Use of the frc gene as a molecular marker to characterize oxalate-oxidizing bacterial abundance and diversity structure in soil

J Microbiol Methods. 2009 Feb;76(2):120-7. doi: 10.1016/j.mimet.2008.09.020. Epub 2008 Sep 30.


Oxalate catabolism, which can have both medical and environmental implications, is performed by phylogenetically diverse bacteria. The formyl-CoA-transferase gene was chosen as a molecular marker of the oxalotrophic function. Degenerated primers were deduced from an alignment of frc gene sequences available in databases. The specificity of primers was tested on a variety of frc-containing and frc-lacking bacteria. The frc-primers were then used to develop PCR-DGGE and real-time SybrGreen PCR assays in soils containing various amounts of oxalate. Some PCR products from pure cultures and from soil samples were cloned and sequenced. Data were used to generate a phylogenetic tree showing that environmental PCR products belonged to the target physiological group. The extent of diversity visualised on DGGE pattern was higher for soil samples containing carbonate resulting from oxalate catabolism. Moreover, the amount of frc gene copies in the investigated soils was detected in the range of 1.64x10(7) to 1.75x10(8)/g of dry soil under oxalogenic tree (representing 0.5 to 1.2% of total 16S rRNA gene copies), whereas the number of frc gene copies in the reference soil was 6.4x10(6) (or 0.2% of 16S rRNA gene copies). This indicates that oxalotrophic bacteria are numerous and widespread in soils and that a relationship exists between the presence of the oxalogenic trees Milicia excelsa and Afzelia africana and the relative abundance of oxalotrophic guilds in the total bacterial communities. This is obviously related to the accomplishment of the oxalate-carbonate pathway, which explains the alkalinization and calcium carbonate accumulation occurring below these trees in an otherwise acidic soil. The molecular tools developed in this study will allow in-depth understanding of the functional implication of these bacteria on carbonate accumulation as a way of atmospheric CO(2) sequestration.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acyl Coenzyme A / analysis*
  • Acyl Coenzyme A / genetics*
  • Acyl Coenzyme A / metabolism
  • Bacterial Typing Techniques
  • Biodiversity
  • Biomarkers
  • Calcium Carbonate / analysis
  • Calcium Carbonate / metabolism
  • Calcium Oxalate / analysis
  • Calcium Oxalate / metabolism
  • DNA Primers
  • Electrophoresis, Polyacrylamide Gel / methods
  • Genes, Bacterial*
  • Oxalobacteraceae / classification
  • Oxalobacteraceae / genetics*
  • Oxalobacteraceae / isolation & purification*
  • Oxalobacteraceae / metabolism
  • Phylogeny
  • Polymerase Chain Reaction / methods*
  • Soil Microbiology*


  • Acyl Coenzyme A
  • Biomarkers
  • DNA Primers
  • formyl-coenzyme A
  • Calcium Oxalate
  • Calcium Carbonate