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Pontibacter humi sp. nov., Isolated from Mountain Soil

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Abstract

A Gram-negative, aerobic, non-motile, rod-shaped bacterial strain, designated as SWU8T, was isolated from a mountain soil collected in Seoul Women’s University campus at South Korea. Phylogenic analysis, using 16S rRNA gene sequence of the new isolate, showed that strain SWU8T belongs to the genus Pontibacter. The highest sequence similarities were 96.2 % with Pontibacter saemangeumensis GCM0142T, 95.5 % with Pontibacter toksunensis ZLD-7T, 95.3 % with Pontibacter roseus DSM 17521T, and 95.1 % with Pontibacter odishensis JC130T. Chemotaxonomic data showed that the most abundant fatty acids were summed feature 4 (comprising iso-C17:1 I/anteiso-C17:1 B; 26.9 %), iso-C15:0 (25.6 %), and iso-C17:0 3OH (10.6 %), and major polar lipid was phosphatidylethanolamine. The DNA G+C content of strain SWU8T was 48.5 mol%. Together, the phenotypic, phylogenetic, and chemotaxonomic data supported that strain SWU8T presents a novel species of the genus Pontibacter, for which the name Pontibacter humi sp. nov. is proposed. The type strain is SWU8T (=KEMC 9004-131T = JCM 19178T).

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References

  1. Collins MD, Jones D (1981) Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 45(2):316–354

    CAS  PubMed Central  PubMed  Google Scholar 

  2. Dai J, Xu M, Peng F, Jiang F, Chen X, Wang Z, Fang C (2013) Pontibacter soli sp. nov., isolated from the soil of a Populus rhizosphere in Xinjiang, China. Antonie van Leeuwenhoek. doi:10.1007/s10482-013-0053-8

    Google Scholar 

  3. Dastager SG, Raziuddin QS, Deepa CK, Li WJ, Pandey A (2010) Pontibacter niistensis sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 60(Pt 12):2867–2870. doi:10.1099/ijs.0.019935-0

    Article  CAS  PubMed  Google Scholar 

  4. Doetsch, R. N. (1981) Determinative methods of light microscopy. In: Gerhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA, Krieg NR, Phillips GH (eds) Manual of methods for general bacteriology. American Society for Microbiology, Washington, pp 21–33

  5. Dwivedi V, Niharika N, Lal R (2013) Pontibacter lucknowensis sp. nov., isolated from a hexachlorocyclohexane dump site. Int J Syst Evol Microbiol 63(1):309–313. doi:10.1099/ijs.0.040147-0

    Article  CAS  PubMed  Google Scholar 

  6. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  7. Fitch WM (1971) Toward defining the course of evolution: minimum change for a specified tree topology. Syst Zool 20(4):406–416

    Article  Google Scholar 

  8. Frank JA, Reich CI, Sharma S et al (2008) Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 74:2461–2470

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  9. Gosink JJ, Woese CR, Staley JT (1998) Polaribactger gen. nov., with three new species, P. irgensii sp. nov., P. franzmannii sp. nov. and P. filamentus sp. nov., gas vacuolate polare marine bacteria of the Cytophaga-Flavobacterium-Bactgerodes group and reclassification of ‘Flectobacillus glomeraatus’ as Polaribacer glomeratus comb. nov. Int J Syst Bacteriol 48:223–235

    Article  PubMed  Google Scholar 

  10. Joung Y, Kim H, Ahn TS, Jon K (2011) Pontibacter salisaro sp. nov., isolated from a clay tablet solar saltern in Korea. J Microbiol 49(2):290–293. doi:10.1007/s12275-011-0093-6

    Article  CAS  PubMed  Google Scholar 

  11. Joung Y, Kim H, Lee BI, Kang H, Jang TY, Kwon OS, Joh K (2013) Pontibacter jeungdoensis sp. nov., isolated from a solar saltern in Korea. J Microbiol 51(4):531–535. doi:10.1007/s12275-013-2324-5

    Article  CAS  PubMed  Google Scholar 

  12. Kang JY, Joung Y, Chun J, Kim H, Joh K, Jahng KY (2013) Pontibacter saemangeumensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 63(Pt2):565–569. doi:10.1099/ijs.0.039867-0

    Article  CAS  PubMed  Google Scholar 

  13. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721. doi:10.1099/ijs.0.038075-0

    Article  CAS  PubMed  Google Scholar 

  14. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16(2):111–120

    Article  CAS  PubMed  Google Scholar 

  15. Komagata K, Suzuki KI (1987) Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–205

    Article  CAS  Google Scholar 

  16. Larkin JM, Borrall R (1984) Deoxyribonucleic acid base compositions, and homology of “Microcyclus”, Pontibacter, and similar organisms. Int J Syst Bacteriol 34(2):211–215

    Article  CAS  Google Scholar 

  17. Minnikin DE, O’Donnella AG, Goodfellowb M, Aldersonb G, Athalyeb M, Schaala A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2(5):233–241. doi:10.1016/0167-7012(84)90018-6

    Article  CAS  Google Scholar 

  18. Nedashkovskaya OI, Kim SB, Suzuki M, Shevchenko LS, Lee, Lee KH, Park, Frolova GM, Oh HW, Bae KS, Park HY, Mikhailov VV (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 Nedashkovskaya et al. 2003. Int J Syst Evol Microbiol 55(Pt 6):2583–2588. doi:10.1099/ijs.0.63819-0

