1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 69, Issue 8

sp. nov., a psychrophilic bacterium isolated from pelagic sediment of the Ross Sea (Antarctica), and reclassification of Kim . 2012 as a later heterotypic synonym of Bowman . 1997 Free

Abstract

Two Gram-stain-negative, rod-shaped, facultatively anaerobic, iron-reducing bacterial strains, designated M2 and R106, were isolated from pelagic surface-sediment of the Ross Sea, Antarctica. The 16S rRNA gene sequence analysis revealed that strains M2 and R106 were affiliated to the genus and formed a distinct subline in a robust clade encompassing , , and with a range of sequence similarities of 98.1–98.9 %. Overall genome relatedness indices indicated that M2 and R106 represented a single genomic species, which was clearly distinguishable from the phylogenetically close relatives with lower values of species delineation thresholds. Cells of M2 grew optimally at 10–15 °C and pH 6.5 in the presence of 3.0–4.0 % (w/v) sea salts. The polar lipids of M2 comprised phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminophospholipids, an unidentified aminolipid and an unidentified phospholipid. Quinones were Q-7, Q-8, MK-7 and MMK-7. The major cellular fatty acids (>10 %) were Cω7 and/or Cω6, C and Cω8. The DNA G+C content was 42.2 mol%. On the basis of the phenotypic, phylogenetic, genomic and chemotaxonomic features, we propose the name sp. nov. with the type strain M2 (=KCCM 43257 =JCM 32090) and the reclassification of as a later heterotypic synonym of .

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Antarctic , new species , pelagic sediment , psychrophilic and Shewanella psychromarinicola
© 2019 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003490
2019-08-01
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/8/2415.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003490&mimeType=html&fmt=ahah

