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**Geoscientific Model Development**
An interactive open-access journal of the European Geosciences Union

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- About
- Editorial board
- Articles
- Special issues
- Highlight articles
- Manuscript tracking
- Subscribe to alerts
- Peer-review process
- For authors
- For editors and referees
- EGU publications
- Imprint
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- About
- Editorial board
- Articles
- Special issues
- Highlight articles
- Manuscript tracking
- Subscribe to alerts
- Peer-review process
- For authors
- For editors and referees
- EGU publications
- Imprint
- Data protection

- Abstract
- Introduction
- Model description
- Stand-alone sensitivity analysis and case studies
- Coupled pre-industrial Earth system model simulations
- Scope of applicability and model limitations
- Conclusions
- Code availability
- Appendix A: Reaction network
- Appendix B: Sensitivity analysis
- Appendix C: Prescribed burial flux fields
- Author contributions
- Competing interests
- Acknowledgements
- References
- Supplement

**Model description paper**
09 Jul 2018

**Model description paper** | 09 Jul 2018

OMEN-SED 1.0: a novel, numerically efficient organic matter sediment diagenesis module for coupling to Earth system models

^{1}BRIDGE, School of Geographical Sciences, University of Bristol, Clifton, Bristol BS8 1SS, UK^{2}Department of Earth Sciences, University of California, Riverside, CA 92521, USA^{3}BGeosys, Department Geoscience, Environment & Society (DGES), Université Libre de Bruxelles, Brussels, Belgium^{4}Earth System Science, University of Exeter, North Park Road, Exeter EX4 4QE, UK

^{1}BRIDGE, School of Geographical Sciences, University of Bristol, Clifton, Bristol BS8 1SS, UK^{2}Department of Earth Sciences, University of California, Riverside, CA 92521, USA^{3}BGeosys, Department Geoscience, Environment & Society (DGES), Université Libre de Bruxelles, Brussels, Belgium^{4}Earth System Science, University of Exeter, North Park Road, Exeter EX4 4QE, UK

**Correspondence**: Dominik Hülse (dominik.huelse@ucr.edu)

**Correspondence**: Dominik Hülse (dominik.huelse@ucr.edu)

Abstract

Back to toptop
We present the first version of
OMEN-SED (Organic Matter ENabled SEDiment model), a new, one-dimensional
analytical early diagenetic model resolving organic matter cycling and
the associated biogeochemical dynamics in marine sediments designed to be coupled
to Earth system models. OMEN-SED explicitly describes organic matter
(OM) cycling and the associated dynamics of the most important
terminal electron acceptors (i.e. O_{2} , NO_{3}, SO_{4}) and
methane (CH_{4}), related reduced substances (NH_{4}, H_{2}S),
macronutrients (PO_{4}) and associated pore water quantities
(ALK, DIC). Its reaction network accounts for the most
important primary and secondary redox reactions, equilibrium reactions,
mineral dissolution and precipitation, as well as adsorption and desorption
processes associated with OM dynamics that affect the dissolved and solid
species explicitly resolved in the model. To represent a redox-dependent
sedimentary P cycle we also include a representation of the formation and
burial of Fe-bound P and authigenic Ca–P minerals. Thus, OMEN-SED is able to
capture the main features of diagenetic dynamics in marine sediments and
therefore offers similar predictive abilities as a complex, numerical
diagenetic model. Yet, its computational efficiency allows for its coupling to
global Earth system models and therefore the investigation of coupled global
biogeochemical dynamics over a wide range of climate-relevant timescales.
This paper provides a detailed description of the new sediment model, an
extensive sensitivity analysis and an evaluation of OMEN-SED's
performance through comprehensive comparisons with observations and results
from a more complex numerical model. We find that solid-phase and dissolved pore
water profiles for different ocean depths are reproduced with good accuracy
and simulated terminal electron acceptor fluxes fall well within the range of
globally observed fluxes. Finally, we illustrate its application in an Earth
system model framework by coupling OMEN-SED to the Earth system model cGENIE
and tune the OM degradation rate constants to optimise the fit of simulated
benthic OM contents to global observations. We find that the simulated sediment
characteristics of the coupled model framework, such as OM degradation rates,
oxygen penetration depths and sediment–water interface fluxes, are generally
in good agreement with observations and in line with what one would expect on
a global scale. Coupled to an Earth system model, OMEN-SED is thus a powerful
tool that will not only help elucidate the role of benthic–pelagic exchange
processes in the evolution and the termination of a wide
range of climate events, but will also allow for a direct comparison of model
output with the sedimentary record – the most important climate archive on
Earth.

How to cite

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How to cite.

Hülse, D., Arndt, S., Daines, S., Regnier, P., and Ridgwell, A.: OMEN-SED 1.0: a novel, numerically efficient organic matter sediment diagenesis module for coupling to Earth system models, Geosci. Model Dev., 11, 2649–2689, https://doi.org/10.5194/gmd-11-2649-2018, 2018.

1 Introduction

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Marine surface sediments are key components in the Earth system. They host
the largest carbon reservoir within the surficial Earth system, provide the
primary long-term sink for atmospheric CO_{2}, recycle nutrients and
represent the most important geochemical archive used for deciphering past
changes in biogeochemical cycles and climate (e.g. Berner, 1991;
Archer and Maier-Reimer, 1994;
Ridgwell and Zeebe, 2005;
Arndt et al., 2013). Physical and
chemical processes in sediments (i.e. diagenetic processes) depend on the
water column and vice versa: diagenesis is controlled by the external supply
of solid material (e.g. organic matter, calcium carbonate, opal) from the
water column and is affected by overlying bottom water concentrations of
solutes. At the same time, sediments impact the water column directly either
through the short- and long-term storage of deposited material or the diagenetic
processing of deposited material and the transport of terminal electron acceptors
(e.g. O_{2}, SO_{4}) into the sediments, as well as metabolic
products (e.g. nutrients, DIC) to the overlying bottom waters. This
so-called benthic–pelagic coupling is essential for understanding global
biogeochemical cycles and climate (e.g. Archer and Maier-Reimer, 1994; Archer et al., 2000; Soetaert et al., 2000; Mackenzie, 2005).

The biological primary production of organic matter (OM, generally represented in
its simple form CH_{2}O in Reaction R1) and the
reverse process of degradation can be written in a greatly simplified
reaction as

$$\begin{array}{}\text{(R1)}& {\mathrm{CO}}_{\mathrm{2}}+{\mathrm{H}}_{\mathrm{2}}\mathrm{O}\rightleftharpoons {\mathrm{CH}}_{\mathrm{2}}\mathrm{O}+{\mathrm{O}}_{\mathrm{2}}.\end{array}$$

On geological timescales, production of OM is generally greater than
degradation, which results in some organic matter being buried in marine
sediments and oxygen accumulating in the atmosphere. Thus, the burial of OM deep
into the sediment leads to net oxygen input to and CO_{2} removal from
the atmosphere (Berner, 2004). On shorter timescales, the
upper few metres of the sediments where early diagenesis occurs are
specifically important, as this zone controls whether a substance is recycled
to the water column or buried for a longer period of time in the deeper
sediments (Hensen et al., 2006). Most biogeochemical cycles and
reactions in this part of marine sediments can be related either directly or
indirectly to the degradation of organic matter
(Middelburg et al., 1993; Arndt et al., 2013). Oxygen and
nitrate, for instance, the highest energy-yielding electron acceptors, are
preferentially consumed in the course of the degradation of organic matter,
resulting in the release of ammonium and phosphorus to the pore water. As
such, the degradation of OM in the sediments can profoundly affect the oxygen and
nutrient inventory of the ocean and thus primary productivity
(Van Cappellen and Ingall, 1994; Lenton and Watson, 2000). Furthermore,
organic matter degradation releases metabolic CO_{2} to the pore water,
causing it to have a lower pH and carbonate ion concentration, thus provoking
the dissolution of calcium carbonate CaCO_{3}
(Emerson and Bender, 1981).

Benthic nutrient recycling from marine sediments has been suggested to play a
key role for climate and ocean biogeochemistry throughout Earth history. For
example, feedbacks between phosphorus storage and erosion from shelf
sediments and marine productivity have been hypothesised to play an important
role for glacial–interglacial atmospheric CO_{2} changes
(Broecker, 1982; Ruttenberg, 1993). Furthermore,
benthic nutrient recycling from anoxic sediments has been invoked to explain
the occurrence of more extreme events in Earth history, for instance oceanic
anoxic events (OAEs; e.g. Van Cappellen and Ingall, 1994; Mort et al., 2007; Tsandev and Slomp, 2009). OAEs represent severe
disturbances of the global carbon, oxygen and nutrient cycles of the ocean
and are usually characterised by widespread bottom water anoxia and photic
zone euxinia (Jenkyns, 2010). One way to explain the
genesis and persistence of OAEs is increased oxygen demand due to enhanced
primary productivity. Increased nutrient inputs to fuel primary productivity
may in turn have come from marine sediments as the burial efficiency of
phosphorus declines when bottom waters become anoxic
(Ingall and Jahnke, 1994; Van Cappellen and Ingall, 1994). The recovery from
OAE-like conditions is thought to involve the permanent removal of excess
CO_{2} from the atmosphere and ocean by burying carbon in the form of
organic matter in marine sediments (e.g. Arthur et al., 1988; Jarvis et al., 2011), which is consistent with the geological record of
widespread black shale formation (Stein et al., 1986). Models
capable of simulating not only the expansion and intensification of oxygen
minimum zones, but also of predicting how the underlying sediments interact
are hence needed.

Quantifications of diagenetic processes in the sediments are possible through
the application of idealised mathematical representations, or so-called
diagenetic models (see e.g. Berner, 1980; Boudreau, 1997). A plethora of different approaches have been
developed, mainly following two distinct directions (see Arndt et al., 2013, for an
overview). The first involves state-of-the-art vertically
resolved numerical models simulating the entire suite of essential coupled
redox and equilibrium reactions within marine sediments (e.g. BRNS,
Aguilera et al.,
2005; CANDI,
Boudreau,
1996; MEDIA,
Meysman et al., 2003; MUDS,
Archer et al., 2002; STEADYSED,
Van Cappellen and Wang, 1996).
These “complete”, multi-component steady-state or non-steady-state models
thus resolve the resulting characteristic redox zonation of marine sediments
by explicitly accounting for oxic OM degradation, denitrification,
oxidation by manganese and iron (hydr)oxides, sulfate reduction and
methanogenesis as well as the reoxidation of reduced byproducts (i.e.
NH_{4}, Mn^{2+}, Fe^{2+}, H_{2}S, CH_{4}; see
e.g. Regnier et al., 2011). Furthermore, they incorporate various
mineral dissolution and precipitation reactions, as well as fast equilibrium
sorption processes, for example of NH_{4}, PO_{4} and metal ions
(i.e. Mn^{2+}, Fe^{2+} and Mg^{2+};
compare Van Cappellen and Wang, 1996; Meysman et al., 2003). Modelled,
depth-dependent transport processes usually comprise advection, diffusion,
bioturbation and bio-irrigation. This group of diagenetic models generally
describes OM degradation via a so-called multi-G approach
(Jørgensen, 1978; Berner, 1980), thus dividing the
bulk organic matter pool into a number of compound classes that are
characterised by different degradabilities *k*_{i}. Alternative approaches,
so-called continuum models (Middelburg, 1989;
Boudreau and Ruddick, 1991), assume a continuous distribution of reactive types
but, although conceptually superior, are much less popular
(Arndt et al., 2013). These complex, multi-component models have
great potential for quantifying diagenetic dynamics at sites where
comprehensive observational datasets are available to constrain its model
parameters (see e.g. Boudreau et al., 1998; Wang and Van Cappellen, 1996; Thullner et al., 2009, for applications). However, due to the
high degree of coupled processes and depth-varying parameters, the diagenetic
equation needs to be solved numerically, thus resulting in a very high
computational demand and consequently rendering their application in an Earth
system model (ESM) framework with a large number of grid points prohibitive.
Additionally, their global applicability is seriously compromised by the
restricted transferability of model parameters from one site to the global
scale (Arndt et al., 2013).

The second group of diagenetic models emerged during the early days of
diagenetic modelling when computing power was severely restricted
(e.g. Berner, 1964). These models solve the diagenetic
equation analytically, thus providing an alternative and computationally more
efficient approach. Finding an analytical solution, especially when complex
reaction networks are to be considered, is not straightforward and analytical
models are thus usually less sophisticated and comprehensive than numerical
models and generally require the assumption of steady-state conditions. It
has been shown that the complexity of the reaction network can be reduced by
dividing the sediment column into distinct zones and accounting for the most
pertinent biogeochemical processes within each zone, thus increasing the
likelihood of finding an analytical solution without oversimplifying the
problem. Analytical approaches with distinct biogeochemical zones were
implemented and used in the 1970s and 1980s to describe observed pore
water profiles (e.g. Vanderborght and Billen, 1975; Vanderborght et al., 1977; Billen, 1982; Goloway and Bender, 1982; Boudreau and Westrich, 1984) and later for inclusion into multi-box ecosystem
models (e.g. Ruardij and Van Raaphorst, 1995; Gypens et al., 2008) and global
Earth system models (Tromp et al., 1995). However, in addition to the
oxic zone these models generally only describe one anoxic zone explicitly,
either a denitrification (Vanderborght and Billen, 1975; Billen, 1982; Goloway and Bender, 1982; Ruardij and Van Raaphorst, 1995; Gypens et al., 2008) or a sulfate reduction zone
(Boudreau and Westrich, 1984; Tromp et al., 1995). Furthermore, the
approaches of Vanderborght and Billen (1975),
Goloway and Bender (1982) and Tromp et al. (1995) do not
explicitly account for reduced species (i.e. NH_{4} and H_{2}S).

In most current ESMs sediment–water dynamics are either neglected or treated
in a very simplistic way (Soetaert et al., 2000; Hülse et al., 2017). Most Earth system models of intermediate
complexity (EMICs) and also some of the higher-resolution Earth
system–climate models represent the sediment–water interface either as a
reflective or a conservative–semi-reflective
boundary (Hülse et al., 2017). Thus, all particulate material deposited on
the sea floor is either instantaneously consumed (reflective boundary), or a
fixed fraction is buried in the sediments (conservative–semi-reflective boundary). Both
highly simplified approaches furthermore completely neglect the exchange of
solute species through the sediment–water interface and therefore cannot
resolve the complex benthic–pelagic coupling. However, due to their
computational efficiency, both representations are often used in global
biogeochemical models (e.g. Najjar et al., 2007; Ridgwell et al., 2007; Goosse et al., 2010). Analytical diagenetic models
represent the most complex description of diagenetic dynamics in Earth system
models. Examples of global ESMs employing a vertically resolved diagenetic
model are NorESM (Tjiputra et al., 2013) and HAMOCC
(Palastanga et al., 2011; Ilyina et al., 2013), both using a version
of Heinze et al. (1999). None of the EMICs reviewed by
Hülse et al. (2017) use such a sediment representation. DCESS
(Shaffer et al., 2008) and MBM
(Munhoven, 2007) are box models employing a
vertically resolved diagenetic model. These analytic models account for the
most important transport processes (i.e. advection, bioturbation and
molecular diffusion) through basic parameterisations and include fewer
biogeochemical reactions, which are generally restricted to the upper,
bioturbated 10 cm of the sediments. Pore water species explicitly
represented in DCESS (Shaffer et al., 2008) and the HAMOCC model
of Heinze et al. (1999) and Palastanga et al. (2011) are
restricted to DIC, TA, PO_{4} and O_{2}. The MEDUSA model
(Munhoven, 2007) considers CO_{2},
${\mathrm{HCO}}_{\mathrm{3}}^{-}$, ${\mathrm{CO}}_{\mathrm{3}}^{\mathrm{2}-}$ and O_{2}. Other species produced or
consumed during OM degradation are neglected. Thus, with oxygen being the
only TEA explicitly modelled, the influence of reduced species is only
implicitly included in the boundary conditions for O_{2}. A newer
version of the HAMOCC model is a notable exception, as
Ilyina et al. (2013) include NO_{3} and denitrification
explicitly. Furthermore, the version of Palastanga et al. (2011)
represents a redox-dependent explicit sedimentary phosphorus cycle. Yet, the
reoxidation of reduced byproducts, so-called secondary redox reactions (e.g.
oxidation of NH_{4}, H_{2}S or CH_{4}), or sorption processes
are not included in any of the discussed models. Furthermore, these global
models assume that the sedimentary organic matter pool is composed of just a
single compound class which is either degraded with a globally invariant
degradation rate constant (Munhoven, 2007) or a
fixed rate constant depending on local oxygen concentrations
(Shaffer et al., 2008; Palastanga et al., 2011).

Obviously, such a simplification of the OM pool can neither account for the
observed vast structural complexity in natural organic matter and its
resulting different degradation rates nor for the rapid decrease in OM
degradability in the uppermost centimetres of the sediments
(Arndt et al., 2013). It has been suggested that at least a 3G
approach is necessary to accurately represent organic matter dynamics in this
part of the sediments where most OM is degraded
(e.g. Soetaert et al., 1996). Even more restrictive is the use of
O_{2} as the only TEA and the complete absence of reduced substances and
related secondary redox reactions. For the majority of the modern sediments
(i.e. in the deep ocean) O_{2} is the primary electron acceptor;
however, recent model and data studies have reported that sulfate reduction
is the dominant degradation pathway on a global average (with
contributions of 55–76 % Canfield et al., 2005; Jørgensen and Kasten, 2006; Thullner et al., 2009). Oxygen becomes progressively less important as
TEA with decreasing sea-floor depth and sulfate reduction has been shown to
account for 83 % of OM degradation in coastal sediments
(Krumins et al., 2013). In these environments most O_{2} is used
to reoxidise reduced substances produced during anaerobic degradation
(Canfield et al., 2005; Thullner et al., 2009). Thus, the in situ
production of e.g. NO_{3} and SO_{4} through the oxidation of
NH_{4} and H_{2}S forms an important sink for O_{2} which is
entirely neglected in current sediment representations in global models. In
addition, the lack of anoxic degradation pathways in these models limits
their application to oxic oceans. Currently no analytical sediment model
exists that can be used under anoxic conditions. Due to the lack of an
appropriate sedimentary P cycle (with the exception of the HAMOCC
version of Palastanga et al., 2011), no current global ESM is able to
model the redox-dependent P release from marine sediments and its
implications for primary productivity, global biogeochemical cycles and
climate. A sediment model suitable for coupling to an ESM and enabling a wide
range of paleo-questions to be addressed has to provide a robust
quantification of organic (and inorganic) carbon burial fluxes, benthic
uptake and return fluxes of oxygen,
growth-limiting nutrients and reduced species, as well as anoxic degradation
pathways. As a consequence, the reaction network must account for the most
important primary and secondary redox reactions, equilibrium reactions,
mineral precipitation and dissolution,
and adsorption and desorption,
resulting in a complex set of coupled reaction–transport equations.

Therefore, we developed the Organic Matter ENabled SEDiment model (OMEN-SED), a new, one-dimensional, numerically efficient diagenetic model. OMEN-SED builds upon and stands in the tradition of earlier stand-alone, analytical diagenetic models (Vanderborght et al., 1977; Billen, 1982; Goloway and Bender, 1982; Boudreau, 1991) and analytical diagenetic models developed for coupling to regional-scale ecosystem or global Earth system models (Ruardij and Van Raaphorst, 1995; Tromp et al., 1995; Heinze et al., 1999; Gypens et al., 2008).

OMEN-SED is the first analytical model to explicitly describe OM cycling and the associated dynamics of the most important TEAs (i.e. O_{2},
NO_{3}, SO_{4}), related reduced substances (NH_{4},
H_{2}S), the full suite of secondary redox reactions, macronutrients
(PO_{4}) and the associated pore water quantities (ALK, DIC).
To represent a redox-dependent sedimentary P cycle we consider the formation
and burial of Fe-bound P and authigenic Ca–P minerals. Thus, while OMEN-SED
captures most of the features of a complex, numerical diagenetic model, its
computational efficiency allows for coupling to global Earth system models
and therefore the investigation of coupled global biogeochemical dynamics
over different timescales. Here, the model is presented as a 2G approach;
however, OMEN-SED can be easily extended to a multi-G approach. The first
part of the paper provides a detailed description of OMEN-SED
(Sect. 2). This includes descriptions of the
general model approach (Sect. 2.1), the
conservation equations for all explicitly represented biogeochemical tracers
(Sect. 2.2) and a summary of global
relationships used to constrain reaction and transport parameters in OMEN-SED
(Sect. 2.4). In addition, a generic algorithm is
described which is used to match internal boundary conditions and to
determine the integration constants for the analytical solutions
(Sect. 2.3). In order to validate the stand-alone
version of OMEN-SED, the second part of the paper performs an extensive
sensitivity analysis for the most important model parameters, and resulting
sediment–water interface fluxes are compared with a global database
(Sect. 3.1). In addition, the results of the stand-alone model are
compared with observed pore water profiles from different ocean depths
(Sect. 3.2), and OMEN-SED simulations of TEA fluxes along
a typical ocean transect are compared with observations and results from a
complete, numerical diagenetic model (Sect. 3.3).
Thereafter, OMEN-SED is coupled to the carbon-centric version of the
GENIE Earth system model
(cGENIE; Ridgwell et al., 2007, Sect. 4.1).
Sensitivity studies are carried out using this coupled model and modelled
organic matter concentrations in the surface sediments are compared to a
global database
(Seiter et al., 2004, Sect. 4.2).
We finally discuss potential applicabilities of OMEN-SED and critically
analyse model limitations (Sect. 5).

