Fix typos and enhance text clarity in 09-bgc-model.Rmd

09-bgc-model.Rmd

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 Cockburn Sound has undergone significant water quality changes over many decades, shaped by both natural processes and intense human activity. Understanding how nutrients and other pollutants move through the system has proved challenging, in part because the Sound receives inputs from many different sources. These include atmospheric deposition, groundwater inflows, stormwater and urban drainage, industrial and wastewater discharges, as well as nutrients released from within the seabed itself. Although direct river flows to Cockburn Sound are limited, nutrient concentrations commonly rise near the shoreline and at discharge points, and occasional large flow events from the Swan–Canning Estuary can also influence local water quality.
 
-From the 1950s through to the 1980s, Cockburn Sound experienced severe eutrophication—an excess of nutrients that fuelled high algal productivity and reduced water clarity. During this period, wastewater and industrial effluents increased substantially, and the construction of the Garden Island causeway in the 1970s further reduced flushing of nutrients to the open ocean. The combined effect of these pressures was dramatic: more than 80% of the seagrass meadows were lost, largely due to nutrient enrichment and growth of epiphytes that blocked light from reaching the leaves.
+From the 1950s through to the 1980s, Cockburn Sound experienced severe eutrophication — an excess of nutrients that fuelled high algal productivity and reduced water clarity. During this period, wastewater and industrial effluents increased substantially, and the construction of the Garden Island causeway in the 1970s further reduced flushing of nutrients to the open ocean. The combined effect of these pressures was dramatic: more than 80% of the seagrass meadows were lost, largely due to nutrient enrichment and growth of epiphytes that blocked light from reaching the leaves.
 
 Significant management efforts have since helped reduce nutrient loads, particularly through improved wastewater treatment and redirecting discharges offshore. However, the legacy of historical inputs remains. Nutrient-rich groundwater continues to enter the Sound, sandy sediments store large historical nutrient loads, and internal recycling of nitrogen and phosphorus still contributes substantially to the nutrients available in the water column. While concentrations of nitrogen and phosphorus have declined in recent decades, improvements in water clarity and phytoplankton biomass have been slower and less consistent. Fish kills, algal blooms, and episodes of low-oxygen bottom waters continue to be reported. In addition, hypersaline brine from the desalination plant has been shown to form dense plumes that may settle near the seabed, reinforcing stratification and making hypoxia more likely under certain conditions.
 
-Together, these patterns highlight that nutrient dynamics in Cockburn Sound are shaped by a combination of external loads, internal cycling, and physical processes such as mixing, stratification, and ocean exchange. Assessing these interactions requires an integrated approach capable of linking hydrodynamics, nutrient budgets, biological processes, and local management actions. An advanced biogeochemical model provides this capability. It allows us to explore how nutrients move through the system today, identify key environmental risks, and evaluate how future changes—such as dredging, coastal development, or climate-driven shifts in flows and temperatures—may influence water quality.
+Together, these patterns highlight that nutrient dynamics in Cockburn Sound are shaped by a combination of external loads, internal cycling, and physical processes such as mixing, stratification, and ocean exchange. Assessing these interactions requires an integrated approach capable of linking hydrodynamics, nutrient budgets, biological processes, and local management actions. An advanced biogeochemical model provides this capability. It allows us to explore how nutrients move through the system today, identify key environmental risks, and evaluate how future changes — such as dredging, coastal development, or climate-driven shifts in flows and temperatures — may influence water quality.
 
 Developing such a model relies on a firm understanding of the broader physical environment (discussed in earlier chapters) and the many sources of nutrients entering the system. Previous studies have shown that nitrogen, in particular, plays a central role in controlling productivity in the region. Even small inputs can drive substantial ecological responses in this naturally low-nutrient coastal setting. Although overall nitrogen concentrations have decreased due to improved management, phytoplankton biomass remains elevated at several locations, reinforcing the need to quantify both external inputs and internal nutrient cycling.
 
@@ -34,7 +34,7 @@ Submarine groundwater discharge (SGD) has emerged as a dominant nitrogen source
 
 ### Local stormwater inputs
 
-The latest estimates from our field survey suggest that maximum contribution of nutrients from stormwater directly to Cockburn Sound could be less than about 0.1 tonnes/year, though there is a high degree of uncertainty due to sparse observations in stormwater fluxes and their nutrient concentrations (Bekele et al., 2023). Due to the low nutrient load brought by stormwater it does not play a major role and was ot included in early versions. From version 1.7.2 estimates of stormwater have been included.
+The latest estimates from our field survey suggest that maximum contribution of nutrients from stormwater directly to Cockburn Sound could be less than about 0.1 tonnes/year, though there is a high degree of uncertainty due to sparse observations in stormwater fluxes and their nutrient concentrations (Bekele et al., 2023). Due to the low nutrient load brought by stormwater it does not play a major role and was not included in early versions. From version 1.7.2 estimates of stormwater have been included.
 
 
 ### Wastewater treatment plants (WWTPs) inputs
@@ -70,7 +70,7 @@ For the current study, the CSIEM model configuration mirrors the industrial inpu
 
 ### Nutrient load trend and summary 
 
-An summary of nutrient loads is presented in Table 9.2 presenting a structure summary of each input and major flux path that has been reported, with literature review of nutrient balance terms.
+A summary of nutrient loads is presented in Table 9.2 presenting a structure summary of each input and major flux path that has been reported, with literature review of nutrient balance terms.
 
 **Table 9.2**. Summary of nutrient sources estimated from literature review and CSIEM
 
@@ -127,7 +127,7 @@ An summary of nutrient loads is presented in Table 9.2 presenting a structure su
 
 ## Variability in Benthic Recycling
 
-The varied benthic (bottom) substrates across Cockburn Sound, Owen Anchorage and farther afield play a critical role in regualting and recycling carbon and nutrients, and therefore controlling water quality. To assess the current state of the Cockburn environment and to simulate future scenarios, the rates of flux across the sediment–water interface for O\(_2\) and nutrients area therefore critical factors to be resolved. In this section, field studies and prior modelling of the sediment were used as data sources for the purposes of defining the necessary parameters needed for setup and configuration of the biogeochemical model. 
+The varied benthic (bottom) substrates across Cockburn Sound, Owen Anchorage and farther afield play a critical role in regulating and recycling carbon and nutrients, and therefore controlling water quality. To assess the current state of the Cockburn environment and to simulate future scenarios, the rates of flux across the sediment–water interface for O\(_2\) and nutrients area therefore critical factors to be resolved. In this section, field studies and prior modelling of the sediment were used as data sources for the purposes of defining the necessary parameters needed for setup and configuration of the biogeochemical model. 
 
 Four major sources of information were used to determine benthic fluxes: