## 2 Materials and Methods
### Primary Production Measurements  
Primary production was measured during submergence at all sites in November 2017 and 2018, and at TAU-O, TAU-T and RAG in June 2018. On each sampling date, an Odyssey PAR (photosynthetically active radiation) logger (Dataflow Systems, Melbourne, FL, USA) was deployed in the middle of each site and on the shore to capture light availability at the sediment and water surface, respectively. Two benthic flux chambers were deployed in each plot for approximately 4 h during a midday high tide. Each chamber base (50 cm \(\times\) 50 cm \(\times\) 15 cm) was inserted 5 cm into the sediment at low tide and equipped with a light and temperature logger (HOBO Pendant(r)). On the incoming tide, chambers were sealed with a Perspex dome lid and any air bubbles removed, encapsulating 41 L of seawater over the sediment surface. An opaque shade cloth covered one of the two chamber lids per plot to block out all sunlight, while the other lid was left uncovered to receive ambient sunlight. Immediately after the chambers were sealed and at the end of the incubation, one 60 mL seawater sample was collected from each chamber to provide initial and final dissolved oxygen concentrations. Seawater dissolved oxygen concentration was measured on-site immediately after sampling using a handheld optical probe (PreSens FIBOX 3 LCD trace v7). In June and November 2018, this was supplemented with a dissolved oxygen logger (PME miniDOT) deployed within each chamber recording at a 1-min sampling frequency.  
Emerged primary production was assessed within 10 d of the submerged measurements in June 2018 at TAU-O, TAU-T and RAG, and at all sites in November 2018 over a midday low tide. For the full emerged period, an Odyssey PAR light logger was deployed in the middle of the site to capture ambient  
\begin{table}
\begin{tabular}{l c c c c} \hline  & **March 2017** & **November 2017 (T1)** & **June 2018 (T2)** & **November 2018 (T3)** \\ \hline Sediment nutrient enrichment & \(\surd\) & & \(\surd\) & \(\surd\) & \\ Characterisation of site PAR & & & & \\ Primary production measures & & & & \\ Submerged (O\({}_{2}\) flux) & & \(\surd\) & \(\surd\) & \(\surd\) \\ Emerged (CO\({}_{2}\) flux) & & & \(\surd\) & \(\surd\) \\ Sediment characteristics & & \(\surd\) & \(\surd\) & \(\surd\) \\ Macrofaunal composition & & \(\surd\) & & \(\surd\) \\ \hline \end{tabular} PAR = photosynthetically active radiation.  
\end{table}
Table 1: Experiment timeline and parameters measured. T1 and T3 sampling includes all 6 sites, T2 sampling includes only 3 (TAU-O, TAU-T and RAG).  
light availability. Once the site was drained of water, one chamber base in each plot was inserted 5 cm into the sediment. During each measurement, the chamber contained an Odyssey PAR light logger, a pressure vent, a thermocouple measuring chamber air temperature and a battery-powered fan. The fan maintained airflow and gentle mixing to ensure no dead spaces were created inside the chamber which could alter the diffusion of gases from the sediment [39]. A Perspex lid was then fitted over the chamber and connected to an infrared gas analyser (LI-COR 8100A Automated Soil CO\({}_{2}\) Flux System) where air was continuously circulated between the analyser and the chamber. Measurements of CO\({}_{2}\) concentration (ppm) were recorded at a frequency of 1 Hz for a total incubation period of 5 min. This method has been shown to provide a reliable quantification of CO\({}_{2}\) exchange in intertidal habitats, with a 5 min period resulting in a stable diffusion of CO\({}_{2}\) without increasing the humidity within the chamber [25; 40]. Light incubations were conducted before an opaque shade cloth was placed over the chamber base and allowed to acclimate for 20 min prior to an additional CO\({}_{2}\) incubation performed in dark conditions.