1887

Abstract

Strain F21, a marine, aerobic, Gram-negative, rod-shaped bacterium, was isolated from seashore sand sampled in Pohang, Republic of Korea. Cells of strain F21 were non-motile, catalase-positive, oxidase-positive, non-spore-forming and formed pinkish-red colonies on marine agar. The strain grew optimally at 37°C, pH 7 and in the presence of 2–3 % NaCl (w/v). Analysis of the 16S rRNA gene sequence of strain F21 revealed that it belonged to the genus , family , with similarity values of 98.1 and 96.8 % to DSM 16067 and IMSNU 14014, respectively. When comparing the genome sequence of F21 with those of the type strains of six species of the genus , the values obtained were below the thresholds for analyses of average nucleotide identity (71.8–92.7 %) and DNA–DNA hybridization using the Genome-to-Genome Distance Calculator (14.7–75.2 %). The DNA G+C content of strain F21 was 42.0 mol%. The chemotaxonomic characteristics of F21 included MK-7 as the predominant isoprenoid quinone, iso-C, iso-C 3-OH and summed feature 3 (Cω6 and/or Cω7) as major cellular fatty acids, and phosphatidylcholine and phosphatidylethanolamine as major polar lipids. On the basis of phenotypic and chemotaxonomic properties, phylogenetic distinctiveness, and genomic data, we named strain F21 as sp. nov. and proposed that strain F21 (=KEMB 2250–007= KCTC 72106=JCM 33187) in the genus represents a novel species.

Funding
This study was supported by the:
  • Ministry of Land, Infrastructure and Transport (Award 19SCIP-B103706-05)
    • Principle Award Recipient: Keun-Hyeok Yang
  • Ministry of Education, Science and Technology (Award NRF-2017M3A9B8065734)
    • Principle Award Recipient: Sang-Seob Lee
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2019-12-13
2024-12-07
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References

  1. Bowman JP, Nichols CM, Gibson JAE. Algoriphagus ratkowskyi gen. nov., sp. nov., Brumimicrobium glaciale gen. nov., sp. nov., Cryomorpha ignava gen. nov., sp. nov. and Crocinitomix catalasitica gen. nov., sp. nov., novel flavobacteria isolated from various polar habitats. Int J Syst Evol Microbiol 2003; 53:1343–1355 [View Article]
    [Google Scholar]
  2. Tiago I, Mendes V, Pires C, Morais PV, Veríssimo A. Chimaereicella alkaliphila gen. nov., sp. nov., a Gram-negative alkaliphilic bacterium isolated from a nonsaline alkaline groundwater. Syst Appl Microbiol 2006; 29:100–108 [View Article]
    [Google Scholar]
  3. Ahmed I, Yokota A, Fujiwara T. Chimaereicella boritolerans sp. nov., a boron-tolerant and alkaliphilic bacterium of the family Flavobacteriaceae isolated from soil. Int J Syst Evol Microbiol 2007; 57:986–992 [View Article]
    [Google Scholar]
  4. Yoon JH, Yeo SH, Oh TK. Hongiella marincola sp. nov., isolated from sea water of the East Sea in Korea. Int J Syst Evol Microbiol 2004; 54:1845–1848 [View Article]
    [Google Scholar]
  5. Yi H, Chun J. Hongiella mannitolivorans gen. nov., sp. nov., Hongiella halophila sp. nov. and Hongiella ornithinivorans sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 2004; 54:157–162 [View Article]
    [Google Scholar]
  6. Nedashkovskaya OI, Vancanneyt M, Van Trappen S, Vandemeulebroecke K, Lysenko AM et al. Description of Algoriphagus aquimarinus sp. nov., Algoriphagus chordae sp. nov. and Algoriphagus winogradskyi sp. nov., from sea water and algae, transfer of Hongiella halophila Yi and Chun 2004 to the genus Algoriphagus as Algoriphagus halophilus comb. nov. and emended descriptions of the genera Algoriphagus Bowman et al. 2003 and Hongiella Yi and Chun 2004. Int J Syst Evol Microbiol 2004; 54:1757–1764 [View Article]
    [Google Scholar]
  7. Nedashkovskaya OI, Kim SB, Kwon KK, Shin DS, Luo X et al. Proposal of Algoriphagus vanfongensis sp. nov., transfer of members of the genera Hongiella Yi and Chun 2004 emend. Nedashkovskaya et al. 2004 and Chimaereicella Tiago et al. 2006 to the genus Algoriphagus, and emended description of the genus Algoriphagus Bowman et al. 2003 emend. Nedashkovskaya et al. 2004. Int J Syst Evol Microbiol 2007; 57:1988–1994 [View Article]
    [Google Scholar]
  8. Parte AC. LPSN--list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 2014; 42:D613–D616 [View Article]
    [Google Scholar]
  9. Oh KH, Kang SJ, Lee SY, Park S, Oh TK et al. Algoriphagus namhaensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2012; 62:575–579 [View Article]
