Until recently, denitrification was thought to be the only significant pathway for N ₂ formation and, in turn, the removal of nitrogen in aquatic sediments. The discovery of anaerobic ammonium oxidation in the laboratory suggested that alternative metabolisms might be present in the environment. By using a combination of ¹⁵ N-labeled NH ₄ ⁺ , NO ₃ ⁻ , and NO ₂ ⁻ (and ¹⁴ N analogues), production of ²⁹ N ₂ and ³⁰ N ₂ was measured in anaerobic sediment slurries from six sites along the Thames estuary. The production of ²⁹ N ₂ in the presence of ¹⁵ NH ₄ ⁺ and either ¹⁴ NO ₃ ⁻ or ¹⁴ NO ₂ ⁻ confirmed the presence of anaerobic ammonium oxidation, with the stoichiometry of the reaction indicating that the oxidation was coupled to the reduction of NO ₂ ⁻ . Anaerobic ammonium oxidation proceeded at equal rates via either the direct reduction of NO ₂ ⁻ or indirect reduction, following the initial reduction of NO ₃ ⁻ . Whether NO ₂ ⁻ was directly present at 800 μM or it accumulated at 3 to 20 μM (from the reduction of NO ₃ ⁻ ), the rate of ²⁹ N ₂ formation was not affected, which suggested that anaerobic ammonium oxidation was saturated at low concentrations of NO ₂ ⁻ . We observed a shift in the significance of anaerobic ammonium oxidation to N ₂ formation relative to denitrification, from 8% near the head of the estuary to less than 1% at the coast. The relative importance of anaerobic ammonium oxidation was positively correlated ( P < 0.05) with sediment organic content. This report of anaerobic ammonium oxidation in organically enriched estuarine sediments, though in contrast to a recent report on continental shelf sediments, confirms the presence of this novel metabolism in another aquatic sediment system.

River deltas are particularly important in the marine carbon cycle as they represent the transition between terrestrial and marine carbon: linked to major burial zones, they are reprocessing zones where large carbon fluxes can be mineralized. In order to estimate this mineralization, sediment oxygen uptake rates were measured in continental shelf sediments and river prodelta over different seasons near the outlet of the Rhône River in the Mediterranean Sea. On a selected set of 10 stations in the river prodelta and nearby continental shelf, in situ diffusive oxygen uptake (DOU) and laboratory total oxygen uptake (TOU) measurements were performed in early spring and summer 2007 and late spring and winter 2008. In and ex situ DOU did not show any significant differences except for shallowest organic rich stations. Sediment DOU rates show highest values concentrated close to the river mouth (approx. 20 mmol O₂ m⁻² d⁻¹) and decrease offshore to values around 4.5 mmol O₂ m⁻² d⁻¹ with lowest gradients in a south west direction linked to the preferential transport of the finest riverine material. Core incubation TOU showed the same spatial pattern with an averaged TOU/DOU ratio of 1.2±0.4. Temporal variations of sediment DOU over different sampling periods, spring summer and late fall, were limited and benthic mineralization rates presented a stable spatial pattern. A flood of the Rhône River occurred in June 2008 and delivered up to 30 cm of new soft muddy deposit. Immediately after this flood, sediment DOU rates close to the river mouth dropped from around 15–20 mmol O₂ m⁻² d⁻¹ to values close to 10 mmol O₂ m⁻² d⁻¹, in response to the deposition near the river outlet of low reactivity organic matter associated to fine material. Six months later, the oxygen distribution had relaxed back to its initial stage: the initial spatial distribution was found again underlining the active microbial degradation rates involved and the role of further deposits. These results highlight the immediate response of the sediment oxygen system to flood deposit and the rapid relaxation of this system towards its initial state (6 months or less) potentially linked to further deposits of reactive material.