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Sediment iron-sulphur chemistry examples

Implementation

Fe-S chemistry is implemented by three PALEO reactions ReactionFeSaq, ReactionFeSm, ReactionPyrH2S, see PALEOaqchem documentation for details

ReactionFeSaq: equilibrium chemistry of FeII, H2S, FeS system

Represents two equilibrium reactions as algebraic constraints to define primary species [Fe2++] and [HS-] in terms of:

  • total [S-II] = [HS-] + [H2S] + [FeSaq]
  • total [FeII] = [Fe++] + [FeSaq]

given a provided fixed value of [H+]

H2S        <--> H+ + HS-         eqb. const. K_H2S
FeSaq + H+ <--> Fe++ + HS-       eqb. const K2_FeSaq

ReactionFeSm: FeS precipitation/dissolution

Represents 

[FeSaq] <--> [FeSm]

as a fast precipitation dissolution reaction

ReactionPyrH2S: Pyrite formation by the "H2S" (Berzelius) mechanism

FeSm + H2S -> FeS2pyr + H2

at rate 

R_Pyr_H2S * [FeSm] * [H2S]

Sediment configurations and experiments

NB: these are illustrative model test configurations only, and are not scientifically validated !!

Physical environment and organic matter input from PALEOexamples\src\sediment\boudreau1996\README.md, from (Boudreau, 1996) shelf and shelf/slope cases.

Fe reactions with FeHR, FeMR, FePR iron oxide phases from Dale (2015), Van Cappellen & Wang (1996), with Fe-S system with explicit treatment of FeS from Rickard and Luther (2007), Lenton & Daines (2017), van de Velde (2021).

TODO

  • not checked rate constants carefully
  • physical configuration and organic matter input is illustrative only
  • no Mn

Oxygen, sulphur, iron, with iron-sulphur interaction and pyrite, iron oxide burial

julia> include("PALEO_examples_sediment_Fe_pyr_x15.jl")

Set of 15 columns, all with same shelf environment, Corg input with two reactivity fractions (a combination of the high-reactivity fraction from the shelf/slope case, and the low reactivity fraction from the rise case), excess Fe input:

  • Columns 1-5 with [SO4] 28 mM (high modern value), decreasing values of [O2], with bioturbation
  • Columns 6-10 with [SO4] 28 mM (high modern value), decreasing values of [O2], no bioturbation
  • Columns 11-15 with zero [O2], no bioturbation decreasing values of [SO4]

Parameters for Fe cycle modified to create a high Fe test case, and increase FeS2pyr oxidation

  • FeHR input ~0.6 mol m-2 yr-1 (comparable to Van Cappellen & Wang 1996 test case, ~x10 higher than a standard modern shelf value?)
  • decrease FeMR limiting concentration for remineralization by x2 vs Van Cappellen & Wang 1996 value (NB: the "Monod" inhibition here is not the same as the linear form they used)
  • increase FeS2pyr oxidation rate constant x10

Demonstrates (cf van de Velde & Meysman (2016)):

  • Pyrite oxidation with modern [O2] and bioturbated sediment resulting in (2*FeS2)/(S reduction) of ~0.1, increases once [O2] drops below ~100 uM, cf Canfield & Farquar (2009)
  • (non bioturbated oxic sediment with modern [O2] stays mostly oxic with little S reduction hence low pyrite burial)
  • Zero oxygen (and non bioturbated) sediment shows high SR, (2*FeS2)/(S reduction) of ~0.5 hence high pyrite burial until [SO4] drops to ~100uM (down a factor of two at ~1 Mm), presumably set by the remin [SO4] dependence (inhibition below 1 mM), cf Habicht (2002)

Test case with pyrite burial

julia> include("PALEO_examples_sediment_Fe_pyr.jl")

Boudreau (1996) test cases with Corg, O2, SO4/H2S, P, Fe-S and pyrite burial. Three columns: shelf/slope, rise, rise (no bioturbation)

POC stoichiometry Corg, P only (no N) to simplify test of alkalinity budget, ie check alkalinity flux from SO4 and FeII solute fluxes = soluteflux_TAlk (as solid phase inputs and output make no contribution to alkalinity budget).

julia> PALEOmodel.get_array(paleorun.output, "fluxOceanfloor.soluteflux_SmIIaqtot", (cell=1, tmodel=1e12)).values
0.00021099944013347013

julia> PALEOmodel.get_array(paleorun.output, "fluxOceanfloor.soluteflux_SO4", (cell=1, tmodel=1e12)).values
-0.0745449641168272  # net sulphate input balanced by FeS / FeS2 burial

julia> PALEOmodel.get_array(paleorun.output, "fluxOceanfloor.soluteflux_FeIIaqtot", (cell=1, tmodel=1e12)).values
0.0012053409002682764

julia> PALEOmodel.get_array(paleorun.output, "fluxOceanfloor.soluteflux_TAlk", (cell=1, tmodel=1e12)).values
0.15150061203704088

julia> -2*-0.0745449641168272 + 2*0.0012053409002682764
0.15150061003419096 # check alkalinity flux from SO4 and FeII fluxes = soluteflux_TAlk

Test case with Fe only, no Fe-S or pyrite burial

julia> include("PALEO_examples_sediment_Fe.jl")

Boudreau (1996) test cases with Corg, O2, SO4/H2S, P, Fe, no Fe-S or pyrite Three columns: shelf/slope, rise, rise (no bioturbation)

References