Pontibacter oryzae sp. nov., a carotenoid-producing species isolated from a rice paddy field

  • Geeta Chhetri
  • Jiyoun Kim
  • Hyungdong Kim
  • Inhyup Kim
  • Taegun SeoEmail author
Original Paper


A taxonomic study using a polyphasic approach was performed on a Gram-stain negative, red-pink, aerobic, non-motile, asporogenous, rod-shaped bacterium, designated strain KIRANT, isolated from soil collected from a rice paddy field. The 16S rRNA gene sequence analysis showed that strain KIRANT is phylogenetically related to Pontibacter actiniarum KMM 6156T, Pontibacter korlensis X14-1T, Pontibacter odishensis JC130T, Pontibacter litorisediminis YKTF-7T and Pontibacter aurantiacus NP1T (97.6, 97.5, 97.3, 97.3 and 96.7% sequence similarity, respectively). The major fatty acids of strain KIRANT were identified as iso-C15:0, iso-C15:0 3-OH and summed feature 4. The predominant menaquinone was identified as MK-7. The polar lipid profile was found to consist of phosphatidylethanolamine, four unidentified phospholipids, an unidentified glycolipid, an unidentified aminolipid and four unidentified lipids. The genome of strain KIRANT has a G + C content of 48.3 mol%. The in silico DNA–DNA hybridization and average nucleotide identity values between strain KIRANT and the closely related strains P. actiniarum KMM 6156T and P. korlensis X14-1T were 21.2%/21.8% and 76.4%/75.1%, respectively. On the basis of the data from phenotypic tests and genotypic differences between strain KIRANT and its close phylogenetic relatives, strain KIRANT is concluded to represent a new species belonging to the genus Pontibacter, for which the name Pontibacter oryzae sp. nov. is proposed. The type strain is KIRANT (= KACC 19815T = JCM 32880T).


Paddy field Carotenoid Phylogenetic analysis Cell morphology New taxa Cytophagaceae 



We thank Prof Dr. Bernhard Schink (University of Konstanz, Konstanz, Germany) for the suggested species names. This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (NRF-2017R1A2B4009448).

Compliance with ethical standards

Conflict of interest

The authors declare that there is no conflict of interest.

Ethical standards

This study does not describe any experimental work related to human.

Supplementary material

10482_2019_1298_MOESM1_ESM.docx (6 mb)
Supplementary material 1 (DOCX 6174 kb)


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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Geeta Chhetri
    • 1
  • Jiyoun Kim
    • 1
  • Hyungdong Kim
    • 1
  • Inhyup Kim
    • 1
  • Taegun Seo
    • 1
    Email author
  1. 1.Department of Life ScienceDongguk University-SeoulGoyangSouth Korea

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