2 Model description

Back to toptop
OMEN-SED is implemented as a FORTRAN version that can be easily coupled to
any pelagic, biogeochemical model via the coupling routine
**OMEN_SED_main**. In addition, OMEN-SED exists as a
stand-alone version implemented in MATLAB and the entire model can be
executed on a standard personal computer in less than 0.1 s. The source code
of both the FORTRAN and the MATLAB stand-alone version and
instructions for executing OMEN-SED and for plotting model results are
available as a Supplement to this paper.

The following section provides a detailed description of OMEN-SED and the fundamental equations underlying the model are highlighted. Tables 1 and A1 summarise the biogeochemical reaction network and Tables 9 and 10 provide a glossary of model parameters along with their respective units.

In OMEN-SED, the calculation of benthic uptake, recycling and burial fluxes is based on the vertically resolved conservation equation for solid and dissolved species in porous media (e.g. Berner, 1980; Boudreau, 1997):

$$\begin{array}{}\text{(1)}& {\displaystyle}\mathit{\xi}{\displaystyle \frac{\partial {C}_{i}}{\partial t}}=-{\displaystyle \frac{\partial}{\partial z}}\left(-\mathit{\xi}{D}_{i}{\displaystyle \frac{\partial {C}_{i}}{\partial z}}+\mathit{\xi}w{C}_{i}\right)+\mathit{\xi}\sum _{j}{R}_{i}^{j},\end{array}$$

where *C*_{i} is the concentration of biogeochemical species *i*, and *ξ*
equals the porosity *ϕ* for solute species and (1−*ϕ*) for solid
species. The term *z* is the sediment depth, *t* denotes the time, *D*_{i} is
the apparent diffusion coefficient of species *i*, *w* is the advection
rate and ${\sum}_{j}{R}_{i}^{j}$ represents
the sum of all biogeochemical rates *j* affecting species *i*.

OMEN-SED accounts for both the advective and the diffusive transport of solid
and dissolved species. They are buried in the sediment according to a
constant advection rate *w*, thus
neglecting the effect of sediment compaction (i.e. $\frac{\partial \mathit{\varphi}}{\partial z}=\mathrm{0}$) due to mathematical constraints. The molecular
diffusion of dissolved species is described by Fick's law applying a
species-specific apparent diffusion coefficient, *D*_{mol,i}. In
addition, the activity of infaunal organisms in the bioturbated zone is
simulated using a diffusive term (e.g. Boudreau, 1986),
with a constant bioturbation coefficient *D*_{bio} in the
bioturbated zone, while *D*_{bio} is set to zero below the maximum
bioturbation depth, *z*_{bio}. The pumping activity by burrow-dwelling
animals and the resulting ventilation of tubes, the so-called bio-irrigation,
is encapsulated in a factor *f*_{ir} that enhances the molecular
diffusion coefficient (hence, ${D}_{i,\mathrm{0}}={D}_{\mathrm{mol},i}\cdot {f}_{\mathrm{ir}}$; Soetaert et al., 1996). The reaction network of OMEN-SED
accounts for the most important primary and secondary redox reactions,
equilibrium reactions, mineral dissolution and precipitation, and
the adsorption and desorption
processes associated with OM dynamics that affect the dissolved and solid
species explicitly resolved in the model.
Tables 1 and A1
provide a summary of the reactions and biogeochemical tracers considered in
OMEN-SED together with their respective reaction stoichiometries.

All parameters in Eq. (1), apart from porosity
and burial rate, may vary with sediment depth and many reaction rate
expressions depend on the concentration of other species. Expressing
Eq. (1) for a set of chemical species thus
results in a non-linear, coupled set of equations that can only be solved
numerically. However, OMEN-SED is designed for coupling to Earth system
models and therefore cannot afford a computationally expensive numerical
solution. Instead, similar to early analytical diagenetic models, a
computationally efficient analytical solution to
Eq. (1) can be derived by (1) assuming steady-state conditions (i.e.$\frac{\partial {C}_{i}}{\partial t}=\mathrm{0}$) and (2) reducing
the vertical variability in parameters and reaction rate expressions by
dividing the sediment column into a number of functional biogeochemical zones
(Fig. 1; compare e.g. Billen, 1982; Goloway and Bender, 1982; Ruardij and Van Raaphorst, 1995; Tromp et al., 1995; Gypens et al., 2008, for similar
solutions). More
specifically, OMEN-SED follows Berner (1980) by dividing the
sediment column into (I) a bioturbated and (II) a non-bioturbated zone
defined by an imposed, constant bioturbation depth *z*_{bio}
(Fig. 1). Furthermore, it resolves the dynamic redox
stratification of marine sediments by dividing the sediment into (1) an oxic
zone delineated by the oxygen penetration depth *z*_{ox}; (2) a
denitrification (or nitrogenous) zone situated between *z*_{ox} and
the nitrate penetration depth ${z}_{{\mathrm{NO}}_{\mathrm{3}}}$; (3) a sulfate reduction zone
situated between ${z}_{{\mathrm{NO}}_{\mathrm{3}}}$ and the sulfate penetration depth
${z}_{{\mathrm{SO}}_{\mathrm{4}}}$; and (4) a methanogenic zone situated below
${z}_{{\mathrm{SO}}_{\mathrm{4}}}$ (Fig. 1). Although in each of these
zones Eq. (1) is applied with depth invariant
parameters, parameter values may differ across zones. The biogeochemical
zones are linked by stating continuity in both concentrations and fluxes at
the dynamic, internal boundaries (${z}_{\mathrm{b}}\in \mathit{\{}{z}_{\mathrm{bio}},{z}_{\mathrm{ox}},{z}_{{\mathrm{NO}}_{\mathrm{3}}},{z}_{{\mathrm{SO}}_{\mathrm{4}}}\mathit{\}}$; compare
e.g. Billen, 1982; Ruardij and Van Raaphorst, 1995). Note that these
boundaries are dynamic because their depth varies in response to changing
ocean boundary conditions and forcings (see Sect. 2.3.1 for
details). Furthermore, the maximum bioturbation depth is not restricted to a
specific biogeochemical zone, and hence OMEN-SED allows bioturbation to occur in
the anoxic zones of the sediment (here all zones *z*>*z*_{ox}
combined).

The formulation of the reaction term in Eq. (1)
varies between zones and encapsulates the most pertinent reaction processes
within the respective zone (see Sect. 2.2), thus
simplifying the mathematical description of the reaction network while
retaining most of its biogeochemical complexity. One such simplification is
that solid-phase iron and manganese oxidants and their reductants are not
considered in the reaction network. All consumption and production processes
of dissolved species related to the degradation of organic matter are a
function of the organic matter concentration. Because organic matter
degradation is described as a first-order degradation, these processes can be
expressed as a series of exponential terms (${\sum}_{j}{\mathit{\alpha}}_{j}\mathrm{exp}(-{\mathit{\beta}}_{j}z)$; see Eq. 2). In addition, slow adsorption and desorption
and mineral precipitation processes can be expressed as zero- or first-order
(reversible) reactions (*Q*_{m} or *k*_{l}⋅*C*_{i} in Eq. 2).
Fast adsorption is described as an instantaneous equilibrium reaction using a
constant adsorption coefficient *K*_{i}. The reoxidation of reduced substances
is accounted for implicitly by adding a
(consumption and production) flux to
the internal boundary conditions (see Sect. 2.2.2,
2.2.3 and 2.2.4). This simplification has been used
previously by Gypens et al. (2008) for nitrate and ammonium and can be
justified as it has been shown that reoxidation mainly occurs within a thin
layer at the oxic–anoxic interface (Soetaert et al., 1996). The general
reaction–transport equation underlying OMEN-SED is thus given by

$$\begin{array}{ll}{\displaystyle \frac{\partial {C}_{i}}{\partial t}}& {\displaystyle}=\mathrm{0}={\displaystyle \frac{{D}_{i}}{\mathrm{1}+{K}_{i}}}{\displaystyle \frac{{\partial}^{\mathrm{2}}{C}_{i}}{\partial {z}^{\mathrm{2}}}}-w{\displaystyle \frac{\partial {C}_{i}}{\partial z}}-{\displaystyle \frac{\mathrm{1}}{\mathrm{1}+{K}_{i}}}\\ \text{(2)}& {\displaystyle}& {\displaystyle}\left(\sum _{j}{\mathit{\alpha}}_{j}\mathrm{exp}(-{\mathit{\beta}}_{j}z)+\sum _{l}{k}_{l}\cdot {C}_{i}-\sum _{m}{Q}_{m}\right),\end{array}$$

where 1∕*β*_{j} can be interpreted as the length scale and *α*_{j} as
the relative importance (or the magnitude at *z*=0) of reaction *j*
(Boudreau, 1997);
*k*_{l} represents generic first-order reaction rate constants and *Q*_{m} represents zero-order (or constant) reaction rates.

The analytical solution to Eq. (2) is of the general form

$$\begin{array}{ll}{\displaystyle}{C}_{i}\left(z\right)& {\displaystyle}=A\cdot \mathrm{exp}\left(az\right)+B\cdot \mathrm{exp}\left(bz\right)+\sum _{j}{\displaystyle \frac{{\mathit{\alpha}}_{j}}{D{\mathit{\beta}}_{j}^{\mathrm{2}}-w{\mathit{\beta}}_{j}-{\sum}_{l}{k}_{l}}}\\ \text{(3)}& {\displaystyle}& {\displaystyle}\cdot \mathrm{exp}(-{\mathit{\beta}}_{j}z)+{\displaystyle \frac{{\sum}_{m}{Q}_{m}}{{\sum}_{l}{k}_{l}}},\end{array}$$

with

$$\begin{array}{ll}{\displaystyle}& {\displaystyle}a={\displaystyle \frac{w-\sqrt{{w}^{\mathrm{2}}+\mathrm{4}\cdot D\cdot {\sum}_{l}{k}_{l}}}{\mathrm{2}\cdot D}},\\ \text{(4)}& {\displaystyle}& {\displaystyle}b={\displaystyle \frac{w+\sqrt{{w}^{\mathrm{2}}+\mathrm{4}\cdot D\cdot {\sum}_{l}{k}_{l}}}{\mathrm{2}\cdot D}}\end{array}$$

where *A* and *B* are integration constants that can be determined by
applying a set of internal boundary conditions (see
Sect. 2.3) and $D=\frac{{D}_{i}}{\mathrm{1}+{K}_{i}}$.

Based on Eq. (2) and its analytical solution
Eq. (3), OMEN-SED returns the
fraction of particulate organic carbon (POC) buried in the sediment,
*f*_{POC}, and the benthic uptake and return fluxes ${F}_{{C}_{i}}$ of
dissolved species *C*_{i} (in mol cm^{−2} yr^{−1}) in response to the
dynamic interplay of transport and reaction processes under changing boundary
conditions and forcings:

$$\begin{array}{}\text{(5)}& {\displaystyle}{f}_{\mathrm{POC}}& {\displaystyle}={\displaystyle \frac{\mathrm{POC}\left({z}_{\mathrm{max}}\right)}{\mathrm{POC}\left(\mathrm{0}\right)}},\text{(6)}& {\displaystyle}{F}_{{C}_{i}}& {\displaystyle}=\mathit{\varphi}\left(\mathrm{0}\right)\left({D}_{i}{\displaystyle \frac{\partial {C}_{i}\left(z\right)}{\partial z}}{|}_{z=\mathrm{0}}-w\cdot {C}_{i}\left(\mathrm{0}\right)\right),\end{array}$$

where *w* is the deposition rate, *D*_{i} is the diffusion coefficient and
POC(0), POC(*z*_{max}) and *C*_{i}(0) denote the
concentration of POC and dissolved species *i* at the sediment–water
interface (SWI) and at the lower sediment boundary, respectively.

The following sections provide a detailed description of the conservation equations and analytical solutions for each chemical species that is resolved in this version of OMEN-SED.

In marine sediments, organic matter (or in the following called particulate
organic carbon, POC) is degraded by heterotrophic activity coupled to the
sequential utilisation of terminal electron acceptors (TEAs) according to the
free energy gain of the half-reaction (${\mathrm{O}}_{\mathrm{2}}>{\mathrm{NO}}_{\mathrm{3}}^{-}>{\mathrm{MnO}}_{\mathrm{2}}>\mathrm{Fe}(\mathrm{OH}{)}_{\mathrm{3}}>{\mathrm{SO}}_{\mathrm{4}}^{\mathrm{2}-}$;
e.g. Stumm and Morgan, 2012). Once all TEAs are depleted, organic matter is
degraded via methanogenesis. Here, organic matter degradation is described
via a multi-G model approach (Jørgensen, 1978), dividing
the bulk OM into a number *i* of discrete compound classes POC_{i}
characterised by class-specific first-order degradation rate constants *k*_{i}.
The conservation equation for organic matter dynamics is thus given by

$$\begin{array}{}\text{(7)}& {\displaystyle \frac{\partial {\mathrm{POC}}_{i}}{\partial t}}=\mathrm{0}={D}_{{\mathrm{POC}}_{i}}{\displaystyle \frac{{\partial}^{\mathrm{2}}{\mathrm{POC}}_{i}}{\partial {z}^{\mathrm{2}}}}-w{\displaystyle \frac{\partial {\mathrm{POC}}_{i}}{\partial z}}-{k}_{i}\cdot {\mathrm{POC}}_{i},\end{array}$$

with ${D}_{{\mathrm{POC}}_{i}}={D}_{\mathrm{bio}}$ for *z*≤*z*_{bio} and
${D}_{{\mathrm{POC}}_{i}}=\mathrm{0}$ for *z*>*z*_{bio}. Integration of
Eq. (7) yields the following general solutions for the
bioturbated and non-bioturbated layers.

$$\begin{array}{ll}{\displaystyle}& {\displaystyle}\text{(I) Bioturbated zone}\phantom{\rule{0.25em}{0ex}}(z\le {z}_{\mathrm{bio}})\\ \text{(8)}& {\displaystyle}& {\displaystyle}{\mathrm{POC}}_{i}^{\mathrm{I}}\left(z\right)={A}_{\mathrm{1}i}\cdot \mathrm{exp}\left({a}_{\mathrm{1}i}z\right)+{B}_{\mathrm{1}i}\cdot \mathrm{exp}\left({b}_{\mathrm{1}i}z\right){\displaystyle}& {\displaystyle}\text{(II) Non-bioturbated zone}\phantom{\rule{0.25em}{0ex}}({z}_{\mathrm{bio}}<z)\\ \text{(9)}& {\displaystyle}& {\displaystyle}{\mathrm{POC}}_{i}^{\mathrm{II}}\left(z\right)={A}_{\mathrm{2}i}\cdot \mathrm{exp}\left({a}_{\mathrm{2}i}z\right)\end{array}$$

In the above equations,

$$\begin{array}{ll}{\displaystyle}& {\displaystyle}{a}_{\mathrm{1}i}={\displaystyle \frac{w-\sqrt{{w}^{\mathrm{2}}+\mathrm{4}\cdot {D}_{{\mathrm{POC}}_{i}}\cdot {k}_{i}}}{\mathrm{2}\cdot {D}_{{\mathrm{POC}}_{i}}}},\\ \text{(10)}& {\displaystyle}& {\displaystyle}{b}_{\mathrm{1}i}={\displaystyle \frac{w+\sqrt{{w}^{\mathrm{2}}+\mathrm{4}\cdot {D}_{{\mathrm{POC}}_{i}}\cdot {k}_{i}}}{\mathrm{2}\cdot {D}_{{\mathrm{POC}}_{i}}}},\phantom{\rule{1em}{0ex}}{a}_{\mathrm{2}i}=-{\displaystyle \frac{{k}_{i}}{w}}.\end{array}$$

Determining the integration constants (${A}_{\mathrm{1},i},\phantom{\rule{0.33em}{0ex}}{B}_{\mathrm{1},i},\phantom{\rule{0.33em}{0ex}}{A}_{\mathrm{2},i}$)
requires the definition of a set of boundary conditions
(Table 2). For organic matter, OMEN-SED applies a known
concentration at the sediment–water interface and assumes continuity across
the bottom of the bioturbated zone, *z*_{bio}. When OMEN-SED is
coupled to an ESM, the POC depositional flux from the coupled ocean model is
converted to a concentration by solving the flux divergence
Eq. (51). The integration constants (${A}_{\mathrm{1},i},\phantom{\rule{0.33em}{0ex}}{B}_{\mathrm{1},i},\phantom{\rule{0.33em}{0ex}}{A}_{\mathrm{2},i}$) are thus given by the following.

$$\begin{array}{ll}\text{(11)}& {\displaystyle}{B}_{\mathrm{1}i}& {\displaystyle}\stackrel{\mathrm{BC}\mathrm{1})}{=}{\mathrm{POC}}_{\mathrm{0}i}-{A}_{\mathrm{1}i}{\displaystyle}{A}_{\mathrm{2}i}& {\displaystyle}\stackrel{\mathrm{BC}\mathrm{2})}{=}{\displaystyle \frac{{A}_{\mathrm{1}i}\cdot \mathrm{exp}\left({a}_{\mathrm{1}i}{z}_{\mathrm{bio}}^{-}\right)+{B}_{\mathrm{1}i}\cdot \mathrm{exp}\left({b}_{\mathrm{1}i}{z}_{\mathrm{bio}}^{-}\right)}{\mathrm{exp}\left({a}_{\mathrm{2}i}{z}_{\mathrm{bio}}^{+}\right)}}\\ {\displaystyle}{A}_{\mathrm{1}i}& {\displaystyle}\stackrel{\mathrm{BC}\mathrm{3})}{=}-{\displaystyle \frac{{B}_{\mathrm{1}i}{b}_{\mathrm{1}i}\cdot \mathrm{exp}\left({b}_{\mathrm{1}i}{z}_{\mathrm{bio}}^{-}\right)}{{a}_{\mathrm{1}i}\cdot \mathrm{exp}\left({a}_{\mathrm{1}i}{z}_{\mathrm{bio}}^{-}\right)}}\end{array}$$

See Sect. 2.3.1 for further details on how to find the analytical solution.

OMEN-SED explicitly accounts for oxygen consumption by the aerobic
degradation of organic matter within the oxic zone and the oxidation
of reduced species (i.e. NH_{4}, H_{2}S) produced in the anoxic
zones of the sediment. In the oxic zone (*z*<*z*_{ox}), aerobic
degradation consumes oxygen with a fixed O_{2}:C ratio (O_{2}C,
Table 10). A predefined fraction,
${\mathit{\gamma}}_{{\mathrm{NH}}_{\mathrm{4}}}$, of the ammonium produced during the aerobic degradation
of OM is nitrified to nitrate, consuming 2 moles of oxygen per mole of
ammonium produced. In addition, OMEN-SED implicitly accounts for oxygen
consumption due to the oxidation of reduced species (NH_{4}, H_{2}S)
produced below the oxic zone through the flux boundary condition at the
dynamically calculated oxygen penetration depth *z*_{ox} (see
Sect. 2.4.2 for details). All oxygen
consumption processes can thus be formulated as a function of organic matter
degradation. The conservation equation for oxygen is given by

$$\begin{array}{ll}{\displaystyle \frac{\partial {\mathrm{O}}_{\mathrm{2}}}{\partial t}}& {\displaystyle}=\mathrm{0}={D}_{{\mathrm{O}}_{\mathrm{2}}}{\displaystyle \frac{{\partial}^{\mathrm{2}}{\mathrm{O}}_{\mathrm{2}}}{\partial {z}^{\mathrm{2}}}}-w{\displaystyle \frac{\partial {\mathrm{O}}_{\mathrm{2}}}{\partial z}}-{\displaystyle \frac{\mathrm{1}-\mathit{\varphi}}{\mathit{\varphi}}}\sum _{i}{k}_{i}\\ \text{(12)}& {\displaystyle}& {\displaystyle}\cdot [{\mathrm{O}}_{\mathrm{2}}\mathrm{C}+\mathrm{2}{\mathit{\gamma}}_{{\mathrm{NH}}_{\mathrm{4}}}{\mathrm{NC}}_{i}]\cdot {\mathrm{POC}}_{i}\left(z\right).\end{array}$$

For illustrative purposes, we here substitute the analytical solution for
the POC depth profile and provide the analytical solution. The remaining
paragraphs only outline the general equation, whose analytical solution can
be derived in an identical manner. Substituting Eqs. (8) and
(9) for POC_{i(z)} and Eq. (11) for
*B*_{1i} gives the following.