    [Google Scholar]
  10. Shahina M, Hameed A, Lin SY, Lai WA, Hsu YH et al. Description of Algoriphagus taiwanensis sp. nov., a xylanolytic bacterium isolated from surface seawater, and emended descriptions of Algoriphagus mannitolivorans, Algoriphagus olei, Algoriphagus aquatilis and Algoriphagus ratkowskyi . Antonie van Leeuwenhoek 2014; 106:1031–1040 [View Article]
    [Google Scholar]
  11. Lee DH, Kahng HY, Lee SB. Algoriphagus jejuensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2012; 62:409–413 [View Article]
    [Google Scholar]
  12. Alegado RA, Grabenstatter JD, Zuzow R, Morris A, Huang SY et al. Algoriphagus machipongonensis sp. nov., co-isolated with a colonial choanoflagellate. Int J Syst Evol Microbiol 2013; 63:163–168 [View Article]
    [Google Scholar]
  13. Jung YT, Lee JS, Yoon JH. Algoriphagus aestuarii sp. nov., a member of the Cyclobacteriaceae isolated from a tidal-flat sediment of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2015; 65:3439–3446 [View Article]
    [Google Scholar]
  14. Jia X, Jia B, Kim KH, Jeon CO. Algoriphagus aestuariicola sp. nov., isolated from estuary sediment. Int J Syst Evol Microbiol 2017; 67:914–919 [View Article]
    [Google Scholar]
  15. Park S, Park JM, Lee KC, Yoon JH. Algoriphagus boseongensis sp. nov., a member of the family Cyclobacteriaceae isolated from a tidal flat. Antonie van Leeuwenhoek 2014; 105:523–531 [View Article]
    [Google Scholar]
  16. Kang H, Weerawongwiwat V, Jung MY, Myung SC, Kim W. Algoriphagus chungangensis sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2013; 63:648–653 [View Article]
    [Google Scholar]
  17. Li Y, Yan S, Yang Q, Qi Z, Zhang XH et al. Algoriphagus faecimaris sp. nov., isolated from coastal sediment. Int J Syst Evol Microbiol 2011; 61:2856–2860 [View Article]
    [Google Scholar]
  18. Sun QL, Sun L. Description of Algoriphagus iocasae sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2017; 67:243–249 [View Article]
    [Google Scholar]
  19. Park S, Ha MJ, Yoon SY, Jung YT, Yoon JH. Algoriphagus litorisediminis sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2016; 66:5437–5443 [View Article]
    [Google Scholar]
  20. Park S, Kang S, Oh K, Oh T, Yoon J. Algoriphagus lutimaris sp. nov., isolated from a tidal flat sediment; 2016200–204
  21. Han JR, Geng QL, Wang FQ, Du ZJ, Chen GJ. Algoriphagus marinus sp. nov., isolated from marine sediment and emended description of the genus Algoriphagus . Int J Syst Evol Microbiol 2017; 67:2412–2417 [View Article]
    [Google Scholar]
  22. Han JR, Zhao JX, Wang ZJ, Chen GJ, Du ZJ. Algoriphagus resistens sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2017; 67:1275–1280 [View Article]
    [Google Scholar]
  23. Kim H, Joung Y, Joh K. Algoriphagus taeanensis sp. nov., isolated from a tidal flat, and emended description of Algoriphagus hitonicola . Int J Syst Evol Microbiol 2014; 64:21–26 [View Article]
    [Google Scholar]
  24. Yoon JH, Kang SJ, Oh TK. Algoriphagus locisalis sp. nov., isolated from a marine solar saltern. Int J Syst Evol Microbiol 2005; 55:1635–1639 [View Article]
    [Google Scholar]
  25. Yoon JH, Kang SJ, Jung SY, Lee CH, Oh TK. Algoriphagus yeomjeoni sp. nov., isolated from a marine solar saltern in the Yellow Sea, Korea. Int J Syst Evol Microbiol 2005; 55:865–870 [View Article]
    [Google Scholar]
  26. Park S, Park JM, Yoon JH. Algoriphagus marisflavi sp. nov., isolated from water of an estuary environment. Int J Syst Evol Microbiol 2017; 67:4168–4174 [View Article]
    [Google Scholar]
  27. Park S, Park JM, Yoon JH. Algoriphagus marisflavi sp. nov., isolated from water of an estuary environment. Int J Syst Evol Microbiol 2017; 67:4168–4174 [View Article]
    [Google Scholar]
  28. Yang C, Li Y, Guo Q, Lai Q, Zheng T et al. Algoriphagus zhangzhouensis sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2013; 63:1621–1626 [View Article]
    [Google Scholar]
  29. Copa-Patiño JL, Arenas M, Soliveri J, Sánchez-Porro C, Ventosa A. Algoriphagus hitonicola sp. nov., isolated from an athalassohaline lagoon. Int J Syst Evol Microbiol 2008; 58:424–428 [View Article]
    [Google Scholar]
  30. Van Trappen S, Vandecandelaere I, Mergaert J, Swings J. Algoriphagus antarcticus sp. nov., a novel psychrophile from microbial mats in Antarctic lakes. Int J Syst Evol Microbiol 2004; 54:1969–1973 [View Article]
    [Google Scholar]
