1887

Abstract

A group of rod-shaped, aerobic, Gram-stain-negative, gliding bacteria producing flexirubin-type pigment was isolated from environmental samples collected in Antarctica in 2009–2014. Phylogenetic analysis of the almost complete 16S rRNA gene sequences revealed two separated branches belonging to the genus Flavobacterium . Group I (n=8), represented by strain CCM 8826, shared the highest sequence similarity to Flavobacterium collinsii 983-08 (98.8 %) and Flavobacterium saccharophilum DSM 1811 (98.4 %), and group II (n=4) represented by strain CCM 8827 shared the highest similarity to Flavobacterium aquidurense WB 1.1-56 (99.6 %). High genetic homogeneity of both groups, separation from each other and from phylogenetically close Flavobacterium species was verified by the rep-PCR fingerprinting method. DNA–DNA hybridization confirmed low genomic relatedness between strain CCM 8826 and F. collinsii 983-08 and F. saccharophilum DSM 1811 (18 and 28 %, respectively) and between strain CCM 8827 and F. aquidurense WB 1.1-56 (27 %). Chemotaxonomic analyses of strains CCM 8826 and CCM 8827 revealed the respiratory quinone to be MK-6, the major identified polar lipid was phosphatidylethanolamine and the predominant polyamine was sym-homospermidine. The common major fatty acids were C15 : 0 iso, C17 : 0 iso 3OH, C15 : 1 iso G, Summed Feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), C15 : 0 iso 3OH and additionally, C15 : 0 anteiso among group II members. All analyses confirmed that strains of group I and II represent two novel species of the genus Flavobacterium , for which the names Flavobacterium chryseum sp. nov. (type strain CCM 8826=P3160=LMG 30615) and Flavobacterium psychroterrae sp. nov. (type strain CCM 8827=P3922=LMG 30616) are proposed.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002952
2018-08-10
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/10/3132.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002952&mimeType=html&fmt=ahah

References

  1. Bergey DH, Harrison FC, Breed RS, Hammer BW, Huntoon FM et al. (editors) Bergey’s Manual of Determinative Bacteriology Baltimore: Williams & Wilkins; 1923
    [Google Scholar]
  2. Kuo I, Saw J, Kapan DD, Christensen S, Kaneshiro KY et al. Flavobacterium akiainvivens sp. nov., from decaying wood of Wikstroemia oahuensis, Hawai'i, and emended description of the genus Flavobacterium. Int J Syst Evol Microbiol 2013; 63:3280–3286 [View Article][PubMed]
    [Google Scholar]
  3. Bernardet JF, Bowman JP. Flavobacterium. In Bergey’s Manual of Systematics of Archaea and Bacteria John Wiley & Sons, Ltd; 2015
    [Google Scholar]
  4. Yoon JH, Kang SJ, Oh TK. Flavobacterium soli sp. nov., isolated from soil. Int J Syst Evol Microbiol 2006; 56:997–1000 [View Article][PubMed]
    [Google Scholar]
  5. Zhang G, Xian W, Chu Q, Yang J, Liu W et al. Flavobacterium terriphilum sp. nov., isolated from soil. Int J Syst Evol Microbiol 2016; 66:4276–4281 [View Article][PubMed]
    [Google Scholar]
  6. Dong K, Chen F, Du Y, Wang G. Flavobacterium enshiense sp. nov., isolated from soil, and emended descriptions of the genus Flavobacterium and Flavobacterium cauense, Flavobacterium saliperosum and Flavobacterium suncheonense. Int J Syst Evol Microbiol 2013; 63:886–892 [View Article][PubMed]
    [Google Scholar]
  7. Ao L, Zeng XC, Nie Y, Mu Y, Zhou L et al. Flavobacterium arsenatis sp. nov., a novel arsenic-resistant bacterium from high-arsenic sediment. Int J Syst Evol Microbiol 2014; 64:3369–3374 [View Article][PubMed]
    [Google Scholar]
  8. Chen WM, Chen YL, Sheu SY. Flavobacterium brevivitae sp. nov., isolated from river water. Int J Syst Evol Microbiol 2016; 66:1705–1712 [View Article][PubMed]
    [Google Scholar]
