Carbon cycling at the estuarine interface:

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Carbon cycling at the estuarine interface:

a new model for regional and global scale assessment

by Chiara Volta

A dissertation submitted in fulfillment of the requirements for the degree of

Doctor of Philosophy (Sciences)

in theUniversité Libre de Bruxelles - March 2016 -

Promotor: Prof. Dr. P. Regnier

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“Essentially, all models are wrong, but some are useful.”

George E. P. Box, 1979

To Juza

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SUMMARY

The qualitative and quantitative understanding of carbon fluxes between the different Earth reservoirs is essential for a robust estimation of the global carbon budget and for a reliable assessment of the impact of additional carbon inputs from human activities on the climate of our planet. Estuaries are aquatic environments extending between the river and the coast, typically recognized as important transition zones controlling the elemental fluxes from the terrestrial to the oceanic compartment of the Earth system. Despite their active biogeochemical processing, no monitoring system or modelling approach is currently able to represent the wide variety of estuarine systems worldwide. As a consequence, estuaries are currently excluded from estimates of the carbon budget at global scale and their overall global filtering effect is still poorly constrained.

The overarching goal of this thesis is to develop a diagnostic and predictive model to quantify the estuarine CO2dynamics across scales - from catchment to the globe - using an approach that explicitly resolves the strong physical and biogeochemical gradients typically observed in these systems. Due to their wide distribution all over the Earth, especially within highly populated regions, and their strong processing of land-derived matter, the focus of our research is here on alluvial estuaries.

Chapter 1 provides fundamental definitions and descriptions of estuaries, as well as an assessment of their role in the global carbon cycle. This analysis highlights the lack of quantitative tools to gauge the effect of the estuarine filter on the riverine carbon loads

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knowledge gap.

Chapter 2 presents the rationale behind the novel modelling approach (C-GEM, Carbon- Generic Estuary Model) developed in the framework of this thesis. First, a detailed overview of the dominant physical and biogeochemical processes that control transformations and fluxes of carbon and associated bio-elements (nitrogen, phosphorous and silica) along the estuarine gradient is provided. The tight link between geometry, hydrodynamics and scalar transport in alluvial estuaries, as well as their transient and non-linear dynamics is also highlighted. The most important biogeochemical processes are then discussed in terms of key biogeochemical indicators, such as the Net Ecosystem Metabolism (NEM), air-water CO2 fluxes, nutrient filtering capacity and element budgets. Finally, trends in estuarine biogeochemical dynamics across different geometries and environmental scenarios are briefly explored with C-GEM. These preliminary results are discussed in the context of improving the modelling of estuarine carbon and CO2 dynamics at regional and global scales.

Chapter 3 provides a detailed description of C-GEM, both in terms of structure and set-up. The model relies on a novel theoretical framework that recognizes the strong interdependence between the estuarine geometry, its hydrodynamics and biogeochemistry. This interdependence allows using an idealized representation of the estuarine shape to capture the biogeochemical dynamics of a given system. C-GEM’s idealized geometries only require the specification of a few geometrical characteristics, such as the estuarine length, the convergence of its banks and the average water depth. For any system, this information is readily available from local maps, satellite imagery (e.g. Google Earth) or from existing empirical relationships. The resulting model structure reduces computational time and data requirements in such a way that C-GEM can perform simultaneously multiannual simulations for a large number of estuarine systems, including those that are poorly surveyed. In this chapter, C-GEM’s performance is evaluated through comprehensive model-data and

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model-model comparisons in the funnel-shaped Scheldt estuary (BE/NL), one of the best- surveyed tidal estuaries in the world. Results reveal that longitudinal steady-state profiles of oxygen, ammonium, nitrate and silica are generally in good agreement with measured data. In addition, simulated, system-wide integrated reaction rates of the main pelagic biogeochemical processes are comparable with those obtained using a high-resolution, two- dimensional RTM. Finally, a sensitivity analysis of the effect of geometrical and reaction parameter values on the estuarine biogeochemical functioning indicates that the lack of an objective framework for solid transport and biogeochemical process parameterization remains a significant hurdle towards regional and global applications of C-GEM. The need for a global compilation of model parameter values that can help identify common trends and possible relationships between parameters and controlling factors, such as climate, catchment characteristics and anthropogenic pressure, is thus clearly emphasized.

In Chapter 4, the domain of applicability of C-GEM is extended by combining the modelling approach developed in the previous chapter with a generic set of forcing conditions and parameter values representative of average temperate conditions worldwide.

Forcings are extracted from well-established high-resolution environmental databases (e.g.

