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Volume 70, Issue 6

sp. nov., isolated from a deep-sea seamount Free

Abstract

The Gram-stain-negative, rod-shaped, facultative anaerobic, motile bacterial strain, designated TP390, was isolated from a seamount near the Yap Trench in the tropical western Pacific. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain TP390 was related to the genus and had highest 16S rRNA gene sequence identity with the type strain of EC11 (97.8 %). Sequence similarities to all other type strains of current species of the genus were below 97 %. The predominant cellular fatty acids were iso-C and iso-CG. The quinone system for strain TP390 comprised predominantly menaquinone MK-6 and the polar lipid profile contained phosphatidylethanolamine, four unknown aminolipids, one glycolipid and six unknown polar lipids. The genomic DNA G+C content of strain TP390 was 31.2 mol%. In addition, the maximum values of DNA–DNA hybridization (DDH) and average nucleotide identity (ANI) between strain TP390 with KCTC 42149 were 22.60 and 80.01% respectively. Combined data from phenotypic, phylogenetic, DDH and ANI data demonstrated that the strain TP390 is representative of a novel species of the genus , for which we propose the name sp. nov. (type strain TP390=KACC 18559=CGMCC 1.15398).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Flavobacterium and seamount
Funding
This study was supported by the:
  • the Science & Technology Basic Resources Investigation Program of China (Award 2017FY100804)
    • Principle Award Recipient: De-Chao Zhang
  • the Senior User Project of RV KEXUE (Award KEXUE2019G09)
    • Principle Award Recipient: De-Chao Zhang
© 2020 The Authors
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2020-05-18
2024-04-26
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References

