1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 64, Issue Pt_2

gen. nov., sp. nov., of the family isolated from surface seawater, and emended descriptions of the genera and Free

Abstract

A Gram-staining-negative, orange-pigmented, strictly aerobic, carotenoid-producing, rod-shaped, non-flagellated, non-spore-forming bacterium, motile by gliding, designated strain CC-AMO-30D, was isolated from surface seawater collected near Taichung harbour, Taiwan. Strain CC-AMO-30D shared pairwise 16S rRNA gene sequence similarities of 94.8, 93.7 and 92.5 % with the type strains of the type species of the genera , and , respectively, and formed a distinct monophyletic lineage in phylogenetic trees. The major fatty acids (≥5 % of total) were iso-C G, iso-C, iso-C 3-OH, iso-C 3-OH, iso-C and anteiso-C. The polar lipid profile consisted of phosphatidylethanolamine, four unidentified lipids, two unidentified aminolipids and an unidentified phospholipid. The major polyamine was the triamine -homospermidine. The DNA G+C content was 47.1 mol% and the predominant respiratory quinone was menaquinone-6 (MK-6). Based on the phylogenetic distinctiveness and distinguishing phenotypic characteristics, strain CC-AMO-30D represents 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 is CC-AMO-30D ( = JCM 18552 = BCRC 80469). Emended descriptions of the genera and are also proposed.

  • Published Online:
Funding
This study was supported by the:
  • Ministry of Education, Taiwan, ROC
© 2014 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.054627-0
2014-02-01
2023-10-02
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/64/2/533.html?itemId=/content/journal/ijsem/10.1099/ijs.0.054627-0&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, 403–410.[PubMed] [CrossRef]
    [Google Scholar]
  2. Bernardet J.-F. ( 2011 ). Family I. Flavobacteriaceae Reichenbach 1992. . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 4, pp. 106–111. Edited by Krieg N. R., Ludwig W., Whitman W. B., Hedlund B. P., Paster B. J., Staley J. T., Ward N., Brown D., Parte A. . New York:: Springer;.
     [Google Scholar]
  3. Bernardet J.-F., Nakagawa Y. ( 2006 ). An introduction to the family Flavobacteriaceae . . In The Prokaryotes, , 3rd edn., vol. 7, pp. 455–480. Edited by Dworkin M., Falkow S., Rosenberg E., Schleifer K. H., Stackebrandt E. . New York:: Springer;. [View Article]
    [Google Scholar]
  4. 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, 1049–1070. [View Article] [PubMed]
    [Google Scholar]
  5. Collins M. D. ( 1985 ). Analysis of isoprenoid quinones. . Methods Microbiol 18, 329–366. [View Article]
    [Google Scholar]
  6. Embley T. M., Wait R. ( 1994 ). Structural lipids of eubacteria. . In Chemical Methods in Prokaryotic Systematics, pp. 121–161. Edited by Goodfellow M., O’Donnell A. G. . Chichester:: Wiley;.
     [Google Scholar]
  7. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368–376. [View Article] [PubMed]
    [Google Scholar]
  8. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783–791. [View Article]
    [Google Scholar]
  9. Fitch W. M. ( 1971 ). Towards defining the course of evolution: minimum change for a specific tree topology. . Syst Zool 20, 406–416. [View Article]
    [Google Scholar]
  10. GCG ( 1995 ). Wisconsin Package Version 8.1 Program Manual. Madison, WI:: Computer Group;.
     [Google Scholar]
  11. Hameed A., Arun A. B., Ho H.-P., Chang C.-M., Rekha P. D., Lee M.-R., Singh S., Young C.-C. ( 2011 ). Supercritical carbon dioxide micronization of zeaxanthin from moderately thermophilic bacteria Muricauda lutaonensis CC-HSB-11T . . J Agric Food Chem 59, 4119–4124. [View Article] [PubMed]
    [Google Scholar]
  12. 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, 37–45. [View Article] [PubMed]
    [Google Scholar]
  13. Hameed A., Shahina M., Lin S.-Y., Cho J. C., Lai W.-A., Young C.-C. ( 2013a ). 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 (in press). [View Article] [PubMed]
    [Google Scholar]
  14. Hameed A., Shahina M., Lin S.-Y., Lai W.-A., Hsu Y.-H., Liu Y.-C., Young C.-C. ( 2013b ). 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 (in press). [View Article] [PubMed]
    [Google Scholar]
  15. 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, 557–561.[PubMed]
    [Google Scholar]
  16. Kämpfer P., Kroppenstedt R. M. ( 1996 ). Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. . Can J Microbiol 42, 989–1005. [View Article]
    [Google Scholar]
  17. Khan S. T., Nakagawa Y., Harayama S. ( 2007 ). Galbibacter mesophilus gen. nov., sp. nov., a novel member of the family Flavobacteriaceae . . Int J Syst Evol Microbiol 57, 969–973. [View Article] [PubMed]
    [Google Scholar]
  18. 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 ( 2012 ). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol 62, 716–721. [View Article] [PubMed]
    [Google Scholar]
  19. Kimura M. ( 1980 ). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. . J Mol Evol 16, 111–120. [View Article] [PubMed]
    [Google Scholar]
  20. Kirchman D. L. ( 2002 ). The ecology of Cytophaga-Flavobacteria in aquatic environments. . FEMS Microbiol Ecol 39, 91–100.[PubMed]
    [Google Scholar]
  21. 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, 159–167. [View Article]
    [Google Scholar]
  22. 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, 233–241. [View Article]
    [Google Scholar]
  23. Montero-Calasanz M. D., 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 emendation of the species Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium . . Int J Syst Evol Microbiol (in press). [View Article] [PubMed]
    [Google Scholar]
  24. Murray R. G. E., Doetsch R. N., Robinow C. F. ( 1994 ). Determinative and cytological light microscopy. . In Methods for General and Molecular Bacteriology, pp. 21–41. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
     [Google Scholar]
  25. Quan Z.-X., Xiao Y.-P., Roh S. W., Nam Y.-D., Chang H.-W., Shin K.-S., Rhee S.-K., Park Y.-H., Bae J.-W. ( 2008 ). Joostella marina gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from the East Sea. . Int J Syst Evol Microbiol 58, 1388–1392. [View Article] [PubMed]
    [Google Scholar]
  26. Reichenbach H. ( 1992 ). The order Cytophagales. . In The Prokaryotes, , 2nd edn., pp. 3631–3675. Edited by Balows A., Trüper H. G., Dworkin M., Harder W., Schleifer K. H. . New York:: Springer;. [CrossRef]
    [Google Scholar]
  27. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406–425.[PubMed]
    [Google Scholar]
  28. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids. . USFCC Newsl 20, 16.
     [Google Scholar]
  29. Scherer P., Kneifel H. ( 1983 ). Distribution of polyamines in methanogenic bacteria. . J Bacteriol 154, 1315–1322.[PubMed]
    [Google Scholar]
  30. 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, 3415–3422. [View Article] [PubMed]
    [Google Scholar]
  31. Shindo K., Kikuta K., Suzuki A., Katsuta A., Kasai H., Yasumoto-Hirose M., Matsuo Y., Misawa N., Takaichi S. ( 2007 ). Rare carotenoids, (3R)-saproxanthin and (3R,2′S)-myxol, isolated from novel marine bacteria (Flavobacteriaceae) and their antioxidative activities. . Appl Microbiol Biotechnol 74, 1350–1357. [View Article] [PubMed]
    [Google Scholar]
  32. Smibert R. M., Krieg N. R. ( 1994 ). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607–654. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
     [Google Scholar]
  33. 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, 2731–2739. [View Article] [PubMed]
    [Google Scholar]
  34. 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, 4876–4882. [View Article] [PubMed]
    [Google Scholar]
  35. 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, 249–266. [View Article] [PubMed]
    [Google Scholar]
  36. Watts D., MacBeath J. R. ( 2001 ). Automated fluorescent DNA sequencing on the ABI PRISM 310 Genetic Analyzer. . Methods Mol Biol 167, 153–170.[PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.054627-0
Loading
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, 533 (2014); https://doi.org/10.1099/ijs.0.054627-0
/content/journal/ijsem/10.1099/ijs.0.054627-0
/content/journal/ijsem/10.1099/ijs.0.054627-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month Most Cited RSS feed

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