World Ocean Atlas, GLORICH) and global statistical models (e.g. GlobalNEWS2), while a generic set of biogeochemical parameters is obtained from a comprehensive literature survey of estuarine modelling studies (∼50). This model set-up is applied to three idealized geometries, whose hydro-geometrical characteristics span the wide diversity of estuarine morphological characteristics. Results from simulations performed for the present decade predict that about 20-40% of the river carbon is lost as CO2 through outgassing along the estuarine filter, which translates into a first order estimate of the total CO2outgassing flux from all tidal estuaries worldwide comprised between 0.04 and 0.07 Pg C yr⁻¹. Prospective simulations for the year 2050 suggest that the carbon dynamics will only marginally be affected by river load changes (C, N, P, Si), whereas the expected increase in atmospheric CO2partial pressure in the future will trigger a significant reduction of the CO2outgassing

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Finally, Chapter 5 provides the first application of C-GEM at the scale of a regional sea.

Here, the overall carbon export and CO2outgassing from all tidal estuaries discharging into the North Sea are quantified. Simulations are first performed for the most important tidal estuaries in terms of freshwater inputs (Scheldt, Elbe, Ems, Weser, Humber and Thames) and model results are used to estimate an average estuarine filtering efficiency with respect to land-derived carbon. This filtering capacity is then applied to the carbon inputs incoming from all rivers discharging into tidal estuaries bordering the North Sea. Results reveal that for yearly-averaged conditions, only about 15% of the total (organic and inorganic) carbon inputs is lost as CO2 to the atmosphere before reaching the coast. The carbon export is largely occurring in the inorganic form (>90%), a result that highlights the very intense processing of organic carbon within the systems. Simulation results indicate that the CO₂ outgassing is mainly induced by heterotrophic degradation processes, while nitrification only plays a marginal role through its impact on pH. In addition, they reveal a significant contribution of the ventilation of riverine CO2to the estuarine CO2emission, although this contribution strongly depends on the physico-chemical characteristics of the incoming river waters. Overall, our results suggest that the estuarine carbon filtering capacity and their contribution to the atmospheric CO2budget might not be as high as previously thought.

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CHAPTER I

General Introduction

1.1 Introduction

Carbon is arguably one of the most essential elements for the life on Earth as we know it. It is not only able to create stable and complex organic molecules that represent the building-blocks of all living-organisms, but in its gaseous forms in the atmosphere, such as carbon dioxide (CO2) and methane (CH4) mainly, it also helps to maintain a suitable temperature for life by trapping the infrared emission emitted by the Earth that would otherwise escape into the space (Mitchell et al., 1995;Raven and Johnson, 2001;Sabine and Feely, 2002). In addition to the biosphere and the atmosphere, carbon is also distributed in other Earth’s system compartments, including the hydrosphere, the lithosphere, as well as the cryosphere, and it is moves between all these pools following the so-called global carbon cycle (Archer, 2010). In the carbon cycle, reservoirs dynamically interact with one another by exchanging carbon through a myriad of physical, biological, chemical and geological transformations that operate on varying timescales ranging, for instance, from seconds (e.g.

gas dissolution in water), days (e.g. photosynthesis/respiration cycle of plants), seasons and years (e.g. growth/decay cycle of plants and animals) to millennia (e.g. sediment burial/rock weathering cycle) (Fig. 1.1).

Since 1750, human activities, such as burning fossil fuel and oil, as well as land-use and land-cover changes have released huge amounts of carbon in the atmosphere (∼550 Pg C;Ciais et al., 2013), mainly as CO2, and major concerns about how and how much this additional flux has altered or will modify the global carbon cycle and, ultimately, the Earth climate have motivated a great deal of interest in the scientific community in the last three

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Figure 1.1: Simplified representation of the global carbon cycle showing the typical turnover scales for carbon exchange through the major reservoirs. Modified afterCiais et al., 2013.

decades (e.g. Emanuel et al., 1984; Bolin, 1986; IPCC Report, 1990, 1996, 2001, 2007, 2013;Post et al., 1990;Wollast et al., 1993;Ver et al., 1999;Falkowski et al., 2000;Janzen, 2004;Le Quéré et al., 2009, 2015). To date, combinations of data, algorithms, statistics and model applications have led to significant advances in key areas, from climate history to predicting future scenarios at a global scale (e.g.Petit, 1999;Rahmstorf, 2002;Bauer et al., 2003;Moss et al., 2010), and have highlighted that anthropogenically-induced changes in the global carbon cycle, as well as in the biogeochemical cycling of associated bio-elements, such as nitrogen, phosphorous and silica, are becoming evident (Wollast and Mackenzie, 1989;Vitousek et al., 1997;Mackenzie et al., 2002;Gruber and Galloway, 2008;Laruelle et al., 2009a). For instance, the ocean, which was likely a source of carbon for the atmosphere prior to 1750, became a sink during the 20th century due to the anthropogenically-induced increase of the atmospheric CO2partial pressure above the oceanic value, which triggers CO2dissolution rather than outgassing (Fig. 1.2;Ciais et al., 2013).

