1887

Abstract

A taxonomic study performed on 17 Gram-stain-negative rod-shaped bacterial strains originating from the Antarctic environment is described. Initial phylogenetic analysis using 16S rRNA gene sequencing differentiated the strains into four groups belonging to the genus Pedobacter but they were separated from all hitherto described Pedobacter species. Group I (n=8) was closest to Pedobacter aquatilis (97.8 % 16S rRNA gene sequence similarity). Group II (n=2) and group III (n=4) were closely related (98.8 % 16S rRNA gene sequence similarity) and had Pedobacter jejuensis as their common nearest neighbour. Group IV (n=3) was distantly delineated from the remaining Pedobacter species. Differentiation of the analysed strains into four clusters was further confirmed by repetitive sequence-based PCR fingerprinting, ribotyping, DNA–DNA hybridization and phenotypic traits. Common to representative strains for the four groups were the presence of major menaquinone MK-7, sym-homospermidine as the major polyamine, phosphatidylethanolamine, two unidentified lipids (L2, L5) and an unidentified aminolipid (AL2) as the major polar lipids, presence of an alkali-stable lipid, and C16:1ω7c/C16:1ω6c (summed feature 3), iso-C15:0 and iso-C 17:0 3-OH as the major fatty acids, which corresponded to characteristics of the genus Pedobacter . The obtained results showed that the strains analysed represent four novel species of the genus Pedobacter , for which the names Pedobacter jamesrossensis sp. nov. (type strain CCM 8689=LMG 29684), Pedobacter lithocola sp. nov. (CCM 8691=LMG 29685), Pedobacter mendelii sp. nov. (CCM 8685=LMG 29688) and Pedobacter petrophilus sp. nov. (CCM 8687=LMG 29686) are proposed.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001749
2017-05-22
2019-09-21
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/5/1499.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001749&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 [CrossRef][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 Planctomycetesvol. 4 New York, USA: Springer; 2010; pp.339–351
    [Google Scholar]
  3. Da X, Jiang F, Chang X, Ren L, Qiu X et al. Pedobacter ardleyensis sp. nov., isolated from soil in Antarctica. Int J Syst Evol Microbiol 2015;65:3841–3846 [CrossRef]
    [Google Scholar]
  4. Qiu X, Qu Z, Jiang F, Ren L, Chang X et al. Pedobacter huanghensis sp. nov. and Pedobacter glacialis sp. nov., isolated from Arctic glacier foreland. Int J Syst Evol Microbiol 2014;64:2431–2436 [CrossRef][PubMed]
    [Google Scholar]
  5. 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 [CrossRef][PubMed]
    [Google Scholar]
  6. Edwards U, Rogall T, Blöcker H, Emde M, Böttger EC. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 1989;17:7843–7853 [CrossRef][PubMed]
    [Google Scholar]
  7. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012;62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  8. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006;8:152–155
    [Google Scholar]
  9. 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][PubMed]
    [Google Scholar]
  10. Švec P, Nováková D, Žáčková L, Kukletová M, Sedláček I. Evaluation of (GTG)5-PCR for rapid identification of Streptococcus mutans. Antonie van Leeuwenhoek 2008;94:573–579 [CrossRef]
    [Google Scholar]
  11. Cleenwerck I, Vandemeulebroecke K, Janssens D, Swings J. Re-examination of the genus Acetobacter, with descriptions of Acetobacter cerevisiae sp. nov. and Acetobacter malorum sp. nov. Int J Syst Evol Microbiol 2002;52:1551–1558 [CrossRef][PubMed]
    [Google Scholar]
  12. Mesbah M, Whitman WB. Measurement of deoxyguanosine/thymidine ratios in complex mixtures by high-performance liquid chromatography for determination of the mole percentage guanine + cytosine of DNA. J Chromatogr A 1989;479:297–306 [CrossRef]
    [Google Scholar]
  13. 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 [CrossRef]
    [Google Scholar]
  14. Goris J, Suzuki K-Ichiro, Vos PD, Nakase T, Kersters K. Evaluation of a microplate DNA–DNA hybridization method compared with the initial renaturation method. Can J Microbiol 1998;44:1148–1153 [CrossRef]
    [Google Scholar]
