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Abstract

A novel actinobacterium, strain K3-2, was isolated in pure culture from a thawing ancient ice wedge at Mammoth Mountain (Eastern Siberia, Russia). Colonies of strain K3-2 were yellowish orange; cells had the fine structure typical of Gram-positive bacteria, were non-motile short rods and were non-spore-forming. Strain K3-2 was mesophilic (optimum growth at 28 °С), but capable of growing at 4 °С. The cell-wall peptidoglycan of strain K3-2 contained lysine (the diagnostic diamino acid), glutamic acid, alanine, ornithine, glycine and serine. The polar lipids were phosphatidylglycerol, lysophosphatidylserine, three unidentified phospholipids and glycolipids. The major fatty acids were anteiso-C and C. The only menaquinone detected was MK-8(H). 16S rRNA gene analysis indicated that strain K3-2 belongs to the genus . The closest taxonomically described relatives were Kis4-28 and PS-14-7, with 97.20 and 97.20 % 16 s rRNA gene sequence similarity, respectively. The average nucleotide identity value of the whole genome sequence between strain K3-2 and Kis4-28 was 78.9 %. DNA–DNA relatedness values between strain K3-2 and DSM 21801 (=Kis4-28) and VKPM Ac 2044 (=PS-14-7) were 41 and 47 %. Thus, strain K3-2 represents a novel species of the genus for which the name sp. nov. is proposed. The type strain is K3-2 (DSM 103859=VKM Ас−2719).

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2019-11-15
2020-12-04
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References

  1. Hamada M, Iino T, Tamura T, Iwami T, Harayama S et al. Serinibacter salmoneus gen. nov., sp. nov., an actinobacterium isolated from the intestinal tract of a fish, and emended descriptions of the families Beutenbergiaceae and Bogoriellaceae . Int J Syst Evol Microbiol 2009; 59:2809–2814 [CrossRef]
    [Google Scholar]
  2. Hamada M, Shibata C, Nurkanto A, Ratnakomala S, Lisdiyanti P et al. Serinibacter tropicus sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove, and emended description of the genus Serinibacter . Int J Syst Evol Microbiol 2015; 65:1151–1154 [CrossRef]
    [Google Scholar]
  3. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics New York: John Wiley & Sons; 1991 pp 115–175
    [Google Scholar]
  4. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symposium Series 1999; 41:95–98
    [Google Scholar]
  5. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef]
    [Google Scholar]
  6. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef]
    [Google Scholar]
  7. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [CrossRef]
    [Google Scholar]
  8. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [CrossRef]
    [Google Scholar]
  9. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef]
    [Google Scholar]
  10. Wilson K. Preparation of genomic DNA from bacteria. Curr Protoc Mol Biol 2001; 56:2.4.1–2.4.2 [CrossRef]
    [Google Scholar]
  11. 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 [CrossRef]
    [Google Scholar]
  12. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The seed and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [CrossRef]
    [Google Scholar]
  13. Rodriguez-R LM. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 2016:e1900v1
    [Google Scholar]
  14. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [CrossRef]
    [Google Scholar]
  15. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993
    [Google Scholar]
  16. Komagata K, Yamada K, Ogawa H. Taxonomic studies on coryneform bacteria I. division of bacterial cells. J Gen Appl Microbiol 1969; 15:243–259
    [Google Scholar]
  17. Krulwich TA, Pate JL. Ultrastructural explanation for snapping postfission movements in Arthrobacter crystallopoietes . J Bacteriol 1971; 105:408–412
    [Google Scholar]
  18. Zavarzina DG, Tourova TP, Kuznetsov BB, Bonch-Osmolovskaya EA, Slobodkin AI. Thermovenabulum ferriorganovorum gen. nov., sp. nov., a novel thermophilic, anaerobic, endospore-forming bacterium. Int J Syst and Evol Microbiol 2002; 52:1737–1743
    [Google Scholar]
  19. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American society for microbiology; 1994 pp 607–654
    [Google Scholar]
  20. Goodfellow M. Numerical taxonomy of some Nocardioform bacteria. J Gen Microbiol 1971; 69:33–80 [CrossRef]
    [Google Scholar]
  21. Potekhina NV, Streshinskaya GM, Tul’skaya EM, Shashkov AS. Cell wall teichoic acids in the taxonomy and characterization of gram-positive bacteria. In Rainey FA, Oren A. (editors) Methods in Microbiology 38 Elsevier: Academic Press; 2011 pp 131–164
    [Google Scholar]
  22. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477
    [Google Scholar]
  23. Trofimova L, Ksenofontov A, Mkrtchyan G, Graf A, Baratova L et al. Quantification of rat brain amino acids: analysis of the data consistency. Curr Anal Chem 2016; 12:349–356 [CrossRef]
    [Google Scholar]
  24. Nichols BW. Separation of the lipids of photosynthetic tissues: improvements in analysis by thin-layer chromatography. Biochim Biophys Acta 1963; 70:417–422 [CrossRef]
    [Google Scholar]
  25. Benning C, Huang ZH, Gage DA. Accumulation of a novel glycolipid and a betaine lipid in cells of Rhodobacter sphaeroides grown under phosphate limitation. Arch Biochem Biophys 1995; 317:103–111 [CrossRef]
    [Google Scholar]
  26. Kates M. Techniques of lipidology: Isolation, analysis and identification of lipids. In Work TS, Work E. (editors) Laboratory Techniques in Biochemistry and Molecular Biology Amsterdam: North-Holland Publishing Company; 1972 pp 267–610
    [Google Scholar]
  27. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316–354
    [Google Scholar]
  28. Collins MD. Analysis of isoprenoid quinones. Meth Microbiol 1985; 18:329–366
    [Google Scholar]
  29. Ley JD, Cattoir H, Reynaerts A. The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 1970; 12:133–142 [CrossRef]
    [Google Scholar]
  30. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961; 3:208–IN1 [CrossRef]
    [Google Scholar]
  31. 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 [CrossRef]
    [Google Scholar]
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