Description of gen. nov., sp. nov. and reclassification of three related members of the genus in the genus gen. nov. Free

Abstract

A previously undescribed aerobic, non-sporulating bacterium, strain G1A_585, was isolated from an oligotrophic freshwater lake in Bavaria, Germany. The rod-shaped cells were Gram-stain-negative and non-motile. Based on 16S rRNA gene sequence similarity, strain G1A_585 was a member of the family and shared <95.2 % similarity with type strains of all members of the most closely related genus, . Phyogenetically, the isolate shared a root with strains of three marine species, DSM 16223, DSM 22363 and DSM 22379. The polar lipids of strain G1A_585 were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, sphingoglycolipids, three glycolipids and one unknown lipid. Ubiquinone-10 was the dominant quinone (93.1 %) and ubiquinone-9 (6.5 %) was also detected. The major cellular fatty acids were summed feature 8 (Cω7 and/or Cω6; 38.2 %); Cω7 (33.6 %) and C 2-OH (17.8 %). The major polyamine was spermidine and traces of 1,3-diaminopropane, putrescine and spermine were also detected. The DNA G+C content of strain G1A_585 was 55.7 mol% and the isolate was oxidase- and catalase-positive. Based on the phylogenetic relationship, the low DNA G+C content compared with most other members of the genus and the presence of signature nucleotides in the 16S rRNA gene sequence, a novel species in a new genus and species, gen. nov., sp. nov., is proposed; the type strain of is G1A_585 ( = DSM 25081  = LMG 26646). Because DSM 16223, DSM 22363 and DSM 22379 form a phylogenetic group together with strain G1A_585 that is clearly separated from all other known strains and share signature nucleotides, these three strains are reclassified as members of the proposed novel genus : comb. nov. (type strain SW-151 = DSM 16223 = KCTC 12232), comb. nov. (type strain FR1087 = DSM 22363 = IMSNU 14132 = KCTC 12763 = JCM 14161) and comb. nov. (type strain FR1093 = DSM 22379 = IMSNU 14133 = KCTC 12764 = JCM 14162).

Funding
This study was supported by the:
  • Deutsche Forschungsgemeinschaft (Award OV 20/19-1 and OV 20/17-1)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.043133-0
2013-04-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/63/4/1342.html?itemId=/content/journal/ijsem/10.1099/ijs.0.043133-0&mimeType=html&fmt=ahah

References

  1. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. ( 1997 ). Gapped blast and psi-blast: a new generation of protein database search programs. . Nucleic Acids Res 25, 33893402. [View Article] [PubMed]
    [Google Scholar]
  2. Asker D., Beppu T., Ueda K. (. 2007 ). Sphingomonas jaspsi sp. nov., a novel carotenoid-producing bacterium isolated from Misasa, Tottori, Japan. . Int J Syst Evol Microbiol 57, 14351441. [View Article] [PubMed]
    [Google Scholar]
  3. Balkwill D. L., Frederickson J. K., Romine M. F. (. 2006 ). Sphingomonas and related genera. . Prokaryotes 7, 605629. [View Article]
    [Google Scholar]
  4. Bartscht K., Cypionka H., Overmann J. (. 1999 ). Evaluation of cell activity and of methods for the cultivation of bacteria from a natural lake community. . FEMS Microbiol Ecol 28, 249259. [View Article]
    [Google Scholar]
  5. Basta T., Buerger S., Stolz A. (. 2005 ). Structural and replicative diversity of large plasmids from sphingomonads that degrade polycyclic aromatic compounds and xenobiotics. . Microbiology 151, 20252037. [View Article] [PubMed]
    [Google Scholar]
