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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 67, Issue 12

sp. nov., a heavy-metal-tolerant bacterium isolated from deep-sea sediment Free

Abstract

A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium, designated B1, was isolated from deep-sea sediment collected from the South Atlantic Ocean. Cells of strain B1 grew in medium containing 0.5–6.0 % (w/v) NaCl (optimum 1.0–2.0 %), at pH 5.5–7.5 (optimum pH 7.0) and at 15–37 °C (optimum 30 °C). Aesculin, starch and Tweens 20, 40 and 60 were hydrolysed. The strain was able to grow in medium containing a high concentration of Co (10 mM). The 16S rRNA gene sequence of strain B1 shared high similarity with respect to DSM 16471 (97.7 %), and exhibited less than 97.0 % sequence similarity with the type strains of other species with validly published names. Phylogenetic analyses revealed that strain B1 fell within the cluster comprising species and formed an independent lineage. The average nucleotide identity and DNA–DNA hybridization values between strain B1 and DSM 16471 were 72.0 % and 17.6 %, respectively. Strain B1 contained menaquinone 6 (MK-6) as the sole isoprenoid quinone and iso-C 3-OH, iso-C and iso-C G as the predominant cellular fatty acids. The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and two unidentified lipids. The DNA G+C content was 39.7 mol%. According to the phylogenetic, chemotaxonomic and phenotypic data, B1 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is B1 (=CGMCC 1.15508=KCTC 52882=MCCC 1K03318).

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Keyword(s): Flavobacteria , heavy-metal-tolerant and Maribacter
© 2017 IUMS
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2017-12-01
2024-04-19
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References

