sp. nov., a psychrotolerant bacterium isolated from forest soil Free

Abstract

Strain K-4-11-1, a psychrotolerant, light salmon-coloured, Gram-stain-negative, non-motile and rod-shaped bacterium, was isolated from forest soil of Kyonggi University, Suwon, South Korea. It was able to grow at 0–32 °C, at pH 5.0–10.0 and with 0–1.5 % (w/v) NaCl. This strain was taxonomically characterized by a polyphasic approach. Based on 16S rRNA gene sequence analysis, strain K-4-11-1 belongs to the genus and is closely related to THG-45 (98.75 % sequence similarity), G-1 (98.48 %), DS-57 (98.20 %), PB92 (97.92 %) and 15-52 (97.84 %). The only respiratory quinone was menaquinone-7. The major polar lipids were phosphatidylethanolamine and unidentified glycolipids. The predominant fatty acids of strain K-4-11-1 were summed feature 3 (Cω7 and/or Cω6), iso-C, iso-C 3-OH, anteiso-C and summed feature 9 (iso-Cω9 and/or C 10-methyl). The genomic DNA G+C content of this novel strain was 38.3 mol%. The DNA–DNA relatedness values between strain K-4-11-1 and KACC 14530, KACC 14287, KACC 13766, KACC 13768 and KACC 11317 were 40.0, 36.3, 37.0, 32.3 and 29.7 %, respectively. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this novel strain from its closest phylogenetic neighbours. Thus, strain K-4-11-1 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is K-4-11-1 (=KEMB 9005-574=KACC 19174=JCM 31916).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002428
2017-12-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/12/5120.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002428&mimeType=html&fmt=ahah

