gen. nov., sp. nov., a new member of the family isolated from a cave soil Free

Abstract

A novel Gram-stain-positive, actinobacterial strain, designated C5-26, was isolated from soil from a natural cave in Jeju, Republic of Korea, and its taxonomic position was investigated using a polyphasic approach. The organism was aerobic, and cells were non-spore-forming, non-motile cocci that occurred singly, in pairs, in triplets, in tetrads, in short chains or in irregular clusters. Colonies of the cells were circular, convex, entire and white. The peptidoglycan type was A4α with an -Ser-Asp interpeptide bridge. The whole-cell sugars comprised glucose, rhamnose, mannose, arabinose, galactose and ribose. The major menaquinone was MK-8(H). The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unidentified phospholipid. The major fatty acids were iso-C and iso-C h. The size of the draft genome was 5.32 Mbp with depth of coverage of 161×. The G+C content of the genomic DNA was 67.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that the novel isolate belonged to the family and formed a distinct subcluster at the base of the radiation of the genus . Highest sequence similarities of the novel isolate were found to the type strains of (96.2 %), (95.4 %), (95.4 %) and (95.3 %). The whole genome-based phylogeny supported the novelty of the isolate at the genus level in the family . On the basis of data from this polyphasic study, strain C5-26 (=KCTC 39632=DSM 108676) represents a novel species of a new genus in the family , for which the name gen. nov., sp. nov. is proposed.

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2020-04-28
2024-03-29
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References

