1887

Abstract

A Gram-stain-negative, aerobic, light-pink, short rod-shaped, non-spore-forming bacterial strain was isolated from biological soil crust sampled in the Hopq Desert, Inner Mongolia, China, designated MIMBbqt21. The G+C content of the genomic DNA was 55.1 mol%. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain MIMBbqt21 belonged to the genus Hymenobacter and had the highest sequence similarity to Hymenobacter cavernae K1E01-27 (94.35 %). Cell growth could be observed at 4–29 °C (optimum, 24 °C), pH of 6.0–8.6 (optimum, 6.0) and in the presence of 1 % (w/v) NaCl (optimum, 0 %). The major fatty acids of strain MIMBbqt21 were iso-C15 : 0, C16 : 1 ω5c and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c). The main polar lipids were phosphatidylethanolamine, five unidentified aminophospholipids, an unidentified glycolipid and four unidentified polar lipids. The sole respiratory quinone was menaquinone MK-7. Based on the results of the phylogenetic, chemotaxonomic and phenotypic studies, strain MIMBbqt21 could be distinguished from all known Hymenobacter species and represents a novel species, for which the name Hymenobacter crusticola sp. nov. is proposed. The type strain is MIMBbqt21 (=MCCC 1K01312=KCTC 42804).

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2018-12-21
2019-10-18
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References

