Biogeosciences, 9, 4087-4097, 2012
www.biogeosciences.net/9/4087/2012/
doi: 10.5194/bg-9-4087-2012
© Author(s) 2012. CC Attribution 3.0 License.
Biogeosciences
The role of alkalinity generation in controlling the fluxes of CO2
during exposure and inundation on tidal flats
P. A. Faber1, A. J. Kessler1, J. K. Bull1,1. D. M cKelvie2 3, F. J. R. M eysman4, and P. L. M. Cook1
1 Water Studies Centre, School of Chemistry, Monash University, Victoria 3800, Australia
2School of Chemistry, The University of Melbourne, Victoria 3010, Australia
3School of Geography, Earth and Environmental Sciences, University of Plymouth, Plymouth PL48AA, UK
4Department of Ecosystem Studies, Royal Netherlands Institute for Sea Research (NIOZ), Korringaweg 7, 4401 NT Yerseke,
The Netherlands
Correspondence to: P. A. Faber (peter.faber@monash.edu)
Received: 2 April 2012 - Published in Biogeosciences Discuss.: 9 May 2012
Revised: 3 August 2012 - Accepted: 30 August 2012 - Published: 23 October 2012
Abstract. Dissolved inorganic carbon (DIC), gaseous CO 2
and alkalinity fluxes from intertidal sediments were investi­
gated during periods of exposure and inundation, using lab­
oratory core incubations, previously published field data and
reactive transport model simulations. In the incubations and
previous field data, it was found that during periods of alka­
linity production (attributed to the accumulation of reduced
sulfur species within the sediment), the flux of DIC out of
the sediment was greater during inundation than the gaseous
CO 2 flux during exposure by a factor of up to 1.8. This find­
ing was supported by computational simulations which in­
dicated that large amounts of sulfate reduction and reduced
sulfur burial (FeS) induce an alkalinity flux from the sed­
iment during high tide conditions. Model simulations also
found that the amount of reactive Fe in the sediment was a
major driver of net alkalinity production. Our finding that
CO 2 fluxes can be significantly lower than total metabolism
during exposure has implications for how total metabolism is
quantified on tidal flats.
1
Introduction
Tidal flats are highly dynamic and biogeochemically ac­
tive environments, that are characterised by the deposition
of allochthonous organic matter as well as high in situ
rates of primary production by microphytobenthos (Joye
et al., 2009). The quantification of organic carbon produc­
tion and mineralisation in these environments is compli­
cated by the fact that tidal flats are periodically inundated.
This means that fluxes of inorganic carbon should ideally
be measured both during inundation (as dissolved inorganic
carbon DIC = [CO 2 ] + [HCO(("] + [CO 3 - ]) and exposure (as
gaseous CO 2 ). In practice, the quantification of inorganic
carbon fluxes during the inundation of tidal flats is logistically complex because they are covered by a shallow layer of
turbid water and often experience high currents. Moreover,
the determination of DIC in aqueous samples is also more
time consuming and technically challenging than the analy­
sis of CO 2 in gas samples. Typically, most studies of benthic
metabolism on tidal flats only measure gaseous fluxes of CO 2
during exposure (Migné et al., 2005: Middelburg et al., 1996)
or DIC flux during inundation (Cai et al., 1999).
Relatively few studies have included direct measurement
of inorganic carbon fluxes during both exposure and inunda­
tion of tidal flats and these studies show different outcomes.
Alongi et al. (1999) found very similar exchange rates dur­
ing both inundation and exposure. By contrast, Gribsholt and
Kristensen (2003) and Cook et al. (2004) found consistently
higher rates of inorganic carbon exchange during inundation
on un-vegetated tidal flat sediments, where the flux during in­
undation increased by a factor of ~ 2. A number of possible
explanations exist for these differences. Firstly, solute trans­
port processes are very different between inundation and ex­
posure periods. During inundation, all three forms of the car­
bonate system (CO 2 , HCO^ and CO 3 - ) can be transported
across the sediment interface, whereas during exposure, only
gaseous CO 2 can diffuse into the atmosphere. Furthermore,
Published by Copernicus Publications on behalf o f the European Geosciences Union.
4088
P. A. Faber et al.: The role of alkalinity generation
bio-irrigation is w ell know n to enhance solute exchange in
sedim ents (Kristensen, 1988). T his process w ill cease upon
exposure, and w ould result in a reduction o f the C O 2 flux
during exposure as com pared to the inundated DIC flux. S ec­
ondly, alkalinity generation, caused by the burial o f reduced
m etal sulfides and/or calcium carbonate dissolution, is of­
ten observed at high rates in shallow w aters and intertidal
sedim ents (Thom as et al., 2009; C ook et al., 2004; F ergu­
son et al., 2003). A lkalinity cannot escape the sedim ent dur­
ing low tide and, therefore, w ill tend to accum ulate near the
sedim ent-w ater interface. T his w ill lead to a shift tow ards in2_
creased H C O 3 and CO 3 and decreased C O 2 and, hence, a
reduced gaseous C O 2 flux during exposure.
H owever, there are also reasons w hy the C O 2 flux m ight
be enhanced during exposure. A change in C O 2 transfer
during exposure to the atm osphere m ay occur due to the
higher diffusion o f C O 2 in the atm osphere (IO - 5 com pared
to 1 0 _ 9 m 2 s _1) and the decreased thickness o f the diffusive
boundary layer during exposure (Brotas et al., 1990).
To date, none o f these factors have been explored, exper­
im entally or theoretically. A basic understanding o f the ex­
change dynam ics o f inorganic carbon is required for the d e­
sign o f studies aim ing to quantify the fluxes o f inorganic car­
bon betw een tidal flats and the atm osphere and coastal w a­
ters. H ere, w e used data from controlled laboratory experi­
m ents and a num eric diagenetic m odel to investigate the dy­
nam ics o f inorganic carbon exchange in the intertidal zone.
