1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 3

sp. nov. and sp. nov., isolated from tidal flats in the Yellow Sea in Korea No Access

Abstract

Two bacterial strains (designated as YSTF-M11 and TSTF-M6) were isolated from tidal flat sediments of the Yellow Sea, Republic of Korea, and taxonomically characterized. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain YSTF-M11 clusters with the type strains of species and strain TSTF-M6 clusters with the type strains of , and . Strains YSTF-M11 and TSTF-M6 exhibited 16S rRNA gene sequence similarity values of 97.5–98.9 % and 94.1–97.2 % to the type strains of four species and to the type strains of four species, respectively. An UBCG tree based on genomic sequences and a tree based on AAI showed that strains YSTF-M11 and TSTF-M6 form a cluster with the type strains of species and with the type strains of , and , respectively. The ANI and dDDH values between genomic sequences of strain YSTF-M11 and the type strains of four species and between those of strain TSTF-M6 and the type strains of the three species were in ranges of 74.0–75.9 and 18.2–19.7 % and 74.7–75.5 and 18.8–19.3 %, respectively. The DNA G+C contents of strains YSTF-M11 and TSTF-M6 were 60.3 and 61.9 % based on their genomic sequences. Both strains contained Q-10 as the predominant ubiquinone and C 7 as the major fatty acid. Strains YSTF-M11 and TSTF-M6 were separated from recognized species and , and , respectively, by their phenotypic properties together with the phylogenetic and genetic distinctiveness. Based on data presented in this study, strains YSTF-M11 (=KACC 21642 =NBRC 115155) and TSTF-M6 (=KACC 21643 =NBRC 115154) are considered to represent novel species of the genera and , respectively, for which the names sp. nov. and sp. nov. are proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Loktanella gaetbulisp. nov , Novel species , Polyphasic taxonomy and Roseobacter insulaesp. nov
Funding
This study was supported by the:
  • Rural Development Administration (Award PJ015247)
    • Principle Award Recipient: Jung-HoonYoon
  • National Institute of Biological Resources (Award project on survey of indigenous species of Korea)
    • Principle Award Recipient: Jung-HoonYoon
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005794
2023-03-31
2024-05-09
Loading full text...

Full text loading...

