sp. nov., isolated from lake sediment Free

Abstract

A Gram-stain-negative, facultatively aerobic, rod-shaped, motile by gliding and pink-pigmented bacterial strain, designated ELS1360, was isolated from a lake sediment sample collected in Inner Mongolia, PR China. Strain ELS1360 grew optimally at 33 °C, at pH 6.5–7.0 and without NaCl. Strain ELS1360 exhibited 97.3, 97.1 and 96.9 % 16S rRNA gene sequence similarities to HMF3095, JCM 30328 and JCM 30327, respectively, and 90.4–96.9 % to other members of the genus . Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strain ELS1360 belonged to the genus and clustered with JCM 30328 and JCM 30327. The predominant cellular fatty acids were iso-C, summed feature 3 and Cω5. Strain ELS1360 contained MK-7 as the sole menaquinone. The major polar lipids contained phosphatidylethanolamine and two unidentified lipids. The genomic DNA G+C content of strain ELS1360 was 57.1 mol%. Based on the results of our phylogenetic, phenotypic, genotypic and chemotaxonomic analyses, it is concluded that strain ELS1360 represents a novel species within the genus , for which the name sp. nov. is proposed. The type strain is ELS1360 (=KCTC 62449=MCCC 1H00319).

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 31770002)
    • Principle Award Recipient: Zong-Jun Du
  • Science and Technology Basic Resources Investigation Program of China (Award 2017FY100300)
    • Principle Award Recipient: Zong-Jun Du
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2020-01-21
2024-03-29
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References

