1887

Abstract

A novel bacterium, designated as strain AM134, was isolated from the gut of a purple sea urchin () gathered from the coastal waters of Dokdo, Korea. Strain AM134 was Gram-stain-negative, both catalase- and oxidase-positive, strictly aerobic and showed a rod-coccus cell cycle. Optimum growth occurred at 30 °C, in the presence of 2 % (w/v) NaCl and at pH 7. The 16S rRNA gene sequence analysis showed that strain AM134 belonged to the genus in the family and had high 16S rRNA gene sequence similarity (>97 %) with F-104 (98.9 % similarity) and Ni-2088 (98.6 % similarity). The polar lipid profile of strain AM134 was composed of phosphatidylethanolamine, phosphatidylserine, three unidentified aminophospholipids, two unidentified phospholipids, an unidentified amino lipid and six unidentified lipids. The major respiratory quinone was identified as ubiquinone-8 (Q-8). The major cellular fatty acids were summed feature 8 (Cω6 and/or Cω7) and C. The DNA–DNA hybridization analysis showed that the strain shared less than 28 % genomic relatedness with DSM 18651 (27±3 %) and ATCC 700307 (15±1 %). The G+C content of the genomic DNA was 56.1 mol%. The results of the phylogenetic, phenotypic and genotypic analyses suggest that strain AM134 represents a novel species in the genus , for which the name is proposed. The type strain is AM134 (=KACC 18258=JCM 30400).

Keyword(s): Microbulbifer , novel and sea urchin
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001731
2017-04-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/4/998.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001731&mimeType=html&fmt=ahah

