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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 9

sp. nov., isolated from deep sea sediment of the Mariana Trench Free

Abstract

A Gram-stain-negative, light pink-coloured, rod-shaped, flagellated and facultative anaerobic bacterial strain, designated MT2928, was isolated from deep-sea sediment collected from the Mariana Trench. Growth of strain MT2928 occurred optimally at 28 °C, pH 8.0–9.0 and in the presence of 1.0–2.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MT2928 belongs to the genus and has the highest sequence similarity to GYSW-23 (96.6 %). Genomic analysis indicated that strain MT2928 contains a circular chromosome of 4 199 362 bp with G+C content of 67.2 mol%. The strain did not produce bacteriochlorophyll a, but produced carotenoid. The predominant respiratory quinone of MT2928 was ubiquinone-10. The polar lipids of MT2928 contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified lipids and two unidentified phospholipids. The major fatty acids of strain MT2928 contained summed feature 8 (C 7 or/and C 6), C and summed feature 2 (iso-C I and/or C 3-OH). On the basis of phylogenetic, physiological, biochemical and other phenotypic properties, strain MT2928 represents a novel species of the genus , and the name sp. nov. is proposed with the type species MT2928 (=MCCC 1K05575=JCM 34320).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Mariana Trench , Pontivivens , Rhodobacteraceae and sediment
Funding
This study was supported by the:
  • Key Technology Research and Development Program of Shandong (Award 2018YFC0310801)
    • Principle Award Recipient: Qing-leiSun
  • Grants of the National Key R&D Program of China (Award 2018YFC0310603)
    • Principle Award Recipient: JianZhang
© 2021 Yantai University Yantai, Shandong CHINA
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2021-09-14
2024-10-13
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References

  1. Buchan A, González JM, Moran MA. Overview of the marine Roseobacter lineage. Appl Environ Microbiol 2005; 71:5665–5677 [View Article] [PubMed]
     [Google Scholar]
  2. Cai X, Wang Y, Yang X, Liu J, Wu Y et al. Paraphaeobacter pallidus gen. nov., sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2017; 67:2520–2526 [View Article] [PubMed]
     [Google Scholar]
  3. Feng T, Jeong SE, Kim KH, Park HY, Jeon CO. Aestuariicoccus marinus gen. nov., sp. nov., isolated from sea-tidal flat sediment. Int J Syst Evol Microbiol 2018; 68:260–265 [View Article] [PubMed]
     [Google Scholar]
  4. Park S, Jung YT, Won SM, Park JM, Yoon JH. Thalassobius aquaeponti sp. nov., an alphaproteobacterium isolated from seawater. Antonie van Leeuwenhoek 2014; 106:535–542 [View Article] [PubMed]
     [Google Scholar]
  5. Park S, Park JM, Park DS, Yoon JH. Litoreibacter ponti sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2014; 64:3810–3815 [View Article] [PubMed]
     [Google Scholar]
  6. Park S, Won SM, Park JM, Jung YT, Yoon JH. Pontivivens insulae gen. nov., sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2015; 65:2896–2902 [View Article] [PubMed]
     [Google Scholar]
  7. 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]
  8. 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]
  9. 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]
  10. Rzhetsky A, Nei M. A simple method for estimating and testing minimum-evolution trees. Mol Biol 1992; 9:945–967
     [Google Scholar]
  11. 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]
  12. 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]
  13. 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]
  14. 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]
  15. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2010; 25:1754–1760
     [Google Scholar]
  16. 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]
  17. 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]
  18. 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]
  19. 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]
  20. Medema MH, Blin K, Cimermancic P, 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–W346 [View Article]
     [Google Scholar]
  21. 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]
  22. 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]
  23. 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]
  24. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC News Lett 1990; 20:1–6
     [Google Scholar]
  25. 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]
  26. Zhuang L, Lin B, Xu L, Li G, Wu C-J et al. Erythrobacter spongiae sp. nov., isolated from marine sponge. Int J Syst Evol Microbiol 2019; 69:1111–1116 [View Article] [PubMed]
     [Google Scholar]
  27. 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]
  28. 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]
  29. 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]
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Pontivivens ytuae sp. nov., isolated from deep sea sediment of the Mariana Trench
Int J Syst Evol Microbiol 71, 004967 (2021); https://doi.org/10.1099/ijsem.0.004967
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