  1. 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 [CrossRef][PubMed]
    [Google Scholar]
  2. Buczolits S, Denner EB, Kämpfer P, Busse HJ. 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 [CrossRef][PubMed]
    [Google Scholar]
  3. Han L, Wu SJ, Qin CY, Zhu YH, Lu ZQ 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 [CrossRef][PubMed]
    [Google Scholar]
  4. Rickard AH, Stead AT, O'May GA, Lindsay S, Banner M et al. Adhaeribacter aquaticus gen. nov., sp. nov., a Gram-negative isolate from a potable water biofilm. Int J Syst Evol Microbiol 2005;55:821–829 [CrossRef][PubMed]
    [Google Scholar]
  5. Kang JY, Chun J, Jahng KY. Nibribacter koreensis gen. nov., sp. nov., isolated from estuarine water. Int J Syst Evol Microbiol 2013;63:4663–4668 [CrossRef][PubMed]
    [Google Scholar]
  6. Nedashkovskaya OI, Kim SB, Suzuki M, Shevchenko LS, Lee MS et al. Pontibacter actiniarum gen. nov., sp. nov., a novel member of the phylum 'Bacteroidetes', and proposal of Reichenbachiella gen. nov. as a replacement for the illegitimate prokaryotic generic name Reichenbachia Nedashkovskaya et al. 2003. Int J Syst Evol Microbiol 2005;55:2583–2588 [CrossRef][PubMed]
    [Google Scholar]
  7. Abaydulla G, Luo X, Shi J, Peng F, Liu M et al. Rufibacter tibetensis gen. nov., sp. nov., a novel member of the family cytophagaceae isolated from soil. Antonie van Leeuwenhoek 2012;101:725–731 [CrossRef][PubMed]
    [Google Scholar]
  8. 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 [CrossRef][PubMed]
    [Google Scholar]
  9. Zhu HZ, Yang L, Muhadesi JB, Wang BJ, Liu SJ. Hymenobacter cavernae sp. nov., isolated from a karst cave. Int J Syst Evol Microbiol 2017;67:4825–4829 [CrossRef][PubMed]
    [Google Scholar]
  10. Reddy GS, 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 [CrossRef][PubMed]
    [Google Scholar]
  11. Parte AC. LPSN—list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 2014;42:D613–D616 [CrossRef][PubMed]
    [Google Scholar]
  12. Belnap J, Weber B BB. Biological soil crusts as an organizing principle in drylands. In Weber B, Belnap J. (editors) Biological Soil Crusts: An Organizing Principle in Drylands Switzerland: Springer, Cham; 2017; pp.3–13
    [Google Scholar]
  13. Liu L, Liu Y, Hui R, Xie M. Recovery of microbial community structure of biological soil crusts in successional stages of Shapotou desert revegetation, northwest China. Soil Biology and Biochemistry 2017;107:125–128 [CrossRef]
    [Google Scholar]
  14. Bates ST, Nash TH, Sweat KG, Garcia-Pichel F. Fungal communities of lichen-dominated biological soil crusts: Diversity, relative microbial biomass, and their relationship to disturbance and crust cover. J Arid Environ 2010;74:1192–1199 [CrossRef]
    [Google Scholar]
  15. Xu JL, Liu QM, Yu HS, Jin FX, Lee ST et al. Hymenobacter daecheongensis sp. nov., isolated from stream sediment. Int J Syst Evol Microbiol 2009;59:1183–1187 [CrossRef][PubMed]
    [Google Scholar]
  16. Klassen JL, Foght JM. Characterization of Hymenobacter isolates from Victoria Upper Glacier, Antarctica reveals five new species and substantial non-vertical evolution within this genus. Extremophiles 2011;15:45–57 [CrossRef][PubMed]
    [Google Scholar]
  17. Du H, Jiao N, Hu Y, Zeng Y. Diversity and distribution of pigmented heterotrophic bacteria in marine environments. FEMS Microbiol Ecol 2006;57:92–105 [CrossRef][PubMed]
    [Google Scholar]
  18. Swindell SR. Sequence Data Analysis Guidebook New York: Humana Press; 1997; pp.75–89
    [Google Scholar]
  19. Yoon SH, Ha SM, 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 [CrossRef][PubMed]
    [Google Scholar]
  20. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004;32:1792–1797 [CrossRef][PubMed]
    [Google Scholar]
  21. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for Bigger Datasets. Mol Biol Evol 2016;33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  22. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215:403–410 [CrossRef][PubMed]
    [Google Scholar]
  23. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  24. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  25. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20:406–416 [CrossRef]
    [Google Scholar]
  26. 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 [CrossRef][PubMed]
    [Google Scholar]
  27. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  28. Du Y, Yuan B, Zeng Y, Meng J, Li H et al. Draft genome sequence of the cellulolytic bacterium Clavibacter sp. CF11, a Strain Producing Cold-Active Cellulase. Genome Announc 2015;3:e01304e01314 [CrossRef][PubMed]
    [Google Scholar]
  29. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982;44:992–993[PubMed]
    [Google Scholar]
  30. Wolfe AJ, Berg HC. Migration of bacteria in semisolid agar. Proc Natl Acad Sci USA 1989;86:6973–6977 [CrossRef][PubMed]
    [Google Scholar]
  31. Dong X, Cai M. Determinative Manual for Routine Bacteriology Beijing: Scientific Press (English translation); 2001
    [Google Scholar]
  32. Sedláček I, Králová S, Kýrová K, Mašlaňová I, Busse HJ et al. Red-pink pigmented Hymenobacter coccineus sp. nov., Hymenobacter lapidarius sp. nov. and Hymenobacter glacialis sp. nov., isolated from rocks in Antarctica. Int J Syst Evol Microbiol 2017;67:1975–1983 [CrossRef][PubMed]
    [Google Scholar]
  33. Bauer AW, Kirby WM, Sherris JC, Turck M. Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 1966;45:493–496 [CrossRef][PubMed]
    [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]
  35. Liu Q, Xamxidin M, Sun C, Cheng H, Meng FX et al. Marinobacter fuscus sp. nov., a marine bacterium of Gammaproteobacteria isolated from surface seawater. Int J Syst Evol Microbiol 2018;68:3156–3162 [CrossRef][PubMed]
    [Google Scholar]
  36. Komagata K, Suzuki K. Lipids and cell-wall analysis in bacterial systematics. Methods Microbiol 1987;19:161–207
    [Google Scholar]
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