1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 7

sp. nov., isolated from deep-sea sediment of the Pacific Ocean Free

Abstract

A Gram-strain-negative, rod-shaped, aerobic bacterium, designated 216_PA32_1, was isolated from deep-sea sediment of the Pacific Ocean. Cells of strain 216_PA32_1 were non-motile, oxidase-positive and catalase-negative. The strain could grow at temperatures of 10–45 °C (optimum, 32–35 °C), at pH 5.0–10.0 (optimum, 6.0–7.0) and at salinities of 0–10% (optimum, 2–8%). The principal fatty acid (>10 %) was summed feature 8 (C 6/7). The sole respiratory quinone was Q10 (100 %). The polar lipids included phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, two unidentified phospholipids and five unidentified aminolipids. The G+C content of the chromosomal DNA was 66.3 mol%. According to the 16S rRNA gene similarity, strain 216_PA32_1 showed the highest sequence similarity to JLT 1210 (97.3 %), followed by SS011B1-20 (97.1 %). Phylogenetic trees indicated that strain 216_PA32_1 clustered with strain SS011B1-20. The average nucleotide identity and the DNA–DNA hybridization values between strain 216_PA32_1 and all species of the genus were below 79.5 and 20.6%, respectively. A combination of the phylogenetic, phenotypic, chemotaxonomic and genomic evidence demonstrated that strain 216_PA32_1 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is 216_PA32_1 (=MCCC 1A14128=KCTC 72688).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): deep-sea sediment , Pacific Ocean , Pseudooceanicola pacificus sp. nov. and taxonomy
Funding
This study was supported by the:
  • COMRA program (Award DY135-B2-01)
    • Principle Award Recipient: Zongze Shao
  • the Key Research Program of Frontier Sciences of the Chinese Academy of Sciences (Award QYZDJ-SSW-DQC018-02)
    • Principle Award Recipient: Zhiqiang Yu
  • Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program (Award 2017BT01Z134)
    • Principle Award Recipient: Zhiqiang Yu
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004298
2020-06-24
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/7/4372.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004298&mimeType=html&fmt=ahah

References

  1. Lai Q, Li G, Liu X, Du Y, Sun F et al. Pseudooceanicola atlanticus gen. nov. sp. nov., isolated from surface seawater of the Atlantic Ocean and reclassification of Oceanicola batsensis, Oceanicola marinus, Oceanicola nitratireducens, Oceanicola nanhaiensis, Oceanicola antarcticus and Oceanicola flagellatus, as Pseudooceanicola batsensis comb. nov., Pseudooceanicola marinus comb. nov., Pseudooceanicola nitratireducens comb. nov., Pseudooceanicola nanhaiensis comb. nov., Pseudooceanicola antarcticus comb. nov., and Pseudooceanicola flagellatus comb. nov. Antonie van Leeuwenhoek 2015; 107:1065–1074 [View Article][PubMed]
     [Google Scholar]
  2. Cho J-C, Giovannoni SJ. Oceanicola granulosus gen. nov., sp. nov. and Oceanicola batsensis sp. nov., poly-beta-hydroxybutyrate-producing marine bacteria in the order 'Rhodobacterales'. Int J Syst Evol Microbiol 2004; 54:1129–1136 [View Article][PubMed]
     [Google Scholar]
  3. Lin K-Y, Sheu S-Y, Chang P-S, Cho J-C, Chen W-M. Oceanicola marinus sp. nov., a marine alphaproteobacterium isolated from seawater collected off Taiwan. Int J Syst Evol Microbiol 2007; 57:1625–1629 [View Article][PubMed]
     [Google Scholar]
  4. Zheng Q, Chen C, Wang Y-N, Jiao N. Oceanicola nitratireducens sp. nov., a marine alphaproteobacterium isolated from the South China Sea. Int J Syst Evol Microbiol 2010; 60:1655–1659 [View Article][PubMed]
     [Google Scholar]
  5. Huo Y-Y, Li Z-Y, You H, Wang C-S, Post AF et al. Oceanicola antarcticus sp. nov. and Oceanicola flagellatus sp. nov., moderately halophilic bacteria isolated from seawater. Int J Syst Evol Microbiol 2014; 64:2975–2979 [View Article][PubMed]
     [Google Scholar]
  6. Huang M-M, Guo L-L, Wu Y-H, Lai Q-L, Shao Z-Z et al. Pseudooceanicola lipolyticus sp. nov., a marine alphaproteobacterium, reclassification of Oceanicola flagellatus as Pseudooceanicola flagellatus comb. nov. and emended description of the genus Pseudooceanicola . Int J Syst Evol Microbiol 2018; 68:409–415 [View Article][PubMed]
     [Google Scholar]
  7. Gu J, Guo B, Wang Y-N, Yu S-L, Inamori R et al. Oceanicola nanhaiensis sp. nov., isolated from sediments of the South China Sea. Int J Syst Evol Microbiol 2007; 57:157–160 [View Article][PubMed]
     [Google Scholar]
  8. Skerman VBD. A Guide to the Identification of the Genera of Bacteria, 2nd edn. Baltimore: Williams & Wilkins; 1967
     [Google Scholar]
  9. Yin Q, Song ZM, Liang J, Wang Y, Zheng X et al. Pseudooceanicola onchidii sp. nov., isolated from a marine invertebrate from the South China Sea. Int J Syst Evol Microbiol 2019ijsem003905
     [Google Scholar]
  10. Chen M-H, Sheu S-Y, Chen CA, Wang J-T, Chen W-M. Roseivivax isoporae sp. nov., isolated from a reef-building coral, and emended description of the genus Roseivivax. Int J Syst Evol Microbiol 2012; 62:1259–1264 [View Article][PubMed]
     [Google Scholar]
  11. 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]
  12. Chun J, Lee J-H, Jung Y, Kim M, Kim S et al. Eztaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 2007; 57:2259–2261 [View Article][PubMed]
     [Google Scholar]
  13. 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][PubMed]
     [Google Scholar]
  14. 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]
  15. 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]
  16. Rzhetsky A, Nei M. Statistical properties of the ordinary least-squares, generalized least-squares, and minimum-evolution methods of phylogenetic inference. J Mol Evol 1992; 35:367–375 [View Article][PubMed]
     [Google Scholar]
  17. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  18. 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]
  19. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically United database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article][PubMed]
     [Google Scholar]
  20. 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]
  21. 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]
  22. 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]
  23. 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]
  24. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article][PubMed]
     [Google Scholar]
  25. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the AD hoc Committee on reconciliation of approaches to bacterial Systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
     [Google Scholar]
  26. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI; 1990
     [Google Scholar]
  27. YH W, Xu L, Zhou P, Wang CS, Oren A et al. Brevirhabdus pacificus gen. nov., sp. nov., isolated from deep-sea sediment in a hydrothermal vent field. Int J Syst Evol Microbiol 2015; 64:3645–3651
     [Google Scholar]
  28. Kates M. Techniques of Lipidology, 2nd ed. rev.. Amsterdam: Elsevier; 1986 pp 106–107
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004298
Loading
Pseudooceanicola pacificus sp. nov., isolated from deep-sea sediment of the Pacific Ocean
Int J Syst Evol Microbiol 70, 4372 (2020); https://doi.org/10.1099/ijsem.0.004298
/content/journal/ijsem/10.1099/ijsem.0.004298
/content/journal/ijsem/10.1099/ijsem.0.004298
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