The generation of acidity from oxidation of pyrite in acid sulfate soils requires the transport of oxygen into the soil profile. The sink for this oxygen will not only be the chemical reaction with pyrite but the biological processes associated with both microbial and plant respiration. The biological sinks in burning the oxygen (O₂) will release CO₂. The respiratory quotient which is the molar volume ratio of O₂ : CO₂ varies between 1.3 and 0.7 depending on the source of the organic matter being oxidised, but is generally 1.0. The oxidation of pyrite by oxygen will, by comparison with the biological processes, produce minor amounts of CO₂ (if any) by reaction with intrinsic carbonate minerals.

Gas samplers were installed into the soil at various depths and samples collected from these at approximately fortnightly intervals. The samples were analysed by gas chromatography and the CO₂ and O₂ profiles obtained. The flux of these gases was calculated and the difference between these attributed to the oxidation of pyrite. The flux difference varied over the period of sampling and on average gave an in situ oxidation rate of 11.5 tonnes H₂SO₄/ha.year. This is considerably more that the rate of export of acidity from this site and would explain the considerable actual acidity storage in these soils.

A model is developed for steady state transport of oxygen into soils with an exponentially decreasing biological sink with depth and an exponentially increasing chemical (pyrite) sink with depth. The model is developed in non-dimensional variables, which allows the relative strengths and rates of increase or decrease in sink terms to be explored. This model does not explicitly treat the flow of oxygen in macropores. Other models that do explicitly calculate macropore flow are compared and found to give similar results. These results suggest that the use of biological or other sinks near the soil surface could be a useful method for reducing the oxidation rate of pyrite in acid sulfate soils.