Abstract
A Gram-stain-negative, aerobic, motile and rod-shaped bacterium was isolated from pebbles collected from the coast near Taejongdae Park, Busan, South Korea. Phylogenetic analysis based on 16S rRNA gene sequence analysis revealed that strain DHUNG17T belonged to the family Sphingomonadaceae, and it showed the highest sequence similarity found with Sphingopyxis panaciterrulae DCY34T (98.4%) and Sphingopyxis granuli TFAT (98.4%). The strain grew at 10–45 °C, at pH 5.0–9.0 and with 0–12% (w/v) NaCl. Chemotaxonomic data revealed that strain DHUNG17T possessed ubiquinone Q-10 as the predominant respiratory lipoquinone. The predominant fatty acids were C16: 0, C18: 0, summed feature 4 (C16: 1 ω7c and/or C15: 0 iso 2-OH) and summed feature 8 (C19: 1 ω6c and/or unknown 18.864). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and a sphingoglycolipid and spermidine were detected as the major polyamines. Strain DHUNG17T was able to produce carotenoid-type pigment. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values with its closest neighbors were 79.3–81.7% and 22.0–24.4%, respectively. The genome of strain DHUNG17T is 3,129,415 bp long with a DNA G + C content of 64.7% and encodes 2,951 predicted proteins, 3 rRNAs and 47 tRNAs. Gene related to transportation of polycyclic aromatic hydrocarbons (PAHs) was found in the genome of strain DHUNG17T. According to the genotypic, phylogenetic and chemotaxonomic data, strain DHUNG17T represents a novel species within the genus Sphingopyxis, for which the name Sphingopyxis lutea sp. nov. is proposed. The type strain is DHUNG17T (= KACC 21746T = NBRC 114643T).
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Data availability
The draft genome and 16S rRNA gene sequences of strain DHUNG17T have been deposited in GenBank/EMBL/DDBJ under accession numbers JAERPO000000000 and MN956702 respectively.
Abbreviations
- ANI:
-
Average amino acid identity
- MEGA:
-
Molecular evolutionary genetics analysis
- NJ:
-
Neighbor-joining
- ML:
-
Maximum-likelihood
- MP:
-
Maximum-parsimony
- ME:
-
Minimum evolution
- UBCG:
-
Up-to-date bacterial core gene
- DPG:
-
Diphosphatidylglycerol
- PE:
-
Phosphatidylethanolamine
- PG:
-
Phosphatidylcholine
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Funding
This work was supported by a grant from the National Institute of Biological Resources (NIBR), funded by the Ministry of Environment (MOE) of the Republic of Korea (NIBR202102205), and by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (2020R1F1A1072647).
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GC isolated the bacterium and drafted the manuscript. IK helped with the analysis of taxonomic data and performed the phenotypic and biochemical characterization; TS designed and supervised the study, and edited the original draft.
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Chhetri, G., Kim, I. & Seo, T. Sphingopyxis lutea sp. nov., a novel moderately halotolerant bacterium isolated from pebbles. Arch Microbiol 204, 406 (2022). https://doi.org/10.1007/s00203-022-03042-1
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DOI: https://doi.org/10.1007/s00203-022-03042-1