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Volume 69, Issue 4

sp. nov., isolated from arctic soil Free

Abstract

A bacterial strain, designated N-1-3-6, was isolated from a soil sample collected from the arctic regions. The cells were short rods, Gram-stain-negative, catalase- and oxidase-positive. Growth was observed with 0–12 % (w/v) NaCl, with optimal growth at 0.5–2 %, and at pH 6.0–9.0, with optimum of pH 7.0, and a growth temperature of 10–45 °C, with an optimum of 28–37 °C. Phylogenetic analysis based on the 16S rRNA gene placed N-1-3-6 in the genus with the closest relative being 5DNS001, exhibiting 95.3 % 16S rRNA pairwise similarity. A polyphasic taxonomic study, including phenotypic, chemotaxonomic and molecular analyses, was performed to clarify its taxonomic position. N-1-3-6 contained MK-6 as the predominant menaquinone. Polar lipids consisted of phosphatidylethanolamine and several unidentified aminolipids, phospholipids and lipids. The principal fatty acids (>10 %) were iso-C (26.9 %), summed feature 3 [Cω7cω6 (17.2 %)] and iso-C 3-OH (14.7 %). The DNA G+C content of N-1-3-6 was 47.7 mol%. On the basis of its phenotypic and genotypic properties, strain N-1-3-6 should be classified as representing a novel species of the genus , for which the name sp. nov. is proposed, with the type strain N-1-3-6 (=MCCC 1A06047=KCTC 52339).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Arctic , Sinomicrobium soli sp. nov. , soil and taxonomy
Funding
This study was supported by the:
  • China Ocean Mineral Resources RandD Association program (Award No. DY135-B-01)
  • Xiamen Ocean Economic Innovation and Development Demonstration Project (Award 16PZP001SF16)
  • National Infrastructure of Natural Resources for Science and Technology Program of China (Award NIMR-2017-9)
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2019-02-12
2024-04-25
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References

  1. Xu Y, Tian XP, Liu YJ, Li J, Kim CJ et al. Sinomicrobium oceani gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from marine sediment. Int J Syst Evol Microbiol 2013; 63:1045–1050 [View Article][PubMed]
     [Google Scholar]
  2. Cheng B, Li C, Lai Q, Du M, Shao Z et al. Sinomicrobium pectinilyticum sp. nov., a pectinase-producing bacterium isolated from alkaline and saline soil, and emended description of the genus Sinomicrobium . Int J Syst Evol Microbiol 2014; 64:2939–2943 [View Article][PubMed]
     [Google Scholar]
  3. Lai Q, Cao J, Yuan J, Li F, Shao Z. Celeribacter indicus sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium from deep-sea sediment and reclassification of Huaishuia halophila as Celeribacter halophilus comb. nov. Int J Syst Evol Microbiol 2014; 64:4160–4167 [View Article][PubMed]
     [Google Scholar]
  4. Liu C, Shao Z. Alcanivorax dieselolei sp. nov., a novel alkane-degrading bacterium isolated from sea water and deep-sea sediment. Int J Syst Evol Microbiol 2005; 55:1181–1186 [View Article][PubMed]
     [Google Scholar]
  5. 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]
  6. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731–2739 [View Article][PubMed]
     [Google Scholar]
  7. 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]
  8. 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]
  9. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  10. Rzhetsky A, Nei M. A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 1992; 9:945–967
     [Google Scholar]
  11. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
     [Google Scholar]
  12. 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]
  13. 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]
  14. 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]
  15. Auch AF, Klenk HP, Göker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2010; 2:142–148 [View Article][PubMed]
     [Google Scholar]
  16. 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]
  17. 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]
  18. Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E et al. Microbial genomic taxonomy. BMC Genomics 2013; 14:913 [View Article][PubMed]
     [Google Scholar]
  19. Fautz E, Reichenbach H. A simple test for flexirubin-type pigments. FEMS Microbiol Lett 1980; 8:87–91 [View Article]
     [Google Scholar]
  20. Skerman VBD. A Guide to the Identification of the Genera of Bacteria, 2nd ed. Baltimore: Williams & Wilkins; 1967
     [Google Scholar]
  21. Liu X, Lai Q, Du Y, Li G, Sun F et al. Tamlana nanhaiensis sp. nov., isolated from surface seawater collected from the South China Sea. Antonie van Leeuwenhoek 2015; 107:1189–1196 [View Article][PubMed]
     [Google Scholar]
  22. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc 1990
     [Google Scholar]
  23. Collins M. Isoprenoid quinone analyses in bacterial classification and identification. Society for Applied Bacteriology Technical Series 1985267–287
     [Google Scholar]
  24. Kates M. Techniques of Lipidology. , 2nd ed. rev.,. Elsevier: Amsterdam; 1986 pp. 241–246
  25. Bowman JP, Mccammon SA, Lewis T, Skerratt JH, Brown JL et al. Psychroflexus torquis gen. nov., sp. nov., a psychrophilic species from Antarctic sea ice, and reclassification of Flavobacterium gondwanense (Dobson et al. 1993) as Psychroflexus gondwanense gen. nov., comb. nov. Microbiology 1998; 144:1601–1609 [View Article][PubMed]
     [Google Scholar]
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Sinomicrobium soli sp. nov., isolated from arctic soil
Int J Syst Evol Microbiol 69, 1070 (2019); https://doi.org/10.1099/ijsem.0.003273
/content/journal/ijsem/10.1099/ijsem.0.003273
/content/journal/ijsem/10.1099/ijsem.0.003273
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