References

  1. Steyn PL, Segers P, Vancanneyt M, Sandra P, Kersters K et al. Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. proposal of the family Sphingobacteriaceae fam. nov. Int J Syst Bacteriol 1998; 48:165–177 [View Article][PubMed]
    [Google Scholar]
  2. Margesin R, Shivaji S. Genus II. Pedobacter Steyn, Segers, Vancanneyt, Sandra, Kersters and Joubert 1998, 171VP . In Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ et al. (editors) Bergey’s Manual of Systematic Bacteriology The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes vol. 4 New York: Springer; 2010 pp. 339–351
    [Google Scholar]
  3. Dahal RH, Kim J. Pedobacter humicola sp. nov., a member of the genus Pedobacter isolated from soil. Int J Syst Evol Microbiol 2016; 66:2205–2211 [View Article][PubMed]
    [Google Scholar]
  4. Yang JE, Son HM, Lee JM, Shin HS, Park SY et al. Pedobacter ginsenosidimutans sp. nov., with ginsenoside-converting activity. Int J Syst Evol Microbiol 2013; 63:4396–4401 [View Article][PubMed]
    [Google Scholar]
  5. Gordon NS, Valenzuela A, Adams SM, Ramsey PW, Pollock JL et al. Pedobacter nyackensis sp. nov., Pedobacter alluvionis sp. nov. and Pedobacter borealis sp. nov., isolated from Montana flood-plain sediment and forest soil. Int J Syst Evol Microbiol 2009; 59:1720–1726 [View Article][PubMed]
    [Google Scholar]
  6. Li AH, Liu HC, Zhou YG. Pedobacter alpinus sp. nov., isolated from a plateau lake. Int J Syst Evol Microbiol 2015; 65:3782–3787 [View Article][PubMed]
    [Google Scholar]
  7. Gallego V, García MT, Ventosa A. Pedobacter aquatilis sp. nov., isolated from drinking water, and emended description of the genus Pedobacter . Int J Syst Evol Microbiol 2006; 56:1853–1858 [View Article][PubMed]
    [Google Scholar]
  8. Zhou Z, Jiang F, Wang S, Peng F, Dai J et al. Pedobacter arcticus sp. nov., a facultative psychrophile isolated from Arctic soil, and emended descriptions of the genus Pedobacter, Pedobacter heparinus, Pedobacter daechungensis, Pedobacter terricola, Pedobacter glucosidilyticus and Pedobacter lentus . Int J Syst Evol Microbiol 2012; 62:1963–1969 [View Article][PubMed]
    [Google Scholar]
  9. Vanparys B, Heylen K, Lebbe L, de Vos P. Pedobacter caeni sp. nov., a novel species isolated from a nitrifying inoculum. Int J Syst Evol Microbiol 2005; 55:1315–1318 [View Article][PubMed]
    [Google Scholar]
  10. Lee HG, Kim SG, Im WT, Oh HM, Lee ST. Pedobacter composti sp. nov., isolated from compost. Int J Syst Evol Microbiol 2009; 59:345–349 [View Article][PubMed]
    [Google Scholar]
  11. Margesin R, Spröer C, Schumann P, Schinner F. Pedobacter cryoconitis sp. nov., a facultative psychrophile from alpine glacier cryoconite. Int J Syst Evol Microbiol 2003; 53:1291–1296 [View Article][PubMed]
    [Google Scholar]
  12. Du J, Singh H, Ngo HT, Won KH, Kim KY et al. Pedobacter daejeonensis sp. nov. and Pedobacter trunci sp. nov., isolated from an ancient tree trunk, and emended description of the genus Pedobacter . Int J Syst Evol Microbiol 2015; 65:1241–1246 [View Article][PubMed]
    [Google Scholar]
  13. Luo X, Wang Z, Dai J, Zhang L, Li J et al. Pedobacter glucosidilyticus sp. nov., isolated from dry riverbed soil. Int J Syst Evol Microbiol 2010; 60:229–233 [View Article][PubMed]
    [Google Scholar]
  14. Cho H, Ahn JH, Weon HY, Joa JH, Kwon SW et al. Pedobacter lycopersici sp. nov., isolated from the rhizosphere of tomato plant (Solanum lycopersicum L.). Int J Syst Evol Microbiol 2016; 66:5406–5411 [View Article][PubMed]
    [Google Scholar]
  15. Derichs J, Kämpfer P, Lipski A. Pedobacter nutrimenti sp. nov., isolated from chilled food. Int J Syst Evol Microbiol 2014; 64:1310–1316 [View Article][PubMed]
    [Google Scholar]
  16. Hwang CY, Choi DH, Cho BC. Pedobacter roseus sp. nov., isolated from a hypertrophic pond, and emended description of the genus Pedobacter . Int J Syst Evol Microbiol 2006; 56:1831–1836 [View Article][PubMed]
    [Google Scholar]
  17. Chaudhary DK, Kim J. Novosphingobium naphthae sp. nov., from oil-contaminated soil. Int J Syst Evol Microbiol 2016; 66:3170–3176 [View Article][PubMed]
    [Google Scholar]
  18. Chaudhary DK, Kim J. Chryseobacterium nepalense sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2017; 67:646–652 [View Article][PubMed]
    [Google Scholar]
  19. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961; 3:208–218 [View Article]
    [Google Scholar]
  20. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008; 74:2461–2470 [View Article][PubMed]
    [Google Scholar]
  21. Yoon SH, Sm H, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 2017: (in press)
    [Google Scholar]
  22. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article][PubMed]
    [Google Scholar]
  23. Hall TA. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41:95–98
    [Google Scholar]
  24. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425[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 [View Article]
    [Google Scholar]
  26. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  27. 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 [View Article][PubMed]
    [Google Scholar]
  28. 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 [View Article][PubMed]
    [Google Scholar]
  29. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  30. Yarza P, Richter M, Peplies J, Euzeby J, Amann R et al. The All-Species Living Tree Project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008; 31:241–250 [View Article][PubMed]
    [Google Scholar]
  31. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994; 44:846–849 [View Article]
    [Google Scholar]
  32. Doetsch RN. Determinative methods of light microscopy. In Gerhardt P. (editor) Manual of Methods for General Bacteriology Washington, DC: American Society for Microbiology; 1981 pp. 21–33
    [Google Scholar]
  33. Powers EM. Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol 1995; 61:3756–3758[PubMed]
    [Google Scholar]
  34. Chaudhary DK, Kim J. Arvibacter flaviflagrans gen. nov., sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2016; 66:4347–4354 [View Article][PubMed]
    [Google Scholar]
  35. Breznak JA, Costilow RN. Physicochemical factors in growth. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR et al. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: American Society for Microbiology; 2007 pp. 309–329
    [Google Scholar]
  36. Hemraj V, Diksha S, Avneet G. A review on commonly used biochemical test for bacteria. Innovare J Life Sci 2013; 1:1–7
    [Google Scholar]
  37. Chaudhary DK, Kim J. Sphingomonas naphthae sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2016; 66:4621–4627 [View Article][PubMed]
    [Google Scholar]
  38. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM et al. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: ASM Press; 2007 pp. 330–393
    [Google Scholar]
  39. 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]
  40. Cowan ST, Steel KJ. Manual for the Identification of Medical Bacteria London: Cambridge University Press; 1965
    [Google Scholar]
  41. Reichenbach H. The order Cytophagales . In Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH et al. (editors) The Prokaryotes, 2nd ed. vol. 4 New York: Springer; 1992 pp. 3631–3675 [Crossref]
    [Google Scholar]
  42. Joubert JJ, van Rensburg EJ, Pitout MJ. A plate method for demonstrating the breakdown of heparin and chrondroitin sulphate by bacteria. J Microbiol Methods 1984; 2:197–202 [View Article]
    [Google Scholar]
  43. 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]
  44. Komagata K, Suzuki K. Lipids and cell wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–203 [Crossref]
    [Google Scholar]
  45. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [View Article]
    [Google Scholar]
  46. 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]
  47. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark DE: MIDI Inc; 1990
    [Google Scholar]
  48. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 1989; 39:159–167 [View Article]
    [Google Scholar]
  49. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 1989; 39:224–229 [View Article]
    [Google Scholar]
  50. Švec P, Králová S, Busse HJ, Kleinhagauer T, Pantůček R et al. Pedobacter jamesrossensis sp. nov., Pedobacter lithocola sp. nov., Pedobacter mendelii sp. nov. and Pedobacter petrophilus sp. nov., isolated from the Antarctic environment. Int J Syst Evol Microbiol 2017; 67:1499–1507 [View Article][PubMed]
    [Google Scholar]
  51. 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 [View Article]
    [Google Scholar]
  52. Yoon JH, Kang SJ, Oh TK. Pedobacter terrae sp. nov., isolated from soil. Int J Syst Evol Microbiol 2007; 57:2462–2466 [View Article][PubMed]
    [Google Scholar]
  53. Roh SW, Quan ZX, Nam YD, Chang HW, Kim KH et al. Pedobacter agri sp. nov., from soil. Int J Syst Evol Microbiol 2008; 58:1640–1643 [View Article][PubMed]
    [Google Scholar]
  54. Kwon SW, Kim BY, Lee KH, Jang KY, Seok SJ et al. Pedobacter suwonensis sp. nov., isolated from the rhizosphere of Chinese cabbage (Brassica campestris). Int J Syst Evol Microbiol 2007; 57:480–484 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002428
Loading
/content/journal/ijsem/10.1099/ijsem.0.002428
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited Most Cited RSS feed