1887

Abstract

A novel facultatively methanol-utilizing bacterial strain, SM30, was isolated from rice rhizosphere. Strain SM30 was Gram-stain-negative, aerobic, motile, short rods, and grew optimally at pH 7 and at 28 °C. It could tolerate 0 to 2 % (w/v) NaCl. Based on 16S rRNA gene sequence comparisons, strain SM30 was most closely related to Pleomorphomonas oryzae DSM 16300, with a low similarity of 94.17 %. One of the lanthanide metals, lanthanum, could enhance its growth slightly on methanol. Phylogenetic trees, based on the mxaF, xoxF and cpn60 genes of SM30 showed its distinct phylogenetic position with respect to species with validly published names. Polymerase chain reaction (PCR) amplification of the nifH and growth on nitrogen-free medium indicated that strain SM30 is a diazotroph. The major cellular fatty acids were summed feature 8 (containing 18 : 1ω7c and 18 : 1ω6c) and cyclo 19 : 0ω8c. The major quinone was ubiquinone 10. The DNA G+C content was 74.6 mol%. Based on the genotypic and phenotypic characteristics, strain SM30 represents a novel genus and species, for which the name Oharaeibacter diazotrophicus gen. nov., sp. nov. is proposed with the type strain SM30 (=NBRC 111955=DSM 102969).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001660
2017-04-03
2019-10-17
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/3/576.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001660&mimeType=html&fmt=ahah

References

  1. Pol A, Heijmans K, Harhangi HR, Tedesco D, Jetten MS et al. Methanotrophy below pH 1 by a new Verrucomicrobia species. Nature 2007;450:874–878 [CrossRef][PubMed]
    [Google Scholar]
  2. Anthony C. The Biochemistry of Methylotrophs London: Academic Press; 1982
    [Google Scholar]
  3. Keltjens JT, Pol A, Reimann J, Op den Camp HJ. PQQ-dependent methanol dehydrogenases: rare-earth elements make a difference. Appl Microbiol Biotechnol 2014;98:6163–6183 [CrossRef][PubMed]
    [Google Scholar]
  4. Vu HN, Subuyuj GA, Vijayakumar S, Good NM, Martinez-Gomez NC et al. Lanthanide-dependent regulation of methanol oxidation systems in Methylobacterium extorquens AM1 and their contribution to methanol growth. J Bacteriol 2016;198:1250–1259 [CrossRef][PubMed]
    [Google Scholar]
  5. Richardson IW, Anthony C. Characterization of mutant forms of the quinoprotein methanol dehydrogenase lacking an essential calcium ion. Biochem J 1992;287:709–715 [CrossRef][PubMed]
    [Google Scholar]
  6. Ghosh M, Avezoux A, Anthony C, Harlos K, Blake CC. X-ray structure of PQQ-dependent methanol dehydrogenase. EXS 1994;71:251–260[PubMed]
    [Google Scholar]
  7. Harris TK, Davidson VL. Replacement of enzyme-bound calcium with strontium alters the kinetic properties of methanol dehydrogenase. Biochem J 1994;300:175–182 [CrossRef][PubMed]
    [Google Scholar]
  8. Chistoserdova L, Lidstrom ME. Molecular and mutational analysis of a DNA region separating two methylotrophy gene clusters in Methylobacterium extorquens AM1. Microbiology 1997;143:1729–1736 [CrossRef][PubMed]
    [Google Scholar]
  9. Hibi Y, Asai K, Arafuka H, Hamajima M, Iwama T et al. Molecular structure of La3+-induced methanol dehydrogenase-like protein in Methylobacterium radiotolerans. J Biosci Bioeng 2011;111:547–549 [CrossRef][PubMed]
    [Google Scholar]
  10. Wu ML, Wessels JC, Pol A, Op den Camp HJ, Jetten MS et al. XoxF-type methanol dehydrogenase from the anaerobic methanotroph “Candidatus Methylomirabilis oxyfera”. Appl Environ Microbiol 2015;81:1442–1451 [CrossRef][PubMed]