  6. Bruns A., Cypionka H., Overmann J. (. 2002 ). Cyclic AMP and acyl homoserine lactones increase the cultivation efficiency of heterotrophic bacteria from the central Baltic Sea. . Appl Environ Microbiol 68, 39783987. [View Article] [PubMed]
    [Google Scholar]
  7. Bruns A., Nübel U., Cypionka H., Overmann J. (. 2003 ). Effect of signal compounds and incubation conditions on the culturability of freshwater bacterioplankton. . Appl Environ Microbiol 69, 19801989. [View Article] [PubMed]
    [Google Scholar]
  8. Busse H.-J., Auling G. (. 1988 ). Polyamine patterns as a chemotaxonomic marker within the Proteobacteria . . Syst Appl Microbiol 11, 18. [View Article]
    [Google Scholar]
  9. Busse H.-J., Denner E. B. M., Buczolits S., Salkinoja-Salonen M., Bennasar A., Kämpfer P. (. 2003 ). Sphingomonas aurantiaca sp. nov., Sphingomonas aerolata sp. nov. andSphingomonas faeni sp. nov., air- and dustborne and Antarctic, orange-pigmented, psychrotolerant bacteria, and emended description of the genus Sphingomonas . . Int J Syst Evol Microbiol 53, 12531260. [View Article] [PubMed]
    [Google Scholar]
  10. Cashion P., Holder-Franklin M. A., McCully J., Franklin M. (. 1977 ). A rapid method for the base ratio determination of bacterial DNA. . Anal Biochem 81, 461466. [View Article] [PubMed]
    [Google Scholar]
  11. Chen C., Zheng Q., Wang Y.-N., Yan X.-J., Hao L.-K., Du X., Jiao N. (. 2010 ). Stakelama pacifica gen. nov., sp. nov., a new member of the family Sphingomonadaceae isolated from the Pacific Ocean. . Int J Syst Evol Microbiol 60, 28572861. [View Article] [PubMed]
    [Google Scholar]
  12. Choi J.-H., Kim M.-S., Jung M.-J., Roh S. W., Shin K.-S., Bae J.-W. (. 2010 ). Sphingopyxis soli sp. nov., isolated from landfill soil. . Int J Syst Evol Microbiol 60, 16821686. [View Article] [PubMed]
    [Google Scholar]
  13. Denner E. B. M., Paukner S., Kämpfer P., Moore E. R. B., Abraham W.-R., Busse H.-J., Wanner G., Lubitz W. (. 2001 ). Sphingomonas pituitosa sp. nov., an exopolysaccharide-producing bacterium that secretes an unusual type of sphingan. . Int J Syst Evol Microbiol 51, 827841. [View Article] [PubMed]
    [Google Scholar]
  14. Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. (. 1994 ). Methods for General and Molecular Bacteriology. Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  15. Gich F., Overmann J. (. 2006 ). Sandarakinorhabdus limnophila gen. nov., sp. nov., a novel bacteriochlorophyll a-containing, obligately aerobic bacterium isolated from freshwater lakes. . Int J Syst Evol Microbiol 56, 847854. [View Article] [PubMed]
    [Google Scholar]
  16. Gich F., Schubert K., Bruns A., Hoffelner H., Overmann J. (. 2005 ). Specific detection, isolation, and characterization of selected, previously uncultured members of the freshwater bacterioplankton community. . Appl Environ Microbiol 71, 59085919. [View Article] [PubMed]
    [Google Scholar]
  17. Glöckner F. O., Zaichikov E., Belkova N., Denissova L., Pernthaler J., Pernthaler A., Amann R. (. 2000 ). Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria. . Appl Environ Microbiol 66, 50535065. [View Article] [PubMed]
    [Google Scholar]
  18. Godoy F., Vancanneyt M., Martínez M., Steinbüchel A., Swings J., Rehm B. H. (. 2003 ). Sphingopyxis chilensis sp. nov., a chlorophenol-degrading bacterium that accumulates polyhydroxyalkanoate, and transfer of Sphingomonas alaskensis to Sphingopyxis alaskensis comb. nov.. Int J Syst Evol Microbiol 53, 473477. [View Article] [PubMed]
    [Google Scholar]