References

  1. Oren A, Garrity GM. Valid publication of the names of forty-two phyla of prokaryotes. Int J Syst Evol Microbiol 2021; 71:5056 [View Article]
     [Google Scholar]
  2. Shiba T. Roseobacter litoralis gen. nov., sp. nov., and Roseobacter denitrificans sp. nov., aerobic pink-pigmented bacteria which contain bacteriochlorophyll a. Syst Appl Microbiol 1991; 14:140–145 [View Article]
     [Google Scholar]
  3. Van Trappen S, Mergaert J, Swings J. Loktanella salsilacus gen. nov., sp. nov., Loktanella fryxellensis sp. nov. and Loktanella vestfoldensis sp. nov., new members of the Rhodobacter group, isolated from microbial mats in Antarctic lakes. Int J Syst Evol Microbiol 2004; 54:1263–1269 [View Article]
     [Google Scholar]
  4. Liang KYH, Orata FD, Boucher YF, Case RJ. Roseobacters in a sea of poly- and paraphyly: whole genome-based taxonomy of the family Rhodobacteraceae and the proposal for the split of the “Roseobacter Clade” into a novel family, Roseobacteraceae fam. nov. Front Microbiol 2021; 12:683109 [View Article]
     [Google Scholar]
  5. Wirth JS, Whitman WB. Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera. Int J Syst Evol Microbiol 2018; 68:2393–2411 [View Article] [PubMed]
     [Google Scholar]
  6. Oren A, Garrity GM. Notification list. Notification that new names and new combinations have appeared in volume 68, part 7 of the IJSEM. Int J Syst Evol Microbiol 2018; 68:3077–3079
     [Google Scholar]
  7. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article] [PubMed]
     [Google Scholar]
  8. Ivanova EP, Zhukova NV, Lysenko AM, Gorshkova NM, Sergeev AF et al. Loktanella agnita sp. nov. and Loktanella rosea sp. nov., from the north-west Pacific Ocean. Int J Syst Evol Microbiol 2005; 55:2203–2207 [View Article]
     [Google Scholar]
  9. Hosoya S, Yokota A. Loktanella atrilutea sp. nov., isolated from seawater in Japan. Int J Syst Evol Microbiol 2007; 57:1966–1969 [View Article] [PubMed]
     [Google Scholar]
  10. Jung YT, Park S, Lee JS, Yoon JH. Roseobacter ponti sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2017; 67:2189–2194 [View Article]
     [Google Scholar]
  11. Muramatsu S, Kanamuro M, Sato-Takabe Y, Hirose S, Muramatsu Y et al. Roseobacter cerasinus sp. nov., isolated from a fish farm. Int J Syst Evol Microbiol 2020; 70:4920–4926 [View Article]
     [Google Scholar]
  12. Yoon J-H, Lee ST, Kim S-B, Kim WY, Goodfellow M et al. Restriction fragment length polymorphism analysis of PCR-amplified 16S ribosomal DNA for rapid identification of Saccharomonospora strains. Int J Syst Bacteriol 1997; 47:111–114 [View Article]
     [Google Scholar]
  13. Yoon JH, Kim H, Kim IG, Kang KH, Park YH. Erythrobacter flavus sp. nov., a slight halophile from the East Sea in Korea. Int J Syst Evol Microbiol 2003; 53:1169–1174 [View Article]
     [Google Scholar]
  14. Lee I, Chalita M, Ha S-M, Na S-I, Yoon S-H et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [View Article]
     [Google Scholar]
  15. 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]
     [Google Scholar]
  16. 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]
     [Google Scholar]
  17. Yoon SH, Ha SM, 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]
     [Google Scholar]
  18. 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]
     [Google Scholar]
  19. 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]
     [Google Scholar]
  20. Kim D, Park S, Chun J. Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity. J Microbiol 2021; 59:476–480 [View Article]
     [Google Scholar]
  21. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci 2005; 102:2567–2572 [View Article]
     [Google Scholar]
  22. 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]
  23. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009; 106:19126–19131 [View Article]
     [Google Scholar]
  24. Komagata K, Suzuki K. Lipids and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
     [Google Scholar]
  25. Park S, Won SM, Kim H, Park DS, Yoon JH. Aestuariivita boseongensis gen. nov., sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2014; 64:2969–2974 [View Article]
     [Google Scholar]
  26. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note vol 101 Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  27. 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]
  28. Embley TM, Wait R. Structural lipids of eubacteria. In Goodfellow M, O’Donnel AG. eds Modern Microbial Methods. Chemical Methods in Prokaryotic Systematics Chichester: John Wiley & Sons; 1994 pp 121–161
     [Google Scholar]
  29. Moon YG, Seo SH, Lee SD, Heo MS. Loktanella pyoseonensis sp. nov., isolated from beach sand, and emended description of the genus Loktanella. Int J Syst Evol Microbiol 2010; 60:785–789 [View Article] [PubMed]
     [Google Scholar]
  30. Yoon J-H, Jung Y-T, Lee J-S. Loktanella litorea sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2013; 63:175–180 [View Article] [PubMed]
     [Google Scholar]
  31. Lányí B. Classical and rapid identification methods for medically important bacteria. Methods Mocrobiol 1987; 19:1–67
     [Google Scholar]
  32. Barrow GI, Feltham RKA. Cowan and Steel’s Manual for the Identification of Medical Bacteria, 3rd. edn Cambridge: Cambridge University Press; 1993 [View Article]
     [Google Scholar]
  33. Bruns A, Rohde M, Berthe-Corti L. Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North Sea intertidal sediment. Int J Syst Evol Microbiol 2001; 51:1997–2006 [View Article]
     [Google Scholar]
  34. Baumann P, Baumann L. The marine Gram-negative eubacteria: genera Photobacterium, Beneckea, Alteromonas, Pseudomonas, and Alcaligenes. In Starr MP, Stolp H, Trüper HG, Balows A, Schlegel HG. eds The Prokaryotes Berlin: Springer; 1981 pp 1302–1331
     [Google Scholar]
  35. Cohen-Bazire G, Sistrom WR, Stanier RY. Kinetic studies of pigment synthesis by non-sulfur purple bacteria. J Cell Comp Physiol 1957; 49:25–68 [View Article]
     [Google Scholar]
  36. Staley JT. Prosthecomicrobium and Ancalomicrobium: new prosthecate freshwater bacteria. J Bacteriol 1968; 95:1921–1942 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005794
Loading
Roseobacter insulae sp. nov. and Loktanella gaetbuli sp. nov., isolated from tidal flats in the Yellow Sea in Korea
Int J Syst Evol Microbiol 73, 005794 (2023); https://doi.org/10.1099/ijsem.0.005794
/content/journal/ijsem/10.1099/ijsem.0.005794
/content/journal/ijsem/10.1099/ijsem.0.005794
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