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Volume 72, Issue 8

sp. nov., isolated from intertidal sediment No Access

Abstract

A Gram-stain-negative, obligately aerobic bacterium, designated as HS1C4-1, was isolated from a sediment sample from the tidal zone of the Haicang Coast, Xiamen, Fujian Province, PR China. The strain was yellowish-coloured, non-gliding, rod-shaped and motile, with a single polar flagellum. Cells of HS1C4-1 were oxidase- and catalase-positive. The strain could grow at 15–55 °C (optimum 37 °C), pH 6.0–10.0 (optimum, pH 7.0–9.0), in the presence of 0–12 % (optimum, 1 %) NaCl (w/v). Phylogenetic analysis based on the 16S rRNA gene sequences indicated that HS1C4-1 represented a member of the genus , and shared the highest similarity to CGMCC 1.10267 (97.6 %). Digital DNA–DNA hybridization values and average nucleotide identity between HS1C4-1 and all the species of genus were 18.7–20.2 % and 77.3–78.4 %, respectively. The principal fatty acids (>10 %) were C cyclo ω8 (50.5 %) and summed feature 8 (Cω7 and/or Cω6; 29.1%). Q-10 was the sole respiratory quinone. The polar lipids included diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids and six unidentified lipids. The G+C content of the chromosomal DNA was 62.9 %. On the basis of phylogenetic, phenotypic, chemotaxonomic and genomic characteristics, HS1C4-1 represents a novel species within the genus , for which the name sp. nov. is proposed. The type strain is HS1C4-1 (=MCCC 1A18759=KCTC 92097).

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  • Accepted:
  • Published Online:
Keyword(s): Pelagibacterium xiamenense , sediment , taxonomy and Xiamen
© 2022 The Authors
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2022-08-04
2024-12-13
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References

  1. Xu X-W, Huo Y-Y, Wang C-S, Oren A, Cui H-L et al. Pelagibacterium halotolerans gen. nov., sp. nov. and Pelagibacterium luteolum sp. nov., novel members of the family Hyphomicrobiaceae. Int J Syst Evol Microbiol 2011; 61:1817–1822 [View Article]
     [Google Scholar]
  2. Li Q, Xu Y, Liu K, Cai L, Fu Y et al. Pelagibacterium nitratireducens sp.nov., a marine Alphaproteobacterium isolated from the East China Sea. Curr Microbiol 2013; 66:450–455 [View Article] [PubMed]
     [Google Scholar]
  3. Yang N, Sun C. Pelagibacterium lixinzhangensis sp. nov., a novel member of the genus Pelagibacterium. Curr Microbiol 2016; 72:551–556 [View Article] [PubMed]
     [Google Scholar]
  4. Lu H, Xing P, Phurbu D, Tang Q, Wu Q. Pelagibacterium montanilacus sp. nov., an alkaliphilic bacterium isolated from Lake Cuochuolong on the Tibetan Plateau. Int J Syst Evol Microbiol 2018; 68:2220–2225 [View Article] [PubMed]
     [Google Scholar]
  5. Liu B-T, Wang C, Wang X-M, Chen G-J, Du Z-J. Pelagibacterium lacus sp. nov., isolated from lake water. Int J Syst Evol Microbiol 2019; 69:1807–1813 [View Article] [PubMed]
     [Google Scholar]
  6. Jang H-J, Song J, Joung Y, Cho J-C. Pelagibacterium sediminicola sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 2019; 69:2651–2657 [View Article] [PubMed]
     [Google Scholar]
  7. Wei W, Xing K, Wang K, Hu X, Zhang X et al. Pelagibacterium limicola sp. nov., isolated from a soda alkali-saline soil. Arch Microbiol 2021; 203:2681–2687 [View Article] [PubMed]
     [Google Scholar]
  8. Liu CL, Shao ZZ. Alcanivorax dieselolei sp. nov., a novel alkane-degrading bacterium isolated from sea water and deep-sea sediment. Int J Syst Evol Microbiol 2005; 55:1181–1186 [View Article] [PubMed]
     [Google Scholar]
  9. Park S-C, Won S. Evaluation of 16S rRNA databases for taxonomic assignments using mock community. Genomics Inform 2018; 16:e24 [View Article] [PubMed]
     [Google Scholar]
  10. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article] [PubMed]
     [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] [PubMed]
     [Google Scholar]
  12. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
     [Google Scholar]
  13. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 2014; 42:D206–14 [View Article] [PubMed]
     [Google Scholar]
  14. 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]
  15. 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] [PubMed]
     [Google Scholar]
  16. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprintse1900v1 2016; 4: [View Article]
     [Google Scholar]
  17. Kuykendall LD, Roy MA, O’neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988; 38:358–361 [View Article]
     [Google Scholar]
  18. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. Usfcc Newsl 1990
     [Google Scholar]
  19. Collins MD. Isoprenoid quinone analyses in bacterial classification and identification society for applied bacteriology technical. J Appl Microbiol 1985
     [Google Scholar]
  20. 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]
  21. Wang G, Yu K, Wang Y, Su H, Wu H et al. Pelagibacterium lentulum sp. nov., a marine bacterium from the culture broth of Picochlorum sp. 122. Int J Syst Evol Microbiol 2017; 67:3182–3185 [View Article] [PubMed]
     [Google Scholar]
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Pelagibacterium xiamenense sp. nov., isolated from intertidal sediment
Int J Syst Evol Microbiol 72, 005462 (2022); https://doi.org/10.1099/ijsem.0.005462
/content/journal/ijsem/10.1099/ijsem.0.005462
/content/journal/ijsem/10.1099/ijsem.0.005462
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