Currently, global carbon budgets, as for example that reported by the last Assessment Report (AR5) of the Intergovernmental Panel of Climate Change (IPCC Report, 2013), are

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1.1. INTRODUCTION

LAND (ΔC=0.05+0.9) INLAND WATERS (ΔC≈0)

ESTUARIES (ΔC≈0)COASTAL OCEAN (ΔC=+0.05)

OPEN OCEAN (ΔC=+2.4) SEDIMENTS & BEDROCK(ΔC=0.5+0.45)

FOSSIL FUEL RESERVES (ΔC=-7.9)

ATMOSPHERE(ΔC=-0.55+4.2) 1.1+0.9+ 0.8+0.20.85+0.10.65+0.1

-0.4 5+2.3

0+0.2 0.25+?

-0.4 5+0.1 5

0.7+0.5 0.2+0.1 1.15+1.7

0.2 0.2 +0.1 5

0.15-0.0 5

0.2+0.4 0.4 +0.1

0.3+0.0 5

0+7.9

FFFFFFFFFW1 ATM3G ATM1ATM2ATM5ATM6ATM4ATM7 0.15

FFF FW2 FB1FB2FB3FB4

F1 F2 F3 F4

FW1 CO2 uptake by bedrock weathering FG Geological fluxes FATM1 CO2 uptake by open ocean FATM2 CO2 uptake by coastal ocean FATM3 CO2 emissions from estuaries FATM4 CO2 uptake/releas from mangroves and salt marshes FATM5 CO2 emissions from inland waters FATM6 Autochthonous C input to inland waters FATM7 Net CO2 flux between atmosphere and land* FFF C input from fossil fuel combustion F1 C export from land to inland waters F2 C export from inland waters to estuaries F3 C export from estuaries to coastal ocean F4 C export from coastal to open ocean FB1 C burial in open ocean sediments FB2 C burial in coastal ocean sediments FB3 C burial in estuarine sediments FB4 C burial in inland water sediments FW2 C input from bedrock weathering 90% certainty that fluxes correspond to estimations 95% certainty that estimates are within 50% the reported values 95% certainty that estimates are within 100% the reported values Uncertainties are larger than 100%

LOAC Figure1.2:Present-daycarbonfluxes(inPgCyr−1 )andanthropogenicperturbations.FigureredrawnfromRegnieretal.,2013a.Black numbersrepresentthenaturalcarboncyclepriorto1750,whilerednumberscorrespondtotheadditionalanthropogenicdisturbances. ∆CrefertovariationsinreservoirCmasses.FluxesarefromRegnieretal.,2013a.Thegreyboxhighlightscarbonfluxesalongthe Land-OceanAquaticContinuumzone(LOAC),includinginlandwaters,estuariesandcoastalseas,whiletheenvironmentalinterfaceof interestofthisstudyishighlightedinbold.StarsindicatetheconfidenceintervalassociatedtofluxesestimatesasreportedintheIPCC Report(2013)andinRegnieretal.(2013a).∗ NetfluxincludingCuptakethroughphotosynthesisandCemissionsfromlanduse,fires, ricepaddies,wetlandsandheterotrophicdegradation.+ Theanthropogenicperturbationincludesanadditionalfluxfromsewage(0.1Pg Cyr−1 ).

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typically estimated by considering fluxes between the major carbon reservoirs on Earth (i.e.

atmosphere, ocean and land) and their human perturbations, but ignoring biogeochemically dynamic and variable environments, such as the interface along the Land-Ocean Aquatic Continuum zone (LOAC), including rivers, estuaries and coastal seas (Mackenzie et al., 2012;Regnier et al., 2013a). Recent estimates indicate that anthropogenic activities may have increased the carbon flux from the LOAC to the open ocean of about 0.1 Pg C per year since 1750 and released an additional 0.35 Pg C yr⁻¹ to the atmosphere (Fig. 1.2;

Regnier et al., 2013a). The magnitude of this perturbation thus suggests that the LOAC should be included in global carbon budget calculations. However, although several research projects, such as those affiliated to the international LOICZ (Land-Ocean Interactions in the Coastal Zone) Program (Gordon et al., 1996), have focused their attention on the quantitative significance of each LOAC’s compartment at global scale, the quantification of the carbon export to the ocean, the role of the LOAC in terms of CO2 exchange fluxes with the atmosphere and the extent to which these fluxes have been impacted by human disturbances are still associated to very large uncertainties (Bauer et al., 2013; Le Quéré et al., 2013;Regnier et al., 2013a) (Fig. 1.2). In addition, althoughRegnier et al.(2013a) calculated large, but similar uncertainties associated to global estimations of CO2vertical fluxes in rivers, estuaries and coastal zones, they also highlighted that very little quantitative information is currently available to constrain the effect of human perturbations on estuarine systems.

