1887

Abstract

A bacterial strain designated LYH-15 was isolated from a freshwater fish pond in Taiwan and characterized using a polyphasic taxonomy approach. Cells of LYH-15 were Gram-staining-negative, aerobic, motile by means of a single polar flagellum, poly-β-hydroxybutyrate-containing, non-spore forming, straight rods and formed light-coral-colored colonies. Growth occurred at 15–40 °C (optimum, 30 °C), at pH 5.0–9.0 (optimum, pH 7.0) and with 0–0.5 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that LYH-15 forms a distinct phyletic line within the order Burkholderiales , with less than 94 % sequence similarity to its closest relatives with validly published names. The predominant fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The major isoprenoid quinone was Q-8 and the DNA G+C content was 63.8 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several uncharacterized lipids. The major polyamines were 2-hydroxyputrescine and putrescine. On the basis of the genotypic and phenotypic data, LYH-15 represents a novel species of a new genus in the order Burkholderiales , for which the name Piscinibacterium candidicorallinum gen. nov., sp. nov. is proposed. The type strain is LYH-15 (=BCRC 80969=LMG 29480=KCTC 52168).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001505
2016-12-01
2019-10-13
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/12/5260.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001505&mimeType=html&fmt=ahah

References

  1. Anandham R., Indiragandhi P., Kwon S. W., Sa T. M., Jeon C. O., Kim Y. K., Jee H. J..( 2010;). Pandoraea thiooxydans sp. nov., a facultatively chemolithotrophic, thiosulfate-oxidizing bacterium isolated from rhizosphere soils of sesame (Sesamum indicum L.). . Int J Syst Evol Microbiol 60: 21–26. [CrossRef] [PubMed]
    [Google Scholar]
  2. Anzai Y., Kudo Y., Oyaizu H..( 1997;). The phylogeny of the genera Chryseomonas, Flavimonas, and Pseudomonas supports synonymy of these three genera. . Int J Syst Bacteriol 47: 249–251. [CrossRef] [PubMed]
    [Google Scholar]
  3. Baldani J. I., Baldani V. L. D., Seldin L., Döbereiner J..( 1986;). Characterization of Herbaspirillum seropedicae gen. nov., sp. nov., a root-associated nitrogen-fixing bacterium. . Int J Syst Bacteriol 36: 86–93. [CrossRef]
    [Google Scholar]
  4. Baldani J. I., Pot B., Kirchhof G., Falsen E., Baldani V. L. D., Olivares F. L., Hoste B., Kersters K., Hartmann A. et al.( 1996;). Emended description of Herbaspirillum; inclusion of [Pseudomonas] rubrisubalbicans, a mild plant pathogen, as Herbaspirillum rubrisubalbicans comb. nov.; and classification of a group of clinical isolates (EF group 1) as Herbaspirillum species 3. .46 802–810. [CrossRef]
  5. Beveridge T. J., Lawrence J. R., Murray R. G. E..( 2007;). Sampling and staining for light microscopy. . In Methods for General and Molecular Bacteriology, , 3rd edn., pp. 19–33. Edited by Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder L. R.. Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  6. Bowman J. P..( 2000;). Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. . Int J Syst Evol Microbiol 50: 1861–1868. [CrossRef]
    [Google Scholar]
  7. Breznak J. A., Costilow R. N..( 2007;). Physicochemical factors in growth. . In Methods for General and Molecular Bacteriology, , 3rd edn., pp. 309–329. Edited by Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder L. R.. Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  8. Busse J., Auling G..( 1988;). Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. . Syst Appl Microbiol 11: 1–8. [CrossRef]
