1887

Abstract

A Gram-staining-negative, strictly aerobic, yellowish-orange, flexirubin-positive, rod-shaped, non-flagellated, non-spore-forming and non-gliding marine bacterium, designated strain CC-PY-50, was isolated from estuarine water off Pingtung, Taiwan. The strain produced zeaxanthin as a major carotenoid pigment, and showed highest pairwise 16S rRNA gene sequence similarity to T-y7 (93.9 %) followed by KMM 6217 (93.8 %), YCS-16 (93.7 %) and other members of the family (<93.7 %). Strain CC-PY-50 established a distinct phyletic lineage associated with LYYY01 (93.1 % sequence similarity) with poor bootstrap support during neighbour-joining and maximum-likelihood phylogenetic analyses (37 % for each). The polar lipid profile of strain CC-PY-50 was determined to accommodate large numbers of unknown lipids including major amounts of three unidentified aminolipids and two unidentified lipids, and moderate amounts of an unidentified phospholipid, an unidentified glycolipid and an unidentified lipid. In addition, phosphatidylethanolamine was also detected in significant amounts. The major (>5 % of total) fatty acids were iso-C, iso-C G, iso-C 3-OH, C and Cω6 and/or Cω7. The DNA G+C content was 37.1 mol% and menaquinone-6 (MK-6) was the sole respiratory quinone. Based on the phylogenetic evidence and several distinguishing phenotypic and chemotaxonomic features, strain CC-PY-50 is proposed to represent a novel genus and species of the family , for which the name gen. nov., sp. nov. is proposed. The type strain of the type species gen. nov., sp. nov. is CC-PY-50 ( = JCM 19743 = BCRC 80747). Emended descriptions of the species and are also proposed.

Funding
This study was supported by the:
  • Ministry of Education, Taiwan
  • R.O.C.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.066852-0
2015-02-01
2024-04-26
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/65/2/336.html?itemId=/content/journal/ijsem/10.1099/ijs.0.066852-0&mimeType=html&fmt=ahah

