1887

Abstract

A Gram-staining-negative, strictly aerobic, long-rod shaped with no flagellum and yellow-pigmented bacterium designated strain ZXX205, was isolated from the hadal seawater at the depth of 7500 m in the Mariana Trench, Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences placed strain ZXX205 within the genus and strain ZXX205 was most closely related to KCTC 52348 and KCTC 22026 with 96.9 % and 96.6 % sequence similarity, respectively. The sequence similarities to all other type strains were 96.3 % or less, and to the type strain LMG 22492 was 94.1 %. Growth occurred in the presence of 0–9.0 % (w/v) NaCl (optimum 3.0 %), at 4–45 °C (optimum 28 °C) and pH 6.0–9.0 (optimum pH 7.5). The sole respiratory quinone was menaquinone 6 (MK-6). The dominant cellular fatty acids (>10 %) of strain ZXX205 were iso-C, iso-C G, iso-C 3-OH and iso-C. The polar lipids profile contained predominantly phosphatidylethanolamine, four glycolipids, four unidentified aminolipids and three unidentified lipids. The genomic DNA G+C content was 35.5 %. The DNA–DNA relatedness (DDH) values between strain ZXX205 and the most closely related species and were 21.1 and 20.4 %, respectively. Based on polyphasic taxonomic analysis, strain ZXX205 is considered to represent a novel species in the genus of the family , for which the name is proposed. The type strain is ZXX205 (=MCCC 1K03851=JCM 33665).

Funding
This study was supported by the:
  • Fundamental Research Funds for Central Universities of the Central South University (Award Nos. 201762009 and 201762017)
    • Principle Award Recipient: Xiao-HuaZhang
  • Innovative Research Group Project of the National Natural Science Foundation of China (Award Nos. 91751202 and 41730530)
    • Principle Award Recipient: Xiao-HuaZhang
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004687
2021-02-08
2024-04-24
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/71/3/ijsem004687.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004687&mimeType=html&fmt=ahah

