1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 3

sp. nov., isolated from pond sediment No Access

Abstract

A Gram-stain-negative, strictly aerobic, oxidase-positive, catalase-negative, motile by gliding, creamy white-pigmented bacterium, designated strain S2-8, isolated from a sediment sample from a Wiyang pond in the Republic of Korea, was subjected to polyphasic taxonomic analysis. Growth was observed at 10–40 °C (optimum: 30 °C), pH 7–8 and 0–0.5% NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain S2-8 belonged to the family in the phylum Bacteroidota and was closely related to HR-AV, DSM 3403 and R2A36-4 with 97.2, 96.7 and 93.7 % 16S rRNA gene sequence similarities, respectively. Average nucleotide identity and digital DNA–DNA hybridization values for these type strains were 72.0–75.2% and 21.2–21.9 %, respectively. The major respiratory quinone is menaquinone-7. The major fatty acids were iso-C, iso-C 3-OH and summed feature 3 (comprising C 7 and/or C 6). The major polar lipids were phosphatidylethanolamine, two unidentified amino acids and four unidentified lipids. The G+C content of genomic DNA was 37.9 mol%. Based on polyphasic taxonomic analysis, it was observed that strain S2-8 is a novel species belonging to the genus , for which the name sp. nov. is proposed. The type strain is S2-8 (= KACC 22266= JCM 34533).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): new taxa , pond sediment , Solitalea lacus and taxonomy
Funding
This study was supported by the:
  • Nakdonggang National Institute of Biological Resources (Award NNIBR202201104)
    • Principle Award Recipient: NotApplicable
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005743
2023-03-20
2024-04-28
Loading full text...

Full text loading...

References

  1. Weon H-Y, Kim B-Y, Lee C-M, Hong S-B, Jeon Y-A et al. Solitalea koreensis gen. nov., sp. nov. and the reclassification of [Flexibacter] canadensis as Solitalea canadensis comb. nov. Int J Syst Evol Microbiol 2009; 59:1969–1975 [View Article]
     [Google Scholar]
  2. Christensen P. Flexibacter canadensis sp. nov. Int J Syst Bacteriol 1980; 30:429–432 [View Article]
     [Google Scholar]
  3. Lee Y, Jeon CO. Solitalea longa sp. nov., isolated from freshwater and emended description of the genus Solitalea. Int J Syst Evol Microbiol 2018; 68:2826–2831 [View Article] [PubMed]
     [Google Scholar]
  4. Jones AM, Knowles R. Denitrification in Flexibacter canadensis. Can J Microbiol 1990; 36:430–434
     [Google Scholar]
  5. Jung JY, Kang HK, Jin HM, Han S-S, Kwon YC et al. Companilactobacillus pabuli sp. nov., a lactic acid bacterium isolated from animal feed. Int J Syst Evol Microbiol 2019; 71: [View Article] [PubMed]
     [Google Scholar]
  6. 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]
  7. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article] [PubMed]
     [Google Scholar]
  8. 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]
  9. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  10. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree Topology. Syst Zool 1971; 20:406 [View Article]
     [Google Scholar]
  11. 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]
     [Google Scholar]
  12. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
     [Google Scholar]
  13. 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]
  14. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007; 73:5261–5267 [View Article] [PubMed]
     [Google Scholar]
  15. Jung JY, Han K-I, Jin HM, Nam YH, Kang HK et al. Complete genome sequence of Lacticaseibacillus paracasei strain NSMJ15. Microbiol Resour Announc 2021; 10:e0103021 [View Article]
     [Google Scholar]
  16. Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013; 10:563–569 [View Article] [PubMed]
     [Google Scholar]
  17. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014; 9:e112963 [View Article]
     [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. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 2007; 35:W182–5 [View Article]
     [Google Scholar]
  20. Arndt D, Grant JR, Marcu A, Sajed T, Pon A et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 2016; 44:W16–21 [View Article] [PubMed]
     [Google Scholar]
  21. Biswas A, Staals RHJ, Morales SE, Fineran PC, Brown CM. CRISPRDetect: a flexible algorithm to define CRISPR arrays. BMC Genomics 2016; 17:356 [View Article]
     [Google Scholar]
  22. Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res 2020; 48:D517–D525 [View Article]
     [Google Scholar]
  23. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35 [View Article] [PubMed]
     [Google Scholar]
  24. Xu L, Dong Z, Fang L, Luo Y, Wei Z et al. OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res 2019; 47:W52–W58 [View Article]
     [Google Scholar]
  25. Alanjary M, Steinke K, Ziemert N. AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Res 2019; 47:W276–W282 [View Article]
     [Google Scholar]
  26. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article]
     [Google Scholar]
  27. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article]
     [Google Scholar]
  28. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article]
     [Google Scholar]
  29. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR 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]
  30. 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]
  31. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article]
     [Google Scholar]
  32. Bernardet J-F, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [View Article]
     [Google Scholar]
  33. Lányí B. Classical and rapid identification methods for medically important bacteria. Methods Microbiol 1988; 19:1–67
     [Google Scholar]
  34. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P. eds Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  35. Komagata K, Suzuki K. Lipids and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
     [Google Scholar]
  36. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids, Technical note #101 Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  37. 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]
  38. Embley TM, Wait R. Structural lipids of eubacteria. In Goodfellow M, O’Donnell AG. eds Modern Microbial Methods. Chemical Methods in Prokaryotic Systematics Chichester: John Wiley & Sons; 1994 pp 121–161
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005743
Loading
Solitalea lacus sp. nov., isolated from pond sediment
Int J Syst Evol Microbiol 73, 005743 (2023); https://doi.org/10.1099/ijsem.0.005743
/content/journal/ijsem/10.1099/ijsem.0.005743
/content/journal/ijsem/10.1099/ijsem.0.005743
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