References

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. ( 1990 ). Basic local alignment search tool. . J Mol Biol 215, 403410. [View Article] [PubMed]
    [Google Scholar]
  2. Arun A. B., Chen W.-M., Lai W.-A., Chao J. H., Rekha P. D., Shen F.-T., Singh S., Young C.-C. ( 2009a ). Muricauda lutaonensis sp. nov., a moderate thermophile isolated from a coastal hot spring. . Int J Syst Evol Microbiol 59, 27382742. [View Article] [PubMed]
    [Google Scholar]
  3. Arun A. B., Chen W.-M., Lai W.-A., Chou J.-H., Shen F.-T., Rekha P. D., Young C. C. ( 2009b ). Lutaonella thermophila gen. nov., sp. nov., a moderately thermophilic member of the family Flavobacteriaceae isolated from a coastal hot spring. . Int J Syst Evol Microbiol 59, 20692073. [View Article] [PubMed]
    [Google Scholar]
  4. Bauer M., Kube M., Teeling H., Richter M., Lombardot T., Allers E., Würdemann C. A., Quast C., Kuhl H. & other authors ( 2006 ). Whole genome analysis of the marine BacteroidetesGramella forsetii’ reveals adaptations to degradation of polymeric organic matter. . Environ Microbiol 8, 22012213. [View Article] [PubMed]
    [Google Scholar]
  5. Bernardet J.-F., Nakagawa Y. ( 2006 ). An introduction to the family Flavobacteriaceae . . In The Prokaryotes, a Handbook on the Biology of Bacteria, pp. 455480. Edited by Dworkin M., Falkow S., Rosenberg E., Schleifer K. H., Stackebrandt E. . New York:: Springer;.
    [Google Scholar]
  6. Bernardet J.-F., Segers P., Vancanneyt M., Berthe F., Kersters K., Vandamme P. ( 1996 ). 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 46, 128148. [View Article]
    [Google Scholar]
  7. Bernardet J.-F., Nakagawa Y., Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes ( 2002 ). Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. . Int J Syst Evol Microbiol 52, 10491070. [View Article] [PubMed]
    [Google Scholar]
  8. Collins M. D. ( 1985 ). Analysis of isoprenoid quinones. . Methods Microbiol 18, 329366. [View Article]
    [Google Scholar]
  9. Embley T. M., Wait R. ( 1994 ). Structural lipids of eubacteria. . In Chemical Methods in Prokaryotic Systematics, pp. 121161. Edited by Goodfellow M., O’Donnell A. G. . Chichester:: Wiley;.
    [Google Scholar]
  10. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368376. [View Article] [PubMed]
    [Google Scholar]
  11. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783791. [View Article]
    [Google Scholar]
  12. Fitch W. M. ( 1971 ). Towards defining the course of evolution: minimum change for a specific tree topology. . Syst Biol 20, 406416. [View Article]
    [Google Scholar]
  13. Garrity G. M., Holt J. G. ( 2001 ). The road map to the Manual . . In Bergey’s Manual of Systematic Bacteriology, pp. 119166. Edited by Boone D. R., Castenholz R. W., Garrity G. M. . New York:: Springer;. [View Article]
    [Google Scholar]
  14. GCG ( 1995 ). Wisconsin Package Version 8.1 Program Manual. Madison, WI:: Computer Group;.
    [Google Scholar]
  15. Gómez-Consarnau L., González J. M., Coll-Lladó M., Gourdon P., Pascher T., Neutze R., Pedrós-Alió C., Pinhassi J. ( 2007 ). Light stimulates growth of proteorhodopsin-containing marine Flavobacteria . . Nature 445, 210213. [View Article] [PubMed]
    [Google Scholar]
  16. González J. M., Fernández-Gómez B., Fernàndez-Guerra A., Gómez-Consarnau L., Sánchez O., Coll-Lladó M., Del Campo J., Escudero L., Rodríguez-Martínez R. & other authors ( 2008 ). Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria). . Proc Natl Acad Sci U S A 105, 87248729. [View Article] [PubMed]
    [Google Scholar]
  17. Hameed A., Shahina M., Lin S.-Y., Sridhar K. R., Young L.-S., Lee M.-R., Chen W.-M., Chou J.-H., Young C.-C. ( 2012 ). Siansivirga zeaxanthinifaciens gen. nov., sp. nov., a novel zeaxanthin-producing member of the family Flavobacteriaceae isolated from coastal seawater of Taiwan. . FEMS Microbiol Lett 333, 3745. [View Article] [PubMed]
    [Google Scholar]