The need for robust estimations of the role of estuaries in the global carbon cycle, on the one hand, and for methods allowing to quantify the estuarine response to anthropogenic disturbances, on the other hand, have motivated the research presented in this study. Here, an innovative modelling approach is developed and proposed as a diagnostic and prognostic tool for local, regional and potentially global applications in alluvial estuaries. Alluvial systems are aquatic environments between a river and the coast that originates from marine and riverine sediment deposition in a costal plain area (Savenije, 2012). They are of

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1.2. WHAT IS AN ESTUARY?

relevance for the carbon budget not only because of their wide distribution all over the Earth, especially within highly populated region, but also because of their strong biogeochemical processing of land-derived matter (Laruelle, 2009; Wollast, 2003). The overarching goal of this research is to develop a flexible, cost-efficient model that, combined with highly- resolved databases for environmental conditions and model parameters, can be used to derive robust estuarine biogeochemical mass budgets across scales - from catchment to the globe. In addition, the target is also to propose a modelling approach that is compatible with the current construct of Earth-System Models of the coupled biogeochemical cycles and the climate system (Collins et al., 2011).

1.2 What is an estuary?

Estuaries are commonly recognized as the downstream zone of a river entering the coastal ocean. However, the exact definition of estuaries, and in particular the exact location of the starting and ending point of estuaries along the aquatic land-ocean continuum, has kept the scientific community busy for a long time. The need for a more accurate terminology was identified for the first time in 1958 during the Venice symposium (Venice System, 1958;

Elliott and McLusky, 2002). Nonetheless, scientists had to wait almost ten years to have the first rigorous definition of what an estuary is. In 1967, Pritchard first defined an estuary as

“a semi-enclosed coastal body of water, which has a free connection with the open sea, and within which seawater is measurably diluted with freshwater derived from land drainage”.

Hence, an aquatic environment can be defined as an estuary if 1) it is a semi-enclosed basin, whose circulation pattern is largely influenced by its lateral boundaries, 2) it has a free connection with the adjacent coastal zone, which guarantees a continuous exchange of water between the estuary and the ocean and 3) it is characterized by a salinity gradient and, thus, by a density gradient, which drives the estuarine water circulation. Following this definition, very different land-ocean transition systems, such as for instance coastal plain estuaries, fjords and deltas can be regarded as estuaries. On the other hand, the salinity-based definition of Pritchard explicitly excludes freshwater environments subject to

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tides, which effects can be observed far beyond the upstream limit of saline water intrusion.

To fill this gap,Fairbridge(1980) extended the estuarine domain to include the freshwater zone influenced by tides, the so-called tidal river. Fairbridge recalled the origin of the word

“estuary” from the Latin aestus, meaning tide, and defined an estuary as “an inlet of the sea reaching into a river valley as far as the upper limit of tidal rise, usually being divisible into three sectors: 1) a marine or lower estuary, in free connection with the open sea, 2) a middle estuary subject to strong salt and freshwater mixing and 3) an upper or fluvial estuary, characterized by freshwater but subject to strong tidal action. The limits between these sectors are variable and subject to constant changes in the river discharge”. Pritchard’s and Fairbridge’s definitions are visually compared in Fig. 1.3. Nowadays, the exact position

Figure 1.3: Schematic representation of the definitions of an estuary according toPritchard (1967) andFairbridge(1980). S=salinity. The total length of an estuary and the extent of its sub-zones can vary in response to different freshwater inputs from upstream rivers.

of the upper estuarine limit is still debated. However, although Pritchard’s definition has been widely adopted in estuarine science during decades, recent studies in tidal freshwater regions of estuaries reveal that these zones can act as important components of the estuarine systems (e.g Vanderborght et al., 2007; Arndt et al., 2009; Amann et al., 2014) and thus suggest that the definition proposed by Fairbridge may be more suitable. The latter is thus chosen as the theoretical basis of this dissertation.

