Marine Chemistry 168 (2015) 6979

Contents lists available at ScienceDirect

Marine Chemistry
journal homepage: www.elsevier.com/locate/marchem

Methane and carbon dioxide dynamics in a subtropical estuary over a diel

cycle: Insights from automated in situ radioactive and stable
isotope measurements
Damien T. Maher a,, Kirsten Cowley b, Isaac R. Santos a, Paul Macklin a, Bradley D. Eyre a
a
b

Centre for Coastal Biogeochemistry, School of Environment, Science and Engineering, Southern Cross University, PO Box 157, Lismore, NSW 2480, Australia
Department of Environment & Geography, Macquarie University, NSW 2109, Australia

a r t i c l e

i n f o

Article history:
Received 1 September 2014
Received in revised form 22 October 2014
Accepted 31 October 2014
Available online 8 November 2014
Keywords:
Airwater gas exchange
Greenhouse gas
Carbon stable isotopes
Floodplain
Coastal acid sulfate soils
Wetland

a b s t r a c t
Estuaries have high rates of primary production and respiration and can be hotspots for carbon dioxide and
methane enriched submarine groundwater discharge. Here, we report high resolution pCO2, CH4, 13CCO2,
13CCH4 and radon (222Rn, a natural groundwater tracer) observations along North Creek estuary, Australia
(S2848, E15334) during four spatial surveys over a diurnal cycle in January 2013 (summer). There were distinct tidal and diurnal differences in estuarine pCO2 and CH4, which lead to tidal differences of 3.6 fold and 5 fold
in the estimated CO2 and CH4 diffusive water to air uxes respectively, and up to a 2.4 fold difference in diurnal
ux estimates of CH4. Carbon stable isotopes revealed tidal and diurnal differences in the source 13C value of CO2
and CH4, and minor CH4 oxidation within the estuary. The CO2 outgassing rates based on the spatial surveys were
different than the outgassing derived from three xed time series stations along the estuary. There was
agreement between the methods in the lower and upper estuary where pCO2 had a relatively low range over
the study (~ 600 atm and 3000 atm respectively). However, in the mangrove surrounded mid estuary
where pCO2 ranged from ~1450 to 11,000 atm over a tidal cycle, uxes estimated by the survey method were
~30% of the time series estimates. This study highlights the importance of considering tidal and diurnal variability
when estimating the ux of CO2 and CH4 from estuaries, and discusses how a combination of diurnal
(productivity/respiration) and tidal (groundwater/mixing) processes may drive surface water pCO2 and CH4
over short-term time scales.
2014 Elsevier B.V. All rights reserved.

1. Introduction
Atmospheric concentrations of CO2 have increased by approximately 40% since the industrial revolution and, concurrently, atmospheric
CH4 concentrations have more than doubled since pre-industrial times
(IPCC, 2007). There is still a paucity of data from a number of biomes
to adequately constrain the global CO2 and CH4 cycles. Despite the relatively small surface area, global estuarine CO2 degassing is estimated to
be as large as the CO2 uptake by the continental shelf (Borges, 2005;
Borges et al., 2005; Cai, 2011), but large uncertainties remain in estimates of the global estuarine CO2 ux (Laruelle et al., 2010; Borges
and Abril, 2011; Cai, 2011; Maher and Eyre, 2012). Even fewer estimates
are available on the global estuarine CH4 ux (Borges and Abril, 2011;
Oritz-Llorente and Alvarez-Cobelas, 2012). Difculties in calculating
global emissions of CO2 and CH4 from estuaries include the lack of empirical data on controlling factors, the high degree of spatial and

Corresponding author.
E-mail address: damien.maher@scu.edu.au (D.T. Maher).

http://dx.doi.org/10.1016/j.marchem.2014.10.017
0304-4203/ 2014 Elsevier B.V. All rights reserved.

temporal variability in these systems, and the lack of data in subtropical

and tropical systems.
Previous studies have found high temporal and spatial variability in
pCO2 and CH4 concentrations within estuarine systems (Sansone et al.,
1999; Middelburg et al., 2002; Chen et al., 2008; Macklin et al.,2014).
However it has generally been observed that estuarine systems are
net sources of CO2 and CH4 to the atmosphere. Typically pCO2
and dissolved CH4 concentrations are measured during a spatial survey
or at xed time series stations, however these sampling strategies
may not adequately measure the high degree of both spatial and temporal variability often found in estuarine systems. Fixed time series measurements using automated instrumentation (e.g. Atkins et al., 2013)
capture temporal variability extremely well, with the resolution of measurements typically at the scale of minutes. However the measurements
are restricted to a single location, preventing assessment of spatial variation. Survey methods using continuous underway measurements or
discrete sampling offer the advantage of determining spatial variation,
and are therefore the most commonly utilized method for estimating
estuary-wide uxes. However single surveys do not capture variability
induced by diel and tidal cycles, which may be signicant. For example

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D.T. Maher et al. / Marine Chemistry 168 (2015) 6979

