sp. nov. and sp. nov. isolated from soil and tree bark, respectively Free

Abstract

Two novel strains (HMF3257 and HMF4905), isolated from freshwater and bark samples, were investigated to determine their relationships within and between species of the genus by using a polyphasic approach. They were aerobic, Gram-stain-negative, non-motile and rod-shaped bacteria. The major fatty acids (>10%) in both strains were identified as summed feature 3 (C 7 and/or C 6) and C 5, while strains HMF3257 and HMF4905 contained a moderately high amount of C and iso-C, respectively. The predominant respiratory quinone was MK-7 for both strains. In addition to phosphatidylethanolamine and one unidentified glycolipid, the polar lipid profile of strain HMF3257 consisted of three unidentified aminophospholipids, one unidentified aminolipid and two unidentified polar lipids, and that of strain HMF4905 consisted of one unidentified aminophospholipid, two unidentified aminolipids and three unidentified polar lipids. The DNA G+C contents of strains HMF3257 and HMF4905 were 47.2 and 46.4 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains HMF3257 and HMF4905 are closely related to 15J9-8 (97.0 % sequence similarity), while sharing 97.4 % sequence similarity with each other. The average nucleotide identity value between strains HMF3257 and HMF4905 was 81.1 %, and the digital DNA–DNA hybridization value between these two strains was 24.4 %. Based on the above data, strains HMF3257 and HMF4905 represent two novel members within the genus , for which the names sp. nov. and sp. nov. are proposed, respectively. The type strain of is HMF3257 (=KCTC 62463=NBRC 112670) and type strain of is HMF4905 (=KCTC 72779=NBRC 114270).

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2020-09-03
2024-03-29
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References

  1. Migula W. Über ein neues system Der Bakterien, Arbeiten AUS dem Bakteriologischen Institut Der Technischen Hochschule zu Karlsruhe; 1894; 1235–238
  2. Finster KW, Herbert RA, Lomstein BA. Spirosoma spitsbergense sp. nov. and Spirosoma luteum sp. nov., isolated from a high Arctic permafrost soil, and emended description of the genus Spirosoma . Int J Syst Evol Microbiol 2009; 59:839–844 [View Article][PubMed]
    [Google Scholar]
  3. Ahn J-H, Weon H-Y, Kim S-J, Hong S-B, Seok S-J et al. Spirosoma oryzae sp. nov., isolated from rice soil and emended description of the genus Spirosoma . Int J Syst Evol Microbiol 2014; 64:3230–3234 [View Article][PubMed]
    [Google Scholar]
  4. Joo ES, Lee J-J, Cha S, Jheong W, Seo T et al. Spirosoma pulveris sp. nov., a bacterium isolated from a dust sample collected at Chungnam province, South Korea. J Microbiol 2015; 53:750–755 [View Article][PubMed]
    [Google Scholar]
  5. Kim S-J, Ahn J-H, Weon H-Y, Hong S-B, Seok S-J et al. Spirosoma aerophilum sp. nov., isolated from an air sample. Int J Syst Evol Microbiol 2016; 66:2342–2346 [View Article][PubMed]
    [Google Scholar]
  6. Okiria J, Ten LN, Lee J-J, Lee S-Y, Cho Y-J et al. Spirosoma litoris sp. nov., a bacterium isolated from beach soil. Int J Syst Evol Microbiol 2017; 67:4986–4991 [View Article][PubMed]
    [Google Scholar]
  7. Kim D-U, Lee H, Lee S, Park S, Yoon J-H et al. Spirosoma metallilatum sp. nov., isolated from an automotive air conditioning system. Int J Syst Evol Microbiol 2018; 68:523–528 [View Article][PubMed]
    [Google Scholar]
  8. Li W, Lee SY, Kang IK, Ten LN, Jung HY. Spirosoma pomorum sp. nov., isolated from apple orchard soil. J Microbiol 2018; 56:90–96 [View Article][PubMed]
    [Google Scholar]
  9. Kim MK, Back C-G, Jung H-Y, Srinivasan S. Complete genome sequence of Spirosoma radiotolerans, a gamma-radiation-resistant bacterium isolated from rice field in South Korea. J Biotechnol 2015; 208:11–12 [View Article][PubMed]
    [Google Scholar]
  10. Kim MK, Kim J-Y, Kim SJ, Kim MJ, Lee JY et al. Complete genome sequence of Spirosoma pulveris JSH 5-14T, a bacterium isolated from a dust sample. Mol Cell Toxicol 2017; 13:373–378 [View Article]
    [Google Scholar]
  11. Hucker GJ. A new modification and application of the Gram stain. J Bacteriol 1921; 6:395–397 [View Article][PubMed]
    [Google Scholar]
  12. Brown AE. Benson's Microbiological Application Laboratory Manual in General Microbiology, 10th ed. New York: McGraw-Hill; 2007
    [Google Scholar]
  13. Bernardet JF, 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
    [Google Scholar]
  14. CLSI Performance standards for antimicrobial disk susceptibility testing: approved standard. CLSI document M02-A11, 11th ed. PA: Clinical and Laboratory Standards Institute; 2012
    [Google Scholar]
  15. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  16. 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]
  17. Collins MD. Analysis of isoprenoid quinones. In Gottschalk G. editor Methods in Microbiology 18 New York: Acad. Press; 1985 pp 329–366
    [Google Scholar]
  18. Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013; 10:563–569 [View Article][PubMed]
    [Google Scholar]
  19. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article][PubMed]
    [Google Scholar]
  20. 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][PubMed]
    [Google Scholar]
  21. 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 [View Article][PubMed]
    [Google Scholar]
  22. 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]
  23. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  24. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article][PubMed]
    [Google Scholar]
  25. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991 pp 125–175
    [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; 67:1613–1617 [View Article][PubMed]
    [Google Scholar]
  27. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28:1823–1829 [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 Zool 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. Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HN. editor Mammalian Protein Metabolism New York: Academic Press; 1969 pp 21–132
    [Google Scholar]
  33. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  34. Kim M, Oh H-S, Park S-C, 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 [View Article][PubMed]
    [Google Scholar]
  35. Okiria J, Ten LN, Park S-J, Lee S-Y, Lee DH et al. Spirosoma migulaei sp. nov., isolated from soil. J Microbiol 2017; 55:927–932 [View Article][PubMed]
    [Google Scholar]
  36. Lail K, Sikorski J, Saunders E, Lapidus A, Glavina Del Rio T et al. Complete genome sequence of Spirosoma linguale type strain (1T). Stand Genomic Sci 2010; 2:176–184 [View Article][PubMed]
    [Google Scholar]
  37. Fries J, Pfeiffer S, Kuffner M, Sessitsch A. Spirosoma endophyticum sp. nov., isolated from Zn- and Cd-accumulating Salix caprea. Int J Syst Evol Microbiol 2013; 63:4586–4590 [View Article][PubMed]
    [Google Scholar]
  38. Montero-Calasanz MdelC, Göker M, Rohde M, Spröer C, Schumann P et al. Chryseobacterium oleae sp. nov., an efficient plant growth promoting bacterium in the rooting induction of olive tree (Olea europaea L.) cuttings and emended descriptions of the genus Chryseobacterium, C. daecheongense, C. gambrini, C. gleum, C. joostei, C. jejuense, C. luteum, C. shigense, C. taiwanense, C. ureilyticum and C. vrystaatense . Syst Appl Microbiol 2014; 37:342–350 [View Article][PubMed]
    [Google Scholar]
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