In particular, w e focus on the role o f alkalinity generation
by anaerobic respiration in the retardation o f the C O 2 efflux
during exposure relative to D IC export to the w ater colum n.
2
2.1
M aterials and m ethods
E xperim ental
M uddy sedim ent (Grain size: 48 % 300 p m -1 mm; 8 % 2 0 0 300 pm ; 3 9 % 100-200 pm; 5 % 6 2 -1 0 0 pm and p oros­
ity = 0.81 m l w ater cm - 3 ) w as collected from an intertidal
flat located in the Yarra Estuary, A ustralia (37.833° S,
145.0229° E). The sedim ent w as sieved (1 m m mesh) to re­
m ove m acrofauna and hom ogenised. T he total inorganic car­
bon content o f the sedim ent w as < 0.1 % w / w . T he sedim ent
w as then placed in a shallow tray and gently stirred w hilst b e­
ing aerated for 1 day to oxidise reduced solutes before being
packed into 8 core liners (7 cm diam eter) to a depth o f 5 cm.
This depth layer w as chosen to represent the diagenetically
active depth. Figure 1 represents the experim ental setup that
w as used. The cores had stirrer bars inserted to gently stir
the w ater colum n. A peristaltic pum p system transferred am ­
bient sea w ater collected from P ort Phillip Bay in and out
o f the cores (Salinity = 35, Tem perature = 20 °C ). The pum p­
ing regim e follow ed a regular six hourly cycle o f inundation
and exposure that m im icked a sem i-diurnal tide. T he inlet o f
the tubes in the core w as recessed slightly into the sedim ent
Biogeosciences, 9, 4087-4097, 2012
6 hours
High tid e condition
Low tid e condition
r \
I S to p p er
Pum pand
w a te rre se rv o ir
Pum pand
J
.
w a te rre selervoir
rv o ir J
rH ead sp a ce
C J
S ed im en t
S edim ent
core
Fig. 1. Diagram of the experimental setup, showing the conditions
of simulated tides. TA and DIC are sampled from the water col­
umn during inundation (high tide) and CO2 is sampled from the
headspace during exposure (low tide). MS refers to a magnetic stir­
rer bar.
surface, so that all the overlying w ater could be rem oved,
leaving no ponding o f w ater on the surface during exposure.
C arbon m ineralisation processes in natural system s can be
highly dynam ic reflecting pulsed inputs o f organic m atter
(OM ), for exam ple, deposition o f phytodetritus. This pulsed
occurrence o f carbon m ineralisation is highly relevant, driv­
ing cycles o f solute reduction and oxidation, w hich in turn
drives alkalinity production and consum ption. To sim ulate a
pulse o f organic m atter, h a lf o f the cores had 0.38 g b aker’s
yeast added to them after 71 days (+O M treatm ent), w hile
the rem aining cores did not receive this organic m atter input
(—OM ). D uring inundation, the flux o f D IC w as determ ined
by covering the cores w ith sealed lids and taking 4 -5 w ater
sam ples during sedim ent inundation. T he DIC flux w as d e­
term ined as the slope o f D IC concentration versus tim e m u l­
tiplied by the w ater height. T he pH w as sim ultaneously m ea­
sured as the w ater sam ple fo r alkalinity w as taken. D uring
exposure, the flux o f gaseous C O 2 w as m easured by sam ­
pling the gas headspace o f the sealed core. A gain, the C O 2
flux w as determ ined as the slope o f C O 2 concentration v er­
sus tim e m ultiplied by the headspace height. C O 2 w as sam ­
pled using evacuated 3 ml draw blood collection vials (Vacutainers, B ecton D ickinson) and analysed using Flow Injec­
tion A nalysis (Satienperakul et al., 2004). A lkalinity sam ­
ples w ere filtered (Bonnet, 0.45 pm polyethersulfone) and
preserved w ith 2 0 p lH g C l 2 (6 % w / v ) . T hey w ere stored in
glass vials and refrigerated at 4 ° C for less than one w eek
before analysis using a m odified G ran titration (A lm gren et
al., 1983). pH w as determ ined at 20 °C using a pH electrode
(Hach PHC301 connected to an H Q 40d m eter), calibrated
w ith N BS buffers. D IC concentrations in the w ater colum n
w ere calculated using alkalinity and pH, w ith the constants
found in R oy et al. (1993). T he m ethod for total Fe analysis
o f the dried sedim ent w as m odified from Lord (1982), u s­
ing a 24 h citrate/bi carbonate/dithi oni te extraction for easily
extractable Fe, follow ed by a 24 h concentrated nitric acid
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P. A. Faber et al.: The role of alkalinity generation
digestion. The extracts w ere then analysed using atom ic ab­
sorption spectroscopy (AAS).
2.2
M odel formulation
The reactive transport m odel follow s the standard form u­
lation for early diagenetic m odels of m arine sedim ents
(Boudreau, 1997; M eysm an et al., 2003). The m odel sim ­
ulates the depth profiles of solutes and solids, as w ell as the
fluxes across the sedim ent-w ater interface, based on the mass
balance equations
Solutes: cp~dCr
sr
dx
(pDi
9C .
J2vi,kRk
dx
k
dCf
Solids: (1 - < p ) - ÿ j - = J 2 vi,kRk
w here C pw and C f are the concentrations o f a solute and
solid com pound, respectively. No advective processes are in­
cluded in the model, as negligible sedim entation occurred
during the incubations. The porosity <p is assum ed constant
w ith depth. For solutes, the only transport process is m olec­
ular diffusion. The diffusion coefficient Z)¡ is calculated as
a function o f tem perature and salinity using the R package
m arelac (Soetaert et al., 2010) and subsequently corrected
for tortuosity according to the m odified W iessberg relation
of Boudreau (1996). The quantities R t represent the reac­
tion rates, w here ry^ is the stoichiom eric coefficient o f the
r-th species in the k-th reaction. The reaction set includes
three m ineralisation pathw ays (aerobic respiration, dissim ilatory iron reduction and sulfate reduction) for two fractions
of organic m atter (fast and slow decaying), the form ation of
iron sulfide and pyrite, and the reoxidation o f reduced com ­
pounds in pore w ater (ferrous iron, free sulfide) and solid
phase (iron sulfides and pyrite). The full set o f 13 reactions
is given in Table 1. T he rate expressions for these reactions
follow the standard kinetic rate law s and are given in Table 2.
