Long-term effects of mineral versus organic fertilizers on activity and structure of the methanotrophic community in agricultural soils

Environ Microbiol. 2003 Oct;5(10):867-77. doi: 10.1046/j.1462-2920.2003.00477.x.


Agricultural practices, such as mineral nitrogen fertilization, have an impact on the soil's ability to oxidize methane, but little is known about the shifts in the methanotrophic community composition associated with these practices. Therefore, the long-term effect of both mineral (NH4NO3) and organic (manure and GFT-compost) fertilizer applications on the soil methanotrophic community activity and structure were investigated. Both high and low affinity methane oxidation rates were lower in the soil treated with mineral fertilizer compared to the other soils. An enhanced nitrate concentration was observed in the mineral fertilized soil but nitrate did not show a direct affect on the high affinity methane oxidation. In contrast, the low affinity methane oxidation was slowed down by increased nitrate concentrations, which suggests a direct effect of nitrate on low affinity methane oxidation. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene fragments specific for methanotrophs revealed a distinct community between the mineral and organic fertilized soils as extra Type I methanotrophic bands (phylotypes) became visible in the organic fertilized soils. These phylotypes were not visible in the patterns of the added organic fertilizers suggesting an indirect effect of the organic fertilizers on the methanotrophic community. Additionally, a molecular analysis was performed after the low affinity methane oxidation test. The enhanced methane concentrations used in the test enriched certain low affinity methanotrophs in the organic fertilized soils but not in the mineral fertilized soil. Supporting the molecular and functional observations, fatty acids characteristic for methanotrophs were less abundant in the soil treated with mineral fertilizer compared to the soil treated with compost. In conclusion, the function and molecular and chemical composition of the methanotrophic community are all altered in soil fertilized with mineral fertilizer.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alphaproteobacteria / classification
  • Alphaproteobacteria / metabolism*
  • Crops, Agricultural
  • Fatty Acids / chemistry
  • Fatty Acids / metabolism
  • Fertilizers*
  • Gammaproteobacteria / classification
  • Gammaproteobacteria / metabolism*
  • Manure / microbiology*
  • Methane / metabolism*
  • Methylococcaceae / metabolism*
  • Minerals / chemistry
  • Minerals / metabolism
  • Nitrates / metabolism
  • Oxidation-Reduction
  • Phylogeny
  • Quaternary Ammonium Compounds / metabolism
  • RNA, Ribosomal, 16S / analysis
  • Soil
  • Soil Microbiology


  • Fatty Acids
  • Fertilizers
  • Manure
  • Minerals
  • Nitrates
  • Quaternary Ammonium Compounds
  • RNA, Ribosomal, 16S
  • Soil
  • Methane