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Puget Sound Georgia Basin Model

Sediment Diagenesis Module and Hypoxia


Low concentrations of DO have been measured throughout the Salish Sea and are at hypoxic levels (< 2 mg/L) in selected sub-basins. Recent modeling investigations using the prior version of the Salish Sea Model (e.g. Khangaonkar et al. 2012, Roberts et. al. 2014) showed that that low concentrations occur throughout much of the Salish Sea due to the intrusion of water with naturally occurring low DO from the Pacific Ocean. However, some regions of Puget Sound are also significantly influenced by human nutrient contributions. In those investigations, sediment water interaction was prescribed as being uniform fluxes of nutrients and DO. The model worked reasonably well in most sub-basins but could not achieve domain-wide calibration for near-bed LOW DO levels. With prescribed uniform sediment fluxes, hypoxia in regions such as Lynch Cove region of Hood Canal could not be reproduced satisfactorily.

The new version of the Salish Sea Model (Khangaonkar et al. 2018) includes a sediment diagenesis module which allows direct coupled interaction between the water column and sediments through the processes of organic sediment settling, burial, and remineralization. The sediment module generates nutrient fluxes including sediment oxygen demand. With the help of this improvement, the large region of hypoxia in Hood Canal that extends over 30-40 km during its peak has been reproduced as shown in the Figure below. The model also correctly represents hypoxia in Penn Cove and East Sound-waterbodies previously identified as potential areas of concern based on monitoring data. Other areas of concern identified through model results include the Henderson Bay in South Puget Sound and Port Susan Bay.

Comparison of the area and duration of hypoxic bottom layer waters in the Salish Sea Model, with and without land-based loads, based on the Year 2014 simulation. The bottom layer in the model occupies the lower 15% of the water column. (a) hypoxia-duration map - Y2014 baseline (b) hypoxia-duration map - Y2014 without land-based loads.

Note: Land-based loads include rivers, watershed runoff, and wastewater discharges


Module Formulation and Theory

Sediment diagenesis theory is described in detail in Pelletier et al. (2017a) and Bianucci et al. (2018) and is briefly summarized here. Sediment diagenesis is the process where biogeochemical processes transform the nutrients delivered to the sediments from particles settling from the water column and release a portion of the nutrients back into the water column. The process also consumes oxygen. A portion of the nutrients are buried as well, where they are permanently lost from the active system (see schematic below).

Sediment Diagenesis Schematic (Source: Pelletier et al. 2017a)

As the algae bloom, they transform dissolved material into particulate matter. As the algae die, a fraction settles to the bottom. Zooplankton that feed on the algae also produce wastes that settle to the bottom as a flux of particles. These combined fluxes fuel processes within the sediments. A variety of physical and biogeochemical processes act on the organic matter in the sediments. Microbes decompose the organic matter in the sediment which consumes oxygen. Plants and animals physically rework the sediments in a process known as bioturbation. Decomposition and oxidation of organic matter transforms nutrients and release them back to the water column. Sediment oxygen levels decline from bottom water concentrations to near zero within a few millimeters to centimeters of the water surface, which produces strong gradients. These gradients contribute to diffusion into the sediments as oxygen is used to fuel decomposition of organic matter. This exerts a sediment oxygen demand (SOD) on the water column. The decomposition of organic nitrogen generates ammonium and also creates a gradient that pushes ammonium out of the sediments and into the water column.

The Sediment Diagenesis Module in the Salish Sea Model code (FVCOM-ICM) is an implementation based on the Di Toro et al. (2001) model of sediment oxygen demand in the ICM framework. The model was cross checked using bench mark tests with the well-documented WASP modeling framework developed by EPA (Martin and Wool 2013) shown in the process diagram below, also based on the same Di Toro et. al. (2001) formulation.

Basic structure of the Sediment Diagenesis Module (SDM). (Martin and Wool, 2013)

The Sediment Diagenesis Module numerically integrates the mass balance equations for chemical constituents in two layers of sediment. Layer 1: A relatively thin aerobic layer at the sediment water interface with variable thickness that is dynamically calculated. Layer 2: A thicker anaerobic layer with thickness equal to the total sediment depth of 10 minus the depth of the aerobic layer. Particulate organic matter (POM) initially decomposes rapidly in the sediments, but then slows down as the more labile fraction is consumed. In order to capture this process, the settled POM is fractioned to one of three "G classes" based on overall reactivity. The three G classes represent a relatively rapidly decomposing labile class (G1), a more refractory form (G2), and a relatively inert form (G3). The decomposition of the three G classes of POM occurs in layer 2.



1. Di Toro, D.M. 2001. Sediment Flux Modeling, Wiley-Interscience, New York, New York. 624 pp. ISBN: 978-0-471-13535-7.

2. Martin, J.L. and T.A. Wool. 2013. Supplement to Water Analysis Simulation Program User Documentation. WASP Sediment diagenesis Routines: Model Theory and Users Guide. U.S. Environmental Protection Agency, Region 4, Atlanta GA.

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