Bio-sediment coupling to represent detritus (how to implement)

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Eugen
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Joined: Wed Apr 06, 2016 4:36 pm
Location: University of Liege

Bio-sediment coupling to represent detritus (how to implement)

#1 Unread post by Eugen »

Dear ROMS community,

For the purpose of a project I need to couple the sediment and a biological model (to account for detritus that settles down and (partially) being buried and removed from the chemical cycles).

Based on my search through the ROMS code, there is by far no coupling.

Several bio-models (such as Fennel) do have a cpp BIOSEDIMENT, but the settling detritus is being instantaneously converted to nutrients at the deepest water grid cell, this is too much of a simplification.

Am I correct that that coupling is not yet provided in the official ROMS release?

And how do you think it would be easiest to implement it from the logical point of view? I imagine, that I could reserve a sediment class for the detritus, call the sediment model and transform all the detritus in the lowest grid cell into this sediment class, that can settle down and become a part of the sediment bed. In contrast, if particles of this sediment class move up due to mixing or upwelling, they will automatically convert to nutrients.

Is it a good way to solve the coupling problem?
Evgeny Ivanov

PostDoc,
MAST, University of Liege, Belgium

kfennel
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Re: Bio-sediment coupling to represent detritus (how to implement)

#2 Unread post by kfennel »

Hi Eugen,

Please look at these papers:
Moriarty et al., Impact of seabed resuspension on oxygen and nitrogen dynamics in the northern Gulf of Mexico: A numerical modeling study, Journal of Geophysical Research-Oceans 123, 7237-7263 (2018)
https://agupubs.onlinelibrary.wiley.com ... 18JC013950

Moriarty et al., The roles of resuspension, diffusion and biogeochemical processes on oxygen dynamics offshore of the Rhône River, France: a numerical modeling study, Biogeosciences 14, 1919-1946 (2017)
http://www.biogeosciences.net/14/1919/2 ... 9-2017.pdf

I suggest you contact Julia Moriarty (Julia.Moriarty@colorado.edu) directly to obtain the code.

Good luck,
Katja

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Eugen
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Re: Bio-sediment coupling to represent detritus (how to implement)

#3 Unread post by Eugen »

Dear Katja,

Many thanks for the response and the articles ! This is exactly what we were looking for :)

Evgeny
Evgeny Ivanov

PostDoc,
MAST, University of Liege, Belgium

jmoriarty
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Joined: Fri Feb 07, 2020 2:00 am
Location: University of Colorado Boulder

Re: Bio-sediment coupling to represent detritus (how to implement)

#4 Unread post by jmoriarty »

Hi Eugen,

To follow up on Katja's email, the code for the coupling from Moriarty et al., 2017, 2018, and 2021 papers is available in model repositories (see links in the specific papers). Thanks to Katja for providing the first two links. Here's the 2021 paper, too: https://link.springer.com/article/10.10 ... 20-00763-8 . The main difference between the 2018 and 2021 versions is that the 2021 version allows inorganic and organic particles to influence light attenuation/phytoplankton growth in the biogeochemistry module, whereas the 2018 one does not. Also, they use different water column biogeochemistry models (Fennel vs. ECB) because I was working in different systems.

In all three studies/codes, the detritus from the water column biogeochemistry model becomes part of a class of seabed organic matter that can be advected/mixed downwards in the seabed due to bioturbation or burial (just like inorganic sediments in the CSTMS model), resuspended back into the water column (again, just like inorganic sediments in the CSTMS model), or remineralize (based on the Soetaert seabed diagenetic model). If it's resuspended, the seabed organic matter is not instantaneously remineralized, but a fraction of it will become remineralized, depending on the associated remineralization rate constant and how long it is in the water column.

Best,
Julia

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Eugen
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Re: Bio-sediment coupling to represent detritus (how to implement)

#5 Unread post by Eugen »

Dear Julia,

Thanks a lot for the explanation !

This model is exactly what we need, I'm very glad this implementation exists.

Evgeny
Evgeny Ivanov

PostDoc,
MAST, University of Liege, Belgium

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