  9. Li DD, Liu C, Zhang YQ, Wang XJ, Wang N et al. Flavobacterium arcticum sp. nov., isolated from Arctic seawater. Int J Syst Evol Microbiol 2017; 67:1070–1074 [View Article][PubMed]
    [Google Scholar]
  10. Yi H, Oh HM, Lee JH, Kim SJ, Chun J. Flavobacterium antarcticum sp. nov., a novel psychrotolerant bacterium isolated from the Antarctic. Int J Syst Evol Microbiol 2005; 55:637–641 [View Article][PubMed]
    [Google Scholar]
  11. Yi H, Chun J. Flavobacterium weaverense sp. nov. and Flavobacterium segetis sp. nov., novel psychrophiles isolated from the Antarctic. Int J Syst Evol Microbiol 2006; 56:1239–1244 [View Article][PubMed]
    [Google Scholar]
  12. Humphry DR, George A, Black GW, Cummings SP. Flavobacterium frigidarium sp. nov., an aerobic, psychrophilic, xylanolytic and laminarinolytic bacterium from Antarctica. Int J Syst Evol Microbiol 2001; 51:1235–1243 [View Article][PubMed]
    [Google Scholar]
  13. Van Trappen S, Vandecandelaere I, Mergaert J, Swings J. Flavobacterium degerlachei sp. nov., Flavobacterium frigoris sp. nov. and Flavobacterium micromati sp. nov., novel psychrophilic bacteria isolated from microbial mats in Antarctic lakes. Int J Syst Evol Microbiol 2004; 54:85–92 [View Article][PubMed]
    [Google Scholar]
  14. Kim JH, Choi BH, Jo M, Kim SC, Lee PC. Flavobacterium faecale sp. nov., an agarase-producing species isolated from stools of Antarctic penguins. Int J Syst Evol Microbiol 2014; 64:2884–2890 [View Article][PubMed]
    [Google Scholar]
  15. Bernardet J-F, Segers P, Vancanneyt M, Berthe F, Kersters K et al. Cutting a Gordian Knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (Basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 1996; 46:128–148 [View Article]
    [Google Scholar]
  16. Touchon M, Barbier P, Bernardet JF, Loux V, Vacherie B et al. Complete genome sequence of the fish pathogen Flavobacterium branchiophilum. Appl Environ Microbiol 2011; 77:7656–7662 [View Article][PubMed]
    [Google Scholar]
  17. Kavan J, Ondruch J, Nývlt D, Hrbáček F, Carrivick JL et al. Seasonal hydrological and suspended sediment transport dynamics in proglacial streams, James Ross Island, Antarctica. Geogr Ann Ser Phys Geogr 2017; 99:38–55 [View Article]
    [Google Scholar]
  18. Nedbalová L, Nývlt D, Kopáček J, Šobr M, Elster J. Freshwater lakes of Ulu Peninsula, James Ross Island, north-east Antarctic Peninsula: origin, geomorphology and physical and chemical limnology. Antarct Sci 2013; 25:358–372 [View Article]
    [Google Scholar]
  19. Kopalová K, Nedbalová L, Nývlt D, Elster J, van de Vijver B. Diversity, ecology and biogeography of the freshwater diatom communities from Ulu Peninsula (James Ross Island, NE Antarctic Peninsula). Polar Biol 2013; 36:933–948 [View Article]
    [Google Scholar]
  20. 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 [View Article][PubMed]
    [Google Scholar]
  21. Huang X, Madan A. CAP3: A DNA sequence assembly program. Genome Res 1999; 9:868–877 [View Article][PubMed]
    [Google Scholar]
  22. 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 [View Article][PubMed]
    [Google Scholar]
  23. 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]
  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 [View Article][PubMed]
    [Google Scholar]
  25. Romanenko LA, Tanaka N, Svetashev VI, Kurilenko VV, Mikhailov VV. Flavobacterium maris sp. nov. isolated from shallow sediments of the Sea of Japan. Arch Microbiol 2015; 197:941–947 [View Article][PubMed]
    [Google Scholar]
  26. Svec P, Nováková D, Zácková L, Kukletová M, Sedlácek I. Evaluation of (GTG)5-PCR for rapid identification of Streptococcus mutans. Antonie van Leeuwenhoek 2008; 94:573–579 [View Article][PubMed]
    [Google Scholar]
  27. 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 [View Article][PubMed]
    [Google Scholar]
  28. 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]