References

  1. González JM, Mayer F, Moran MA, Hodson RE, Whitman WB. Microbulbifer hydrolyticus gen. nov., sp. nov., and Marinobacterium georgiense gen. nov., sp. nov., Two Marine Bacteria from a Lignin-Rich Pulp Mill Waste Enrichment Community. Int J Syst Evol Microbiol 1997; 47:369–376
    [Google Scholar]
  2. Baba A, Miyazaki M, Nagahama T, Nogi Y. Microbulbifer chitinilyticus sp. nov. and Microbulbifer okinawensis sp. nov., chitin-degrading bacteria isolated from mangrove forests. Int J Syst Evol Microbiol 2011; 61:2215–2220 [View Article][PubMed]
    [Google Scholar]
  3. Miyazaki M, Nogi Y, Ohta Y, Hatada Y, Fujiwara Y et al. Microbulbifer agarilyticus sp. nov. and Microbulbifer thermotolerans sp. nov., agar-degrading bacteria isolated from deep-sea sediment. Int J Syst Evol Microbiol 2008; 58:1128–1133 [View Article][PubMed]
    [Google Scholar]
  4. Vashist P, Nogi Y, Ghadi SC, Verma P, Shouche YS. Microbulbifer mangrovi sp. nov., a polysaccharide-degrading bacterium isolated from an Indian mangrove. Int J Syst Evol Microbiol 2013; 63:2532–2537 [View Article][PubMed]
    [Google Scholar]
  5. Jeong SH, Yang SH, Jin HM, Kim JM, Kwon KK et al. Microbulbifer gwangyangensis sp. nov. and Microbulbifer pacificus sp. nov., isolated from marine environments. Int J Syst Evol Microbiol 2013; 63:1335–1341 [View Article][PubMed]
    [Google Scholar]
  6. Tang SK, Wang Y, Cai M, Lou K, Mao PH et al. Microbulbifer halophilus sp. nov., a moderately halophilic bacterium from north-west China. Int J Syst Evol Microbiol 2008; 58:2036–2040 [View Article][PubMed]
    [Google Scholar]
  7. Wang CS, Wang Y, Xu XW, Zhang DS, Wu YH et al. Microbulbifer donghaiensis sp. nov., isolated from marine sediment of the East China Sea. Int J Syst Evol Microbiol 2009; 59:545–549 [View Article][PubMed]
    [Google Scholar]
  8. Yoon JH, Kim IG, Oh TK, Park YH. Microbulbifer maritimus sp. nov., isolated from an intertidal sediment from the Yellow Sea, Korea. Int J Syst Evol Microbiol 2004; 54:1111–1116 [View Article][PubMed]
    [Google Scholar]
  9. Nishijima M, Takadera T, Imamura N, Kasai H, An KD et al. Microbulbifer variabilis sp. nov. and Microbulbifer epialgicus sp. nov., isolated from Pacific marine algae, possess a rod-coccus cell cycle in association with the growth phase. Int J Syst Evol Microbiol 2009; 59:1696–1707 [View Article][PubMed]
    [Google Scholar]
  10. Camacho M, del Carmen Montero-Calasanz M, Redondo-Gómez S, Rodríguez-Llorente I, Schumann P et al. Microbulbifer rhizosphaerae sp. nov., isolated from the rhizosphere of the halophyte Arthrocnemum macrostachyum. Int J Syst Evol Microbiol 2016; 66:1844–1850 [View Article][PubMed]
    [Google Scholar]
  11. Martin M, Barbeyron T, Martin R, Portetelle D, Michel G et al. The cultivable surface microbiota of the brown alga Ascophyllum nodosum is enriched in macroalgal-polysaccharide-degrading bacteria. Frontiers in Microbiology 2015; 6:1487 [CrossRef]
    [Google Scholar]
  12. Martin M, Portetelle D, Michel G, Vandenbol M. Microorganisms living on macroalgae: diversity, interactions, and biotechnological applications. Appl Microbiol Biotechnol 2014; 98:2917–2935 [View Article][PubMed]
    [Google Scholar]
  13. Sawabe T, Oda Y, Shiomi Y, Ezura Y. Alginate degradation by bacteria isolated from the gut of sea urchins and abalones. Microb Ecol 1995; 30:193–202 [View Article][PubMed]
    [Google Scholar]
  14. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics New York, NY: John Wiley and Sons; 1991 pp. 115–175
    [Google Scholar]
  15. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
    [Google Scholar]
  16. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680[PubMed] [CrossRef]
    [Google Scholar]
  17. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  18. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425[PubMed]
    [Google Scholar]
  19. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1972; 20:406–416 [CrossRef]
    [Google Scholar]
  20. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376[PubMed] [CrossRef]
    [Google Scholar]
  21. Hyun DW, Kim JY, Kim MS, Shin NR, Kim HS et al. Actibacter haliotis sp. nov., isolated from the gut of an abalone, Haliotis discus hannai, and emended description of the genus Actibacter. Int J Syst Evol Microbiol 2015; 65:49–55 [View Article][PubMed]
    [Google Scholar]
  22. Tittsler RP, Sandholzer LA. The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 1936; 31:575–580[PubMed]
    [Google Scholar]
  23. Gonzalez JM, Saiz-Jimenez C. A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. Environ Microbiol 2002; 4:770–773[PubMed] [CrossRef]
    [Google Scholar]
  24. Bae JW, Park YH. Homogeneous versus heterogeneous probes for microbial ecological microarrays. Trends Biotechnol 2006; 24:318–323 [View Article][PubMed]
    [Google Scholar]
  25. Bae JW, Rhee SK, Nam YD, Park YH. Generation of subspecies level-specific microbial diagnostic microarrays using genes amplified from subtractive suppression hybridization as microarray probes. Nucleic Acids Res 2005; 33:e113 [View Article][PubMed]
    [Google Scholar]
  26. Chang HW, Sung Y, Kim KH, Nam YD, Roh SW et al. Development of microbial genome-probing microarrays using digital multiple displacement amplification of uncultivated microbial single cells. Environ Sci Technol 2008; 42:6058–6064[PubMed] [CrossRef]
    [Google Scholar]
  27. Loy A, Schulz C, Lücker S, Schöpfer-Wendels A, Stoecker K et al. 16S rRNA gene-based oligonucleotide microarray for environmental monitoring of the betaproteobacterial order "Rhodocyclales". Appl Environ Microbiol 2005; 71:1373–1386 [View Article][PubMed]
    [Google Scholar]
  28. Brenner DJ. Deoxyribonucleic acid reassociation in the taxonomy of enteric bacteria. Int J Syst Evol Microbiol 1973; 23:298–307
    [Google Scholar]
  29. Tindall BJ, Rosselló-Móra R, Busse HJ, Ludwig W, Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60:249–266 [View Article][PubMed]
    [Google Scholar]
  30. Wayne L, Brenner D, Colwell R, Grimont P, Kandler O et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [CrossRef]
    [Google Scholar]
  31. MIDI Sherlock Microbial Identification System Operating Manual, Version 3.0 Newark, DE: MIDI, Inc. In; 1999
    [Google Scholar]
  32. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids Newark: DE: MIDI Inc; 1990
    [Google Scholar]
  33. Xin H, Itoh T, Zhou P, Suzuki K, Kamekura M et al. Natrinema versiforme sp. nov., an extremely halophilic archaeon from Aibi salt lake, Xinjiang, China. Int J Syst Evol Microbiol 2000; 50:1297–1303 [View Article][PubMed]
    [Google Scholar]
  34. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316–354[PubMed]
    [Google Scholar]
  35. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. Fems Microbiol Lett 1990; 66:199–202 [CrossRef]
    [Google Scholar]
  36. Collins MD, Jones D. A note on the separation of natural mixtures of bacterial ubiquinones using reverse-phase partition thin-layer chromatography and high performance liquid chromatography. J Appl Bacteriol 1981; 51:129–134[PubMed] [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001731
Loading
/content/journal/ijsem/10.1099/ijsem.0.001731
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error