For sim plicity, w e have assum ed that processes such as nitri­
fication and denitrification have a negligible effect on alka­
linity fluxes in this system.
2.3
pH model
The set o f acid-base reactions governing the pH dynam ics in
the pore w ater includes the carbonate, borate, sulfide and w a­
ter equilibria. The im pact of dissociation reactions involving
phosphate, am m onium , silicate and dissolved organic com ­
pounds w as assum ed negligible. The associated total alkalin­
ity and total species are hence defined as:
A t = [H C O 3-] + 2 [C O 2“ ] + [B (OH)¡"] + [H S“ ] + [O H “ ] - [H+]
S u m C 0 2 = [ C 0 2] + [H C O J]
CO 2 -
Sum BO H 3 = [B (O H )3] + [B (O H )“ ]
S u m H 2 S = [H S “ ] + [H 2 S]
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4089
Table 1. K inetic reactions included in the reaction set.
R1
R2
{CFHOfi + O2 —> H2O
{CH2 0 } f + 4 FeO O H + 8 H + ^
R3
R4
{CH20 } f + \ SO)]“ + \ H + - * CO 2 + \ H “ + H 2 0
{CH20 } s + 0 2 -* CO 2 + H 20
4 Fe2+ + CO2 + 7 H 2 O
R5
{CH20 } s + 4 FeO O H + 8 H + -* 4 Fe2+ + C 0 2 + 7 H 20
R6
{CH20 } s + 1 SO 2“ + | H +
R7
H S“ + 2 O2 - * SO)]“ + H+
R8
Fe2+ + \ 0 2 + I H 20 - * FeO O H + 2 H +
CO2 +
+ H 20
R9
8 FeO O h = H S - + 15 H + -* SO^4_ + 12 H 20
RIO
Fe2+ + H S“ - * FeS + H +
R ll
¿W-*
r FeO
1 CW
T ow4
FeS + I 0 2 + 2
I 1
H120
OW
Hll +
SO)]“ + 2 H +
R12
FeS + I SO)]“
R13
FeS2 +
O2
|
I H S - + I H + -* FeS2 + H 20
F e O O H + 2 SO',2 4H +
h 2o
4
The associated equilibrium constants w ere calculated as a
function o f tem perature and salinity using AquaEnv, a dedi­
cated R -package for acid-base and C O 2 system calculations
(Hofm ann et al., 2010).
2.4
Boundary conditions and initial state
The cyclic process o f inundation and exposure w as sim u­
lated by regular sw itching betw een two sets o f boundary
conditions. U nder inundation, the concentration of solutes at
the sedim ent-w ater interface w as fixed to that o f the overlying w ater (which w as set at constant pH and solute con­
centrations) , w hile a fixed flux w as im posed for the solids.
T hese fluxes w ere set to zero for all solid com ponents dur­
ing the w hole sim ulation period (zero deposition assum ed
- see above), apart from organic matter, w hich received a
pulse input at 71 days. To m odel this pulse input, the organic
m atter w as added uniform ly to the top 2 mm o f the sedim ent
at a total concentration o f ~ 2500 pinoi C ^ O g “ 1 dry sed­
im ent and fractionated betw een the fast-decaying fraction
(75% ) and the slow -decaying fraction (25% ), a ratio used
by W estrich and B erner (1984) (who also included a third,
non-reactive fraction in their model.)
U nder exposed conditions, only the volatile solutes O 2
and C O 2 have an exchange w ith the overlying atm osphere,
w hich is m odelled using the convective boundary flux J =
ká ( C eq — C) w ith ká the piston velocity and C eq the gas con­
centration in equilibrium w ith the atm osphere. A t the lower
boundary o f the sedim ent dom ain a no-flux condition w as
im posed (fluxes across the bottom boundary are zero) for all
com pounds over the w hole sim ulation period.
The reduced Fe (FeS and FeS 2 ) concentration w as ini­
tially set to 0 and the O 2 concentration in the pore w a­
ter w as set to equilibrium w ith the atm ospheric concen­
tration. A uniform profile o f slow -decaying organic m at­
ter (~ 2500 pm ol C H 2 O g “ 1 dry sedim ent), and either 19 or
95 pinoi F e g “ 1 dry sedim ent w as imposed. These latter val­
ues w ere determ ined to be the extrem e low and high Fe
Biogeosciences, 9, 4087-4097, 2012
4090
P. A. Faber et al.: The role of alkalinity generation
Table 2. K inetic rate expressions for the reactions included in the
reaction set.
N ii in — (1
V ) f in si [ C H 2 O f ]
, = ( 1 - ¥ > ) * s 1o w [ C H 2 O s
Ri =
[0 2]
[0 2] + Ko, m
[FeOOH]
Rz =
Rs =
[S 0 4 ~ ]
[S° r ]
Ri =
R o2
[FeOOH] + KpeOOH [ 0 2] + K q 2
KpeOOH
R o2
2- [FeOOH] + ^FeOOH [ 0 2] + K q 2 '
+
OL)A
2.6
[ ° 2]
„s
[0 2] + Kq m
[FeOOH]
r5
=
r6
=
Rl
= # H 2S - O x [ 0 2 ]
K o2
[FeOOH] + KpeOOH [ 0 2] + K q 2 '
K o2
KpeOOH
[FeOOH] + KpeOOH [ 0 2] + K q 2 '
[S ° 4 ~ ]
[S°r]-
■K S O 2 -
HS-
R& = Ç*Fe-Ox [pe2+ [0 2]_
Tfg = (1 - <P) ^FeOOH-FFS [FeOOH] [H SR w = U 'irS . lomi |^Fe
j [HS
]
^11 = (1 - ¥>) ^FeS-Ox [FeS] [ 0 2]
^12 — (1 ~ (P) ^FeS2.form [FeS] H S~
^13 = (1 - ¥ ,)*FeS2-Ox[FeS2] 0 2]
concentrations, as m easured by a total Fe extraction at the
conclusion o f the experim ent.