  1. Bergey DH, Harrison FC, Breed RS, Hammer BW, Huntoon FM et al. Genus II. Flavobacterium gen. nov. Bergey’s Manual of Determinative Bacteriology Baltimore: Williams and Wilkins; 1923 pp 97–117
     [Google Scholar]
  2. Bernardet J-F, Segers P, Vancanneyt M, Berthe F, Kersters K et al. Cutting a Gordian Knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (Basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 1996; 46:128–148 [View Article]
     [Google Scholar]
  3. Dong K, Chen F, Du Y, Wang G. Flavobacterium enshiense sp. nov., isolated from soil, and emended descriptions of the genus Flavobacterium and Flavobacterium cauense, Flavobacterium saliperosum and Flavobacterium suncheonense. Int J Syst Evol Microbiol 2013; 63:886–892 [View Article][PubMed]
     [Google Scholar]
  4. Kang JY, Chun J, Jahng KY. Flavobacterium aciduliphilum sp. nov., isolated from freshwater, and emended description of the genus Flavobacterium . Int J Syst Evol Microbiol 2013; 63:1633–1638 [View Article][PubMed]
     [Google Scholar]
  5. Kuo I, Saw J, Kapan DD, Christensen S, Kaneshiro KY et al. Flavobacterium akiainvivens sp. nov., from decaying wood of Wikstroemia oahuensis, Hawai'i, and emended description of the genus Flavobacterium . Int J Syst Evol Microbiol 2013; 63:3280–3286 [View Article][PubMed]
     [Google Scholar]
  6. Bernardet J-F, Bowman JP. The genus Flavobacterium . In Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E. (editors) The Prokaryotes: A Handbook on the Biology of Bacteria 7, 3rd ed. New York, NY: Springer; 2006 pp 481–531
     [Google Scholar]
  7. Bernardet J-F, Bowman JP. Genus I. Flavobacterium Bergey, et al. 1923. In Whitman W. editor Bergey's Manual of Systematic Bacteriology 4, 2nd ed. Baltimore: Williams & Wilkins; 2011 pp 112–154
     [Google Scholar]
  8. DD L, Liu C, Zhang YQ, Wang XJ, Wang N et al. Flavobacterium arcticum sp. nov., isolated from Arctic seawater. Int J Syst Evol Microbiol 2007; 67:1070–1074
     [Google Scholar]
  9. Nupur Bhumika V, Srinivas TNR, Kumar PA. Flavobacterium nitratireducens sp. nov., an amylolytic bacterium of the family Flavobacteriaceae isolated from coastal surface seawater. Int J Syst Evol Microbiol 2013; 63:2490–2496 [View Article][PubMed]
     [Google Scholar]
  10. Nedashkovskaya OI, Balabanova LA, Zhukova NV, Kim S-J, Bakunina IY et al. Flavobacterium ahnfeltiae sp. nov., a new marine polysaccharide-degrading bacterium isolated from a Pacific red alga. Arch Microbiol 2014; 196:745–752 [View Article][PubMed]
     [Google Scholar]
  11. Park S-H, Kim J-Y, Kim Y-J, Heo M-S. Flavobacterium jejuensis sp. nov., isolated from marine brown alga Ecklonia cava . J Microbiol 2015; 53:756–761 [View Article][PubMed]
     [Google Scholar]
  12. Kaur I, Kaur C, Khan F, Mayilraj S. Flavobacterium rakeshii sp. nov., isolated from marine sediment, and emended description of Flavobacterium beibuense Fu et al. 2011. Int J Syst Evol Microbiol 2012; 62:2897–2902 [View Article][PubMed]
     [Google Scholar]
  13. Park S, Choi J, Choi SJ, Yoon J-H. Flavobacterium sediminilitoris sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2018; 68:630–635 [View Article][PubMed]
     [Google Scholar]
  14. Ren Q, Yu M, Li Y, Zhang Y, Shi X et al. Flavobacterium ovatum sp. nov., a marine bacterium isolated from an Antarctic intertidal sandy beach. Int J Syst Evol Microbiol 2018; 68:795–800 [View Article][PubMed]
     [Google Scholar]
  15. Yi H, Oh H-M, Lee J-H, Kim S-J, Chun J. Flavobacterium antarcticum sp. nov., a novel psychrotolerant bacterium isolated from the Antarctic. Int J Syst Evol Microbiol 2005; 55:637–641 [View Article][PubMed]
     [Google Scholar]
  16. Zhang D-C, Liu Y-X, Huang H-J, Wu J. Pseudoalteromonas profundi sp. nov., isolated from a deep-sea seamount. Int J Syst Evol Microbiol 2016; 66:4416–4421 [View Article][PubMed]
     [Google Scholar]
  17. Zhang D-C, Liu Y-X, Huang H-J. Novosphingobium profundi sp. nov. isolated from a deep-sea seamount. Antonie van Leeuwenhoek 2017; 110:19–25 [View Article][PubMed]
     [Google Scholar]
  18. Liu J, Sun Y-W, Zhang D-D, Li S-N, Zhang D-C. Oceanisphaera marina sp. nov., isolated from a deep-sea seamount. Int J Syst Evol Microbiol 2017; 67:1996–2000 [View Article][PubMed]
     [Google Scholar]
  19. Wang Q, Sun Y-W, Liu J, Zhang D-C. Rheinheimera marina sp. nov., isolated from a deep-sea seamount. Int J Syst Evol Microbiol 2018; 68:266–270 [View Article][PubMed]
     [Google Scholar]
  20. Sambrook J, Russell DW. Molecular Cloning: a Laboratory Manual Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press; 2001
     [Google Scholar]
  21. Zhang D-C, Redzic M, Schinner F, Margesin R. Glaciimonas immobilis gen. nov., sp. nov., a member of the family Oxalobacteraceae isolated from alpine glacier cryoconite. Int J Syst Evol Microbiol 2011; 61:2186–2190 [View Article][PubMed]
     [Google Scholar]
  22. Kim O-S, Cho Y-J, Lee K, Yoon S-H, 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]
  23. 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][PubMed]
     [Google Scholar]
  24. 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]
  25. 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]
  26. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article][PubMed]
     [Google Scholar]
  27. 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]
  28. 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]
  29. Yoon S-H, Ha S-M, 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][PubMed]
     [Google Scholar]
  30. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
     [Google Scholar]
  31. Lechner M, Findeiss S, Steiner L, Marz M, Stadler PF et al. Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinformatics 2011; 12:124 [View Article][PubMed]
     [Google Scholar]
  32. Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
     [Google Scholar]
  33. 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]
  34. Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 1992; 8:275–282 [View Article][PubMed]
     [Google Scholar]
  35. Süßmuth R, Eberspächer J, Haag R, Springer W. Biochemisch-mikrobiologisches Praktikum Stuttgart: Georg Thieme Verlag; 1987
     [Google Scholar]
  36. Margesin R, Gander S, Zacke G, Gounot AM, Schinner F. Hydrocarbon degradation and enzyme activities of cold-adapted bacteria and yeasts. Extremophiles 2003; 7:451–458 [View Article][PubMed]
     [Google Scholar]
  37. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press (English translation); 2001
     [Google Scholar]
  38. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, Technical Note 101. Newark, DE: MIDI; 1990
     [Google Scholar]
  39. Zhang D-C, Wang H-X, Liu H-C, Dong X-Z, Zhou P-J. Flavobacterium glaciei sp. nov., a novel psychrophilic bacterium isolated from the China No.1 glacier. Int J Syst Evol Microbiol 2006; 56:2921–2925 [View Article][PubMed]
     [Google Scholar]
  40. Altenburgera P, Kämpferb P, Makristathisc A, Lubitza W, Bussea H-J. Classification of bacteria isolated from a medieval wall painting. J Biotechnol 1996; 47:39–52 [View Article]
     [Google Scholar]
  41. Stolz A, Busse H-J, Kämpfer P. Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol 2007; 57:572–576 [View Article][PubMed]
     [Google Scholar]
  42. 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]
  43. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202 [View Article]
     [Google Scholar]
  44. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
     [Google Scholar]
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Flavobacterium profundi sp. nov., isolated from a deep-sea seamount
Int J Syst Evol Microbiol 70, 3633 (2020); https://doi.org/10.1099/ijsem.0.004205
/content/journal/ijsem/10.1099/ijsem.0.004205
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