    Article  CAS  PubMed  Google Scholar 

  19. Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, New York

    Google Scholar 

  20. Raichand R, Kaur I, Singh NK, Mayilraj S (2011) Pontibacter rhizosphera sp. nov., isolated from rhizosphere soil of an Indian medicinal plant Nerium indicum. Antonie Van Leeuwenhoek 100(1):129–135. doi:10.1007/s10482-011-9573-2

    Article  PubMed  Google Scholar 

  21. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406–425

    CAS  PubMed  Google Scholar 

  22. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. MIDI Inc., Newark

    Google Scholar 

  23. Singh AK, Garg N, Lata P, Kumar R, Negi V, Vikram S, Lal R (2013) Pontibacter indicus sp. nov., isolated from hexachlorocyclohexane (HCH) contaminated soil. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.055319-0

    Google Scholar 

  24. Singh AK, Garg N, Sangwan N, Negi V, Kumar R, Vikram S, Lal R (2013) Pontibacter ramchanderi sp. nov., isolated from hexachlorocyclohexane-contaminated pond sediment. Int J Syst Evol Microbiol 63(Pt 8):2829–2834. doi:10.1099/ijs.0.045948-0

    Article  CAS  PubMed  Google Scholar 

  25. Subhash Y, Tushar L, Sasikala C, Ramana CV (2013) Erythrobacter odishensis sp. nov. and Pontibacter odishensis sp. nov. isolated from a dry soil of a solar saltern. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.052183-0

    Google Scholar 

  26. Suresh K, Mayilraj S, Chakrabarti T (2006) Effluviibacter roseus gen. nov., sp. nov., isolated from muddy water, belonging to the family “Flexibacteraceae”. Int J Syst Evol Microbiol 56(Pt7):1703–1707. doi:10.1099/ijs.0.64144-0

    Article  CAS  PubMed  Google Scholar 

  27. Tamaoka J, Komagata K (1984) Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25:125–128

    Article  CAS  Google Scholar 

  28. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731–2739. doi:10.1093/molbev/msr121

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  29. 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(24):4876–4882. doi:10.1093/nar/25.24.4876

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  30. 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(Pt 1):99–103. doi:10.1099/ijs.0.011395-0

    Article  CAS  PubMed  Google Scholar 

  31. Xu M, Wang Y, Dai J, Jiang F, Rahman E, Peng F, Fang C (2012) Pontibacter populi sp. nov., isolated from the soil of a Euphrates poplar (Populus euphratica) forest. Int J Syst Evol Microbiol 62(Pt 3):665–670. doi:10.1099/ijs.0.030122-0

    Article  CAS  PubMed  Google Scholar 

  32. Zhang L, Zhang Q, Luo X, Tang Y, Dai J, Li Y, Wang Y, Chen G, Fang C (2008) Pontibacter korlensis sp. nov., isolated from the desert of Xinjiang, China. China. Int J Syst Evol Microbiol 58(Pt 5):1210–1214. doi:10.1099/ijs.0.65667-0

    Article  CAS  Google Scholar 

  33. Zhang L, Zhu L, Wei L, Li C, Wang Y, Shen X (2013) Pontibacter toksunensis sp. nov., isolated from soil, and emended descriptions of Pontibacter roseus and Pontibacter akesuensis. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.053165-0

    Google Scholar 

  34. Zhou Y, Wang X, Liu H, Zhang KY, Zhang YQ, Lai R, Li WJ (2007) Pontibacter akesuensis sp. nov., isolated from a desert soil in China. Int J Syst Evol Microbiol 57(Pt 2):321–325. doi:10.1099/ijs.0.64716-0

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

This work was supported by a research Grant from Seoul Women’s University (2013).

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Authors and Affiliations

  1. Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul, 139-774, Republic of Korea

    Sathiyaraj Srinivasan, Jae-Jin Lee & Myung Kyum Kim

  2. Department of Life Science, Graduate School of Kyonggi University, 94-6 Iui-dong Yeongtong-gu, Suwon, 433-760, Republic of Korea

    Sathiyaraj Srinivasan & Sang-Seob Lee

Authors
  1. Sathiyaraj Srinivasan
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  2. Jae-Jin Lee
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  3. Sang-Seob Lee
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  4. Myung Kyum Kim
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Correspondence to Sang-Seob Lee or Myung Kyum Kim.

Additional information

The NCBI GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain SWU8T (=KEMC 9004-131T = JCM 19178T) is KF975403.

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Fig. S1

Maximum-parsimony phylogenetic tree based on the 16S rRNA gene sequences of strain SWU8T and related taxa. Numbers at branch nodes present bootstrap values (>50 %) obtained by percentage of 1,000 replicates. Bar 20 substitutions per nucleotide position. Reichenbachiella agariperforans KMM 3525T was used as an out-group. (PPTX 80 kb)

Fig. S2

Maximum-likelihood phylogenetic tree based on the 16S rRNA gene sequences of strain SWU8T and related taxa. Numbers at branch nodes present bootstrap values (>50 %) obtained by percentage of 1,000 replicates. Bar 0.02 substitutions per nucleotide position. Reichenbachiella agariperforans KMM 3525T was used as an out-group. (PPTX 79 kb)

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Srinivasan, S., Lee, JJ., Lee, SS. et al. Pontibacter humi sp. nov., Isolated from Mountain Soil. Curr Microbiol 69, 263–269 (2014). https://doi.org/10.1007/s00284-014-0580-1

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