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Puget Sound Georgia Basin Model

pH and Ocean Acidification


Schematic diagram of the carbon cycle in the coastal and estuarine system

The Blue-Ribbon Panel of scientists, tribes, and shellfish managers appointed by former Governor Christine Gregoire recommended future research, monitoring, and actions to understand, prevent or mitigate, and adapt to the acidification of Washington State marine waters. The panel recommended efforts to quantify how much regional human sources (water nutrients and air emissions) exacerbate the effects of the upwelled Pacific Ocean water and global atmospheric CO2 on the acidification of marine waters. PNNL and Ecology have developed a planning document (Long et al. 2014) that summarizes the initial approach recommended to simulate the impacts of regional human sources on acidification. The effort is based on a strong belief that it may be possible to manage nutrient pollution and modify our fisheries and water-quality management practices to minimize potential impacts from ocean acidification. Monitoring and modeling can help forecast conditions and adapt our activities to minimize the adverse effects.

Model Formulation

Biogeochemical processes such as algal growth and die-off affect total inorganic carbon in the water column and therefore affect pH. We know that shallow sub-basins in Puget Sound and Georgia Basin regions of Salish Sea are highly productive, which results in almost complete depletion of nutrients during the spring and summer algae blooms. Discharge of nutrient pollutants into the Salish Sea during these periods could lead to eutrophic conditions. High levels of algae during the daytime lead to super-saturated dissolved oxygen (DO) levels. The same algae during the nighttime produce copious amounts of carbon dioxide (CO2) through respiration resulting in reduced pH. At the conclusion of the spring and summer blooms, algae die, decay, and settle to sediments, leading to conditions suitable for hypoxia. The decaying algae also release large amounts of inorganic carbon back to the water column. Data from sub-basins of Puget Sound show sharp drops in pH correlated to nighttime respiration. This problem is exacerbated by ocean acidification and upwelling.

Carbonate chemistry and pH model as incorporated in the Salish Sea Model is described in detail in Pelletier et al. (2017b) and Bianucci et al. (2018) and is briefly summarized here.

Key physical and biogeochemical processes and pathways including human contributions in the coastal zone

The existing model of the Salish Sea, conducts carbon-based biogeochemical simulations and is well suited for incorporating acidification kinetics. The approach selected by the project team was to modify the existing FVCOM-ICM model to include relevant new quantities in the computational domain. Specifically, total dissolved inorganic carbon (TDIC) and total alkalinity (TA) were included as state variables in advection, transport, and turbulent mixing computations. Aragonite saturation and pH are secondary quantities computed based on predicted values of TDIC and TA. The parameters of the CO2 system, pH, and calcium solubility are computed based any two of the four measurable parameters (TA, TDIC, pH, and fCO2 or pCO2) using the CO2SYS framework of Lewis and Wallace (1998).

TA in the water column increases due to processes that produce NH4 or consume NO3, while consumption of NH4 and production of NO3 decreases TA. Therefore, TA in the model increases due to new primary production, remineralization of LDON and RDON, water column denitrification, and sediment fluxes of NH4; it decreases due to regenerated primary production, water column nitrification, and sediment fluxes of NO3. The processes that consume DIC are primary production and water column nitrification. Production of DIC occurs through remineralization of LDOC and RDOC, water column denitrification, phytoplankton losses by predation, basal metabolism and photorespiration, and sediment fluxes. The model also includes air-sea exchange of CO2, which can either increase or decrease DIC depending on whether the surface partial pressure of CO2 (pCO2) is lower or higher than the atmospheric pCO2.

Simulation of Carbonate Chemistry and pH in Salish Sea

Time series of surface model values (black lines) for seven variables (rows) and four stations (columns). Overlapped observations belong to CTD casts (blue triangles) and bottles (red circles) for 2008; diamonds and crosses correspond to other years in the panels for DIC (µmol kg–1), TA (µmol kg–1), pH (total scale), and OA (blue diamonds for PRISM, pink crosses for ECY-MMUdata). (Bianucci et al. 2018)


Lewis, E. and D. Wallace. 1998. Program Developed for CO2 System Calculations, Oakland Ridge National Laboratory, Technical report # ORNL/CDLAC-105.

Salish Sea Model Overview

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