    [Google Scholar]
  11. Chu F, Lidstrom ME. XoxF acts as the predominant methanol dehydrogenase in the type I methanotroph Methylomicrobium buryatense. J Bacteriol 2016;198:1317–1325 [CrossRef][PubMed]
    [Google Scholar]
  12. Krishnamurthy N, Gupta CK. Extractive Metallurgy of Rare Earths Boca Raton, FL: CRC Press; 2004;[CrossRef]
    [Google Scholar]
  13. Chistoserdova L. Lanthanides: new life metals?. World J Microbiol Biotechnol 2016;32:138 [CrossRef][PubMed]
    [Google Scholar]
  14. Whittenbury R, Phillips KC, Wilkinson JF. Enrichment, isolation and some properties of methane-utilizing bacteria. J Gen Microbiol 1970;61:205–218 [CrossRef][PubMed]
    [Google Scholar]
  15. Alamgir KM, Masuda S, Fujitani Y, Fukuda F, Tani A. Production of ergothioneine by Methylobacterium species. Front Microbiol 2015;6:1185 [CrossRef][PubMed]
    [Google Scholar]
  16. Gerhardt P, Murray RGE, Wood WA, Krieg NR. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
    [Google Scholar]
  17. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P. (editor) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp.607–654
    [Google Scholar]
  18. Eckert B, Weber OB, Kirchhof G, Halbritter A, Stoffels M et al. Azospirillum doebereinerae sp. nov., a nitrogen-fixing bacterium associated with the C4-grass Miscanthus. Int J Syst Evol Microbiol 2001;51:17–26 [CrossRef][PubMed]
    [Google Scholar]
  19. Suarez C, Ratering S, Geissler-Plaum R, Schnell S. Hartmannibacter diazotrophicus gen. nov., sp. nov., a phosphate-solubilizing and nitrogen-fixing alphaproteobacterium isolated from the rhizosphere of a natural salt-meadow plant. Int J Syst Evol Microbiol 2014;64:3160–3167 [CrossRef]
    [Google Scholar]
  20. Pol A, Barends TR, Dietl A, Khadem AF, Eygensteyn J et al. Rare earth metals are essential for methanotrophic life in volcanic mudpots. Environ Microbiol 2014;16:255–264 [CrossRef][PubMed]
    [Google Scholar]
  21. Bogart JA, Lewis AJ, Schelter EJ. DFT study of the active site of the XoxF-type natural, cerium-dependent methanol dehydrogenase enzyme. Chemistry 2015;21:1743–1748 [CrossRef][PubMed]
    [Google Scholar]
  22. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959;37:911–917 [CrossRef][PubMed]
    [Google Scholar]
  23. Tamaoka J, Katayama-Fujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. Journal of Applied Bacteriology 1983;54:31–36 [CrossRef]
    [Google Scholar]
  24. Ghosh R, Quayle JR. Phenazine ethosulfate as a preferred electron acceptor to phenazine methosulfate in dye-linked enzyme assays. Anal Biochem 1979;99:112–117 [CrossRef][PubMed]
    [Google Scholar]
  25. Tani A, Sahin N, Matsuyama Y, Enomoto T, Nishimura N et al. High-throughput identification and screening of novel Methylobacterium species using whole-cell MALDI-TOF/MS analysis. PLoS One 2012;7:e40784 [CrossRef][PubMed]
    [Google Scholar]
  26. Noguchi T, Kumagai M, Kuninaka A. Analysis of base composition of sequenced DNA's by high performance liquid chromatography of their nuclease P1 hydrolysate. Agric Biol Chem 1988;52:2355–2356
    [Google Scholar]
  27. Wright ES, Yilmaz LS, Noguera DR. DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences. Appl Environ Microbiol 2012;78:717–725 [CrossRef][PubMed]
    [Google Scholar]
  28. 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]
  29. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 2007;35:7188–7196 [CrossRef][PubMed]
    [Google Scholar]
  30. Gascuel O. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol 1997;14:685–695 [CrossRef][PubMed]
