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Journal of Geophysical Research: Biogeosciences
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Supporting Information for
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Chesapeake Bay nitrogen fluxes derived from a land-estuarine ocean biogeochemical
modeling system: Model description, evaluation and nitrogen budgets
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Yang Feng1, Marjorie A. M. Friedrichs1, John Wilkin2, Hanqin Tian3, Qichun Yang3, Eileen E.
Hofmann4, Jerry D. Wiggert5 and Raleigh R. Hood6
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1Virginia
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2Institute
3International
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Institute of Marine Science, College of William and Mary, Gloucester Point, Virginia
of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey
Center for Climate and Global Change Research and School of Forestry and Wildlife Sciences, Auburn
University, Auburn, Alabama
4Center
5Department
6Horn
for Coastal Physical Oceanography, Old Dominion University, Norfolk, Virginia
of Marine Science, University of Southern Mississippi, Stennis Space Center, Mississippi
Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland
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Contents of this file
Model Equations for Biogeochemistry
Additional Supporting Information (Files uploaded separately)
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Model Equations for Biogeochemistry
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The biogeochemical source/sink equations for the estuarine biogeochemical model state
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variables that specifically pertain to the nitrogen cycle are described in the below text as well as
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summarized in Tables A1 and A2. Model function symbols are defined in Table A3, and
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parameter definitions and values are provided in Table A4 (see appendix in the text).
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Phytoplankton
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Phytoplankton are increased by primary production and decreased by grazing, mortality,
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aggregation and sinking. Two additional processes, exudation to semi-labile DON and
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ammonium were added. The exudation to ammonium pool was limited by coupled water column
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nitrification/denitrification through the low oxygen condition. Changes in phytoplankton due to
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those biological processes are finally determined as:
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¶P
¶P
= [1- g - ( fNTR + fDNF )w ] m0 LI (LNO3 + LNH 4 )P - gZ - mP P - t (DS + P)P - wP
¶t
¶t
(1)
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Chlorophyll
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The sources and sinks of chlorophyll are consistent with those for phytoplankton:
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¶[Chl]
= r[Chl ] [1- g - ( f NTR + fDNF )w ] m 0 LI (LNO3 + LNH 4 )[Chl]
¶t
Z
¶[Chl]
-g [Chl]- mP [Chl]- t (DS + P)[Chl]- wP
P
¶z
(2)
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Zooplankton, Small and large detritus
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The zooplankton source term is the assimilation of phytoplankton. The loss terms represent
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excretion and mortality. The efficiency of the assimilation is β, and the remainder (1- β)Z is lost
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to semi-labile DON and ammonium through sloppy feeding and to large detritus by fecal pellet
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production.
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æ
¶Z
P2 ö
= b gZ - ç lBM + lE b
Z - mZ Z 2
2÷
¶t
KP + P ø
è
(3)
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Small and large detritus
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Phytoplankton and zooplankton mortality is transferred into the small and large detritus pools,
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respectively. Phytoplankton and small detritus aggregate to large detritus. Following Druon et al.
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[2010], part of the small and large detritus pools are transferred to semi-labile DON by bacterial
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solubilization with an efficiency of δN. The remaining detrital material is remineralized. The
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remineralization rate is limited by water column nitrification and denitrification processes.
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¶DS
¶D
= mP P - t (DS + P)DS - éëdN + (1- dN ) ( fNTR + fDNF )ùû rDS DS - wS S
¶t
¶z
(4)
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¶DL
¶D
= (1- b )(1- l )gZ + mZ Z 2 + t (DS + P)2 - éëdN + (1- dN ) ( fNTR + fDNF )ùû rDL DL - wL L
¶t
¶z
(5)
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Semi-labile and refractory DON
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Semilabile DON may be gained through phytoplankton exudation, sloppy feeding, bacterial
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solubilization, and lost through remineralization. The rate of remineralization is limited by
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temperature as well as nitrification/denitrification.