References

  1. Macdonell MT, Colwell RR. Phylogeny of the Vibrionaceae, and recommendation for two new genera, Listonella and Shewanella . Syst Appl Microbiol 1985; 6:171–182 [View Article]
     [Google Scholar]
  2. Ivanova EP, Flavier S, Christen R. Phylogenetic relationships among marine Alteromonas-like proteobacteria: emended description of the family Alteromonadaceae and proposal of Pseudoalteromonadaceae fam. nov., Colwelliaceae fam. nov., Shewanellaceae fam. nov., Moritellaceae fam. nov., Ferrimonadaceae fam. nov., Idiomarinaceae fam. nov. and Psychromonadaceae fam. nov. Int J Syst Evol Microbiol 2004; 54:1773–1788 [View Article][PubMed]
     [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][PubMed]
     [Google Scholar]
  4. Yun BR, Park S, Kim MK, Park J, Kim SB. Shewanella saliphila sp. nov., Shewanella ulleungensis sp. nov. and Shewanella litoralis sp. nov., isolated from coastal seawater. Int J Syst Evol Microbiol 2018; 68:2960–2966 [View Article][PubMed]
     [Google Scholar]
  5. Bowman JP. Shewanella. In Whitman WB, Rainey F, Kämpfer P, Trujillo M, Chun J et al. (editors) Bergey's Manual of Systematics of Archaea and Bacteria 2015
     [Google Scholar]
  6. Bowman JP, Mccammon SA, Nichols DS, Skerratt JH, Rea SM et al. Shewanella gelidimarina sp. nov. and Shewanella frigidimarina sp. nov., novel Antarctic species with the ability to produce eicosapentaenoic acid (20:5ω3) and grow anaerobically by dissimilatory Fe(III) reduction. Int J Syst Bacteriol 1997; 47:1040–1047 [View Article][PubMed]
     [Google Scholar]
  7. Bozal N, Montes MJ, Tudela E, Jiménez F, Guinea J. Shewanella frigidimarina and Shewanella livingstonensis sp. nov. isolated from Antarctic coastal areas. Int J Syst Evol Microbiol 2002; 52:195–205 [View Article][PubMed]
     [Google Scholar]
  8. Bozal N, Montes MJ, Miñana-Galbis D, Manresa A, Mercadé E. Shewanella vesiculosa sp. nov., a psychrotolerant bacterium isolated from an Antarctic coastal area. Int J Syst Evol Microbiol 2009; 59:336–340 [View Article][PubMed]
     [Google Scholar]
  9. Kim SJ, Park SJ, Oh YS, Lee SA, Shin KS et al. Shewanella arctica sp. nov., an iron-reducing bacterium isolated from Arctic marine sediment. Int J Syst Evol Microbiol 2012; 62:1128–1133 [View Article][PubMed]
     [Google Scholar]
  10. Englen MD, Kelley LC. A rapid DNA isolation procedure for the identification of Campylobacter jejuni by the polymerase chain reaction. Lett Appl Microbiol 2000; 31:421–426 [View Article][PubMed]
     [Google Scholar]
  11. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991 pp. 115–175
     [Google Scholar]
  12. Anzai Y, Kudo Y, Oyaizu H. The phylogeny of the genera Chryseomonas, Flavimonas, and Pseudomonas supports synonymy of these three genera. Int J Syst Bacteriol 1997; 47:249–251 [View Article][PubMed]
     [Google Scholar]
  13. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article][PubMed]
     [Google Scholar]
  14. 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]
  15. Cole JR, Wang Q, Fish JA, Chai B, Mcgarrell DM et al. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 2014; 42:D633–D642 [View Article][PubMed]
     [Google Scholar]
  16. 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]
  17. 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]
  18. 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]
  19. 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]
  20. Swofford DL, Olsen GJ, Waddell PJ, Hillis DM. Phylogenetic inference. In Hiillis DM, Moritz D, Mable BK. (editors) Molecular Systematics Sunderland, MA: Sinauer Associates; 1996 pp. 407–514
     [Google Scholar]
  21. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  22. Cho BC, Hardies SC, Jang GI, Hwang CY. Complete genome of streamlined marine actinobacterium Pontimonas salivibrio strain CL-TW6T adapted to coastal planktonic lifestyle. BMC Genomics 2018; 19:625 [View Article][PubMed]
     [Google Scholar]
  23. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
     [Google Scholar]
  24. 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][PubMed]
     [Google Scholar]
  25. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article][PubMed]
     [Google Scholar]
  26. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article][PubMed]
     [Google Scholar]
  27. Bushnell B. BBMap: A Fast, Accurate, Splice-Aware Aligner. Lawrence Berkeley National Laboratory, Report Number: LBNL-7065E. Berkeley, CA: 2014
     [Google Scholar]
  28. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M et al. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 2012; 28:1647–1649 [View Article][PubMed]
     [Google Scholar]
  29. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P 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][PubMed]
     [Google Scholar]
  30. Auch AF, von Jan M, Klenk HP, Göker M. Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article][PubMed]
     [Google Scholar]
  31. Venkateswaran K, Moser DP, Dollhopf ME, Lies DP, Saffarini DA et al. Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov. Int J Syst Bacteriol 1999; 49:705–724 [View Article][PubMed]