$$\begin{array}{ll}{\displaystyle}& {\displaystyle}\text{(I) Bioturbated zone}\phantom{\rule{0.25em}{0ex}}(z\le {z}_{\mathrm{bio}})\\ {\displaystyle}& {\displaystyle \frac{\partial {\mathrm{O}}_{\mathrm{2}}^{\mathrm{I}}}{\partial t}}=\mathrm{0}\stackrel{\mathrm{8}\mathit{\&}\mathrm{11}}{=}{D}_{{\mathrm{O}}_{\mathrm{2}}}^{\mathrm{I}}{\displaystyle \frac{{\partial}^{\mathrm{2}}{\mathrm{O}}_{\mathrm{2}}}{\partial {z}^{\mathrm{2}}}}-w{\displaystyle \frac{\partial {\mathrm{O}}_{\mathrm{2}}}{\partial z}}-{\displaystyle \frac{\mathrm{1}-\mathit{\varphi}}{\mathit{\varphi}}}\sum _{i}{k}_{i}\\ {\displaystyle}& {\displaystyle}\phantom{\rule{1em}{0ex}}\cdot [{\mathrm{O}}_{\mathrm{2}}\mathrm{C}+\mathrm{2}{\mathit{\gamma}}_{{\mathrm{NH}}_{\mathrm{4}}}{\mathrm{NC}}_{i}]\cdot ({A}_{\mathrm{1}i}\cdot [\mathrm{exp}\left({a}_{\mathrm{1}i}z\right)-\mathrm{exp}\left({b}_{\mathrm{1}i}z\right)]\\ {\displaystyle}& {\displaystyle}\phantom{\rule{1em}{0ex}}+{\mathrm{POC}}_{\mathrm{0}i}\cdot \mathrm{exp}\left({b}_{\mathrm{1}i}z\right))\\ {\displaystyle}& {\displaystyle}\text{(II) Non-bioturbated zone}\phantom{\rule{0.25em}{0ex}}({z}_{\mathrm{bio}}<z<{z}_{\mathrm{ox}})\\ {\displaystyle}& {\displaystyle \frac{\partial {{\mathrm{O}}_{\mathrm{2}}}^{\mathrm{II}}}{\partial t}}=\mathrm{0}\stackrel{9}{=}{D}_{{\mathrm{O}}_{\mathrm{2}}}^{\mathrm{II}}{\displaystyle \frac{{\partial}^{\mathrm{2}}{\mathrm{O}}_{\mathrm{2}}}{\partial {z}^{\mathrm{2}}}}-w{\displaystyle \frac{\partial {\mathrm{O}}_{\mathrm{2}}}{\partial z}}-{\displaystyle \frac{\mathrm{1}-\mathit{\varphi}}{\mathit{\varphi}}}\sum _{i}{k}_{i}\\ {\displaystyle}& {\displaystyle}\phantom{\rule{1em}{0ex}}\cdot [{\mathrm{O}}_{\mathrm{2}}\mathrm{C}+\mathrm{2}{\mathit{\gamma}}_{{\mathrm{NH}}_{\mathrm{4}}}{\mathrm{NC}}_{i}]\cdot ({A}_{\mathrm{2}i}\cdot \mathrm{exp}({a}_{\mathrm{2}i}z\left)\right)\end{array}$$

${D}_{{\mathrm{O}}_{\mathrm{2}}}^{\mathrm{I}}$ and ${D}_{{\mathrm{O}}_{\mathrm{2}}}^{\mathrm{II}}$ denote the
O_{2} diffusion coefficient for the bioturbated and non-bioturbated
zone, respectively. The term $\frac{\mathrm{1}-\mathit{\varphi}}{\mathit{\varphi}}$ accounts for the volume
conversion from solid to dissolved phase and NC_{i} is the nitrogen to
carbon ratio in POC. Integration yields the following analytical solution for
each zone.

$$\begin{array}{ll}{\displaystyle}& {\displaystyle}\text{(I) Bioturbated zone}\phantom{\rule{0.25em}{0ex}}(z\le {z}_{\mathrm{bio}}):\\ {\displaystyle}& {\displaystyle}{{\mathrm{O}}_{\mathrm{2}}}^{\mathrm{I}}\left(z\right)={A}_{{\mathrm{O}}_{\mathrm{2}}}^{\mathrm{1}}+{B}_{{\mathrm{O}}_{\mathrm{2}}}^{\mathrm{1}}\cdot \mathrm{exp}\left({b}_{{\mathrm{O}}_{\mathrm{2}}}^{\mathrm{1}}z\right)+\sum _{i}{\mathrm{\Phi}}_{\mathrm{1},i}^{\mathrm{I}}\cdot \mathrm{exp}\left({a}_{\mathrm{1}i}z\right)\\ \text{(13)}& {\displaystyle}& {\displaystyle}\phantom{\rule{1em}{0ex}}+\sum _{i}{\mathrm{\Phi}}_{\mathrm{1},i}^{\mathrm{II}}\cdot \mathrm{exp}\left({b}_{\mathrm{1}i}z\right)+\sum _{i}{\mathrm{\Phi}}_{\mathrm{1},i}^{\mathrm{III}}\cdot \mathrm{exp}\left({b}_{\mathrm{1}i}z\right){\displaystyle}& {\displaystyle}\text{(II) Non-bioturbated zone}\phantom{\rule{0.25em}{0ex}}({z}_{\mathrm{bio}}<z<{z}_{\mathrm{ox}})\\ {\displaystyle}& {\displaystyle}{{\mathrm{O}}_{\mathrm{2}}}^{\mathrm{II}}\left(z\right)={A}_{{\mathrm{O}}_{\mathrm{2}}}^{\mathrm{2}}+{B}_{{\mathrm{O}}_{\mathrm{2}}}^{\mathrm{2}}\cdot \mathrm{exp}\left({b}_{{\mathrm{O}}_{\mathrm{2}}}^{\mathrm{2}}z\right)\\ \text{(14)}& {\displaystyle}& {\displaystyle}\phantom{\rule{1em}{0ex}}+\sum _{i}{\mathrm{\Phi}}_{i,\mathrm{2}}^{\mathrm{I}}\cdot \mathrm{exp}\left({a}_{\mathrm{2}i}z\right)\end{array}$$

with

$$\begin{array}{ll}{\displaystyle}& {\displaystyle}{b}_{{\mathrm{O}}_{\mathrm{2}}}^{\mathrm{1}}={\displaystyle \frac{w}{{D}_{{\mathrm{O}}_{\mathrm{2}}}^{\mathrm{I}}}},\phantom{\rule{1em}{0ex}}{b}_{{\mathrm{O}}_{\mathrm{2}}}^{\mathrm{2}}={\displaystyle \frac{w}{{D}_{{\mathrm{O}}_{\mathrm{2}}}^{\mathrm{II}}}}\\ {\displaystyle}& {\displaystyle}{\mathrm{\Phi}}_{\mathrm{1},i}^{\mathrm{I}}={\displaystyle \frac{\mathrm{1}-\mathit{\varphi}}{\mathit{\varphi}}}\cdot {\displaystyle \frac{{k}_{i}\cdot ({\mathrm{O}}_{\mathrm{2}}\mathrm{C}+\mathrm{2}{\mathit{\gamma}}_{{\mathrm{NH}}_{\mathrm{4}}}{\mathrm{NC}}_{i})\cdot {A}_{\mathrm{1}i}}{{D}_{{\mathrm{O}}_{\mathrm{2}}}^{\mathrm{I}}(-{a}_{\mathrm{1}i}{)}^{\mathrm{2}}-w\cdot (-{a}_{\mathrm{1}i})}},\\ {\displaystyle}& {\displaystyle}{\mathrm{\Phi}}_{\mathrm{1},i}^{\mathrm{II}}=-{\displaystyle \frac{\mathrm{1}-\mathit{\varphi}}{\mathit{\varphi}}}\cdot {\displaystyle \frac{{k}_{i}\cdot ({\mathrm{O}}_{\mathrm{2}}\mathrm{C}+\mathrm{2}{\mathit{\gamma}}_{{\mathrm{NH}}_{\mathrm{4}}}{\mathrm{NC}}_{\mathrm{i}})\cdot {A}_{\mathrm{1}i}}{{D}_{{\mathrm{O}}_{\mathrm{2}}}^{\mathrm{I}}(-{b}_{\mathrm{1}i}{)}^{\mathrm{2}}-w\cdot (-{b}_{\mathrm{1}i})}}\\ {\displaystyle}& {\displaystyle}{\mathrm{\Phi}}_{\mathrm{1},i}^{\mathrm{III}}={\displaystyle \frac{\mathrm{1}-\mathit{\varphi}}{\mathit{\varphi}}}\cdot {\displaystyle \frac{{k}_{i}\cdot ({\mathrm{O}}_{\mathrm{2}}\mathrm{C}+\mathrm{2}{\mathit{\gamma}}_{{\mathrm{NH}}_{\mathrm{4}}}{\mathrm{NC}}_{i})\cdot {\mathrm{POC}}_{\mathrm{0}i}}{{D}_{{\mathrm{O}}_{\mathrm{2}}}^{\mathrm{I}}(-{b}_{\mathrm{1}i}{)}^{\mathrm{2}}-w\cdot (-{b}_{\mathrm{1}i})}}\\ {\displaystyle}& {\displaystyle}{\mathrm{\Phi}}_{i,\mathrm{2}}^{\mathrm{I}}:={\displaystyle \frac{\mathrm{1}-\mathit{\varphi}}{\mathit{\varphi}}}\cdot {\displaystyle \frac{{k}_{i}\cdot ({\mathrm{O}}_{\mathrm{2}}\mathrm{C}+\mathrm{2}{\mathit{\gamma}}_{{\mathrm{NH}}_{\mathrm{4}}}{\mathrm{NC}}_{i})\cdot {A}_{\mathrm{2}i}}{{D}_{{\mathrm{O}}_{\mathrm{2}}}^{\mathrm{II}}(-{a}_{\mathrm{2}i}{)}^{\mathrm{2}}-w\cdot (-{a}_{\mathrm{2}i})}}\end{array}$$

Determining the four integration constants (${A}_{{\mathrm{O}}_{\mathrm{2}}}^{\mathrm{1}},\phantom{\rule{0.125em}{0ex}}{B}_{{\mathrm{O}}_{\mathrm{2}}}^{\mathrm{1}},\phantom{\rule{0.125em}{0ex}}{A}_{{\mathrm{O}}_{\mathrm{2}}}^{\mathrm{2}},\phantom{\rule{0.125em}{0ex}}{B}_{{\mathrm{O}}_{\mathrm{2}}}^{\mathrm{2}}$; see
Sect. 2.3 for details) and the a priori
unknown oxygen penetration depth requires the definition of five boundary
conditions (see Table 3). At the sediment–water interface,
OMEN-SED applies a Dirichlet condition (i.e. known concentration) and assumes
concentration and flux continuity across the bottom of the bioturbated zone,
*z*_{bio}. The oxygen penetration depth *z*_{ox} marks the
lower boundary and is dynamically calculated as the depth at which
O_{2}(*z*)=0. Therefore, OMEN-SED applies a Dirichlet boundary condition
O_{2}(*z*_{ox})=0. In addition, a flux boundary is applied that
implicitly accounts for the oxygen consumption by the partial oxidation of
NH_{4} and H_{2}S diffusing into the oxic zone from below (BC
4.2; Table 3). It is assumed that respective fractions
(${\mathit{\gamma}}_{{\mathrm{NH}}_{\mathrm{4}}}$ and ${\mathit{\gamma}}_{{\mathrm{H}}_{\mathrm{2}}\mathrm{S}}$) are directly reoxidised
at the oxic–anoxic interface and the remaining fraction escapes reoxidation
(or is precipitated as pyrite, *γ*_{FeS}). OMEN-SED iteratively
solves for *z*_{ox} by first testing if there is oxygen left at
*z*_{max} (i.e. O_{2}(*z*_{max})>0). If that is not the
case, it determines the root for the flux boundary condition 4.2
(Table 3). If *z*_{ox}=*z*_{max}, a zero
diffusive flux boundary condition is applied as a lower boundary condition.

Nitrogen dynamics in OMEN-SED are controlled by the metabolic production of
ammonium, nitrification, denitrification and ammonium adsorption.
Ammonium is produced by organic matter degradation in both the oxic and
anoxic zones, while denitrification consumes nitrate in the denitrification
zone with a fixed NO_{3}:C ratio (NO_{3}C;
Table 10). Anaerobic ammonium oxidation
(anammox) is implicitly included in the model. The organic nitrogen released
during denitrification is assumed to be directly oxidised with nitrite to
N_{2} through a coupling between denitrification and anammox.

The adsorption of ammonium to sediment particles is formulated as an equilibrium process with a constant equilibrium adsorption coefficient ${K}_{{\mathrm{NH}}_{\mathrm{4}}}$, thus assuming that the adsorption is fast compared to the characteristic timescales of transport processes (Wang and Van Cappellen, 1996). In addition, a defined fraction, ${\mathit{\gamma}}_{{\mathrm{NH}}_{\mathrm{4}}}$, of metabolically produced ammonium is directly nitrified to nitrate in the oxic zone, while the nitrification of upward-diffusing ammonium produced in the sulfidic and methanic zones is implicitly accounted for in the boundary conditions. The conservation equations for ammonium and nitrate are thus given by the following.

$$\begin{array}{ll}{\displaystyle}& {\displaystyle}\text{(1) Oxic zone}\phantom{\rule{0.25em}{0ex}}(z\le {z}_{\mathrm{ox}})\\ {\displaystyle}& {\displaystyle \frac{\partial {{\mathrm{NO}}_{\mathrm{3}}}^{\mathrm{I}}}{\partial t}}=\mathrm{0}={D}_{{\mathrm{NO}}_{\mathrm{3}}}{\displaystyle \frac{{\partial}^{\mathrm{2}}{{\mathrm{NO}}_{\mathrm{3}}}^{\mathrm{I}}}{\partial {z}^{\mathrm{2}}}}-w{\displaystyle \frac{\partial {{\mathrm{NO}}_{\mathrm{3}}}^{\mathrm{I}}}{\partial z}}\\ \text{(15)}& {\displaystyle}& {\displaystyle}\phantom{\rule{1em}{0ex}}+{\mathit{\gamma}}_{{\mathrm{NH}}_{\mathrm{4}}}{\displaystyle \frac{\mathrm{1}-\mathit{\varphi}}{\mathit{\varphi}}}\cdot \sum _{i}{\mathrm{NC}}_{i}\cdot {k}_{i}\cdot {\mathrm{POC}}_{i}\left(z\right){\displaystyle}& {\displaystyle \frac{\partial {{\mathrm{NH}}_{\mathrm{4}}}^{\mathrm{I}}}{\partial t}}=\mathrm{0}={\displaystyle \frac{{D}_{{\mathrm{NH}}_{\mathrm{4}}}}{\mathrm{1}+{K}_{{\mathrm{NH}}_{\mathrm{4}}}}}{\displaystyle \frac{{\partial}^{\mathrm{2}}{{\mathrm{NH}}_{\mathrm{4}}}^{\mathrm{I}}}{\partial {z}^{\mathrm{2}}}}-w{\displaystyle \frac{\partial {{\mathrm{NH}}_{\mathrm{4}}}^{\mathrm{I}}}{\partial z}}\\ \text{(16)}& {\displaystyle}& {\displaystyle}\phantom{\rule{1em}{0ex}}+{\displaystyle \frac{\mathrm{1}-{\mathit{\gamma}}_{{\mathrm{NH}}_{\mathrm{4}}}}{\mathrm{1}+{K}_{{\mathrm{NH}}_{\mathrm{4}}}}}\cdot {\displaystyle \frac{\mathrm{1}-\mathit{\varphi}}{\mathit{\varphi}}}\cdot \sum _{i}{\mathrm{NC}}_{i}\cdot {k}_{i}\cdot {\mathrm{POC}}_{i}\left(z\right){\displaystyle}& {\displaystyle}\text{(2) Denitrification (or nitrogenous) zone}\phantom{\rule{0.25em}{0ex}}({z}_{\mathrm{ox}}<z\le {z}_{{\mathrm{NO}}_{\mathrm{3}}})\\ {\displaystyle}& {\displaystyle \frac{\partial {{\mathrm{NO}}_{\mathrm{3}}}^{\mathrm{II}}}{\partial t}}=\mathrm{0}={D}_{{\mathrm{NO}}_{\mathrm{3}}}{\displaystyle \frac{{\partial}^{\mathrm{2}}{{\mathrm{NO}}_{\mathrm{3}}}^{\mathrm{II}}}{\partial {z}^{\mathrm{2}}}}-w{\displaystyle \frac{\partial {{\mathrm{NO}}_{\mathrm{3}}}^{\mathrm{II}}}{\partial z}}\\ \text{(17)}& {\displaystyle}& {\displaystyle}\phantom{\rule{1em}{0ex}}-{\displaystyle \frac{\mathrm{1}-\mathit{\varphi}}{\mathit{\varphi}}}{\mathrm{NO}}_{\mathrm{3}}\mathrm{C}\cdot \sum _{i}{k}_{i}\cdot {\mathrm{POC}}_{i}\left(z\right)\text{(18)}& {\displaystyle}& {\displaystyle \frac{\partial {{\mathrm{NH}}_{\mathrm{4}}}^{\mathrm{II}}}{\partial t}}=\mathrm{0}={\displaystyle \frac{{D}_{{\mathrm{NH}}_{\mathrm{4}}}}{\mathrm{1}+{K}_{{\mathrm{NH}}_{\mathrm{4}}}}}{\displaystyle \frac{{\partial}^{\mathrm{2}}{{\mathrm{NH}}_{\mathrm{4}}}^{\mathrm{II}}}{\partial {z}^{\mathrm{2}}}}-w{\displaystyle \frac{\partial {{\mathrm{NH}}_{\mathrm{4}}}^{\mathrm{II}}}{\partial z}}{\displaystyle}& {\displaystyle}\text{(3) Sulfidic and methanic zone}\phantom{\rule{0.25em}{0ex}}({z}_{{\mathrm{NO}}_{\mathrm{3}}}<z\le {z}_{\mathrm{max}})\\ {\displaystyle}& {\displaystyle \frac{\partial {{\mathrm{NH}}_{\mathrm{4}}}^{\mathrm{III}}}{\partial t}}=\mathrm{0}={\displaystyle \frac{{D}_{{\mathrm{NH}}_{\mathrm{4}}}}{\mathrm{1}+{K}_{{\mathrm{NH}}_{\mathrm{4}}}}}{\displaystyle \frac{{\partial}^{\mathrm{2}}{{\mathrm{NH}}_{\mathrm{4}}}^{\mathrm{III}}}{\partial {z}^{\mathrm{2}}}}-w{\displaystyle \frac{\partial {{\mathrm{NH}}_{\mathrm{4}}}^{\mathrm{III}}}{\partial z}}\\ \text{(19)}& {\displaystyle}& {\displaystyle}\phantom{\rule{1em}{0ex}}+{\displaystyle \frac{\mathrm{1}}{\mathrm{1}+{K}_{{\mathrm{NH}}_{\mathrm{4}}}}}\cdot {\displaystyle \frac{\mathrm{1}-\mathit{\varphi}}{\mathit{\varphi}}}\cdot \sum _{i}{\mathrm{NC}}_{i}\cdot {k}_{i}\cdot {\mathrm{POC}}_{i}\left(z\right)\end{array}$$

${D}_{{\mathrm{NO}}_{\mathrm{3}}}$ and ${D}_{{\mathrm{NH}}_{\mathrm{4}}}$ denote the diffusion coefficients
for NO_{3} and NH_{4}, which depend on the bioturbation status of
the respective geochemical zone (compare to Sect. 2.3.1).
Integration of Eqs. (15)–(19) yields the
analytical solutions, which are not further developed here but follow the
procedure outlined in Sect. 2.2.2 for oxygen (also see
Sect. 2.3.1 for more details on how to find the analytical
solution). Table 4 summarises the boundary conditions
applied in OMEN-SED to solve
Eqs. (15)–(19) and to find the a
priori unknown nitrate penetration depth, ${z}_{{\mathrm{NO}}_{\mathrm{3}}}$. The model assumes
known bottom water concentrations for both NO_{3} and NH_{4}, the
complete consumption of nitrate at the nitrate penetration depth (in the case
${z}_{{\mathrm{NO}}_{\mathrm{3}}}<{z}_{\mathrm{max}}$) and no change in ammonium flux at
*z*_{max}. In addition, concentration and diffusive flux continuity
across *z*_{bio} and *z*_{ox} is considered for NO_{3}
and NH_{4}. Furthermore, the reoxidation of upward-diffusing reduced
ammonium is accounted for in the oxic–anoxic boundary condition for nitrate
and ammonium. OMEN-SED iteratively solves for ${z}_{{\mathrm{NO}}_{\mathrm{3}}}$ by first
testing if there is nitrate left at *z*_{max} (i.e.
NO_{3}(*z*_{max})>0) and otherwise by finding the root for
the flux boundary condition 6.2 (Table 4).

