1887

Abstract

A novel bacterial strain, designated THS-13, isolated from a freshwater mesocosm in Taiwan, was characterized by taking a polyphasic taxonomic approach. Cells of strain THS-13 were Gram-stain-negative, aerobic, rod-shaped, motile by means of a single polar flagellum and formed translucent white coloured colonies. Growth occurred at 20–35 °C (optimum, 25 °C), at pH 5–8 (pH 6) and with 0–2 % NaCl (1 %). Phylogenetic analyses based on 16S rRNA gene and coding sequences of 92 protein clusters revealed that the strain belonged to the family Nevskiaceae in the class Gammaproteobacteria and represented an independent taxon separated from other genera. Strain THS-13 shared low level of 16S rRNA gene sequence similarity (less than 93.0 %) to members of other genera in the family Nevskiaceae and was most closely related to Nevskia aquatilis F2-63 (92.9 %). Strain THS-13 showed less than 73.4 % average nucleotide identity and less than 23.8 % digital DNA–DNA hybridization identity compared to the type strains of related genera within the family Nevskiaceae . The predominant fatty acids were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and iso-C16 : 0. The major isoprenoid quinone was Q-8 and the DNA G+C content was 67.6 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, an uncharacterized aminophospholipid, an uncharacterized phospholipid and an uncharacterized aminolipid. On the basis of the genotypic and phenotypic data, strain THS-13 represents a novel species of a new genus in the family Nevskiaceae , for which we propose the name Stagnimonas aquatica gen. nov., sp. nov. The type strain is THS-13 (=BCRC 81158=LMG 30925=KCTC 62868).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003365
2019-03-25
2024-04-18
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/6/1606.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003365&mimeType=html&fmt=ahah

