Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 70, Issue 11

sp. nov., isolated from a mussel inhabiting a hydrothermal field in the Okinawa Trough Free

Abstract

A Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped and non-flagellated marine bacterium strain, designated BOM4, was isolated from a mussel inhabiting the Tangyin hydrothermal field of the Okinawa Trough. The growth temperature was in the range of 16–40 °C, and the optimum temperature was 37 °C. Optimal growth occurred at pH 7.0 and in the presence of 1 % (w/v) NaCl. The predominant isoprenoid quinone of strain BOM4 was identified as menaquinone-6 (MK-6). The predominant fatty acids (>10 %) were iso-C(43.8 %) and iso-C 3-OH (17.5 %). The major polar lipids comprised one phosphatidylethanolamine, three unidentified aminolipids and two unidentified lipids. Based on 16S rRNA gene sequence analyses, strain BOM4 was found to be most closely related to JCM 17790 (96.7 %), followed by JLT2011 (96.1 %), GHTF-27 (95.6 %) and RA5-111 (95.5 %) and with lower sequence similarities (93.7- 95.4 %) to other species of the genus . Genome relatedness between strain BOM4 and JCM 17790 was computed using both average nucleotide identity and DNA–DNA hybridization with values of 75.6 and 19.3±2.4 %, respectively. The DNA G+C content of strain BOM4 was 41.4 mol%. On the basis of polyphasic analysis, strain BOM4 was considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is BOM4 (=MCCC 1K03735=JCM 33424).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Gramella bathymodioli , hydrothermal field , mussel and Okinawa Trough
Funding
This study was supported by the:
  • Scientific and Technological Innovation Project of Qingdao National Laboratory for Marine Science and Technology (Award 2016ASKJ14)
    • Principle Award Recipient: Xiao-Hua Zhang
  • The Youth Talent Support Program of the Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao) (Award LMEES-YTSP-2018-02-07)
    • Principle Award Recipient: Min Yu
  • National Natural Science Foundation of China (Award U1706208)
    • Principle Award Recipient: Min Yu
  • National Natural Science Foundation of China (Award 41976137)
    • Principle Award Recipient: Min Yu
  • National Key R&D Program of China (Award 2018YFC0310701)
    • Principle Award Recipient: Min Yu
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004488
2020-09-30
2025-05-23
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/11/5854.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004488&mimeType=html&fmt=ahah