2.5
solved for the unknow n proton concentration using the it­
erative m ethod o f Follow s et al. (2006). U sing this proton
concentration (or equally pH v alu e), the full spéciation could
be calculated o f all chem ical species involved in the acidbase dissociation reactions. The resulting concentrations of
the equilibrium species could then be em ployed in kinetic
rate expressions (specifically, the pore w ater C 0 2 concen­
tration w as needed in the rate expression for the air-sea gas
transfer o f C 0 2). Further details on this pH m odel procedure
are given by Flofm ann et al. (2008).
Description o f model runs
The m odel w as set up to sim ulate the tidal cycles im posed
in the laboratory core incubation experim ents, w hich w ere
exposed and inundated alternately every 6 h.
The model sim ulations provide flux estim ates at each point
in tim e. The fluxes o f TA and DIC during inundation and
C 0 2 fluxes during exposure are reported as the m ean over
the 6 -h exposure/inundation period. T hese reported m ean
values include transient (~ 30 min) spikes in DIC and TA
im m ediately after inundation. The sim ulation extended over
120 days (i.e., 240 tidal cycles), w ith a pulse o f organic m at­
ter added on day 70, sim ulating the addition o f the organic
m atter source in the laboratory experim ents. Table 3 lists an
overview o f param eters values used in m odel sim ulations.
T hese w ere determ ined from m easured properties, literature
values or calibrated to the available dataset. All param eter
values w ere kept constant during the w hole sim ulation pe­
riod (apart from the organic m atter input).
Numerical model solution
2.7
A num erical solution procedure w as im plem ented in the
open-source program m ing language R as fully detailed in
Soetaert and M eysm an (2012). A reactive transport model
essentially consists o f one partial differential equation (PDE)
for each com pound. Together w ith the m ass action laws
o f the acid-base equilibria, these PD Es form a differentialalgebraic system , w hich w as solved using an operator sp lit­
ting approach (Solution m ethod, 3b, as explained in Hofm ann et al., 2008). Follow ing the m ethod-of-lines, the R
package R eacTran uses a finite difference schem e to expand
the spatial derivatives of the PD Es over the sedim ent grid.
This grid w as obtained by dividing the sedim ent dom ain
(thickness L = 5 cm, the approxim ate depth o f the sedim ent
cores in the incubation experim ent) into a uniform grid of
100 sedim ent layers. A fter finite differencing, the resulting
set of O D Es w as integrated using the stiff equation solver
vode from the R -package deSolve.
A t each tim e step, the operator splitting approach o f the
pH model required an additional pH equilibration step. To
this end, the num erical integration o f the O D E system pro­
vided the values o f the reaction invariants (TA, S u m C 0 2 ,
SumF[2S, SumBOF[3) at each future tim e step. Subsequently,
the nonlinear system o f algebraic acid-base expressions w as
Biogeosciences, 9, 4087-4097, 2012
Sensitivity model runs
The sensitivity o f C 0 2 flux to the piston velocity w as in­
vestigated using sim ulations, w here the piston velocity w as
varied from 0.05 to 5 c m h _1. In each sim ulation, the initial
FeO O H concentration w as 19 pm ol F e g - 1 dry sedim ent. For
each value o f the piston velocity, the average flux o f C 0 2
during exposure w as calculated over the com plete sim ula­
tion period (30 tidal cycles). T his procedure w as repeated for
three different initial values o f organic m atter concentration
(2500, 1000 and 6 0 0 p m o lC g _1 dry sedim ent for the slowdecaying fraction, and 5, 2.5 and 1 .3 p m o lC g _ 1 dry sedi­
m ent for the fast-decaying fraction, respectively), to investi­
gate the sensitivity o f C 0 2 flux to the piston velocity under
different am ounts of organic m atter loading.
The availability o f reactive oxidised iron (FeOOH) con­
trols alkalinity production in the sedim ent and, hence, w e
perform ed a second series of sim ulations to investigate the
sensitivity of the m odel tow ards the initial sedim entary
FeO O H concentration. To determ ine the effect of FeOOH
availability on TA production, sim ulations w ere run w ith a
fixed initial concentration o f C H 20 (~ 2500 pm ol C H 20 g - 1
dry sedim ent), but w ith various FeO O H concentrations (7.6,
19 and 95 pm ol F e g - 1 dry sedim ent). T he values of 19 and
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P. A. Faber et al.: The role o f alkalinity generation
4091
Table 3. O verview o f m odel param eter values.
7
6
Constant
Value
Units
Porosity
rho.sed (density of solid
sediment)
Piston velocity
K.fast (highly labile organic
matter)
K.slow (less labile organic
matter)
K _02 (Monod constant for 0 2
consumption)
K_FeOOH (Monod constant
for FeOOH reduction)
0.8
2.6
-
K _S02~ (Monod constant for
1.6
g cm ~ 2
1
25
cm h ~ 4
yr- 1
3.1
dry sedim ent
Alkalinity
4
E
E 33
Ï
2
LL
1
7
yr- 1
0.6
0.005
6
I
o
200*rho.sed
pmol cm~ 2
pmol cm~ 2
19 pmol Fe g
DIC
C 02
pmol cm~ 2
1X
3
4
.1
dry sedim ent
Alkalinity
3
2
0
1.6
X
IO7
p m o P 4 cm 2 yr~ 4
2.0
X
IO4
p m o P 4 cm 2 yr~ 4
7
+OM
co2
160
p m o U 4 cm 2 yr~ 4
0
p m o U 4 cm 2 yr~ 4
2.57
p m o P 4 cm 2 yr~ 4
1 X 10s
p m o P 4 cm 2 yr~ 4
1
p m o P 4 cm 2 yr~ 4
95 pm ol F e g - 1 dry sedim ent are the low and high estim ates
of sedim ent FeO O H concentrations in the core experim ent
sedim ent, respectively. The value o f 7.6 pm ol Fe g - 1 dry sed ­
im ent w as chosen as a low value for a com parison w ith our
estimates.