    [Google Scholar]
  9. Busse H.-J., Bunka S., Hensel A., Lubitz W..( 1997;). Discrimination of members of the family Pasteurellaceae based on polyamine patterns. . Int J Syst Evol Microbiol 47: 698–708. [CrossRef]
    [Google Scholar]
  10. Chen W. M., Laevens S., Lee T. M., Coenye T., De Vos P., Mergeay M., Vandamme P..( 2001;). Ralstonia taiwanensis sp. nov., isolated from root nodules of Mimosa species and sputum of a cystic fibrosis patient. . Int J Syst Evol Microbiol 51: 1729–1735. [CrossRef]
    [Google Scholar]
  11. Chen W.-M., Huang W.-C., Sheu S.-Y..( 2013;). Derxia lacustris sp. nov., a nitrogen-fixing bacterium isolated from a freshwater lake. . Int J Syst Evol Microbiol 63: 965–970. [CrossRef] [PubMed]
    [Google Scholar]
  12. Chung A. P., Tiago I., Nobre M. F., Verissimo A., Morais P. V..( 2013;). Glaciimonas singularis sp. nov., isolated from a uranium mine wastewater treatment plant. . Int J Syst Evol Microbiol 63: 2344–2350. [CrossRef]
    [Google Scholar]
  13. Coenye T., Falsen E., Hoste B., Ohlen M., Goris J., Govan J. R. W., Gillis M., Vandamme P..( 2000;). Description of Pandoraea gen. nov. with Pandoraea apista sp. nov., Pandoraea pulmonicola sp. nov., Pandoraea pnomenusa sp. nov., Pandoraea sputorum sp. nov. and Pandoraea norimbergensis comb. nov. . Int J Syst Evol Microbiol 50: 887–899. [CrossRef]
    [Google Scholar]
  14. Cole J. R., Wang Q., Cardenas E., Fish J., Chai B., Farris R. J., Kulam-Syed-Mohideen A. S., McGarrell D. M., Marsh T. et al.( 2009;). The ribosomal database project: improved alignments and new tools for rRNA analysis. . Nucleic Acids Res 37: D141–D145. [CrossRef]
    [Google Scholar]
  15. Collins M. D..( 1994;). Isoprenoid quinones. . In Chemical Methods in Prokaryotic Systematics, pp. 265–309. Edited by Goodfellow M., O’Donnell A. G.. Chichester:: Wiley;.
    [Google Scholar]
  16. De Smedt J., Bauwens M., Tytgat R., De Ley J..( 1980;). Intra- and intergeneric similarities of ribosomal ribonucleic acid cistrons of free-living, nitrogen-fixing bacteria. . Int J Syst Bacteriol 30: 106–122. [CrossRef]
    [Google Scholar]
  17. Ding L., Yokota A..( 2004;). Proposals of Curvibacter gracilis gen. nov., sp. nov. and Herbaspirillum putei sp. nov. for bacterial isolates isolated from well water and reclassification of [Pseudomonas] huttiensis, [Pseudomonas] lanceolata, [Aquaspirillum] delicatum and [Aquaspirillum] autotrophicum as Herbaspirillum huttiense comb. nov., Curvibacter lanceolatus comb. nov., Curvibacter delicatus comb. nov. and Herbaspirillum autotrophicum comb. nov. . Int J Syst Evol Microbiol 54: 2223–2230. [CrossRef]
    [Google Scholar]
  18. Dobritsa A. P., Reddy M. C. S., Samadpour M..( 2010;). Reclassification of Herbaspirillum putei as a later heterotypic synonym of Herbaspirillum huttiense, with the description of H. huttiense subsp. huttiense subsp. nov. and H. huttiense subsp. putei subsp. nov., comb. nov., and description of Herbaspirillum aquaticum sp. nov. . Int J Syst Evol Microbiol 60: 1418–1426. [CrossRef]
    [Google Scholar]
  19. 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]
  20. Felsenstein J..( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17: 368–376. [CrossRef]
    [Google Scholar]
