Advertisement

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
  • 69 Downloads

Abstract

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).

Keywords

Paddy field Carotenoid Phylogenetic analysis Cell morphology New taxa Cytophagaceae 

Notes

Acknowledgements

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)

References

  1. Aziz RK et al (2008) The RAST server: rapid Annotations Using Subsystems Technology. BMC Genom 9:75.  https://doi.org/10.1186/1471-2164-9-75 CrossRefGoogle Scholar
  2. Bernardet JF, Nakagawa Y, Holmes B, Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes (2002) Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049–1070Google Scholar
  3. Breznak JA, Costilow RN (2007) Physicochemical factors in growth. In: Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR (eds) Methods for general and molecular bacteriology, 3rd edn. American Society for Microbiology, Washington, DC, pp 309–329Google Scholar
  4. Buck JD (1982) Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 44:992–993PubMedPubMedCentralGoogle Scholar
  5. Chhetri G, Yang D, Choi J et al (2018a) Edaphorhabdus rosea gen. nov., sp. nov., a new member of the family Cytophagaceae isolated from soil in South Korea. Antonie Van Leeuwenhoek 111:2385CrossRefPubMedGoogle Scholar
  6. Chhetri G, Yang D, Choi J et al (2018b) Flavobacterium edaphi sp. nov., isolated from soil from Jeju Island, Korea. Arch Microbiol 201(4):539–545CrossRefPubMedGoogle Scholar
  7. Chhetri G, Kim J, Kim I et al (2019a) Pontibacter chitinilyticus sp. nov., a novel chitin-hydrolysing bacterium isolated from soil. Antonie Van Leeuwenhoek.  https://doi.org/10.1007/s10482-019-01235-1 CrossRefPubMedGoogle Scholar
  8. Chhetri, G., Kim, J., Kim, I. et al. (2019b). Lysobacter caseinilyticus, sp. nov., a casein hydrolyzing bacterium isolated from sea-water.  https://doi.org/10.1007/s10482-019-01267-7
  9. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu XW, De Meyer S, Trujillo ME (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466CrossRefPubMedGoogle Scholar
  10. Collins MD, Jones D (1981) Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications. Microbiol Rev 45:316–354PubMedPubMedCentralGoogle Scholar
  11. Fautz E, Reichenbach H (1980) A simple test for flexirubin-type pigments. FEMS Microbiol Lett 8:87–91CrossRefGoogle Scholar
  12. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  13. Fisher JF, Meroueh SO, Mobashery S (2005) Bacterial resistance to beta-lactam antibiotics: compelling opportunism, compelling opportunity. Chem Rev 105:395–424CrossRefGoogle Scholar
  14. Fraser PD, Bramley PM (2004) The biosynthesis and nutritional uses of carotenoids. Prog Lipid Res 43:228–265CrossRefPubMedGoogle Scholar
  15. Hiraishi A, Ueda Y, Ishihara J, Mori T (1996) Comparative lipoquinone analysis of influent sewage and activated sludge by highperformance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42:457–469CrossRefGoogle Scholar
  16. Kai B, Shaw S, Steinke K, Villebro R, Ziemert N, Lee SY, Medema MH, Weber T (2019) antiSMASH 50: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res.  https://doi.org/10.1093/nar/gkz310 CrossRefGoogle Scholar
  17. Kang JY, Joung Y, Chun J, Kim H, Joh K et al (2013) Pontibacter saemangeumensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 63:565–569CrossRefPubMedGoogle Scholar
  18. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH et al (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbial 62:716–721CrossRefGoogle Scholar
  19. Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120CrossRefGoogle Scholar
  20. Komagata K, Suzuki KI (1987) Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–205CrossRefGoogle Scholar
  21. Kumar S, Stecher G, Tamura K (2016) Mega 7: molecular evolutionary genetics analysis in version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874CrossRefPubMedPubMedCentralGoogle Scholar
  22. Kuykendall LD, Roy MA, O’Neill JJ, Devine TE (1988) Fatty acids, antibiotic resistance and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Evol Microbiol 38:358–361Google Scholar
  23. Lee D, Jang JH, Cha S et al (2016) Telluribacter humicola gen. nov., sp. nov., a new member of the family Cytophagaceae isolated from soil in South Korea. Antonie Van Leeuwenhoek 109:1525–1533CrossRefPubMedGoogle Scholar
  24. Meier-Kolthoff JP, Auch AF, Klenk H-P, Goker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60CrossRefGoogle Scholar
  25. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241CrossRefGoogle Scholar
  26. Mukherjee S, Lapidus A, Shapiro N et al (2015) High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1(T) (DSM 17521(T)) isolated from muddy waters of a drainage system in Chandigarh, India. Stand Genomic Sci 10:8.  https://doi.org/10.1186/1944-3277-10-8 CrossRefPubMedPubMedCentralGoogle Scholar
  27. Nedashkovskaya OI, Kim SB, Suzuki M, Shevchenko LS, Lee MS et al (2005) Pontibacter actiniarum gen. nov., sp. nov., a novel member of the phylum ‘Bacteroidetes’, and proposal of Reichenbachiella gen nov as a replacement for the illegitimate prokaryotic generic name Reichenbachia. Int J Syst Evol Microbiol 55:2583–2588CrossRefPubMedGoogle Scholar
  28. Park S, Park JM, Lee KH, Yoon JH (2016) Pontibacter litorisediminis sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 66:4172–4178CrossRefPubMedGoogle Scholar
  29. Piddock LJV (2006) Multidrug-resistance efflux pumps? not just for resistance. Nat Rev Microbiol 4:629–636.  https://doi.org/10.1038/nrmicro1464 CrossRefPubMedGoogle Scholar
  30. Richter M, Rossello-Mora R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131CrossRefGoogle Scholar
  31. Rzhetsky A, Nei M (1992) A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 9:945–967Google Scholar
  32. Singh AK, Garg N, Lal R (2015) Pontibacter chinhatensis sp. nov., isolated from pond sediment containing discarded hexachlorocyclohexane isomer waste. Int J Syst Evol Microbiol 65:2248–2254CrossRefPubMedGoogle Scholar
  33. Singh P, Kumari R, Nayyar N, Lal R (2017) Pontibacter aurantiacus sp. nov. isolated from hexachlorocyclohexane (HCH) contaminated soil. Int J Syst Evol Microbiol 67:1400–1407CrossRefPubMedGoogle Scholar
  34. Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC, pp 607–654Google Scholar
  35. Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152–155Google Scholar
  36. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882CrossRefPubMedPubMedCentralGoogle Scholar
  37. Wang Y, Zhang K, Cai F, Zhang L, Tang Y, Dai J, Fang C (2010) Pontibacter xinjiangensis sp. nov., in the phylum 'Bacteroidetes', and reclassification of [Effluviibacter] roseus as Pontibacter roseus comb. nov. Int J Syst Evol Microbiol 60:99–103CrossRefPubMedGoogle Scholar
  38. Xu L, Zeng XC, Nie Y, Luo X, Zhou E et al (2014) Pontibacter diazotrophicus sp. nov., a novel nitrogen-fixing bacterium of the family Cytophagaceae. PLoS ONE 9:e92294CrossRefPubMedPubMedCentralGoogle Scholar
  39. Zhang L, Zhang QJ, Luo XS, Tang YL, Dai J et al (2008) Pontibacter korlensis sp. nov., isolated from the desert of Xinjiang, China. Int J Syst Evol Microbiol 58:1210–1214CrossRefPubMedGoogle Scholar

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

Personalised recommendations