Below the denitrification zone ($z>{z}_{{\mathrm{NO}}_{\mathrm{3}}}$), organic matter
degradation is coupled to sulfate reduction, consuming sulfate and producing
hydrogen sulfide with a fixed SO_{4}:C ratio (SO_{4}C;
Table 10). In addition, the anaerobic oxidation
of upward-diffusing methane (AOM) produced below the sulfate penetration and
the associated consumption of sulfate and production of sulfide, as well as
the production of sulfate and consumption of sulfide through sulfide
oxidation, are implicitly accounted for through the boundary conditions
(Table 5). In the sulfidic zone a defined fraction of
sulfide, *γ*_{FeS}, can be precipitated as pyrite (in the presented
simulations *γ*_{FeS}=0.0 as we do not want to make any
assumptions about pyrite precipitation). It can be safely assumed that almost
all CH_{4} is oxidised anaerobically in the sediments
(e.g. Reeburgh, 2007, suggests up to 90 %), except for
active (very localised) sites and slope failure, which can, in theory, be
accounted for through the ${\mathit{\gamma}}_{{\mathrm{CH}}_{\mathrm{4}}}$ term. The conservation
equations for sulfate and sulfide are thus given by the following.

$$\begin{array}{ll}{\displaystyle}& {\displaystyle}\text{(1) Oxic and nitrogenous zone}\phantom{\rule{0.25em}{0ex}}(z\le {z}_{{\mathrm{NO}}_{\mathrm{3}}})\\ \text{(20)}& {\displaystyle}& {\displaystyle \frac{\partial {{\mathrm{SO}}_{\mathrm{4}}}^{\mathrm{I}}}{\partial t}}=\mathrm{0}={D}_{{\mathrm{SO}}_{\mathrm{4}}}{\displaystyle \frac{{\partial}^{\mathrm{2}}{{\mathrm{SO}}_{\mathrm{4}}}^{\mathrm{I}}}{\partial {z}^{\mathrm{2}}}}-w{\displaystyle \frac{\partial {{\mathrm{SO}}_{\mathrm{4}}}^{\mathrm{I}}}{\partial z}}\text{(21)}& {\displaystyle}& {\displaystyle \frac{\partial {{\mathrm{H}}_{\mathrm{2}}\mathrm{S}}^{\mathrm{I}}}{\partial t}}=\mathrm{0}={D}_{{\mathrm{H}}_{\mathrm{2}}\mathrm{S}}{\displaystyle \frac{{\partial}^{\mathrm{2}}{{\mathrm{H}}_{\mathrm{2}}\mathrm{S}}^{\mathrm{I}}}{\partial {z}^{\mathrm{2}}}}-w{\displaystyle \frac{\partial {{\mathrm{H}}_{\mathrm{2}}\mathrm{S}}^{\mathrm{I}}}{\partial z}}{\displaystyle}& {\displaystyle}\text{(2) Sulfidic zone}\phantom{\rule{0.25em}{0ex}}({z}_{{\mathrm{NO}}_{\mathrm{3}}}<z\le {z}_{{\mathrm{SO}}_{\mathrm{4}}})\\ {\displaystyle}& {\displaystyle \frac{\partial {{\mathrm{SO}}_{\mathrm{4}}}^{\mathrm{II}}}{\partial t}}=\mathrm{0}={D}_{{\mathrm{SO}}_{\mathrm{4}}}{\displaystyle \frac{{\partial}^{\mathrm{2}}{{\mathrm{SO}}_{\mathrm{4}}}^{\mathrm{II}}}{\partial {z}^{\mathrm{2}}}}-w{\displaystyle \frac{\partial {{\mathrm{SO}}_{\mathrm{4}}}^{\mathrm{II}}}{\partial z}}\\ \text{(22)}& {\displaystyle}& {\displaystyle}\phantom{\rule{1em}{0ex}}-{\displaystyle \frac{\mathrm{1}-\mathit{\varphi}}{\mathit{\varphi}}}\cdot \sum _{i}{\mathrm{SO}}_{\mathrm{4}}\mathrm{C}\cdot {k}_{i}\cdot {\mathrm{POC}}_{i}\left(z\right){\displaystyle}& {\displaystyle \frac{\partial {{\mathrm{H}}_{\mathrm{2}}\mathrm{S}}^{\mathrm{II}}}{\partial t}}=\mathrm{0}={D}_{{\mathrm{H}}_{\mathrm{2}}\mathrm{S}}{\displaystyle \frac{{\partial}^{\mathrm{2}}{{\mathrm{H}}_{\mathrm{2}}\mathrm{S}}^{\mathrm{II}}}{\partial {z}^{\mathrm{2}}}}-w{\displaystyle \frac{\partial {{\mathrm{H}}_{\mathrm{2}}\mathrm{S}}^{\mathrm{II}}}{\partial z}}\\ \text{(23)}& {\displaystyle}& {\displaystyle}\phantom{\rule{1em}{0ex}}+{\displaystyle \frac{\mathrm{1}-\mathit{\varphi}}{\mathit{\varphi}}}\cdot (\mathrm{1}-{\mathit{\gamma}}_{\mathrm{FeS}})\cdot \sum _{i}{\mathrm{SO}}_{\mathrm{4}}\mathrm{C}\cdot {k}_{i}\cdot {\mathrm{POC}}_{i}\left(z\right){\displaystyle}& {\displaystyle}\text{(3) Methanic zone}\phantom{\rule{0.25em}{0ex}}({z}_{{\mathrm{SO}}_{\mathrm{4}}}<z\le {z}_{\mathrm{max}})\\ \text{(24)}& {\displaystyle}& {\displaystyle \frac{\partial {{\mathrm{H}}_{\mathrm{2}}\mathrm{S}}^{\mathrm{III}}}{\partial t}}=\mathrm{0}={D}_{{\mathrm{H}}_{\mathrm{2}}\mathrm{S}}{\displaystyle \frac{{\partial}^{\mathrm{2}}{{\mathrm{H}}_{\mathrm{2}}\mathrm{S}}^{\mathrm{III}}}{\partial {z}^{\mathrm{2}}}}-w{\displaystyle \frac{\partial {{\mathrm{H}}_{\mathrm{2}}\mathrm{S}}^{\mathrm{III}}}{\partial z}}\end{array}$$

${D}_{{\mathrm{SO}}_{\mathrm{4}}}$ and ${D}_{{\mathrm{H}}_{\mathrm{2}}\mathrm{S}}$ denote the diffusion coefficients
for SO_{4} and H_{2}S, which depend on the bioturbation status of
the respective geochemical zone (compare to Sect. 2.3.1).
Integration of Eqs. (20)–(24) yields the
analytical solution and Table 5 summarises the boundary
conditions applied. OMEN-SED assumes known concentrations at the
sediment–water interface and continuity across the bioturbation depth and the
nitrate penetration depth. The reoxidation of reduced H_{2}S to
SO_{4} is accounted for implicitly via the oxic–anoxic boundary
condition for both species, while the reduction of SO_{4} and the associated
production of H_{2}S via AOM is accounted for through the respective
boundary conditions at ${z}_{{\mathrm{SO}}_{\mathrm{4}}}$. In the case
${z}_{{\mathrm{SO}}_{\mathrm{4}}}<{z}_{\mathrm{max}}$, OMEN-SED assumes zero sulfate concentration
at ${z}_{{\mathrm{SO}}_{\mathrm{4}}}$ and its diffusive flux must equal the amount of methane
produced below (with a methane to carbon ratio of MC); in the case
${z}_{{\mathrm{SO}}_{\mathrm{4}}}={z}_{\mathrm{max}}$, a zero diffusive flux condition for sulfate
is considered. OMEN-SED iteratively solves for ${z}_{{\mathrm{SO}}_{\mathrm{4}}}$ by first
testing if there is sulfate left at *z*_{max} (i.e.
SO_{4}(*z*_{max})>0) and otherwise by finding the root for
the flux boundary condition 8.2 (Table 5). At the lower
boundary *z*_{max} zero diffusive flux of H_{2}S is considered.

The biogeochemical description of phosphorus (P) dynamics builds on earlier
models developed by Slomp et al. (1996) and accounts for
phosphorus recycling through organic matter degradation, adsorption onto
sediments and iron(III) hydroxides (Fe-bound P), as well as carbonate
fluorapatite (CFA or authigenic P) formation (see
Fig. 2 for a schematic overview of the sedimentary P cycle).
In the oxic zone of the sediment, PO_{4} liberated through organic
matter degradation can adsorb to iron(III) hydroxides forming Fe-bound P
(or FeP; Slomp et al., 1998). Below the oxic zone, PO_{4} is
not only produced via organic matter degradation but can also be released
from the Fe-bound P pool due to the reduction of iron(III) hydroxides under
anoxic conditions. Furthermore, in these zones phosphate concentrations build
up and pore waters can thus become supersaturated with respect to carbonate
fluorapatite, thus triggering the authigenic formation of CFA
(Van Cappellen and Berner, 1988). Phosphorus bound in these authigenic
minerals represents a permanent sink for reactive phosphorus
(Slomp et al., 1996). As for ammonium, the adsorption of P to
the sediment matrix is treated as an equilibrium process parameterised
with dimensionless adsorption coefficients for the oxic and anoxic zone,
respectively (${K}_{{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{ox}}$,
${K}_{{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{anox}}$; Slomp et al., 1998). The adsorption and
desorption of P to iron(III) hydroxides and authigenic
fluorapatite formation are described as first-order reactions with rate
constants *k*_{s}, *k*_{m} and *k*_{a}, respectively
(Table 10). The rate of the respective process
is calculated as the product of the rate constant and the difference between
the current concentration (of PO_{4} and FeP) and an equilibrium
or asymptotic concentration (Slomp et al., 1996). The asymptotic
Fe-bound P concentration is FeP^{∞} and the equilibrium
concentrations for P sorption and authigenic fluorapatite formation are
${{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{s}}$ and ${{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{a}}$, respectively
(Table 10). The last term in
Eqs. (25) and (26) represents the sorption of
PO_{4} to FeP in the oxic zone, the last term in
Eqs. (27) and (28) is the release of
PO_{4} from the FeP pool and the fourth term in
Eq. (28) represents the permanent loss of PO_{4} to
authigenic fluorapatite formation. The conservation equations for phosphate
and Fe-bound P are thus given by the following.

$$\begin{array}{ll}{\displaystyle}& {\displaystyle}\text{(1) Oxic zone}\phantom{\rule{0.25em}{0ex}}(z\le {z}_{\mathrm{ox}})\\ {\displaystyle}& {\displaystyle \frac{\partial {{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{I}}}{\partial t}}={\displaystyle \frac{{D}_{{\mathrm{PO}}_{\mathrm{4}}}}{\mathrm{1}+{K}_{{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{ox}}}}{\displaystyle \frac{{\partial}^{\mathrm{2}}{{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{I}}}{\partial {z}^{\mathrm{2}}}}-w{\displaystyle \frac{\partial {{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{I}}}{\partial z}}\\ {\displaystyle}& {\displaystyle}\phantom{\rule{1em}{0ex}}+{\displaystyle \frac{\mathrm{1}-\mathit{\varphi}}{\mathit{\varphi}}}{\displaystyle \frac{\mathrm{1}}{\mathrm{1}+{K}_{{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{ox}}}}\sum _{i}\left({\mathrm{PC}}_{i}\cdot {k}_{i}\cdot {\mathrm{POC}}_{i}\left(z\right)\right)\\ \text{(25)}& {\displaystyle}& {\displaystyle}\phantom{\rule{1em}{0ex}}-{\displaystyle \frac{{k}_{s}}{\mathrm{1}+{K}_{{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{ox}}}}({{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{I}}-{{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{s}}){\displaystyle}& {\displaystyle \frac{\partial {\mathrm{FeP}}^{\mathrm{I}}}{\partial t}}={D}_{\mathrm{FeP}}{\displaystyle \frac{{\partial}^{\mathrm{2}}{\mathrm{FeP}}^{\mathrm{I}}}{\partial {z}^{\mathrm{2}}}}-w{\displaystyle \frac{\partial {\mathrm{FeP}}^{\mathrm{I}}}{\partial z}}\\ \text{(26)}& {\displaystyle}& {\displaystyle}\phantom{\rule{1em}{0ex}}+{\displaystyle \frac{\mathit{\varphi}}{\mathrm{1}-\mathit{\varphi}}}{k}_{s}({{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{I}}-{{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{s}}){\displaystyle}& {\displaystyle}\text{(2) Anoxic zones}\phantom{\rule{0.25em}{0ex}}({z}_{\mathrm{ox}}<z\le {z}_{\mathrm{max}})\\ {\displaystyle}& {\displaystyle \frac{\partial {\mathrm{FeP}}^{\mathrm{II}}}{\partial t}}={D}_{\mathrm{FeP}}{\displaystyle \frac{{\partial}^{\mathrm{2}}{\mathrm{FeP}}^{\mathrm{II}}}{\partial {z}^{\mathrm{2}}}}-w{\displaystyle \frac{\partial {\mathrm{FeP}}^{\mathrm{II}}}{\partial z}}\\ \text{(27)}& {\displaystyle}& {\displaystyle}\phantom{\rule{1em}{0ex}}-{k}_{m}({\mathrm{FeP}}^{\mathrm{II}}-{\mathrm{FeP}}^{\mathrm{\infty}}){\displaystyle}& {\displaystyle \frac{\partial {{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{II}}}{\partial t}}={\displaystyle \frac{{D}_{{\mathrm{PO}}_{\mathrm{4}}}}{\mathrm{1}+{K}_{{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{anox}}}}{\displaystyle \frac{{\partial}^{\mathrm{2}}{{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{II}}}{\partial {z}^{\mathrm{2}}}}-w{\displaystyle \frac{\partial {{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{II}}}{\partial z}}\\ {\displaystyle}& {\displaystyle}\phantom{\rule{1em}{0ex}}+{\displaystyle \frac{\mathrm{1}-\mathit{\varphi}}{\mathit{\varphi}}}{\displaystyle \frac{\mathrm{1}}{\mathrm{1}+{K}_{{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{anox}}}}\sum _{i}\left({\mathrm{PC}}_{i}\cdot {k}_{i}\cdot {\mathrm{POC}}_{i}\left(z\right)\right)\\ {\displaystyle}& {\displaystyle}-{\displaystyle \frac{{k}_{a}}{\mathrm{1}+{K}_{{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{anox}}}}({{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{II}}-{{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{a}})\\ \text{(28)}& {\displaystyle}& {\displaystyle}\phantom{\rule{1em}{0ex}}+{\displaystyle \frac{(\mathrm{1}-\mathit{\varphi})}{\mathit{\varphi}}}{\displaystyle \frac{{k}_{m}}{\mathrm{1}+{K}_{{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{anox}}}}({\mathrm{FeP}}^{\mathrm{II}}-{\mathrm{FeP}}^{\mathrm{\infty}})\end{array}$$

${D}_{{\mathrm{PO}}_{\mathrm{4}}}$ denotes the diffusion coefficient for PO_{4}, which
depends on the bioturbation status of the respective geochemical zone, and
*D*_{FeP}=*D*_{bio} for *z*≤*z*_{bio} and
*D*_{FeP}=0 for *z*>*z*_{bio} (compare
to Sect. 2.3.1). Integration of
Eqs. (25)–(28) yields the analytical
solution and Table 6 summarises the boundary conditions
applied in OMEN-SED. The model assumes known bottom water concentrations and
equal concentrations and diffusive fluxes at *z*_{bio} and
*z*_{ox} for both species. Additionally, OMEN-SED considers no change
in phosphate flux and an asymptotic Fe-bound P concentration at
*z*_{max}.

OMEN-SED accounts for the production of dissolved inorganic carbon
(DIC) through organic matter degradation and methane
oxidation. Organic matter degradation produces dissolved inorganic carbon
with a stoichiometric DIC:C ratio of 1:2 in the methanic zone and
1:1 in the rest of the sediment column (DICC^{II} and
DICC^{I}, respectively). DIC production through methane
oxidation is implicitly taken into account through the boundary condition at
${z}_{{\mathrm{SO}}_{\mathrm{4}}}$. A mechanistic description of DIC production from
CaCO_{3} dissolution would lead to significant mathematical problems and
is therefore not included in the current version of OMEN-SED. The
conservation equations for DIC are thus given by the following.

$$\begin{array}{ll}{\displaystyle}& {\displaystyle}\text{(1) Oxic, nitrogenous and sulfidic zone}\phantom{\rule{0.25em}{0ex}}(z\le {z}_{{\mathrm{SO}}_{\mathrm{4}}})\\ {\displaystyle}& {\displaystyle \frac{\partial {\mathrm{DIC}}^{\mathrm{I}}}{\partial t}}=\mathrm{0}={D}_{\mathrm{DIC}}{\displaystyle \frac{{\partial}^{\mathrm{2}}{\mathrm{DIC}}^{\mathrm{I}}}{\partial {z}^{\mathrm{2}}}}-w{\displaystyle \frac{\partial {\mathrm{DIC}}^{\mathrm{I}}}{\partial z}}+{\displaystyle \frac{\mathrm{1}-\mathit{\varphi}}{\mathit{\varphi}}}\\ \text{(29)}& {\displaystyle}& {\displaystyle}\phantom{\rule{1em}{0ex}}\cdot \sum _{i}{\mathrm{DICC}}^{\mathrm{I}}\cdot {k}_{i}\cdot {\mathrm{POC}}_{i}\left(z\right){\displaystyle}& {\displaystyle}\text{(2) Methanic zone}\phantom{\rule{0.25em}{0ex}}({z}_{{\mathrm{SO}}_{\mathrm{4}}}<z\le {z}_{\mathrm{max}})\\ {\displaystyle}& {\displaystyle \frac{\partial {\mathrm{DIC}}^{\mathrm{II}}}{\partial t}}=\mathrm{0}={D}_{\mathrm{DIC}}{\displaystyle \frac{{\partial}^{\mathrm{2}}{\mathrm{DIC}}^{\mathrm{II}}}{\partial {z}^{\mathrm{2}}}}-w{\displaystyle \frac{\partial {\mathrm{DIC}}^{\mathrm{II}}}{\partial z}}+{\displaystyle \frac{\mathrm{1}-\mathit{\varphi}}{\mathit{\varphi}}}\\ \text{(30)}& {\displaystyle}& {\displaystyle}\phantom{\rule{1em}{0ex}}\cdot \sum _{i}{\mathrm{DICC}}^{\mathrm{II}}\cdot {k}_{i}\cdot {\mathrm{POC}}_{i}\left(z\right)\end{array}$$

*D*_{DIC} denotes the diffusion coefficient for DIC
(taking the values for ${\mathrm{HCO}}_{\mathrm{3}}^{-}$ from
Schulz, 2006), which depends on the bioturbation status
of the respective geochemical zone. Integration of
Eqs. (29) and (30) yields the analytical
solution and Table 7 summarises the boundary conditions
applied in OMEN-SED. A Dirichlet condition is applied at the sediment–water
interface. In addition, the model assumes a zero diffusive flux through the
lower boundary *z*_{max} and continuity across the bottom of the
bioturbated zone and the sulfate penetration depth. An additional
flux boundary condition at ${z}_{{\mathrm{SO}}_{\mathrm{4}}}$ implicitly accounts for DIC
production through the anaerobic oxidation of methane (Table 7
Eq. 5).

Organic matter degradation and secondary redox reactions exert a complex
influence on alkalinity (e.g. Jourabchi et al., 2005; Wolf-Gladrow et al., 2007; Krumins et al., 2013). To model alkalinity,
OMEN-SED divides the sediment column into four geochemical zones in which
different equations describe the biogeochemical processes using variable
stoichiometric coefficients (compare values in Table
10). Above *z*_{ox}, the combined
effects of NH_{4} and P release due to aerobic OM degradation
increases alkalinity according to ALK^{OX}, whereas
nitrification decreases alkalinity with stoichiometry
ALK^{NIT}. In the remaining three zones anaerobic OM
degradation generally results in an increase in alkalinity, with the exact
magnitude depending on the nature of the terminal electron acceptor used
(i.e. ALK^{DEN}, ALK^{SUL},
ALK^{MET}). In addition, the effect of secondary redox
reactions, such as nitrification, sulfide and methane oxidation,
and pyrite precipitation are
implicitly accounted for in the boundary conditions. Note that the alkalinity
description in the current version of OMEN-SED does not account for
CaCO_{3} dissolution and precipitation due to the mathematical complexity
of the problem. In OMEN-SED, the conservation equations for alkalinity are
thus given by the following.

