1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 7

sp. nov. and sp. nov., and emended description of the genus No Access

Abstract

Taxonomic positions of six isolates, which were recovered from two different environments in Jeju, Republic of Korea, were examined by a polyphasic analysis. Cells of the isolates were Gram-reaction-negative, facultatively anaerobic, motile and rod-shaped and showed growth at 4–30 °C, pH 4.0–9.0 and with 0–6 (w/v) NaCl. In phylogenomic analysis based on 92 single-copy core genes, it was shown that the isolates belonged to the genus and formed three distinct sublines within the genus. The isolates shared 16S rRNA gene sequence similarities of 97.9–100 % with one another. The isolates contained ubiquinone-8 was as the major isoprenoid quinone. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. The predominant fatty acids were C and C cyclo. The G+C content of their genomic DNA was 52.8–53.1 %. Average nucleotide identity and digital DNA–DNA hybridization values supported that strains SAP-17 and Lac-M11 represented two new species of the genus , whereas strain SAP-10 was a strain of . Based on the results obtained here, sp. nov. (type strain SAP-17=KCTC 72960=NBRC 114723=CCM 9079) and sp. nov. (type strain Lac-M11=KACC 21743=NBRC 114406) are proposed. Also, an emended description of the genus is given on the basis of our physiological and chemotaxonomic results.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Acer pictum , core gene , new species , Rahnella , raw rice wine and tree sap
© 2021 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004893
2021-07-02
2024-04-24
Loading full text...

Full text loading...

References

  1. Izard D, Gavini F, Trinel PA, Lecterc H. Rahnella aquatilis, nouveau member de la family des Enterobacteriaceae. Ann Microbiol (Paris 1979; 130:163–177
     [Google Scholar]
  2. Kämpfer P. Genus Rahnella. Brenner D, Krieg N, Staley J. eds In Bergey’s Manual of Systematic Bacteriology, the Proteobacteria Part B, the Gammaproteobacteria, 2nd. edn Vol 2 New York: Springer; 2005 pp 759–763
     [Google Scholar]
  3. Brady C, Hunter G, Kirk S, Arnold D. Denman, S. Rahnella victoriana sp. nov., Rahnella bruchi sp. nov., Rahnella woolbedingensis sp. nov., classification of Rahnella genomospecies 2 and 3 as Rahnella variigena sp. nov. and Rahnella inusitata sp. nov., respectively and emended description of the genus Rahnella. Syst Appl Microbiool 2014; 37:545–552
     [Google Scholar]
  4. Brenner DJ, Muller HE, Streigerwalt AG, Whitney AM, O’Hara CM et al. Two new Rahnella genomospecies that cannot be phenotypically differentiated from Rahnella aquatilis. Int J Syst Evol Microbiol 1998; 48:1551–1558
     [Google Scholar]
  5. Lee SD, Jeon D, Kim IS, Choe H, Kim JS. Rahnella aceris sp. nov., isolated from sap drawn from Acer pictum. Arch Microbiol 2020; 202:2411–2417 [View Article] [PubMed]
     [Google Scholar]
  6. Oren A, Garrity GM. List of new names and new combinations that have appeared in effective publications outside of the IJSEM and are submitted for valid publication. Int J Syst Evol Microbiol 2021; 71:004600
     [Google Scholar]
  7. Adeolu M, Alnajar S, Naushed S, Gupta RS. Genome-based phylogeny and taxonomy of the “Enterobacteriales”: proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Int J Syst Evol Microbiol 2016; 66:5575–5599
     [Google Scholar]
  8. Hopwood DA, Bibb MJ, Chater KF, Kieser T, Bruton CJ et al. Genetic Manipulation of Streptomyces. A Laboratory Manual Norwich: John Innes Foundation; 1985
     [Google Scholar]
  9. SI N, Kim YO, Yoon SH, SM H, Baek I et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285
     [Google Scholar]
  10. Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article] [PubMed]
     [Google Scholar]
  11. Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol 2011; 7:e1002195 [View Article] [PubMed]
     [Google Scholar]
  12. Katoh K, Standley DM. MAFFT Multiple sequence alignment software version 7: Improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article] [PubMed]
     [Google Scholar]
  13. Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One 2010; 5:e9490 [View Article] [PubMed]
     [Google Scholar]
  14. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article] [PubMed]
     [Google Scholar]
  15. 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; 110:1281–1286
     [Google Scholar]
  16. 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]
  17. Wang J, Zheng ML, Jiao JY, Wang WJ, Li S et al. Serratia microhaemolytica sp. nov., isolated from an artificial lake in Southern China. Antonie van Leeuwenhoek 2019; 112:1447–1456 [View Article] [PubMed]
     [Google Scholar]
  18. Zhang CW, Zhang J, Zhao JJ, Zhao X, Zhao DF et al. Serratia oryzae sp. nov., isolated from rice stems. Int J Syst Evol Microbiol 2017; 67:2928–2933 [View Article] [PubMed]
     [Google Scholar]
  19. Rochter M, Roselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:12196–19131
     [Google Scholar]
  20. 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]
  21. 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]
  22. Fitch WM. Towards defining the course of evolution: minimum change for a specific tree topology. System Zool 1971; 20:406–416
     [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. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 24:4876–4882
     [Google Scholar]
  25. Jukes TH, Cantor CR. Evolution of protein molecules. Munro H. eds In Mammalian Protein Metabolism New York: Academic Press; 1969 pp 21–132
     [Google Scholar]
  26. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  27. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  28. 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
     [Google Scholar]
  29. Kroppenstedt RM. Fatty acid and menaquinone analysis of actinomycetes and related organisms. Goodfellow M, Minnikin D. eds In Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp 173–199
     [Google Scholar]
  30. Minnikin DE, Patal PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977; 27:104–107
     [Google Scholar]
  31. 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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004893
Loading
Rahnella laticis sp. nov. and Rahnella contaminans sp. nov., and emended description of the genus Rahnella
Int J Syst Evol Microbiol 71, 004893 (2021); https://doi.org/10.1099/ijsem.0.004893
/content/journal/ijsem/10.1099/ijsem.0.004893
/content/journal/ijsem/10.1099/ijsem.0.004893
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited 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