  15. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Brenner DJ, Grimont PAD 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]
  16. Atlas RM, Snyder JW. Reagents, stains, and media: Bacteriology. In Versalovic J, Carroll KC, Funke G, Jorgensen JH, Landry ML et al. (editors) Manual of Clinical Microbiology, 10th ed.vol. 1 Washington: ASM Press; 2011; pp.272–303
    [Google Scholar]
  17. Hugh R, Leifson E. The taxonomic significance of fermentative versus oxidative metabolism of carbohydrates by various Gram negative bacteria. J Bacteriol 1953;66:24–26[PubMed]
    [Google Scholar]
  18. Christensen WB. Urea decomposition as a means of differentiating Proteus and paracolon cultures from each other and from Salmonella and Shigella types. J Bacteriol 1946;52:461–466[PubMed]
    [Google Scholar]
  19. Brooks K, Sodeman T. A rapid method for determining decarboxylase and dihydrolase activity. J Clin Pathol 1974;27:148–152 [CrossRef][PubMed]
    [Google Scholar]
  20. Barrow GI, Feltham RKA. Cowan and Steel’s Manual for the Identification of Medical Bacteria, 3rd ed. Great Britain: Cambridge University Press; 1993;[CrossRef]
    [Google Scholar]
  21. Páčová Z, Kocur M. New medium for detection of esterase and gelatinase activity. Zb Bakt Hyg 1984;258:69–73
    [Google Scholar]
  22. Kurup VP, Babcock JB. Use of casein, tyrosine, and hypoxanthine in the identification of nonfermentative Gram-negative bacilli. Med Microbiol Immunol 1979;167:71–75 [CrossRef][PubMed]
    [Google Scholar]
  23. Owens JJ. The egg yolk reaction produced by several species of bacteria. J Appl Bacteriol 1974;37:137–148 [CrossRef][PubMed]
    [Google Scholar]
  24. Lowe GH. The rapid detection of lactose fermentation in paracolon organisms by the demonstration of beta-D-galactosidase. J Med Lab Technol 1962;19:21–25[PubMed]
    [Google Scholar]
  25. Oberhofer TR, Rowen JW. Acetamide agar for differentiation of nonfermentative bacteria. Appl Microbiol 1974;28:720–721[PubMed]
    [Google Scholar]
  26. Ewing WH. Enterobacteriaceae. Biochemical Methods for Group Differentation Public Health Service Publication Nono 734 CDC, Atlanta 1960
  27. Bernardet JF, Nakagawa Y, Holmes B.Subcommittee on the taxonomy of Flavobacterium 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]
  28. CLSI . Performance Standards for Antimicrobial Susceptibility Testing; Twenty-Fifth Informational Supplement (M100–s25) Vol. 35, No. 3 2015
    [Google Scholar]
  29. EUCAST 2015; European committee on antimicrobial susceptibility testing. EUCAST clinical breakpoints - bacteria (version 5.0). http://www.eucast.org
  30. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids MIDI Technical Note 101 Newark,DE: Microbial ID, Inc; 1990
    [Google Scholar]
  31. Altenburger P, Kämpfer P, Makristathis A, Lubitz W, Busse HJ. Classification of bacteria isolated from a medieval wall painting. J Biotechnol 1996;47:39–52 [CrossRef]
    [Google Scholar]
  32. Stolz A, Busse HJ, Kämpfer P. Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol 2007;57:572–576 [CrossRef][PubMed]
    [Google Scholar]
  33. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990;66:199–202 [CrossRef]
    [Google Scholar]
  34. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990;13:128–130 [CrossRef]
    [Google Scholar]
  35. Kato M, Muto Y, Tanaka-Bandoh K, Watanabe K, Ueno K. Sphingolipid composition in Bacteroides species. Anaerobe 1995;1:135–139 [CrossRef][PubMed]
    [Google Scholar]
  36. Naka T, Fujiwara N, Yano I, Maeda S, Doe M et al. Structural analysis of sphingophospholipids derived from Sphingobacterium spiritivorum, the type species of genus Sphingobacterium. Biochim Biophys Acta 2003;1635:83–92 [CrossRef][PubMed]
    [Google Scholar]
  37. Busse HJ, Auling G. Polyamine pattern as a chemotaxonomic marker within the proteobacteria. Syst Appl Microbiol 1988;11:1–8 [CrossRef]
    [Google Scholar]
  38. Busse HJ, Bunka S, Hensel A, Lubitz W. Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 1997;47:698–708 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001749
Loading
/content/journal/ijsem/10.1099/ijsem.0.001749
Loading

Data & Media loading...

Supplementary File 1

PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error