  21. Felsenstein J..( 1993;). phylip (phylogeny inference package). version 3.5c. Distributed by the author. Department of Genome Sciences. . Seattle, USA:: University of Washington;.
  22. Frasson D., Udovičić M., Frey B., Lapanje A., Zhang D. C., Margesin R., Sievers M..( 2015;). Glaciimonas alpina sp. nov. isolated from alpine glaciers and reclassification of Glaciimonas immobilis Cr9-12 as the type strain of Glaciimonas alpina sp. nov. . Int J Syst Evol Microbiol 65: 1779–1785. [CrossRef] [PubMed]
    [Google Scholar]
  23. Garrity G. M., Bell J. A., Lilburn T..( 2005;). Order I. Burkholderiales ord. nov. . In Bergey’s Manual of Systematic Bacteriology (The Proteobacteria), Part C (The Alpha-, Beta-, Delta-, and Epsilonproteobacteria), , 2nd edn.,vol. 2 p. 575. Edited by Brenner D. J., Krieg N. R., Staley J. T., Garrity G. M.. New York:: Springer;.[CrossRef]
    [Google Scholar]
  24. Gomila M., Pinhassi J., Falsen E., Moore E. R. B., Lalucat J..( 2010;). Kinneretia asaccharophila gen. nov., sp. nov., isolated from a freshwater lake, a member of the Rubrivivax branch of the family Comamonadaceae. . IntJ Syst Evol Microbiol 60: 809–814. [CrossRef]
    [Google Scholar]
  25. Goto M., Kuwata H..( 1988;). Rhizobacter daucus gen. nov., sp. nov., the causal agent of carrot bacterial gall. . Int J Syst Bacteriol 38: 233–239. [CrossRef]
    [Google Scholar]
  26. Hall T. A..( 1999;). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. . Nucleic Acids Symp Ser 41: 95–98. [CrossRef]
    [Google Scholar]
  27. Im W.-T., Bae H.-S., Yokota A., Lee S. T..( 2004;). Herbaspirillum chlorophenolicum sp. nov., a 4-chlorophenol-degrading bacterium. . Int J Syst Evol Microbiol 54: 851–855. [CrossRef]
    [Google Scholar]
  28. Imai S., Yoshida R., Endo Y., Fukunaga Y., Yamazoe A., Kasai D., Masai E., Fukuda M..( 2013;). Rhizobacter gummiphilus sp. nov., a rubber-degrading bacterium isolated from the soil of a botanical garden in Japan. . J Gen Appl Microbiol 59: 199–205. [CrossRef] [PubMed]
    [Google Scholar]
  29. Jensen H. L., Petersen E. J., De P. K., Bhattacharya R..( 1960;). A new nitrogen-fixing bacterium: Derxia gummosa nov. gen. nov. spec. . Archiv F ü R Mikrobiologie 36: 182–195. [CrossRef]
    [Google Scholar]
  30. Jin L., Ko S. R., Ahn C. Y., Lee H. G., Oh H.-M..( 2016;). Rhizobacter profundi sp. nov., isolated from freshwater sediment. . Int J Syst Evol Microbiol 66: 1926–1931. [CrossRef] [PubMed]
    [Google Scholar]
  31. Jung S.-Y., Lee M.-H., Oh T.-K., Yoon J.-H..( 2007;). Herbaspirillum rhizosphaerae sp. nov., isolated from rhizosphere soil of Allium victorialis var. platyphyllum. . Int J Syst Evol Microbiol 57: 2284–2288. [CrossRef]
    [Google Scholar]
  32. Kim O.-S., Cho Y.-J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. et al.( 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. [CrossRef]
    [Google Scholar]
  33. Kimura M..( 1983;). The Neutral Theory of Molecular Evolution. Cambridge:: Cambridge University Press;.[CrossRef]
    [Google Scholar]
  34. Kirchhof G., Eckert B., Stoffels M., Baldani J. I., Reis V. M., Hartmann A..( 2001;). Herbaspirillum frisingense sp. nov., a new nitrogen-fixing bacterial species that occurs in C4-fibre plants. . Int J Syst Evol Microbiol 51: 157–168. [CrossRef] [PubMed]
    [Google Scholar]
  35. Kluge A. G., Farris F. S..( 1969;). Quantitative phyletics and the evolution of anurans. . Syst Zool 18: 1–32. [CrossRef]
    [Google Scholar]