  1. Munoz R, Rosselló-Móra R, Amann R. Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov. Syst Appl Microbiol 2016; 39:281–296 [View Article]
    [Google Scholar]
  2. Krieg NR, Ludwig W, Euzéby J, Whitman WB. Phylum XIV. Bacteroidetes phyl. nov. In Krieg JT, Staley DR, Brown DR, Hedlund BP, Paster BJ. (editors) Bergey’s Manual of Systematic Bacteriology 4, 2nd ed. New York, NY: Springer; 2010 pp 25–469
    [Google Scholar]
  3. Hirsch P, Ludwig W, Hethke C, Sittig M, Hoffmann B et al. Hymenobacter roseosalivarius gen. nov., sp. nov. from continental Antartica soils and sandstone: bacteria of the Cytophaga/Flavobacterium/Bacteroides line of phylogenetic descent. Syst Appl Microbiol 1998; 21:374–383 [View Article]
    [Google Scholar]
  4. Buczolits S, Denner EBM, Kämpfer P, Busse H-J. Proposal of Hymenobacter norwichensis sp. nov., classification of 'Taxeobacter ocellatus', 'Taxeobacter gelupurpurascens' and 'Taxeobacter chitinovorans' as Hymenobacter ocellatus sp. nov., Hymenobacter gelipurpurascens sp. nov. and Hymenobacter chitinivorans sp. nov., respectively, and emended description of the genus Hymenobacter Hirsch et al. 1999. Int J Syst Evol Microbiol 2006; 56:2071–2078 [View Article]
    [Google Scholar]
  5. Han L, Wu S-J, Qin C-Y, Zhu Y-H, Lu Z-Q et al. Hymenobacter qilianensis sp. nov., isolated from a subsurface sandstone sediment in the permafrost region of Qilian Mountains, China and emended description of the genus Hymenobacter . Antonie van Leeuwenhoek 2014; 105:971–978 [View Article]
    [Google Scholar]
  6. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article]
    [Google Scholar]
  7. Kang H, Cha I, Kim H, Joh K. Hymenobacter aquatilis sp. nov., isolated from a mesotrophic artificial lake. Int J Syst Evol Microbiol 2018; 68:2036–2041 [View Article]
    [Google Scholar]
  8. Jiang F, Danzeng W, Zhang Y, Zhang Y, Jiang L et al. Hymenobacter rubripertinctus sp. nov., isolated from Antarctic tundra soil. Int J Syst Evol Microbiol 2018; 68:663–668 [View Article]
    [Google Scholar]
  9. Ohn J-E, Ten LN, Kim B-O, Cho Y-J, Jung H-Y. Hymenobacter rufus sp. nov., a bacterium isolated from soil. Int J Syst Evol Microbiol 2018; 68:2983–2989 [View Article]
    [Google Scholar]
  10. Liu L, Zhou E-M, Jiao J-Y, Manikprabhu D, Ming H et al. Hymenobacter latericoloratus sp. nov. and Hymenobacter luteus sp. nov., isolated from freshwater sediment. Antonie van Leeuwenhoek 2015; 107:165–172 [View Article]
    [Google Scholar]
  11. Chen W-M, Chen W-T, Young C-C, Sheu S-Y. Hymenobacter gummosus sp. nov., isolated from a spring. Int J Syst Evol Microbiol 2017; 67:4728–4735 [View Article]
    [Google Scholar]
  12. Sheu S-Y, Li Y-S, Young C-C, Chen W-M. Hymenobacter pallidus sp. nov., isolated from a freshwater fish culture pond. Int J Syst Evol Microbiol 2017; 67:2915–2921 [View Article]
    [Google Scholar]
  13. Lee J-J, Lee Y-H, Park S-J, Lee S-Y, Park S et al. Hymenobacter seoulensis sp. nov., isolated from river water. Int J Syst Evol Microbiol 2017; 67:596–601 [View Article]
    [Google Scholar]
  14. Liu Q-Q, Wang Y, Li J, Du Z-J, Chen G-J. Saccharicrinis carchari sp. nov., isolated from a shark, and emended descriptions of the genus Saccharicrinis and Saccharicrinis fermentans . Int J Syst Evol Microbiol 2014; 64:2204–2209 [View Article]
    [Google Scholar]
  15. Fang D-B, Han J-R, Liu Y, Du Z-J. Seonamhaeicola marinus sp. nov., isolated from marine algae. Int J Syst Evol Microbiol 2017; 67:4857–4861 [View Article]
    [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]
    [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]
    [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]
    [Google Scholar]
  19. Haft DH, DiCuccio M, Badretdin A, Brover V, Chetvernin V et al. Refseq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res 2018; 46:D851–D860 [View Article]
    [Google Scholar]
  20. Lee I, Chalita M, Ha S-M, Na S-I, Yoon S-H 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]
  21. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. Dna-Dna hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article]
    [Google Scholar]
  22. 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]
    [Google Scholar]
  23. Blin K, Wolf T, Chevrette MG, Lu X, Schwalen CJ et al. antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res 2017; 45:W36–W41 [View Article]
    [Google Scholar]
  24. Kanehisa M, Sato Y, Morishima K, BlastKOALA MK. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 2016; 428:726–731 [View Article]
    [Google Scholar]
  25. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [View Article]
    [Google Scholar]
  26. Konstantinidis KT, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J 2017; 11:2399–2406 [View Article]
    [Google Scholar]
  27. Bowman JP. Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 2000; 50:1861–1868 [View Article]
    [Google Scholar]
  28. Dong XZ, Cai MY. (editors) Chapter 14. Determination of biochemical characteristics. Manual for the Systematic Identification of General Bacteria Beijing: Science Press; 2001
    [Google Scholar]
  29. Bernardet J-F, Nakagawa Y, Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes 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]
    [Google Scholar]
  30. Reddy GSN, Garcia-Pichel F. Description of Hymenobacter arizonensis sp. nov. from the southwestern arid lands of the United States of America. Antonie van Leeuwenhoek 2013; 103:321–330 [View Article]
    [Google Scholar]
  31. Klassen JL, Foght JM. Differences in carotenoid composition among Hymenobacter and related strains support a tree-like model of carotenoid evolution. Appl Environ Microbiol 2008; 74:2016–2022 [View Article]
    [Google Scholar]
  32. CLSI Performance Standards for Antimicrobial Susceptibility Testing. , Twenty-Second Informational Supplement. 2012
  33. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
    [Google Scholar]
  34. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
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