It has recently been hypothesized that bulk denitrification rates in carbonate sands may be enhanced by reactions occurring in the intra-granular pores, cracks and crevices. We tested this hypothesis using a series of flow and reactive transport models spanning from the pore-scale (∼mm) to the continuum scales (∼10 cm bedforms). Pore-scale simulations solved the coupled Navier–Stokes and Brinkman equations and represented flow-through reactor experiments previously performed on coral reef sands. The results revealed that intra-granular transport and reactions can explain over-all denitrification enhancement. A sensitivity study with a single grain diffusive transport model showed that in the majority of cases, the resultant increase in denitrification was not coupled to nitrification within a single grain. Only for large grain diameters of 2 and 4 mm was coupled nitrification–denitrification important. In most cases, coupled nitrification–denitrification instead arose as conditions became more reducing along a flow path, as is the case in quartz sands without intragranular pores. An intra-granular reaction rate based on a single grain model was incorporated into a continuum-scale Darcy flow and reactive transport model for a rippled sand bed, where porewater flow is driven by the turbulent current over the ripple. The results of the Darcy-scale model suggest that intra-granular pores increase the amount of slow-flowing areas within which coupled nitrification–denitrification can occur. We conclude that the complex advective flow field does not strongly inhibit denitrification enhancement by carbonate sand grains, as it does in silica sands. Thus, intra-granular reactions may enhance bulk denitrification in carbonate sediment with porous grains under natural advective conditions
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