3
Í
o
-1
0
S 0 2~ reduction)
k_H2S.Ox (Kinetic constant
for H 2S oxidation)
k_Fe.Ox (Kinetic constant for
Fe oxidation)
k_FeS.Ox (Kinetic constant for
FeS oxidation)
k_FeS2.Ox (Kinetic constant
for FeS2 oxidation)
k_Fe.H2S (Kinetic constant for
F eO O H /H 2S redox reaction)
k_FeS.form (Kinetic constant
for FeS formation)
k_FeS2.form (Kinetic constant
for FeS2 formation)
■*= 5
9 5 pmol F e g
DIC
co 2
Results
Experimental
There w as little variation in the DIC fluxes over the entire
course o f the experim ent in the —OM treatm ent w ith a m ean
value o f 1.3 m m ol m - 2 h - 1 over the 120 days (Fig. 2). In the
+OM treatm ent, DIC fluxes w ere the sam e as the —OM treat­
m ent w ithin experim ental uncertainty in the first 70 days of
the experim ent before the organic m atter w as added (Fig. 2).
A fter the organic m atter addition, DIC fluxes substantially
increased to a m axim um o f ~ 5.0 m m ol m - 2 h- 1 , and then
decreased again to ~ 2 . 0 m m ol m - 2 h - 1 over a tim e period of
40 days after organic m atter addition. A lkalinity fluxes w ere
initially high in both —OM and +OM treatm ents, steadily
decreasing from > 1.4 m m ol m - 2 h - 1 at the start of the ex­
perim ent to attain a negligible alkalinity flux after 60 days.
The m ost likely explanation for this observation is that there
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DIC
Alkalinity
Alkalinity
D ays
Fig. 2. S im ulated m ean fluxes o f C 0 2 during exposure (C O g),
dissolved inorganic carbon (DIC) and alkalinity during inundation
in the com puter sim ulation w ith 95 and 19 pm ol F e g - 1 sedim ent
( d/ w) and laboratory core incubation fluxes w ith (+OM) and w ith ­
out (—OM) added organic m atter. E rror bars are standard deviations
across 10 replicates.
w as build-up of iron sulfides, w hose rate o f form ation slowed
over tim e. We hypothesise that initially, a large pool of
Fe (III) w as form ed during sedim ent pre-treatm ent, w hich
w as subsequently reduced to m etal sulfides. D issim ilatoiy
iron reduction produces alkalinity (TA : DIC = 8 , see R9 in
Table 2), but as the pool o f Fe (III) is depleted, alkalinity pro­
duction w ill decrease over tim e. A fter the pulsed addition of
organic matter, alkalinity fluxes increased rapidly to a m ax­
im um o f 3.0 m m ol m - 2 h - 1 before decreasing again rapidly.
The C O 2 fluxes during exposure w ere initially very low in
both treatm ents (~ O .lO m m o lm - 2 h- 1 ). In the —OM treat­
ment, the C O 2 flux increased after 60 days, coinciding w ith
Biogeosciences, 9, 4087-4097, 2012
4092
P. A. Faber et al.: The role of alkalinity generation
the decrease and cessation of alkalinity fluxes (fluxes not
significantly different from zero, shown by the error bars).
In the +OM treatment, there was an increase in CO 2 fluxes
after the addition of organic matter, reaching a maximum
of ~ 2.5 mmol m - 2 h- 1 . The CO 2 fluxes decreased again to
~ 0.60 mmol m - 2 h - 1 at the conclusion of the experiment.
3.2
M odel simulations
To match with the laboratory experiments, the data from the
model were truncated before 20 days (Fig. 2). From day 20
to 70, the simulation yielded inundated DIC fluxes between
~ 1.2 and ~ 1.4 mmol m - 2 h- 1 . Immediately after the OM
addition at day 70, the DIC flux increased to a maximum
of ~ 5.7 m m olm - 2 h- 1 . The TA flux decreased from ~ 0.48
to ~ 0.40 mmol m - 2 h - 1 before the OM addition, then in­
creased to a maximum of ~ 0.74 mmol m - 2 h - 1 after the ad­
dition. The CO 2 flux during exposure was between ~ 0.66
and ~ 1.0m m olm - 2 h - 1 before the OM addition, and rose
to a maximum of ~ 3.6 m m olm - 2 h - 1 after the addition of
the OM, then decreasing again to ~ 1.2 mmol m - 2 h - 1 by the
end of the simulation. The peak flux during the simulation is
shifted forward in time relative to the core incubations indi­
cating a delayed response of organic matter mineralisation
under experimental conditions. This is expected, as the bac­
terial community first needs to grow to consume the bioavailable organic matter. In the computer simulation, no lag phase
occurs, as the model formulation does not include popula­
tion growth and, thus, assumes an instantaneous response of
microbial metabolism.
In the model simulations, DIC fluxes were consistently
higher during inundation than CO 2 fluxes during the cor­
responding exposure periods (Fig. 3). The discrepancy be­
tween DIC and gaseous CO 2 fluxes appears to increase with
increasing respiration, shown by the divergence of the sim­
ulation data from the 1 : 1 line as DIC flux increases. This
pattern was very similar to that previously observed for in­
tact sediments collected from tidal flats (Cook et al., 2004)
(Fig. 3).
