1887

Abstract

A Gram-staining negative, aerobic, oval-shaped bacterium, designated strain PTG4-2, was isolated from deep-sea sediment of the Indian Ocean. Growth was observed with 1–9 % (w/v) NaCl with optimal growth with 3 %, at pH 6.0–10.0 with an optimum of pH 7.0, and at 4–40 °C with an optimum of 30 °C. Positive for catalase and oxidase. The results of a 16S rRNA gene sequence comparison indicated that PTG4-2 was most closely related to JL1095 (97.3 %), followed by J103 (96.5 %), all other species shared <93 % sequence similarity. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that PTG4-2 forms a distinct lineage within the genus , and revealed that the genus forms a novel family-level clade in the order . The ANI and the DNA–DNA hybridization estimate values between PTG4-2 and two type strains ( JL1095 and J103) were 79.9–76.2 % and 23.1–20.8 %, respectively. PTG4-2 contained Q-10 as the predominant ubiquinone. The principal fatty acids (>5 %) were summed feature 8 [C 7/6 (72.2 %)], C (8.4 %), C 7 (6.4 %) and C (6.3 %). The polar lipids consisted of phosphatidylglycerol, three unidentified phospholipids, two unidentified glycolipids, one unidentified aminolipid and one unknown lipid. The DNA G+C content of PTG4-2 is 69.2 mol%. On the basis of the polyphasic taxonomic evidence presented in this study, PTG4-2 should be classified as representing a novel species of the genus , for which the name sp. nov. is proposed, with the type strain PTG4-2 (=MCCC 1A01274=KCTC 52323). In addition, a novel family, fam. nov., is proposed to accommodate the genus .

Funding
This study was supported by the:
  • Xiamen Ocean Economic Innovation and Development Demonstration Project (Award 16PZP001SF16)
  • China Ocean Mineral Resources RandD Association program (Award No. DY135-B2-01)
  • National Infrastructure of Microbial Resources of China (Award NIMR-2018-9)
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2019-02-27
2024-12-09
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References

  1. Garrity GM, Holt JG. The road map to the manual. Bergey’s Manual of Systematic Bacteriology 2001119–166
    [Google Scholar]
  2. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article]
    [Google Scholar]
  3. Wt I, Kim SH, Kim MK, Ten LN, Lee ST. Pleomorphomonas koreensis sp. nov., a nitrogen-fixing species in the order Rhizobiales . Int J Syst Evol Microbiol 2006; 56:1663–1666
    [Google Scholar]
  4. Hou L, Zhang Y, Sun J, Xie X. Acuticoccus yangtzensis gen. nov., sp. nov., a novel member in the family Rhodobacteraceae, isolated from the surface water of the Yangtze Estuary. Curr Microbiol 2015; 70:176–182 [View Article]
    [Google Scholar]
  5. Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2017; 67:529–531 [View Article]
    [Google Scholar]
  6. Yin Q, Liang J, Zhang L, Ma K, Hu Z-L et al. Acuticoccus kandeliae sp. nov., isolated from rhizosphere soil of the mangrove plant Kandelia, and emended description of Acuticoccus yangtzensis . Int J Syst Evol Microbiol 2018; 68:3316–3321 [View Article]
    [Google Scholar]
  7. Lai Q, Cao J, Yuan J, Li F, Shao Z. Celeribacter indicus sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium from deep-sea sediment and reclassification of Huaishuia halophila as Celeribacter halophilus comb. nov. Int J Syst Evol Microbiol 2014; 64:4160–4167 [View Article]
    [Google Scholar]
  8. Liu C, Shao Z. 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. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article]
    [Google Scholar]
  10. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol and Evol 1987; 4:406–425
    [Google Scholar]
  11. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  12. Rzhetsky A, Nei M. A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 1992; 9:945–967
    [Google Scholar]
  13. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731–2739 [View Article]
    [Google Scholar]
  14. 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]
    [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][PubMed]
    [Google Scholar]
  17. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article]
    [Google Scholar]
  18. Goris J, Klappenbach JA, Vandamme P, Coenye T, Konstantinidis KT 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]
    [Google Scholar]
  19. 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]
  20. 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][PubMed]
    [Google Scholar]
  21. Auch AF, Klenk H-P, Göker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2010; 2:142–148 [View Article]
    [Google Scholar]
  22. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article]
    [Google Scholar]
  23. Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E et al. Microbial genomic taxonomy. BMC Genomics 2013; 14:913 [View Article]
    [Google Scholar]
  24. Zuo G, Hao B. CVTree3 web server for whole-genome-based and alignment-free prokaryotic phylogeny and taxonomy. Genomics Proteomics Bioinformatics 2015; 13:321–331 [View Article]
    [Google Scholar]
  25. Liu X, Lai Q, Du Y, Li G, Sun F et al. Tamlana nanhaiensis sp. nov., isolated from surface seawater collected from the South China Sea. Antonie van Leeuwenhoek 2015; 107:1189–1196 [View Article]
    [Google Scholar]
  26. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  27. Collins M. Isoprenoid quinone analyses in bacterial classification and identification. Soc Appl Bacteriol Tech Ser 1985267–287
    [Google Scholar]
  28. Kates M. Techniques of Lipidology, 2nd ed. Amsterdam: Elsevier; 1986 pp. 106241–107246
    [Google Scholar]
  29. Yin Q, Liang J, Zhang L, Ma K, Hu Z-L et al. Acuticoccus kandeliae sp. nov., isolated from rhizosphere soil of the mangrove plant Kandelia, and emended description of Acuticoccus yangtzensis . Int J Syst Evol Microbiol 2018; 68:3316–3321 [View Article]
    [Google Scholar]
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