1887

Abstract

A novel Gram-reaction-negative bacterial strain, designated Ka43, was isolated from agricultural soil and characterised using a polyphasic approach to determine its taxonomic position. On the basis of 16S rRNA gene sequence analysis, the strain shows highest similarity (97.1 %) to E50. Cells of strain Ka43 are aerobic, motile, short rods. The major fatty acids are summed feature 3 (C 7 and/or iso-C 2-OH), C 7 and C. The only isoprenoid quinone is Q-8. The polar lipid profile includes phosphatidylethanolamine, phosphatidylglycerol, four phospholipids, two lipids and an aminolipid. The assembled genome of strain Ka43 has a total length of 4.2 Mb and the DNA G+C content is 51.6 mol%. Based on phenotypic data, including chemotaxonomic characteristics and analysis of the 16S rRNA gene sequences, it was concluded that strain Ka43 represents a novel species in the genus , for which the name sp. nov. is proposed. The type strain of the species is strain Ka43 (=LMG 31577=NCAIM B.02637).

Funding
This study was supported by the:
  • Magyar Tudományos Akadémia (Award BO/00342/18)
    • Principle Award Recipient: ÁkosTóth
  • NVKP (Award 16-1-2016-0009)
    • Principle Award Recipient: JózsefKukolya
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004805
2021-05-17
2022-01-24
Loading full text...

Full text loading...

