1887

Abstract

Strain AHQ-12, isolated from a freshwater lake in Taiwan, was characterized using a polyphasic taxonomy approach. Cells of strain AHQ-12 were Gram-staining-negative, aerobic, non-motile, non-spore forming, straight rods and formed translucent white-coloured colonies. Optimal growth occurred at 20 °C, pH 6.0 and with 0 % NaCl. The predominant fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The major isoprenoid quinone was Q-8, and the DNA G+C content was 50.4 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several uncharacterized aminophospholipids and lipids. The major polyamine was cadaverine. 16S rRNA gene sequence analysis demonstrated that this isolate was unique, showing less than 91 % sequence similarity to its closest relatives, including members of the genera Ralstonia (89.7–90.8 %), Cupriavidus (88.8–90.3 %), Polynucleobacter (88.2–89.5 %), Burkholderia (86.6–90.3 %) and Pandoraea (89.2–90.1 %). Phylogenetic analyses demonstrated that strain AHQ-12 formed a distinct clade closely related to species of the family Burkholderiaceae . On the basis of the phylogenetic inference and phenotypic data, strain AHQ-12 should be classified as a novel species of a new genus in the family Burkholderiaceae , for which the name Formosimonas limnophila gen. nov., sp. nov. is proposed. The type strain is AHQ-12 (=BCRC 80690=LMG 27847=KCTC 32501).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001561
2017-02-20
2019-10-20
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/1/17.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001561&mimeType=html&fmt=ahah

References

  1. Garrity GM, Bell JA, Lilburn T. Family I. Burkholderiaceae fam. nov. In Brenner DJ, Krieg NR, Staley JT, Garrity GM. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd ed.vol. 2 (The Proteobacteria), Part C (The Alpha-, Beta-, Delta-, and Epsilonproteobacteria) New York: Springer; 2005; pp.575[CrossRef]
    [Google Scholar]
  2. Chen WM, Laevens S, Lee TM, Coenye T, De Vos P et al. Ralstonia taiwanensis sp. nov., isolated from root nodules of Mimosa species and sputum of a cystic fibrosis patient. Int J Syst Evol Microbiol 2001;51:1729–1735 [CrossRef][PubMed]
    [Google Scholar]
  3. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991;173:697–703 [CrossRef][PubMed]
    [Google Scholar]
  4. Anzai Y, Kudo Y, Oyaizu H. The phylogeny of genera Chryseomonas, Flavimonas, and Pseudomonas supports synonymy of these three genera. Int J Syst Bacteriol 1997;47:249–251 [CrossRef][PubMed]
    [Google Scholar]
  5. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012;62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  6. Cole JR, Wang Q, Cardenas E, Fish J, Chai B et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 2009;37:D141–D145 [CrossRef][PubMed]
    [Google Scholar]
  7. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999;41:95–98
    [Google Scholar]
  8. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  9. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007;23:2947–2948 [CrossRef][PubMed]
    [Google Scholar]
  10. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983;[CrossRef]
    [Google Scholar]
  11. Saitou N, Nei M. The neighbor-joining method: a new method for constructing phylogenetic trees. Mol Biol Evol 1987;4:406–425[PubMed]
    [Google Scholar]
  12. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  13. Kluge AG, Farris FS. Quantitative phyletics and the evolution of anurans. Syst Zool 1969;18:1–32 [CrossRef]
    [Google Scholar]
