1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 6

sp. nov., isolated from a tidal mudflat No Access

Abstract

A Gram-reaction-negative, aerobic, motile, rod-shaped bacterium, designated GH3-8, was isolated from rhizosphere mudflats of halophytes on the seashore of Gangwha Island, Republic of Korea. Growth was observed at pH 4–10 (optimum, pH 7–8), at 4–40 °C (optimum, 37 °C) and in the presence of 0.5–20 % (w/v) NaCl (optimum, 4 %). The predominant respiratory quinone was Q-9. The major fatty acids were C ω7, C, summed feature 3 (C ω7 and/or C ω6) and C 3OH. The polar lipids contained phosphatidylethanolamine, phosphatidylglycerol, an unidentified phosphoglycolipid, an unidentified phosphoglycoaminolipid, an unidentified glycoaminolipid, two unidentified phospholipids and two unidentified lipids. Phylogenetic analysis based on 16S rRNA gene sequences exhibited that the isolate belonged to the family , with the most closely related species, (98.1 % sequence similarity) and (97.9 %). Sequence similarity values between the isolate and other representatives of the family were all below 95.3 %. The values of average nucleotide identity between strain GH3-8 and members of the genus were 73.42 % with CCM 8464 and 72.38 % with DSM 22428. Strain GH3-8 showed digital DNA–DNA hybridization values of 18.5–18.6 % with members of the genus . Based on phenotypic and chemotaxonomic distinctiveness together with low overall genomic relatedness indices and phylogenetic data, the isolate is considered to represent a new species of the genus , for which the name sp. nov. is proposed, with the type strain GH3-8 (=KCTC 62127=NBRC 113214).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Carex scabrifolia , Halomonadaceae , halophytes: Suaeda japonica and Larsenimonas rhizosphaerae
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005930
2023-06-20
2024-05-03
Loading full text...

Full text loading...

References

  1. León MJ, Sánchez-Porro C, de la Haba RR, Llamas I, Ventosa A. Corrigendum to “Larsenia salina gen. nov., sp. nov., a new member of the family Halomonadaceae based on multilocus sequence analysis” [Syst. Appl. Microbiol. 37 (October (7)) (2014) 480–487]. Syst Appl Microbiol 2015; 38:77 [View Article]
     [Google Scholar]
  2. León MJ, Sánchez-Porro C, de la Haba RR, Llamas I, Ventosa A. Larsenia salina gen. nov., sp. nov., a new member of the family Halomonadaceae based on multilocus sequence analysis. Syst Appl Microbiol 2014; 37:480–487 [View Article] [PubMed]
     [Google Scholar]
  3. Xia Z-J, Wu H-Z, Cui C-X, Chen Q, Zhao G-Y et al. Larsenimonas suaedae sp. nov., a moderately halophilic, endophytic bacterium isolated from the halophyte Suaeda salsa. Int J Syst Evol Microbiol 2016; 66:2952–2958 [View Article] [PubMed]
     [Google Scholar]
  4. Lane DJ. 16S/23S rRNA Sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematics London: John Wiley and Sons; 1991 pp 115–144
     [Google Scholar]
  5. 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; 25:4876–4882 [View Article] [PubMed]
     [Google Scholar]
  6. Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HN. eds Mammalian Protein Metabolism New York: Academic Press; 1969 pp 21–132
     [Google Scholar]
  7. 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]
  8. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [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. System Zool 1971; 20:406 [View Article]
     [Google Scholar]
  11. de la Haba RR, Márquez MC, Papke RT, Ventosa A. Multilocus sequence analysis of the family Halomonadaceae. Int J Syst Evol Microbiol 2012; 62:520–538 [View Article] [PubMed]
     [Google Scholar]
  12. Oren A, Ventosa A. Subcommittee on the taxonomy of Halobacteriaceae and Subcommittee on the taxonomy 344 of Halomonadaceae (Minute 12). Int J Syst Evol Microbiol 2013; 63:3540–3544 [View Article]
     [Google Scholar]
  13. Gao P, Lu H, Xing P, Wu QL. Halomonas rituensis sp. nov. and Halomonas zhuhanensis sp. nov., isolated from natural salt marsh sediment on the Tibetan Plateau. Int J Syst Evol Microbiol 2020; 70:5217–5225 [View Article] [PubMed]
     [Google Scholar]
  14. 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] [PubMed]
     [Google Scholar]
  15. Hyatt D, Chen G-L, 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]
  16. Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol 2011; 7:e1002195 [View Article] [PubMed]
     [Google Scholar]
  17. 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]
  18. 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]
  19. 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]
  20. 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]
     [Google Scholar]
  21. 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]
  22. 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] [PubMed]
     [Google Scholar]
  23. 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]
  24. MacFaddin JF. Biochemical Tests for Identification of Medical Bacteria. 2nd edn Baltimore: Williams & Wilkins; 1980
     [Google Scholar]
  25. Arahal DR, Vreeland RH, Litchfield CD, Mormile MR, Tindall BJ et al. Recommended minimal standards for describing new taxa of the family Halomonadaceae. Int J Syst Evol Microbiol 2007; 57:2436–2446 [View Article] [PubMed]
     [Google Scholar]
  26. Collins MD. Anaysis of isoprenoid quinones. Methods Microbiol 1985; 18:329–366
     [Google Scholar]
  27. Kroppenstedt RM. Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Goodfellow M, Minnikin DE. eds Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp 173–199
     [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 [View Article]
     [Google Scholar]
  29. 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]
  30. 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.0.005930
Loading
Larsenimonas rhizosphaerae sp. nov., isolated from a tidal mudflat
Int J Syst Evol Microbiol 73, 005930 (2023); https://doi.org/10.1099/ijsem.0.005930
/content/journal/ijsem/10.1099/ijsem.0.005930
/content/journal/ijsem/10.1099/ijsem.0.005930
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