  19. Guindon S., Dufayard J. F., Lefort V., Anisimova M., Hordijk W., Gascuel O. (. 2010 ). New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. . Syst Biol 59, 307321. [View Article] [PubMed]
    [Google Scholar]
  20. Jaspers E., Nauhaus K., Cypionka H., Overmann J. (. 2001 ). Multitude and temporal variability of ecological niches as indicated by the diversity of cultivated bacterioplankton. . FEMS Microbiol Ecol 36, 153164. [View Article] [PubMed]
    [Google Scholar]
  21. Jenkins C. L., Andrewes A. G., McQuade T. J., Starr M. P. (. 1979 ). The pigment of Pseudomonas paucimobilis is a carotenoid (nostoxanthin) rather than a brominated aryl-polyene (xanthomonadin). . Curr Microbiol 3, 14. [View Article]
    [Google Scholar]
  22. Jogler M., Siemens H., Chen H., Bunk B., Sikorski J., Overmann J. (. 2011 ). Identification and targeted cultivation of abundant novel freshwater sphingomonads and analysis of their population substructure. . Appl Environ Microbiol 77, 73557364. [View Article] [PubMed]
    [Google Scholar]
  23. Kalnenieks U. (. 2006 ). Physiology of Zymomonas mobilis: some unanswered questions. . Adv Microb Physiol 51, 73117. [View Article] [PubMed]
    [Google Scholar]
  24. Kämpfer P., Arun A. B., Young C.-C., Busse H.-J., Kassmannhuber J., Rossello-Mora R., Geueke B., Rekha P. D., Chen W.-M. (. 2012 ). Proposal of Sphingomicrobium lutaoense gen. nov. sp. nov., isolated from a coastal hot spring. . Int J Syst Evol Microbiol 62, 13261330. [CrossRef]
    [Google Scholar]
  25. Kim M. K., Im W.-T., Ohta H., Lee M., Lee S.-T. (. 2005 ). Sphingopyxis granuli sp. nov., a beta-glucosidase-producing bacterium in the family Sphingomonadaceae in alpha-4 subclass of the Proteobacteria . . J Microbiol 43, 152157.[PubMed]
    [Google Scholar]
  26. Kim M. K., Schubert K., Im W.-T., Kim K.-H., Lee S.-T., Overmann J. (. 2007 ). Sphingomonas kaistensis sp. nov., a novel alphaproteobacterium containing pufLM genes. . Int J Syst Evol Microbiol 57, 15271534. [View Article] [PubMed]
    [Google Scholar]
  27. Kim B.-S., Lim Y. W., Chun J. (. 2008 ). Sphingopyxis marina sp. nov. and Sphingopyxis litoris sp. nov., isolated from seawater. . Int J Syst Evol Microbiol 58, 24152419. [View Article] [PubMed]
    [Google Scholar]
  28. Lane D. J. (. 1991 ). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115175. Edited by Stackebrandt E., Goodfellow M. . Chichester, UK:: Wiley;.
    [Google Scholar]
  29. Lee M., Ten L. N., Lee H.-W., Oh H. W., Im W.-T., Lee S.-T. (. 2008 ). Sphingopyxis ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea. . Int J Syst Evol Microbiol 58, 23422347. [View Article] [PubMed]
    [Google Scholar]
  30. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, Buchner A., Lai T., Steppi S. et al. ( 2004 ). arb: a software environment for sequence data. . Nucleic Acids Res 32, 13631371. [View Article] [PubMed]
    [Google Scholar]
  31. Maruyama T., Park H. D., Ozawa K., Tanaka Y., Sumino T., Hamana K., Hiraishi A., Kato K. (. 2006 ). Sphingosinicella microcystinivorans gen. nov., sp. nov., a microcystin-degrading bacterium. . Int J Syst Evol Microbiol 56, 8589. [View Article] [PubMed]
    [Google Scholar]
  32. Mesbah M., Premachandran U., Whitman W. B. (. 1989 ). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. . Int J Syst Bacteriol 39, 159167. [View Article]
    [Google Scholar]
  33. Reasoner D. J., Geldreich E. E. (. 1985 ). A new medium for the enumeration and subculture of bacteria from potable water. . Appl Environ Microbiol 49, 17.[PubMed]
    [Google Scholar]
  34. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. . Newark, DE:: MIDI Inc;.