  1. Nedashkovskaya OI, Kim SB, Han SK, Lysenko AM, Rohde M et al. Maribacter gen. nov., a new member of the family Flavobacteriaceae, isolated from marine habitats, containing the species Maribacter sedimenticola sp. nov., Maribacter aquivivus sp. nov., Maribacter orientalis sp. nov. and Maribacter ulvicola sp. nov. Int J Syst Evol Microbiol 2004; 54:1017–1023 [View Article][PubMed]
     [Google Scholar]
  2. Barbeyron T, Carpentier F, L'Haridon S, Schüler M, Michel G et al. Description of Maribacter forsetii sp. nov., a marine Flavobacteriaceae isolated from North Sea water, and emended description of the genus Maribacter . Int J Syst Evol Microbiol 2008; 58:790–797 [View Article][PubMed]
     [Google Scholar]
  3. Nedashkovskaya OI, Kim SB, Mikhailov VV. Maribacter stanieri sp. nov., a marine bacterium of the family Flavobacteriaceae . Int J Syst Evol Microbiol 2010; 60:214–218 [View Article][PubMed]
     [Google Scholar]
  4. Weerawongwiwat V, Kang H, Jung MY, Kim W. Maribacter chungangensis sp. nov., isolated from a green seaweed, and emended descriptions of the genus Maribacter and Maribacter arcticus . Int J Syst Evol Microbiol 2013; 63:2553–2558 [View Article][PubMed]
     [Google Scholar]
  5. Lo N, Jin HM, Jeon CO. Maribacter aestuarii sp. nov., isolated from tidal flat sediment, and an emended description of the genus Maribacter . Int J Syst Evol Microbiol 2013; 63:3409–3414 [View Article][PubMed]
     [Google Scholar]
  6. Hu J, Yang QQ, Ren Y, Zhang WW, Zheng G et al. Maribacter thermophilus sp. nov., isolated from an algal bloom in an intertidal zone, and emended description of the genus Maribacter . Int J Syst Evol Microbiol 2015; 65:36–41 [View Article][PubMed]
     [Google Scholar]
  7. Jackson SA, Kennedy J, Morrissey JP, O'Gara F, Dobson AD. Maribacter spongiicola sp. nov. and Maribacter vaceletii sp. nov., isolated from marine sponges, and emended description of the genus Maribacter . Int J Syst Evol Microbiol 2015; 65:2097–2103 [View Article][PubMed]
     [Google Scholar]
  8. Yoon JH, Kang SJ, Lee SY, Lee CH, Oh TK. Maribacter dokdonensis sp. nov., isolated from sea water off a Korean island, Dokdo. Int J Syst Evol Microbiol 2005; 55:2051–2055 [View Article][PubMed]
     [Google Scholar]
  9. Nedashkovskaya OI, Vancanneyt M, de Vos P, Kim SB, Lee MS et al. Maribacter polysiphoniae sp. nov., isolated from a red alga. Int J Syst Evol Microbiol 2007; 57:2840–2843 [View Article][PubMed]
     [Google Scholar]
  10. Zhang GI, Hwang CY, Kang SH, Cho BC. Maribacter antarcticus sp. nov., a psychrophilic bacterium isolated from a culture of the Antarctic green alga Pyramimonas gelidicola . Int J Syst Evol Microbiol 2009; 59:1455–1459 [View Article][PubMed]
     [Google Scholar]
  11. Cho KH, Hong SG, Cho HH, Lee YK, Chun J et al. Maribacter arcticus sp. nov., isolated from Arctic marine sediment. Int J Syst Evol Microbiol 2008; 58:1300–1303 [View Article][PubMed]
     [Google Scholar]
  12. Kim KH, Jin HM, Jeong HI, Jeon CO. Maribacter lutimaris sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2016; 66:1773–1778 [View Article][PubMed]
     [Google Scholar]
  13. Jung YT, Lee JS, Yoon JH. Maribacter caenipelagi sp. nov., a member of the Flavobacteriaceae isolated from a tidal flat sediment of the Yellow Sea in Korea. Antonie van Leeuwenhoek 2014; 106:733–742 [View Article][PubMed]
     [Google Scholar]
  14. Nies DH. Microbial heavy-metal resistance. Appl Microbiol Biotechnol 1999; 51:730–750 [View Article][PubMed]
     [Google Scholar]
  15. Monsieurs P, Moors H, van Houdt R, Janssen PJ, Janssen A et al. Heavy metal resistance in Cupriavidus metallidurans CH34 is governed by an intricate transcriptional network. Biometals 2011; 24:1133–1151 [View Article][PubMed]
     [Google Scholar]
  16. Xu XW, Wu YH, Zhou Z, Wang CS, Zhou YG et al. Halomonas saccharevitans sp. nov., Halomonas arcis sp. nov. and Halomonas subterranea sp. nov., halophilic bacteria isolated from hypersaline environments of China. Int J Syst Evol Microbiol 2007; 57:1619–1624 [View Article][PubMed]
     [Google Scholar]
  17. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article][PubMed]
     [Google Scholar]
  18. 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][PubMed]
     [Google Scholar]
  19. Ludwig W, Strunk O, Westram R, Richter L, Meier H et al. ARB: a software environment for sequence data. Nucleic Acids Res 2004; 32:1363–1371 [View Article][PubMed]
     [Google Scholar]
  20. Yarza P, Richter M, Peplies J, Euzeby J, Amann R et al. The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008; 31:241–250 [View Article][PubMed]
     [Google Scholar]
  21. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 2007; 35:7188–7196 [View Article][PubMed]
     [Google Scholar]
  22. 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 [View Article][PubMed]
     [Google Scholar]
  23. 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]
  24. 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]
  25. 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]
  26. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  27. 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]
  28. Cai MY, Dong XZ. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
     [Google Scholar]
  29. Wu YH, Xu L, Meng FX, Zhang DS, Wang CS et al. Altererythrobacter atlanticus sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2014; 64:116–121 [View Article][PubMed]
     [Google Scholar]
  30. Farmer III JJ, Janda JM, Brenner FW, Cameron DN, Birkhead KM et al. Genus I. Vibrio Pacini 1854, 411AL . In Garrity GM, Brenner DJ, Krieg NR, Staley JT. (editors) Bergey's Manual of Systematic Bacteriology, 2nd ed. vol. 2 The Proteobacteria, Part B, The Gammaproteobacteria New York: Springer; 1854 pp. 494–546
     [Google Scholar]
  31. Zhang H, Sekiguchi Y, Hanada S, Hugenholtz P, Kim H et al. Gemmatimonas aurantiaca gen. nov., sp. nov., a Gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov. Int J Syst Evol Microbiol 2003; 53:1155–1163 [View Article][PubMed]
     [Google Scholar]
  32. Leifson E. Determination of carbohydrate metabolism of marine bacteria. J Bacteriol 1963; 85:1183–1184[PubMed]
     [Google Scholar]
  33. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. 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, 3rd ed. Washington, DC: ASM Press; 2007 pp. 330–393
     [Google Scholar]
  34. Zhang YZ, Fang MX, Zhang WW, Li TT, Wu M et al. Salimesophilobacter vulgaris gen. nov., sp. nov., an anaerobic bacterium isolated from paper-mill wastewater. Int J Syst Evol Microbiol 2013; 63:1317–1322 [View Article][PubMed]
     [Google Scholar]
  35. Xu XW, Huo YY, Wang CS, Oren A, Cui HL et al. Pelagibacterium halotolerans gen. nov., sp. nov. and Pelagibacterium luteolum sp. nov., novel members of the family Hyphomicrobiaceae . Int J Syst Evol Microbiol 2011; 61:1817–1822 [View Article][PubMed]
     [Google Scholar]
  36. Tang M, Wang G, Xiang W, Chen C, Wu J et al. Maribacter flavus sp. nov., isolated from a cyanobacterial culture pond. Int J Syst Evol Microbiol 2015; 65:3997–4002 [View Article][PubMed]
     [Google Scholar]
  37. 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][PubMed]
     [Google Scholar]
  38. Moore L, Moore E, Murray R, Stackebrandt E, Starr M. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol 1987; 37:463–464 [Crossref]
     [Google Scholar]
  39. Bernardet J-F, Order I. Flavobacteriales ord. nov. In Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ. et al. (editors) Bergey's Manual of Systematic Bacteriology, 2nd ed. vol. 4 New York: Springer; 2010 pp. 105–314
     [Google Scholar]
  40. Bernardet JF, Nakagawa Y, Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes 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]
  41. Park S, Jung YT, Won SM, Yoon JH. Maribacter litorisediminis sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2016; 66:4236–4242 [View Article][PubMed]
     [Google Scholar]
  42. Park S, Jung YT, Park JM, Won SM, Yoon JH et al. Maribacter confluentis sp. nov., isolated from the junction between the ocean and a freshwater spring. Int J Syst Evol Microbiol 2015; 65:3079–3085 [View Article][PubMed]
     [Google Scholar]
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Maribacter cobaltidurans sp. nov., a heavy-metal-tolerant bacterium isolated from deep-sea sediment
Int J Syst Evol Microbiol 67, 5261 (2017); https://doi.org/10.1099/ijsem.0.002458
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