$$\begin{array}{ll}{\displaystyle}& {\displaystyle}\text{(1) Oxic zone}\phantom{\rule{0.25em}{0ex}}(z\le {z}_{\mathrm{ox}})\\ {\displaystyle}& {\displaystyle \frac{\partial {\mathrm{ALK}}^{\mathrm{I}}}{\partial t}}=\mathrm{0}={D}_{\mathrm{ALK}}{\displaystyle \frac{{\partial}^{\mathrm{2}}{\mathrm{ALK}}^{\mathrm{I}}}{\partial {z}^{\mathrm{2}}}}-w{\displaystyle \frac{\partial {\mathrm{ALK}}^{\mathrm{I}}}{\partial z}}\\ {\displaystyle}& {\displaystyle}\phantom{\rule{1em}{0ex}}+{\displaystyle \frac{\mathrm{1}-\mathit{\varphi}}{\mathit{\varphi}}}\cdot \sum _{i}\left({\mathrm{ALK}}^{\mathrm{NIT}}\cdot {\displaystyle \frac{{\mathit{\gamma}}_{{\mathrm{NH}}_{\mathrm{4}}}}{\mathrm{1}+{K}_{{\mathrm{NH}}_{\mathrm{4}}}}}{\mathrm{NC}}_{i}+{\mathrm{ALK}}^{\mathrm{OX}}\right)\\ \text{(31)}& {\displaystyle}& {\displaystyle}\phantom{\rule{1em}{0ex}}\cdot {k}_{i}\cdot {\mathrm{POC}}_{i}\left(z\right){\displaystyle}& {\displaystyle}\text{(2) Denitrification or nitrogenous zone}\phantom{\rule{0.25em}{0ex}}({z}_{\mathrm{ox}}<z\le {z}_{{\mathrm{NO}}_{\mathrm{3}}})\\ {\displaystyle}& {\displaystyle \frac{\partial {\mathrm{ALK}}^{\mathrm{II}}}{\partial t}}=\mathrm{0}={D}_{\mathrm{ALK}}{\displaystyle \frac{{\partial}^{\mathrm{2}}{\mathrm{ALK}}^{\mathrm{II}}}{\partial {z}^{\mathrm{2}}}}-w{\displaystyle \frac{\partial {\mathrm{ALK}}^{\mathrm{II}}}{\partial z}}\\ \text{(32)}& {\displaystyle}& {\displaystyle}\phantom{\rule{1em}{0ex}}+{\displaystyle \frac{\mathrm{1}-\mathit{\varphi}}{\mathit{\varphi}}}\cdot \sum _{i}{\mathrm{ALK}}^{\mathrm{DEN}}\cdot {k}_{i}\cdot {\mathrm{POC}}_{i}\left(z\right){\displaystyle}& {\displaystyle}\text{(3) Sulfidic zone}\phantom{\rule{0.25em}{0ex}}({z}_{{\mathrm{NO}}_{\mathrm{3}}}<z\le {z}_{{\mathrm{SO}}_{\mathrm{4}}})\\ {\displaystyle}& {\displaystyle \frac{\partial {\mathrm{ALK}}^{\mathrm{III}}}{\partial t}}=\mathrm{0}={D}_{\mathrm{ALK}}{\displaystyle \frac{{\partial}^{\mathrm{2}}{\mathrm{ALK}}^{\mathrm{III}}}{\partial {z}^{\mathrm{2}}}}-w{\displaystyle \frac{\partial {\mathrm{ALK}}^{\mathrm{III}}}{\partial z}}\\ \text{(33)}& {\displaystyle}& {\displaystyle}\phantom{\rule{1em}{0ex}}+{\displaystyle \frac{\mathrm{1}-\mathit{\varphi}}{\mathit{\varphi}}}\cdot \sum _{i}{\mathrm{ALK}}^{\mathrm{SUL}}\cdot {k}_{i}\cdot {\mathrm{POC}}_{i}\left(z\right){\displaystyle}& {\displaystyle}\text{(4) Methanic zone}\phantom{\rule{0.25em}{0ex}}({z}_{{\mathrm{SO}}_{\mathrm{4}}}<z\le {z}_{\mathrm{max}})\\ {\displaystyle}& {\displaystyle \frac{\partial {\mathrm{ALK}}^{\mathrm{IV}}}{\partial t}}=\mathrm{0}={D}_{\mathrm{ALK}}{\displaystyle \frac{{\partial}^{\mathrm{2}}{\mathrm{ALK}}^{\mathrm{IV}}}{\partial {z}^{\mathrm{2}}}}-w{\displaystyle \frac{\partial {\mathrm{ALK}}^{\mathrm{IV}}}{\partial z}}\\ \text{(34)}& {\displaystyle}& {\displaystyle}\phantom{\rule{1em}{0ex}}+{\displaystyle \frac{\mathrm{1}-\mathit{\varphi}}{\mathit{\varphi}}}\cdot \sum _{i}{\mathrm{ALK}}^{\mathrm{MET}}\cdot {k}_{i}\cdot {\mathrm{POC}}_{i}\left(z\right)\end{array}$$

*D*_{ALK} denotes the diffusion coefficient for alkalinity
(taking the values for ${\mathrm{HCO}}_{\mathrm{3}}^{-}$ from
Schulz, 2006), which depends on the bioturbation status
of the respective geochemical zone. Integration of
Eqs. (31)–(34) yields the analytical
solution and Table 8 summarises the boundary conditions
applied in OMEN-SED. A Dirichlet boundary condition is applied at the
sediment–water interface. The decrease in alkalinity due to the oxidation of
reduced species produced in the anoxic zones and due to the precipitation of
pyrite (with stoichiometry ALK^{NIT},
${\mathrm{ALK}}^{{\mathrm{H}}_{\mathrm{2}}\mathrm{S}}$ and ALK^{FeS}) is implicitly taken
into account through the flux boundary condition at *z*_{ox}
(Table 8 Eq. 5). Furthermore, the oxidation of methane by
sulfate reduction increases alkalinity with stoichiometry
ALK^{AOM}, which is accounted for through the flux boundary
condition at ${z}_{{\mathrm{SO}}_{\mathrm{4}}}$ (Table 8 Eq. 9). At the lower
boundary *z*_{max} a zero diffusive flux condition is applied.

The integration constants of all general analytical solutions derived above change in response to changing boundary conditions. Thus, OMEN-SED has to redetermine integration constants for each dynamic zone (i.e. ${z}_{\mathrm{ox}},{z}_{\mathrm{bio}},{z}_{{\mathrm{NO}}_{\mathrm{3}}}$ and ${z}_{{\mathrm{SO}}_{\mathrm{4}}}$) at every time step for all biogeochemical species. The bioturbation boundary poses a particular challenge as it can theoretically occur in any of the dynamic geochemical zones (Fig. 3). Therefore, in order to generalise and simplify this recurring boundary matching problem, an independent, generic algorithm (generic boundary condition matching) is implemented (rather than using multiple fully-worked-out algebraic solutions for each possible case and every biogeochemical species). As a consequence, the algorithm only has to solve a two-simultaneous-equation problem.

As discussed in Sect. 2.1, the solution to the
general steady-state transport-reaction equation (Eq. 2)
for a generic species *C* is of the general form

$$\begin{array}{ll}{\displaystyle}C\left(z\right)& {\displaystyle}=A\cdot \mathrm{exp}\left(az\right)+B\cdot \mathrm{exp}\left(bz\right)+\sum _{j}{\displaystyle \frac{{\mathit{\alpha}}_{j}}{D{\mathit{\beta}}_{j}^{\mathrm{2}}-w{\mathit{\beta}}_{j}-k}}\\ \text{(35)}& {\displaystyle}& {\displaystyle}\cdot \mathrm{exp}(-{\mathit{\beta}}_{j}z)+{\displaystyle \frac{Q}{k}}\end{array}$$

and can therefore be expressed as

$$\begin{array}{}\text{(36)}& {\displaystyle}C\left(z\right)=A\cdot E\left(z\right)+B\cdot F\left(z\right)+G\left(z\right),\end{array}$$

where *E*(*z*) and *F*(*z*) are the homogeneous solutions to the ODE, *G*(*z*) the
particular integral (collectively called the basis functions), and *A* and *B*
are the integration constants that must be determined using the boundary
conditions (shown in Fig. 3 for the whole
sediment column).

Each internal boundary matching problem (i.e. excluding *z*=0 and
*z*=*z*_{max}) involves matching continuity and flux for the two
solutions to the respective reaction–transport equation above (*C*_{U}(*z*)
“upper”) and below (*C*_{L}(*z*) “lower”) the dynamic boundary at *z*=*z*_{b}.

$$\begin{array}{}\text{(37)}& {\displaystyle}{C}_{\mathrm{U}}\left(z\right)& {\displaystyle}={A}_{\mathrm{U}}\cdot {E}_{\mathrm{U}}\left(z\right)+{B}_{\mathrm{U}}\cdot {F}_{\mathrm{U}}\left(z\right)+{G}_{\mathrm{U}}\left(z\right)\text{(38)}& {\displaystyle}{C}_{\mathrm{L}}\left(z\right)& {\displaystyle}={A}_{\mathrm{L}}\cdot {E}_{\mathrm{L}}\left(z\right)+{B}_{\mathrm{L}}\cdot {F}_{\mathrm{L}}\left(z\right)+{G}_{\mathrm{L}}\left(z\right)\end{array}$$

OMEN-SED generally applies concentration continuity and flux boundary conditions at its internal dynamic boundaries.

Continuity (where for
generality we allow a discontinuity *V*_{b}):

$$\begin{array}{ll}\text{(39)}& {\displaystyle}& {\displaystyle}{C}_{\mathrm{U}}\left({z}_{\mathrm{b}}\right)={C}_{\mathrm{L}}\left({z}_{\mathrm{b}}\right)+{V}_{b}.{\displaystyle}& {\displaystyle}\text{Flux}:\\ \text{(40)}& {\displaystyle}& {\displaystyle}{D}_{\mathrm{U}}{C}_{\mathrm{U}}^{\prime}\left({z}_{\mathrm{b}}\right)+w{C}_{\mathrm{U}}\left({z}_{\mathrm{b}}\right)={D}_{\mathrm{L}}{C}_{\mathrm{L}}^{\prime}\left({z}_{\mathrm{b}}\right)+w{C}_{\mathrm{L}}\left({z}_{\mathrm{b}}\right)+{F}_{b},\end{array}$$

where *w* is advection, *D* represents the diffusion coefficients and *F*_{b} is any
flux discontinuity (e.g. resulting from secondary redox reactions).
Considering that the advective flux above and below the boundary is equal
(i.e. *w**C*_{U}(*z*_{b})=*w**C*_{L}(*z*_{b})) and substituting the general
ODE solutions (37) and (38), the boundary
conditions can be represented as two equations connecting the four
integration constants:

$$\begin{array}{ll}{\displaystyle}& {\displaystyle}\left(\begin{array}{cc}{E}_{\mathrm{U}}& {F}_{\mathrm{U}}\\ {D}_{\mathrm{U}}{E}_{\mathrm{U}}^{\prime}& {D}_{\mathrm{U}}{F}_{\mathrm{U}}^{\prime}\end{array}\right)\left(\begin{array}{c}{A}_{\mathrm{U}}\\ {B}_{\mathrm{U}}\end{array}\right)=\left(\begin{array}{cc}{E}_{\mathrm{L}}& {F}_{\mathrm{L}}\\ {D}_{\mathrm{L}}{E}_{\mathrm{L}}^{\prime}& {D}_{\mathrm{L}}{F}_{\mathrm{L}}^{\prime}\end{array}\right)\left(\begin{array}{c}{A}_{\mathrm{L}}\\ {B}_{\mathrm{L}}\end{array}\right)\\ \text{(41)}& {\displaystyle}& {\displaystyle}+\left(\begin{array}{c}{G}_{\mathrm{L}}-{G}_{\mathrm{U}}+{V}_{b}\\ {D}_{\mathrm{L}}{G}_{\mathrm{L}}^{\prime}-{D}_{\mathrm{U}}{G}_{\mathrm{U}}^{\prime}+{F}_{b}-w{V}_{b}\end{array}\right),\end{array}$$

where the ODE solutions *E*, *F* and *G* are all evaluated at *z*_{b}.
Equation (41) can now be solved to give *A*_{U} and *B*_{U} as a
function of the integration constants from the layer below (*A*_{L} and *B*_{L}),
thereby constructing a piecewise solution for both layers with just two
integration constants (this is implemented in the function
**benthic_utils.matchsoln** of OMEN-SED):

$$\begin{array}{}\text{(42)}& {\displaystyle}\left(\begin{array}{c}{A}_{\mathrm{U}}\\ {B}_{\mathrm{U}}\end{array}\right)=\left(\begin{array}{cc}{c}_{\mathrm{1}}& {c}_{\mathrm{2}}\\ {c}_{\mathrm{3}}& {c}_{\mathrm{4}}\end{array}\right)\left(\begin{array}{c}{A}_{\mathrm{L}}\\ {B}_{\mathrm{L}}\end{array}\right)+\left(\begin{array}{c}{d}_{\mathrm{1}}\\ {d}_{\mathrm{2}}\end{array}\right).\end{array}$$

Using Eq. (42), *C*_{U}(*z*) in
Eq. (37) can now be rewritten as a function of
*A*_{L} and *B*_{L} (implemented in
**benthic_utils.xformsoln**):

$$\begin{array}{ll}{\displaystyle}{C}_{\mathrm{U}}\left(z\right)=& {\displaystyle}\phantom{\rule{0.25em}{0ex}}({c}_{\mathrm{1}}{A}_{\mathrm{L}}+{c}_{\mathrm{2}}{B}_{\mathrm{L}}+{d}_{\mathrm{1}})\cdot {E}_{\mathrm{U}}\left(z\right)+({c}_{\mathrm{3}}{A}_{\mathrm{L}}+{c}_{\mathrm{4}}{B}_{\mathrm{L}}+{d}_{\mathrm{2}})\\ \text{(43)}& {\displaystyle}& {\displaystyle}\cdot {F}_{\mathrm{U}}\left(z\right)+{G}_{\mathrm{U}}\left(z\right),\end{array}$$

and hence the “transformed” basis functions ${E}_{\mathrm{U}}^{*}\left(z\right),\phantom{\rule{0.33em}{0ex}}{F}_{\mathrm{U}}^{*}\left(z\right)$ and ${G}_{\mathrm{U}}^{*}\left(z\right)$ can be defined such that

$$\begin{array}{}\text{(44)}& {\displaystyle}{C}_{\mathrm{U}}\left(z\right)={A}_{\mathrm{L}}\cdot {E}_{\mathrm{U}}^{*}\left(z\right)+{B}_{\mathrm{L}}\cdot {F}_{\mathrm{U}}^{*}\left(z\right)+{G}_{\mathrm{U}}^{*}\left(z\right),\end{array}$$

where

$$\begin{array}{ll}{\displaystyle}{E}_{\mathrm{U}}^{*}\left(z\right)& {\displaystyle}={c}_{\mathrm{1}}{E}_{\mathrm{U}}\left(z\right)+{c}_{\mathrm{3}}{F}_{\mathrm{U}}\left(z\right)\\ \text{(45)}& {\displaystyle}{F}_{\mathrm{U}}^{*}\left(z\right)& {\displaystyle}={c}_{\mathrm{2}}{E}_{\mathrm{U}}\left(z\right)+{c}_{\mathrm{4}}{F}_{\mathrm{U}}\left(z\right){\displaystyle}{G}_{\mathrm{U}}^{*}\left(z\right)& {\displaystyle}={G}_{\mathrm{U}}\left(z\right)+{d}_{\mathrm{1}}{E}_{\mathrm{U}}\left(z\right)+{d}_{\mathrm{2}}{F}_{\mathrm{U}}\left(z\right).\end{array}$$

Equations (42), (44) and (45) can now be consecutively applied for each of the dynamic biogeochemical zone boundaries (Fig. 3) starting at the bottom of the sediment column. The net result is a piecewise solution for the whole sediment column with just two integration constants (coming from the lowest layer), which can then be solved for by applying the boundary conditions at the sediment–water interface and the bottom of the sediments.

The bioturbation boundary affects the diffusion coefficient of the modelled
solutes and the conservation equation of organic matter (and thereby
the exact form of each reaction–transport equation). This boundary is
particularly inconvenient as it can in principle occur in the middle of any
of the dynamically shifting biogeochemical zones and therefore generate
multiple cases (Fig. 3). The GBCM algorithm
described above is thus not only used to construct a piecewise solution for
the whole sediment column, but also to abstract out the bioturbation
boundary. For each biogeochemical zone the “bioturbation status” is
initially tested (i.e. fully bioturbated, fully non-bioturbated or crossing
the bioturbation boundary). Therefore, the upper and lower boundaries for the
different zones (e.g. for the nitrogenous zone *z*_{U}=*z*ox, ${z}_{\mathrm{L}}={z}_{{\mathrm{NO}}_{\mathrm{3}}}$) and the respective reactive terms and diffusion
coefficients (bioturbated and non-bioturbated) are passed over to the routine
**zTOC.prepfg_l12** in which the bioturbation status is
determined. In the case that the bioturbation depth is located within this zone (i.e.
${z}_{\mathrm{U}}<{z}_{\mathrm{bio}}<{z}_{\mathrm{L}}$) a piecewise solution for this layer is
constructed. Therefore, the reactive terms and diffusion coefficients are
handed over to the routines **zTOC.calcfg_l1** and
**zTOC.calcfg_l2**, which calculate the basis functions (${E}_{\mathrm{U}},{F}_{\mathrm{U}},{G}_{\mathrm{U}}$ and ${E}_{\mathrm{L}},{F}_{\mathrm{L}},{G}_{\mathrm{L}}$) and their derivatives for the bioturbated and
the non-bioturbated part of this specific geochemical zone. The concentration
and flux for both solutions at *z*_{bio} are matched and the
coefficients ${c}_{\mathrm{1}},{c}_{\mathrm{2}},{c}_{\mathrm{3}},{c}_{\mathrm{4}},{d}_{\mathrm{1}}$ and *d*_{2} (as in
Eq. 42) are calculated by the routine
**benthic_utils.matchsoln**. These coefficients and the
“bioturbation status” of the layer are passed back to the main GBCM
algorithm in which they can be used by the routine
**benthic_utils.xformsoln** to calculate the “transformed”
basis functions (${E}_{\mathrm{U}}^{*}\left(z\right),\phantom{\rule{0.33em}{0ex}}{F}_{\mathrm{U}}^{*}\left(z\right),\phantom{\rule{0.33em}{0ex}}{G}_{\mathrm{U}}^{*}\left(z\right)$) such that both layers are
expressed in the same basis (compare
Eqs. 43–45).

For instance, in the case of sulfate, **zTOC.prepfg_l12** is
called three times before the actual profile is calculated (once per zone:
oxic, nitrogenous, sulfidic) and hands back the information about the
“bioturbation status” of the three layers and the coefficients ${c}_{\mathrm{1}},{c}_{\mathrm{2}},{c}_{\mathrm{3}},{c}_{\mathrm{4}},{d}_{\mathrm{1}}$ and *d*_{2} for the biogeochemical zone including the bioturbation
depth. When calculating the complete piecewise solution for the sediment
column, this information is passed to the function
**zTOC.calcfg_l12**, which sorts out the correct solution type
to use. The main GBCM algorithm therefore never needs to know whether it is
dealing with a piecewise solution (i.e. matched across the bioturbation
boundary) or a “simple” solution (i.e. the layer is fully bioturbated or
fully non-bioturbated).

The following section provides a summary of global relationships used to constrain reaction and transport parameters in OMEN-SED. Table 9 synthesises sediment and transport parameters, while Table 10 provides an overview of all biogeochemical parameters used in OMEN-SED.

The burial of sediments and pore water is directly related to the
accumulation of new material on the sea floor (i.e.
sedimentation, Burdige, 2006). This results in a downward
advective flux of older sediment material and pore water in relation to the
sediment–water interface. When coupled to an ocean model, its sedimentation
flux can be readily used in OMEN-SED. The stand-alone version of OMEN-SED
uses the empirical global relationship between the sediment accumulation rate
(*w* in cm yr^{−1}) and sea-floor depth (*z* in m) of
Burwicz et al. (2011):

$$\begin{array}{}\text{(46)}& {\displaystyle}w={\displaystyle \frac{{w}_{\mathrm{1}}}{\mathrm{1}+(\frac{z}{z\mathrm{1}}{)}^{c\mathrm{1}}}}+{\displaystyle \frac{{w}_{\mathrm{2}}}{\mathrm{1}+(\frac{z}{z\mathrm{2}}{)}^{c\mathrm{2}}}},\end{array}$$

with parameter values as found in the original study (i.e.
*w*_{1}=0.117 cm yr^{−1}, *w*_{2}=0.006 cm yr^{−1}, *z*1=200 m,
*z*2=4000 m, *c*1=3, *c*2=10). As an option we include the parameterisation
of Middelburg et al. (1997):

$$\begin{array}{}\text{(47)}& {\displaystyle}w=\mathrm{3.3}\times {\mathrm{10}}^{-\mathrm{0.87478367}-\mathrm{0.00043512}\cdot z}.\end{array}$$

As mentioned before (Sect. 2.1), the diffusion
coefficient of species *i* is calculated as
${D}_{i}={D}_{i,\mathrm{0}}+{D}_{\mathrm{bio}}={D}_{\mathrm{mol},i}\cdot {f}_{\mathrm{ir}}+{D}_{\mathrm{bio}}$ for dissolved species and
*D*_{i}=*D*_{bio} for solid species. The bioturbation coefficient
*D*_{bio} (cm^{2} yr^{−1}) is constant in the bioturbated zone and
also follows the empirical relationship by Middelburg et al. (1997):

$$\begin{array}{}\text{(48)}& {\displaystyle}{D}_{\mathrm{bio}}=\mathrm{5.2}\times {\mathrm{10}}^{\mathrm{0.76241122}-\mathrm{0.00039724}\cdot z}.\end{array}$$

Observations indicate that bioturbation is largely restricted to the upper
10 cm of the sediments and is only marginally related to sea-floor depth
(e.g. Boudreau, 1998; Teal et al., 2010). Therefore, OMEN-SED
imposes a globally invariant bioturbation depth *z*_{bio} of 10 cm.
In the case that the bottom water oxygen concentration is low (here
< 4.5 nmol cm^{−3}, which is often used to define suboxic waters;
e.g. Morrison et al., 1999; Karstensen et al., 2008) infaunal activity is
assumed to cease and *z*_{bio}=0.01 cm. We choose a low value
unequal to zero in order to simplify the implementation of the model. This
approach ensures that the sediment column always consists of a bioturbated
(even though very small for the low oxygen condition) and a non-bioturbated
zone, and thus the same GBCM algorithm can be used to solve the conservation
equations. Furthermore, when OMEN-SED is coupled to an Earth system model the
same method can be used to convert the POC depositional flux into an SWI
concentration (i.e. the flux needs to be converted assuming bioturbation; see
Sect. 4.1).

