1887

Abstract

A facultative anaerobic, rod-shaped, endospore-forming and non-motile bacterium was isolated from permafrost sediment cores in the Kolyma lowland, Siberia, Russia. The permafrost isolate clustered with members of the genus Cohnella on the basis of 16S rRNA gene sequence analysis and showed the highest sequence similarity to Cohnella saccharovorans CJ22 (96.3 %), followed by Cohnella cellulosilytica FCN3-3 (96.0 %) and Cohnella panacarvi KCTC 13060 (96.0 %). The chemotaxonomic characteristics (quinone system, cellular fatty acids and polar lipid profile) of strain 20.16 were consistent with members of the genus Cohnella . The peptidoglycan diaminoacids included meso-diaminopimelic acid and a small amount of ll-diaminopimelic acid. The molar ratio and composition of major amino acids (meso-diaminopimelic acid, alanine, and glutamic acid) correspond to the peptydoglycan type A1γ. The estimated genome size of strain 20.16 is 4.34 Mb (lower than those in other Cohnella species). The genome has a G+C content of 50.5 mol% and encodes 4843 predicted genes, of these 4740 are protein-coding ones. The results of chemotaxonomic, physiological and biochemical characterization allowed clear differentiation of strain 20.16 from the closest Cohnella species. Based on data provided, a new species Cohnella kolymensis sp. nov. is proposed, with 20.16 (=VKM B-2846=DSM 104983) as the type strain.

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2018-07-17
2019-12-15
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References