  14. Rzhetsky A, Nei M. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 1993;10:1073–1095[PubMed]
    [Google Scholar]
  15. Felsenstein J. PHYLIP (phylogeny inference package), version 3.5c. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA 1993
  16. Beveridge TJ, Lawrence JR, Murray RGE. Sampling and staining for light microscopy. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR. (editors) Methods for General and Molecular Bacteriology, 3rd ed Washington, DC: American Society for Microbiology; 2007; pp.19–33
    [Google Scholar]
  17. Powers EM. Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol 1995;61:3756–3758[PubMed]
    [Google Scholar]
  18. Schlegel HG, Lafferty R, Krauss I. The isolation of mutants not accumulating poly-β-hydroxybutyric acid. Arch Mikrobiol 1970;71:283–294 [CrossRef][PubMed]
    [Google Scholar]
  19. Spiekermann P, Rehm BHA, Kalscheuer R, Baumeister D, Steinbüchel A. 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 1999;171:73–80 [CrossRef][PubMed]
    [Google Scholar]
  20. Breznak JA, Costilow RN. Physicochemical factors in growth. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: American Society for Microbiology; 2007; pp.309–329
    [Google Scholar]
  21. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: American Society for Microbiology; 2007; pp.330–393
    [Google Scholar]
  22. Wen CM, Tseng CS, Cheng CY, Li YK. Purification, characterization and cloning of a chitinase from Bacillus sp. NCTU2. Biotechnol Appl Biochem 2002;35:213–219 [CrossRef][PubMed]
    [Google Scholar]
  23. Bowman JP. 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 2000;50:1861–1868 [CrossRef][PubMed]
    [Google Scholar]
  24. Nokhal TH, Schlegel HG. Taxonomic study of Paracoccus denitrificans. Int J Syst Bacteriol 1983;33:26–37 [CrossRef]
    [Google Scholar]
  25. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  26. Embley TM, Wait R. Structural lipids of eubacteria. In Goodfellow M, O’Donnell AG. (editors) Chemical Methods in Prokaryotic Systematics Chichester: Wiley; 1994; pp.121–161
    [Google Scholar]
  27. Busse HJ, Auling G. Polyamine pattern as chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 1988;11:1–8 [CrossRef]
    [Google Scholar]
  28. Busse HJ, Bunka S, Hensel A, Lubitz W. Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 1997;47:698–708 [CrossRef]
    [Google Scholar]
  29. Collins MD. Isoprenoid quinones. In: Goodfellow M, O’Donnell AG. (editors) Chemical Methods in Prokaryotic Systematics Chichester: Wiley; 1994; pp.265–309
    [Google Scholar]
  30. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high- performance liquid chromatography. Int J Syst Bacteriol 1989;39:159–167 [CrossRef]
    [Google Scholar]
  31. Ludwig W, Strunk O, Klugbauer S, Klugbauer N, Weizenegger M et al. Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 1998;19:554–568 [CrossRef][PubMed]
    [Google Scholar]
  32. Yabuuchi E, Kosako Y, Yano I, Hotta H, Nishiuchi Y. Transfer of two Burkholderia and an Alcaligenes species to Ralstonia gen. nov.: proposal of Ralstonia pickettii (Ralston, Palleroni and Doudoroff 1973) comb. nov., Ralstonia solanacearum (Smith 1896) comb. nov. and Ralstonia eutropha (Davis 1969) comb. nov. Microbiol Immunol 1995;39:897–904[PubMed][CrossRef]
    [Google Scholar]
  33. De Baere T, Steyaert S, Wauters G, Des Vos P, Goris J et al. Classification of Ralstonia pickettii biovar 3/'thomasii' strains (Pickett 1994) and of new isolates related to nosocomial recurrent meningitis as Ralstonia mannitolytica sp. nov. Int J Syst Evol Microbiol 2001;51:547–558 [CrossRef][PubMed]