References

  1. Nedashkovskaya OI, Kim SB, Han SK, Snauwaert C, Vancanneyt M et al. Winogradskyella thalassocola gen. nov., sp. nov., Winogradskyella epiphytica sp. nov. and Winogradskyella eximia sp. nov., marine bacteria of the family Flavobacteriaceae . Int J Syst Evol Microbiol 2005; 55:49–55 [View Article][PubMed]
    [Google Scholar]
  2. Yoon B-J, Byun H-D, Kim J-Y, Lee D-H, Kahng H-Y et al. Winogradskyella lutea sp. nov., isolated from seawater, and emended description of the genus Winogradskyella . Int J Syst Evol Microbiol 2011; 61:1539–1543 [View Article][PubMed]
    [Google Scholar]
  3. Nedashkovskaya OI, Vancanneyt M, Kim SB, Zhukova NV. Winogradskyella echinorum sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from the sea urchin Strongylocentrotus intermedius . Int J Syst Evol Microbiol 2009; 59:1465–1468 [View Article][PubMed]
    [Google Scholar]
  4. Ivanova EP, Christen R, Gorshkova NM, Zhukova NV, Kurilenko VV et al. Winogradskyella exilis sp. nov., isolated from the starfish Stellaster equestris, and emended description of the genus Winogradskyella . Int J Syst Evol Microbiol 2010; 60:1577–1580 [View Article][PubMed]
    [Google Scholar]
  5. Nedashkovskaya OI, Kukhlevskiy AD, Zhukova NV. Winogradskyella ulvae sp. nov., an epiphyte of a Pacific seaweed, and emended descriptions of the genus Winogradskyella and Winogradskyella thalassocola, Winogradskyella echinorum, Winogradskyella exilis and Winogradskyella eximia. Int J Syst Evol Microbiol 2012; 62:1450–1456 [View Article][PubMed]
    [Google Scholar]
  6. Begum Z, Srinivas TNR, Manasa P, Sailaja B, Sunil B et al. Winogradskyella psychrotolerans sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from Arctic sediment. Int J Syst Evol Microbiol 2013; 63:1646–1652 [View Article][PubMed]
    [Google Scholar]
  7. Lee JH, Kang JW, Shin SB, Seong CN. Winogradskyella flava sp. nov., isolated from the brown alga, Sargassum fulvellum . Int J Syst Evol Microbiol 2017; 67:3540–3546 [View Article][PubMed]
    [Google Scholar]
  8. Park S, Park J-M, Won S-M, Bae KS, Yoon J-H. Winogradskyella wandonensis sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2014; 64:1520–1525 [View Article][PubMed]
    [Google Scholar]
  9. Zhang D-C, Liu Y-X, Huang H-J, Weber K, Margesin R. Winogradskyella sediminis sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2016; 66:3157–3163 [View Article][PubMed]
    [Google Scholar]
  10. Franco A, Busse H-J, Schubert P, Wilke T, Kämpfer P et al. Winogradskyella pocilloporae sp. nov. isolated from healthy tissue of the coral Pocillopora damicornis . Int J Syst Evol Microbiol 2018; 68:1689–1696 [View Article][PubMed]
    [Google Scholar]
  11. Park S, Park J-M, Won S-M, Yoon J-H. Winogradskyella crassostreae sp. nov., isolated from an oyster (Crassostrea gigas). Int J Syst Evol Microbiol 2015; 65:2890–2895 [View Article][PubMed]
    [Google Scholar]
  12. Schellenberg J, Busse H-J, Hardt M, Schubert P, Wilke T et al. Winogradskyella haliclonae sp. nov., isolated from a marine sponge of the genus Haliclona . Int J Syst Evol Microbiol 2017; 67:4902–4910 [View Article][PubMed]
    [Google Scholar]
  13. Zhao X, Liu J, Zhou S, Zheng Y, Wu Y et al. Diversity of culturable heterotrophic bacteria from the Mariana Trench and their ability to degrade macromolecules. Mar Life Sci Technol 2020; 2:181–193 [View Article]
    [Google Scholar]
  14. Nunoura T, Takaki Y, Hirai M, Shimamura S, Makabe A et al. Hadal biosphere: insight into the microbial ecosystem in the deepest Ocean on earth. Proc Natl Acad Sci U S A 2015; 112:E1230–E1236 [View Article][PubMed]
    [Google Scholar]
  15. Liu J, Zheng Y, Lin H, Wang X, Li M et al. Proliferation of hydrocarbon-degrading microbes at the bottom of the Mariana Trench. Microbiome 2019; 7:47 [View Article][PubMed]
    [Google Scholar]
  16. Nunoura T, Hirai M, Yoshida-Takashima Y, Nishizawa M, Kawagucci S et al. Distribution and niche separation of planktonic microbial communities in the water columns from the surface to the Hadal waters of the Japan Trench under the eutrophic Ocean. Front Microbiol 2016; 7:1261 [View Article][PubMed]
    [Google Scholar]
  17. Peoples LM, Donaldson S, Osuntokun O, Xia Q, Nelson A et al. Vertically distinct microbial communities in the Mariana and Kermadec trenches. PLoS One 2018; 13:e0195102 [View Article][PubMed]
    [Google Scholar]
  18. Ausubel F, Brent R, Kingston R, Moore D, Seidman J. Short protocols in molecular biology: a Compendium of Methods from Current Protocols in Molecular Biology, 3rd ed. New York: Wiley; 1995
    [Google Scholar]
  19. Zhang Z, Yu C, Wang X, Yu S, Zhang X-H. Arcobacter pacificus sp. nov., isolated from seawater of the South Pacific Gyre. Int J Syst Evol Microbiol 2016; 66:542–547 [View Article][PubMed]
    [Google Scholar]
  20. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:18 [View Article][PubMed]
    [Google Scholar]
  21. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article][PubMed]
    [Google Scholar]
  22. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with glimmer. Bioinformatics 2007; 23:673–679 [View Article][PubMed]
    [Google Scholar]
  23. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article][PubMed]
    [Google Scholar]
  24. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 [View Article][PubMed]
    [Google Scholar]
  25. Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL et al. Rfam: updates to the RNA families database. Nucleic Acids Res 2009; 37:D136–D140 [View Article][PubMed]
    [Google Scholar]
  26. 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; 67:16131617 [View Article][PubMed]
    [Google Scholar]
  27. 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]
  28. 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]
  29. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  30. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
    [Google Scholar]
  31. 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]
  32. 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]
  33. Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res 2016; 44:D286–D293 [View Article]
    [Google Scholar]
  34. Beveridge TJ, Lawrence JR, Murray RG. Sampling and staining for light microscopy. Methods for General and Molecular Microbiology, 3rd ed. American Society of Microbiology; 2007 pp 19–33
    [Google Scholar]
  35. Bernardet J-F, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [View Article][PubMed]
    [Google Scholar]
  36. Zhou S, Ren Q, Li Y, Liu J, Wang X et al. Abyssibacter profundi gen. nov., sp. nov., a marine bacterium isolated from seawater of the Mariana Trench. Int J Syst Evol Microbiol 2018; 68:3424–3429 [View Article][PubMed]
    [Google Scholar]
  37. Yu C, Yu S, Zhang Z, Li Z, Zhang X-H. Oceanobacillus pacificus sp. nov., isolated from a deep-sea sediment. Int J Syst Evol Microbiol 2014; 64:1278–1283 [View Article][PubMed]
    [Google Scholar]
  38. Bernardet JF, Bowman JP. The Genus Flavobacterium New York: Springer; 2006
    [Google Scholar]
  39. Yoon J-H, Lee K-C, Kho YH, Kang KH, Kim C-J et al. Halomonas alimentaria sp. nov., isolated from jeotgal, a traditional Korean fermented seafood. Int J Syst Evol Microbiol 2002; 52:123–130 [View Article][PubMed]
    [Google Scholar]
  40. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC News Lett 1990; 20:1–6
    [Google Scholar]
  41. Xie C-H, Yokota A. Phylogenetic analyses of Lampropedia hyalina based on the 16S rRNA gene sequence. J Gen Appl Microbiol 2003; 49:345–349 [View Article][PubMed]
    [Google Scholar]
  42. 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]
  43. Collins MD, Shah HN. Fatty acid, menaquinone and polar lipid composition of Rothia dentocariosa. Arch Microbiol 1984; 137:247–249 [View Article]
    [Google Scholar]
  44. Komagata K, Suzuki K-I. 4 Lipid and Cell-Wall Analysis in Bacterial Systematics Methods in microbiology: Elsevier; 1988 pp 161–207
    [Google Scholar]
  45. Montero-Calasanz MDC, 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][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004687
Loading
/content/journal/ijsem/10.1099/ijsem.0.004687
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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