Archives of Microbiology

, Volume 200, Issue 5, pp 829–833 | Cite as

Efficient methanol-degrading aerobic bacteria isolated from a wetland ecosystem

  • Kavitha Thulasi
  • Arjun Jayakumar
  • Aneesh Balakrishna Pillai
  • Vinod Kumar Gopalakrishnapillai Sankaramangalam
  • Harikrishnan Kumarapillai
Short Communication


Methylotrophs present in the soil play an important role in the regulation of one carbon compounds in the environment, and thereby aid in mitigating global warming. The study envisages the isolation and characterization of methanol-degrading bacteria from Kuttanad wetland ecosystem, India. Three methylotrophs, viz. Achromobacter spanius KUT14, Acinetobacter sp. KUT26 and Methylobacterium radiotolerans KUT39 were isolated and their phylogenetic positions were determined by constructing a phylogenetic tree based on 16S rDNA sequences. In vitro activity of methanol dehydrogenase enzyme, responsible for methanol oxidation was evaluated and the genes involved in methanol metabolism, mxaF and xoxF were partially amplified and sequenced. The specific activity of methanol dehydrogenase (451.9 nmol min−1 mg−1) observed in KUT39 is the highest, reported ever to our knowledge from a soil bacterium. KUT14 recorded the least activity of 50.15 nmol min−1 mg−1 and is the first report on methylotrophy in A. spanius.


Methanol Methanol dehydrogenase Methylotroph MxaF gene 16S rDNA 



The authors are grateful to Prof. M. Radhakrishna Pillai, Director, RGCB for the facilities provided. This work was financially supported by Department of Environment and Climate Change (DoECC), Govt. of Kerala, India (DoECC/E2/RD-49/165/12 dated 14-03-2013).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

203_2018_1509_MOESM1_ESM.pdf (170 kb)
Supplementary material 1 (PDF 170 KB)
203_2018_1509_MOESM2_ESM.pdf (235 kb)
Supplementary material 2 (PDF 235 KB)