    [Google Scholar]
  34. Coenye T, Goris J, De Vos P, Vandamme P, Lipuma JJ. Classification of Ralstonia pickettii-like isolates from the environment and clinical samples as Ralstonia insidiosa sp. nov. Int J Syst Evol Microbiol 2003;53:1075–1080 [CrossRef][PubMed]
    [Google Scholar]
  35. Vaneechoutte M, Kämpfer P, De Baere T, Falsen E, Verschraegen G. Wautersia gen. nov., a novel genus accommodating the phylogenetic lineage including Ralstonia eutropha and related species, and proposal of Ralstonia [Pseudomonas] syzygii (Roberts et al. 1990) comb. nov. Int J Syst Evol Microbiol 2004;54:317–327 [CrossRef][PubMed]
    [Google Scholar]
  36. Safni I, Cleenwerck I, De Vos P, Fegan M, Sly L et al. Polyphasic taxonomic revision of the Ralstonia solanacearum species complex: proposal to emend the descriptions of Ralstonia solanacearum and Ralstonia syzygii and reclassify current R. syzygii strains as Ralstonia syzygii subsp. syzygii subsp. nov., R. solanacearum phylotype IV strains as Ralstonia syzygii subsp. indonesiensis subsp. nov., banana blood disease bacterium strains as Ralstonia syzygii subsp. celebesensis subsp. nov. and R. solanacearum phylotype I and III strains as Ralstonia pseudosolanacearum sp. nov. Int J Syst Evol Microbiol 2014;64:3087–3103 [CrossRef][PubMed]
    [Google Scholar]
  37. Makkar NS, Casida LE Jr. Cupriavidus necator gen. nov., sp. nov.: a nonobligate bacterial predator of bacteria in soil. Int J Syst Bacteriol 1987;37:323–326 [CrossRef]
    [Google Scholar]
  38. Coenye T, Falsen E, Vancanneyt M, Hoste B, Govan JRW et al. Classification of Alcaligenes faecalis-like isolates from the environment and human clinical samples as Ralstonia gilardii sp. nov. Int J Syst Bacteriol 1999;49:405–413 [CrossRef][PubMed]
    [Google Scholar]
  39. Coenye T, Vandamme P, LiPuma JJ. Ralstonia respiraculi sp. nov., isolated from the respiratory tract of cystic fibrosis patients. Int J Syst Evol Microbiol 2003;53:1339–1342 [CrossRef][PubMed]
    [Google Scholar]
  40. Sahin N, Işik K, Tamer AU, Goodfellow M. Taxonomic position of "Pseudomonas oxalaticus" strain Ox1T (DSM 1105T) (Khambata and Bhat, 1953) and its description in the genus Ralstonia as Ralstonia oxalatica comb. nov. Syst Appl Microbiol 2000;23:206–209 [CrossRef][PubMed]
    [Google Scholar]
  41. Goris J, De Vos P, Coenye T, Hoste B, Janssens D et al. Classification of metal-resistant bacteria from industrial biotopes as Ralstonia campinensis sp. nov., Ralstonia metallidurans sp. nov. and Ralstonia basilensis Steinle et al. 1998 emend. Int J Syst Evol Microbiol 2001;51:1773–1782 [CrossRef][PubMed]
    [Google Scholar]
  42. Kageyama C, Ohta T, Hiraoka K, Suzuki M, Okamoto T et al. Chlorinated aliphatic hydrocarbon-induced degradation of trichloroethylene in Wautersia numadzuensis sp. nov. Arch Microbiol 2005;183:56–65 [CrossRef][PubMed]
    [Google Scholar]
  43. Sato Y, Nishihara H, Yoshida M, Watanabe M, Rondal JD et al. Cupriavidus pinatubonensis sp. nov. and Cupriavidus laharis sp. nov., novel hydrogen-oxidizing, facultatively chemolithotrophic bacteria isolated from volcanic mudflow deposits from Mt. Pinatubo in the Philippines. Int J Syst Evol Microbiol 2006;56:973–978 [CrossRef][PubMed]
    [Google Scholar]
  44. Cuadrado V, Gomila M, Merini L, Giulietti AM, Moore ERB. Cupriavidus pampae sp. nov., a novel herbicide-degrading bacterium isolated from agricultural soil. Int J Syst Evol Microbiol 2010;60:2606–2612 [CrossRef][PubMed]
