1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 69, Issue 12

sp. nov., isolated from water sampled from a rice paddy field Free

Abstract

Strain TER-1 was isolated from water sampled from a rice paddy field in Taiwan. Cells were Gram-negative, aerobic, motile, rod-shaped and formed pink-coloured colonies. Optimal growth occurred at 25–30 °C, pH 6–7 and in the presence of 0.5 % NaCl. Strain TER-1 could grow on C1 compounds such as methanol, formic acid, methylamine and dimethylamine as sole carbon source, and carry methanol dehydrogenase gene, which supports its methylotrophic metabolism. The results of phylogenetic analyses based on the 16S rRNA gene sequence, methanol dehydrogenase gene sequence and coding sequences of 92 protein clusters indicated that strain TER-1 formed a phylogenetic lineage in the genus . Strain TER-1 was most closely related to AR24 with 96.8 % 16S rRNA gene sequence similarity. Strain TER-1 showed 77.1–82.8 % average nucleotide identity and 16.4–20.2 % digital DNA–DNA hybridization identity with the strains of other species. The major fatty acid of strain TER-1 was Cω7. The predominant hydroxy fatty acid was C 3-OH. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and two uncharacterized lipids. The only isoprenoid quinone was Q-10. The genomic DNA G+C content of strain TER-1 was 71.9 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain TER-1 should be classified in a novel species of the genus , for which the name sp. nov. is proposed. The type strain is TER-1 (=BCRC 81157=LMG 30931=KCTC 62864).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Alphaproteobacteria , Methylobacteriaceae , Methylobacterium oryzihabitans , Rhizobiales and rice paddy field
© 2019 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003693
2019-12-01
2024-04-18
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/12/3843.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003693&mimeType=html&fmt=ahah

References

  1. Patt TE, Cole GC, Hanson RS. Methylobacterium, a new genus of facultatively methylotrophic bacteria. Int J Syst Bacteriol 1976; 26:226–229
     [Google Scholar]
  2. Green PN, Bousfield IJ. Emendation of Methylobacterium (Patt, Cole, and Hanson 1976); Methylobacterium rhodinum (Heumann 1962) comb. nov. corrig. Methylobacterium radiotolerans (Ito & Iizuka 1971) comb. nov. corrig.; and Methylobacterium mesophilicum (Austin & Goodfellow 1979) comb. nov. Int J Syst Bacteriol 1983; 33:875–877
     [Google Scholar]
  3. 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]
  4. Green PN, Ardley JK. Review of the genus Methylobacterium and closely related organisms: a proposal that some Methylobacterium species be reclassified into a new genus, Methylorubrum gen. nov. Int J Syst Evol Microbiol 2018; 68:2727–2748 [View Article][PubMed]
     [Google Scholar]
  5. Kelly DP, McDonald IR, Wood AP. The family Methylobacteriaceae . In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F et al. (editors) The Prokaryotes-Alphaproteobacteria and Betaproteobacteria, 4th ed. Berlin: Springer; 2014 pp. 313–340
     [Google Scholar]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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]
  12. 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]
  13. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376[PubMed]
     [Google Scholar]
  14. Kluge AG, Farris FS. Quantitative phyletics and the evolution of anurans. Syst Zool 1969; 18:1–32
     [Google Scholar]
  15. 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]
  16. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983
     [Google Scholar]
  17. 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]
  18. Nei M, Kumar S. Molecular Evolution and Phylogenetics New York: Oxford University Press; 2000
     [Google Scholar]
  19. Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 2016; 32:3047–3048 [View Article][PubMed]
     [Google Scholar]
  20. Lee I, Chalita M, Ha SM, Na SI, Yoon SH et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [View Article][PubMed]
     [Google Scholar]
  21. 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]
  22. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][PubMed]
     [Google Scholar]
  23. Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ et al. Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Mol Biol Evol 2017; 34:2115–2122 [View Article][PubMed]
     [Google Scholar]
  24. Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res 2016; 44:D286–D293 [View Article][PubMed]
     [Google Scholar]
  25. Ramachandran A, Walsh DA. Investigation of XoxF methanol dehydrogenases reveals new methylotrophic bacteria in pelagic marine and freshwater ecosystems. FEMS Microbiol Ecol 2015; 91:fiv105 [View Article][PubMed]
     [Google Scholar]
  26. 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]
  27. 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]
  28. 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]
  29. 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]
  30. 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]
  31. 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]
  32. Schlegel HG, Lafferty R, Krauss I. The isolation of mutants not accumulating poly-beta-hydroxybutyric acid. Arch Mikrobiol 1970; 71:283–294[PubMed]
     [Google Scholar]
  33. 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]
  34. 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]
  35. 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]
  36. 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]
  37. 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 Pt 5:1861–1868 [View Article][PubMed]
     [Google Scholar]
  38. 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]
  39. Nokhal TH, Schlegel HG. Taxonomic study of Paracoccus denitrificans . Int J Syst Bacteriol 1983; 33:26–37
     [Google Scholar]
  40. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  41. 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]
  42. Collins MD. Isoprenoid quinones. In Goodfellow M, O’Donnell AG. (editors) Chemical Methods in Prokaryotic Systematics Chichester: Wiley; 1994 pp. 265–309
     [Google Scholar]
  43. Gallego V, García MT, Ventosa A. Methylobacterium isbiliense sp. nov., isolated from the drinking water system of Sevilla, Spain. Int J Syst Evol Microbiol 2005; 55:2333–2337 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003693
Loading
Methylobacterium oryzihabitans sp. nov., isolated from water sampled from a rice paddy field
Int J Syst Evol Microbiol 69, 3843 (2019); https://doi.org/10.1099/ijsem.0.003693
/content/journal/ijsem/10.1099/ijsem.0.003693
/content/journal/ijsem/10.1099/ijsem.0.003693
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited 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