Skip to main content
Article thumbnail
Location of Repository

Molecular ecology of facultative methanotrophs

By M. Tanvir Rahman


Methylocella spp. are facultative methanotrophs, able to grow not only on one\ud carbon molecules e.g., methane or methanol, but also on multi-carbon compounds\ud e.g., acetate, succinate and malate.\ud PCR-based molecular techniques were developed and validated to target the 16S\ud rRNA genes of all the species of the genus Methylocella present in environmental\ud samples. DNA extracted from a variety of environmental samples screened by PCR\ud to determine the environmental distribution of Methylocella spp. Methylocella were\ud found to be widely distributed, not only in acidic environments, but also in neutral\ud and alkaline environments. New primers targeting the mmoX gene of Methylocella\ud spp. that encoded the α-subunit of methane monooxygenases were designed. A\ud SYBR® green-based real-time quantitative PCR assay was developed and validated\ud using these Methylocella mmoX gene-targeting primers. The abundance of\ud Methylocella spp. present in selected environmental samples was quantified using\ud the newly developed real-time quantitative PCR assay\ud A series of 13CH4 DNA-SIP experiments were carried either in the presence or\ud absence of 12C acetate in microcosms containing Moor House peat soil to investigate\ud the effect of acetate (0.5 mM) on the ability of Methylocella silvestris to oxidize\ud methane. Methane oxidation data indicated that acetate repressed the ability of\ud Methylocella silvestris to oxidize methane in peat soil microcosms. 13CH4 DNA-SIP\ud experiments revealed that in presence of acetate, Methylocella silvestris did not\ud utilize methane as a carbon source, suggesting that acetate might be the alternative\ud source of carbon. However, when 13C-labelled acetate DNA-SIP experiments were\ud carried out, Methylocella spp. were not found to be dominant acetate utilizers in the\ud peat soil microcosms. Methylocella spp. seem to have been outcompeted by more\ud efficient acetate utilizers such as Brevundimonas and Burkholderia.\ud To identify genes that might be involved in the utilization of methane or acetate,\ud Methylocella silvestris whole genome transcriptomics experiments were carried out.\ud All the genes of the sMMO gene cluster were found to be highly upregulated during\ud growth on methane. In addition to the sMMO gene cluster, a gene encoding Fur was\ud also found to be highly upregulated during growth on methane. During growth on\ud acetate, a gene cluster encoding glycine dehydrogenase was found to be highly\ud upregulated. Microarray experiments carried out here provided potential candidate\ud genes for further characterization by gene knockout based studies. Further work is\ud also required to validate the microarray findings.\ud A study was carried out on forest soils derived from Swedish islands that were at\ud different successional stages. All islands were found to be positive for the presence\ud of Methylocella spp., and identity of composition of other methanotrophs were\ud determined using a pmoA-diagnostic microarray. All the islands were dominated by\ud Methylococcus, Methylosinus and methanotrophs of the uncultivated RA14 clade.\ud The diversity of methanotrophs was higher in late successional islands compared to\ud mid and early successional islands. In addition the diversity of methanotrophs\ud decreased as the soil depth increased

Topics: QR
OAI identifier:

Suggested articles


  1. (1970). A new sensitive and specific test for the detection of aldehydes: formation of 6-mercapto-3-substituted-striazolo [4,3-b]-s-tetrazines. doi
  2. (1971). An N-methyl glutamate dehydrogenase from Pseudomonas M.A. doi
  3. (1985). Bacterial reduction of trimethylamine oxide. doi
  4. (1977). Biochemical parameters of glutamine synthetase from Klebsiella aerogenes.
  5. (1985). Biodegradation of N-nitrosodimethylamine in aqueous and soil systems.
  6. (2002). Biomineralization of an organophosphorous pesticide, monocrotophos, by soil bacteria. doi
  7. (2002). Broad-host-range cre-lox system for antibiotic marker recycling in gram-negative bacteria.
  8. (2007). Characterization of theanine-forming enzyme from Methylovorus mays no. 9 in respect to utilization of theanine production. doi
  9. (2008). Cloning and expression of Methylovorus mays no. 9 gene encoding gamma-glutamylmethylamide synthetase: an enzyme usable in theanine formation by coupling with the alcoholic fermentation system of baker’s yeast. doi
  10. (1993). Cloning, sequencing, expression and regulation of structural gene for the copper/topa quininecontaining methylamine oxidase from Arthrobacter strain P1, a gram-positive facultative methylotroph.
  11. (1995). Discovery of the ammonium substrate site on glutamine synthetase, a third cation binding site. Protein Sci. doi
  12. (1998). Electroporation of pink-pigmented methylotrophic bacteria. doi
  13. (2005). Evidence for the presence of a CmuA methyltransferase pathway in novel marine methyl halide-oxidising bacteria. doi
  14. (1994). Genetic organization of mau gene cluster in Methylobacterium extorquens AM1: complete nucleotide sequence and generation and characteristics of mau mutants.
  15. (2010). Genetics of the glutamate-mediated methylamine utilization pathway in the facultative methylotrophic beta-proteobacterium Methyloversatilis universalis FAM5. doi
  16. (1969). Glutamylmethylamide: a new intermediate in the metabolism of methylamine.
  17. (2008). Intracellular organic osmolytes: function and regulation. doi
  18. (2007). MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. doi
  19. (2008). Metabolic, phylogenetic and ecological diversity of the methanogenic doi
  20. (2003). Methylocella silvestris sp. nov., a novel methanotrophic bacterium isolated from an acidic forest cambisol. doi
  21. (2005). Methylocella species are facultatively methanotrophic. doi
  22. (2000). Molecular analysis of the pmo (particulate methane monooxygenase) operons from two type II methanotrophs. doi
  23. (1971). N-methylglutamate synthetase: purification and properties of the enzyme.
  24. (1942). Preparation of -alkylamides of glutamic acid. doi
  25. (1990). Primary metabolic pathway of methylamine in Methylophaga sp. doi
  26. (1976). Primary metabolic pathways of methylated amines in Hyphomicrobium vulgare. Mikrobiologiia 45:41–47.
  27. (1992). Purification and characterization of -glutamylmethylamide synthetase from Methylophaga sp. doi
  28. (1995). Purification and characterization of a new -glutamylmethylamide-dissimilating enzyme system from Methylophaga sp. doi
  29. (1987). Purification and properties of methylamine dehydrogenase from Paracoccus denitrificans. doi
  30. (2005). Regulation of methane oxidation in the facultative methanotroph Methylocella silvestris BL2. doi
  31. (1995). Sequence analysis of sarcosine oxidase and nearby genes reveals homologies with key enzymes of folate one-carbon metabolism. doi
  32. (1977). Solubilization, partial purification and properties of N-methylglutamate dehydrogenase from Pseudomonas aminovorans.
  33. (1984). Study of odorous compounds produced by putrefaction of foods. doi
  34. (1970). The analytical chemistry of nitrogen and its compounds. Wiley Interscience, doi
  35. (1982). The biochemistry of methylotrophs. doi
  36. (1997). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. doi
  37. (1976). The demonstration of two discrete enzymes catalyzing the synthesis of glutamine and -glutamylmethylamide in Pseudomonas MS. doi
  38. (1966). The enzymatic synthesis of N-methylglutamic acid.
  39. (1983). The utilization of methylamine-nitrogen by the methazotrophic bacterium Pseudomonad P.

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.