  1. Anthony C (1971) Prosthetic group of an alcohol dehydrogenase of a Pseudomonad. In: McCormick DB, Wright LD (eds) Methods in enzymology, vol XVIII. Academic Press, New York, pp 808–813Google Scholar
  2. Boden R, Thomas E, Savani P, Kelly DP, Wood AP (2008) Novel methylotrophic bacteria isolated from the river Thames (London, UK). Environ Microbiol 10:3225–3236. CrossRefPubMedGoogle Scholar
  3. Borodina E, Kelly DP, Schumann P, Rainey FA, Ward-Rainey N, Wood AP (2002) Enzymes of dimethyl sulfone metabolism and the phylogenetic characterization of the facultative methylotrophs Arthrobacter sulfonivorans sp. nov., Arthrobacter methylotrophus sp. nov., and Hyphomicrobium sulfonivorans sp. nov. Arch Microbiol 177:173–183. CrossRefPubMedGoogle Scholar
  4. Bowman J (2006) The methanotrophs—the families Methanococcaceae and Methylocystaceae. In: Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The prokaryotes: vol 5 proteobacteria alpha and beta subclasses. Springer, New York, pp 273–275Google Scholar
  5. Cappuccino JG, Sherman N (2011) Microbiology: a laboratory manual, 9th edn. Pearson Benjamin Cummings, HalamanGoogle Scholar
  6. Chistoserdova L (2011) Modularity of methylotrophy, revisited. Environ Microbiol 13:2603–2622. CrossRefPubMedGoogle Scholar
  7. Chistoserdova L, Kalyuzhnaya MG, Lidstrom ME (2009) The expanding world of methylotrophic metabolism. Annu Rev Microbiol 63:477–499. CrossRefPubMedPubMedCentralGoogle Scholar
  8. Clinical Laboratory Standards Institute (2006) Performance standards for antimicrobial disk susceptibility tests; Approved standard—9th ed. CLSI document M2-A9. 26:1. Clinical Laboratory Standards Institute, WayneGoogle Scholar
  9. De Vries GE, Arfman N, Terpstra P, Dijkhuizenl L (1992) Cloning, expression, and sequence analysis of the Bacillus methanolicus Cl methanol dehydrogenase gene. J Bacteriol 174:5346–5353. CrossRefPubMedPubMedCentralGoogle Scholar
  10. Del Rocío Bustillos-Cristales M, Corona-Gutierrez I, Castañeda-Lucio M, Águila-Zempoaltécatl C, Seynos-García E, Hernández-Lucas I, Muñoz-Rojas J, Medina-Aparicio L, Fuentes-Ramírez LE (2017) Culturable facultative methylotrophic bacteria from the cactus Neobuxbaumia macrocephala possess the locus xoxF and consume methanol in the presence of Ce3+ and Ca2+. Microbes Environ 32:244–251. CrossRefPubMedPubMedCentralGoogle Scholar
  11. Duine JA, Frank J, Berkhout MPJ (1984) NAD-dependent, PQQ-containing methanol dehydrogenase: a bacterial dehydrogenase in a multienzyme complex. FEBS Lett 168:217–221CrossRefPubMedGoogle Scholar
  12. Faria D, LokaBharathi PA (2006) Marine and estuarine methylotrophs: their abundance, activity and identity. Curr Sci 90:984–989Google Scholar
  13. Ghosh A, Goyal A, Jain RK (2007) Study of methanol-induced phenotypic changes in a novel strain of Acinetobacter lwoffi. Arch Microbiol 188:533–539. CrossRefPubMedGoogle Scholar
  14. Green PN, Bousfield IJ (1983) 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 33:875–877. CrossRefGoogle Scholar
  15. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95–98Google Scholar
  16. Hanson RS, Hanson TE (1996) Methanotrophic bacteria. Microbiol Rev 60:439–471PubMedPubMedCentralGoogle Scholar
  17. Harley P, Greenberg J, Niinemets U, Guenther A (2007) Environmental controls over methanol emission from leaves. Biogeosciences 4:1083–1099. 2007CrossRefGoogle Scholar
  18. Hibi Y, Asai K, Arafuka H, Hamajima M, Iwama T, Kawai K (2011) Molecular structure of La3+-induced methanol dehydrogenase-like protein in Methylobacterium radiotolerans. J Biosci Bioeng 111:547–549. CrossRefPubMedGoogle Scholar
  19. Iguchi H, Yurimoto H, Sakai Y (2015) Interactions of methylotrophs with plants and other heterotrophic bacteria. Microorganisms 3:137–151. CrossRefPubMedPubMedCentralGoogle Scholar
  20. Jahng DJ, Kim CS, Hanson RS, Wood TK (1996) Optimization of trichloroethylene degradation using soluble methane monooxygenase of Methylosinus trichosporium OB3b expressed in recombinant bacteria Biotechnol Bioeng 51:349–359.<349::AID-BIT10>3.0.CO;2-HCrossRefPubMedGoogle Scholar
  21. Jhala YK, Vyas RV, Shelat HN, Patel HK, Patel HK, Patel KT (2014) Isolation and characterization of methane utilizing bacteria from wetland paddy ecosystem. World J Microbiol Biotechnol 30:1845–1860. CrossRefPubMedGoogle Scholar