     [Google Scholar]
  32. Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T et al. Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. Nucleic Acids Res 2017; 45:D535–D542 [View Article][PubMed]
     [Google Scholar]
  33. 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]
  34. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996–1004 [View Article][PubMed]
     [Google Scholar]
  35. Lefort V, Longueville JE, Gascuel O. SMS: Smart Model Selection in PhyML. Mol Biol Evol 2017; 34:2422–2424 [View Article][PubMed]
     [Google Scholar]
  36. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010; 59:307–321 [View Article][PubMed]
     [Google Scholar]
  37. Zhong C, Han M, Yu S, Yang P, Li H et al. Pan-genome analyses of 24 Shewanella strains re-emphasize the diversification of their functions yet evolutionary dynamics of metal-reducing pathway. Biotechnol Biofuels 2018; 11:193 [View Article][PubMed]
     [Google Scholar]
  38. 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]
  39. Collins MD. Analysis of isoprenoid quinones. Methods Microbiol 1985; 18:329–366
     [Google Scholar]
  40. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
     [Google Scholar]
  41. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp. 607–654
     [Google Scholar]
  42. Skerman VBD. A Guide to the Identification of the Genera of Bacteria, 2nd ed. Baltimore: Williams & Wilkins; 1967
     [Google Scholar]
  43. Hwang CY, Lee I, Cho Y, Lee YM, Baek K et al. Rhodococcus aerolatus sp. nov., isolated from subarctic rainwater. Int J Syst Evol Microbiol 2015; 65:465–471 [View Article][PubMed]
     [Google Scholar]
  44. Hwang CY, Cho BC. Cohaesibacter gelatinilyticus gen. nov., sp. nov., a marine bacterium that forms a distinct branch in the order Rhizobiales, and proposal of Cohaesibacteraceae fam. nov. Int J Syst Evol Microbiol 2008; 58:267–277 [View Article][PubMed]
     [Google Scholar]
  45. Lovley DR, Giovannoni SJ, White DC, Champine JE, Phillips EJ et al. Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals. Arch Microbiol 1993; 159:336–344 [View Article][PubMed]
     [Google Scholar]
  46. Coates JD, Lonergan DJ, Philips EJ, Jenter H, Lovley DR. Desulfuromonas palmitatis sp. nov., a marine dissimilatory Fe(III) reducer that can oxidize long-chain fatty acids. Arch Microbiol 1995; 164:406–413 [View Article][PubMed]
     [Google Scholar]
  47. Miller TL, Wolin MJ. A serum bottle modification of the Hungate technique for cultivating obligate anaerobes. Appl Microbiol 1974; 27:985–987[PubMed]
     [Google Scholar]
  48. Cappuccino JG, Sherman N. Microbiology: a Laboratory Manual, 6th ed. Menlo Park, CA: Benjamin/Cummings; 2002
     [Google Scholar]
  49. Høvik Hansen G, Sørheim R. Improved method for phenotypical characterization of marine bacteria. J Microbiol Methods 1991; 13:231–241 [View Article]
     [Google Scholar]
  50. Lyman J, Fleming RH. Composition of sea water. J Mar Res 1940; 3:134–146
     [Google Scholar]
  51. 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][PubMed]
     [Google Scholar]
  52. 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]
  53. 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]
  54. Rosselló-Mora R, Amann R. The species concept for prokaryotes. FEMS Microbiol Rev 2001; 25:39–67 [View Article][PubMed]
     [Google Scholar]
  55. Morita RY. Psychrophilic bacteria. Bacteriol Rev 1975; 39:144–167[PubMed]
     [Google Scholar]
  56. Brettar I, Christen R, Höfle MG. Shewanella denitrificans sp. nov., a vigorously denitrifying bacterium isolated from the oxic-anoxic interface of the Gotland Deep in the central Baltic Sea. Int J Syst Evol Microbiol 2002; 52:2211–2217 [View Article][PubMed]
     [Google Scholar]
  57. Park HY, Jeon CO. Shewanella aestuarii sp. nov., a marine bacterium isolated from a tidal flat. Int J Syst Evol Microbiol 2013; 63:4683–4690 [View Article][PubMed]
     [Google Scholar]
  58. Chang HW, Roh SW, Kim KH, Nam YD, Jeon CO et al. Shewanella basaltis sp. nov., a marine bacterium isolated from black sand. Int J Syst Evol Microbiol 2008; 58:1907–1910 [View Article][PubMed]
     [Google Scholar]
  59. Wang MQ, Sun L. Shewanella inventionis sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2016; 66:4947–4953 [View Article][PubMed]
     [Google Scholar]
  60. Ivanova EP, Sawabe T, Gorshkova NM, Svetashev VI, Mikhailov VV et al. Shewanella japonica sp. nov. Int J Syst Evol Microbiol 2001; 51:1027–1033 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003490
Loading
Shewanella psychromarinicola sp. nov., a psychrophilic bacterium isolated from pelagic sediment of the Ross Sea (Antarctica), and reclassification of Shewanella arctica Kim et al. 2012 as a later heterotypic synonym of Shewanella frigidimarina Bowman et al. 1997
Int J Syst Evol Microbiol 69, 2415 (2019); https://doi.org/10.1099/ijsem.0.003490
/content/journal/ijsem/10.1099/ijsem.0.003490
/content/journal/ijsem/10.1099/ijsem.0.003490
Loading

Data & Media loading...

Supplements

Supplementary File 1

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