sp. nov., isolated from a freshwater river, reclassification of as comb. nov., and emended description of the genus Free

Abstract

A novel Gram-negative, aerobic, non-motile, ovoid to rod-shaped bacterium, designated NBD-18, was isolated from a freshwater river in Taiwan. Optimal growth occurred at 30 °C, at pH 6 and in the absence of NaCl. The predominant fatty acids of strain NBD-18 were C, summed feature 3 (C 7 and/or C 6), C cyclo and summed feature 8 (C 7 and/or C 6). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidyldimethylethanolamine. The major polyamine was putrescine. The major isoprenoid quinone was Q-8. The genomic DNA G+C content of strain NBD-18 was 50.9 %. Strain NBD-18 was most closely related to LMG 29303 and HZ20 at a 16S rRNA gene sequence similarity of 97.7 %. 16S rRNA gene sequence similarity between LMG 29303 and HZ20 was 97.7 %. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set indicated that strain NBD-18, LMG 29303 and HZ20 are affiliated with the same genus. Digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity values among these three strains supported that they belong to the same genus and that strain NBD-18 represents a novel species. Thus, HZ20 should be reclassified as comb. nov. based on the rules for priority of publication and validation. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain NBD-18 represents a novel species in the genus , for which the name sp. nov. is proposed. The type strain is NBD-18 (=BCRC 81197=LMG 31338).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004538
2020-10-28
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/12/6381.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004538&mimeType=html&fmt=ahah

References

  1. Carlier A, Cnockaert M, Fehr L, Vandamme P, Eberl L. Draft genome and description of Orrella dioscoreae gen. nov. sp. nov., a new species of Alcaligenaceae isolated from leaf acumens of Dioscorea sansibarensis . Syst Appl Microbiol 2017; 40:11–21 [View Article][PubMed]
    [Google Scholar]
  2. Ying J-J, Zhang S-L, Huang C-Y, Xu L, Zhao Z et al. Algicoccus marinus gen. nov. sp. nov., a marine bacterium isolated from the surface of brown seaweed Laminaria japonica . Arch Microbiol 2019; 201:943–950 [View Article][PubMed]
    [Google Scholar]
  3. Beveridge TJ, Lawrence JR, Murray RGE et al. Sampling and staining for light microscopy.. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR et al. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: American Society for Microbiology;; 2007 pp pp. 19–.33
    [Google Scholar]
  4. Schlegel HG, Lafferty R, Krauss I. The isolation of mutants not accumulating poly-β-hydroxybutyric acid. Arch Mikrobiol 1970; 71:283–294 [View Article][PubMed]
    [Google Scholar]
  5. Spiekermann P, Rehm BH, Kalscheuer R, Baumeister D, Steinbüchel A. A sensitive, viable-colony staining method using Nile red for direct screening of bacteria that accumulate polyhydroxyalkanoic acids and other lipid storage compounds. Arch Microbiol 1999; 171:73–80 [View Article][PubMed]
    [Google Scholar]
  6. Breznak JA, Costilow RN. Physicochemical factors in growth. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: American Society for Microbiology; 2007 pp 309–329
    [Google Scholar]
  7. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematic. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: American Society for Microbiology; 2007 pp 330–393
    [Google Scholar]
  8. Wen C-M, Tseng C-S, Cheng C-Y, Li Y-K. Purification, characterization and cloning of a chitinase from Bacillus sp. NCTU2. Biotechnol Appl Biochem 2002; 35:213–219 [View Article][PubMed]
    [Google Scholar]
  9. Bowman JP. Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 2000; 50:1861–1868 [View Article][PubMed]
    [Google Scholar]
  10. Chang S-C, Wang J-T, Vandamme P, Hwang J-H, Chang P-S et al. Chitinimonas taiwanensis gen. nov., sp. nov., a novel chitinolytic bacterium isolated from a freshwater pond for shrimp culture. Syst Appl Microbiol 2004; 27:43–49 [View Article][PubMed]
    [Google Scholar]
  11. Nokhal TH, Schlegel HG. Taxonomic study of Paracoccus denitrificans . Int J Syst Bacteriol 1983; 33:26–37
    [Google Scholar]
  12. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  13. Embley TM, Wait R. Structural lipids of eubacteria. In Goodfellow M, O’Donnell AG. (editors) Chemical Methods in Prokaryotic Systematics Chichester: Wiley; 1994 pp 121–161
    [Google Scholar]
  14. Busse HJ, Auling G. Polyamine pattern as chemotaxonomic marker within the Proteobacteria . Syst Appl Microbiol 1988; 11:1–8
    [Google Scholar]
  15. Busse HJ, Bunka S, Hensel A, Lubitz W. Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 1997; 47:698–708
    [Google Scholar]
  16. Collins MD. Isoprenoid quinones. In Goodfellow M, O’Donnell AG. (editors) Chemical Methods in Prokaryotic Systematics Chichester: Wiley; 1994 pp 265–309
    [Google Scholar]
  17. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article][PubMed]
    [Google Scholar]
  18. 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]
  19. Yoon S-H, Ha S-M, 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]
  20. 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]
  21. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41:95–98
    [Google Scholar]
  22. 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]
  23. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  24. Kluge AG, Farris FS. Quantitative phyletics and the evolution of anurans. Syst Zool 1969; 18:1–32
    [Google Scholar]
  25. 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]
  26. Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 2016; 32:3047–3048 [View Article][PubMed]
    [Google Scholar]
  27. 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]
  28. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][PubMed]
    [Google Scholar]
  29. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article][PubMed]
    [Google Scholar]
  30. Oren A 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]
  31. 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]
  32. 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]
  33. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article][PubMed]
    [Google Scholar]
  34. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  35. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe Magazine 2014; 9:111–118
    [Google Scholar]
  36. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article][PubMed]
    [Google Scholar]
  37. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [View Article][PubMed]
    [Google Scholar]
  38. Sun C, Xu L, Ying JJ, Zhang SL, Huang CY et al. Complete genome sequence of Bordetella sp. HZ20 sheds light on the ecological role of bacterium without algal-polysaccharides degrading abilities in the brown seaweed-abundant environment. Mar Genomics 2018; 42:49–52
    [Google Scholar]
  39. Blom J, Kreis J, Spänig S, Juhre T, Bertelli C et al. EDGAR 2.0: an enhanced software platform for comparative gene content analyses. Nucleic Acids Res 2016; 44:W22–W28 [View Article][PubMed]
    [Google Scholar]
  40. Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2019; 69:5–9 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004538
Loading
/content/journal/ijsem/10.1099/ijsem.0.004538
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed