1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 8

sp. nov., isolated from the deep-sea cold seep sediment of South China Sea No Access

Abstract

In this study, we report a Gram-stain-negative, rod-shaped, non-pigmented, motile and aerobic bacterium named strain MTZ26, which was isolated from deep-sea sediment sampled at a cold seep in the South China Sea. Growth of strain MTZ26 occurred at 4–40 °C (optimum, 25–30 °C), pH 6.0–10.0 (optimum, 7.0–8.0) and with 1.0–11.0 % (w/v) NaCl (optimum, 6.0–8.0 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MTZ26 belonged to the genus and was closely related to PSC101 (97.5 % sequence similarity) and KDW4 (97.5 %). Genomic analysis indicated that strain MTZ26 contains a circular chromosome of 3 331 814 bp with G+C content of 42.2 mol%. The predominant respiratory quinone of MTZ26 was ubiquinone-8. The polar lipids of MTZ26 contained phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminophospholipid and one unidentified phospholipid. The major fatty acids of strain MTZ26 contained C C C, C ω8, C 3-OH, C 3-OH, C ω8 and summed feature 8 (C ω7 or/and C ω6). Results of phylogenetic, physiological, biochemical and morphological analyses suggested that strain MTZ26 represents a novel species of the genus , and the name sp. nov. is proposed with the type strain MTZ26 (=MCCC 1K05568=JCM 34321).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Alphaproteobacteria , cold seep , Psychrosphaera and sediment
Funding
This study was supported by the:
  • National Key R&D Program of China (Award 2018YFC0310603)
    • Principle Award Recipient: ZhangJian
  • National Key R&D Program of China (Award 2018YFC0310801)
    • Principle Award Recipient: SunQing-lei
© 2021 Yantai University Yantai, Shandong CHINA
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004983
2021-08-25
2024-04-28
Loading full text...

Full text loading...

References

  1. Park S, Yoshizawa S, Hamasaki K, Kogure K, Yokota A. Psychrosphaera saromensis gen. nov., sp. nov., within the family Pseudoalteromonadaceae, isolated from Lake Saroma, Japan. J Gen Appl Microbiol 2010; 56:475–480 [View Article] [PubMed]
     [Google Scholar]
  2. Pheng S, Ayyadurai N, Park AY, Kim SG. Psychrosphaera aquimarina sp. nov., a marine bacterium isolated from seawater collected from Asan Bay, Republic of Korea. Int J Syst Evol Microbiol 2017; 67:4820–4824 [View Article] [PubMed]
     [Google Scholar]
  3. Lee JH, Baik KS, Kim D, Seong CN. Psychrosphaera aestuarii sp. nov. and Psychrosphaera haliotis sp. nov., isolated from the marine environment, and emended description of the genus Psychrosphaera. Int J Syst Evol Microbiol 2014; 64:1952–1957 [View Article] [PubMed]
     [Google Scholar]
  4. Lane DJ. 16S/23S rRNA sequencing. Stackebrandt E, Goodfellow M. eds In Nucleic Acids Techniques in Bacterial Systematics Chichester: John Wiley & Sons; 1991 pp 115–147
     [Google Scholar]
  5. Kim OS, Cho YJ, Lee K, Yoon SH, Kimet 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]
  6. 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]
  7. Rzhetsky A, Nei M. A simple method for estimating and testing minimum-evolution trees. Mol Biol 1992; 9:945–967
     [Google Scholar]
  8. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003; 52:696–704 [View Article] [PubMed]
     [Google Scholar]
  9. 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]
  10. 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]
  11. Berlin K, Koren S, Chin CS, Drake JP, Landolin JM et al. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat Biotechnol 2015; 33:623 [View Article] [PubMed]
     [Google Scholar]
  12. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2010; 25:1754–1760
     [Google Scholar]
  13. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2014; 25:1043–1055
     [Google Scholar]
  14. 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] [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. Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 2011; 8:785–786 [View Article] [PubMed]
     [Google Scholar]
  17. Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P et al. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 2011; 39:W339–46 [View Article]
     [Google Scholar]
  18. Lee I, Ouk Kim Y, Park SC, 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]
  19. Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  20. Xu P, Li W-J, Tang S-K, Zhang Y-Q, Chen G-Z et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family “Oxalobacteraceae” isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article] [PubMed]
     [Google Scholar]
  21. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC News Lett 1990; 20:1–6
     [Google Scholar]
  22. 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 Meth 1984; 2:233–241 [View Article]
     [Google Scholar]
  23. Meier-Kolthoff JP, Goker M, Sproer C, Klenk HP. When should a DDH experiment be mandatory in microbial taxonomy. Arch Microbiol 2013; 195:413–418 [View Article] [PubMed]
     [Google Scholar]
  24. 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]
  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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004983
Loading
Psychrosphaera ytuae sp. nov., isolated from the deep-sea cold seep sediment of South China Sea
Int J Syst Evol Microbiol 71, 004983 (2021); https://doi.org/10.1099/ijsem.0.004983
/content/journal/ijsem/10.1099/ijsem.0.004983
/content/journal/ijsem/10.1099/ijsem.0.004983
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