  18. Hameed A., Shahina M., Lin S.-Y., Cho J.-C., Lai W.-A., Young C.-C. ( 2013 ). Kordia aquimaris sp. nov., a zeaxanthin-producing member of the family Flavobacteriaceae isolated from surface seawater, and emended description of the genus Kordia . . Int J Syst Evol Microbiol 63, 47904796. [View Article] [PubMed]
    [Google Scholar]
  19. Hameed A., Shahina M., Lin S.-Y., Lai W.-A., Hsu Y.-H., Liu Y.-C., Young C.-C. ( 2014a ). Aquibacter zeaxanthinifaciens gen. nov., sp. nov., a zeaxanthin-producing bacterium of the family Flavobacteriaceae isolated from surface seawater, and emended descriptions of the genera Aestuariibaculum and Gaetbulibacter . . Int J Syst Evol Microbiol 64, 138145. [View Article] [PubMed]
    [Google Scholar]
  20. Hameed A., Shahina M., Lin S.-Y., Lai W.-A., Liu Y.-C., Hsu Y.-H., Cheng I.-C., Young C.-C. ( 2014b ). Robertkochia marina gen. nov., sp. nov., of the family Flavobacteriaceae, isolated from surface seawater, and emended descriptions of the genera Joostella and Galbibacter . . Int J Syst Evol Microbiol 64, 533539. [View Article] [PubMed]
    [Google Scholar]
  21. Hameed A., Shahina M., Lin S.-Y., Liu Y.-C., Lai W.-A., Young C.-C. ( 2014 c). Gramella oceani sp. nov., a zeaxanthin-producing bacterium of the family Flavobacteriaceae isolated from marine sediment. . Int J Syst Evol Microbiol 64, 26752681. [View Article] [PubMed]
    [Google Scholar]
  22. Heiner C. R., Hunkapiller K. L., Chen S. M., Glass J. I., Chen E. Y. ( 1998 ). Sequencing multimegabase-template DNA with BigDye terminator chemistry. . Genome Res 8, 557561.[PubMed]
    [Google Scholar]
  23. Jooste P. J. ( 1985 ). The taxonomy and significance of Flavobacterium–Cytophaga strains from daily sources. . PhD thesis , University of the Orange Free State, Bloemfontein, South Africa;.
    [Google Scholar]
  24. Kämpfer P., Kroppenstedt R. M. ( 1996 ). Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. . Can J Microbiol 42, 9891005. [View Article]
    [Google Scholar]
  25. Khan S. T., Nakagawa Y., Harayama S. ( 2007 ). Sediminibacter furfurosus gen. nov., sp. nov. and Gilvibacter sediminis gen. nov., sp. nov., novel members of the family Flavobacteriaceae . . Int J Syst Evol Microbiol 57, 265269. [View Article] [PubMed]
    [Google Scholar]
  26. Kim O.-S., Cho Y.-J., Lee K., Yoon S.-H., Kim M., Na H., Park S.-C., Jeon Y. S., Lee J.-H. & other authors ( 2012a ). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol 62, 716721. [View Article] [PubMed]
    [Google Scholar]
  27. Kim S. B., Nedashkovskaya O. I., Zhukova N. V., Kuchlevskiy A. D., Mikhailov V. V. ( 2012b ). Corallibacter vietnamensis gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae . . Int J Syst Evol Microbiol 62, 569574. [View Article] [PubMed]
    [Google Scholar]
  28. Kimura M. ( 1980 ). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. . J Mol Evol 16, 111120. [View Article] [PubMed]
    [Google Scholar]
  29. Kirchman D. L. ( 2002 ). The ecology of Cytophaga-Flavobacteria in aquatic environments. . FEMS Microbiol Ecol 39, 91100.[PubMed]
    [Google Scholar]
  30. Kwon Y. M., Choi D., Yang S.-H., Kwon K. K., Kim S.-J. ( 2014 ). Hoppeia youngheungensis gen. nov., sp. nov., a member of the Flavobacteriaceae isolated from tidal flat sediment, and emended descriptions of the genus Sediminibacter and Sediminibacter furfurosus . . Int J Syst Evol Microbiol 64, 20532059. [View Article] [PubMed]
    [Google Scholar]
  31. Li Y., Bai S., Yang C., Lai Q., Zhang H., Chen Z., Wei J., Zheng W., Tian Y., Zheng T. ( 2013 ). Mangrovimonas yunxiaonensis gen. nov., sp. nov., isolated from mangrove sediment. . Int J Syst Evol Microbiol 63, 20432048. [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. Minnikin D. E., O’Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J. H. ( 1984 ). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. . J Microbiol Methods 2, 233241. [View Article]
    [Google Scholar]
