sp. nov., isolated from a marine sand Free

Abstract

A Gram-stain-negative, aerobic, non-spore-forming, motile by gliding and rod-shaped bacterial strain, designated HSMS-1, was isolated from a marine sand collected from the Yellow Sea, Republic of Korea, and identified by a polyphasic taxonomic approach. The neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that HSMS-1 fell within the clade comprising the type strains of species of the genus . HSMS-1 exhibited 16S rRNA gene sequence similarity values of 99.0 and 98.7 % to the type strains of and and of 93.3–98.5 % to the type strains of the other species of the genus . The ANI and dDDH values between HSMS-1 and the type strains of , , , , and were 72.6–79.3 % and 17.4–22.2 %, respectively. Mean DNA–DNA relatedness value between HSMS-1 and the type strain of was 18 %. HSMS-1 contained MK-6 as the predominant menaquinone and iso-C, anteiso-C, iso-C 3-OH and iso-C as the major fatty acids. The major polar lipid of HSMS-1 was phosphatidylethanolamine. The DNA G+C content of HSMS-1 from genomic sequence data was 39.2 %. Distinguishing phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that HSMS-1 is separated from recognized species of the genus . On the basis of the data presented, strain HSMS-1 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is HSMS-1(=KACC 19899=NBRC 113648).

Funding
This study was supported by the:
  • Rural Development Administration (Award PJ013743)
    • Principle Award Recipient: Jung-Hoon Yoon
  • National Institute of Biological Resources (Award project on survey of indigenous species of Korea)
    • Principle Award Recipient: Jung-Hoon Yoon
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003845
2019-11-12
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/2/909.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003845&mimeType=html&fmt=ahah