References

  1. Henrici AT, Johnson D, Bacteria S. Stalked bacteria, a new order of Schizomycetes. J Bacteriol 1935; 29:3–4
    [Google Scholar]
  2. Parte AC. LPSN - list of prokaryotic names with standing in nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article][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 [View Article][PubMed]
    [Google Scholar]
  4. Anzai Y, Kudo Y, Oyaizu H. The phylogeny of the genera Chryseomonas, Flavimonas, and Pseudomonas supports synonymy of these three genera. Int J Syst Bacteriol 1997; 47:249–251 [View Article][PubMed]
    [Google Scholar]
  5. 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 [View Article][PubMed]
    [Google Scholar]
  6. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article][PubMed]
    [Google Scholar]
  7. 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 [View Article][PubMed]
    [Google Scholar]
  8. 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]
  9. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  10. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  11. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Syst Zool 1969; 18:1–32 [View Article]
    [Google Scholar]
  12. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  13. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983
    [Google Scholar]
  14. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article][PubMed]
    [Google Scholar]
  15. Nei M, Kumar S. Molecular Evolution and Phylogenetics New York: Oxford University Press; 2000
    [Google Scholar]
  16. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
    [Google Scholar]
  17. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [View Article][PubMed]
    [Google Scholar]
  18. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article][PubMed]
    [Google Scholar]
  19. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  20. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  21. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article][PubMed]
    [Google Scholar]
  22. Na SI, Kim YO, Yoon SH, Ha SM, Baek I et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article][PubMed]
    [Google Scholar]
  23. Beveridge TJ, Lawrence JR, Murray RGE. Sampling and staining for light microscopy. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR et al. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: American Society for Microbiology; 2007 pp. 19–33
    [Google Scholar]
  24. 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]
  25. Schlegel HG, Lafferty R, Krauss I. The isolation of mutants not accumulating poly-beta-hydroxybutyric acid. Arch Mikrobiol 1970; 71:283–294 [View Article][PubMed]
    [Google Scholar]
  26. Spiekermann P, Rehm BH, 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 [View Article][PubMed]
    [Google Scholar]
  27. Breznak JA, Costilow RN. Physicochemical factors in growth. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR et al. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: American Society for Microbiology; 2007 pp. 309–329
    [Google Scholar]
  28. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparativesystematic. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR et al. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: American Society for Microbiology; 2007 pp. 330–393
    [Google Scholar]
  29. 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 [View Article][PubMed]
    [Google Scholar]
  30. 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 [View Article][PubMed]
    [Google Scholar]
  31. 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 [View Article][PubMed]
    [Google Scholar]
  32. Nokhal T-H, Schlegel HG. Taxonomic study of Paracoccus denitrificans . Int J Syst Bacteriol 1983; 33:26–37 [View Article]
    [Google Scholar]
  33. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Netwark, DE: MIDI Inc; 1990
    [Google Scholar]
  34. 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]
  35. Collins MD. Isoprenoid quinones. In Goodfellow M, O’Donnell AG. (editors) Chemical Methods in Prokaryotic Systematics Chichester: Wiley; 1994 pp. 265–309
    [Google Scholar]
  36. Ludwig W, Strunk O, Klugbauer S, Klugbauer N, Weizenegger M et al. Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 1998; 19:554–568 [View Article][PubMed]
    [Google Scholar]
  37. Stürmeyer H, Overmann J, Babenzien HD, Cypionka H. Ecophysiological and phylogenetic studies of Nevskia ramosa in pure culture. Appl Environ Microbiol 1998; 64:1890–1894[PubMed]
    [Google Scholar]
  38. Weon HY, Kim BY, Son JA, Song MH, Kwon SW et al. Nevskia soli sp. nov., isolated from soil cultivated with Korean ginseng. Int J Syst Evol Microbiol 2008; 58:578–580 [View Article][PubMed]
    [Google Scholar]
  39. Kim SJ, Weon HY, Kim YS, Park IC, Son JA et al. Nevskia terrae sp. nov., isolated from soil. Int J Syst Evol Microbiol 2011; 61:1226–1229 [View Article][PubMed]
    [Google Scholar]
  40. Leandro T, França L, Nobre MF, Schumann P, Rosselló-Móra R et al. Nevskia aquatilis sp. nov. and Nevskia persephonica sp. nov., isolated from a mineral water aquifer and the emended description of the genus Nevskia . Syst Appl Microbiol 2012; 35:297–301 [View Article][PubMed]
    [Google Scholar]
  41. Palleroni NJ, Port AM, Chang HK, Zylstra GJ. Hydrocarboniphaga effusa gen. nov., sp. nov., a novel member of the α-Proteobacteria active in alkane and aromatic hydrocarbon degradation. Int J Syst Evol Microbiol 2004; 54:1203–1207 [View Article][PubMed]
    [Google Scholar]
  42. Liu Y, Song XF, Jiang JT, Liu YH, Xu CJ et al. Hydrocarboniphaga daqingensis sp. nov., isolated from a freshwater lake. Int J Syst Evol Microbiol 2011; 61:408–411 [View Article][PubMed]
    [Google Scholar]
  43. Kim MK, Kim YJ, Cho DH, Yi TH, Soung NK et al. Solimonas soli gen. nov., sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2007; 57:2591–2594 [View Article][PubMed]
    [Google Scholar]
  44. Zhou Y, Zhang YQ, Zhi XY, Wang X, Dong J et al. Description of Sinobacter flavus gen. nov., sp. nov., and proposal of Sinobacteraceae fam. nov. Int J Syst Evol Microbiol 2008; 58:184–189 [View Article][PubMed]
    [Google Scholar]
  45. Friedrich MM, Lipski A. Alkanibacter difficilis gen. nov., sp. nov. and Singularimonas variicoloris gen. nov., sp. nov., hexane-degrading bacteria isolated from a hexane-treated biofilter. Int J Syst Evol Microbiol 2008; 58:2324–2329 [View Article][PubMed]
    [Google Scholar]
  46. Sheu SY, Cho NT, Arun AB, Chen WM. Proposal of Solimonas aquatica sp. nov., reclassification of Sinobacter flavus Zhou et al. 2008 as Solimonas flava comb. nov. and singularimonas variicoloris Friedrich and Lipski 2008 as Solimonas variicoloris comb. nov. and emended descriptions of the genus Solimonas and its type species Solimonas soli. Int J Syst Evol Microbiol 2011; 61:2284–2291 [View Article][PubMed]
    [Google Scholar]
  47. Kim SJ, Moon JY, Weon HY, Ahn JH, Chen WM et al. Solimonas terrae sp. nov., isolated from soil. Int J Syst Evol Microbiol 2014; 64:1218–1222 [View Article][PubMed]
    [Google Scholar]
  48. Lee Y, Lee B, Lee K, Jeon CO. Solimonas fluminis sp. nov., isolated from a freshwater river. Int J Syst Evol Microbiol 2018; 68:2755–2759 [View Article][PubMed]
    [Google Scholar]
  49. Zhang XQ, Sun C, Wang CS, Zhang X, Zhou X et al. Sinimarinibacterium flocculans gen. nov., sp. nov., a gammaproteobacterium from offshore surface seawater. Int J Syst Evol Microbiol 2015; 65:3541–3546 [View Article][PubMed]
    [Google Scholar]
  50. Losey NA, Stevenson BS, Verbarg S, Rudd S, Moore ER et al. Fontimonas thermophila gen. nov., sp. nov., a moderately thermophilic bacterium isolated from a freshwater hot spring, and proposal of Solimonadaceae fam. nov. to replace Sinobacteraceae Zhou et al. 2008. Int J Syst Evol Microbiol 2013; 63:254–259 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003365
Loading
/content/journal/ijsem/10.1099/ijsem.0.003365
Loading

Data & Media loading...

Supplements

Supplementary File 1

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