Active methanotrophs in two contrasting North American peatland ecosystems revealed using DNA-SIP

Microb Ecol. 2012 Feb;63(2):438-45. doi: 10.1007/s00248-011-9902-z. Epub 2011 Jul 5.


The active methanotroph community was investigated in two contrasting North American peatlands, a nutrient-rich sedge fen and nutrient-poor Sphagnum bog using in vitro incubations and (13)C-DNA stable-isotope probing (SIP) to measure methane (CH(4)) oxidation rates and label active microbes followed by fingerprinting and sequencing of bacterial and archaeal 16S rDNA and methane monooxygenase (pmoA and mmoX) genes. Rates of CH(4) oxidation were slightly, but significantly, faster in the bog and methanotrophs belonged to the class Alphaproteobacteria and were similar to other methanotrophs of the genera Methylocystis, Methylosinus, and Methylocapsa or Methylocella detected in, or isolated from, European bogs. The fen had a greater phylogenetic diversity of organisms that had assimilated (13)C, including methanotrophs from both the Alpha- and Gammaproteobacteria classes and other potentially non-methanotrophic organisms that were similar to bacteria detected in a UK and Finnish fen. Based on similarities between bacteria in our sites and those in Europe, including Russia, we conclude that site physicochemical characteristics rather than biogeography controlled the phylogenetic diversity of active methanotrophs and that differences in phylogenetic diversity between the bog and fen did not relate to measured CH(4) oxidation rates. A single crenarchaeon in the bog site appeared to be assimilating (13)C in 16S rDNA; however, its phylogenetic similarity to other CO(2)-utilizing archaea probably indicates that this organism is not directly involved in CH(4) oxidation in peat.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alphaproteobacteria / classification*
  • Alphaproteobacteria / genetics*
  • Alphaproteobacteria / isolation & purification
  • Archaea / classification
  • Archaea / genetics
  • Archaea / isolation & purification
  • DNA, Bacterial / analysis
  • DNA, Bacterial / genetics
  • Denaturing Gradient Gel Electrophoresis
  • Ecosystem
  • Gammaproteobacteria / classification*
  • Gammaproteobacteria / genetics*
  • Gammaproteobacteria / isolation & purification
  • Hydrogen-Ion Concentration
  • Methane / metabolism*
  • Molecular Sequence Data
  • New York
  • Oxidation-Reduction
  • Oxygenases / analysis
  • Oxygenases / genetics
  • Phylogeny
  • Polymerase Chain Reaction
  • RNA, Ribosomal, 16S / analysis
  • RNA, Ribosomal, 16S / genetics
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Soil / chemistry*
  • Soil Microbiology*
  • Wetlands


  • DNA, Bacterial
  • RNA, Ribosomal, 16S
  • Soil
  • Oxygenases
  • methane monooxygenase
  • Methane

Associated data

  • GENBANK/HQ844528
  • GENBANK/HQ844529
  • GENBANK/HQ844530
  • GENBANK/HQ844531
  • GENBANK/HQ844532
  • GENBANK/HQ844533
  • GENBANK/HQ844534
  • GENBANK/HQ844535
  • GENBANK/HQ844536
  • GENBANK/HQ844537
  • GENBANK/HQ844538
  • GENBANK/HQ844539
  • GENBANK/HQ844540
  • GENBANK/HQ844541
  • GENBANK/HQ844542
  • GENBANK/HQ844543
  • GENBANK/HQ844544
  • GENBANK/HQ844545
  • GENBANK/HQ844546
  • GENBANK/HQ844547
  • GENBANK/HQ844548
  • GENBANK/HQ844549
  • GENBANK/HQ844550
  • GENBANK/HQ844551
  • GENBANK/HQ844552
  • GENBANK/HQ844553
  • GENBANK/HQ844554
  • GENBANK/HQ844555
  • GENBANK/JN022611