CO2 and CH4 concentrations in mangrove creeks and marshes can vary
by up to an order of magnitude over a tidal cycle (e.g. Borges et al.,
2003; Wang and Cai, 2004; Bouillon et al., 2007; Gatland et al., 2014),
and signicant diel variability in pCO2 and CH4 concentrations driven
by photosynthesis and respiration has been observed in estuarine
macrophyte beds (Maher et al., 2013b; Saderne et al., 2013). Therefore,
careful consideration of diel and tidal effects upon pCO2 and CH4
concentrations need to be assessed when calculating whole system
uxes.
A combination of factors may drive the diurnal and tidal variation of
CO2 and CH4 uxes in estuaries. Estuaries can have high productivity
and respiration rates (Kemp et al., 1997; McGlathery et al., 2001;
Middelburg and Herman, 2007; Maher and Eyre, 2012) which inuence
pCO2 on diurnal scales through the uptake (photosynthesis) and release
(respiration) of CO2 during day and night periods, respectively. Diel cycles may also inuence surface water CH4 concentrations, with previous
studies nding light-induced inhibition of CH4 oxidation rates in freshwater lakes (Murase and Sugimoto, 2005; Tang et al., 2014). In addition,
productivity and respiration driven cycles of sediment oxygen dynamics
may lead to oscillation in aerobic methane oxidation and methane production rates (King et al., 1990; Maher et al., 2013b), and methylated
substrates produced by phytoplankton have been shown to sustain
aerobic CH4 production in the ocean (Karl et al., 2008).
The actions of tides can deliver groundwater enriched in solutes
through tidal pumping, directly inuencing surface water pCO2
and CH4 (Borges et al., 2003; Dulaiova et al., 2006; Bouillon et al.,
2007; Kristensen et al., 2008; Dorsett et al., 2011; Atkins et al., 2013).
In addition, groundwater can deliver dissolved organic matter (Santos
et al., 2008; Bauer and Bianchi, 2011) and nutrients (Gleeson et al.,
2013; Charbonnier et al., 2013; Santos et al., 2013; Makings et al.,
2014) to surface waters, which may indirectly inuence pCO2 through
enhanced autotrophic and/or heterotrophic metabolism. Therefore calculations of estuarine airwater CO2 and CH4 uxes determined by surveys of surface water pCO2 and CH4 that do not capture tidal and diurnal
variability may produce inaccurate estimates.
Determining the major drivers of estuarine surface water pCO2 and
CH4 involves disentangling the various tidal and diel processes. Recent
development of cavity ring-down spectroscopy (CRDS) for high resolution in situ measurements of 13CCO2 and 13CCH4 may help
constrain the source 13C value of the dissolved CO2 and CH4 pools
(Bass et al., 2013; Maher et al., 2013b; Gatland et al., 2014), thereby
giving insights into the processes controlling surface water pCO2 and
CH4 concentrations. For example, respiration will produce CO2 with a
similar 13C to the organic matter source (Lin and Ehleringer, 1997),
and the dominant CH4 production pathways produce CH4 with differing
13C values (Whiticar et al., 1986). In addition, development of high
precision continuous measurement of in situ 222Rn (a natural groundwater tracer with a half-life of 3.84 days) now enables qualitative and
quantitative assessment of groundwater input to estuaries (Dulaiova
et al., 2005; Peterson et al., 2010). By combining simultaneous measurements of surface water 222Rn, pCO2, CH4, and 13CCO2 and 13CCH4 insights into the contribution of biological (e.g. primary production/
respiration) versus hydrological (e.g. groundwater and surface runoff)
drivers of surface water CO2 and CH4 concentrations can be gained.
We hypothesize that estimates of CO2 and CH4 uxes from estuaries
will vary signicantly over diurnal and tidal cycles, due to tidal pumping
and ecosystem metabolism. We tested this hypothesis by undertaking
four surveys over a 24 hour period along a small shallow estuary making
continuous underway measurements of 222Rn, pCO2, pCH4, 13CCO2
and 13CCH4 along with other physico-chemical parameters (wind
speed, temperature, dissolved oxygen, chromophoric dissolved organic
matter, chlorophyll a, and alkalinity). In addition three xed time series
stations were simultaneously deployed along the length of the estuary
measuring pCO2 and 222Rn to compare water to air ux estimates and
temporal variability in concentrations between the survey and the
xed time series method.

