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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 2

sp. nov., isolated from surface sediment of the Terra Nova Bay, Antarctica Free

Abstract

Polyphasic taxonomic analysis was performed to characterize a novel bacterium, which was isolated from surface sediment of the Terra Nova Bay, Antarctica, and designated as R04H25. The cells of the isolate were Gram-stain-negative, aerobic, non-motile, slightly curved rods. Growth occurred at 4–42 °C, pH 7.0–9.5, and in 1–15 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences indicated that strain R04H25 formed an independent lineage within the genus and its nearest neighbours were 908033 (98.2 %), PIM1 (98.1 %), W11 (97.8 %), 908087 (97.1 %) and PIN1 (97.0 %). The average nucleotide identities between strain R04H25 and the nearest neighbours were 76.2–77.7 %. The major fatty acids were iso-C, summed feature 9, iso-C, C and iso-C 3-OH. The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminophospholipid, three unidentified glycolipids and two unidentified lipids. The predominant respiratory quinone was ubiquinone 8. The genomic DNA G+C content was 48.2 mol%. On the basis of the phylogenetic, physiological and chemotaxonomic results, we propose a novel species named as sp. nov. in the genus , with the type strain R04H25 (=GDMCC 1.1503=KCTC 62911).

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): Alteromonadales , Antarctica , marine sediment , polyphasic taxonomy and Pseudidiomarina
Funding
This study was supported by the:
  • GDAS' Special Project of Science and Technology Development (Award 2018GDASCX-0909)
  • Pearl River S&T Nova Program of Guangzhou (Award 201806010065)
    • Principle Award Recipient: Anzhang Li
  • Science and Technology Plan Project of Guangzhou (Award 201704020088)
    • Principle Award Recipient: Hong-Hui Zhu
  • Guangdong Province Science and Technology Innovation Strategy Special Fund (Award 2018B020205002)
    • Principle Award Recipient: Anzhang Li
  • Science and Technology Plan Project of Guangdong (Award 2018B020205003)
    • Principle Award Recipient: Not Applicable
  • National Natural Science Foundation of China (Award 31600008)
© 2020 The Authors
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2019-11-07
2024-04-18
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References