¶[DON ]SL
= gm0 LI (LNO3 + LNH 4 )P + (1- b )le gZ + d N (rDS DS + rDL DL )
¶t
k[ DON ]SL T
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-r[ DON ]SL e
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The refractory DON does not participate directly in the biogeochemical cycling, however it does
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affect light attenuation.
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Nitrate
( fNTR + fDNF )[DON ]SL
(6)
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Nitrate is taken up by phytoplankton during photosynthesis and produced through nitrification. In
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addition, nitrate is lost to the atmosphere as nitrogen gas through water column denitrification,
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the rate of which is limited by the availability of oxygen. The time rate of change due to
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biological process for nitrate is:
¶[NO3 ]
k
T
= -m0 LI LNO3 P - hDNF éë fDNF, fWC ùûmin (1- dN ) ( rDS DS + rDL DL ) + r[ DON ]SL e [ DON ]SL [DON ]SL
¶t
{
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+ nf NTR [NH 4 ]
}
(7)
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Ammonium
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The sources of ammonium include phytoplankton exudation and sloppy feeding, zooplankton
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excretion, and remineralization of small detritus, large detritus and semi-labile organic nitrogen.
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The sinks of ammonium include nitrification and uptake by phytoplankton. The time rate of
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change due to biological processes for ammonium is:
é
æ
¶[NH 4 ]
P 2 öù
= m0 éë-LNH 4 + ( f NTR + fDNF )(LNO3 + LNH 4 )w ùû LI P + ê(1- b )l (1- e )g + ç lBM + lE b
÷ú Z
¶t
K P + P 2 øû
è
ë
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{
+( f NTR + fDNF ) (1- dN ) ( rDS DS + rDL DL ) + r[ DON ]SL e
k[ DON ]SL T
}
[DON ]SL - nf NTR [NH 4 ]
(8)
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Inorganic Suspended Solids
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Inorganic suspended solids do not participate in the water column biogeochemical cycle,
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however they do affect light attenuation. Concentrations of ISS are reduced by sinking and
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increased by seabed resuspension.
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¶[ISS]
¶[ISS]
= -wISS
¶t
¶z
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Dissolved Oxygen
(9)
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The oxygen increased or decreased due to the above biological processes with the
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stoichiometry
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ammonium. The phytoplankton exudated semi-labile DOC during photosynthesis. The semi-
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labile DOC exudation process does not follow the Redfield ratio. Druon et al. [2010] describe a
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carbon excess-based semi-labile DOC exudation process, which is the carbohydrate production
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over the nutrient-based part. The oxygen produced by the synthesis of carbohydrates (carbon
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excess uptake) has a one to one molar ratio following the equation: CO2 +H20 + energy ->
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(CH2O) + O2. The oxygen uptake from oxidation of DON with a C to N ratio of
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therefore, the oxygen production by this part is
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hO :NO =138 :16 and hO2 :NH4 =106 :16 when consuming 1 mole of nitrate or
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hC:N = 6.6,
g ChC:N m0 LI (1- LNH - LNO )P .
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In addition to the biochemical sources and sinks of oxygen, there is gas exchange
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across the air-sea interface, which modified the oxygen concentration in the top layer. The air-
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sea oxygen exchange was calculated as
vkO2
vkO2 Dz ([O2 ]sat -[O2 ])
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where
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calculated from Garcia and Gordon [1992].