The fluxes of gaseous CO 2 during exposure and the
fluxes of DIC and TA during exposure were highly sensi­
tive to initial Fe concentrations in the sediment. This can
be evaluated by calculating the mean fluxes over the pe­
riod before the organic matter pulse (Fig. 4). The high
Fe concentration resulted in a lower CO 2 flux during ex­
posure (~ 0.65 vs. ~ 0.35 mmol m - 2 h - 1 for the 19 and
95 pmol F e g - 1 dry sediment). There was also a large dis­
crepancy between alkalinity fluxes, where the high Fe con­
centration resulted in a higher TA flux (0.80 mmol m - 2 h - 1
versus 1.4 m m olm - 2 h - 1 for the 19 and 9 5 p m o lF e g - 1
dry sediment simulations). The difference between DIC
fluxes were smaller, with a flux of ~ 1 . 8 mmol m - 2 h - 1
for the simulation with 95 pmol F e g - 1 dry sediment and
~ 1. 6 mmol m - 2 h - 1 for the simulation with 19 pmol Fe g - 1
dry sediment.
Biogeosciences, 9, 4087-4097, 2012
I n c u b a te d C o re s
C o o k e t al 2 0 0 4
1:1 line
C 0 2 vs DIC (simulation)
0
1
2
3
4
5
E x p o s e d C 0 3 flux (m m ol m"2 h"1)
Fig. 3. F luxes o f dissolved inorganic carbon (DIC) versus exposed
C O 2 fluxes for tw o experim ental datasets and a m odel sim ulation.
Incubated core experim ents represent both the + and —O M trea t­
m ents.
3.3
Simulation profiles
The profile of FeOOH in the top 0.5 cm of sediment changed
dramatically upon the addition of the organic matter pulse to
the top 0.2 cm (Fig. 5). The profile taken two tidal cycles be­
fore the pulse shows the FeOOH reaching ~ 15 pmol F e g - 1
dry sediment in the surface layer and decreasing with in­
creasing depth. One tidal cycle after the addition of organic
matter, FeOOH has begun to oxidise, with the concentration
in the top 0.2 cm falling to a maximum of 2 pmol F e g - 1 dry
sediment in the surface layer. Below 0.2 cm, the FeOOH pro­
file is similar between the two times, as the organic matter
concentration has not changed in this domain.
4
4.1
Discussion
Alkalinity producing reactions
The production of alkalinity can be attributed to several key
processes: ammonia release, net denitrification, net sulfate
reduction and to a lesser extent, dissolved organic carbon
release (Hammond et al., 1999). Berner et al. (1970) pro­
posed the idea of sulfate reduction as an alkalinity producing
process. It was noted that sulfate reduction coupled with the
precipitation of the stable iron sulfides FeS and FeS 2 pro­
duces one mole of alkalinity per mole of carbon mineralised
(Berner et al., 1970) (Eq. 1).
6CH 20 + 3 S 0 2 - + 2FeOOH
FeS + FeS2 + 6HCO:r + 4H 20
(1)
In this representation of sulfate reduction, the supply of
Fe (III) to the sediment enables the burial of reduced sul­
fur compounds as iron sulfides (FeS) or pyrite (FeS2 ).
This burial of reduced sulfur prevents sulfide oxidation and,
www.biogeosciences.net/9/4087/2012/
P. A. Faber et al.: The role of alkalinity generation
4093
2.0
0.0
Ö 1.6
0.1
0.2
—
F e OOH b e fo re OM addition
■■ O ■ F eO O H a fte r OM addition
0.3
0.6
0.4
0.7
0.6
0.5
0
2
4
6
8
10
12
14
16
ftm ol F e g"' d ry s e d im e n t
0.4
Fig. 5. A sim ulation show ing the FeO O H concentration before and
0.3
after an organic m atter pulse w ith initial FeO O H concentration of
1 9 p m o lg - 1 sedim ent (d/ w). Note: T he step around 0 .2 c m is due
to the pulse o f organic m atter added to only the top 0.2 cm.
0.2
1.6
7 .6 pm ol F e g
d ry se d im e n t
-1
E
19 pm ol F e g
“5
9 5 (omoi F e g
d ry se d im e n t
-1
d ry se d im e n t
E
E
X
D
<
I-
03
D
C
T3
C
0.2
20
10
0
30
40
50
Tim e a fte r F e an d o rg an ic c a rb o n addition (d ay s)
Fig. 4. Fluxes o f dissolved inorganic carbon (DIC), exposed C O 2
and alkalinity fluxes for a sim ulation o f a 50 day period w ith an im ­
posed profile o f 7.6, 19 and 95 p m o lg - 1 sedim ent (d / w ) FeO O H .
hence, it prevents the alkalinity generated by sulfate reduc­
tion being consum ed again (Eq. 2).
H S- +
2
O 2 -> SO 4 - + H +
(2)
U pon exposure to oxygen, iron sulfides can also oxidise,
leading to alkalinity consum ption (and, hence, no net alka­
linity generation by sulfate reduction) (Eq. 3).
FeS +
2
.2 5 O 2 +
2
.5 H 2
0
F e( 0 H ) 3 + S 0 f2 + 2H +
(3)
However, the rate o f this reaction is typically low er than that
o f free sulfide oxidation (see Table 3). M ore importantly, one
requires a suitable transport process, that either m oves the re­
duced sulfur com pounds upw ards to the oxic zone (like biotu rbation), or transfers oxygen dow n into anoxic layers (like
bio-irrigation). In the experim ental setup here, such transport
processes are not present.
H u and Cai (2011) review ed the factors controlling alka­
linity generation in ocean m argins in sedim ent and concluded
www.biogeosciences.net/9/4087/2012/
that the burial o f pyrite and the denitrification o f N O 3 d e­
rived from the continents w ere the only net sources o f al­
kalinity in ocean m argin sedim ents. A s the cycling o f su l­
fur is closely linked w ith that o f iron, w e included both su l­
fur and iron geochem istry in the diagenetic m odel. In our
experim ents, denitrification w as unlikely to be a significant
source o f alkalinity generation because o f the lack o f NO3
in the overlying w ater o f our incubations. C oupled nitrifica­
tion denitrification w ill not results in significant net alkalin­
ity generation (Hu and Cai, 2011). Consequently, w e did not
m odel the effect o f denitrification on alkalinity in this m odel.
