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Understanding and quantifying the scope and scale of sedimentary services in the German Baltic Sea (SECOS II)

For general information please visit the SECOS homepage [1] or the IOW project database [2].

Work Package 2.3. Modelling sediment services under changing environmental conditions and the influence of macrofaunal key species

The task of work package 2.3 was to model important processes at the sediment-water-interface and in the sediment which are indicative of the retention and long term fate of nutrients. These include:

  • sedimentation rates of organic material,
  • oxygen, nitrogen, phosphorus, and carbon fluxes at the sediment-water-interface,
  • transformation of eutrophic substances into non-reactive forms, e.g. nitrate removal via denitrification,
  • burial of nitrogen and phosphorus compounds in deep sediment layers.

To do this, the Ecological ReGional Ocean Model (ERGOM) was extended to include vertically resolved sediment biogeochemistry (ERGOM SED 1.0) [3,4].

The extended coupled benthic and pelagic diagenetic model includes:

  • continuation of the water column model ERGOM into the pore water of the sediments,
  • vertically resolved representation of the upper sediment layers (~22cm)
  • non-local bio-diffusion in 1D
  • realistic representation of the sediment processes, similar to Reed et al. [2011], iron and manganese oxides, iron monosulfide, pyrite, adsorption of solutes to clay minerals, predictive calculation of pore water pH

Biogeochemical and physical processes at the sediment-water-interface and involved state variables in the extended ERGOM-SED model (source: Hagen Radtke, IOW)

Figure 1: Biogeochemical and physical processes at the sediment-water-interface and involved state variables in the extended ERGOM-SED model (source: Hagen Radtke, IOW).

All model simulations for SECOS were performed on High Performance Computing (HPC) clusters of the HLRN (North-German Supercomputing Alliance) [5].

An example of the annual mean modelled oxygen fluxes into the sediment is shown below. The fluxes are highest in the vicinity of the coast, where eutrophication also is highest. In contrast, they are lower in central basins, which contain larger amounts of organic material. White areas indicate regions where the substrate is characterized by rocky seafloor, hence, no biogeochemical processes are activated.

A detailed evaluation of the model results is ongoing.

Annual mean Oxygen flux into the sediment [mmol m -2 d -1]. Mean daily values from 1991 to 1999 are plotted. White regions indicate regions where the substrate is characterized by rocky seafloor, therefore, no biogeochemical processes are activated (source: Bronwyn Cahill, IOW).

Figure 2: Annual mean Oxygen flux into the sediment [mmol m-2 d-1]. Mean daily values from 1991 to 1999 are plotted. White regions indicate regions where the substrate is characterized by rocky seafloor, therefore, no biogeochemical processes are activated (source: Bronwyn Cahill, IOW).


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Links and references:

  1. SECOS homepage: secos.deutsche-kuestenforschung.de/projekt-secos-synthese.html
  2. SECOS in IOW project database: www.io-warnemuende.de/project/141/secos_ii.html
  3. ERGOM homepage: ergom.net/
  4. Radtke, Hagen, et al. "Ecological ReGional Ocean Model with vertically resolved sediments (ERGOM SED 1.0): Coupling benthic and pelagic biogeochemistry of the south-western Baltic Sea." Geosci. Model Dev. (2019): 275-320. doi: 10.5194/gmd-12-275-2019
  5. SECOS computing project at the North-German Supercomputing Alliance (HLRN, project id: mvk00035): zulassung.hlrn.de/kurzbeschreibungen/mvk00035.pdf

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Model experiments performed within SECOS

Table of Content


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General Information

ERGOM was extended by a 3D sediment model in the SECOS project. The extended ERGOM is denoted as ERGOM SED. The new ERGOM SED model has been documented in Geoscientific Model Development (Radtke et al., 2019, doi: 10.5194/gmd-12-275-2019). The default ERGOM is equipped with an one-layer sediment and includes considerably less benthic processes.


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Purpose of the Experiments

Forty years of hindcast simulations were performed with the new ERGOM SED and the old ERGOM (with one-layer sediment) in order to evaluate benefits of the extended ERGOM version. The simulations extended from 1961 to 2000. The full model output (including processes) was saved only for the last 11 years (1990-2000) to save disk space.

Additionally, one climate run following the A1B scenario was performed to assess the impact of climate change on sediment processes (100 years reduced output; 20 years full output).


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Area and time coverage

  • regional model: western Baltic Sea (model ran for the whole Baltic Sea; detailed sediment data and validation only for western Baltic Seat)
  • initialisation time: 240 years spin up on lower resolution of 9 n.m. (six iterations of 40-year period 1961-2000)
  • first output time stamp, hindcast, reduced output: 31.08.1961
  • first output time stamp, hindcast, full output: 01.01.1990
  • last output time stamp, hindcast: 31.12.2000
  • first output time stamp, scenario A1B, reduced output: 14.02.2001
  • first output time stamp, scenario A1B, full output: 01.01.2080
  • last output time stamp, scenario A1B: 31.12.2099

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Specific information

naming convention

model runinternal run/folder name
hindcast, default ERGOM 1-3nm_CLM_C20_8
hindcast, ERGOM SED, reduced output 1-3nm_CLM_C20_5
hindcast, ERGOM SED, full output 1-3nm_CLM_C20_9
scenario, ERGOM SED, reduced output 1-3nm_CLM_A1B_1
scenario, ERGOM SED, full output 1-3nm_CLM_A1B_2

 

Spezific namelist setup

Atmospheric forcing and open boundary conditions

  • hindcast: CLM C20 forcing
  • scenario: CLM coastDat A1B

Known errors and shortcomings and corrections

Please see Radtke et al. (2019, doi: 10.5194/gmd-12-275-2019) or contact Hagen Radtke.

Configuration and code files

Output variables

Please see IOW THREDDS server (all variables available there).

Storage of the results

Place of Storage Path
IOW Storage /silod4/dneumann/00_permanent_data/published_data/SECOS/online
THREDDS, internal http://thredds.io-warnemuende.de:8080/thredds/secos/catalog_secos.html
THREDDS, external https://thredds-iow.io-warnemuende.de/thredds/projects/secos/catalog_secos.html

Derived data sets

none


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Contact and Questions

Please see the data set description in the IOWMETA database for contact options.


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