Skip to main content
SpringerLink
Log in

Taxonomy of oxalotrophic Methylobacterium strains

  • Original Paper
  • Published:
Naturwissenschaften Aims and scope Submit manuscript

Abstract

Most of the oxalotrophic bacteria are facultative methylotrophs and play important ecological roles in soil fertility and cycling of elements. This study gives a detailed picture of the taxonomy and diversity of these bacteria and provides new information about the taxonomical variability within the genus Methylobacterium. Twelve mesophilic, pink-pigmented, and facultatively methylotrophic oxalate-oxidizing strains were included in this work that had been previously isolated from the soil and some plant tissues by the potassium oxalate enrichment method. The isolates were characterized using biochemical tests, cellular lipid profiles, spectral characteristics of carotenoid pigments, G+C content of the DNA, and 16S rDNA sequencing. The taxonomic similarities among the strains were analyzed using the simple matching (S SM) and Jaccard (S J) coefficients, and the UPGMA clustering algorithm. The phylogenetic position of the strains was inferred by the neighbor-joining method on the basis of the 16S rDNA sequences. All isolates were Gram-negative, facultatively methylotrophic, oxidase and catalase positive, and required no growth factors. Based on the results of numerical taxonomy, the strains formed four closely related clusters sharing ≥85% similarity. Analysis of the 16S rDNA sequences demonstrated that oxalotrophic, pink-pigmented, and facultatively methylotrophic strains could be identified as members of the genus Methylobacterium. Except for M. variabile and M. aquaticum, all of the Methylobacterium type strains tested had the ability of oxalate utilization. Our results indicate that the capability of oxalate utilization seems to be an uncommon trait and could be used as a valuable taxonomic criterion for differentiation of Methylobacterium species.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  • Anthony C, Zatman LJ (1964) The microbial oxidation of methanol: I. Isolation and properties of Pseudomonas sp. M27. Biochem J 92:609–614

    PubMed  CAS  Google Scholar 

  • Aragno M, Schlegel HG (1992) The mesophilic hydrogen-oxidizing (knallgas) bacteria. In: Balows A, Trüper HG, Dworkin M, Harder W, Schleifer K-H (eds) The prokaryotes. A handbook on the biology of bacteria: ecophysiology, isolation, identification, applications. 2nd edn. Springer, Berlin, pp 344–384

    Google Scholar 

  • Bassalik K (1913) Über die Verarbeitung der Oxalsäure durch Bacillus extorquens n. sp. Jahrb Wiss Bot 53:255–302

    Google Scholar 

  • Bousfield IJ, Green PN (1985) Reclassification of bacteria of the genus Protomonas Urakami and Komagata 1984 in the genus Methylobacterium (Patt, Cole, and Hanson) emend. Green and Bousfield 1983. Int J Syst Bacteriol 35:209

    Article  Google Scholar 

  • Braissant O, Verrecchia EP, Aragno M (2002) Is the contribution of bacteria to terrestrial carbon budget greatly underestimated. Naturwissenschaften 89:366–370

    Article  PubMed  CAS  Google Scholar 

  • Braissant O, Cailleau G, Aragno M, Verrecchia EP (2004) Biologically induced mineralization in the tree Milicia excelsa (Moraceae): its causes and consequences to the environment. Geobiology 2:59–66

    Article  CAS  Google Scholar 

  • Chandra TS, Shethna YI (1977) Microbial metabolism of oxalate and one-carbon compounds. J Indian Inst Sci A 59:26–52

    CAS  Google Scholar 

  • Corpe WA, Rheem S (1989) Ecology of the methylotrophic bacteria on living leaf surfaces. FEMS Microbiol Ecol 62:243–250

    Article  CAS  Google Scholar 

  • Doronina NV, Trotsenko YA, Tourova TP, Kuznetsov BB, Leisinger T (2000) Methylophlia helvetica sp. nov. and Methylobacterium dichloromethanicum sp. nov.—novel aerobic facultatively methylotrophic bacteria utilizing dichloromethane. Syst Appl Microbiol 23:210–218

    PubMed  CAS  Google Scholar 

  • Euzeby JP (1997) List of bacterial names with standing in nomenclature: a folder available on the Internet. Int J Syst Bacteriol 47:590–592

