1887

Abstract

A Gram-stain-negative, ovoid or rod-shaped, non-flagellated, motile-by-gliding and aerobic bacteria, designated S10-8, was isolated from marine sediment of the Yellow Sea. Colonies of strain S10-8 had a pink-red pigmentation and its cells were approximately 0.5–0.8 μm×1.0–2.5 μm in size. Growth occurred at 10–45 °C (optimally at 33–37 °C), in the presence of 0–12.0 % NaCl (optimally at 2.0–5.0 %, w/v) and at pH 5.0–8.5 (optimally at pH 7.0–7.5). Phylogenetic analysis of the 16S rRNA gene indicated that strain S10-8 is a member of the genus within the family , and the 16S rRNA gene sequence similarity of strain S10-8 to its closest relative KCTC 12367 was 96.9 %. Strain S10-8 contained MK-7 as the predominant menaquinone and summed feature 4 (iso-C I and/or anteiso-C B) and iso-C as the major fatty acids. The major polar lipids were phosphatidylethanolamine, an unidentified aminophospholipid and an unidentified lipid. The size of the draft genome was 4 623 791 bp and the G+C content was 53.5 mol%. There were low DNA-DNA hybridization values (<48.3±5.2 %) and average nucleotide identity values (<86.5 %) between strain S10-8 and the most closely related recognized species. Therefore, we propose a novel species in the genus to accommodate the novel isolate: sp. nov. (type strain S10-8=KCTC 42769=ACCC 19859).

Funding
This study was supported by the:
  • National Basic Research Program of China (973 Program) (Award 2017YFD0201401)
    • Principle Award Recipient: GuishanZhang
  • National Natural Science Foundation of China (Award NSFC No. 31670113)
    • Principle Award Recipient: GuishanZhang
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2021-10-11
2021-10-25
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References