2. Methods
2.1. Study site
North Creek is a small subtropical estuary located on the North Coast
of New South Wales, Australia (Fig. 1). The estuary is shallow (average
depth ~ 2 m) and well mixed with a tidal range of ~ 2 m. The region
has a mean annual rainfall of 1863 mm with the wetter months occurring over summer and autumn. Intense rain events associated with
tropical low-pressure systems contribute a majority of this rain to the
catchment (Eyre and Pont, 2003). The hydrology of North Creek has
been modied signicantly in the last 100 years, through extensive
drainage of wetland areas, which have been converted to agricultural
land. An extensive drainage network including oodgates was constructed to facilitate drainage and prevent tidal inundation (King,
2003). Groundwater has been found to account for up to ~76% of surface
waters of the upper reaches of North Creek (Atkins et al., 2013), but
earlier investigations did not assess the mid and lower estuarine
sections.
For the purposes of this study, the estuary was divided into
three zones (Fig. 1). The rst zone, the lower estuary, comprises of
large marine inuenced tidal ats. Land usage is largely residential,
with the city of Ballina (population ~ 8000) surrounding the lower estuary. Riparian vegetation is largely absent however there are small
patches of remnant mangrove, salt marsh and river-at forest communities. The mid-reaches (hereafter termed mid-estuary) is
located within Ballina Nature Reserve, with an intact riparian zone
of mangrove and swamp sclerophyll forests (King, 2003). The
upper reach (hereafter termed upper estuary) is highly modied. It
has been straightened to provide drainage for agriculture (predominantly sugar cane cultivation) and is generally devoid of riparian
vegetation.
2.2. Spatial survey
Four spatial surveys were conducted over two consecutive tidal
cycles starting on the 15th of January 2013. A boat was driven at 5
6 km h 1 along North Creek with surveys starting during the
two low (pre-dusk and pre-dawn) and two high tides (~ midday and
~ midnight) to investigate tidal and diurnal inuences on pCO2 and
CH4 concentrations. Water was pumped continuously from a depth
of ~ 0.5 m at a ow rate of ~ 3 L min1 using a Rule bilge pump to a
showerhead equilibrator, and 222Rn, CO2 and CH4 were measured in
a dried closed gas loop using the system described in Santos et al.
(2012). 222Rn was measured at 10 minute intervals using a RAD7
radon detector. The RAD7 uses a silicon semi-conductor to count the
positively charged 218Po and 214Po daughters. Dissolved 222Rn concentrations were then calculated using the temperature and salinity function of solubility (Schubert et al., 2012). pCO2, pCH4, 13CCO2 and
13CCH4 were measured from the same gas stream using a cavity
ring down spectrometer (CRDS, Picarro G2201-i) at ~ 1 second intervals and then averaged over 1 minute intervals (Maher et al.,
2013b). The xCO2 and xCH4 (i.e. dry CO2 and CH4 concentrations measured by the CRDS) were converted to in situ pCO2 and CH4 using standards equations (Pierrot et al., 2009) with pCH4 converted to
concentrations using the solubility coefcients of Yamamoto et al.
(1976).
Four calibration gases (two CO2 and two CH4) were analyzed prior to
each survey. CO2 standards had a concentration of 306 ppm (13C
CO2 = 14.4) and 2017 ppm (13CCO2 = 17.1) with the 13C
values referenced using an Isotope Ratio Mass Spectrometer (IRMS)
which was referenced to NIST certied standards. CH4 standards had a
concentration of 3 ppm (13CCH4 = 45.9) and 200 ppm (13C
CH4 = 40.1). The 13CCH4 values of the standards were obtained
by running the standards through a factory calibrated CRDS, and were
later referenced against certied standards obtained from Isometric

D.T. Maher et al. / Marine Chemistry 168 (2015) 6979

71

Fig. 1. Location of study area including discrete survey sampling locations (black circles), time series locations (white crosses) and estuary section classication (color coded) (For
interpretation of the references to color in this gure legend, the reader is referred to the web version of this article.).

Instruments (Tiso 1, 13CCH4 = 38.3 0.2 and Liso1, 13CCH4 =

66.5 0.2). Accuracy of CO2 concentrations was better than 1 ppm
and 13CCO2 accuracy for a 5 min average was better than 0.5. CH4
concentration accuracy was better than 80 ppb. 13CCH4 accuracy for
a 5 min averaging interval was better than 0.6 for both Tiso1 and
Liso1 standards.
Additional physico-chemical water quality parameters including
dissolved oxygen (DO), salinity, pH, chromophoric dissolved organic

matter (CDOM, expressed as Quinine Sulfate Equivalents QSE), and

chlorophylla were measured at one minute intervals throughout the
surveys using a Hydrolab DS5 sonde and Wetlabs Triplet urometer.
Instantaneous wind speed was measured using an onboard sonic
anemometer (Airmar PB200). DO concentrations were converted to
apparent oxygen utilization (AOU):
AOU = [O2] [O2]

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D.T. Maher et al. / Marine Chemistry 168 (2015) 6979

Fig. 2. Solute distribution during the four estuarine surveys (D HT = day high tide, D LT = day low tide, N HT = night high tide, N LT = night low tide). A. salinity, B. apparent oxygen
utilization (AOU), C. chlorophyll a, D. chromophoric dissolved organic matter (CDOM), E. 222Rn concentration, F. windspeed, G. dissolved inorganic carbon (DIC), H. alkalinity.

where [O2] is the measured DO, and [O2] is the oxygen concentration at
100% saturation, calculated as a function of temperature and salinity
(Benson and Krause, 1984).
Discrete samples for alkalinity (TAlk) analysis were collected at 7
equidistant spaced stations along the estuary (~ every 2 km; Fig. 1)
during each survey. Samples were ltered through 0.7 m GFF lters
into 30 mL polycarbonate vials, and stored at 4 C until analysis within
2 days. TAlk was determined by Gran Titration using an automated titration system (Metrohm Titrando), using standardized 0.01 M HCl
and referenced to Dickson Certied Reference Material (Batch 122).
Dissolved inorganic carbon (DIC) was calculated from pCO2 and TAlk
using the CO2SYS program (Lewis and Wallace, 1998) using the carbonic acid disassociation constants of Mehrbach et al. (1973) as
retted by Dickson and Millero (1987). Excess DIC is dened as the
amount of DIC transferred to the atmosphere as CO2 after complete
waterair equilibration (Abril et al., 2000) and was calculated as the
difference between in situ DIC and equilibrium DIC both of which
were calculated using CO2SYS using TAlk and pCO2, and assuming
atmospheric pCO2 of 400 atm.