  29. Goris J, Suzuki KI, 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 [View Article]
    [Google Scholar]
  30. 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]
  31. 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 [View Article][PubMed]
    [Google Scholar]
  32. Atlas RM. Handbook of Microbiological Media, 4th ed. Washington, DC: ASM Press; 2010
    [Google Scholar]
  33. 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]
  34. 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]
  35. Brooks K, Sodeman T. A rapid method for determining decarboxylase and dihydrolase activity. J Clin Pathol 1974; 27:148–152 [View Article][PubMed]
    [Google Scholar]
  36. Barrow GI, Feltham RKA. (editors) Cowan and Steel’s Manual for the Identification of Medical Bacteria, 3rd ed. Cambridge: Cambridge University Press; 1993
    [Google Scholar]
  37. Pácová Z, Kocur M. New medium for detection of esterase and gelatinase activity. Zentralbl Bakteriol Mikrobiol Hyg A 1984; 258:69–73[PubMed]
    [Google Scholar]
  38. 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 [View Article][PubMed]
    [Google Scholar]
  39. Ali Z, Cousin S, Frühling A, Brambilla E, Schumann P et al. Flavobacterium rivuli sp. nov., Flavobacterium subsaxonicum sp. nov., Flavobacterium swingsii sp. nov. and Flavobacterium reichenbachii sp. nov., isolated from a hard water rivulet. Int J Syst Evol Microbiol 2009; 59:2610–2617 [View Article][PubMed]
    [Google Scholar]
  40. Owens JJ. The egg yolk reaction produced by several species of bacteria. J Appl Bacteriol 1974; 37:137–148 [View Article][PubMed]
    [Google Scholar]
  41. 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]
  42. Oberhofer TR, Rowen JW. Acetamide agar for differentiation of nonfermentative bacteria. Appl Microbiol 1974; 28:720–721[PubMed]
    [Google Scholar]
  43. Ewing WH. Enterobacteriaceae. Biochemical methods for group differentiation U.S. Pub. Health Serv. Pub. No. 734 Washington, DC: U.S. Gov. Printing Office; 1960
    [Google Scholar]
  44. Atlas R, Snyder J. Reagents, stains, and media: bacteriology. Manual of Clinical Microbiology, 11th ed. Washington, DC: ASM Press; 2015
    [Google Scholar]
  45. CLSI Performance Standards for Antimicrobial Susceptibility Testing; Twenty-Fifth Informational Supplement (M100-S25) Wayne, PA: Clinical and Laboratory Standards Institute.; 2015
    [Google Scholar]
  46. Nokhal T-H, Schlegel HG. Taxonomic study of Paracoccus denitrificans. Int J Syst Bacteriol 1983; 33:26–37 [View Article]
    [Google Scholar]
  47. Whitman KA. Finfish and shellfish bacteriology manual: techniques and procedures. Finfish Shellfish Bacteriol Man Tech Proced 2004 www.cabdirect.org/cabdirect/abstract/20043074815 [accessed 1 March 2018]
    [Google Scholar]
  48. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  49. Altenburger P, Kämpfer P, Makristathis A, Lubitz W, Busse H-J. Classification of bacteria isolated from a medieval wall painting. J Biotechnol 1996; 47:39–52 [View Article]
    [Google Scholar]
  50. Busse J, Auling G. Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 1988; 11:1–8 [View Article]
    [Google Scholar]
  51. Stolz A, Busse HJ, Kämpfer P. Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol 2007; 57:572–576 [View Article][PubMed]
    [Google Scholar]
  52. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [View Article]
    [Google Scholar]
  53. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
    [Google Scholar]
  54. Busse H-J, 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 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002952
Loading
/content/journal/ijsem/10.1099/ijsem.0.002952
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
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