Bio-irrigation (i.e. the pumping activity by burrow-dwelling animals) exchanges
burrow water with overlying water and may enhance the SWI flux of solutes
(Aller, 1984, 1988). Several approaches exist to
incorporate this into a 1-D diagenetic model, for instance as a non-local
transport–exchange process (Boudreau, 1984; Emerson et al., 1984) or as an enhancement factor of the molecular
diffusion coefficient (Devol and Christensen, 1993; Soetaert et al., 1996). In
OMEN-SED the latter approach is applied and the apparent “bio-diffusion”
coefficient is calculated as ${D}_{i,\mathrm{0}}={D}_{\mathrm{mol},i}\cdot {f}_{\mathrm{ir}}$.
Soetaert et al. (1996) derived an empirical relationship between
*f*_{ir} and sea-floor depth (${f}_{\mathrm{ir}}=\mathrm{Min}\mathit{\{}\mathrm{1};\mathrm{15.9}\cdot {z}^{-\mathrm{0.43}}\mathit{\}}$) based on observations from
Archer and Devol (1992) and Devol and Christensen (1993), which is used in
OMEN-SED. The specific molecular diffusion coefficients *D*_{mol,i}
are corrected for sediment porosity *ϕ* and tortuosity *F* and are linearly
interpolated for an ambient temperature *T* (in ^{∘}C) using zero-degree
coefficients ${D}_{i}^{\mathrm{0}}$ and temperature-dependent diffusion coefficients ${D}_{i}^{T}$
(Soetaert et al., 1996):

$${D}_{\mathrm{mol},i}=({D}_{i}^{\mathrm{0}}+{D}_{i}^{T}\cdot T)\cdot {\displaystyle \frac{\mathrm{1}}{\mathit{\varphi}\cdot F}}.$$

Tortuosity can be expressed in terms of porosity as $F=\frac{\mathrm{1}}{{\mathit{\varphi}}^{m}}$
(Ullman and Aller, 1982) with the exponent *m* varying according to the
type of sediment (here *m*=3 is used representing muddy sediments with high
porosity). Values for ${D}_{i}^{T}$ and ${D}_{i}^{\mathrm{0}}$ are summarised in
Table 9 and are adapted from
Li and Gregory (1974), Schulz (2006) and
Gypens et al. (2008).

The first-order organic matter degradation constants of compound class *i*,
*k*_{i} (yr^{−1}), are assumed invariant along the sediment column and
therefore independent of the nature of the terminal electron acceptor. The
rate constants can be altered manually to fit observed sediment profiles
(compare modelled profiles in Sect. 3.2) or related to a
master variable provided by a coupled Earth system model (e.g. sedimentation
rate; see Sect. 4.2). The partitioning
of the bulk OM pool into reactivity classes (*f*_{i}) needs to be specified
manually in the stand-alone version or can be provided by the ESM. Organic
matter degradation releases N, P and DIC to the pore water using Redfield
molar ratios (Redfield, 1963) and consumes TEA with specific
stoichiometries (O_{2}C, NO_{3}C, SO_{4}C) as summarised in
Table 10. Table A1 in
the Appendix provides a list of reactions and their stoichiometries as
implemented in OMEN-SED. The effect of OM degradation, secondary redox
reactions and pyrite precipitation on total alkalinity is also accounted for
via reaction-specific stoichiometries representing the release of
NH_{4}, H_{2}S and P and is based on
Jourabchi et al. (2005). In reality, the reoxidation of
reduced substances produced during OM degradation may be incomplete. Yet, in
OMEN-SED we have to assume their complete, instantaneous reoxidation at
*z*_{ox} to allow for an analytical solution. In order to relax this
assumption for cases in which it can be justified, we include a “switch” to
allow part of the NH_{4}, H_{2}S and CH_{4} flux to escape
reoxidation. The secondary redox parameters (i.e. ${\mathit{\gamma}}_{{\mathrm{NH}}_{\mathrm{4}}}$,
${\mathit{\gamma}}_{{\mathrm{H}}_{\mathrm{2}}\mathrm{S}}$, ${\mathit{\gamma}}_{{\mathrm{CH}}_{\mathrm{4}}}$) therefore account for the
fraction of reduced substances that are reoxidised and would ideally be
parameterised, for instance, in relation to bottom water oxygen concentration
or oxygen penetration depth (*z*_{ox}). Gypens et al. (2008),
for example, expressed ${\mathit{\gamma}}_{{\mathrm{NH}}_{\mathrm{4}}}$ as a function of oxygen
penetration depth (${\mathit{\gamma}}_{{\mathrm{NH}}_{\mathrm{4}}}=\mathrm{0.243}\cdot \mathrm{ln}\left({z}_{\mathrm{ox}}\right)+\mathrm{1.8479}$) based on a fitting exercise to a
numerical model and showed that the fraction varies between 0.2 for
*z*_{ox}=0.1 cm and 1.0 for *z*_{ox}>3 cm. Due to
mathematical constraints in OMEN-SED for finding an analytical solution to
the model equations these fractions take constant values generally
representing oxygenated deep sea conditions. However, when coupled to an ESM,
${\mathit{\gamma}}_{{\mathrm{H}}_{\mathrm{2}}\mathrm{S}}$ becomes dependent on the bottom water oxygenation
state. That is, ${\mathit{\gamma}}_{{\mathrm{H}}_{\mathrm{2}}\mathrm{S}}=\mathrm{1.0}$ for oxic bottom waters and a
user-defined value ${\mathit{\gamma}}_{{\mathrm{H}}_{\mathrm{2}}\mathrm{S}}<\mathrm{1.0}$ for anoxic bottom waters. The
parameter *γ*_{FeS} represents the fraction of sulfide that is
precipitated as pyrite in the sulfidic zone. The majority of H_{2}S
produced by sulfate reduction is reoxidised, but it is estimated that ∼10–25 % is eventually buried as pyrite
(Bottrell and Newton, 2006). However, this fraction can vary
significantly over geological timescales (Berner, 1984). If
a user does not want to make any assumptions about pyrite precipitation, it
can be set to zero (as in the results presented here). The instantaneous
equilibrium adsorption coefficients of NH_{4} and PO_{4}
(${K}_{{\mathrm{NH}}_{\mathrm{4}}}$, ${K}_{{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{ox}}$,
${K}_{{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{anox}}$) are based on
Wang and Van Cappellen (1996) and Slomp et al. (1998),
respectively. The first-order rate constants for the sorption of PO_{4}
to Fe oxides (*k*_{s}), the release of PO_{4} from Fe-bound P due
to Fe-oxide reduction (*k*_{m}) and authigenic CFA precipitation
(*k*_{a}), as well as the pore water
equilibrium concentrations for P sorption and CFA precipitation
(${{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{s}}$, ${{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{a}}$) and the asymptotic
concentration for Fe-bound P (FeP^{∞}) are taken from
Slomp et al. (1996). See Table 10
for a complete summary of the parameters and their values.

3 Stand-alone sensitivity analysis and case studies

Back to toptop
Model parameters implicitly account for processes that are not explicitly
resolved. They are notoriously difficult to constrain and thus a primary
source of uncertainty for numerical and analytical models, in particular on
the global scale and/or in data-poor areas. A comprehensive sensitivity
analysis can help quantify this uncertainty and identify the most sensitive
parameters. More specifically, sensitivity analysis is used to investigate
how the variations in the outputs (${y}_{\mathrm{1}},\phantom{\rule{0.33em}{0ex}}\mathrm{\dots},\phantom{\rule{0.33em}{0ex}}{y}_{N}$) of a model can be
attributed to variations in the different input parameters (${x}_{\mathrm{1}},\phantom{\rule{0.33em}{0ex}}\mathrm{\dots},\phantom{\rule{0.33em}{0ex}}{x}_{M}$; Pianosi et al., 2016). Different types of sensitivity
indices, which quantify the relative influence of parameter *x*_{i} on output
*y*_{j} with a scalar *S*_{i,j} (for $i\in \mathit{\{}\mathrm{1},\phantom{\rule{0.33em}{0ex}}\mathrm{\dots},\phantom{\rule{0.33em}{0ex}}M\mathit{\}}$ and $j\in \mathit{\{}\mathrm{1},\phantom{\rule{0.33em}{0ex}}\mathrm{\dots},\phantom{\rule{0.33em}{0ex}}N\mathit{\}}$), can be calculated, ranging from simple one-at-a-time
methods to statistical evaluations of the output distribution (e.g.
variance-based or density-based approaches; Pianosi et al., 2016). The
latter indices take values between zero and one (${S}_{i,j}\in [\mathrm{0},\mathrm{1}]$), where
zero indicates a non-influential parameter and a higher value a more
influential parameter. Here, sensitivity analysis is used mainly to identify
which parameters have the largest impact on the different model outputs and
therefore require more careful calibration. As the probability density
functions of our model outputs (i.e. the resulting SWI fluxes) are generally
highly skewed towards extreme organic matter degradation rates (not shown),
variance-based sensitivity indices may not be a suitable proxy for output
uncertainty (Pianosi et al., 2016). Hence, instead the
density-based PAWN method by Pianosi and Wagener (2015) is employed which
considers the entire conditional and unconditional cumulative distribution
function (CDF) of the model output rather than its variance only. The
unconditional CDF, *F*_{y}(*y*), of output *y* is obtained when all uncertain
parameters (${x}_{\mathrm{1}},\phantom{\rule{0.33em}{0ex}}\mathrm{\dots},\phantom{\rule{0.33em}{0ex}}{x}_{M}$) are varied simultaneously, and the
conditional CDFs, ${F}_{y|{x}_{i}}\left(y\right)$, are obtained when all inputs but the *i*th
parameter are varied (i.e. *x*_{i} is fixed to a so-called conditioning value).
The sensitivity index of parameter *i* is measured by the distance between
the two CDFs using the Kolmogorov–Smirnov statistic
(Kolmogorov, 1933; Smirnov, 1939), i.e.

$$\begin{array}{}\text{(49)}& {\displaystyle}{S}_{i}=\underset{{x}_{i}}{max}\underset{y}{max}\left|{F}_{y}\right(y)-{F}_{y|{x}_{i}}(y\left)\right|.\end{array}$$

Since ${F}_{y|{x}_{i}}\left(y\right)$ accounts for what happens when the variability due to
*x*_{i} is removed, the distance between the two CDFs provides a measure of the
effects of *x*_{i} on the output *y*. Due to the model complexity it is
impossible to compute the sensitivity indices analytically. Therefore, they
are approximated from a Latin hypercube sampling of parameter inputs and
calculated outputs. For a brief description of the methodology, see
Fig. 4. For more details, we refer
the interested reader to Pianosi and Wagener (2015).

Sources: (1) Arndt et al. (2013); (2) Van Cappellen and Wang (1996); (3) Krom and Berner (1980); (4) Gypens et al. (2008); (5) Slomp et al. (1996); (6) Van Cappellen and Berner (1988).

The PAWN method, as implemented within the Sensitivity Analysis for Everyone
(SAFE) MATLAB toolbox (Pianosi et al., 2015), is used to investigate *M*=11 model parameters for ranges as specified in
Table 11. Sensitivity indices for all resulting
SWI fluxes for two idealised sediment conditions (i.e. anoxic at 400 m and
oxic at 4000 m; see Table 12) are calculated. We use
NU = 200 samples to estimate the unconditional CDF, NC = 100 samples
to estimate the conditional CDFs and *n*=10 conditioning points. Thus, as
${\mathrm{N}}_{\mathrm{eval}}=\mathrm{200}+\mathrm{100}\cdot \mathrm{10}\cdot \mathrm{11}$, 11 200 model evaluations are
performed for each sediment condition. The resulting indices are then
translated into a colour code and summarised in a pattern plot to simplify
comparison (Fig. 5).

Figure 5 summarises the results of the sensitivity
analysis as a colour map. Results indicate that generally the most
significant parameters for all model outputs are the degradation rate
constant for the labile OM pool (*k*_{1}) and the fraction of this pool to the
total OM stock (*f*_{1}). Other parameters play a minor role for the
SWI fluxes, with the exception of the secondary redox parameters (i.e.
${\mathit{\gamma}}_{{\mathrm{NH}}_{\mathrm{4}}},\phantom{\rule{0.33em}{0ex}}{\mathit{\gamma}}_{{\mathrm{H}}_{\mathrm{2}}\mathrm{S}}$) in the oxic scenario. Here,
NH_{4}, SO_{4} and H_{2}S fluxes are very sensitive to changes
in ${\mathit{\gamma}}_{{\mathrm{NH}}_{\mathrm{4}}}$ and ${\mathit{\gamma}}_{{\mathrm{H}}_{\mathrm{2}}\mathrm{S}}$, as these parameters
determine how much of the respective TEA is produced in situ via reoxidation,
thus affecting the resulting SWI fluxes. For the oxic scenario, the
reoxidation of H_{2}S produced in the sulfidic layer has also a strong
influence on alkalinity (${\mathit{\gamma}}_{{\mathrm{H}}_{\mathrm{2}}\mathrm{S}}$; Table 8, Eq. 5)
as it decreases alkalinity by 2 moles per mole of S oxidised
(${\mathrm{ALK}}^{{\mathrm{H}}_{\mathrm{2}}\mathrm{S}}$; Table 10). However,
these high sensitivities are partially caused by the wide range of allowed
values (${\mathit{\gamma}}_{{\mathrm{NH}}_{\mathrm{4}}}$, ${\mathit{\gamma}}_{{\mathrm{NH}}_{\mathrm{4}}}\in [\mathrm{0.5};\mathrm{1.0}]$). Yet,
for oxic deep sea conditions it is more likely that reduced substances are
almost completely reoxidised (e.g. Hensen et al., 2006). For the
anoxic scenario the secondary redox parameters are essentially
non-influential as no O_{2} is available for the reoxidation of reduced
substances. Especially for the oxic condition the PO_{4} SWI flux
appears to be insensitive to P-related parameters (i.e.
${K}_{{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{ox}}$, ${K}_{{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{anox}}$, *k*_{s}, *k*_{m},
*k*_{a}) as the majority is absorbed to Fe oxides. The
sensitivities change if other PO_{4}-related equilibrium
concentrations ${{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{s}}$, ${{\mathrm{PO}}_{\mathrm{4}}}^{\mathrm{a}}$ and
FeP^{∞} are used (not shown). Overall the results of the
sensitivity analysis are in line with what one would expect from a diagenetic
model and thus provide grounds to confirm that OMEN-SED provides sensible
results. The parameterisation of the organic matter pools (*f*_{1}) and their
degradation rate constants (*k*_{1}, *k*_{2}) is critical, especially when the
model is used in a global Earth system model framework, as these parameters,
as well as the *γ* parameters, can have a very important influence on
the flux of dissolved species through the SWI. At the same time these are the
weakest constrained parameters. Thus, one should rather choose
*γ* values close to 1 and consider carefully where a relaxation of the
“all reoxidised” assumption is appropriate. In contrast, the importance of
the OM degradation rate constants cannot be overemphasised. Therefore, much
care should be given to how these are parameterised in coupled simulations
and a range of different plausible scenarios should be tested to quantify
uncertainty.

Because of the strong sensitivity of model results to OM degradation rate
parameters, we further explore the sensitivity of simulated sediment–water
exchange fluxes to variations in organic matter degradation parameters by
varying *k*_{1}, *f*_{1} and $\stackrel{\mathrm{\u0303}}{{k}_{\mathrm{2}}}$ while all other model parameters
are set to their default values
(Tables 9 and
10). Minimum and maximum values for *k*_{1},
$\stackrel{\mathrm{\u0303}}{{k}_{\mathrm{2}}}$ and *f*_{1} in the shallow ocean are as in
Table 11. For the deep sea condition we account
for the presence of more refractory OM by sampling ${f}_{\mathrm{1}}\in [\mathrm{0.02},\mathrm{0.3}]$,
whereas the variation of *k*_{1} and $\stackrel{\mathrm{\u0303}}{{k}_{\mathrm{2}}}$ is as in the shallow
ocean. The parameter space is sampled using another Latin hypercube approach
with sample sizes of *N*=3500 for each idealised sediment condition.
Figure 6 summarises the results of the
sensitivity study, and the ranges of observed O_{2} and NO_{3}
sediment–water interface fluxes extracted from a global database
(Stolpovsky et al., 2015) are indicated on the colour scale. The colour
patterns in Fig. 6a and b reveal the complex
interplay between the amount of labile OM *f*_{1} and its degradation rate
*k*_{1} for the resulting SWI fluxes of NO_{3} in anoxic sediments and
O_{2} in aerobic sediments. In general, a higher degradation rate in
combination with more labile OM available leads to a higher SWI flux.
However, higher fluxes extend over a larger range of *k*_{1} values when the
amount of labile OM *f*_{1} is high. The absence of a colour pattern in
Fig. 6c highlights the limited interaction of
the two model parameters for NO_{3} SWI fluxes under oxic conditions.
Figure 6 shows that SWI fluxes can vary widely
over the range of plausible organic matter degradation parameters and that
simulated fluxes generally fall within the range of observed SWI fluxes.
However, a large number of different *k*−*f* combinations can result in
SWI fluxes that fall within the observed ranges reported by
Stolpovsky et al. (2015), further emphasising the care that should be
devoted to constraining OM degradation parameters.

In order to illustrate the capabilities of OMEN-SED, comprehensive datasets
from the Santa Barbara Basin (Reimers et al., 1996), the Iberian margin and the Nazaré Canyon (Epping et al., 2002) are
modelled. Modelled profiles are compared with measured pore water data from
different depths including the continental shelf (108 m) and the lower slope
(2213 m) located at the Iberian margin, the upper slope (585 m) from the
Santa Barbara Basin and a deep sea site (4298 m) in the Nazaré Canyon.
The Santa Barbara Basin is characterised by anoxic bottom waters, high POC
concentrations and varved sediments (Reimers et al., 1990), and therefore
the depth of bioturbation in OMEN-SED is restricted to the upper 0.01 cm. In
the uppermost sediments iron(III) hydroxides are reduced, releasing
Fe^{2+}, which reacts with sulfide to form iron sulfides. Thus, the
Fe cycle exerts a strong control on sulfide concentrations in the
sediments of this basin (Reimers et al., 1996). In addition, the
sediments are generally supersaturated with respect to carbonate fluorapatite
by and below 2 cm (Reimers et al., 1996). The Iberian margin,
situated in the north-eastern Atlantic, generally belongs to the more
productive regions of the global ocean (Longhurst et al., 1995);
however, seasonal changes in upwelling creates a strong temporal variability
in primary productivity and organic carbon deposition. Submarine canyons in
this area (like the Nazaré Canyon) may deliver organic carbon from the
shelf to the ocean interior (van Weering et al., 2002; Epping et al., 2002). For a more detailed description of the study areas
and the experimental work, the interested reader is referred to the
publications by Reimers et al. (1996) and
Epping et al. (2002).

In OMEN-SED sediment characteristics and boundary conditions are set to the
observed values where available (Table 13). Other
sediment characteristics (e.g. sedimentation rate, porosity, density),
stoichiometric factors and secondary reaction parameters are set to the
default value (see Tables 9 and
10). Organic matter is modelled as two
fractions with different first-order degradation rate constants. The POC and
pore water profiles were manually fitted by optimising the POC partitioning
into the fast- and slow-degrading pool and their respective first-order
degradation rate constants (priority is given to reproducing the POC and
O_{2} profiles). For phosphorus the equilibrium concentration for
authigenic P formation (${\mathrm{PO}}_{\mathrm{4}}^{\mathrm{a}}$) was adjusted to fit the
PO_{4} concentration at *z*_{max}.

Figure 7 compares modelled and observed sediment
profiles for the Santa Barbara Basin and the Iberian margin. Results show
that OMEN-SED is able to capture the main diagenetic features across a range
of different environments without changing model parameters (other than the
four we tuned, i.e. *k*_{1}, *k*_{2}, *f*_{1} and ${\mathrm{PO}}_{\mathrm{4}}^{\mathrm{a}}$) to
site-specific conditions. For the two open Iberian margin stations (108 and
2213 m) OMEN-SED fits all observations well. OMEN-SED does especially well
at a sea-floor depth (SFD) of 2213 m by reproducing the deep O_{2}
penetration and the subsurface maximum in NO_{3} concentration due to
the nitrification of NH_{4} (note that NH_{4} is overestimated at
this SFD). For the anoxic Santa Barbara Basin (585 m) the decrease in
SO_{4} and the increase in ALK concentration with sediment depth
is well represented, indicating the importance of sulfate reduction as the
primary pathway of OM degradation at this site (compare
with Meysman et al., 2003). However, a misfit is observed for H_{2}S
and PO_{4} in the upper 20 cm of this sediment core. The discrepancy
for H_{2}S can be explained by high iron(III) hydroxide concentrations,
which is reduced to degrade organic matter (especially in the 2–4 cm depth
interval), therefore placing the beginning of the sulfate reduction zone and
the production of H_{2}S in the deeper sediments
(Reimers et al., 1996). Iron processes are currently not dynamically
represented in OMEN-SED. In addition, produced dissolved Fe reacts
with H_{2}S to form iron sulfides (e.g. pyrite, FeS_{2}) and thus
further inhibits the rise of H_{2}S (Reimers et al., 1990). The
iron cycle also plays a critical role for phosphorus, as the reduction of
iron(III) hydroxides in the surface sediments releases sorbed phosphate,
leading to pore waters around and below 2 cm which are supersaturated with
respect to fluorapatite, thus initiating CFA precipitation.
Reimers et al. (1996) could even show that the accumulation of
CFA is mainly restricted to the near-surface sediments (∼5 cm)
instead of throughout the sediment column. As OMEN-SED currently does not
include an iron cycle and Fe-bound P and CFA processes are highly
parameterised, the model is not able to capture these complex,
non-steady-state phosphorus dynamics at this specific site. For the Nazaré
Canyon station (4298 m) satisfactory fits could be realised apart from
NH_{4}. However, Epping et al. (2002) also could not obtain a
better fit using the diagenetic model OMEXDIA. They suggested non-local
solute exchange resulting from bio-irrigation as responsible for the higher
NH_{4} concentrations at this site, which is neglected in their model
and in OMEN-SED. Furthermore, the fractured POC profile (indicating episodic
depositional events through the canyon) could have been approximated using a
different partitioning of the bulk POC into the labile and refractory pool
with different degradation rate constants, thus potentially leading to a
better fit of the NH_{4} profile. In general, better approximations of
the data could have potentially been acquired by applying a sensitivity study
using different NC ratios (e.g. Epping et al., 2002, report different ratios from Redfield
stoichiometry) and exploring the parameter space for
the secondary reaction parameters (${\mathit{\gamma}}_{{\mathrm{NH}}_{\mathrm{4}}}$,
${\mathit{\gamma}}_{{\mathrm{H}}_{\mathrm{2}}\mathrm{S}}$). However, considering these generalisations and our
assumption of steady state, which might not be valid, particularly for the
complex Santa Barbara Basin, the shallow core and the Nazaré Canyon, which
are affected by seasonality and biology, OMEN-SED generally reproduces the
observed pore water trends and hence captures the main diagenetic processes.