  34. Montero-Calasanz M. C., Göker M., Rohde M., Spröer C., Schumann P., Busse H.-J., Schmid M., Tindall B. J., Klenk H.-P., Camacho M. ( 2013 ). Chryseobacterium hispalense sp. nov., a plant-growth-promoting bacterium isolated from a rainwater pond in an olive plant nursery, and emended descriptions of Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium . . Int J Syst Evol Microbiol 63, 43864395. [View Article] [PubMed]
    [Google Scholar]
  35. Murray R. G. E., Doetsch R. N., Robinow C. F. ( 1994 ). Determinative and cytological light microscopy. . In Methods for General and Molecular Bacteriology, pp. 2141. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  36. O’Sullivan L. A., Weightman A. J., Fry J. C. ( 2002 ). New degenerate Cytophaga-Flexibacter-Bacteroides-specific 16S ribosomal DNA-targeted oligonucleotide probes reveal high bacterial diversity in River Taff epilithon. . Appl Environ Microbiol 68, 201210. [View Article] [PubMed]
    [Google Scholar]
  37. Park S., Lee J.-S., Lee K.-C., Yoon J.-H. ( 2013 ). Geojedonia litorea gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from coastal seawater. . Antonie van Leeuwenhoek 103, 12551262. [View Article] [PubMed]
    [Google Scholar]
  38. Reichenbach H. ( 1992 ). The order Cytophagales . . In The Prokaryotes, , 2nd edn., vol. 4, pp. 36313675. Edited by Balows A., Trüper H. G., Dworkin M., Harder W., Schleifer K.-H. . Berlin, Heidelberg, New York:: Springer;. [View Article]
    [Google Scholar]
  39. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  40. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids. . USFCC Newsl 20, 16.
    [Google Scholar]
  41. Shahina M., Hameed A., Lin S.-Y., Hsu Y.-H., Liu Y.-C., Cheng I.-C., Lee M.-R., Lai W.-A., Lee R.-J., Young C.-C. ( 2013 ). Sphingomicrobium astaxanthinifaciens sp. nov., an astaxanthin-producing glycolipid-rich bacterium isolated from surface seawater and emended description of the genus Sphingomicrobium . . Int J Syst Evol Microbiol 63, 34153422. [View Article] [PubMed]
    [Google Scholar]
  42. Shahina M., Hameed A., Lin S.-Y., Lee R.-J., Lee M.-R., Young C.-C. ( 2014 ). Gramella planctonica sp. nov., a zeaxanthin-producing bacterium isolated from surface seawater, and emended descriptions of Gramella aestuarii and Gramella echinicola . . Antonie van Leeuwenhoek 105, 771779. [View Article] [PubMed]
    [Google Scholar]
  43. Smibert R. M., Krieg N. R. ( 1994 ). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607654. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  44. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. ( 2011 ). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28, 27312739. [View Article] [PubMed]
    [Google Scholar]
  45. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G. ( 1997 ). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. . Nucleic Acids Res 25, 48764882. [View Article] [PubMed]
    [Google Scholar]
  46. Tindall B. J., Rosselló-Móra R., Busse H.-J., Ludwig W., Kämpfer P. ( 2010 ). Notes on the characterization of prokaryote strains for taxonomic purposes. . Int J Syst Evol Microbiol 60, 249266. [View Article] [PubMed]
    [Google Scholar]
  47. Watts D., MacBeath J. R. ( 2001 ). Automated fluorescent DNA sequencing on the ABI PRISM 310 Genetic Analyzer. . Methods Mol Biol 167, 153170.[PubMed]
    [Google Scholar]
  48. Yang S.-J., Oh H.-M., Chung S., Cho J.-C. ( 2009 ). Antarcticimonas flava gen. nov., sp. nov., isolated from Antarctic coastal seawater. . J Microbiol 47, 517523. [View Article] [PubMed]
    [Google Scholar]
  49. Yoshizawa S., Kawanabe A., Ito H., Kandori H., Kogure K. ( 2012 ). Diversity and functional analysis of proteorhodopsin in marine Flavobacteria . . Environ Microbiol 14, 12401248. [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.066852-0
Loading
/content/journal/ijsem/10.1099/ijs.0.066852-0
Loading

Data & Media loading...

Supplements

Supplementary Data

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