  36. Kumar S., Stecher G., Tamura K..( 2016;). mega7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. . Mol Biol Evol 33: 1870–1874. [CrossRef]
    [Google Scholar]
  37. Lagier J.-C., Gimenez G., Robert C., Raoult D., Fournier P.-E..( 2012;). Non-contiguous finished genome sequence and description of Herbaspirillum massiliense sp. nov. . Stand Genomic Sci 7: 200–209. [CrossRef]
    [Google Scholar]
  38. Lechner U., Brodkorb D., Geyer R., Hause G., Hartig C., Auling G., Fayolle-Guichard F., Piveteau P., Muller R. H., Rohwerder T..( 2007;). Aquincola tertiaricarbonis gen. nov., sp. nov., a tertiary butyl moiety-degrading bacterium. . Int J Syst Evol Microbiol 57: 1295–1303. [CrossRef]
    [Google Scholar]
  39. Ludwig W., Strunk O., Klugbauer S., Klugbauer N., Weizenegger M., Neumaier J., Bachleitner M., Schleifer K. H..( 1998;). Bacterial phylogeny based on comparative sequence analysis. . Electrophoresis 19: 554–568. [CrossRef]
    [Google Scholar]
  40. 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. [CrossRef]
    [Google Scholar]
  41. Nakatsu C. H., Hristova K., Hanada S., Meng X. Y., Hanson J. R., Scow K. M., Kamagata Y..( 2006;). Methylibium petroleiphilum gen. nov., sp. nov., a novel methyl tert-butyl ether-degrading methylotroph of the Betaproteobacteria. . Int J Syst Evol Microbiol 56: 983–989. [CrossRef]
    [Google Scholar]
  42. Nokhal T. H., Schlegel H. G..( 1983;). Taxonomic study of Paracoccus denitrificans. . Int J Syst Bacteriol 33: 26–37. [CrossRef]
    [Google Scholar]
  43. Powers E. M..( 1995;). Efficacy of the Ryu nonstaining KOH technique for rapidly determining Gram reactions of food-borne and waterborne bacteria and yeasts. . Appl Environ Microbiol 61: 3756–3758.[PubMed]
    [Google Scholar]
  44. Rapala J., Berg K. A., Lyra C., Niemi R. M., Manz W., Suomalainen S., Paulin L., Lahti K..( 2005;). Paucibacter toxinivorans gen. nov., sp. nov., a bacterium that degrades cyclic cyanobacterial hepatotoxins microcystins and nodularin. . Int J Syst Evol Microbiol 55: 1563–1568. [CrossRef]
    [Google Scholar]
  45. Rothballer M., Schmid M., Klein I., Gattinger A., Grundmann S., Hartmann A..( 2006;). Herbaspirillum hiltneri sp. nov., isolated from surface-sterilized wheat roots. . Int J Syst Evol Microbiol 56: 1341–1348. [CrossRef]
    [Google Scholar]
  46. Rzhetsky A., Nei M..( 1993;). Theoretical foundation of the minimum-evolution method of phylogenetic inference. . Mol Biol Evol 10: 1073–1095.[PubMed]
    [Google Scholar]
  47. Sahin N., Tani A., Kotan R., Sedlacek I., Kimbara K., Tamer A. U..( 2011;). Pandoraea oxalativorans sp. nov., Pandoraea faecigallinarum sp. nov. and Pandoraea vervacti sp. nov., isolated from oxalate-enriched culture. . Int J Syst Evol Microbiol 61: 2247–2253. [CrossRef]
    [Google Scholar]
  48. Saitou N., Nei M..( 1987;). The neighbor-joining method: a new method for constructing phylogenetic trees. . Mol Biol Evol 4: 406–425.[PubMed]
    [Google Scholar]
  49. Sasser M..( 1990;). Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, , MIDI Technical Note 101.. Newark, DE:: MIDI Inc;.
    [Google Scholar]
  50. Schlegel H. G., Lafferty R., Krauss I..( 1970;). The isolation of mutants not accumulating poly-β-hydroxybutyric acid. . Arch Mikrobiol 71: 283–294. [CrossRef]
    [Google Scholar]
  51. Song J., Cho J. C..( 2007;). Methylibium aquaticum sp. nov., a betaproteobacterium isolated from a eutrophic freshwater pond. . Int J Syst Evol Microbiol 57: 2125–2128. [CrossRef] [PubMed]
    [Google Scholar]