References

  1. 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][PubMed]
     [Google Scholar]
  2. 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][PubMed]
     [Google Scholar]
  3. Shahina M, Hameed A, Lin SY, Lee RJ, Lee MR et al. Gramella planctonica sp. nov., a zeaxanthin-producing bacterium isolated from surface seawater, and emended descriptions of Gramella aestuarii and Gramella echinicola. Antonie van Leeuwenhoek 2014; 105:771–779 [View Article][PubMed]
     [Google Scholar]
  4. Panschin I, Huang S, Meier-Kolthoff JP, Tindall BJ, Rohde M et al. Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050T (DSM 19838T) and Gramella portivictoriae UST040801-001T (DSM 23547T), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriae Lau et al. 2005. Stand Genomic Sci 2016; 11:16 [View Article]
     [Google Scholar]
  5. Tang K, Lin Y, Han Y, Jiao N. Characterization of potential polysaccharide utilization systems in the marine bacteroidetes Gramella flava JLT2011 using a multi-omics approach. Front Microbiol 2017; 8:13 [View Article]
     [Google Scholar]
  6. Reintjes G, Arnosti C, Fuchs BM, Amann R. An alternative polysaccharide uptake mechanism of marine bacteria. ISME J 2017; 11:1640–1650 [View Article][PubMed]
     [Google Scholar]
  7. Kabisch A, Otto A, König S, Becher D, Albrecht D et al. Functional characterization of polysaccharide utilization loci in the marine bacteroidetes 'Gramella forsetii' KT0803. ISME J 2014; 8:1492–1502 [View Article][PubMed]
     [Google Scholar]
  8. Yang Z, Xiao X, Zhang Y. Microbial diversity of sediments from an inactive hydrothermal vent field, Southwest Indian Ridge. Mar Life Sci Technol 2020; 2:73–86 [View Article]
     [Google Scholar]
  9. Wang L, Yu M, Liu Y, Liu J, Wu Y et al. Comparative analyses of the bacterial community of hydrothermal deposits and seafloor sediments across Okinawa Trough. J Marine Syst 2018; 180:162–172 [View Article]
     [Google Scholar]
  10. Yu T, Yin Q, Song X, Zhao R, Shi X et al. Aquimarina longa sp. nov., isolated from seawater, and emended description of Aquimarina muelleri. Int J Syst Evol Microbiol 2013; 63:1235–1240 [View Article][PubMed]
     [Google Scholar]
  11. Moore ERB, Arnscheidt A, Krüger A, Strömpl C, Mau M et al. Simplified protocols for the preparation of genomic DNA from bacterial cultures. Molecular Microbial Ecology Manual 1999; 1:1–15
     [Google Scholar]
  12. 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][PubMed]
     [Google Scholar]
  13. Yoon SH, Ha S-M, 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][PubMed]
     [Google Scholar]
  14. 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][PubMed]
     [Google Scholar]
  15. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
     [Google Scholar]
  16. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  17. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  18. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article][PubMed]
     [Google Scholar]
  19. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article][PubMed]
     [Google Scholar]
  20. Beveridge TJ, Lawrence JR, Murray RG et al. Sampling and staining for light microscopy. In Reddy CA, Beveridge TJ, Breznak TA, Marzluf G, Schmidt TM et al. (editors) Methods for General and Molecular Microbiology Washington, DC: American Society for Microbiology; 2007 pp 19–33
     [Google Scholar]
  21. 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 [View Article][PubMed]
     [Google Scholar]
  22. Tindall BJ, Sikorski J, Smibert RA, Krieg NR et al. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM et al. (editors) Methods for General and Molecular Microbiology Washington, DC: American Society for Microbiology; 2007 pp 330–393
     [Google Scholar]
  23. Hsu SC, Lockwood JL. Powdered chitin agar as a selective medium for enumeration of actinomycetes in water and soil. Appl Microbiol 1975; 29:422–426 [View Article][PubMed]
     [Google Scholar]
  24. Bernardet JF, Bowman JP. The genus Flavobacterium. Prokaryotes 2006; 7:481–531
     [Google Scholar]
  25. Yoon JH, Lee KC, Kho YH, Kang KH, Kim CJ et al. Halomonas alimentaria sp. nov., isolated from jeotgal, a traditional Korean fermented seafood. Int J Syst Evol Microbiol 2002; 52:123–130 [View Article][PubMed]
     [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. Xie CH, Yokota A. Phylogenetic analyses of Lampropedia hyaline based on the 16S rRNA gene sequence. J Gen Appl Microbiol 2003; 49:345–349 [View Article][PubMed]
     [Google Scholar]
  28. 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]
  29. Collins MD, Shah HN. Fatty acid, menaquinone and polar lipid composition of Rothia dentocariosa. Arch Microbiol 1984; 137:247–249 [View Article]
     [Google Scholar]
  30. Komagata K, Suzuki KI. 4 lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1988; 19:161–207
     [Google Scholar]
  31. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article][PubMed]
     [Google Scholar]
  32. Yoon SH, Ha S-min, 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]
  33. 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]
  34. Contreras-Moreira B, Vinuesa P. GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl Environ Microbiol 2013; 79:7696–7701 [View Article][PubMed]
     [Google Scholar]
  35. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article][PubMed]
     [Google Scholar]
  36. Lin H, Yu M, Wang X, Zhang XH. Comparative genomic analysis reveals the evolution and environmental adaptation strategies of vibrios. BMC Genomics 2018; 19:135 [View Article][PubMed]
     [Google Scholar]
  37. 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][PubMed]
     [Google Scholar]
  38. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article][PubMed]
     [Google Scholar]
  39. Liu K, Li S, Jiao N, Tang K. Gramella flava sp. nov., a member of the family Flavobacteriaceae isolated from seawater. Int J Syst Evol Microbiol 2014; 64:165–168 [View Article][PubMed]
     [Google Scholar]
  40. 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][PubMed]
     [Google Scholar]
  41. Park S, Yoon SY, Jung YT, Won S-M, Yoon JH et al. Gramella sediminilitoris sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2016; 66:2704–2710 [View Article][PubMed]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.004488
Loading
Gramella bathymodioli sp. nov., isolated from a mussel inhabiting a hydrothermal field in the Okinawa Trough
Int J Syst Evol Microbiol 70, 5854 (2020); https://doi.org/10.1099/ijsem.0.004488
/content/journal/ijsem/10.1099/ijsem.0.004488
/content/journal/ijsem/10.1099/ijsem.0.004488
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

PDF

Most cited Most Cited RSS feed

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