D issolved organic m atter and HPOjj- have been show n to
contribute to alkalinity fluxes (Cai et al., 2010), but reactions
involving sulfur (and it interactions w ith iron) are the m ajor
processes controlling the alkalinity balance w ithin the sed ­
im ent and, hence, only these processes are considered. We
are confident that the m odel used here represents the critical
anaerobic alkalinity-generating processes that are im portant
in our experim ental set up.
4.2
Model sensitivity towards piston velocity
A t piston velocities > l c m h - 1 the CO 2 efflux reached a
stable value and this asym ptotic CO 2 efflux increased p ro ­
portionally w ith initial organic m atter content (or total m in ­
eralisation) (Fig. 6 ). D ecreasing the piston velocity below
0 .5 c m h _ 1 reduced CO 2 fluxes during sedim ent exposure.
T his can be attributed to the slow er efflux o f CO 2 for a given
C O 2 concentration gradient (transport control), and a slow er
flux o f O 2 into the sedim ent resulting in less aerobic respi­
ration. Indeed, w e found the rate o f aerobic respiration to
decrease w ith decreasing piston velocity (data not shown).
Initially w e thought that the alkalinity flux w ould rem ain
Biogeosciences, 9, 4087-4097, 2012
4094
P. A. Faber et al.: The role of alkalinity generation
E
o
Low m ineralisation rate
M edium m ineralisation rate
High m ineralisation rate
E
E
X
0.6
=5
CM
O
o
■o
o
in
o
Q_
0.4
0.2
X
LII
0.0
0
1
2
3
4
5
6
P isto n V elocity (cm h'1)
Fig. 6. E xposed flux o f C O 2 w ith v arying piston velocity and respi­
ration rate. Low, m edium and high m ineralisation rates refer to peak
D IC productions o f approx. 600, 1300 and 2 6 0 0 p m o lm _2 h - 1 , re­
spectively.
constant upon changing piston velocity. It w as noted, how ­
ever, that there w as an increase in alkalinity production by
7 % as the piston velocity w as decreased from 5 to 0.05 (data
not shown) indicating that anaerobic respiration accounted
for a greater proportion of the total respiration. H igher respi­
ration rates w ere m ore sensitive to decreasing piston veloci­
ties. We concluded that w hen the piston velocity is greater
than l c m h - 1 , exchange w ill be lim ited by production of
C O 2 (reaction control), rather than transport across the airw ater interface (Fig. 6 ). For the rem ainder of the sim ulations,
the piston velocity w as fixed at 1 cm h _ 1 , the low est o f values
found by various researchers across the w ater-air interface in
estuarine and riverine system s, as sum m arised by Raym ond
et al. (2 0 0 0 ).
4.3
Agreement o f simulations with experimental data
There w as a general agreem ent betw een experim ental flux
data and the m odel sim ulations. Both m odel and experim en­
tal data show ed that DIC fluxes from the sedim ent during
tidal inundation are higher than C O 2 fluxes during exposure.
This difference w as m ost pronounced at the start o f the exper­
im ent and after the addition of organic matter. A t the start of
the experim ents there w as a rapid alkalinity generation w hich
can be explained by the form ation of FeS as the Fe (III) ini­
tially present w ithin the surface sedim ent w as reduced. A fter
the pulse of organic matter, the oxygen penetration in the sed­
im ent is reduced and a higher rate o f anaerobic carbon m in­
eralisation takes place. This leads then to increased rates of
reduced sulfur production, FeS burial and net alkalinity pro­
duction. The reduction of Fe in the surface o f the sedim ent
leads to a transient alkalinity flux and associated increase
in the discrepancy betw een gaseous C O 2 flux and DIC flux
(Fig. 5). This observation is seen in both the m odel and the
Biogeosciences, 9, 4087-4097, 2012
laboratory incubations, although there is a slight offset due
to the fact that there is a delay in the m axim um respiration
rate in the laboratory incubations com pared to the model.
In our sim ulations, reduced sulfur production continues
after FeO O H is exhausted, but it is reoxidised as free su l­
fide diffuses upw ards into the oxygenated surface layers of
sedim ent. N onetheless, a relatively sm all alkalinity flux still
leaves the sedim ent, as there is som e build up of H 2 S in the
sedim ent pore w aters (The diffusion o f sulfide into the oxic
layer, and its subsequent oxidation is slow er than its produc­
tion w ithin the deeper layers o f the sedim ent).
The dynam ics of this sim ulation/experim ent have strong
environm ental relevance being representative o f a resuspen­
sion event or the deposition o f fresh sedim ent from the catch­
m ent and the deposition o f organic matter. This highlights
the im portance o f environm ental dynam ics in controlling the
relative loss o f C O 2 and D IC from intertidal sedim ent. In­
deed, in coastal sedim ents, periodically high fluxes o f alka­
linity are observed follow ing periods o f high organic m atter
input (Ferguson et ah, 2003a). Hargrave and Phillips (1981)
note the significance o f short-term organic m atter deposition,
w ith high supply rates, relative to m ineralisation rates, caus­
ing a burial o f organic m atter in deeper, anoxic layers o f the
sedim ent.
4.4
M odel sensitivity towards sedimentary iron
The sensitivity o f the m odel (Fig. 7) to solid-phase iron (Fe)
suggests that the delivery o f fresh (oxidised) Fe controls how
m uch m ineralised carbon is exported to the atm osphere (as
C O 2 ) versus the ocean (as alkalinity). In the sim ulation, a
large input o f Fe leads to a higher rate o f alkalinity pro­
duction through F eS 2 burial (FeOOH consum ption), and a
corresponding low er C O 2 efflux during exposure (Fig. 4).