  1. Nedashkovskaya OI, Kim SB, Suzuki M, Shevchenko LS, Lee MS. 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 2005; 55:2583–2588 [View Article] [PubMed]
    [Google Scholar]
  2. Munoz R, Rosselló-Móra R, Amann R. Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov. Syst Appl Microbiol 2016; 39:281–296 [View Article] [PubMed]
    [Google Scholar]
  3. Singh P, Kumari R, Nayyar N, Lal R. Pontibacter aurantiacus sp. nov. isolated from hexachlorocyclohexane (HCH) contaminated soil. Int J Syst Evol Microbiol 2017; 67:1400–1407 [View Article] [PubMed]
    [Google Scholar]
  4. Cao HJ, Nie Y, Zeng XC, Xu LH, He ZC et al. Pontibacter yuliensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2014; 69:968–972
    [Google Scholar]
  5. Chhetri G, Kim J, Kim H, Kim I, Seo T. Pontibacter oryzae sp. nov., a carotenoid-producing species isolated from a rice paddy field. Antonie van Leeuwenhoek 2019; 112:1705–1713 [View Article] [PubMed]
    [Google Scholar]
  6. Dwivedi V, Niharika N, Lal R. Pontibacter lucknowensis sp. nov., isolated from ahexachlorocyclohexane dump site. Int J Syst Evol Microbiol 2013; 63:309–313 [View Article] [PubMed]
    [Google Scholar]
  7. Kang JY, Joung Y, Chun J, Kim H, Joh K et al. Pontibacter saemangeumensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2013; 63:565–569 [View Article] [PubMed]
    [Google Scholar]
  8. Singh AK, Garg N, Sangwan N, Negi V, Kumar R et al. Pontibacter ramchanderi sp. nov., isolated from hexachlorocyclohexane-contaminated pond sediment. Int J Syst Evol Microbiol 2013; 63:2829–2834 [View Article] [PubMed]
    [Google Scholar]
  9. Srinivasan S, Lee JJ, Lee SS, Kim MK. Pontibacter humi sp. nov., isolated from mountain soil. Curr Microbiol 2014; 69:263–269 [View Article] [PubMed]
    [Google Scholar]
  10. Subhash Y, Sasikala C, Ramana CV. Pontibacter ruber sp. nov.and Pontibacter deserti sp. nov., isolated from the desert. Int J Syst Evol Microbiol 2014; 64:1006–1011 [View Article] [PubMed]
    [Google Scholar]
  11. Subhash Y, Tushar L, Sasikala C, Ramana CV. Erythrobacter odishensis sp. nov. and Pontibacter odishensis sp. nov. isolated from dry soil of a solar saltern. Int J Syst Evol Microbiol 2013; 63:4524–4532 [View Article] [PubMed]
    [Google Scholar]
  12. Wang Y, Zhang KD, Cai F, Zhang L, Tang YL et al. Pontibacter xinjiangensis sp. nov., in the phylum “Bacteroidetes”, and reclassification of [Effluviibacter] roseus as Pontibacter roseus comb. nov. Int J Syst Evol Microbiol 2010; 60:99–103 [View Article] [PubMed]
    [Google Scholar]
  13. Xu LH, Zeng XC, Nie Y, Luo XS, Zhou EM et al. Pontibacter diazotrophicus sp. nov., a novel nitrogen-fixing bacterium of the family Cytophagaceae. PLoS One 2014; 9:e92294
    [Google Scholar]
  14. Xu MB, Wang Y, Dai J, Jiang F, Rahman E et al. Pontibacter populi sp. nov., isolated from the soil of a Euphrates poplar (Populus euphratica) forest. Int J Syst Evol Microbiol 2012; 62:665–670 [View Article] [PubMed]
    [Google Scholar]
  15. Zhang L, Zhang QJ, Luo XS, Tang YL, Dai J et al. Pontibacter korlensis sp. nov., isolated from the desert of Xinjiang, China. Int J Syst Evol Microbiol 2008; 58:1210–1214 [View Article] [PubMed]
    [Google Scholar]
  16. Zhang L, Zhang KD, Cai F, Lei Z, Tang YL et al. Pontibacter toksunensis sp. nov., isolated from soil, and emended descriptions of Pontibacter roseus and Pontibacter akesuensis. Int J Syst Evol Microbiol 2013; 63:4462–4468 [View Article] [PubMed]
    [Google Scholar]
  17. Zhou Y, Wang X, Liu H, Zhang KY, Zhang YQ. Pontibacter akesuensis sp. nov., isolated from a desert soil in China. Int J Syst Evol Microbiol 2007; 57:321–325 [View Article] [PubMed]
    [Google Scholar]
  18. Park S, Park JM, Lee KH, Yoon JH. Pontibacter litorisediminis sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2016; 66:4172–4178 [View Article] [PubMed]
    [Google Scholar]
  19. Smibert RM, Krieg NR. Phenotypic characterization. Gerhardt P, Murray R, Wood W, Krieg N. eds In Methods for General, Molecular Bacteriology Washington, DC USA: ASM Press; 1994 pp 607–654
    [Google Scholar]
  20. Dong XZ, Cai MY. Determination of biochemical characteristics. In Manual for the Systematic Identification of General Bacteria Beijing: Science Press; 2001 pp 370–398
    [Google Scholar]
  21. Fraser SL, Jorgensen JH. Reappraisal of the antimicrobial susceptibilities of Chryseobacterium and Flavobacterium species and methods for reliable susceptibility testing. Antimicrob Agents Chemother 1997; 41:2738–2741 [View Article] [PubMed]
    [Google Scholar]
  22. Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 2011; 27:863–864 [View Article] [PubMed]
    [Google Scholar]
  23. Li RQ, Li YR, Kristiansen K, Wang J. SOAP: Short Oligonucleotide Alignment Program. Bioinformatics 2008; 24:713–714 [View Article] [PubMed]
    [Google Scholar]
  24. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010; 20:265–272 [View Article] [PubMed]
    [Google Scholar]
  25. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW et al. Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2014; 25:1043–1055
    [Google Scholar]
  26. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007; 23:673–679 [View Article] [PubMed]
    [Google Scholar]
  27. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article] [PubMed]
    [Google Scholar]
  28. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 [View Article] [PubMed]
    [Google Scholar]
  29. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article] [PubMed]
    [Google Scholar]
  30. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. MolBiolEvol 2016; 33:1870–1874 [View Article]
    [Google Scholar]
  31. De Ley J, Cattoir H, Reynaerts A. The quantitative measurement of DNA hybridization from renaturation rates. Eur JBiochem 1970; 12:133–142
    [Google Scholar]
  32. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  33. Auch AF, Henz SR, Holland BR, Göker M. Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences. BMC Bioinformatics 2006; 7:350 [View Article] [PubMed]
    [Google Scholar]
  34. Vincent L, Richard D, Olivier G. FastME 2.0: A comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article] [PubMed]
    [Google Scholar]
  35. Chun J, Oren A, Ventosa A, Christensen H, Ruiz AD et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
    [Google Scholar]
  36. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
    [Google Scholar]
  37. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M et al. Versatile and open software for comparing large genomes. Genome Biol 2004; 5:R12 [View Article] [PubMed]
    [Google Scholar]
  38. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
    [Google Scholar]
  39. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
    [Google Scholar]
  40. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI technical note 101. Newark DE, USA: MIDI Inc; 1990
    [Google Scholar]
  41. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article] [PubMed]
    [Google Scholar]
  42. Tindall BJ, Sikorski J, Smibert RM, Kreig NR et al. Phenotypic characterization and the principles of comparative systematics. Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T. eds In Methods for General and Molecular Microbiology, 3rd. edn Washington, DC USA: ASM Press; 2007 pp 330–393
    [Google Scholar]
  43. Tao L, Yao H, Kasai H, Misawa N, Cheng Q. A carotenoid synthesis gene cluster from Algoriphagus sp. KK10202C with a novel fusion-type lycopene beta-cyclase gene. Mol Genet Genomics 2006; 276:79–86 [View Article] [PubMed]
    [Google Scholar]
  44. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464
    [Google Scholar]
  45. Graham PH, Sadowsky MJ, Keyser HH, Barnet YM, Bradley RS et al. Proposed minimal standards for the description of new genera and species of root- and stem-nodulating bacteria. Int J Syst Bacteriol 1991; 41:582–587 [View Article]
    [Google Scholar]
  46. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article] [PubMed]
    [Google Scholar]
  47. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
    [Google Scholar]
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