2.3. Time series

Three time series stations, measuring pCO2 and 222Rn and physicochemical water quality parameters were installed within the three sections of the estuary (Fig. 1) between 12.07 pm on the 14th of January
and 12.42 pm on the 16th of January 2013. 222Rn was sampled at 30
minutes intervals using a RAD7 radon detector. Differential nondispersive infrared (NDIR) gas analyzers were used to measure CO2
at one-minute intervals (Licor 7000 at the downstream and midstream
sites, and Licor Li-820 at the upstream site). The downstream Licor was
calibrated prior to deployment using 0 ppm, 306 ppm and 2017 ppm
standards (Coregas, Australia). The mid- and upper estuary Licor instruments were calibrated with 0 ppm, 2017 ppm and 10,000 ppm
standards (Coregas, Australia). A submersible pump (Rule bilge
pump) was used to deliver water to a showerhead equilibrator from
which a closed air loop was continuously pumped through the Rad7
and NDIR analyzers (Santos et al., 2012). Temperature, dissolved oxygen, salinity, and pH, were also monitored at 10 minute intervals at
these sites using calibrated Hydrolab DS5x sondes.

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73

Table 1
Key estuarine characteristics during the four spatial surveys. Fluxes are integrated over the 6 hour period centered on the survey. D HT = day high tide survey, D LT = day low tide survey,
N HT = night high tide survey, N LT = night low tide survey.

D HT
D LT
N HT
N LT

Estuary
volume
(m3)

Ave
depth
(m)

Ave k600
(m d1)

Total
CH4
(mol)

Total excess
DIC
(mol)

Total AOU
(mol)

222

Rn
inventory
(dpm)

Total atmospheric
CO2 ux
(mol)

Total atmospheric
CH4 ux
(mol)

13CCO2 Source
()

13CCH4 Source
()

6,043,801
2,993,108
5,471,821
2,613,022

3.17
1.57
2.87
1.38

2.75
1.70
0.98
1.14

44
48
72
89

36,1219
48,8579
43,7376
52,0909

12,584
43,581
84,977
13,4646

1.81 109
3.01 109
3.33 109
N.D.

6139
22,151
7003
18,957

2
11
5
16

20.44 (0.09)
22.16 (0.08)
20.39 (0.12)
22.22 (0.09)

59.59 (0.12)
60.08 (0.16)
65.17 (0.08)
63.76 (0.17)

where k is the gas transfer velocity of CO2 or CH4 (cm h1), is the solubility coefcient of CO2 (Weiss, 1974) or CH4 (Yamamoto et al., 1976),
and C is the difference between pCO2 and pCH4 in the air and surface
water (atm). Positive numbers indicate a ux from the water to the
atmosphere while negative numbers indicate atmosphere to water
exchange. Gas transfer velocities of sparingly soluble gases such as
CO2 and CH4 are dependent on aqueous boundary layer turbulence
(Broecker and Peng, 1982). Determining gas transfer velocities when
calculating CO2 and CH4 uxes can be problematic due to the high degree of heterogeneity in environmental conditions, which is particularly
true for shallow tidal systems such as estuaries (Raymond and Cole,
2001). CO2 and CH4 uxes have been calculated using the gas transfer
parameterization of Borges et al. (2004b):

This empirical relationship which was established for the Scheldt estuary was used due to the similar morphological characteristics of the
Scheldt estuary and North Creek estuary (Atkins et al., 2013). It is important to note, however, that the relationship between wind speed
and k600 in estuaries is likely to be site specic (Borges et al., 2004a).
In situ Schmidt numbers of CO2 and CH4 were calculated using the
equations of Wanninkhof (1992) from in situ temperature and salinity
assuming a linear relationship of the Schmidt number and salinity
between salinities of 0 and 35. To calculate estuary-wide uxes from
the spatial surveys, ux rates from each individual point were interpolated using the spline with barrier methods in ARC GIS (Maher and Eyre,
2012). To calculate estuary-wide uxes from the time series data, we
assumed that the measured pCO2 at each of the time series stations
was representative of the entire section they were situated within (as
dened in Fig. 1). We used wind speed data from the surveys to calculate time specic rates, as described for the surveys, and scaled the rates
to the entire section based on section specic areas. The one minute
uxes from each section were integrated over the same time period that
the surveys were undertaken, and divided by the total estuarine area
and number of days to compare estuary-wide uxes based on surveys
and time series methods.

k600 = 5.141u0.758
10

2.5. Estuarine inventory

where k600 is the gas transfer velocity (cm h1) normalized to a Schmidt
number of 600, and u10 is the wind speed at a height of 10 m (m s1).

Hydrographic survey data from the New South Wales Department of

Environment and Heritage was used to produce a 10 m 10 m grid

2.4. Flux calculations

Airwater gas exchange rates are controlled by gas solubility, the
concentration gradient between the water and air phase and the gas
transfer velocity:
F = kC

Fig. 3. Distribution of pCO2, dissolved CH4, 13CCO2, and 13CCH4 during the four estuarine surveys.(D HT = day high tide, D LT = day low tide, N HT = night high tide, N LT = night
low tide).

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D.T. Maher et al. / Marine Chemistry 168 (2015) 6979

resolution ( 0.1 m) digital elevation model (DEM). Estuarine CH4

loads for each survey (i.e. the total mass of dissolved CH4 within the entire estuary), were calculated by integrating an interpolated GIS raster
of CH4 concentration constructed using ARC GIS, with the bathymetric
DEM (corrected for tidal height during each survey). The same mass
loading method was used to calculate estuarine inventory of 222Rn,
AOU and excess DIC. Due to the shallow depth (average of 2.3 m) and
generally narrow channel (Fig. 1), homogenous vertical and cross
creek distribution in concentrations were assumed. The tidal height
was assumed to be constant throughout each survey. Surveys were
initiated 1 h prior to high and low tides, and surveys took ~2 h to complete. This resulted in a maximum depth variation of ~12 cm over the
duration of individual surveys, which leads to an error of between 4%
and 9% for the four surveys based on the average estuary depth during
each survey.
2.6. Isotopic characterization of CO2 and CH4 sources
To estimate the isotope value of the CH4 and CO2 sources during each
survey we used the linear model developed for atmospheric CO2 isotopic source characterization in the form of:
obsCobs = sCobs Cbg(bg s)
where C and are concentration and 13C, respectively, and the subscripts obs, bg and s refer to the observed, background and source values
(Miller and Tans, 2003), respectively. By plotting obsCobs (y) against
Cobs (x) (MillerTans plots) the slope of the line is equal to s.