  1. Jean WD, Shieh WY, Chiu HH. Pseudidiomarina taiwanensis gen. nov., sp. nov., a marine bacterium isolated from shallow coastal water of An-Ping Harbour, Taiwan, and emended description of the family Idiomarinaceae . Int J Syst Evol Microbiol 2006; 56:899–905 [View Article]
     [Google Scholar]
  2. Taborda M, Antunes A, Tiago I, Veríssimo A, Nobre MF et al. Description of Idiomarina insulisalsae sp. nov., isolated from the soil of a sea salt evaporation pond, proposal to transfer the species of the genus Pseudidiomarina to the genus Idiomarina and emended description of the genus Idiomarina . Syst Appl Microbiol 2009; 32:371–378 [View Article]
     [Google Scholar]
  3. Liu Y, Lai Q, Shao Z. Genome-based analysis reveals the taxonomy and diversity of the family Idiomarinaceae . Front Microbiol 2018; 9:2453 [View Article]
     [Google Scholar]
  4. Zhong ZP, Liu Y, Liu HC, Wang F, Song L et al. Idiomarina planktonica sp. nov., isolated from a saline lake. Int J Syst Evol Microbiol 2014; 64:3411–3416 [View Article]
     [Google Scholar]
  5. Song L, Ren F, Huang Y, Dai X, Zhou Y. Idiomarina indica sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2013; 63:2497–2500 [View Article]
     [Google Scholar]
  6. Chen MH, Sheu SY, Chen CA, Wang JT, Chen WM. Idiomarina aquimaris sp. nov., isolated from the reef-building coral Isopora palifera . Int J Syst Evol Microbiol 2012; 62:1536–1542 [View Article]
     [Google Scholar]
  7. Lee JC, Yun BS, Kim YS, Whang KS. Idiomarina halophila sp. nov., isolated from a solar saltern sediment. Int J Syst Evol Microbiol 2015; 65:1268–1273 [View Article]
     [Google Scholar]
  8. Wu YH, Shen YQ, Xu XW, Wang CS, Oren A et al. Pseudidiomarina donghaiensis sp. nov. and Pseudidiomarina maritima sp. nov., isolated from the East China Sea. Int J Syst Evol Microbiol 2009; 59:1321–1325 [View Article]
     [Google Scholar]
  9. Kwon SW et al. Idiomarina homiensis sp. nov., isolated from seashore sand in Korea. Int J Syst Evol Microbiol 2006; 56:2229–2233 [View Article]
     [Google Scholar]
  10. Jean WD, Leu TY, Lee CY, Chu TJ, Lin SY et al. Pseudidiomarina marina sp. nov. and Pseudidiomarina tainanensis sp. nov. and reclassification of Idiomarina homiensis and Idiomarina salinarum as Pseudidiomarina homiensis comb. nov. and Pseudidiomarina salinarum comb. nov., respectively. Int J Syst Evol Microbiol 2009; 59:53–59 [View Article]
     [Google Scholar]
  11. Du J, Lai Q, Liu Y, Du Y, Liu X et al. Idiomarina atlantica sp. nov., a marine bacterium isolated from the deep sea sediment of the North Atlantic Ocean. Antonie van Leeuwenhoek 2015; 107:393–401 [View Article]
     [Google Scholar]
  12. Fan X, Zhu Y, Gu P, Li Y, Xiao G et al. Bacterial community compositions of propylene oxide saponification wastewater treatment plants. RSC Adv 2017; 7:22347–22352 [View Article]
     [Google Scholar]
  13. Shahriari Moghadam M, Ebrahimipour G, Abtahi B, Ghassempour A, Hashtroudi MS. Biodegradation of polycyclic aromatic hydrocarbons by a bacterial consortium enriched from mangrove sediments. J Environ Health Sci Eng 2014; 12:114 [View Article]
     [Google Scholar]
  14. 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]
     [Google Scholar]
  15. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article]
     [Google Scholar]
  16. Lee I, Chalita M, Ha SM, Na SI, Yoon SH et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [View Article]
     [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. Kim M, Oh HS, Park SC, 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]
  19. 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]
     [Google Scholar]
  20. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:1912619131 [View Article]
     [Google Scholar]
  21. 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]
  22. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM. (editors) Methods for General and Molecular Microbiology, 3rd ed. Washington, DC: American Society of Microbiology; 2007 pp 330–393
     [Google Scholar]
  23. Li AZ, Lin LZ, Zhang MX, Zhu HH. Arenibacter antarcticus sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2017; 67:4601–4605 [View Article]
     [Google Scholar]
  24. Lanyi B. Classical and rapid identification methods for medically important bacteria. Methods in Microbiology 1988; 19:1–67
     [Google Scholar]
  25. Li AZ, Han XB, Lin LZ, Zhang MX, Zhu HH et al. Gramella antarctica sp. nov., isolated from marine surface sediment. Int J Syst Evol Microbiol 2018; 68:358–363
     [Google Scholar]
  26. 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]
  27. Poddar A, Lepcha RT, Mukherjee D, Bhattacharyya D, Das SK. Comparative analysis of 16S rRNA signature sequences of the genus Idiomarina and Idiomarina woesei sp. nov., a novel marine bacterium isolated from the Andaman Sea. Res Microbiol 2014; 165:501–507 [View Article]
     [Google Scholar]
  28. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article]
     [Google Scholar]
  29. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [View Article]
     [Google Scholar]
  30. 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]
     [Google Scholar]
  31. Montero-Calasanz MdelC, Göker M, Rohde M, Spröer C, Schumann P et al. Chryseobacterium hispalense sp. nov., a plant-growth-promoting bacterium isolated from a rainwater pond in an olive plant nursery, and emended descriptions of Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium . Int J Syst Evol Microbiol 2013; 63:4386–4395 [View Article]
     [Google Scholar]
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Pseudidiomarina gelatinasegens sp. nov., isolated from surface sediment of the Terra Nova Bay, Antarctica
Int J Syst Evol Microbiol 70, 708 (2020); https://doi.org/10.1099/ijsem.0.003760
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