  52. Spiekermann P., Rehm B. H. A., Kalscheuer R., Baumeister D., Steinbüchel A..( 1999;). A sensitive, viable-colony staining method using Nile red for direct screening of bacteria that accumulate polyhydroxyalkanoic acids and other lipid storage compounds. . Arch Microbiol 171: 73–80. [CrossRef]
    [Google Scholar]
  53. Spring S., Kampfer P., Ludwig W., Schleifer K.-H..( 1996;). Polyphasic characterization of the genus Leptothrix: new descriptions of Leptothrix mobilis sp. nov. and Leptothrix discophora sp. nov. nom. rev. and emended description of Leptothrix cholodnii emend. . Syst Appl Microbiology 19: 634–643. [CrossRef]
    [Google Scholar]
  54. Stackebrandt E., Verbarg S., Frühling A., Busse H. J., Tindall B. J..( 2009;). Dissection of the genus Methylibium: reclassification of Methylibium fulvum as Rhizobacter fulvus comb. nov., Methylibium aquaticum as Piscinibacter aquaticus gen. nov., comb. nov. and Methylibium subsaxonicum as Rivibacter subsaxonicus gen. nov., comb. nov. and emended descriptions of the genera Rhizobacter and Methylibium. . Int J Syst Evol Microbiol 59: 2552–2560. [CrossRef] [PubMed]
    [Google Scholar]
  55. 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. [CrossRef]
    [Google Scholar]
  56. Tindall B. J., Sikorski J., Smibert R. A., Krieg N. R..( 2007;). Phenotypic characterization and the principles of comparative systematics. . In Methods for General and Molecular Bacteriology, , 3rd edn., pp. 330–393. Edited by Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder L. R.. Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  57. Valverde A., Velázquez E., Gutiérrez C., Cervantes E., Ventosa A., Igual J. M..( 2003;). Herbaspirillum lusitanum sp. nov., a novel nitrogen-fixing bacterium associated with root nodules of Phaseolus vulgaris. . Int J Syst Evol Microbiol 53: 1979–1983. [CrossRef]
    [Google Scholar]
  58. Wei L., Si M., Long M., Zhu L., Li C., Shen X., Wang Y., Zhao L., Zhang L..( 2015;). Rhizobacter bergeniae sp. nov., isolated from the root of Bergenia scopulosa. . Int J Syst Evol Microbiol 65: 479–484. [CrossRef]
    [Google Scholar]
  59. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J..( 1991;). 16S ribosomal DNA amplification for phylogenetic study. . J Bacteriol 173: 697–703. [CrossRef]
    [Google Scholar]
  60. Wen C. M., Tseng C. S., Cheng C. Y., Li Y. K..( 2002;). Purification, characterization and cloning of a chitinase from Bacillus sp. NCTU2. . Biotechnol Appl Biochem 35: 213–219. [CrossRef]
    [Google Scholar]
  61. Xie C. H., Yokota A..( 2004;). Phylogenetic analyses of the nitrogen-fixing genus Derxia. . J Gen Appl Microbiol 50: 129–135. [CrossRef]
    [Google Scholar]
  62. Yoon M. H., Ten L. N., Im W. T., Lee S. T..( 2007;). Methylibium fulvum sp. nov., a member of the Betaproteobacteria isolated from ginseng field soil, and emended description of the genus Methylibium. . Int J Syst Evol Microbiol 57: 2062–2066. [CrossRef]
    [Google Scholar]
  63. Zhang D. C., Redzic M., Schinner F., Margesin R..( 2011;). Glaciimonas immobilis gen. nov., sp. nov., a member of the family Oxalobacteraceae isolated from alpine glacier cryoconite. . Int J Syst Evol Microbiol 61: 2186–2190. [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001505
Loading
/content/journal/ijsem/10.1099/ijsem.0.001505
Loading

Data & Media loading...

Supplementary File 1

PDF

Most Cited This Month

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