There was a distinct offset in the spatial distribution of 13CCO2 between high tide and low tide surveys in the lower and mid-estuaries,
with low tide surveys having 13CCO2 values ~ 2 depleted for a
given distance from the mouth (Fig. 3C). 13CCO2 values converged
at the most upstream location for all tides at ~19. Spatial distribution of 13CCH4 values differed between each survey, with least depleted values during the D HT survey and most depleted values in the lower
half of the estuary during the N LT survey. (Fig. 3D). During the high tide
surveys 13CCH4 generally showed an upstream depletion in 13C
value, while during the low tide surveys, 13CCH4, values decreased
from the lower to mid-estuary then increased from the mid to upper
estuary.
Salinity was relatively constant at the lower estuary time series station (Fig. 4A), and displayed a clear tidal trend at the mid estuary
(Fig. 4B) and upper estuary stations (Fig. 4C). Time series station pCO2
and 222Rn generally followed a tidal trend at all three time series
stations. pCO2 ranged from ~ 5001200 atm, 140012,000 atm and
40006000 atm at the lower (Fig. 4A), mid (Fig. 4B) and upper estuary
(Fig. 4C) stations, respectively. Highest 222Rn concentrations (up to
~4200 dpm m3) were measured in the mid-estuary (Fig. 4B) and the
lowest concentrations were measured in the lower estuary (Fig. 4A).
The highest 222Rn concentrations and pCO2 values at the mid estuary
station exceeded the highest survey values by ~2 fold.
There was a distinct difference in overall estimated diffusive CO2 and
CH4 uxes between high and low tides. The integrated estuary-wide
CO2 ux during the D HT survey was 19.32 mmol CO2 m2 d1 while
the D LT was 69.70 mmol CO2 m2 d1 (Fig. 5). The difference between

3. Results
Salinity ranged between ~ 36 and 10 throughout the study and
was similar during the day high tide (D HT) survey and night high
tide (N HT) survey (Fig. 2A). Both low tide surveys also had similar salinity distribution (Fig. 2A). AOU ranged from ~ 5 to 110 mol kg1
(Fig. 2B), and showed a general upstream increase during each survey.
During both high tides, AOU increased to ~ 110 mol kg1 within the
mid estuary and remained at this level in the upper estuary. During
both low tides, AOU increased from the lower estuary to the midestuary and then decreased in the upper estuary where AOU declined
to ~10 mol kg1 during the day low tide (D LT). Chlorophyll a concentrations increased in the upstream direction under all tidal regimes and
during both low tide surveys chlorophyll a was ~2 fold higher within
the upper estuary (Fig. 2C). CDOM had a general upstream increase in
concentrations however there were distinctively higher mid estuary
concentrations, and lower upper estuary concentrations during each
of the low tide surveys (Fig. 2D). 222Rn showed a general upstream
increase, however the D LT survey shows a mid-estuary maximum,
with a decrease upstream (Fig. 2E). Due to instrument failure, no
222
Rn data is available for the night low tide (N LT) survey. Wind
speed was generally higher during the two day time surveys and generally lower in the upstream direction (Fig. 2F). Alkalinity and DIC ranged
from 5902583 mol kg1 and 7272499 mol kg1 respectively, and
showed a similar trend along the estuary (Fig. 2G, H).
pCO2 showed a general upstream increase. However during both
low tides, pCO2 showed a decrease in the upstream direction of the
upper estuary (Fig. 3A). Night time pCO2 was generally higher for each
tide than the respective day time pCO2, particularly within the mid estuary. pCO2 in the upper estuary during both high tides were similar
(~6000 atm). CH4 concentrations were highest during the N LT survey,
with concentrations reaching the highest concentration at 12 km
upstream at ~ 150 nmol before decreasing further upstream (Fig. 3B).
Concentrations during the N HT were higher than during the D HT.
Except for the N LT, CH4 concentrations showed a general increase in
the upstream direction, with the highest concentration recorded in
the upper estuary.

Fig. 4. Temporal variability of salinity, pCO2 and 222Rn in the three time series stations.
A. lower estuary, B. mid-estuary and C. upper estuary sites. The * on each graph denotes
the time when surveys passed the time series sites, gray shaded areas represent night time.

D.T. Maher et al. / Marine Chemistry 168 (2015) 6979

Fig. 5. Integrated average estuary-wide water to air uxes of CO2 and CH4 for the four
surveys. D HT = day high tide, D LT = day low tide, N HT = night high tide, N LT =
night low tide.