  1. Kämpfer P, Rosselló-Mora R, Falsen E, Busse HJ, Tindall BJ. Cohnella thermotolerans gen. nov., sp. nov., and classification of 'Paenibacillus hongkongensis' as Cohnella hongkongensis sp. nov. Int J Syst Evol Microbiol 2006;56:781–786 [CrossRef][PubMed]
    [Google Scholar]
  2. Choi JH, Seok JH, Jang HJ, Cha JH, Cha CJ. Cohnella saccharovorans sp. nov., isolated from ginseng soil. Int J Syst Evol Microbiol 2016;66:1713–1717 [CrossRef][PubMed]
    [Google Scholar]
  3. Kämpfer P, Glaeser SP, Busse HJ. Cohnella lubricantis sp. nov., isolated from a coolant lubricant solution. Int J Syst Evol Microbiol 2017;67:466–471 [CrossRef][PubMed]
    [Google Scholar]
  4. Nguyen CP, Lee SS. Cohnella humi sp. nov., isolated from Russian soil. Curr Microbiol 2014;69:525–531 [CrossRef][PubMed]
    [Google Scholar]
  5. Wang LY, Chen SF, Wang L, Zhou YG, Liu HC. Cohnella plantaginis sp. nov., a novel nitrogen-fixing species isolated from plantain rhizosphere soil. Antonie van Leeuwenhoek 2012;102:83–89 [CrossRef][PubMed]
    [Google Scholar]
  6. Wang LY, Wang TS, Chen SF. Cohnella capsici sp. nov., a novel nitrogen-fixing species isolated from Capsicum annuum rhizosphere soil, and emended description of Cohnella plantaginis. Antonie van Leeuwenhoek 2015;107:133–139 [CrossRef][PubMed]
    [Google Scholar]
  7. Jiang F, Dai J, Wang Y, Xue X, Xu M et al. Cohnella arctica sp. nov., isolated from Arctic tundra soil. Int J Syst Evol Microbiol 2012;62:817–821 [CrossRef]
    [Google Scholar]
  8. Zhang T, Barry RG, Knowles K, Heginbottom JA, Brown J. Statistics and characteristics of permafrost and ground‐ice distribution in the Northern Hemisphere. Polar Geogr 1999;23:132–154
    [Google Scholar]
  9. Karlyshev AV, Kudryashova EB, Ariskina EV. Draft genome sequence of "Cohnella kolymensis" B-2846. Genome Announc 2016;4:e01587-15 [CrossRef][PubMed]
    [Google Scholar]
  10. Khlebnikova GM, Gilichinsky DA, Fedorov-Davydov DG, Vorobyeva EA. Quantitative evaluation of microorganisms in permafrost deposits and buried soils. Microbiology 1990;59:106–111
    [Google Scholar]
  11. Gregersen T. Rapid method for distinction of gram-negative from gram-positive bacteria. Eur J Appl Microbiol Biotechnol 1978;5:123–127 [CrossRef]
    [Google Scholar]
  12. Smibert RM, Krieg RN. Phenotypic characterization. In Gerhardt P. (editor) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp.607–654
    [Google Scholar]
  13. Zvyagintsev DG. Methods of Soil Microbiology and Biochemistry, 2nd ed. Moscow: University Press; 1991
    [Google Scholar]
  14. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012;28:1823–1829 [CrossRef][PubMed]
    [Google Scholar]
  15. 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]
  16. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  17. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20:406–416 [CrossRef]
    [Google Scholar]
  18. 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]
  19. 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]
  20. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  21. 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]
  22. Khianngam S, Tanasupawat S, Akaracharanya A, Kim KK, Lee KC et al. Cohnella cellulosilytica sp. nov., isolated from buffalo faeces. Int J Syst Evol Microbiol 2012;62:1921–1925 [CrossRef][PubMed]
    [Google Scholar]
  23. Yoon MH, Ten LN, Im WT. Cohnella panacarvi sp. nov., a xylanolytic bacterium isolated from ginseng cultivating soil. J Microbiol Biotechnol 2007;17:913–918[PubMed]
    [Google Scholar]
  24. 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 [CrossRef][PubMed]
    [Google Scholar]
  25. Cai F, Wang Y, Qi H, Dai J, Yu B et al. Cohnella luojiensis sp. nov., isolated from soil of a Euphrates poplar forest. Int J Syst Evol Microbiol 2010;60:1605–1608 [CrossRef][PubMed]
    [Google Scholar]
  26. Khianngam S, Tanasupawat S, Akaracharanya A, Kim KK, Lee KC et al. Cohnella xylanilytica sp. nov. and Cohnella terrae sp. nov., xylanolytic bacteria from soil. Int J Syst Evol Microbiol 2010;60:2913–2917 [CrossRef][PubMed]
    [Google Scholar]
  27. Jiang F, Dai J, Wang Y, Xue X, Xu M et al. Cohnella arctica sp. nov., isolated from Arctic tundra soil. Int J Syst Evol Microbiol 2012;62:817–821 [CrossRef][PubMed]
    [Google Scholar]
  28. Xie JB, Du Z, Bai L, Tian C, Zhang Y et al. Comparative genomic analysis of N2-fixing and non-N2-fixing Paenibacillus spp.: organization, evolution and expression of the nitrogen fixation genes. PLoS Genet 2014;10:e1004231 [CrossRef][PubMed]
    [Google Scholar]
  29. 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 [CrossRef][PubMed]
    [Google Scholar]
  30. Ash C, Priest FG, Collins MD. Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Antonie van Leeuwenhoek 1993;64:253–260 [CrossRef]
    [Google Scholar]
  31. Dsouza M, Taylor MW, Ryan J, MacKenzie A, Lagutin K et al. Paenibacillus darwinianus sp. nov., isolated from gamma-irradiated Antarctic soil. Int J Syst Evol Microbiol 2014;64:1406–1411 [CrossRef][PubMed]
    [Google Scholar]
  32. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972;36:407–477[PubMed]
    [Google Scholar]
  33. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974;28:226–231[PubMed]
    [Google Scholar]
  34. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981;45:316–354[PubMed]
    [Google Scholar]
  35. 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 [CrossRef]
    [Google Scholar]
  36. Jacin H, Mishkin AR. Separation of carbohydrates on borate-impregnated silica gel g plates. J Chromatogr 1965;18:170–173 [CrossRef][PubMed]
    [Google Scholar]
  37. Dittmer JC, Lester RL. A simple, specific spray for the detection of phospholipids on thin-layer chromatograms. J Lipid Res 1964;5:126–127[PubMed]
    [Google Scholar]
  38. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark: MIDI Inc; 1990
    [Google Scholar]
  39. Härtig C. Rapid identification of fatty acid methyl esters using a multidimensional gas chromatography-mass spectrometry database. J Chromatogr A 2008;1177:159–169 [CrossRef][PubMed]
    [Google Scholar]
  40. García-Fraile P, Velázquez E, Mateos PF, Martínez-Molina E, Rivas R. Cohnella phaseoli sp. nov., isolated from root nodules of Phaseolus coccineus in Spain, and emended description of the genus Cohnella. Int J Syst Evol Microbiol 2008;58:1855–1859 [CrossRef][PubMed]
    [Google Scholar]
  41. Khianngam S, Tanasupawat S, Akaracharanya A, Kim KK, Lee KC et al. Cohnella thailandensis sp. nov., a xylanolytic bacterium from Thai soil. Int J Syst Evol Microbiol 2010;60:2284–2287 [CrossRef][PubMed]
    [Google Scholar]
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