1887

Abstract

A Gram-stain-negative, motile, rod-shaped bacterium, designated CPCC 100842, was isolated from a freshwater reservoir in south-west China. The 16S rRNA gene sequence comparison of strain CPCC 100842 with the available sequences in the GenBank database showed that the isolate was closely related to members of the family Comamonadaceae , with the highest similarities to Simplicispira metamorpha DSM 1837 (98.05 %), Simplicispira limi KCTC 12608 (97.86 %), Simplicispira psychrophila LMG 5408 (97.04 %) and Simplicispira piscis JCM 19291 (97.0 %). In the phylogenetic tree based on 16S rRNA gene sequences, strain CPCC 100842 formed a distinct phylogenetic subclade within the genus Simplicispira . The major cellular fatty acids were as C16 : 0 and summed feature 3 (C16 : 1  ω7c/C16 : 1ω6c). Q-8 was detected as the only respiratory quinone. Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, aminophospholipid and glycolipid were found in the polar lipid extraction. The genomic DNA G+C content was 67.4 mol%. The average nucleotide identity value was 80.4 % by comparing the draft genome sequences of strain CPCC 100842 and S. metamorpha DSM 1837. The DNA–DNA hybridization result between strain CPCC 100842 and S. metamorpha DSM 1837 showed 37±3 % genomic relatedness. On the basis of the genotypic analysis and phenotypic characteristics, we propose that strain CPCC 100842 represents a novel species of the genus Simplicispira in the family Comamonadaceae with the name Simplicispira lacusdiani sp. nov. Strain CPCC 100842 (=KCTC 52093=DSM 102231) is the type strain of the species.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003112
2018-11-15
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/1/129.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003112&mimeType=html&fmt=ahah

References

  1. Grabovich M, Gavrish E, Kuever J, Lysenko AM, Podkopaeva D et al. Proposal of Giesbergeria voronezhensis gen. nov., sp. nov. and G. kuznetsovii sp. nov. and reclassification of [Aquaspirillum] anulus, [A.] sinuosum and [A.] giesbergeri as Giesbergeria anulus comb. nov., G. sinuosa comb. nov. and G. giesbergeri comb. nov., and [Aquaspirillum] metamorphum and [A.] psychrophilum as Simplicispira metamorpha gen. nov., comb. nov. and S. psychrophila comb. nov. Int J Syst Evol Microbiol 2006; 56:569–576 [View Article][PubMed]
    [Google Scholar]
  2. Hylemon PB, Wells JS, Krieg NR, Jannasch HW. The genus Spirillum: a taxonomic study. Int J Syst Bacteriol 1973; 23:340–380 [View Article]
    [Google Scholar]
  3. Lu S, Ryu SH, Chung BS, Chung YR, Park W et al. Simplicispira limi sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2007; 57:31–34 [View Article][PubMed]
    [Google Scholar]
  4. Hyun DW, Oh SJ, Kim MS, Whon TW, Jung MJ et al. Simplicispira piscis sp. nov., isolated from the gut of a Korean rockfish, Sebastes schlegelii. Int J Syst Evol Microbiol 2015; 65:4689–4694 [View Article][PubMed]
    [Google Scholar]
  5. Waksman SA. The Actinomycetes. In Classification, Identification and Description of Genera and Species vol. 2 Baltimore, Maryland: The Williams & Wilkins Company; 1961
    [Google Scholar]
  6. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article][PubMed]
    [Google Scholar]
  7. Yuan LJ, Zhang YQ, Guan Y, Wei YZ, Li QP et al. Saccharopolyspora antimicrobica sp. nov., an actinomycete from soil. Int J Syst Evol Microbiol 2008; 58:1180–1185 [View Article][PubMed]
    [Google Scholar]
  8. 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]
  9. Lee JS, Shin YK, Yoon JH, Takeuchi M, Pyun YR et al. Sphingomonas aquatilis sp. nov., Sphingomonas koreensis sp. nov., and Sphingomonas taejonensis sp. nov., yellow-pigmented bacteria isolated from natural mineral water. Int J Syst Evol Microbiol 2001; 51:1491–1498 [View Article][PubMed]
    [Google Scholar]
  10. Kroppenstedt RM. Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics (Society for Applied Bacteriology Technical Series) vol. 20 Manhattan, NY: Academic Press; 1985 pp. 173–199
    [Google Scholar]
  11. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982; 16:584–586[PubMed]
    [Google Scholar]
  12. Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia. Int J Syst Evol Microbiol 2007; 57:1424–1428 [View Article][PubMed]
    [Google Scholar]
  13. 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]
  14. 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]
  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. 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]
  17. Kimura M. The Neutral Theory of Molecular Evolution Cambridge, Cambridgeshire: Cambridge University Press; 1983
    [Google Scholar]
  18. Kluge AG, Farris JS. Quantitative Phyletics and the Evolution of Anurans. Syst Zool 1969; 18:1–32 [View Article]
    [Google Scholar]
  19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  20. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  21. Yoon SH, Ha SM, 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]
  22. Marmur J, Doty P. Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 1962; 5:109–118 [View Article][PubMed]
    [Google Scholar]
  23. 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]
  24. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International committee on systematic bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003112
Loading
/content/journal/ijsem/10.1099/ijsem.0.003112
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
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