1887

Abstract

A Gram-stain-negative, motile and rod-shaped bacterium, designated strain B2, which can synthesize purple pigments of violacein and dexyoviolacein, was isolated from Tianshan glacier in Xinjiang, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that it was grouped in the genus Massilia with Massilia glaciei B448-2, Massilia eurypsychrophila B528-3 and Massilia psychrophila B1555-1 as its closest relatives (98.2, 97.9 and 97.0 % 16S rRNA gene sequence similarity, respectively). Genomic relatedness between strain B2 and its closest relatives was evaluated using average nucleotide identity, digital DNA–DNA hybridization and average amino acid identity, with values of 77.93–85.08 %, 22.4–23.4 % and 71.54–72.99 %, respectively. Q-8 was the major ubiquinone. The major fatty acids (>5 %) of strain B2 were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C12 : 0 and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The major polar lipids included phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content of strain B2 was 63.51 mol%. Based on genomic relatedness, physiological, biochemical and chemotaxonomic data, strain B2 (=CGMCC 1.6993=DSM 19531=KCTC 32446) is considered to represent a novel species within the genus Massilia , for which the name Massilia violaceinigra sp. nov. is proposed.

Keyword(s): Massilia , new taxa and novel species
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002826
2018-05-31
2019-10-21
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/7/2271.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002826&mimeType=html&fmt=ahah

References

  1. La Scola B, Birtles RJ, Mallet MN, Raoult D. Massilia timonae gen. nov., sp. nov., isolated from blood of an immunocompromised patient with cerebellar lesions. J Clin Microbiol 1998;36:2847–2852[PubMed]
    [Google Scholar]
  2. Kämpfer P, Lodders N, Martin K, Falsen E. Revision of the genus Massilia La Scola et al. 2000, with an emended description of the genus and inclusion of all species of the genus Naxibacter as new combinations, and proposal of Massilia consociata sp. nov. Int J Syst Evol Microbiol 2011;61:1528–1533 [CrossRef][PubMed]
    [Google Scholar]
  3. Altankhuu K, Kim J. Massilia pinisoli sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2016;66:3669–3674 [CrossRef][PubMed]
    [Google Scholar]
  4. Wang H, Lu Y, Xue Y, Ruan Z, Jiang R et al. Separation, purification and structure identification of purple pigments from Duganella B2. J Chem Ind Eng 2008;59:630–635
    [Google Scholar]
  5. Shen L, Liu Y, Gu Z, Xu B, Wang N et al. Massilia eurypsychrophila sp. nov. a facultatively psychrophilic bacteria isolated from ice core. Int J Syst Evol Microbiol 2015;65:2124–2129 [CrossRef][PubMed]
    [Google Scholar]
  6. Embley TM. The linear PCR reaction: a simple and robust method for sequencing amplified rRNA genes. Lett Appl Microbiol 1991;13:171–174 [CrossRef][PubMed]
    [Google Scholar]
  7. 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 [CrossRef][PubMed]
    [Google Scholar]
  8. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006;33:152
    [Google Scholar]
  9. 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 [CrossRef][PubMed]
    [Google Scholar]
  10. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997;25:4876–4882 [CrossRef][PubMed]
    [Google Scholar]
  11. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  12. Rzhetsky A, Nei M. A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 1992;9:945
    [Google Scholar]
  13. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  14. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  15. 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 [CrossRef][PubMed]
    [Google Scholar]
  16. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][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 [CrossRef][PubMed]
    [Google Scholar]
  18. 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 [CrossRef][PubMed]
    [Google Scholar]
  19. 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 [CrossRef][PubMed]
    [Google Scholar]
  20. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  21. 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 [CrossRef][PubMed]
    [Google Scholar]
  22. Qin QL, Xie BB, Zhang XY, Chen XL, Zhou BC et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014;196:2210–2215 [CrossRef][PubMed]
    [Google Scholar]
  23. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014;42:e73 [CrossRef][PubMed]
    [Google Scholar]
  24. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996;42:989–1005 [CrossRef]
    [Google Scholar]
  25. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977;100:221–230 [CrossRef][PubMed]
    [Google Scholar]
  26. Groth I, Schumann P, Rainey FA, Martin K, Schuetze B et al. Demetria terragena gen. nov., sp. nov., a new genus of Actinomycetes isolated from compost soil. Int J Syst Bacteriol 1997;47:1129–1133 [CrossRef][PubMed]
    [Google Scholar]
  27. 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 [CrossRef]
    [Google Scholar]
  28. 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
    [Google Scholar]
  29. Perry LB. Gliding motility in some non-spreading flexibacteria. J Appl Bacteriol 1973;36:227–232 [CrossRef][PubMed]
    [Google Scholar]
  30. Breznak JA, Costilow RN. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC, USA: American Society for Microbiology; 1994; pp.137–154
    [Google Scholar]
  31. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC, USA: American Society for Microbiology; 1994; pp.607–654
    [Google Scholar]
  32. Kim SJ, Ahn JH, Weon HY, Hong SB, Seok SJ et al. Parasegetibacter terrae sp. nov., isolated from paddy soil and emended description of the genus Parasegetibacter. Int J Syst Evol Microbiol 2015;65:113–116 [CrossRef][PubMed]
    [Google Scholar]
  33. Gu Z, Liu Y, Xu B, Wang N, Jiao N et al. Massilia glaciei sp. nov., isolated from the Muztagh glacier. Int J Syst Evol Microbiol 2017;67:4075–4079 [CrossRef][PubMed]
    [Google Scholar]
  34. Guo B, Liu Y, Gu Z, Shen L, Liu K et al. Massilia psychrophila sp. nov., isolated from an ice core. Int J Syst Evol Microbiol 2016;66:4088–4093 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002826
Loading
/content/journal/ijsem/10.1099/ijsem.0.002826
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most Cited This Month

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