    [Google Scholar]
  31. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425[PubMed]
    [Google Scholar]
  32. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010;59:307–321 [CrossRef][PubMed]
    [Google Scholar]
  33. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  34. Neufeld JD, Schäfer H, Cox MJ, Boden R, Mcdonald IR et al. Stable-isotope probing implicates Methylophaga spp and novel Gammaproteobacteria in marine methanol and methylamine metabolism. ISME J 2007;1:480–491 [CrossRef][PubMed]
    [Google Scholar]
  35. Taubert M, Grob C, Howat AM, Burns OJ, Dixon JL et al. XoxF encoding an alternative methanol dehydrogenase is widespread in coastal marine environments. Environ Microbiol 2015;17:3937–3948 [CrossRef][PubMed]
    [Google Scholar]
  36. Sahin N, Gonzalez JM, Iizuka T, Hill JE. Characterization of two aerobic ultramicrobacteria isolated from urban soil and a description of Oxalicibacterium solurbis sp. nov. FEMS Microbiol Lett 2010;307:25–29 [CrossRef][PubMed]
    [Google Scholar]
  37. Bürgmann H, Widmer F, von Sigler W, Zeyer J. New molecular screening tools for analysis of free-living diazotrophs in soil. Appl Environ Microbiol 2004;70:240–247 [CrossRef][PubMed]
    [Google Scholar]
  38. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011;28:2731–2739 [CrossRef][PubMed]
    [Google Scholar]
  39. Xie C-H, Yokota A. Pleomorphomonas oryzae gen. nov., sp. nov., a nitrogen-fixing bacterium isolated from paddy soil of Oryza sativa. Int J Syst Evol Microbiol 2005;55:1233–1237 [CrossRef]
    [Google Scholar]
  40. Im W-T, Kim SH, Kim MK, Ten LN, Lee ST. Pleomorphomonas koreensis sp. nov., a nitrogen-fixing species in the order Rhizobiales. Int J Syst Evol Microbiol 2006;56:1663–1666 [CrossRef]
    [Google Scholar]
  41. Madhaiyan M, Jin TY, Roy JJ, Kim S-J, Weon H-Y et al. Pleomorphomonas diazotrophica sp. nov., an endophytic N-fixing bacterium isolated from root tissue of Jatropha curcas L. Int J Syst Evol Microbiol 2013;63:2477–2483 [CrossRef]
    [Google Scholar]
  42. Yarza P, Richter M, Peplies J, Euzeby J, Amann R et al. The All-Species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008;31:241–250 [CrossRef][PubMed]
    [Google Scholar]
  43. Poroshina MN, Trotsenko YA, Doronina NV. Methylobrevis pamukkalensis gen. nov., sp. nov., a halotolerant restricted facultative methylotroph isolated from saline water. Int J Syst Evol Microbiol 2015;65:1321–1327 [CrossRef][PubMed]
    [Google Scholar]
  44. Biebl H, Pukall R, Lünsdorf H, Schulz S, Allgaier M et al. Description of Labrenzia alexandrii gen. nov., sp. nov., a novel alphaproteobacterium containing bacteriochlorophyll a, and a proposal for reclassification of Stappia aggregata as Labrenzia aggregata comb. nov., of Stappia marina as Labrenzia marina comb. nov. and of Stappia alba as Labrenzia alba comb. nov., and emended descriptions of the genera Pannonibacter, Stappia and Roseibium, and of the species Roseibium denhamense and Roseibium hamelinense. Int J Syst Evol Microbiol 2007;57:1095–1107 [CrossRef][PubMed]
    [Google Scholar]
  45. Bibi F, Jeong JH, Chung EJ, Jeon CO, Chung YR. Labrenzia suaedae sp. nov., a marine bacterium isolated from a halophyte, and emended description of the genus Labrenzia. Int J Syst Evol Microbiol 2014;64:1116–1122 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001660
Loading
/content/journal/ijsem/10.1099/ijsem.0.001660
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