2514 
F. Große et al.: Looking beyond stratification 
Biogeosciences, 13, 2511-2535, 2016 
www.biogeosciences.net/13/2511/2016/ 
A further sink of O2 is nitrification, the bacterial transfor 
mation of ammonium to nitrate. Within ECOHAM, this pro 
cess is light-dependent and links the O2 cycle to the N cycle. 
Nitrification only occurs under aerobic conditions (i.e., con 
centrations > OmgCE L _1 ), which is a realistic constraint for 
the pelagic North Sea environment. It is light-dependent, be 
ing stronger under low light conditions. Pelagic denitrifica 
tion is implemented, but is negligible as it only occurs un 
der anaerobic conditions. Pelagic anaerobic ammonium ox 
idation (anammox) is not implemented, however, it can be 
neglected for the same reason. Except for primary produc 
tion, the biological processes involved in the Ot cycle are 
not temperature-dependent in the present model setup. 
For the representation of the benthic remineralisation pro 
cesses a simple sediment module is used. A layer of zero ex 
tent is defined below the deepest pelagic layer of each water 
column. There the deposited organic matter is collected and 
remineralised (Patsch and Ktihn, 2008). The benthic reminer 
alisation of the organic matter is defined as a first-order pro 
cess with relatively high remineralisation (C, N, P) and disso 
lution rates (Si; opal) preventing year-to-year accumulation 
of deposited matter. The released dissolved inorganic matter 
is returned directly into the pelagic bottom layer. Different 
rates are applied to organic C, N, P and Si resulting in differ 
ent timescales for the release into the pelagic. In ECOHAM, 
the O2 cycle is affected by the benthic remineralisation in 
a direct and indirect way. First, the remineralisation in the 
sediment is accompanied by the direct reduction of the O2 
concentrations in the pelagic bottom layer above. Second, in 
organic nitrogen is released from the sediment in the form of 
ammonium, which can be nitrified within the water column 
under O2 consumption. According to Seitzinger and Giblin 
(1996), who suggested a tight coupling between benthic ni 
trification and denitrification, benthic denitrification depends 
on the benthic O2 consumption in our model. Direct benthic 
nitrification and benthic anammox are neglected as the sedi 
ment has zero vertical extent (Patsch and Ktihn, 2008). 
For a more detailed description of the ECOHAM model, 
including the full set of the differential equations and pa 
rameter settings of ECOHAM, the reader is referred to 
Lorkowski et al. (2012). A detailed description and analysis 
of the O2 module can be found in Müller (2008). 
2.1.1 Model setup and forcing data 
The model domain extends from 15.250° W to 14.083° E and 
from 47.583 to 63.983° N and comprises the entire North 
Sea, large parts of the northwestern European continental 
shelf and parts of the adjacent northeastern Atlantic. The hor 
izontal resolution is 1 /5° with 82 grid points in latitudinal di 
rection and 1 /3° with 88 grid points in longitudinal direction. 
The horizontal grid of the model domain is shown in Fig. 2. 
The vertical dimension with a maximum depth of 4000 m is 
resolved by 31 z-layers with a surface layer of 10 m. The 
vertical has a resolution of 5 m between 10 and 50 m depth. 
Figure 2. Horizontal grid and bottom topography of the 
HAMSOM-ECOHAM model domain. White numbers indicate 
depth levels. Yellow boxes A-D mark the 4x4 regions used for the 
characterisation of key features presented in Sect. 3.3. Black-filled 
boxes (1, 2) mark the validation sites discussed in Sect. 3.1.1. Red 
framed boxes (2-5 ) indicate regions used for the O2 mass balance 
calculations in Sects. 3.4-3.7. 
which is relevant for the calculation of the MLD (Sect. 2.2). 
Below 50 m, the layer thicknesses successively increase with 
depth. 
The model system was run over the period 1977 to 2012. 
HAMSOM was initialised with a monthly-averaged clima 
tology based on the World Ocean Atlas (WOA; Conkright 
et al., 2002). The meteorological forcing was derived from 
NCEP/NCAR reanalysis data (Kalnay et al., 1996; Kistler 
et al., 2001) and provides 6 hourly information for air tem 
perature, cloud coverage, relative humidity, wind speed and 
direction. Short wave radiation was calculated from astro 
nomic insulation and cloud coverage applying a correction 
factor of 0.9 (Lorkowski et al., 2012). The data were interpo 
lated to the model grid and time step according to O’Driscoll 
et al. (2013) and Chen et al. (2014). Daily freshwater run-off 
data for 249 rivers were provided by Cefas and represent an 
updated data set of that used by Lenhart et al. (2010) covering 
the entire simulation period. The same data set encompassed 
nutrient loads used for the ECOHAM. 
At open boundaries, surface elevation was prescribed as 
a fixed (Dirichlet) open boundary condition (OBC) accord 
ing to the M2 tide, while for horizontal transport velocities 
radiation OBCs were applied. For tracers (T and S) radiation 
and radiative-nudging OBCs were used in the case of inflow 
and outflow, respectively. A detailed description of the OBCs