N HT and N LT showed a similar trend with a 2.7 fold increase in CO2

ux at low tide. Estuary-wide uxes of CH4 showed an even greater
difference between tides with the integrated estuary D HT ux of
7 mol CH4 m 2 d 1 while the D LT ux was 36 mol CH4 m 2 d 1
(Fig. 5). CH4 ux during the N HT survey of 17 mol CH4 m2 d1 and
the N LT ux was 51 mol CH4 m2 d1CH4.
The estuarine inventory showed distinct differences in excess DIC,
AOU, CH4 and 222Rn between each survey (Table 1). Despite a smaller
volume of water in the estuary during low tide, inventories were generally higher for all parameters during the low tide surveys. Night time
AOU, excess DIC, CH4 and 222Rn inventories were higher than those during the day time for the same tide. The 13CCH4 value of the source of
CH4 to the estuary ranged from 59.56 to 65.17 over the four
surveys, with values more depleted during the night time surveys
(Table 1). 13CCO2 source values showed no diel difference, but there
was a distinct tidal difference with D HT and D LT values of 20.44
and 22.16 respectively and N HT and N LT values of 20.39
and 22.22 respectively (Table 1). The estuary integrated water to
air ux for each tidal regime (6 hour period) varied from 2 to 16 mol
for CH4 and 6139 to 22151 mol of CO2 (Table 1).
4. Discussion
Estuaries are important in terms of the global carbon cycle. However,
there are few studies on diurnal and tidal variation of CO2 and CH4
concentrations and water to air uxes at the whole estuary scale. This
is likely due to the challenging logistics required. Undertaking four
surveys over a 24 hour period, while at the same time having three
xed time series stations along the length of the estuary may preclude
our strategy from being used in many estuaries. However, the insights
gained from this study are likely to be relevant to other shallow productive estuaries, and/or estuaries inuenced by groundwater inputs, and
may help guide future sampling strategies. There were clear tidal and
diurnal differences in CO2 and CH4 concentrations, 13C values and
estimated diffusive water to air uxes. Further, there were differences
in the estimates of whole estuary water to air CO2 uxes based on
xed time series and survey methods.
Diurnal variability in pCO2 and CH4 can be attributed to four processes; 1) temperature driven differences in gas solubility/thermodynamics,
2) convection in the water column and/or sediment water interface,
3) diel primary production/respiration and methane production/
oxidation cycles and 4) diurnal variability in wind speed and associated
evasion rates. Wind speed was generally higher during the day in the
lower estuary (Fig. 2F). However in the mid and upper estuaries
(where pCO2 and CH4 where highest), wind speeds where generally
similar for the D LT, N HT and N LT surveys, although somewhat higher
for the D HT survey. Average k600 values based on the wind speed
parameterization of Borges et al. (2004b) for each survey were 2.75,

75

1.70, 0.98 and 1.14 m d1 for the D HT, D LT, N HT and N LT surveys respectively. This equates to a loss of 22, 28, 9 and 21% of the CO2 and CH4
inventories in excess of atmospheric equilibrium for the 6 hour period
between the surveys for the D HT, D LT, N HT and N LT surveys, respectively. These differences could explain some of the diurnal variability in
surface water pCO2 and CH4 through increased evasion during the day
when winds are usually stronger.
While we have only used wind speed to determine k600, studies have
found that currents in shallow estuarine systems can contribute significantly to surface turbulence and therefore gas transfer velocity
(Zappa et al., 2003; Borges et al., 2004b; Ho et al., 2014). For example,
Ho et al. (2014) found that by neglecting to include bottom generated
turbulence, k600 was underestimated by between 40 and 70% in the
Shark River estuary. Atkins et al. (2013) found that current driven
evasion dominated water to air uxes of CO2 and 222Rn in the upper
North Creek estuary. Current driven surface turbulence is controlled
by velocity, depth and bottom roughness (O'connor and Dobbins,
1958; Zappa et al., 2003), and therefore would not be subjected to diurnal variability. As such, it is likely that the differences associated with diurnal wind changes are overestimated, due to the lack of current driven
surface turbulence parameterization. Further, integrated estuary-wide
water to air uxes of CO2 and CH4 showed the opposite diurnal trend
to k600 values, with higher or similar estuary integrated uxes at night
(Table 1).
Temperature affects pCO2 through changes in solubility and thermodynamic shifts in the carbonate system, with warmer water having a higher partial pressure of the gas at the same concentration
(Takahashi et al., 1993). Previous studies have found that temperature
can drive diurnal changes in pCO2 in the open ocean (Goyet and
Peltzer, 1997; Bates et al., 1998) and oligotrophic areas of the South
China Sea (Dai et al., 2009), However, diurnal temperature variation
(i.e. warmer water temperatures during the day), would lead to higher
pCO2 during the day and lower pCO2 during the night, the opposite to
what was found during this study. Therefore we can exclude temperature driven changes in solubility as the source of diurnal variability in
surface water pCO2 dynamics during our study.
Diurnal primary production and respiration cycles lead to a lower
pCO2 during the day, driven by CO2 uptake by primary producers, and
higher pCO2 during the night through in situ respiration. The effect of
ecosystem metabolism on estuarine CH4 dynamics is less clear. However, enhanced oxygen production during the day, and depletion during
the night may lead to oscillations in sediment oxygen penetration,
inuencing CH4 production and oxidation rates (King et al., 1990;
Maher et al., 2013b). Ecosystem primary production and respiration
has been found to control pCO2 diurnal variability in the coastal waters
of Tampa Bay (Yates et al., 2007), coral reefs (Gattuso et al., 1993;
Cyronak et al., 2014) and in macrophyte beds (Saderne et al., 2013).
The tight coupling between pCO2 and AOU in the mid- and lower estuaries (i.e. AOU b ~90 mol kg1; Fig. 6C), suggests that in situ biological
processes exerts some control over pCO2 in this section of the estuary. In
addition, a signicant relationship between pCO2 and CDOM, and also
CH4 and CDOM (Fig. 6H) may be indicative of dissolved organic matter
(and associated respiration and/or photodegradation) contributing to in
situ pCO2 and CH4 dynamics.
Interestingly in the upper estuary, there was a sharp decline in AOU
(Fig. 2B) during the two low tide surveys, and the pCO2AOU relationship displayed discontinuity, with AOU decreasing but pCO2 remaining
relatively constant (Fig. 6C). Further, highest chlorophyll a concentrations throughout the study occur at the upstream limit during both of
the low tide surveys (Fig. 2C). This suggests that primary production is
higher in the upper estuary beyond the boundary of the study area,
and during low tide this water ows into the upper estuary section of
the study area. This water is high in oxygen (i.e. low AOU), however
pCO2 remains relatively high. This indicates that a process other than
in situ primary production and respiration are driving pCO2 dynamics
throughout some parts of the estuary. While nitrication can be a