is the gas exchange coefficient for oxygen, and
as in Fennel et al. [2013],
[O2 ]sat
is the oxygen saturation
¶[O2 ]
= +m0 éëhO2 :NO3 LNO3 + hO2 :NH 4 LNH 4 - hO2 :NH 4 f NTRw (LNO3 + LNH 4 )ùû LI P
¶t
é
æ
P 2 öù
-hO2 :NH 4 ê(1- b ) l (1- e ) g + ç lBM + lE b
÷ú Z
K P + P 2 øû
è
ë
{
-hO2 :NH 4 f NTR (1- dN ) ( rDS DS + rDL DL ) + r[ DON ]SL e
k[ DON ]SL T
[DON ]SL
}
-2 f NTR n[NH 4 ]
+g ChC:N m 0 LI (1- LNH 4 - LNO3 )P
+v
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KO2
Dz
([O2 ]sat -[O2 ])
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Bottom boundary conditions
(10)
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The fate of organic matter reaching the benthos includes: (1) resuspension; (2) remineralization;
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(3) burial. The resuspension of the organic matter is back to the water column as DS. The
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fraction of resuspension is ϕ1, which is a function of the bottom stress [Druon et al. 2010]:
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2
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f1 = G Gc , where G = t b + t b is the bottom shear stress, Gc = 0.05Pa is the critical shear
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stress [Xu and Hood, 2006]. Therefore, the time rate of change of small detritus in the model’s
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bottom layer is:
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x
¶DS
¶t
=
z=H
f1
Dz
y
FTON
(11)
FTON = wP P z=H + wDS DS
z=H
+ wDL DL
z=H
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where
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0.5797
f2 = 0.092FBC
, where a maximum of 75% of carbon burial efficiency is applied [Druon et al.
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2010] and
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hC:N wP P z=H + hC :N (wD DS z=H + wD DL z=H ) h =106 /16
C:N
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phytoplankton.
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The rest (1- ϕ1)(1- ϕ2) is remineralized through coupled nitrification and denitrification processes
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in the benthos. The regeneration of the organic matter includes the ammonium form and semi-
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labile DON form, and follows the implementation for sediments below normal oxic waters
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described in Fennel et al. [2006, see their eq. 15]. To account for the observed shift in benthic
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influx and efflux rates that occurs below hypoxic to anoxic overlying waters [Rysgaard et al.,
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1994], an additional term is included to regulate these benthic regeneration rates in response to
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the seasonal transition to hypoxic in the overlying waters. i.e., as hypoxia in the overlying water
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column intensifies, the benthic nitrification-denitrification balance will shift toward the latter.
FBC
is the flux of total organic carbon in the sediment, which is
B
B
S
L
.
is the carbon to nitrogen ratio in
hC :N = 9.3 is the carbon to nitrogen ratio in bottom small and large detritus.
B
B
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. The fraction of the buried organic matter is
The amount of NH4 regenerated is:
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¶[NH 4 ]
(1- f1 )(1- f2 )
= hNF/DNF
FTON (1+ 3LBO2 )
¶t z=H
Dz
LBO2 =
(12)
K BO2
fB (O2 ) - fB (O2max ) f (O ) =
B
2
O2 z=H + K BO2 K BO
1- fB (O2max ) ,
2 is the half-saturation coefficient
,
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Where
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for sediment denitrification, and equals 26.5 mmole-O m-3.
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The amount of semi-labile DON regenerated is:
¶[DON]SL
¶t
= g [ BDON ]SL
z=H
(1- f1 )(1- f2 )
FTON (1+ 3LBO2 )
Dz
(13)
g[ BDON ] = 0.01 is the fraction of bottom semilabile DON produced through coupled
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Where,
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nitrification and denitrification.
SL
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The oxygen consumption during this process is:
¶[O]2
¶t
= -hO2 :NF/DNF
z=H
(1- f1 )(1- f2 )
FTON (1- LBO2 )
Dz
(14)
hNF/DNF and hO :NF/DNF are stoichiometric relations drawn from Fennel et al. [2006].
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The terms
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The term
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and denitrification.
2
h[ BDON ] is the fraction of bottom semilabile DON produced through coupled nitrification
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At the bottom, particles that hit the bottom are resuspended when bottom stress exceeds critical
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shear stress, which is calculated by [Xu and Hood, 2006]
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1
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is the resuspension rate.
x ( G - Gc )
, where
x = 4320 gm-2d-1Pa-