PB92T (97.6 %). The DNA G+C content of the genome was 41.3 mol%; the whole genome length was 5 426 070 bp. The major fatty acids of JBR3-12T were iso-C15 : 0, summed feature 3 (comprising C16 : 1 ω6c and/or C16 : 1 ω7c) and iso-C17 : 0 3-OH. The predominant polar lipid was phosphatidylethanolamine. The predominant quinone was menaquinone-7. Based on its phenotypic, phylogenetic and genotypic features, strain JBR3-12T is proposed to represent a novel species of the genus Pedobacter , for which the name is Pedobacter endophyticus sp. nov. The type strain is JBR3-12T (=KCTC 82363T=NBRC 114901T).

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Cohnella abietis sp. nov., isolated from Korean fir (Abies koreana) rhizospheric soil of Halla mountain

Cited by 11 publications

References 33 publications

Cohnella herbarum sp. nov., isolated from wild grass fermentation broth

Cohnella herbarum sp. nov., isolated from wild grass fermentation broth

Flavobacterium litorale sp. nov., isolated from red alga

Pedobacter endophyticus sp. nov., an endophytic bacterium isolated from Carex pumila

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