  1. Stackebrandt E, Schumann P. Description of Bogoriellaceae fam. nov., Dermacoccaceae fam. nov., Rarobacteraceae fam. nov. and Sanguibacteraceae fam. nov. and emendation of some families of the suborder Micrococcineae . Int J Syst Evol Microbiol 2000; 50:1279–1285 [View Article][PubMed][PubMed]
    [Google Scholar]
  2. Stackebrandt E, Koch C, Gvozdiak O, Schumann P. Taxonomic dissection of the genus Micrococcus: Kocuria gen. nov., Nesterenkonia gen. nov., Kytococcus gen. nov., Dermacoccus gen. nov., and Micrococcus Cohn 1872 gen. emend. Int J Syst Bacteriol 1995; 45:682–692 [View Article][PubMed][PubMed]
    [Google Scholar]
  3. 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 [View Article][PubMed][PubMed]
    [Google Scholar]
  4. Lee L-H, Cheah Y-K, Sidik SM, Xie Q-Y, Tang Y-L et al. Barrientosiimonas humi gen. nov., sp. nov., an actinobacterium of the family Dermacoccaceae . Int J Syst Evol Microbiol 2013; 63:241–248 [View Article][PubMed][PubMed]
    [Google Scholar]
  5. Sugimoto S, Kato T, Ito M, Sakata N, Tsuchida T et al. Branchiibius hedensis gen. nov., sp. nov., an actinobacterium isolated from a Japanese codling (Physiculus japonicus). Int J Syst Evol Microbiol 2011; 61:1195–1200 [View Article][PubMed][PubMed]
    [Google Scholar]
  6. Ruckmani A, Kaur I, Schumann P, Klenk H-P, Mayilraj S. Calidifontibacter indicus gen. nov., sp. nov., a member of the family Dermacoccaceae isolated from a hot spring, and emended description of the family Dermacoccaceae . Int J Syst Evol Microbiol 2011; 61:2419–2424 [View Article][PubMed][PubMed]
    [Google Scholar]
  7. Anzai K, Sugiyama T, Sukisaki M, Sakiyama Y, Otoguro M et al. Flexivirga alba gen. nov., sp. nov., an actinobacterial taxon in the family Dermacoccaceae . J Antibiot 2011; 64:613–616 [View Article][PubMed][PubMed]
    [Google Scholar]
  8. Ara I, Yamamura H, Tsetseg B, Daram D, Ando K. Luteipulveratus mongoliensis gen. nov., sp. nov., an actinobacterial taxon in the family Dermacoccaceae . Int J Syst Evol Microbiol 2010; 60:574–579 [View Article][PubMed][PubMed]
    [Google Scholar]
  9. Kim S-J, Jang Y-H, Ahn J-H, Weon H-Y, Schumann P et al. Rudaeicoccus suwonensis gen. nov., sp. nov., an actinobacterium isolated from the epidermal tissue of a root of a Phalaenopsis orchid. Int J Syst Evol Microbiol 2013; 63:1291–1296 [View Article][PubMed][PubMed]
    [Google Scholar]
  10. Tang S-K, Wu J-Y, Wang Y, Schumann P, Li W-J. Yimella lutea gen. nov., sp. nov., a novel actinobacterium of the family Dermacoccaceae . Int J Syst Evol Microbiol 2010; 60:659–663 [View Article][PubMed][PubMed]
    [Google Scholar]
  11. Ai M-J, Sun Y, Sun H-M, Liu H-Y, Yu L-Y et al. Allobranchiibius huperziae gen. nov., sp. nov., a member of Dermacoccaceae isolated from the root of a medicinal plant Huperzia serrata (Thunb.). Int J Syst Evol Microbiol 2017; 67:4210–4215 [View Article][PubMed][PubMed]
    [Google Scholar]
  12. Lee SD. Tamlicoccus marinus gen. nov., sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2013; 63:1951–1954 [View Article][PubMed][PubMed]
    [Google Scholar]
  13. Parag B, Sasikala C, Ramana CV. Barrientosiimonas endolithica sp. nov., isolated from pebbles, reclassification of the only species of the genus Tamlicoccus, Tamlicoccus marinus Lee 2013, as Barrientosiimonas marina comb. nov. and emended description of the genus Barrientosiimonas . Int J Syst Evol Microbiol 2015; 65:3031–3036 [View Article][PubMed][PubMed]
    [Google Scholar]
  14. Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T et al. Genome-based taxonomic classification of the phylum Actinobacteria . Front Microbiol 2018; 9:9 [View Article][PubMed][PubMed]
    [Google Scholar]
  15. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  16. 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]
  17. 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][PubMed]
    [Google Scholar]
  18. PHYLIP FJ. (phylogeny inference package) version 3.6a. Distributed by the author Seattle, USA: Department of Genome Sciences, University of Washington; 2002
    [Google Scholar]
  19. Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HN. editor Mammalian Protein Metabolism New York: Academic Press; 1969 pp 21–132
    [Google Scholar]
  20. 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][PubMed]
    [Google Scholar]
  21. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed][PubMed]
    [Google Scholar]
  22. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
    [Google Scholar]
  23. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed][PubMed]
    [Google Scholar]
  24. 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]
  25. 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][PubMed]
    [Google Scholar]
  26. 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][PubMed]
    [Google Scholar]
  27. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article][PubMed][PubMed]
    [Google Scholar]
  28. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972; 106:645–668 [View Article]
    [Google Scholar]
  29. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article][PubMed][PubMed]
    [Google Scholar]
  30. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:12196–19131 [View Article][PubMed][PubMed]
    [Google Scholar]
  31. Kang JW, Yang HG, Choi S, Kim YJ, Lee SD. Seongchinamella unica gen. nov.,sp. nov., isolated from a tidal mudflat of beach, and transfer of Halioglobus sediminis to Seongchinamella sediminis comb. nov. and Halioglobus lutimaris to Pseudohalioglobus gen. nov. as Pseudohalioglobus lutimaris comb. nov. Int J Syst Evol Microbiol 2010 in press
    [Google Scholar]
  32. Schumann P. Peptidoglycan structure. Methods Microbiol 2011; 38:101–129
    [Google Scholar]
  33. Saddler GS, Tavecchia P, Lociuro S, Zanol M, Colombo L et al. Analysis of madurose and other actinomycete whole cell sugars by gas chromatography. J Microbiol Methods 1991; 14:185–191 [View Article]
    [Google Scholar]
  34. Collins MD. Anaysis of isoprenoid quinones. Methods Microbiol 1985; 18:329–366
    [Google Scholar]
  35. Kroppenstedt RM. Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp 173–199
    [Google Scholar]
  36. 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]
  37. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977; 27:104–117 [View Article]
    [Google Scholar]
  38. Minnikin DE, Hutchinson IG, Caldicott AB, Goodfellow M. Thin-layer chromatography of methanolysates of mycolic acid-containing bacteria. J Chromatogr A 1980; 188:221–233 [View Article]
    [Google Scholar]
  39. Lee SD, Schumann P. Specibacter cremeus gen. nov., sp. nov., a new member of the family Micrococcaceae isolated from a natural cave. Int J Syst Evol Microbiol 2019; 69:1767–1774 [View Article][PubMed][PubMed]
    [Google Scholar]
  40. Juboi H, Basik AA, Shamsul SSG, Arnold P, Schmitt EK et al. Luteipulveratus halotolerans sp. nov., an actinobacterium (Dermacoccaceae) from forest soil. Int J Syst Evol Microbiol 2015; 65:4113–4120 [View Article][PubMed][PubMed]
    [Google Scholar]
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