    PubMed  CAS  Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  • Fine JB, Sprecher H (1982) Unidimensional thin-layer chromatography of phospholipids on boric acid-impregnated plates. J Lipid Res 23:660–663

    PubMed  CAS  Google Scholar 

  • Green PN (1992) The genus Methylobacterium. In: Balows A, Trüper HG, Dworkin M, Harder W, Schleifer K-H (eds) The prokaryotes. A handbook on the biology of bacteria: ecophysiology, isolation, identification, applications, 2nd edn. Springer, Berlin, pp 2342–2349

    Google Scholar 

  • Hiraishi A, Shimada K (2001) Aerobic anoxygenic photosynthetic bacteria with zinc-bacteriochlorophyll. J Gen Appl Microbiol 47:161–180

    Article  PubMed  CAS  Google Scholar 

  • Holland MA (1997) Methylobacterium and plants. Rec Res Dev Plant Physiol 1:207–213

    Google Scholar 

  • Holland MA, Polacco JC (1994) PPFMs and other covert contaminants: is there more to plant physiology than just plant. Annu Rev Plant Physiol Plant Mol Biol 45:197–209

    Article  CAS  Google Scholar 

  • Ivanova EG, Doronina NV, Trotsenko YA (2001) Aerobic methylobacteria are capable of synthesizing auxins. Microbiologiya 70:452–458

    CAS  Google Scholar 

  • Jenni B, Realini M, Aragno M, Tamer AU (1988) Taxonomy of non H2-lithotrophic, oxalate-oxidizing bacteria related to Alcaligenes eutrophus. Syst Appl Microbiol 10:126–133

    Google Scholar 

  • Jourand P, Giraud E, Bena G, Sy A, Willems A, Gillis M, Dreyfus B, de Lajudie P (2004) Methylobacterium nodulans sp. nov., for a group of aerobic, facultatively methylotrophic, legume root-nodule-forming and nitrogen-fixing bacteria. Int J Syst Evol Microbiol 54:2269–2273

    Article  PubMed  CAS  Google Scholar 

  • Kato Y, Asahara M, Arai D, Goto K, Yokota A (2005) Reclassification of Methylobacterium chloromethanicum and Methylobacterium dichloromethanicum as later subjective synonyms of Methylobacterium extorquens and of Methylobacterium lusitanum as a later subjective synonym of Methylobacterium rhodesianum. J Gen Appl Microbiol 51:287–299

    Article  PubMed  CAS  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitution through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  PubMed  CAS  Google Scholar 

  • Krieg NR, Smibert RM (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. ASM, Washington, DC, pp 607–654

    Google Scholar 

  • Kutschera U, Koopmann V (2005) Growth in liverworts of the Marchantiales is promoted by epiphytic methylobacteria. Naturwissenschaften 92:347–349

    Article  PubMed  CAS  Google Scholar 

  • Kutschera U, Thomas J, Hornschuh M (2007) Cluster formation in liverwort-associated methylobacteria and its implications. Naturwissenschaften 94:687–692

    Article  PubMed  CAS  Google Scholar 

  • Madhaiyan M, Kim B-Y, Poonguzhali S, Kwon S-W, Song M-H, Ryu J-H, Go S-J, Koo B-S, Sa T-M (2007) Methylobacterium oryzae sp. nov., an aerobic, pink-pigmented, facultatively methylotrophic, 1-aminocyclopropane-1-carboxylate deaminase-producing bacterium isolated from rice. Int J Syst Evol Microbiol 57:326–331

    Article  PubMed  CAS  Google Scholar 

  • McDonald IR, Doronina NV, Trotsenko YA, McAnulla C, Murrell JC (2001) Hyphomicrobium chloromethanicum sp. nov. and Methylobacterium chloromethanicum sp. nov., chloromethane-utilizing bacteria isolated from a polluted environment. Int J Syst Evol Microbiol 51:119–122

    PubMed  CAS  Google Scholar 

  • Mehta RJ (1973) Studies on methanol-oxidizing bacteria I. Isolation and growth studies. Antonie van Leeuwanhoek 39:295–302

    Article  CAS  Google Scholar 

  • Raja P, Uma S, Sundaram S (2006) Non-nodulating pink-pigmented facultative Methylobacterium sp. with a functional nifH gene. World J Microbiol Biotechnol 22:1381–1384