  22. Kalyuzhnaya MG, Hristova KR, Lidstrom ME, Chistoserdova L (2008) Characterization of a novel methanol dehydrogenase in representatives of Burkholderiales: implications for environmental detection of methylotrophy and evidence for convergent evolution. J Bacteriol 190:3817–3823. CrossRefPubMedPubMedCentralGoogle Scholar
  23. Kolb S (2009) Aerobic methanol oxidizing bacteria in soil. FEMS Microbiol Lett 300:1–10. CrossRefPubMedGoogle Scholar
  24. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874. CrossRefPubMedGoogle Scholar
  25. Lane DJ (1991) 16S/23S rRNA sequencing. Nucleic acid techniques in bacterial systematices. pp 115–175Google Scholar
  26. Lanigan MD, Vaughan JA, Shiell BJ, Beddome GJ, Michalski WP (2004) Mycobacterial proteome extraction: comparison of disruption methods. Proteomics 4:1094–1100. CrossRefPubMedGoogle Scholar
  27. Lau E, Fisher MC, Steudler PA, Cavanaugh CM (2013) The methanol dehydrogenase gene, mxaF, as a functional and phylogenetic marker for proteobacterial methanotrophs in natural environments. PLoS One 8:1–12. CrossRefGoogle Scholar
  28. Lidstrom ME (2006) Aerobic methylotrophic prokaryotes. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The prokaryotes vol 2 ecophysiology and biochemistry. Springer, New York, pp 618–634Google Scholar
  29. Loew O (1892) Ueber einen Bacillus, welcher Ameisensaure und Formaldehyd assimilieren kann. Centralbl Bakteriol 12:462–465Google Scholar
  30. McTaggart TL, Beck DAC, Setboonsarng U, Shapiro N, Woyke T, Lidstrom ME, Kalyuzhnaya MG, Chistoserdova L (2015) Genomics of methylotrophy in Gram positive methylamine utilizing bacteria. Microorganisms 3:94–112. CrossRefPubMedPubMedCentralGoogle Scholar
  31. Meena KK, Kumar M, Mishra S, Ojha SK, Wakchaure GC, Sarkar B (2015) Phylogenetic study of methanol oxidizers from Chilka lake sediments using genomic and metagenomic approaches. Indian J Microbiol 55:151–162. CrossRefPubMedPubMedCentralGoogle Scholar
  32. Schrader J, Schilling M, Holtmann D, Sell D, Filho MV, Marx A, Vorholt JA (2008) Methanol-based industrial biotechnology: current status and future perspectives of methylotrophic bacteria. Trends Biotechnol 27:107–115. CrossRefPubMedGoogle Scholar
  33. Skovran E, Palmer AD, Rountree AM, Good NM, Lidstrom ME (2011) XoxF is required for expression of methanol dehydrogenase in Methylobacterium extorquens AM1. J Bacteriol 193:6032–6038. CrossRefPubMedPubMedCentralGoogle Scholar
  34. Stoscheck CM (1990) Quantitation of protein. Methods Enzymol 182:50–68CrossRefPubMedGoogle Scholar
  35. Tambekar DH, Ingale MG, Rajgire AV (2013) Isolation and molecular detection of methylotroph from Lonar lake. Biosci Discov 4:176–181Google Scholar
  36. Taubert M, Grob C, Howat AM, Burns OJ, Dixon JL, Chen Y, Murrell JC (2015) XoxF encoding an alternative methanol dehydrogenase is widespread in coastal marine environments. Environ Microbiol 17:3937–3948. CrossRefPubMedGoogle Scholar
  37. Urakamit T, Komagata K (1986) Emendation of Methylobacillus Yordy and Weaver 1977, a genus for methanol utilizing bacteria. Int J Syst Evol Bacteriol 36:502–511. CrossRefGoogle Scholar
  38. Vorob’ev AV, Dedysh SN (2008) Inadequacy of enrichment culture technique for assessing the structure of methanotrophic communities in peat soil. Microbiology 77:504–507. CrossRefGoogle Scholar
  39. Whittenbury R, Phillips KC, Wilkinson JF (1970) Enrichment, isolation and some properties of methane utilizing bacteria. J Gen Microbiol 61:205–218. CrossRefPubMedGoogle Scholar
  40. Yang M, Nightingale P, Beala R, Liss PS, Blomquist B, Fairall C (2013) Atmospheric deposition of methanol over the Atlantic Ocean. PNAS 110:20034–20039. CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Kavitha Thulasi
    • 1
  • Arjun Jayakumar
    • 1
  • Aneesh Balakrishna Pillai
    • 1
  • Vinod Kumar Gopalakrishnapillai Sankaramangalam
    • 2
  • Harikrishnan Kumarapillai
    • 1
  1. 1.Environmental Biology LaboratoryRajiv Gandhi Centre for BiotechnologyThiruvananthapuramIndia
  2. 2.Chemical Biology LaboratoryRajiv Gandhi Centre for BiotechnologyThiruvananthapuramIndia

Personalised recommendations