Both the simulated and measured NOx− flux patterns reflect a gradual replacement of Dw by Dn in the O2 concentration range of 1–4 mg l−1 and Dn prevalence when the O2 concentration exceeds 4 mg l−1 ( Figures 5 and 6). However, the variability of the measured NOx− fluxes, including shifts between influx and efflux,

at higher O2 concentrations indicates the co-existence of both NOx− pathways for denitrification; this is in good agreement with recent denitrification field measurements (Aigars et al. 2013, under review), thus limiting the model’s scope of application. BYL719 Since the experimental results of this study do not cover evidently anoxic conditions, the improved denitrification model should be used with caution, particularly because under sulphidic conditions, microbial denitrification shifts from sediment heterotrophic to water column chemolithotrophic, as reported by e.g. Hietanen et al. (2012) and Dalsgaard et al. (2013). We wish to express our thanks to Maris Skudra, Nina Sunelika, Mintauts Jansons and Alla Ivakina, who supported this study by conducting field measurements and laboratory analysis, as well as to the peer reviewers of the paper, who provided critical and constructive comments. The mineralisation Buparlisib in vitro rate of sediment organic matter mc is described as a first-order process depending on bottom water temperature T and sediment organic nitrogen

concentration cAMP NS, converted into carbon equivalents via a constant carbon/nitrogen ratio rCN assumed for the sediments: equation(1) mc=rCN×NS×amN×ebmn×T.mc=rCN×NS×amN×ebmn×T. The fraction of mineralised organic carbon σ that is oxidised

using terminal electron acceptors other than oxygen increases from 1 – ad to 1 with declining bottom water oxygen concentrations OX: equation(2) ä=1−ad1+e−bd×(OX−cd). The potential denitrification rate dp, assuming that the entire electron acceptor demand not covered by oxygen is provided by denitrification, is then given by equation(3) dp=0.8×σ×rCN×mc,dp=0.8×σ×rCN×mc,where the factor 0.8 expresses the fact that the oxidation of 1 mol organic carbon at oxidation number 0 requires the denitrification of 0.8 mol NO3−. The nitrification rate nx of ammonium released by the mineralisation of sediment organic matter increases with bottom water oxygen concentration until all the ammonium generated is nitrified: equation(4) nx=mcrCN×11+e−ax(bx−OX). If the potential denitrification rate dp exceeds the nitrification rate nx, nitrate diffuses into the sediments depending on the nitrate deficit given by dp – nx, the nitrate concentration in the overlying water NO and the diffusion resistance parameter k. All the nitrate diffusing into the sediment is denitrified (dw): equation(5) dw={(dp−nx)×NOk+NO,dp≥nx,0,dp