    [Google Scholar]
  45. Estrada-de Los Santos P, Martínez-Aguilar L, López-Lara IM, Caballero-Mellado J. Cupriavidus alkaliphilus sp. nov., a new species associated with agricultural plants that grow in alkaline soils. Syst Appl Microbiol 2012;35:310–314 [CrossRef][PubMed]
    [Google Scholar]
  46. Estrada-de Los Santos P, Solano-Rodríguez R, Matsumura-Paz LT, Vásquez-Murrieta MS, Martínez-Aguilar L. Cupriavidus plantarum sp. nov., a plant-associated species. Arch Microbiol 2014;196:811–817 [CrossRef][PubMed]
    [Google Scholar]
  47. Singh P, Kim YJ, Nguyen NL, Hoang VA, Sukweenadhi J et al. Cupriavidus yeoncheonense sp. nov., isolated from soil of ginseng. Antonie van Leeuwenhoek 2015;107:749–758 [CrossRef][PubMed]
    [Google Scholar]
  48. Sun LN, Wang DS, Yang ED, Fang LC, Chen YF et al. Cupriavidus nantongensis sp. nov., a novel chlorpyrifos-degrading bacterium isolated from sludge. Int J Syst Evol Microbiol 2016;66:2335–2341 [CrossRef][PubMed]
    [Google Scholar]
  49. Vandamme P, Goris J, Coenye T, Hoste B, Janssens D et al. Assignment of Centers for Disease Control group IVc-2 to the genus Ralstonia as Ralstonia paucula sp. nov. Int J Syst Bacteriol 1999;49:663–669 [CrossRef][PubMed]
    [Google Scholar]
  50. Heckmann K, Schmidt HJ. Polynucleobacter necessaries gen. nov., sp. nov., an obligately endosymbiotic bacterium living in the cytoplasm of Euplotes aediculatus. Int J Syst Bacteriol 1987;37:456–457 [CrossRef]
    [Google Scholar]
  51. Hahn MW, Lang E, Brandt U, Wu QL, Scheuerl T. Emended description of the genus Polynucleobacter and the species Polynucleobacter necessarius and proposal of two subspecies, P. necessarius subsp. necessarius subsp. nov. and P. necessariussubsp. asymbioticussubsp. nov. Int J Syst Evol Microbiol 2009;59:2002–2009 [CrossRef][PubMed]
    [Google Scholar]
  52. Hahn MW, Lang E, Brandt U, Lünsdorf H, Wu QL et al. Polynucleobacter cosmopolitanus sp. nov., free-living planktonic bacteria inhabiting freshwater lakes and rivers. Int J Syst Evol Microbiol 2010;60:166–173 [CrossRef][PubMed]
    [Google Scholar]
  53. Hahn MW, Lang E, Brandt U, Spröer C. Polynucleobacter acidiphobus sp. nov., a representative of an abundant group of planktonic freshwater bacteria. Int J Syst Evol Microbiol 2011;61:788–794 [CrossRef][PubMed]
    [Google Scholar]
  54. Hahn MW, Lang E, Tarao M, Brandt U. Polynucleobacter rarus sp. nov., a free-living planktonic bacterium isolated from an acidic lake. Int J Syst Evol Microbiol 2011;61:781–787 [CrossRef][PubMed]
    [Google Scholar]
  55. Hahn MW, Minasyan A, Lang E, Koll U, Spröer C. Polynucleobacter difficilis sp. nov., a planktonic freshwater bacterium affiliated with subcluster B1 of the genus Polynucleobacter. Int J Syst Evol Microbiol 2012;62:376–383 [CrossRef][PubMed]
    [Google Scholar]
  56. Yabuuchi E, Kosako Y, Oyaizu H, Yano I, Hotta H et al. Proposal of Burkholderia gen. nov. and transfer of seven species of the genus Pseudomonas homology group II to the new genus, with the type species Burkholderia cepacia (Palleroni and Holmes 1981) comb. nov. Microbiol Immunol 1992;36:1251–1275 [CrossRef][PubMed]
    [Google Scholar]
  57. Gillis M, van van T, Bardin R, Goor M, Hebbar P et al. Polyphasic taxonomy in the genus Burkholderia leading to an emended description of the genus and proposition of Burkholderia vietnamiensis sp. nov. for N2-fixing isolates from rice in Vietnam. Int J Syst Bacteriol 1995;45:274–289 [CrossRef]
    [Google Scholar]