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D.T. Maher et al. / Marine Chemistry 168 (2015) 6979

signicant oxygen consumption process in eutrophic estuaries (Gazeau

et al., 2005) and through H+ production, nitrication concomitantly
increases pCO2, (Frankignoulle et al., 1996), our previous investigations
in North Creek have found relatively low DIN concentrations (up to
4 M, unpublished data) which suggests this may not be a major driver
of AOU or pCO2 in North Creek.
In addition to diurnal variability, during our study, pCO2, CH4, 13C
CO2 and 13CCH4 distribution had marked tidal differences, particularly in the mid-estuary surrounded by mangroves (Fig. 3). There were also
clear differences in the 13C source values and estuarine inventories of
CO2 and CH4 (Table 1). Few studies have assessed the spatial dynamics
of pCO2 over different tides, and to our knowledge there have been no
studies on the tidal inuence on in situ CH4 concentration, 13CCO2
and 13CCH4 distribution along an estuary. Jiang et al. (2008) found
average annual low tide estuary integrated pCO2 was ~ 50% higher

than high tide values for 3 estuaries along the Georgia Coast (USA).
Wang and Cai (2004) also found differences between high and low
tide pCO2 in the nearby Duplin River (Georgia USA), with the greatest
difference occurring during the summer. Tidal variability in estuarine
CH4 concentrations have been previously assessed at xed time series
stations (Dulaiova et al., 2006; Bouillon et al., 2007; Deborde et al.,
2010; Linto et al., 2014) which have found tidal variability in concentrations with higher concentrations during low tide, as found during our
study.
Tidal differences in surface water pCO2 and CH4 concentrations
are driven by a number of processes, including inputs and mixing of
freshwater and oceanic water, inputs of CO2 and CH4 enriched groundwater, lateral inputs from marshes, mangroves and intertidal areas, and
stimulation of in situ primary production and/or respiration by inputs of
organic matter and/or nutrients from any of these processes. There was

Fig. 6. Relationship between: 222Rn and pCO2 (A.), 222Rn and CH4 (B.), AOU and pCO2 (C.), AOU and CH4 (D.), Chlorophyll a and pCO2 (E.), Chlorophyll a and CH4 (F.), CDOM and pCO2
(G.), CDOM and CH4 (H.) during the four estuarine surveys.

