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 taxonomic study was carried out on strain PA15-N-34, which was isolated from deep-sea sediment of Pacific Ocean. The bacterium was Gram-stain-positive, oxidase- and catalase-positive and rod-shaped. Growth was observed at salinity of 0–15.0% NaCl and at temperatures of 10–45 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain PA15-N-34 belonged to the genus , with the highest sequence similarity to MTEO17 (97.7 %), followed by 19 m-6 (97.3 %) and 12 other species of the genus (93.4 %–97.0 %). The average nucleotide identity and DNA–DNA hybridization values between strain PA15-N-34 and type strains of the genus were 71.46–81.78% and 18.7–25.2 %, respectively. The principal fatty acids (>10 %) were summed feature 8 (C 7 and/or C 6; 31.2 %), C (25.0 %) and summed feature 3 (14.6 %). The DNA G+C content was 57.15 mol%. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, four unidentified aminolipids and three unidentified lipids. The novel strain can be differentiated from its closest type strain by a negative test for urease and the presence of diphosphatidylglycerol and aminolipid. The combined genotypic and phenotypic data show that strain PA15-N-34 represents a novel species within the genus , for which the name sp. nov. is proposed, with the type strain PA15-N-34 (=MCCC 1A14738=KCTC 72163).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Alcanivorax sediminis sp. nov. , deep-sea sediment , Pacific Ocean and taxonomy
Funding
This study was supported by the:
  • National Infrastructure of Natural Resources for Science and Technology Program of China (Award (NIMR-2020-9))
    • Principle Award Recipient: Zongze Shao
  • Xiamen Ocean Economic Innovation and Development Demonstration Project (Award (16PZP001SF16))
    • Principle Award Recipient: Zongze Shao
  • National Natural Science Foundation of China (Award (No. 41976107, 91851203))
    • Principle Award Recipient: Zongze Shao
  • COMRA program (Award (No. DY135-B2-01, DY135-E2-5-02))
    • Principle Award Recipient: Zongze Shao
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004285
2020-07-03
2024-09-15
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/7/4280.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004285&mimeType=html&fmt=ahah

References

  1. Yakimov MM, Golyshin PN, Lang S, Moore ER, Abraham WR et al. Alcanivorax borkumensis gen. nov., sp. nov., a new, hydrocarbon-degrading and surfactant-producing marine bacterium. Int J Syst Bacteriol 1998; 48 Pt 2:339–348 [View Article][PubMed]
     [Google Scholar]
  2. Fernández-Martínez J, Pujalte MJ, García-Martínez J, Mata M, Garay E et al. Description of Alcanivorax venustensis sp. nov. and reclassification of Fundibacter jadensis DSM 1 21 78T (Bruns and Berthe-Corti 1999) as Alcanivorax jadensis comb. nov., members of the emended genus Alcanivorax . Int J Syst Evol Microbiol 2003; 53:331–338 [View Article][PubMed]
     [Google Scholar]
  3. Bruns A, Berthe-Corti L. Fundibacter jadensis gen. nov., sp. nov., a new slightly halophilic bacterium, isolated from intertidal sediment. Int J Syst Bacteriol 1999; 49 Pt 2:441–448 [View Article][PubMed]
     [Google Scholar]
  4. 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]
  5. Rivas R, García-Fraile P, Peix A, Mateos PF, Martínez-Molina E et al. Alcanivorax balearicus sp. nov., isolated from Lake Martel. Int J Syst Evol Microbiol 2007; 57:1331–1335 [View Article][PubMed]
     [Google Scholar]
  6. Wu Y, Lai Q, Zhou Z, Qiao N, Liu C et al. Alcanivorax hongdengensis sp. nov., an alkane-degrading bacterium isolated from surface seawater of the straits of Malacca and Singapore, producing a lipopeptide as its biosurfactant. Int J Syst Evol Microbiol 2009; 59:1474–1479 [View Article][PubMed]
     [Google Scholar]