    [Google Scholar]
  35. Sharma P., Verma M., Bala K., Nigam A., Lal R. (. 2010 ). Sphingopyxis ummariensis sp. nov., isolated from a hexachlorocyclohexane dump site. . Int J Syst Evol Microbiol 60, 780784. [View Article] [PubMed]
    [Google Scholar]
  36. Sikorski J., Brambilla E., Kroppenstedt R. M., Tindall B. J. (. 2008 ). The temperature-adaptive fatty acid content in Bacillus simplex strains from ‘Evolution Canyon’, Israel. . Microbiology 154, 24162426. [View Article] [PubMed]
    [Google Scholar]
  37. Srinivasan S., Kim M. K., Sathiyaraj G., Veena V., Mahalakshmi M., Kalaiselvi S., Kim Y.-J., Yang D.-C. (. 2010 ). Sphingopyxis panaciterrulae sp. nov., isolated from soil of a ginseng field. . Int J Syst Evol Microbiol 60, 23582363. [View Article] [PubMed]
    [Google Scholar]
  38. Stead D. E., Sellwood J. E., Wilson J., Viney I. (. 1992 ). Evaluation of a commercial microbial identification system based on fatty acid profiles for rapid, accurate identification of plant pathogenic bacteria. . J Appl Bacteriol 72, 315321. [View Article]
    [Google Scholar]
  39. Stolz A., Schmidt-Maag C., Denner E. B. M., Busse H.-J., Egli T., Kämpfer P. (. 2000 ). Description of Sphingomonas xenophaga sp. nov. for strains BN6T and N, N which degrade xenobiotic aromatic compounds. . Int J Syst Evol Microbiol 50, 3541. [View Article] [PubMed]
    [Google Scholar]
  40. Stolz A., Busse H.-J., Kämpfer P. (. 2007 ). Pseudomonas knackmussii sp. nov.. Int J Syst Evol Microbiol 57, 572576. [View Article] [PubMed]
    [Google Scholar]
  41. Takeuchi M., Kawai F., Shimada Y., Yokota A. (. 1993 ). Taxonomic study of polyethylene glycol-utilizing bacteria: emended description of the genus Sphingomonas and new descriptions of Sphingomonas macrogoltabidus sp. nov., Sphingomonas sanguis sp. nov. and Sphingomonas terrae sp. nov.. Syst Appl Microbiol 16, 227238. [View Article]
    [Google Scholar]
  42. Takeuchi M., Hamana K., Hiraishi A. (. 2001 ). Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. . Int J Syst Evol Microbiol 51, 14051417.[PubMed]
    [Google Scholar]
  43. Tamaoka J., Komagata K. (. 1984 ). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. . FEMS Microbiol Lett 25, 125128. [View Article]
    [Google Scholar]
  44. Tindall B. J. (. 1990a ). Lipid composition of Halobacterium lacusprofundi . . FEMS Microbiol Lett 66, 199202. [View Article]
    [Google Scholar]
  45. Tindall B. J. (. 1990b ). A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. . Syst Appl Microbiol 13, 128130. [View Article]
    [Google Scholar]
  46. Vancanneyt M., Schut F., Snauwaert C., Goris J., Swings J., Gottschal J. C. (. 2001 ). Sphingomonas alaskensis sp. nov., a dominant bacterium from a marine oligotrophic environment. . Int J Syst Evol Microbiol 51, 7379.[PubMed]
    [Google Scholar]
  47. Wittich R. M., Wilkes H., Sinnwell V., Francke W., Fortnagel P. (. 1992 ). Metabolism of dibenzo-p-dioxin by Sphingomonas sp. strain RW1. . Appl Environ Microbiol 58, 10051010.[PubMed]
    [Google Scholar]
  48. Yabuuchi E., Yano I., Oyaizu H., Hashimoto Y., Ezaki T., Yamamoto H. (. 1990 ). Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas . . Microbiol Immunol 34, 99119.[PubMed] [CrossRef]
    [Google Scholar]
  49. Yoon J.-H., Oh T.-K. (. 2005 ). Sphingopyxis flavimaris sp. nov., isolated from sea water of the Yellow Sea in Korea. . Int J Syst Evol Microbiol 55, 369373. [View Article] [PubMed]
    [Google Scholar]
  50. Yoon J.-H., Lee C.-H., Yeo S.-H., Oh T.-K. (. 2005 ). Sphingopyxis baekryungensis sp. nov., an orange-pigmented bacterium isolated from sea water of the Yellow Sea in Korea. . Int J Syst Evol Microbiol 55, 12231227. [View Article] [PubMed]
    [Google Scholar]
  51. Yurkov V., Stackebrandt E., Buss O., Vermeglio A., Gorlenko V., Beatty J. T. (. 1997 ). Reorganization of the genus Erythromicrobium: description of ‘Erythromicrobium sibiricum’ as Sandaracinobacter sibiricus gen. nov., sp. nov., and of ‘Erythromicrobium ursincola’ as Erythromonas ursincola gen. nov., sp. nov.. Int J Syst Bacteriol 47, 11721178. [View Article] [PubMed]
    [Google Scholar]
  52. Zhang D.-C., Liu H.-C., Xin Y.-H., Zhou Y.-G., Schinner F., Margesin R. (. 2010 ). Sphingopyxis bauzanensis sp. nov., a psychrophilic bacterium isolated from soil. . Int J Syst Evol Microbiol 60, 26182622. [View Article] [PubMed]
    [Google Scholar]
  53. Zwart G., Crump B. C., Kamst-Van Agterveld M. P., Hagen F., Han S. (. 2002 ). Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. . Aquat Microb Ecol 28, 141155. [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.043133-0
Loading
/content/journal/ijsem/10.1099/ijs.0.043133-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed