1887

Abstract

A Gram-stain-negative, strictly aerobic, non-motile, rod-shaped, manganese-oxidizing bacterial strain, designated DY6-4, was isolated from the surface sediment of the Pacific Clarion-Clipperton Fracture Zone. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain DY6-4 formed a lineage within the family and was distinct from the most closely related genera , and (94.0–96.0 %, 93.4–96.0 % and 91.9–95.9 % 16S rRNA gene sequence similarity, repectively). Optimal growth occurred in the presence of 1 % (w/v) NaCl, at pH 7.0 and at 28 °C. Strain DY6-4 contained ubiquinone-10 (Q-10) as the major ubiquinone, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and one unidentified aminolipid as the predominant polar lipids, Cω7 and summed feature 3 (Cω7 and/or Cω6) as the main fatty acids (>10 % of the total). The DNA G+C content of strain DY6-4 was 66.6 mol%. On the basis of the polyphasic analyses, strain DY6-4 is considered to represent a novel species of a novel genus in the clade of the family , for which the name gen. nov., sp. nov. is proposed. The type strain is DY6-4 ( = KCTC 42421 = MCCC 1K00502).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.000912
2016-03-01
2020-01-18
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/3/1521.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.000912&mimeType=html&fmt=ahah

References

  1. Beveridge T. J., Lawrence J. G., Murray R. G. E.. 2007; Sampling and staining for light microscopy. In Methods for General and Molecular Microbiology pp19–33Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder L. R.. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  2. Biebl H., Allgaier M., Lünsdorf H., Pukall R., Tindall B. J., Wagner-Döbler I.. 2005; Roseovarius mucosus sp. nov., a member of the Roseobacter clade with trace amounts of bacteriochlorophyll a. Int J Syst Evol Microbiol55:2377–2383 [CrossRef][PubMed]
    [Google Scholar]
  3. Boogerd F. C., de Vrind J. P. M.. 1987; Manganese oxidation by Leptothrix discophora. J Bacteriol169:489–494[PubMed]
    [Google Scholar]
  4. Brinkhoff T., Giebel H. A., Simon M.. 2008; Diversity, ecology, and genomics of the Roseobacter clade: a short overview. Arch Microbiol189:531–539 [CrossRef][PubMed]
    [Google Scholar]
  5. Buchan A., González J. M., Moran M. A.. 2005; Overview of the marine roseobacter lineage. Appl Environ Microbiol71:5665–5677 [CrossRef][PubMed]
    [Google Scholar]
  6. Curson A. R. J., Todd J. D., Sullivan M. J., Johnston A. W. B.. 2011; Catabolism of dimethylsulphoniopropionate: microorganisms, enzymes and genes. Nat Rev Microbiol9:849–859 [CrossRef][PubMed]
    [Google Scholar]
  7. Felsenstein J.. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  8. Ghiorse W. C., Hirsch P.. 1979; An ultrastructural study of ion and manganese deposition associated with extracellular polymers of Pedomicrobium-like budding bacteria. Arch Microbiol123:213–226 [CrossRef]
    [Google Scholar]
  9. Hahnke S., Tindall B. J., Schumann P., Sperling M., Brinkhoff T., Simon M.. 2012; Planktotalea frisia gen. nov., sp. nov., isolated from the southern North Sea. Int J Syst Evol Microbiol62:1619–1624 [CrossRef][PubMed]
    [Google Scholar]
  10. Hansel C. M., Francis C. A.. 2006; Coupled photochemical and enzymatic Mn(II) oxidation pathways of a planktonic Roseobacter-like bacterium. Appl Environ Microbiol72:3543–3549 [CrossRef][PubMed]
    [Google Scholar]
  11. Imhoff J. F.. 2006; The phototrophic Alphaproteobacteria. In (Chief-ed.) Dworkin, Falkow M., Rosenberg S., Schleifer E., Stackebrandt E K.-H. (Eds.), The Prokaryotes, a Handbook on the Biology of Bacteria vol. 5 Proteobacteria: Alpha and Beta Subclasses, 3rd ed.. New York: Springer; pp41–64
    [Google Scholar]
  12. 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 Microbiol62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  13. Kim Y.-O., Park S., Nam B.-H., Lee C., Park J.-M., Kim D.-G., Yoon J.-H.. 2014; Ascidiaceihabitans donghaensis gen. nov., sp. nov., isolated from the golden sea squirt Halocynthia aurantium. Int J Syst Evol Microbiol64:3970–3975 [CrossRef][PubMed]
    [Google Scholar]
  14. Kimura M.. 1980; A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol16:111–120 [CrossRef][PubMed]
    [Google Scholar]
  15. Komagata K., Suzuki K.. 1987; Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol19:161–207 [CrossRef]
    [Google Scholar]
  16. Lenk S., Moraru C., Hahnke S., Arnds J., Richter M., Kube M., Reinhardt R., Brinkhoff T., Harder J., other authors. 2012; Roseobacter clade bacteria are abundant in coastal sediments and encode a novel combination of sulfur oxidation genes. ISME J6:2178–2187 [CrossRef][PubMed]
    [Google Scholar]
  17. Luo H., Moran M. A.. 2014; Evolutionary ecology of the marine Roseobacter clade. Microbiol Mol Biol Rev78:573–587 [CrossRef][PubMed]
    [Google Scholar]
  18. 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 Bacteriol39:159–167 [CrossRef]
    [Google Scholar]
  19. 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 Methods2:233–241 [CrossRef]
    [Google Scholar]
  20. Montero-Calasanz M. delC., 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 Microbiol63:4386–4395 [CrossRef][PubMed]
    [Google Scholar]
  21. Park S., Park J.-M., Kang C.-H., Yoon J.-H.. 2015; Aliiroseovarius pelagivivens gen. nov., sp. nov., isolated from seawater, and reclassification of three species of the genus Roseovarius as Aliiroseovarius crassostreae comb. nov., Aliiroseovarius halocynthiae comb. nov. and Aliiroseovarius sediminilitoris comb. nov. Int J Syst Evol Microbiol65:2646–2652 [CrossRef][PubMed]
    [Google Scholar]
  22. Pukall R., Buntefuss D., Frühling A., Rohde M., Kroppenstedt R. M., Burghardt J., Lebaron P., Bernard L., Stackebrandt E.. 1999; Sulfitobacter mediterraneus sp. nov., a new sulfite-oxidizing member of the α-Proteobacteria. Int J Syst Bacteriol49:513–519 [CrossRef][PubMed]
    [Google Scholar]
  23. Romanenko L. A., Tanaka N., Frolova G. M., Svetashev V. I., Mikhailov V. V.. 2011; Litoreibacter albidus gen. nov., sp. nov. and Litoreibacter janthinus sp. nov., members of the class Alphaproteobacteria isolated from the seashore. Int J Syst Evol Microbiol61:148–154 [CrossRef][PubMed]
    [Google Scholar]
  24. Sass H., Köpke B., Rütters H., Feuerlein T., Dröge S., Cypionka H., Engelen B.. 2010; Tateyamaria pelophila sp. nov., a facultatively anaerobic alphaproteobacterium isolated from tidal-flat sediment, and emended descriptions of the genus Tateyamaria and of Tateyamaria omphalii. Int J Syst Evol Microbiol60:1770–1777 [CrossRef][PubMed]
    [Google Scholar]
  25. Sasser M.. 1990; Identification of bacteria by gas chromatography of cellular fatty acids MIDI Technical Note 101 Newark, DE: MIDI Inc;
    [Google Scholar]
  26. Shiba T.. 1991; Roseobacter litoralis gen. nov., sp. nov., and Roseobacter denitrificans sp. nov., aerobic pink-pigmented bacteria which contain bacteriochlorophyll a. Syst Appl Microbiol14:140–145 [CrossRef]
    [Google Scholar]
  27. Sorokin D. Y.. 1995; Sulfitobacter pontiacusgen. nov., sp. nov. a new heterotrophic bacterium from the Black Sea, specialized on sulfite oxidation. Microbiology64:295–305 (English translation of Mikrobiologiya)
    [Google Scholar]
  28. 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 Evol28:2731–2739 [CrossRef][PubMed]
    [Google Scholar]
  29. 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 Res25:4876–4882 [CrossRef][PubMed]
    [Google Scholar]
  30. Tindall B. J., Sikorski J., Smibert R. M., Krieg N. R.. 2007; Phenotypic characterization and the principles of comparative systematics. In Methods for General and Molecular Microbiology pp330–393Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder L. R.. Washington, DC: American Society for Microbiology; [CrossRef]
    [Google Scholar]
  31. Van Trappen S., Mergaert J., Swings J.. 2004; Loktanella salsilacus gen. nov., sp. nov., Loktanella fryxellensis sp. nov. and Loktanella vestfoldensis sp. nov., new members of the Rhodobacter group, isolated from microbial mats in Antarctic lakes. Int J Syst Evol Microbiol54:1263–1269 [CrossRef][PubMed]
    [Google Scholar]
  32. Xie C.-H., Yokota A.. 2003; Phylogenetic analyses of Lampropedia hyalina based on the 16S rRNA gene sequence. J Gen Appl Microbiol49:345–349 [CrossRef][PubMed]
    [Google Scholar]
  33. Yu T., Yin Q., Song X., Zhao R., Shi X., Zhang X.-H.. 2013; Aquimarina longa sp. nov., isolated from seawater, and emended description of Aquimarina muelleri. Int J Syst Evol Microbiol63:1235–1240 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.000912
Loading
/content/journal/ijsem/10.1099/ijsem.0.000912
Loading

Data & Media loading...

Supplements

Supplementary Data

PDF

Most cited articles

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