References

  1. Bernardet JF. Family I. Flavobacteriaceae Reichenbach 1992. In Krieg NR, Ludwig W, Whitman WB, Hedlund BP, Paster BJ. (editors) Bergey’s Manual of Systematic Bacteriology 4., 2nd ed. New York: Springer; 2011 pp 106–111
    [Google Scholar]
  2. Nedashkovskaya OI, Kim SB, Lysenko AM, Frolova GM, Mikhailov VV et al. Gramella echinicola gen. nov., sp. nov., a novel halophilic bacterium of the family Flavobacteriaceae isolated from the sea urchin Strongylocentrotus intermedius . Int J Syst Evol Microbiol 2005; 55:391–394 [View Article]
    [Google Scholar]
  3. Parte AC. LPSN – list of prokaryotic names with standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article]
    [Google Scholar]
  4. Panschin I, Becher M, Verbarg S, Spröer C, Rohde M et al. Description of Gramella forsetii sp. nov., a marine Flavobacteriaceae isolated from North Sea water, and emended description of Gramella gaetbulicola Cho et al. 2011. Int J Syst Evol Microbiol 2017; 67:697–703 [View Article]
    [Google Scholar]
  5. Li AZ, Han XB, Lin LZ, Zhang MX, Zhu HH. Gramella antarctica sp. nov., isolated from marine surface sediment. Int J Syst Evol Microbiol 2018; 68:358–363 [View Article]
    [Google Scholar]
  6. Shin SK, Kim E, Yi H. Gramella salexigens sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2018; 68:2381–2385 [View Article]
    [Google Scholar]
  7. Lau SCK, Tsoi MMY, Li X, Plakhotnikova I, Dobretsov S et al. Gramella portivictoriae sp. nov., a novel member of the family Flavobacteriaceae isolated from marine sediment. Int J Syst Evol Microbiol 2005; 55:2497–2500 [View Article]
    [Google Scholar]
  8. Cho SH, Chae SH, Cho M, Kim TU, Choi S et al. Gramella gaetbulicola sp. nov., a member of the family Flavobacteriaceae isolated from foreshore soil. Int J Syst Evol Microbiol 2011; 61:2654–2658 [View Article]
    [Google Scholar]
  9. Jeong SH, Jin HM, Jeon CO. Gramella aestuarii sp. nov., isolated from a tidal flat, and emended description of Gramella echinicola . Int J Syst Evol Microbiol 2013; 63:2872–2878 [View Article]
    [Google Scholar]
  10. Hameed A, Shahina M, Lin SY, Liu YC, Lai WA et al. Gramella oceani sp. nov., a zeaxanthin-producing bacterium of the family Flavobacteriaceae isolated from marine sediment. Int J Syst Evol Microbiol 2014; 64:2675–2681 [View Article]
    [Google Scholar]
  11. Park JM, Park S, Won SM, Jung YT, Shin K-S et al. Gramella aestuariivivens sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2015; 65:1262–1267 [View Article]
    [Google Scholar]
  12. Park S, Kim S, Jung YT, Yoon JH. Gramella aquimixticola sp. nov., isolated from water of an estuary environment. Int J Syst Evol Microbiol 2015; 65:4244–4249 [View Article]
    [Google Scholar]
  13. Park S, Yoon SY, Jung YT, Won SM, Yoon JH. Gramella sediminilitoris sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2016; 66:2704–2710 [View Article]
    [Google Scholar]
  14. Yoon JH, Lee ST, Kim SB, Kim WY, Goodfellow M et al. Restriction fragment length polymorphism analysis of PCR-amplified 16S ribosomal DNA for rapid identification of Saccharomonospora strains. Int J Syst Bacteriol 1997; 47:111–114 [View Article]
    [Google Scholar]
  15. Yoon JH, Kim H, Kim IG, Kang KH, Park YH. Erythrobacter flavus sp. nov., a slight halophile from the East Sea in Korea. Int J Syst Evol Microbiol 2003; 53:1169–1174 [View Article]
    [Google Scholar]
  16. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR 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]
    [Google Scholar]
  17. Tritt A, Eisen JA, Facciotti MT, Darling AE. An integrated pipeline for de novo assembly of microbial genomes. PLoS One 2012; 7:e42304 [View Article]
    [Google Scholar]
  18. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article]
    [Google Scholar]
  19. 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]
  20. Lee I, Chalita M, Ha SM, Na SI, Yoon SH et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [View Article]
    [Google Scholar]
  21. Goris J, Klappenbach JA, Vandamme P, Coenye T, Konstantinidis KT 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]
    [Google Scholar]
  22. 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]
    [Google Scholar]
  23. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 2005; 102:2567–2572 [View Article]
    [Google Scholar]
  24. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric deoxyribonucleic acid–deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 1989; 39:224–229 [View Article]
    [Google Scholar]
  25. Komagata K, Suzuki K. Lipids and cell-wall analysis in bacterial Systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  26. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  27. 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]
  28. Embley TM, Wait R. Structural lipids of eubacteria. In Goodfellow M, O’Donnell AG. (editors) Modern Microbial Methods. Chemical Methods in Prokaryotic Systematics Chichester: John Wiley & Sons; 1994 pp 121–161
    [Google Scholar]
  29. Park S, Won SM, Kim H, Park DS, Yoon JH. Aestuariivita boseongensis gen. nov., sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2014; 64:2969–2974 [View Article]
    [Google Scholar]
  30. Bowman JP. Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 2000; 50:1861–1868 [View Article]
    [Google Scholar]
  31. Reichenbach H. The order Cytophagales . In Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH. (editors) The Prokaryotes, A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications, 2nd edn. New York: Springer; 1992 pp 3631–3675
    [Google Scholar]
  32. Bernardet JF, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070
    [Google Scholar]
  33. Lányí B. Classical and rapid identification methods for medically important bacteria. Methods Mocrobiol 1987; 19:1–67
    [Google Scholar]
  34. Bruns A, Rohde M, Berthe-Corti L. Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North Sea intertidal sediment. Int J Syst Evol Microbiol 2001; 51:1997–2006 [View Article]
    [Google Scholar]
  35. Barrow GI, Feltham RKA. Cowan and Steel’s Manual for the Identification of Medical Bacteria , 3rd edn. Cambridge: Cambridge University Press; 1993
    [Google Scholar]
  36. Baumann P, Baumann L. The marine Gram-negative eubacteria: genera Photobacterium, Beneckea, Alteromonas, Pseudomonas, and Alcaligenes . In Starr MP, Stolp H, Trüper HG, Balows A, Schlegel HG. (editors) The Prokaryotes Berlin: Springer; 1981 pp 1302–1331
    [Google Scholar]
  37. Cohen-Bazire G, Sistrom WR, Stanier RY. Kinetic studies of pigment synthesis by non-sulfur purple bacteria. J Cell Comp Physiol 1957; 49:25–68 [View Article]
    [Google Scholar]
  38. Staley JT. Prosthecomicrobium and Ancalomicrobium: new prosthecate freshwater bacteria. J Bacteriol 1968; 95:1921–1942
    [Google Scholar]
  39. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003845
Loading
/content/journal/ijsem/10.1099/ijsem.0.003845
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed