Methodology from Smyth, A. R., Piehler, M. F. and Grabowski, J. H. (2015), Habitat context influences nitrogen removal by restored oyster reefs. J Appl Ecol, 52: 716–725. doi:10.1111/1365-2664.12435

Fluxes across the sediment–water interface were calculated as (Co−Ci) × f/a, where Co is the outflow concentration (μmol L−1), Ci is the inflow concentration, f is the flow rate (0·06 L h−1), and a is the sediment surface area (0·0032 m2). Successive measurements from each core (triplicates for dissolved gas and duplicates for dissolved inorganic nutrients) were averaged to give core-specific values. This results in a net N2flux (gross denitrification – gross nitrogen fixation) and does not distinguish between the sources of N2. Consequently, denitrification refers to net N2 production. Oxygen fluxes were calculated using the concentrations of O2 obtained from the MIMS, presented as sediment oxygen demand (SOD), and serve as an indicator of organic matter quality, such that more labile organic matter is associated with higher SOD (Ferguson, Eyre & Gay 2003). To determine the influence of oyster reefs on sediment N2 fluxes, the change in denitrification between the control and reef habitat pair in each zone was calculated (Kellogg et al. 2014). Denitrification efficiency was computed as the percentage of the dissolved inorganic nitrogen efflux that was N2 (Piehler & Smyth 2011).

Statistical analyses were performed using r 2.13.1 (R Foundation for Statistical Computing 2011). Linear mixed-effects models (lme in R nlme package), where habitat nested in sampling location was included as a random effect for the intercept, were used to investigate the effects of oyster reef presence, habitat context, nitrate concentration (ambient vs. elevated) and the interaction between these factors on response variables. Fluxes of N2, NOx ( [math formula]  +  [math formula] )  [math formula] , denitrification efficiency and SOD were analysed using all three fixed effects. For sediment organic matter, only habitat context and reef presence were included as fixed effects. The effects of ambient vs. elevated nitrate concentration and habitat context on oyster reef-mediated changes in denitrification were also analysed with a mixed-effects model (fixed effects: nitrate concentration × habitat context; random effects: habitat nested in location). Relationships between oyster density and habitat context were made using a mixed-effects model (fixed effects: habitat context; random effects: habitat nested in location). Comparisons were conducted using linear contrasts and judged against an alpha level of 0·05. Interactions were assessed using Tukey's HSD (lsmeans in R lsmeans package). Assumptions of homogeneity were tested using Levene's tests. Regression analyses were used to investigate the effect of oyster density on denitrification. Models with the lowest Akaike's information criterion corrected for small sample sizes (AICc) were chosen.

BCO-DMO Processing Notes:

- column names reformatted to comply with BCO-DMO naming standards.
- lat and lon columns added to correspond with locations.
- nd used to replace all blank cells with no data.