  58. Palleroni NJ. Genus I. Burkholderia In Brenner DJ, Krieg NR, Staley JT, Garrity GM. (editors) Burkholderia. In Bergey’s Manual of Systematic Bacteriology, 2nd ed.vol. 2 (The Proteobacteria), Part C (The Alpha-, Beta-, Delta-, and Epsilonproteobacteria) New York: Springer; 2005; pp.575–600[CrossRef]
    [Google Scholar]
  59. De Smet B, Mayo M, Peeters C, Zlosnik JEA, Spilker T et al. Burkholderia stagnalis sp. nov. and Burkholderia territorii sp. nov., two novel Burkholderia cepacia complex species from environmental and human sources. Int J Syst Evol Microbiol 2015;65:2265–2271 [CrossRef][PubMed]
    [Google Scholar]
  60. Lee JC, Whang KS. Burkholderia humisilvae sp. nov., Burkholderia solisilvae sp. nov. and Burkholderia rhizosphaerae sp. nov., isolated from forest soil and rhizosphere soil. Int J Syst Evol Microbiol 2015;65:2986–2992 [CrossRef][PubMed]
    [Google Scholar]
  61. Coenye T, Falsen E, Hoste B, Ohlén M, Goris J et al. 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 2000;50:887–899 [CrossRef][PubMed]
    [Google Scholar]
  62. Anandham R, Indiragandhi P, Kwon SW, Sa TM, Jeon CO et al. Pandoraea thiooxydans sp. nov., a facultatively chemolithotrophic, thiosulfate-oxidizing bacterium isolated from rhizosphere soils of sesame (Sesamum indicum L.). Int J Syst Evol Microbiol 2010;60:21–26 [CrossRef][PubMed]
    [Google Scholar]
  63. Sahin N, Tani A, Kotan R, Sedlácek I, Kimbara K et al. Pandoraea oxalativorans sp. nov., Pandoraea faecigallinarum sp. nov. and Pandoraea vervacti sp. nov., isolated from oxalate-enriched culture. Int J Syst Evol Microbiol 2011;61:2247–2253 [CrossRef][PubMed]
    [Google Scholar]
  64. Chang SC, Wang JT, Vandamme P, Hwang JH, Chang PS et al. Chitinimonas taiwanensis gen. nov., sp. nov., a novel chitinolytic bacterium isolated from a freshwater pond for shrimp culture. Syst Appl Microbiol 2004;27:43–49 [CrossRef][PubMed]
    [Google Scholar]
  65. Kim BY, Weon HY, Yoo SH, Chen WM, Kwon SW et al. Chitinimonas koreensis sp. nov., isolated from greenhouse soil in Korea. Int J Syst Evol Microbiol 2006;56:1761–1764 [CrossRef][PubMed]
    [Google Scholar]
  66. Joung Y, Lee BI, Kang H, Kim H, Joh K. Chitinimonas viridis sp. nov., isolated from a mesotrophic artificial lake. Int J Syst Evol Microbiol 2014;64:1123–1126 [CrossRef][PubMed]
    [Google Scholar]
  67. Li Y, Zhu H, Lai Q, Lei X, Chen Z et al. Chitinimonas prasina sp. nov., isolated from lake water. Int J Syst Evol Microbiol 2014;64:3005–3009 [CrossRef][PubMed]
    [Google Scholar]
  68. Spring S, Kämpfer P, Schleifer KH. Limnobacter thiooxidans gen. nov., sp. nov., a novel thiosulfate-oxidizing bacterium isolated from freshwater lake sediment. Int J Syst Evol Microbiol 2001;51:1463–1470 [CrossRef][PubMed]
    [Google Scholar]
  69. Lu H, Sato Y, Fujimura R, Nishizawa T, Kamijo T et al. Limnobacter litoralis sp. nov., a thiosulfateoxidizing, heterotrophic bacterium isolated from a volcanic deposit, and emended description of the genus Limnobacter. Int J Syst Evol Microbiol 2011;61:404–407 [CrossRef][PubMed]
    [Google Scholar]
  70. Ohshima S, Sato Y, Fujimura R, Takashima Y, Hamada M et al. Mycoavidus cysteinexigens gen. nov., sp. nov., an endohyphal bacterium isolated from a soil isolate of the fungus Mortierella elongata. Int J Syst Evol Microbiol 2016;66:2052–2057 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001561
Loading
/content/journal/ijsem/10.1099/ijsem.0.001561
Loading

Data & Media loading...

Supplements

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