  31. Liu Y, Li H, Jiang JT, Liu YH, Song XF et al. Algoriphagus aquatilis sp. nov., isolated from a freshwater lake. Int J Syst Evol Microbiol 2009; 59:1759–1763 [View Article]
    [Google Scholar]
  32. Rau JE, Blotevogel KH, Fischer U. Algoriphagus aquaeductus sp. nov., isolated from a freshwater pipe. Int J Syst Evol Microbiol 2012; 62:675–682 [View Article]
    [Google Scholar]
  33. Inan K, Kacagan M, Ozer A, Osman Belduz A, Canakci S. Algoriphagus trabzonensis sp. nov., isolated from freshwater, and emended description of Algoriphagus alkaliphilus . Int J Syst Evol Microbiol 2015; 65:2234–2240 [View Article]
    [Google Scholar]
  34. Yoon JH, Lee MH, Kang SJ, Oh TK. Algoriphagus terrigena sp. nov., isolated from soil. Int J Syst Evol Microbiol 2006; 56:777–780 [View Article]
    [Google Scholar]
  35. Young CC, Lin SY, Arun AB, Shen FT, Chen WM et al. Algoriphagus olei sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2009; 59:2909–2915 [View Article]
    [Google Scholar]
  36. Kohli P, Nayyar N, Sharma A, Singh AK, Lal R. Algoriphagus roseus sp. nov., isolated from a hexachlorocyclohexane-contaminated dumpsite. Int J Syst Evol Microbiol 2016; 66:3558–3565 [View Article]
    [Google Scholar]
  37. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961; 3:IN1208–218 [View Article]
    [Google Scholar]
  38. Kim J, Srinivasan S, You T, Bang JJ, Park S et al. Brevibacterium ammoniilyticum sp. nov., an ammonia-degrading bacterium isolated from sludge of a wastewater treatment plant. Int J Syst Evol Microbiol 2013; 63:1111–1118 [View Article]
    [Google Scholar]
  39. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically United database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article]
    [Google Scholar]
  40. Phillips JL, Gnanakaran S. A data-driven approach to modeling the tripartite structure of multidrug resistance efflux pumps. Proteins 2015; 83:46–65 [View Article]
    [Google Scholar]
  41. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article]
    [Google Scholar]
  42. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article]
    [Google Scholar]
  43. Chow GC. Maximum-Likelihood estimation of misspecified models. Econ Model 1984; 1:134–138 [View Article]
    [Google Scholar]
  44. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
    [Google Scholar]
  45. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article]
    [Google Scholar]
  46. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  47. Takahata N, Kimura M. The neutral theory of molecular evolution. Princ Med Biol 1994; 1:205–234
    [Google Scholar]
  48. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821–829 [View Article]
    [Google Scholar]
  49. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013; 10:563–569 [View Article]
    [Google Scholar]
  50. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The seed and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [View Article]
    [Google Scholar]
  51. 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]
    [Google Scholar]
  52. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article]
    [Google Scholar]
  53. JG C, Sherman N. Microbiology: a Laboratory Manual, 6th Edn. San Francisco, CA: Benjamin Cummings; 2002
    [Google Scholar]
  54. Hayat MA, Miller SE. Negative Staining: Applications and Methods. New York, NY: McGraw-Hill; 1990
    [Google Scholar]
  55. Brown AE. Benson ́S. Microbiological Applications: Laboratory Manual in General Microbiology New York, NY: McGraw-Hill; 2009
    [Google Scholar]
  56. Hudzicki J. Kirby-Bauer Disk Diffusion Susceptibility Test Protocol Washington, DC: American Society for Microbiology; 2009
    [Google Scholar]
  57. Kunitsky C, Gerard O, Sasser M. Identification of microorganisms using fatty acid methyl ester (FAME) analysis and the MIDI Sherlock microbial identification system. Encycl Rapid Microbiol Methods 20061–18
    [Google Scholar]
  58. Tikka T, Al Abduwani J, Costello D. Deliberate self-harming application of superglue in the nose: case report and literature review. J Laryngol Otol 2015; 129:98–100 [View Article]
    [Google Scholar]
  59. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977; 27:104–117 [View Article]
    [Google Scholar]
  60. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [View Article]
    [Google Scholar]
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