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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 8

sp. nov., a CO-utilizing bacterium isolated from tidal flat sediment, and emended description of the genus No Access

Abstract

A novel anaerobic, rod-shaped, non-motile bacterium, designated strain ES005, was isolated from tidal flat sediments near the rhizosphere of at Eulsukdo Island, Republic of Korea. A polyphasic approach revealed that cells of the strain were Gram-stain-positive, catalase- and oxidase-negative, non-spore-forming rods. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain ES005 belonged to the family , class and showed the highest sequence similarity to s (97.52 %) and followed by Z-79820 (96.72%). The OrthoANI value between strain ES005 and was 69.67 %. Strain ES005 grew optimally at 33–37 °C, at pH 6.0–7.0 and in the presence of 1–2 % (w/v) NaCl. Growth in 12.5 % CO atmosphere was observed. Acetate and formate were end products of fructose fermentation and growth on CO. The major cellular fatty acids of strain ES005 were C (39.1 %) and C (26.6 %). The major polar lipids were diphoshatidylgycerol, phosphatidylglycerol and three unidentified phospholipids. The DNA G+C content of strain ES005 was 46.9 mol%. Based on the phenotypic, phylogenetic, genomic and chemotaxonomic features of the isloate, strain ES005 represents a novel species, for which the name sp. nov. is proposed. The type strain is ES005 (=KCTC 25246=JCM 34530)

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Keyword(s): Alkalibacter rhizosphaerae sp. nov. , CO-utilizing and Eubacteriaceae
© 2022 The Authors
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2022-08-24
2024-05-19
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References

  1. Buchanan RE. Studies on the nomenclature and classification of the Bacteria: III. The Families of the Eubacteriales. J Bacteriol 1917; 2:347–350 [View Article]
     [Google Scholar]
  2. Ludwig W, Schleifer K-H, Whitman WB. Revised road map to the phylum Firmicutes. In Bergey’s Manual of Systematic Bacteriology Springer; 2009 pp 1–13
     [Google Scholar]
  3. 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]
  4. Garnova ES, Zhilina TN, Tourova TP, Kostrikina NA, Zavarzin GA. Anaerobic, alkaliphilic, saccharolytic bacterium Alkalibacter saccharofermentans gen. nov., sp. nov. from a soda lake in the Transbaikal region of Russia. Extremophiles 2004; 8:309–316 [View Article]
     [Google Scholar]
  5. Khomyakova M, Merkel A, Novikov A, Klyukina A, Slobodkin A. Alkalibacter mobilis sp. nov., an anaerobic bacterium isolated from a coastal lake. Int J Syst Evol Microbiol 2021; 71:005174 [View Article] [PubMed]
     [Google Scholar]
  6. Namirimu T, Park M-J, Yang S-H, Zo Y-G, Kwon KK. Parashewanella tropica sp. nov., a mesophilic bacterium isolated from a marine sponge from Chuuk lagoon, Federated States of Micronesia, and emended description of the genus Parashewanella. Int J Syst Evol Microbiol 2019; 69:3256–3261 [View Article] [PubMed]
     [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. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
     [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. 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] [PubMed]
     [Google Scholar]
  11. 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]
  12. Kimura M. The neutral theory and molecular evolution. In My Thoughts on Biological Evolution Singapore: Springer; 2020 pp 119–138
     [Google Scholar]
  13. Lee MD. GToTree: a user-friendly workflow for phylogenomics. Bioinformatics 2019; 35:4162–4164 [View Article] [PubMed]
     [Google Scholar]
  14. 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; 11:1–11 [View Article] [PubMed]
     [Google Scholar]
  15. 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]
  16. Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A et al. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res 2014; 42:D231–9 [View Article] [PubMed]
     [Google Scholar]
  17. 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] [PubMed]
     [Google Scholar]
  18. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  19. Tindall BJ, Rosselló-Móra R, Busse H-J, Ludwig W, Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60:249–266 [View Article] [PubMed]
     [Google Scholar]
  20. Skerman VB. A guide to the identification of the genera of bacteria. Acad Med 1960; 35:92
     [Google Scholar]
  21. Kim W, Lee JH, Kwon KK. Abyssisolibacter fermentans gen. nov. sp. nov., isolated from deep sub-seafloor sediment. J Microbiol 2016; 54:347–352 [View Article]
     [Google Scholar]
  22. Lee J, Lee JW, Chae CG, Kwon SJ, Kim YJ et al. Domestication of the novel alcohologenic acetogen Clostridium sp. AWRP: from isolation to characterization for syngas fermentation. Biotechnol Biofuels 2019; 12:1–14 [View Article] [PubMed]
     [Google Scholar]
  23. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101 Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  24. 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]
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Alkalibacter rhizosphaerae sp. nov., a CO-utilizing bacterium isolated from tidal flat sediment, and emended description of the genus Alkalibacter
Int J Syst Evol Microbiol 72, 005495 (2022); https://doi.org/10.1099/ijsem.0.005495
/content/journal/ijsem/10.1099/ijsem.0.005495
/content/journal/ijsem/10.1099/ijsem.0.005495
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