^{a} Derived from Middelburg et al. (1997).^{b} Derived from Van Cappellen and Wang (1995).
^{c} Derived from Conkright et al. (2002). ^{d} Derived from
Boudreau (1997).^{e} Calculated with OMEN-SED from POC_{flux}.

In this section we explore to what degree OMEN-SED is capable of capturing
the dynamics of organic matter degradation pathways and related TEA fluxes as
simulated with a more complete and complex numerical diagenetic model
(Thullner et al., 2009). Therefore, we reproduce the simulations
of typical conditions along a global ocean hypsometry of
Thullner et al. (2009) and compare our modelled TEA fluxes with
the results of the complex model and with observations from
Middelburg et al. (1996). To explore the global degradation of
OM in the sea floor, Thullner et al. (2009) quantified various
diagenetic processes using the Biogeochemical Reaction Network Simulator
(BRNS; Aguilera et al., 2005), a flexible simulation
environment suitable for reactive transport simulations of complex
biogeochemical problems (e.g. Jourabchi et al., 2005; Thullner et al., 2005). Thullner et al. (2009) used sea-floor
depth (SFD) as the master variable and calculated model parameters, such as
*w*, *D*_{bio} and *ϕ*, from existing empirical relationships
(e.g. Van Cappellen and Wang, 1995; Middelburg et al., 1997). Organic matter
degradation was described with a 1G approach, thus assuming a single pool of
organic matter of uniform reactivity. The first-order rate constant was
related to the sediment accumulation rate, *w*
(cm yr^{−1}), following the empirical relationship of
Boudreau (1997):

$$\begin{array}{}\text{(50)}& {\displaystyle}k=\mathrm{0.38}\cdot {w}^{\mathrm{0.59}}.\end{array}$$

This rate constant can be assumed as the mean reactivity of the organic matter fractions which are degraded in the upper, bioturbated 10–20 cm of the sediments. Thus, more reactive fractions (degraded during days or weeks close to the SWI) and more refractory fractions (degraded on longer timescales deeper in the sediments) are not captured by this relationship (Boudreau, 1997). BRNS simulations were performed using boundary conditions and parameters for depths representative of shelf, slope and deep sea sediments (i.e. SFD of 100, 200, 500, 1000, 2000, 3500 and 5000 m). In order to reproduce these results, OMEN-SED is configured here as a 1G model and boundary conditions and model parameters are defined as in Thullner et al. (2009, see Table 14). As OMEN-SED assumes a fixed fraction (i.e. ${\mathit{\gamma}}_{{\mathrm{NH}}_{\mathrm{4}}}$, ${\mathit{\gamma}}_{{\mathrm{H}}_{\mathrm{2}}\mathrm{S}}$) of reduced substances to be reoxidised, which exerts a large impact on the resulting SWI fluxes (compare to Sect. 3.1), two sets of simulations are performed in order to show the range of possible model outputs. In the first set-up 95 % of the reduced substances are reoxidised (i.e. ${\mathit{\gamma}}_{{\mathrm{NH}}_{\mathrm{4}}}={\mathit{\gamma}}_{{\mathrm{H}}_{\mathrm{2}}\mathrm{S}}=\mathrm{0.95}$), and in the second less realistic case, only 5 % are reoxidised (all other model parameters and boundary conditions are equal).

Figure 8 compares simulated SWI fluxes of TEAs (i.e.
O_{2}, NO_{3} and SO_{4}) along the global hypsometry using
OMEN-SED (black lines) with the results of Thullner et al. (2009)
(red lines). Observations for O_{2} and NO_{3} fluxes are taken
from Middelburg et al. (1996). Due to the applied empirical
relations, organic matter flux to the sea floor decreases by 2 orders of
magnitude from 100 to 5000 m and its degradation rate constant by 1 order of
magnitude (Table 14). Therefore, the rate of
organic matter degradation is about 50 times greater at 100 m than at
5000 m (compare to Thullner et al., 2009), thus resulting in a
decrease in TEA fluxes along the hypsometry (Fig. 8). The
95 % reoxidation experiments (dots) show proportionally higher O_{2}
influxes than the 5 % reoxidation experiments (triangles) because more
O_{2} is utilised for the in situ production of NO_{3} and SO_{4}
in the sediments. This is also mirrored by the increased NO_{3} outflux
and decreased SO_{4} influx for shallower SFDs. This is in line with
the results of Thullner et al. (2009), which showed that in situ
production is an important pathway of SO_{4} supply in the sediment
responsible for ∼ 80 % of the total OM degradation at depths
between 100 and 2000 m (in our results SO_{4} is not used for OM
degradation in OMEN-SED below 2000 m). In general, Fig. 8
shows that OMEN-SED captures the main trends in observed and numerically
simulated TEA fluxes well. Results also confirm that higher *γ* values
better represent SWI fluxes for most of the global hypsometry. A slight
overestimation of shallow ocean SWI fluxes (SFD < 200 m) for the high
*γ* scenario indicates that slightly lower *γ* values would better
capture SWI fluxes in these areas where rapid oxygen consumption favours the
escape of reduced species across the SWI.

In addition, observed O_{2} fluxes in the upper 2000 m are generally
encompassed by our total range in predicted OMEN-SED fluxes. Oxygen fluxes
for the deep sea sediments, however, are slightly underestimated. These
deviations can presumably be related to the assumed 1G description of organic
matter degradation, which neglects the more labile OM pool. This highly
reactive pool is degraded close to the sediment surface, thus promoting
higher aerobic degradation rates and higher O_{2} fluxes. Nitrate fluxes
in the upper 500 m of the Atlantic Ocean are well predicted. However, as in
Middelburg et al. (1996) the direction of calculated nitrate
fluxes in the upper 1000 m of the Pacific Ocean differ from the
observations. Middelburg et al. (1996) related these
discrepancies to the globally averaged model parameters and the applied
boundary conditions. They could reduce the disagreements significantly by
using more representative bottom water concentrations for the eastern Pacific
and a higher flux of labile organic matter for their 2G model. By changing
the boundary conditions and the N : C elemental ratio of organic matter for
the whole hypsometry, it is possible to obtain a better model–data fit with
OMEN-SED for the shallow Pacific Ocean (green line in
Fig. 8b). Bohlen et al. (2012) report that the
elemental N : C ratio strongly deviates from Redfield stoichiometry (0.151)
with specifically lower values for the eastern Pacific Ocean. The use of their
globally averaged value of 0.067 allows the modelled and observed
values to be reconciled provided that bottom water conditions are also changed to the low
oxygen and high nitrate levels more likely to be found in the shallow Pacific
Ocean (O_{2}=10 nmol cm^{−3} and NO_{3}=80 nmol cm^{−3}).

4 Coupled pre-industrial Earth system model simulations

Back to toptop
In a final step, we couple OMEN-SED to the carbon-centric version of the GENIE Earth system model (cGENIE; Ridgwell et al., 2007) in order to illustrate how a fully coupled ocean–sediment system can be configured and applied. We start by providing a brief description of cGENIE and the coupling procedure (Fig. 9).

cGENIE is a model of intermediate complexity based on the efficient climate model C-GOLDSTEIN of Edwards and Marsh (2005), featuring a frictional-geostrophic 3-D ocean circulation model coupled to a fast energy–moisture balance 2-D atmosphere together with a dynamic–thermodynamic sea-ice component. The version of cGENIE used here includes the marine geochemical cycling of carbon, oxygen, phosphorus and sulfur (Ridgwell et al., 2007), the preservation of carbonates in deep sea sediments (SEDGEM; Ridgwell and Hargreaves, 2007) and terrestrial weathering (Colbourn et al., 2013). The ocean model is implemented on a 36 × 36 equal-area horizontal grid with 16 vertical levels using the pre-industrial continental configuration and bathymetry as in Archer et al. (2009). A finer grid (72 × 72) is used for the sediments (see Fig. 11c and Ridgwell and Hargreaves, 2007) and OMEN-SED is called by SEDGEM for each wet ocean grid point.

In our Earth system model set-up, we prescribe the burial sediment fluxes of
detrital material, opal and CaCO_{3}, while leaving OMEN-SED to
calculate organic matter preservation. This assumption serves two purposes.
First, the runtime of the model is minimised as steady-state conditions are
reached earlier compared to the ca. 20–50 kyr adjustment time for surface
sediment CaCO_{3} (Ridgwell and Hargreaves, 2007). Second, invariant
flux fields remove feedbacks between OMEN-SED and the calculation of
CaCO_{3} preservation (changes in organic matter preservation affect
CaCO_{3} dissolution and hence sedimentation accumulation rates, which in turn affects the weight percent of organic matter
in the sediments) that would not only lengthen the sediment adjustment time
but also make it impossible to carry out unbiased comparisons between
different assumptions regarding organic matter reactivity in OMEN-SED.

We derive these fields form the data compilation of
Archer (1996) as follows. First, we re-grid the
Archer (1996) interpolated non-carbonate mass accumulation
rate field (NC_{flux}) to the 72 × 72 cGENIE sediment grid.
This field includes detrital material plus opal (plus a minor contribution
from organic matter). We could then directly calculate ∑_{flux}
(total burial flux of all components or total sediment accumulation rate)
from this plus measurements of coretop wt % CaCO_{3}
(*C*_{wtpct}) (Archer, 1996) as ${\sum}_{\mathrm{flux}}={\mathrm{NC}}_{\mathrm{flux}}\cdot (\mathrm{1}-\frac{{C}_{\mathrm{wtpct}}}{\mathrm{100}}{)}^{-\mathrm{1}}$.
However, some of the Archer (1996) database
*C*_{wtpct} values are both close to 100 % and associated with high
NC_{flux} and hence would lead to unrealistically high values for
∑_{flux}. We therefore impose a plausibility filter by also
re-gridding coretop wt % opal (*O*_{wtpct}) and quartz
(*Q*_{wtpct}) and for grid points in which more than one component is
reported and the sum exceeds 100 wt %, normalising the individual
components (for grid points with only a single solid component, no change is
made). We then calculate the individual solid component burial fluxes, and
sum them up. To interpolate between the grid points associated with data, we
iteratively average nearest (adjoining) neighbours. The distribution of the
total burial flux ∑_{flux} (in g cm^{−2} kyr^{−1}) is shown
in Fig. C1 in the Appendix.

Depending on the configuration of the overlying biogeochemical ocean model,
processes can be included or excluded in OMEN-SED and stoichiometric factors
(Table 10) need to be matched between models to
ensure preservation of mass. As nitrogen is not modelled explicitly in the
employed cGENIE configuration, NC_{i}, ALK^{NIT} and
ALK^{DEN} in OMEN-SED are set to zero. cGENIE, however,
implicitly includes the effects of NH_{4} release and its complete
nitrification on alkalinity but neglects the impact of P release. Therefore,
alkalinity stoichiometries for aerobic degradation, sulfate reduction and
methanogenesis are changed to ${\mathrm{ALK}}^{\mathrm{OX}}=-\mathrm{16}/\mathrm{106}$,
${\mathrm{ALK}}^{\mathrm{SUL}}=\mathrm{122}/\mathrm{106}$ and ${\mathrm{ALK}}^{\mathrm{MET}}=-\mathrm{16}/\mathrm{106}$,
respectively (compare to default in Table 10).

Various biogeochemical tracers and parameters are transferred from SEDGEM to
OMEN-SED (see Fig. 9) and are converted into the
required units. Bottom water concentrations of solutes are converted from
mol kg^{−1} to mol cm^{−3} and the depositional flux of POC
(POC_{flux}) is converted from cm^{3} cm^{−2} yr^{−1} to
mol cm^{−2} yr^{−1} assuming an average density of POC of
1.0 g cm^{−3}. Within the water column in cGENIE, POC is partitioned into
two fractions with different degradation length scales of ∼ 590 m and
1 000 000 m. The labile pool thus degrades while sinking through the water
column, whereas the refractory pool is assumed relatively unreactive
(Ridgwell et al., 2007). Thus, depending on sea-floor depth, the
partitioning of bulk POC reaching the sediments is different
(Fig. 10a, b). This information is used by OMEN-SED to
define the parameter *f*_{1}. Other parameters used from cGENIE are sea-floor
depth and local temperature. The sediment accumulation rate (*w*) is taken from the
previous time step of cGENIE; however, it is assured that *w* is not smaller
than the detrital flux (Det_{flux}) to the sediments (e.g. *w*<0 can
occur if initially carbonate-rich sediments are eroded during the spin-up of
cGENIE). In the case (*w*≤Det_{flux} & Det_{flux}=0.0), all POC is remineralised at the ocean floor. Furthermore, a minimum
value of *w*=0.4 cm kyr^{−1} is imposed as OMEN-SED tends to be less
stable for lower values. For comparison, this threshold is crossed for
sea-floor depths below 7000 m when applying the relationship between the
sediment accumulation rate and water depth of
Middelburg et al. (1997) and below 5200 m for the
Burwicz et al. (2011) parameterisation. The bulk POC_{flux}
is separated into the labile and refractory component and the routine to find
the steady-state solution for POC is called. Here, the two POC depositional
fluxes are first converted into SWI concentrations (POC_{i}(*z*=0), in
mol cm^{−3}) by solving the flux divergence equation

$$\begin{array}{}\text{(51)}& {\displaystyle \frac{\partial F}{\partial z}}=-{\displaystyle \frac{\partial}{\partial z}}\left(-\mathit{\xi}{D}_{i}{\displaystyle \frac{\partial {\mathrm{POC}}_{i}}{\partial z}}+\mathit{\xi}w{\mathrm{POC}}_{i}\right)\end{array}$$

for *z*=0. OMEN-SED then computes the fraction of POC preserved in the
sediment (*f*_{POC}, see Eq. 5) and subsequently
calls the routines to find the steady-state solutions for the solute
substances. Note that in this initial coupling the calculated benthic
uptake and return fluxes ${F}_{{C}_{i}}$ of
dissolved species *C*_{i} (compare to Eq. 6) are adjusted
for the advective loss at the lower sediment boundary (*w*⋅*C*_{i}(*z*_{max})) to ensure the conservation of mass in the coupled
model:

$$\begin{array}{}\text{(52)}& {\displaystyle}{F}_{{C}_{i}}=\mathit{\varphi}\left(\mathrm{0}\right)\left({D}_{i}{\displaystyle \frac{\partial {C}_{i}\left(z\right)}{\partial z}}{|}_{z=\mathrm{0}}-w\left[{C}_{i}\left(\mathrm{0}\right)-{C}_{i}\left({z}_{\mathrm{max}}\right)\right]\right).\end{array}$$

In the case that OMEN-SED computes unrealistic results for POC preservation (i.e.
*f*_{POC}<0.0 or *f*_{POC}>1.0) we discard the results
of OMEN-SED and all POC is remineralised at the ocean floor. For the modern
ocean set-up using the adjustments for *w* described above, this has not
occurred and is just installed as a safety check. Finally,
*f*_{POC} and the SWI fluxes of solutes (${F}_{{C}_{i}}$, in
mol cm^{−2} yr^{−1}) are returned to cGENIE. In the case that no POC is
deposited on the sea floor (i.e. POC_{flux}=0), OMEN-SED is not
executed and *f*_{POC} and ${F}_{{C}_{i}}$ for all *i* are set to zero.
In order to reduce memory requirements, the sediment profiles (e.g. as shown
in Fig. 7) are not calculated in the FORTRAN
version of OMEN-SED; however, the boundary conditions are saved and sediment
profiles for specific grid cells, ocean basins and ocean transects can be
plotted at the end of each experiment using the stand-alone MATLAB version of
OMEN-SED.

As shown in our sensitivity analysis (Sect. 3.1) and discussed by
Arndt et al. (2013), the degradation rate constants for OM (*k*_{i})
are the most influential parameters and exert a dominant control on the SWI
flux of redox-sensitive elements and the preservation of organic matter. Yet,
their spatial variability is unknown at the global scale and reported rate
constants in the sediments can vary by about 10 orders of magnitude or more
(Middelburg et al., 1993; Arndt et al., 2013). Furthermore, when
OMEN-SED is coupled to cGENIE, very different timescales have to be
considered for OM degradation in the sediments compared to the water column
(Fig. 10a, b), and thus the diagenetic rate constants
cannot be easily implied by the assumed water column POC flux profiles in
cGENIE. To illustrate this, let us consider the degradation of fresh marine
organic matter as it is transported and degraded along the ocean–sediment
continuum. The bulk material is composed of a complex mixture of different
organic carbon compounds that can be described by a reactivity continuum.
Microbes preferentially degrade the more reactive organic matter compounds
first (Emerson and Hedges, 1988; Wakeham et al., 1997; Lee et al., 2000), resulting in the preferential preservation of more
unreactive compounds and rendering the remaining mixture less and less
reactive with time. Thus, depending on the age of OM (or depth in the water
and sediment column) the reactivity distribution of its compounds changes
significantly (Fig. 10c) and the multi-G (2G in this
case) approximation of this continuum has to take this shift into account.
Figure 10 illustrates these changes in the original
reactivity distribution within an ocean–sediment framework. The reactivity
distribution *t*<1 year represents the organic matter mixture after it
settled through the water column (Fig. 10c). Only the
most reactive OM compounds are remineralised. This explains why the POC flux
in the ocean can be represented with a 1G or pseudo 2G degradation model. In
the sediments, however, much longer timescales have to be considered and a
wider range of more unreactive compounds are degraded. As a consequence,
significant changes in the reactivity distribution already take place in the
upper millimetres of the sediments (*t*∼10 years;
Fig. 10c). Therefore, a broader range of OM reactive
types must be represented by the degradation model to capture the reactivity
spectrum of OM in surface sediments, explaining why at least a pseudo 3G
model (including two degradable and one refractory
fraction; Soetaert et al., 1996; Boudreau, 1997; Stolpovsky et al., 2015) is required. To complicate the situation even
further, different sediment depths can represent very different timescales.
For instance, half a metre of sediment can be deposited within a year in a
coastal setting, while it will represent thousands of years (if not more) of
sedimentation in a deep ocean setting. Therefore, residence times and thus
degradation rate timescales (or OM age) are mainly controlled by sediment
accumulation
rates. For instance, assuming a sediment accumulation
rate of
0.01 cm yr^{−1} for the shallow ocean, OM at 5 cm of depth has been
degraded for approximately 500 years, whereas a deep ocean sediment
accumulation
rate of 0.001 cm yr^{−1} allowed
for OM degradation of approximately 5000 years at the same depth. As a
consequence, organic matter degradation in deep ocean sediments affects a
much wider range of the reactivity continuum and our simple pseudo 3G
approximation of the complex OM mixture needs to reflect this by allowing for
different *k* and *f* values (Fig. 10c). Furthermore, by
assuming steady state in OMEN-SED we assume that deposition fluxes of OM are
constant over the characteristic timescales of the reaction–transport
processes.

Thus, defining appropriate OM degradation rate constants is a major challenge
and source of uncertainty for diagenetic models. The rate constants in models
are either determined through profile fitting for a specific site or, for
global applications, they are related to a single readily available
characteristic (or master variable) of the local environmental conditions.
For instance, considerable effort has been expended to relate the apparent
rate constant for oxic and anoxic OM degradation to sedimentation rate (*w*)
and various empirical relations have been proposed (Toth and Lerman, 1977; Tromp et al., 1995; Boudreau, 1997). Stolpovsky et al. (2015, 2018) suggested empirically derived approaches to constrain
degradation rate constants in a 2G model on a global scale. These approaches
are derived from present-day observations and might help constrain parameters
for present-day applications. However, the problem of constraining 2G
degradation model parameters remains for largely different environmental
conditions encountered in the past that could also prevail in the future
(Arndt et al., 2013). We hence test several alternative schemes in
the coupled OMEN–cGENIE framework. Our objective is not to perform and
discuss a detailed calibration of the coupled models as this is beyond the
scope of this sediment model development paper. Rather, we want to showcase
the feasibility of the model coupling, illustrate the range of results and
thus the information that can be generated with OMEN-SED, and verify that the model
results capture the main observed global benthic biogeochemical features.

