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KMID : 0545120230330101292
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Journal of Microbiology and Biotechnology
2023 Volume.33 No. 10 p.1292 ~ p.1298
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Sphingomonas abietis sp. nov., an Endophytic Bacterium Isolated from Korean Fir
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Lingmin Jiang
Hanna Choe
Yuxin Peng
Jeon Do-Eun
Cho Dong-Hyun
Yue Jiang
Lee Ju-Huck
Kim Cha-Young
Lee Ji-Young
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Abstract
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PAMB 00755T, a bacterial strain, was isolated from Korean fir leaves. The strain exhibits yellow colonies and consists of Gram-negative, non-motile, short rods or ovoid-shaped cells. It displays optimal growth conditions at 20°C, 0% NaCl, and pH 6.0. Results of 16S rRNA gene-based phylogenetic analyses showed that strain PAMB 00755T was most closely related to Sphingomonas chungangi MAH-6T (97.7%) and Sphingomonas polyaromaticivorans B2-7T (97.4%), and ≤96.5% sequence similarity to other members of the genus Sphingomonas. The values of average nucleotide identity (79.9?81.3%), average amino acid identity (73.3?75.9%), and digital DNA?DNA hybridization (73.3?75.9%) were significantly lower than the threshold values for species boundaries; these overall genome-related indexes (OGRI) analyses indicated that the strain represents a novel species. Genomic analysis revealed that the strain has a 4.4-Mbp genome encoding 4,083 functional genes, while the DNA G+C content of the whole genome is 66.1%. The genome of strain PAMB 00755T showed a putative carotenoid biosynthetic cluster responsible for its antioxidant activity. The respiratory quinone was identified as ubiquinone 10 (Q-10), while the major fatty acids in the profile were identified as C18:1ω7c and/or C18:1ω6c (summed feature 8). The major polar lipids of strain PAMB 00755T were diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, and phosphatidylcholine. Based on a comprehensive analysis of genomic, phenotypic, and chemotaxonomic characteristics, we proposed the name Sphingomonas abietis sp. nov. for this novel species, with PAMB 00755T as the type strain (= KCTC 92781T = GDMCC 1.3779T).
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KEYWORD
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Polyphasic taxonomy, Korean fir, phylogeny, AntiSMASH, endophytic bacterium
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