References

  1. Spring S, Scheuner C, Göker M, Klenk H-P. A taxonomic framework for emerging groups of ecologically important marine Gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data. Front Microbiol 2015; 6:281 [View Article][PubMed]
    [Google Scholar]
  2. Winogradsky S. Etudes sur La microbiologie Du sol. sur La degradation de la cellulose dans Le sol. Ann Inst Pasteur 1929; 43:549–633
    [Google Scholar]
  3. Skerman VBD, Sneath PHA, McGowan V. Approved lists of bacterial names. Int J Syst Evol Microbiol 1980; 30:225–420 [View Article]
    [Google Scholar]
  4. Blackall LL, Hayward AC, Sly LI. Cellulolytic and dextranolytic Gram-negative bacteria: revival of the genus Cellvibrio. J Bacteriol 1985; 59:81–97
    [Google Scholar]
  5. Humphry DR, Black GW, Cummings SP. Reclassification of 'Pseudomonas fluorescens subsp. cellulosa' NCIMB 10462 (Ueda et al. 1952) as Cellvibrio japonicus sp. nov. and revival of Cellvibrio vulgaris sp. nov., nom. rev. and Cellvibrio fulvus sp. nov., nom. rev. Int J Syst Evol Microbiol 2003; 53:393–400 [View Article][PubMed]
    [Google Scholar]
  6. Suarez C, Ratering S, Kramer I, Schnell S. Cellvibrio diazotrophicus sp. nov., a nitrogen-fixing bacteria isolated from the rhizosphere of salt meadow plants and emended description of the genus Cellvibrio. Int J Syst Evol Microbiol 2014; 64:481–486 [View Article][PubMed]
    [Google Scholar]
  7. DeBoy RT, Mongodin EF, Fouts DE, Tailford LE, Khouri H et al. Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus. J Bacteriol 2008; 190:5455–5463 [View Article][PubMed]
    [Google Scholar]
  8. Tóth Á, Baka E, Bata-Vidács I, Luzics S, Kosztik J et al. Micrococcoides hystricis gen. nov., sp. nov., a novel member of the family Micrococcaceae, phylum Actinobacteria. Int J Syst Evol Microbiol 2017; 67:2758–2765 [View Article][PubMed]
    [Google Scholar]
  9. Kim O-S, Cho Y-J, Lee K, Yoon S-H, 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]
  10. Sheu S-Y, Huang C-W, Hsu M-Y, Sheu C, Chen W-M. Cellvibrio zantedeschiae sp. nov., isolated from the roots of Zantedeschia aethiopica. Int J Syst Evol Microbiol 2017; 67:3615–3621 [View Article][PubMed]
    [Google Scholar]
  11. Mergaert J, Lednická D, Goris J, Cnockaert MC, De Vos P et al. Taxonomic study of Cellvibrio strains and description of Cellvibrio ostraviensis sp. nov., Cellvibrio fibrivorans sp. nov. and Cellvibrio gandavensis sp. nov. Int J Syst Evol Microbiol 2003; 53:465–471 [View Article][PubMed]
    [Google Scholar]
  12. 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]
  13. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  14. 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]
  15. 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]
  16. Szuróczki S, Khayer B, Spröer C, Toumi M, Szabó A et al. Arundinibacter roseus gen. nov., sp. nov., a new member of the family Cytophagaceae. Int J Syst Evol Microbiol 2019; 69:2076–2081 [View Article][PubMed]
    [Google Scholar]
  17. Rodriguez-R LM, Gunturu S, Harvey WT, Rosselló-Mora R, Tiedje JM et al. The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level. Nucleic Acids Res 2018; 46:W282–W288 [View Article][PubMed]
    [Google Scholar]
  18. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article][PubMed]
    [Google Scholar]
  19. O'Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res 2016; 44:D733–D745 [View Article][PubMed]
    [Google Scholar]
  20. 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]
  21. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article][PubMed]
    [Google Scholar]
  22. Yoon SH, SM H, Lim JM, Kwon SJ. Chun J a large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 10:1281–1286
    [Google Scholar]
  23. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  24. 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]
  25. 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]
  26. Gardner JG. Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus. World J Microbiol Biotechnol 2016; 32:121 [View Article][PubMed]
    [Google Scholar]
  27. Wu Y-R, Lin B, Yu Y. Draft genome sequence of a xylanase-producing bacterial strain, Cellvibrio mixtus J3-8. Genome Announc 2014; 2:e01281–14 [View Article][PubMed]
    [Google Scholar]
  28. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [View Article][PubMed]
    [Google Scholar]
  29. Buck JD. Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993 [View Article][PubMed]
    [Google Scholar]
  30. Barrow GI, Feltham RKA. Cowan and Steel’s Manual for the Identification of Medical Bacteria, 3rd ed. Cambridge: Cambridge University Press; 2004
    [Google Scholar]
  31. Miller LT. A single derivatization method for bacterial fatty acid methyl esters including hydroxy acids. J Clin Microbiol 1982; 16:584–586
    [Google Scholar]
  32. Kuykendall LD, Roy MA, O'Neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988; 38:358–361 [View Article]
    [Google Scholar]
  33. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990a; 13:128–130 [View Article]
    [Google Scholar]
  34. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990b; 66:199–202 [View Article]
    [Google Scholar]
  35. Tindall BJ, Sikorski J, Smibert RM, Kreig NR. Phenotypic characterization and the principles of comparative systematics. Methods for General and Molecular Microbiology, 3rd. 2007 pp 330–393
    [Google Scholar]
  36. Chen W-M, Liu L-P, Sheu S-Y. Cellvibrio fontiphilus sp. nov., isolated from a spring. Int J Syst Evol Microbiol 2017; 67:2532–2537 [View Article][PubMed]
    [Google Scholar]
  37. Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS. Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 2002; 66:506–577 [View Article][PubMed]
    [Google Scholar]
  38. Tóth Á, Barna T, Szabó E, Elek R, Hubert Á et al. Cloning, expression and biochemical characterization of endomannanases from Thermobifida species isolated from different niches. PLoS One 2016; 11:e0155769 [View Article][PubMed]
    [Google Scholar]
  39. Miller GL. Use of dinitrosalicylic acid reagent for determination of reducing sugar. Anal Chem 1959; 31:426–428 [View Article]
    [Google Scholar]
  40. Montella S, Amore A, Faraco V. Metagenomics for the development of new biocatalysts to advance lignocellulose saccharification for bioeconomic development. Crit Rev Biotechnol 2016; 36:998–1009 [View Article][PubMed]
    [Google Scholar]
  41. Ransom-Jones E, McCarthy AJ, Haldenby S, Doonan J, McDonald JE. Lignocellulose-degrading microbial communities in landfill sites represent a repository of unexplored biomass-degrading diversity. mSphere 2017; 2:e00300–00317 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004805
Loading
/content/journal/ijsem/10.1099/ijsem.0.004805
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month 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