In this section we compare modelled mean POC weight percentages (wt %) in
the upper 5 cm of the sediments (POC_{5 cm}) to the global
distribution pattern of POC content in surface sediments (< 5 cm sediment
depth) of Seiter et al. (2004) using different parameterisations for
the degradation rate constants *k*_{1} and *k*_{2}. For our observational target
we take the original POC distribution pattern in $\mathrm{1}{}^{\circ}\times \mathrm{1}{}^{\circ}$ grid resolution (interpolated from > 5500 measurements;
compare to Seiter et al., 2004) and transform it onto the 72×72
SEDGEM grid (Fig. 11). The re-gridding of the
original POC distribution obviously affects the resolution of the data,
especially for the continental margin, as some sites with higher POC wt %
are lost in the re-gridding process (compare e.g. maximum values for the
eastern
Pacific and upwelling waters of the Namibian shelf;
Fig. 11a, b). The colour of the points in
Figs. 12–13
indicates the sea-floor depth (SFD) of the respective cGENIE grid cell. As the
individual data points are highly scattered and in order to see if a certain
relation between *k*_{1} and *k*_{2} performs better for specific ocean depths,
the data points are binned into six uniform depth classes of 1000 m each
(respective mean POC wt % and SFD are represented by the triangles). The
regression line is calculated for the six bin classes and included in the
figures.

To parameterise the reactivity of organic matter in OMEN-SED two different
schemes are tested and compared. First, spatially uniform degradation rate
constants *k*_{1} and *k*_{2} are assumed. By simulating two different pools of
POC in the water column characterised by different degradation length scales
(Ridgwell et al., 2007), cGENIE implicitly accounts for the decrease in
mean POC reactivity with water depth. The rate constants for the more
refractory OM pool, *k*_{2}, are systematically varied and the more labile OM
component, described by *k*_{1}, is assumed to degrade multiple times faster.
Values for these parameters are selected in accordance with the best fit to
the global surface POC observations (Seiter et al., 2004). Although
accounting for the decrease in mean POC reactivity with sea-floor depth, this
approach does not take into account the change in the distribution of organic
matter reactivity types caused by different sediment accumulation rates and thus different
residence timescales in the sediments (Fig. 10).
Therefore, the second approach uses the empirical relationship proposed by
Boudreau (1997), which relates the apparent OM degradation
rate constant in the upper sediments to the sediment accumulation rate, *w* (cm yr^{−1}; see
also Sect. 3.3):

$$\begin{array}{}\text{(53)}& {\displaystyle}{k}_{\mathrm{app}}=\mathrm{0.38}\cdot {w}^{\mathrm{0.59}}.\end{array}$$

Following Boudreau (1997) and Stolpovsky et al. (2015)
it can be assumed that *k*_{app} represents the mean OM reactivity
within the upper 10–20 cm of the sediments. The following assumptions are
made in order to calculate the two degradation rate constants for OMEN-SED:

$$\begin{array}{}\text{(54)}& {\displaystyle}{k}_{\mathrm{app}}& {\displaystyle}={f}_{\mathrm{1}}\cdot {k}_{\mathrm{1}}+(\mathrm{1}-{f}_{\mathrm{1}})\cdot {k}_{\mathrm{2}},\text{(55)}& {\displaystyle}{k}_{\mathrm{1}}& {\displaystyle}=x\cdot {k}_{\mathrm{2}},\end{array}$$

where *x* describes the relation between *k*_{1} and *k*_{2} and is subject to
sensitivity experiments (with values of $x\in \mathit{\{}\mathrm{2},\mathrm{5},\mathrm{8},\mathrm{10},\mathrm{12},\mathrm{15},$ 20,25*}*). Note that the difference between *k*_{1} and *k*_{2} using this approach
is significantly larger as in the globally uniform approach. As the fractions
of labile and refractory OM reaching the sediments *f*_{1} is known from
cGENIE, *k*_{1} and *k*_{2} can be calculated independently for each grid cell.

To simulate steady-state sediment composition we configure the model as a
“closed” system, i.e. one in which there is no loss of CaCO_{3}
through burial. The redox-dependent P cycle in OMEN-SED is not used in these
experiments and all organic phosphorus is returned at the sea floor. To speed
up the calculation and to ensure that ocean redox changes caused by OMEN-SED
do not impact the sediment composition of CaCO_{3}, we use the
prescribed solid fields as described earlier. Apart from the prescribed
fields and the 72×72 sediment grid the model is configured as in
Archer et al. (2009) and atmospheric CO_{2} is restored to a
pre-industrial value of 278 ppmv. First a 20 000 year spin-up is performed
without OMEN-SED being coupled. All presented coupled cGENIE–OMEN simulations
are run for 10 000 years to steady state from this spin-up. OMEN-SED is
called for each grid cell in every time step, feeding back the resulting
SWI fluxes and the fraction of POC preserved in the sediments to cGENIE.

Figure 12 presents results for the
relationship of Boudreau (1997) using the assumptions of
Eqs. (54) and (55) to
calculate *k*_{1} and *k*_{2}. Here, the relation between the two degradation
rate constants (Eq. 55) is changed globally and thus
independent of the sea-floor depth. The cross plots show that it is not
possible to achieve a solution in which all bin classes fall onto or close to
the 1:1 line. Also, the slope of the regression lines is generally much
larger or smaller than 1.0 (with the exception of
Fig. 12c), indicating that the
relationship between depth and observed POC wt % by bin class is not
adequately represented by the model. When looking at the individual bin
classes it can be seen that shallow ocean depths are better represented by
smaller differences between *k*_{1} and *k*_{2} (e.g. ${k}_{\mathrm{1}}=\mathrm{5}\cdot {k}_{\mathrm{2}}$ for
SFD < 1000 m; Fig. 12b) and the deep
ocean by a larger spread (e.g. ${k}_{\mathrm{1}}=\mathrm{25}\cdot {k}_{\mathrm{2}}$ for SFD > 3000 m;
Fig. 12h). These results reflect the
preferential degradation of more reactive organic matter types
(Wakeham et al., 1997; Lee et al., 2000) and thus the change
in the distribution functions of OM reactive types for different OM ages
(Fig. 10c). In the shallow ocean bulk POC consists of
fresher organic matter types on average and is therefore generally more
reactive overall (i.e. higher *k*_{app} due to higher *w* in the
model) as in the deep ocean. In addition, OM at 5 cm of sediment depth in
the deep ocean is generally older than in the shallow ocean due to lower
sediment accumulation rates, and therefore more
reactive types are affected by degradation and a larger spread between *k*
values is needed to capture these dynamics (compare to
Fig. 10c).

Departing from our theoretical considerations (see discussion of
Fig. 10c), we use these observations to create a depth-dependent relationship between the two degradation rate constants, where *x*
in Eq. (55) is a function of SFD and takes values of
*x*=5 for SFD < 1000 m, *x*=8 for 1000 m ≤ SFD < 2000 m,
*x*=12 for 2000 m ≤ SFD < 3000 m and *x*=25 for
SFD ≥ 3000 m for the six SFD bin classes, respectively.
Figure 13 compares this depth-dependent
approach with the best model using spatially uniform degradation rate
constants (*k*_{2}=0.005, ${k}_{\mathrm{1}}=\mathrm{1.3}\cdot {k}_{\mathrm{2}}$). In the depth-dependent
approach all bin classes are close to the 1:1 line and the slope of the
regression line (0.9662) indicates that the relationship between depth and
observed POC wt % for the bin classes is well represented by the model
(Fig. 13a). Using spatially uniform
degradation rate constants, five of the six bin classes are located close to the
1:1 line (Fig. 13b), indicating that
the simpler parameterisation also adequately captures the relationship
between depth and observed POC wt % by bin class. The reason for this is
that BIOGEM provides a depth-dependent POC flux and partitioning between the
two fractions (Fig. 10). The shallowest bin class
(between 0 and 1000 m) represents an exception, as OMEN-SED tends to
overestimate POC preservation for this depth class. However, this could also
be related to the re-gridding of the original POC distribution pattern of
Seiter et al. (2004) onto the SEDGEM grid, as some data grid cells
with higher POC wt % on the continental margin are lost due to the
restricted SEDGEM resolution (compare
to Sect. 4.2). The histograms
(Fig. 13c, d) visualise the difference
between modelled and observed mean POC concentrations and demonstrate the
high density of data points close to the 1:1 line. For the depth-dependent
approach, 92.5 % of the cGENIE grid cells show a difference between
modelled and observed POC concentration of less than 1.0 POC wt %; in
79.9 % of the grid cells, the difference is less than 0.5 POC wt % (for
the globally uniform approach the percentages are 95.37 and 70.95 %).

Both experiments reproduce minimal POC concentrations in the subtropical gyres and generally higher concentrations along the continental margins (Fig. 13e, f). Both experiments, however, underestimate mean POC wt % in the surface sediments of the equatorial eastern Pacific and overestimate POC concentrations in the North Pacific and Southern Ocean (Fig. 13g, h). The depth-dependent approach of Boudreau (1997) shows more spatial variability in POC preservation than the other parameterisation. In general, implementing lower anaerobic degradation rate constants when bottom water oxygen concentrations fall below a threshold value could potentially improve the simulation of higher POC concentrations in areas with high POC input to the sediments (Palastanga et al., 2011).

For the depth-dependent Boudreau (1997) approach modelled
SWI fluxes and sediment characteristics are shown in
Fig. 14. Modelled total POC degradation
(POC_{degr}) rates in the upper sediments decrease from the shelves to
the deep sea by up to 2 orders of magnitude
(Fig. 14b). This is in agreement with
data from the literature (e.g. Middelburg et al., 1993, 1997; Burdige, 2007) and other model results
(e.g. Thullner et al., 2009) which indicate that the highest
degradation rates in marine sediments are found in the coastal ocean
(SFD < 200 m). Oxygen fluxes into the sediments
(Fig. 14c) range from 0.0 for the deep
ocean and sites without OM deposition to values of about 300 µmol cm^{−2} yr^{−1} for the shallow ocean with the highest POC degradation
rates. Influx of SO_{4} into the sediments is rather low (between 0.0
and 23.9 µmol cm^{−2} yr^{−1}) because in OMEN-SED 95 % of produced
H_{2}S is reoxidised to SO_{4}, and therefore sulfate reduction is
mainly driven by in situ sulfide oxidation. However, in general the coupled
model fluxes fall well within the ranges predicted by the stand-alone global
hypsometry experiments (O_{2} between 0.0 and
800 µmol cm^{−2} yr^{−1} and SO_{4} between 0.0 and
about 300 µmol cm^{−2} yr^{−1}; compare to
Sect. 3.3). In accordance with the total POC
degradation rates the release of PO_{4} shows a maximum value of
8.12 nmol cm^{−2} yr^{−1} on the shelves
(Fig. 14d). The relative contribution of
aerobic POC degradation in the upper sediments increases from the shelves to
the deep sea (Fig. 14g), which is also
consistent with estimates from Thullner et al. (2009) who found
that oxygen is responsible for less than 10 % of POC_{degr} at
100 m SFD and for more than 80 % in the deep sea. The oxygen penetration
depth in OMEN-SED increases from values below 1 cm at the shelves to more
than 10 cm in the deep ocean (Figs. 14h
and 15). Small oxygen
penetration depths of a few millimetres are typical for bioturbated sediments
in the coastal ocean (e.g. Wenzhöfer and Glud, 2002) and the oxygen
penetration depth has been shown to increase rapidly with SFD to more than
10 cm in the deep sea (Meile and Van Cappellen, 2003; Glud, 2008).
Fischer et al. (2009) and D'Hondt et al. (2015) even found cores
along a transect in the South Pacific gyre being oxygenated over their entire
length (up to 8 m or even 75 m, respectively), which is consistent with our
model results (not shown). Simulated mean oxygen penetration depths for the
six
depth bin classes also agree well with observations compiled by
Glud (2008) and
Meile and Van Cappellen (2003, Fig. 15).

5 Scope of applicability and model limitations

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Because of the high computational cost associated with resolving benthic dynamics, most Earth system models of intermediate complexity (EMICs) and also some of the higher-resolution Earth system models either completely neglect or merely include a highly simplified representation of benthic–pelagic exchange processes (Hülse et al., 2017). However, benthic–pelagic coupling plays an important role for carbon cycling and the lack of its representation in EMICs compromises our ability to assess the response and recovery of the Earth system to major past, present and future carbon cycle and climate perturbations. As a consequence, there is a need for benthic biogeochemical models that are able to capture the main features of benthic biogeochemical dynamics, but that are at the same time computationally efficient enough to allow for a direct, dynamic coupling to an ocean biogeochemical model. Therefore, we have developed OMEN-SED, a one-dimensional analytical early diagenetic model that offers a predictive ability similar to complex, numerical diagenetic models at a significantly reduced computational cost.

OMEN-SED is thus not problem specific. Its reaction network resolves the most pertinent benthic biogeochemical species and the most important processes that control their cycling and burial in marine sediments. OMEN-SED can thus be coupled to a wide range of regional to global ocean biogeochemical models, EMICs and higher-resolution Earth system models to investigate a wide range of research questions associated with past, present or future carbon and macronutrient cycling. For instance, OMEN-SED can be used to (i) quantify benthic macronutrient recycling from the shallow coastal to the deep open ocean, (ii) investigate the role of benthic–pelagic coupling in the development of past or future ocean anoxia–euxinia, or to (iii) estimate global organic carbon burial in marine sediments. In theory, its scope of applicability thus ranges from the regional to the global and from the seasonal to the millennial timescale. In order to simulate organic matter preservation in the deeper sediments and thus address questions concerning long-term, geological carbon burial the degradation rate constant for the refractory OM pool has to be scaled down. The resulting larger difference between degradation rate constants can be interpreted as being needed to capture the broader range of OM reactivities degraded over the entire sediment column (see Fig. 10). Instead, more collapsed degradation rate constants are needed to model OM degradation in the upper sediments, such as the first 5 cm as shown in Sect. 4.2.2. In addition, the computational efficiency of OMEN-SED allows for the calculation of quantitative sensitivity indices requiring large sample sizes such as variance- or density-based approaches. Therefore, OMEN-SED can also help quantitatively investigate the sensitivity of benthic model output to systematic variations in model parameters when the model has been tuned to a site-specific problem.

However, OMEN-SED is inevitably associated with a certain degree of simplification that may compromise the applicability of the model in its current version under certain circumstances. First, we have assumed steady-state conditions to allow for an analytical solution to the coupled diagenetic equations. This steady-state assumption is only valid if the variability in boundary conditions and fluxes is generally longer than the characteristic timescales of the reaction–transport processes. As a consequence, OMEN-SED is well suited for coupling to EMICs and the investigation of long-term dynamics in sediment–water exchange fluxes, for instance during past extreme climate events. Yet, in its current version, OMEN-SED is not able to predict the transient response of benthic process rates and fluxes to short-term or seasonal variations in boundary conditions. Future versions of OMEN-SED could approximate non-steady-state conditions by incorporating a time-step-dependent relaxation between different steady states, similar to the schemes used in Ruardij and Van Raaphorst (1995) and Arndt and Regnier (2007). Such a pseudo-transient approach would enable the application of OMEN-SED to systems characterised by high-frequency fluctuations in boundary conditions, such as the coastal ocean or estuaries. Furthermore, by their very nature, analytical models do not allow for overlapping biogeochemical zones or depth-dependent porosity, which introduces a certain error to simulation results. However, the energy-yield-dependent sequence of oxidants is generally valid (e.g. Hensen et al., 2006) and the good agreement between OMEN-SED and the results obtained with a fully formulated numerical RTM (allowing for overlapping TEA use and depth-dependent porosity; Sect. 3.3) shows that these are not critical limitations of OMEN-SED, even for shallow sediments.

Although the model explicitly simulates DIC and alkalinity production and
thus has the potential to predict pH profiles within the sediment, a major
limitation at this stage is the lack of an explicit description for
CaCO_{3} precipitation and dissolution coupled to OM decomposition, which
also controls the inorganic carbon system (Krumins et al., 2013). In
addition, the current version of OMEN-SED does not yet explicitly resolve
iron and manganese dynamics (although note that iron is implicitly accounted
for in the PO_{4} equation). This lack currently limits the
applicability of OMEN-SED to iron- and manganese-rich environments, such as
coastal marine environments, upwelling regions or ferruginous oceans. In
addition, it also compromises the ability of OMEN-SED to predict
H_{2}S fluxes in Fe-rich anoxic environments, where high iron pore water
concentrations can deplete pore water H_{2}S by iron-sulfide mineral
precipitation (e.g. Meyers, 2007). Therefore, already
planned future extensions of OMEN-SED include an explicit description of
carbonate dissolution and iron. Also note that our 1-D diffusion–bioturbation
model might not be appropriate to simulate non-accumulating permeable sands
of the coastal ocean.

Finally, just as all global models, the global application of OMEN-SED is
complicated by the lack of an objective global framework for biogeochemical
process parameterisation. The sensitivity study presented here shows that
this lack is particularly critical for OM degradation rate parameters (*k*_{i},
*f*_{i}) and the *γ* values describing the completeness of secondary redox
reactions. A comparison between simulated OM contents and observations
indicates that a depth-dependent *k*−*f* relationship provides the best fit
(Sect. 4.2.2). These results confirm that
reducing the continuous distribution of organic matter reactivities into two
distinct reactivity classes (2G model) requires different *k*−*f* values for
shallow vs. deep ocean sediments because of the largely different reaction
timescales involved (also see Fig. 10). With respect to
*γ* values, model simulations along the global hypsometry
(Sect. 3.3) have shown that high *γ* values
generally capture the main SWI flux features, but have also highlighted that
slightly lower *γ* values would result in a better fit of SWI fluxes to
observations of the shallow ocean.

6 Conclusions

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Here, we have described in detail and tested OMEN-SED, a new, analytical
early diagenetic model resolving organic matter cycling and the associated
biogeochemical dynamics. OMEN-SED has been explicitly designed for coupling
to EMICs and combines biogeochemical complexity with computational
efficiency. It is the first analytical diagenetic model to implicitly
represent methanogenesis and explicitly
represent oxic degradation, denitrification and sulfate reduction,
as well as the
reoxidation of reduced substances, adsorption and desorption, and mineral
precipitation and dissolution. Explicitly resolved pore water species include
O_{2}, NO_{3}, NH_{4}, SO_{4}, H_{2}S, DIC
and ALK and the solid phase includes two degradable fractions of
organic matter, Fe-bound P and authigenic Ca–P minerals.

An extensive sensitive analysis based on the density-based PAWN method
(Pianosi and Wagener, 2015) emphasises the importance of OM degradation rate
parameters (*k*_{i}, *f*_{i}) and thus highlights the need for the development of
an objective global framework to parameterise OM degradation rate
parameters. We have shown that the performance of OMEN-SED at the system
scale is similar to that of a fully formulated, multi-component numerical
model. The new analytical model is able to reproduce observed pore water
profiles across a wide range of depositional environments and captures
observed global patterns of SWI fluxes, oxygen penetration depths,
biogeochemical reaction rates and surface sediment organic matter
contents. Coupled to EMICs or higher-resolution Earth system models, OMEN-SED
is thus well suited to examine the role of sediments in global biogeochemical
cycles in response to a wide range of past or future carbon cycle or climate
perturbations over various timescales.

Code availability

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Code availability.

The OMEN-SED source code (FORTRAN and MATLAB) is provided as a Supplement to this article and is also available for download on the web (Hülse et al., 2018). A ReadMe file for the stand-alone MATLAB version of OMEN-SED describes the source code files and includes instructions for executing the model and plotting the results.

Appendix A: Reaction network

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Appendix B: Sensitivity analysis

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Appendix C: Prescribed burial flux fields

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Supplement

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Supplement.

The supplement related to this article is available online at: https://doi.org/10.5194/gmd-11-2649-2018-supplement.

Author contributions

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Author contributions.

DH and SA designed and implemented the model. SD designed and implemented the boundary matching algorithm and helped with the general code development. DH and AR coupled the two models. DH carried out the simulations and analysed the results. All authors contributed to the design of the simulations, the analysis of the results and the writing of the paper.

Competing interests

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Competing interests.

The authors declare that they have no conflict of interest.

Acknowledgements

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Acknowledgements.

We would like to thank Klaus Wallmann and two anonymous
reviewers for their constructive critiques and insightful comments,
which have improved the paper. We thank Claire Reimers, Filip Meysman,
Martin Thullner, Jack Middelburg, Andy Dale, Katherina Seiter, Christof Meile, Ronny Glud
and the British Oceanographic Data Centre for supplying
the datasets and model results used in this study. We
are also grateful to Francesca Pianosi for helpful insights into sensitivity
analysis. Dominik Hülse was supported by a graduate teaching studentship by
the University of Bristol and a Heising–Simons Foundation award. Sandra Arndt acknowledges funding from the UK Natural Environmental Research Council
(NERC) grant no. NE/I021322/1 and Stuart Daines from the grants NERC JET
(NE/N018508/1) and NERC BETR (NE/P013651/1). Sandra Arndt and
Pierre Regnier were supported by funding from the
European Union Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 643052 (C-CASCADES). Andy Ridgwell
was supported by a Heising–Simons Foundation award and by EU grant
ERC-2013-CoG-617313.

Edited by: Andrew Yool

Reviewed by: Klaus Wallmann and two anonymous referees

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Short summary

We present a 1-D analytical diagenetic model resolving organic matter (OM) cycling and the associated biogeochemical dynamics in marine sediments designed to be coupled to Earth system models (ESMs). The reaction network accounts for the most important reactions associated with OM dynamics. The coupling is described and the OM degradation rate constant is tuned. Various observations, such as pore water profiles, sediment water interface fluxes and OM content, are reproduced with good accuracy.

We present a 1-D analytical diagenetic model resolving organic matter (OM) cycling and the...

Geoscientific Model Development

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