    Article  CAS  Google Scholar 

  • Sahin N (2003) Oxalotrophic bacteria. Res Microbiol 154:399–407

    Article  PubMed  CAS  Google Scholar 

  • Sahin N, Gokler I, Tamer AU (2002) Isolation, characterization and numerical taxonomy of novel oxalate-oxidizing bacteria. J Microbiol 40:109–118

    CAS  Google Scholar 

  • Saitou N, Nei M (1987) The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    PubMed  CAS  Google Scholar 

  • Schoonbeek HJ, Jacquat-Bovet AC, Mascher F, Metraux JP (2007) Oxalate-degrading bacteria can protect Arabidopsis thaliana and crop plants against Botrytis cinerea. Mol Plant–Microbe Interact 20:1535–1544

    Article  PubMed  CAS  Google Scholar 

  • Stepnowski P, Blotevogel K-H, Jastor B (2004) Extraction of carotenoid produced during methanol waste biodegradation. Int Biodeter Biodeg 53:127–132

    Article  CAS  Google Scholar 

  • Sy A, Giraud E, Jourand P, Garcia N, Willems A, de Lajudie P, Prin Y, Neyra M, Gillis M, Boivin-Masson C, Dreyfus B (2001) Methylotrophic Methylobacterium bacteria nodulate and fix nitrogen in symbiosis with legumes. J Bacteriol 183:214–220

    Article  PubMed  CAS  Google Scholar 

  • Tamer AU (1982) Oksalati karbon ve enerji kaynagi olarak kullanan bakteriler üzerinde taksonomik ve fizyolojik bir arastirma. PhD thesis, Ege University, İzmir—Turkey.

  • Tamer AU, Aragno M (1980) Isolement, charactérization et essai d’identification de bactéries capables d’utiliser l’oxalate comme seule source de carbone et d’énergie. Bull Soc Neuchatel Sci Nat 103:91–104

    Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    Article  PubMed  CAS  Google Scholar 

  • Trotsenko YA, Ivanova EG, Doronina NV (2001) Aerobic methylotrophic bacteria as phytosymbionts. Mikrobiologiya 70:725–736

    Google Scholar 

  • Van Aken B, Peres CM, Doty SL, Yoon JM, Schnoor JL (2004) Methylobacterium populi sp. nov., a novel aerobic, pink-pigmented, facultatively methylotrophic, methane-utilizing bacterium isolated from poplar trees (Populus deltoides x nigra DN34). Int J Syst Evol Microbiol 54:1191–1196

    Article  PubMed  CAS  Google Scholar 

  • Xu HX, Kawamura Y, Li N, Zhao LC, Li TM, Li ZY, Shu SN, Ezaki T (2000) A rapid method for determining the G+C content of bacterial chromosomes by monitoring fluorescence intensity during DNA denaturation in a capillary tube. Int J Syst Evol Microbiol 50:1463–1469

    PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported in part by grant no. 105T007 from the Scientific and Technical Research Council of Turkey (TUBITAK). We gratefully acknowledge help by Prof. M. Aragno, N. Jeanneret (University of Neuchatel, Switzerland), and Prof. A.U. Tamer for providing oxalotrophic strains. We also thank Prof. M. Isiloglu for technical support.

Author information

Authors and Affiliations

  1. Egitim Fakultesi, Mugla University, 48170, Kotekli, Mugla, Turkey

    Nurettin Sahin

  2. Microbiological and Analytical Group, Food Research Laboratories, Mitsui Norin Co., Ltd., Fujieda, Shizuoka, 426-0133, Japan

    Yuko Kato

  3. Mantarcilik Arastirma ve Uygulama Merkezi, Mugla University, 48170, Kotekli, Mugla, Turkey

    Ferah Yilmaz

Authors
  1. Nurettin Sahin
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yuko Kato
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ferah Yilmaz
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Nurettin Sahin.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Sahin, N., Kato, Y. & Yilmaz, F. Taxonomy of oxalotrophic Methylobacterium strains. Naturwissenschaften 95, 931–938 (2008). https://doi.org/10.1007/s00114-008-0405-9

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00114-008-0405-9

Keywords

Search

Navigation