The sensitivity o f the m odel to Fe agrees w ith the literature
(Hu and Cai, 2011; B erner et ah, 1970), w hich suggests that
F eS 2 burial is the m ost im portant process controlling alkalin­
ity production. The present w ork show s that in high carbon
system s such as intertidal sedim ents, Fe w ill be the lim iting
species in pyrite burial, despite the role o f carbon as the m e­
diating species in pyrite burial globally (Hu and Cai, 2011).
The tem poral change of TA fluxes also differs consider­
ably. TA flux stabilises after 30 days in the sim ulations w ith
the low er Fe concentrations, w hereas at higher Fe concentra­
tions, TA flux continues to increase. This is due to the reduc­
tion o f all the oxidised Fe, creating a higher net production
of alkalinity. For sim ulations w ith little or no Fe, there is a
higher tem porary sink of H S - in the sedim ent pore w aters
during intense alkalinity production (Fig. 7) as insoluble iron
sulfides cannot form . Subsequent alkalinity consum ption oc­
curs as the H S - is reoxidised. The effect of the reoxidation
of reduced sulfur can be seen in Fig. 7, w hich show s the sim ­
ulation w ith no FeO O H having low er pH and, thus, higher
C O 2 concentration, than the sim ulation w ith 95 pm ol F e g - 1
dry sedim ent. T he alkalinity concentration (as indicated by
www.biogeosciences.net/9/4087/2012/
P. A. Faber et al.: The role of alkalinity generation
4095
o.o
CL
<D
TJ
C 0.3
<D
95 FeOOH
0 FeOOH
E
I d 0.4
<0
0.5
6 .2
6.4
6 .6
6 .8
7 .0
7 .2
7.4
7.6
7.8
8 .0 0.0
0 .2
pH
0.4
0.6
0.8
1.0
1.2
1.4
C 0 2 (mM in porewater)
0.0
o 0.1
0.2
0 0.3
E
I 0-4
0.5
2 .0
2.5
3 .0
3.5
4 .0
4.5
5.0
5 .5
6.0 2.0
2.5
DIC (mM in porewater)
3.0
3.5
4.0
4.5
5.0
1.0
1.2
TA (mM in porewater)
0.0
E
o
Q- 0 .2
o
T5
0.5
0
10
20
ILimol FeOOH
30
40
0.0
0.2
g"1 dry sedim ent
0.4
0.6
0.8
HS" (mM in porewater)
o.o
0.1
£-0 - 2
S 0.3
0.5
0 .0 0
0 .0 5
0 .1 0
0 .1 5
0.20
0 .2 5
0.3 0
0.3 5
0 2 (mM in porewater)
Fig. 7. Profiles o f pH , C O 2, D IC , TA, FeO O H and H S an d O 2 from tw o sim ulations. E m pty circles represent a sim ulation w ith no FeO O H ,
w hereas filled circles represent 95 pm ol g _ 1 sedim ent (d / w) FeO O H .
HCO^" and C O 3 - ) throughout the FeO O H containing profile
is also considerably higher. D uring periods w here respiration
is extrem ely high, H S - has the potential to by-pass the sm all
oxic zone in the sedim ent and so the H S - can reach the w ater
colum n before it is reoxidised. In this situation, the num eric
sim ulation w ill show a net alkalinity flux from the sedim ent.
In reality, im m ediate reoxidation o f H S - in the overlying w a­
ter colum n w ill directly consum e this alkalinity.
W ith regard to carbon budgets, the effect o f anaerobic car­
bon m etabolism is im portant as higher alkalinity export to
the ocean creates a higher C O 2 buffering capacity for the u p ­
www.biogeosciences.net/9/4087/2012/
take of atm ospheric C O 2 . The effect o f anaerobic alkalinity
production on atm ospheric carbon uptake in coastal seas has
been estim ated at up to 60 % o f the total uptake (Thom as et
al., 2009). This is an upper estim ate, as it neglects alkalinity
consum ed during nitrification (Hu and Cai, 2011). In regions
w ith high anthropogenic disturbance, large am ounts o f ter­
restrial carbon is exported tow ards coastal oceans (Frankignoulle et al., 1996, 1998; A bril et al., 2002). Increased
organic carbon loading in estuaries due to anthropogenic
land use represents an anthropogenic carbon source to the
atm osphere upon its breakdown. M ore anthropogenically
Biogeosciences, 9, 4087-4097, 2012
4096
disturbed catchm ents w ill also export m ore sedim ent and,
hence, m ore Fe(III) (Asselm an et al., 2003; W alling, 1999)
to estuaries, w hich may partially offset larger C O 2 em issions
from increased labile organic carbon export to estuaries. The
significance o f this offset rem ains to be investigated.
5
Conclusions
The laboratory data and field data (Cook et al., 2004) and
com puter sim ulations clearly show that gaseous C O 2 fluxes
during exposure on tidal flats are likely to under estim ate
total carbon m ineralisation. This finding has clear im plica­
tions for research in this field, given that total inorganic car­
bon fluxes for intertidal sedim ents have generally been es­
tim ated using only gaseous C O 2 fluxes on the exposed sed ­
im ents (M igné et al., 2005; M iddelburg et al., 1996). The
results o f this study dem onstrate the im portance o f consider­
ing both exposed and inundated fluxes in studies o f intertidal
m etabolism , w hich m ay be quite different, depending on the
extent to w hich there is a net accum ulation o f reduced so ­
lutes.
Acknowledgements. P. Faber acknow ledges the assistance o f an
A ustralian Postgraduate A ssociation scholarship. T his w ork w as
supported by a M onash U niversity faculty o f science early career
researcher grant, as w ell as M onash researcher accelerator grant
to PC. We thank H ans R oy for stim ulating discussions on this w ork.
E dited by: S. W. A. N aqvi
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