  7. Lai Q, Wang L, Liu Y, Fu Y, Zhong H et al. Alcanivorax pacificus sp. nov., isolated from a deep-sea pyrene-degrading consortium. Int J Syst Evol Microbiol 2011; 61:1370–1374 [View Article][PubMed]
     [Google Scholar]
  8. Lai Q, Wang J, Gu L, Zheng T, Shao Z. Alcanivorax marinus sp. nov., isolated from deep-sea water. Int J Syst Evol Microbiol 2013; 63:4428–4432 [View Article][PubMed]
     [Google Scholar]
  9. Rahul K, Sasikala C, Tushar L, Debadrita R, Ramana CV. Alcanivorax xenomutans sp. nov., a hydrocarbonoclastic bacterium isolated from a shrimp cultivation pond. Int J Syst Evol Microbiol 2014; 64:3553–3558 [View Article][PubMed]
     [Google Scholar]
  10. Kyoung Kwon K, Hye Oh J, Yang S-H, Seo H-S, Lee J-H. Alcanivorax gelatiniphagus sp. nov., a marine bacterium isolated from tidal flat sediments enriched with crude oil. Int J Syst Evol Microbiol 2015; 65:2204–2208 [View Article][PubMed]
     [Google Scholar]
  11. Lai Q, Zhou Z, Li G, Li G, Shao Z. Alcanivorax nanhaiticus sp. nov., isolated from deep sea sediment. Int J Syst Evol Microbiol 2016; 66:3651–3655 [View Article][PubMed]
     [Google Scholar]
  12. Yang S, Li M, Lai Q, Li G, Shao Z. Alcanivorax mobilis sp. nov., a new hydrocarbon-degrading bacterium isolated from deep-sea sediment. Int J Syst Evol Microbiol 2018; 68:1639–1643 [View Article][PubMed]
     [Google Scholar]
  13. Song L, Liu H, Cai S, Huang Y, Dai X et al. Alcanivorax indicus sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2018; 68:3785–3789 [View Article][PubMed]
     [Google Scholar]
  14. Liu J, Ren Q, Zhang Y, Li Y, Tian X et al. Alcanivorax profundi sp. nov., isolated from deep seawater of the Mariana Trench. Int J Syst Evol Microbiol 2019; 69:371–376 [View Article][PubMed]
     [Google Scholar]
  15. Lai Q, Yuan J, Gu L, Shao Z. Marispirillum indicum gen. nov., sp. nov., isolated from a deep-sea environment. Int J Syst Evol Microbiol 2009; 59:1278–1281 [View Article][PubMed]
     [Google Scholar]
  16. 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]
  17. 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]
  18. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  19. 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]
  20. 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]
  21. 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]
  22. 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]
  23. 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]
  24. 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]
  25. 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][PubMed]
     [Google Scholar]
  26. 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][PubMed]
     [Google Scholar]
  27. 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]
  28. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Brenner DJ, Grimont PAD 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]
  29. 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]
  30. Skerman VBD. A Guide to the Identification of the Genera of Bacteria, 2nd ed. Baltimore: Williams & Wilkins; 1967
     [Google Scholar]
  31. Sambrook J, Fritsch EF, Maniatis T. Molecular Cloning: a Laboratory Manual, 2nd ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory; 1989
     [Google Scholar]
  32. Dong X-Z, Cai M-Y. Determinative Manual for Routine Bacteriology Beijing: Scientific Press (English translation); 2001
     [Google Scholar]
  33. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI; 1990
     [Google Scholar]
  34. Kates M. Lipid extraction procedures Amsterdam: Techniques of lipidology Elsevier; 1986 pp 100–111
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.004285
Loading
Alcanivorax sediminis sp. nov., isolated from deep-sea sediment of the Pacific Ocean
Int J Syst Evol Microbiol 70, 4280 (2020); https://doi.org/10.1099/ijsem.0.004285
/content/journal/ijsem/10.1099/ijsem.0.004285
/content/journal/ijsem/10.1099/ijsem.0.004285
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