D.T. Maher et al. / Marine Chemistry 168 (2015) 6979

a signicant positive exponential relationship between 222Rn (an

unambiguous groundwater tracer in North Creek, Atkins et al., 2013)
and both pCO2 (all surveys, R2 = 0.88 n = 53, p b 0.001) and CH4 (all
surveys, R2 = 0.88, n = 53, p b 0.001) (Fig. 6A and B) indicating that
groundwater/porewater exchange is closely coupled to surface water
pCO2 and CH4 dynamics (see below). There was also a signicant positive linear relationship between CDOM and 222Rn (R2 = 0.82, n = 53,
p b 0.001), which may simply be a covariance between groundwater
input and CDOM, or, CDOM may be derived from groundwater. The
relationship between CDOM and both CH4 and pCO2 described earlier,
may therefore be due to groundwater derived inputs of dissolved
organic matter as observed in other systems (Santos et al., 2009; Kim
et al., 2012; Maher et al., 2013a).
Temperature driven convection of porewatersurface water exchange may explain diurnal variability in pCO2 and CH4 dynamics.
Rocha (2000) found that temperature driven convection of porewater
in permeable intertidal estuarine sediments may lead to a rapid
exchange of porewater with surface waters, and the process can be orders of magnitude more important than diffusive uxes. As porewaters
are highly enriched in pCO2 and CH4 (Cable et al., 1996; Atkins et al.,
2013), diurnal temperature driven porewater convection could explain
the diurnal patterns found during this study. Interestingly, 222Rn also
showed diurnal variability, with concentrations and inventory higher
during the N HT survey than the D HT survey (Fig. 2E, Table 1), which
implies increased groundwater/porewater inputs during the night.
High night time 222Rn is consistent with observations in a coral reef
lagoon, where the faster cooling of surface waters than underlying
porewater at night was suggested to create a density inversion at the
sediment-water interface that could explain a 15% increase in night
time groundwater discharge (Santos et al., 2011). Further, the estuarine
inventory of CH4, excess DIC, 222Rn and the total estuarine AOU show
higher values during the night than during the day (Table 1). While
primary production and respiration could explain diurnal CH4 and
pCO2 dynamics, clearly the increased 222Rn inventory during the N HT
survey is not linked to biological processes, and implies that temperature driven sediment porewater convection may be a local driver of
surface water chemistry.
Atkins et al. (2013) found that groundwater was the major driver of
surface water pCO2 in the upper section of the North Creek estuary
where agricultural drains cut through the shallow aquifer. In this
study there was a strong relationship between pCO2 and CH4 and
222
Rn throughout the rst three surveys (Fig. 6A and B; 222Rn unavailable during the fourth survey), suggesting that surface water pCO2 and
CH4 is coupled to groundwater/porewater inputs either directly (i.e. inputs of CO2 and CH4 enriched groundwater) or indirectly (e.g. through
groundwater inputs fuelling ecosystem metabolic responses that in
turn inuence surface water pCO2 and CH4).
Whether CH4 is oxidized or uxed to the atmosphere from an estuary has important implications considering CH4 has a global warming
potential (GWP) ~100 times greater than CO2 (the product of CH4 oxidation) over a 20 year time frame (Shindell et al., 2009). The importance
of oxidation as a CH4 sink varies considerably among estuaries, and even
within an estuary. For example Sansone et al. (1999) found evidence of
CH4 oxidation in the Columbia River estuary (USA), but not in four other
estuaries and Upstill-Goddard et al. (2000) found that CH4 oxidation
rates were an order of magnitude lower than atmospheric ux in
North Sea estuaries. Abril and Iversen (2002) found high rates of CH4
oxidation at a brackish water station, but minimal rates in the lower
estuary of Randers Fjord (Denmark) and Abril et al. (2007) found enhanced CH4 oxidation at the estuarine turbidity maximum zone in the
Gironde Estuary in France. The survey 13CCH4 values during this
study suggest that minimal oxidation of CH4 occurred along the estuary
(Fig. 3D). During oxidation, 13CCH4 values become more positive due
to preferential oxidation of the more negative (lighter) CH4 pool by
methanotrophs (Whiticar, 1999). However, lower estuary 13CCH4
are lower than atmospheric equilibrium (approximately 47; Quay

77

et al., 1999) and the 13CCH4 source values (Table 1) are in the range
expected for the acetate reduction pathway (~ 65 to 50;
Whiticar et al., 1986).
Integrated estuary-wide average uxes for the surveys were 19 to
70 mmol m2 d1 for CO2 and 7 to 51 mol m2 d1 for CH4 (Fig. 5).
These uxes fall within the range of uxes reported for estuaries
(Borges and Abril, 2011). Typically, estuarine pCO2 and CH4 are
surveyed once (most likely during the day), and uxes are based on
these single surveys. Alternatively, pCO2 and CH4 may be measured at
a xed time series station, with ux estimates scaled up to the
surrounding area based on those single location concentrations
(e.g. Bouillon et al., 2007; Atkins et al., 2013). Using either of these
methods in isolation, and not accounting for diurnal, tidal and spatial
variability may lead to signicant under or over estimation of total
water to air uxes. While the "four survey" method presented here
may seem most likely to provide accurate estimates, a comparison
with uxes based on the time series data suggest that this may not be
the case for all sections of the estuary (Fig. 7). The large discrepancy between the CO2 ux estimates from the time series and survey data for
the mid estuarine section was due to the surveys not passing through
this section of the estuary during the times of highest pCO2 (see * locations in Fig. 4). This section of the estuary had a pCO2 range of 1400 to
12,000 atm, however the highest pCO2 measured during the survey
was only ~6000 atm. The peak in pCO2 during the time series occurred
23 hours after low tide, after the survey had passed through that section of the estuary. The same is observed for 222Rn, where the highest
survey concentrations were ~ 2200 dpm m3, but at the mid-estuary
time series station concentrations reached ~4000 dpm m3. Therefore
a combination of time series and spatial surveys may be required to
adequately constrain the variability in estuarine pCO2 and CH4 uxes.
5. Conclusion
While it was beyond the scope of this study to quantitatively assess
all the drivers of diurnal and tidal variability in surface water pCO2 and
CH4 dynamics, insights from the high temporal and spatial resolution
time series and survey experiments suggest that a complex interaction
of biological (productivity/respiration), hydrological (groundwater inputs and mixing of riverine and oceanic waters) and physical (temperature driven porewater/groundwater convection and wind driven
evasion) processes occurred. One of the major limitations in scaling up
estuarine water to air greenhouse gas uxes to the global scale is the
paucity of information on diurnal dynamics (Cai, 2011). In this study
we show that this limitation should not be taken lightly, at least for
small shallow productive estuaries that receive some groundwater
input. By neglecting to account for tidal and diurnal differences in
surface water pCO2 and CH4, ux estimates can be signicantly over or

Fig. 7. Comparison of water to air uxes of CO2 estimated from the four spatial surveys
with estimates from the three xed time series locations.

78

D.T. Maher et al. / Marine Chemistry 168 (2015) 6979

under estimated. Research into whether similar diurnal and tidal

differences occur in larger estuaries needs to be undertaken to decrease
uncertainty in estuarine CO2 and CH4 uxes.

Acknowledgments
We acknowledge funding from the Australian Research Council
(DP120101645, LE120100156, LP110200975, LP100200732, and
DE150100581). KC acknowledges the SCU GeoScience Summer School
program for her participation in this study. DTM is funded through an
ARC DECRA Fellowship (DE150100581).

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