Abstract
An aerobic bacterium, designated as PT-12T, was isolated from soil collected from agriculture field, and its taxonomic position was validated through a comprehensive polyphasic methodology. The strain was identified as Gram-stain-negative, non-motile, rod-shaped, and catalase- and oxidase-positive. The yellow-colored colonies showed growth ability at temperature range of 18–37 °C, NaCl content of 0–1.0% (w/v), and at a pH of 6.0–8.0. The 16S rRNA gene and phylogenetic analysis showed that strain PT-12T affiliated with the genus Sphingomonas in the family Sphingomonadaceae, and displayed the highest 16S rRNA nucleotide sequence similarity with Sphingomonas limnosediminicola 03SUJ6T (98.4%). The genome size of strain PT-12T was 2,656,862 bp and the DNA G + C content estimated from genome was 63.5%. The highest values of average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) were observed between strain PT-12T and Sphingomonas segetis YJ09T, accounting to 76.2% and 20.2%, respectively. In addition, both ANI and dDDH values between strain PT-12T and other phylogenetically related neighbors ranged between 69.6% and 76.2% and 18.4% and 20.2%, respectively. Chemotaxonomic features exhibited Q-10 as the only ubiquinone; homospermidine as the major polyamine; summed feature 8 (C18:1ω7c and/or C18:1ω6c), C16:0, and 10-methyl C18:0 as the notable fatty acids; and phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, and sphingoglycolipid as dominating polar lipids. Overall, the comprehensive polyphasic data supported that strain PT-12T represents a novel bacterial species within the genus Sphingomonas. Accordingly, we propose the name Sphingomonas flavescens sp. nov. The type strain is PT-12T (= KCTC 92114T = NBRC 115717T).
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Data availability
The GenBank/EMBL/DDBJ Accession number for the 16S rRNA sequence of strain PT-12T is OK602676. The genome sequence of strain PT-12T has been deposited at DDBJ/ENA/GenBank under the Accession CP133016.
Abbreviations
- dDDH:
-
Digital DNA–DNA hybridization
- KACC:
-
Korean Agricultural Culture Collection
- ANI:
-
Average nucleotide identity
- KCTC:
-
Korean Collection for Type Cultures
- NBRC:
-
NITE Biological Resource Center: Deutsche
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This work was supported by National Institute of Biological Resources funded by the Ministry of Environment (NIBR202102109).
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HL and DK designed the study. HL and DKC performed the experimental work, data analysis, and manuscript draft preparation. DK reviewed and finalized the manuscript, and supervised the project.
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Lee, H., Chaudhary, D.K. & Kim, DU. Sphingomonas flavescens sp. nov., isolated from soil. Arch Microbiol 206, 119 (2024). https://doi.org/10.1007/s00203-024-03851-6
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DOI: https://doi.org/10.1007/s00203-024-03851-6