Because of their location between two different water bodies, a sea and a river, estuaries show both fluvial and marine characteristics, as well as specific behaviors induced by the

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1.3. THE IMPORTANCE OF ESTUARIES

interaction of the two. Riverine characteristics are, for instance, the presence of banks, the freshwater and the downstream advective transport of solutes and solids, whereas marine characteristics are the presence of tides and saline water (Savenije, 2012). On the other hand, the large chemical and energetic gradients can be regarded as specific-estuary features (Prandle, 2009), resulting from physical, chemical, biological and geological processes that interact on very different spatial and temporal scales and respond, at different rates, to a wide array of forcing mechanisms, including tides, riverine discharge, solid and solute inputs from both the land and the sea, as well as winds, water temperature and waves (Powell et al., 1989;Dalrymple et al., 1992;Bianchi, 2007;Arndt et al., 2009;Savenije, 2012) (Fig.

1.4).

Figure 1.4: Conceptual scheme of the coupled processes operating within estuaries.

1.3 The importance of estuaries

Estuaries have always played an important role in human settlement. The continuous supply of nutrients from the surrounding drainage area makes the lands bordering estuaries excellent agricultural sites. Moreover, owing to their geomorphological protected nature and their proximity to the coast, important public infrastructures, such as harbors and cities, often developed along estuarine banks (e.g. New York, Buenos Aires, Hamburg, London, Rotterdam, Jakarta). As a consequence, more than 60% of human population currently lives

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within and around the estuarine watersheds (Alongi, 1998; Bianchi, 2007). In addition, estuaries have an important ecological value since their large nutrient availability also supports unique habitats, hosting thousands of species of birds, mammals, fishes, including most commercially important species, and other wildlife, which depend on estuaries as place to live, feed and reproduce.

From a biogeochemical point of view, the importance of estuaries is essentially related to their ability to act as filters for the solid and solute inputs incoming from the land and flowing towards the sea. Land-derived compounds are chemically and biologically processed along estuaries and, for example, can be adsorbed on fine sediment grains, incorporated in living matter, recycled or exchanged with the atmosphere. As a consequence, the estuarine biogeochemistry may have important implications for the adjacent coastal zone (Cloern, 1999; Rabouille et al., 2001; Crossland et al., 2005; Prandle, 2009; Arndt et al., 2011a;

Slomp, 2011; Regnier et al., 2013a,b). For instance, Nixon et al. (1996) estimated that estuaries flowing into the North Atlantic Ocean could retain between 30 and 65% of the total nitrogen and between 10 and 55% of the total phosphorous that would otherwise be exported to the coasts, while preliminary results presented in Regnier et al. (2013b) suggest that tidal estuaries on the Western European coast may retain between 1 and 60%

of the carbon input from upstream rivers during the summer season. With few exceptions, estuaries are typically recognized as heterotrophic ecosystems (Borges and Abril, 2012;

Maher and Eyre, 2012), where organic matter degradation dominates primary production and generally sustains net regeneration and export of inorganic carbon, as well as high CO₂ emissions to the atmosphere (Regnier et al., 2013a). In addition, the relevant role of these systems as “hot spots” for atmospheric CO2 is also emphasized by the fact that, whilst the total estuarine surface area on Earth represents less than 5% of the continental shelf, CO2

emissions from estuaries (0.15-0.3 Pg C yr⁻¹,Abril and Borges, 2004;Borges, 2005;Borges et al., 2005;Laruelle et al., 2010, 2013;Cai, 2011;Borges and Abril, 2012) are comparable to the CO2uptake by the global oceanic coastal region (0.19-0.45 Pg C yr⁻¹,Borges et al.,

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1.3. THE IMPORTANCE OF ESTUARIES

2005;Cai et al., 2006;Chen and Borges, 2009;Laruelle et al., 2010, 2014).

According to Dürr et al.(2011), estuaries acting as filters of river inputs to the ocean can be distinguished in two main operational types: 1) external filter estuaries, which essentially correspond to large rivers, such as the Mississippi, the Amazon or the Nile, and 2) internal filter estuaries, including alluvial systems, such as small deltas, tidal estuaries and lagoons, and drowned valleys, such as fjords. These five estuarine types and their main characteristics are summarized in Fig. 1.5, while their geographical distribution is shown in Fig. 1.6. Large rivers play a disproportionately important role in transporting dissolved and particulate matter from the land to the coastal ocean and account for approximately 40% of the freshwater discharge entering the ocean (Dürr et al., 2011). Nonetheless, owing to their high freshwater discharge rates, the bulk of biogeochemical transformations in such systems occurs in a plume on the adjacent continental shelf instead of in a physically confined estuary (McKee et al., 2004). As a consequence, large rivers are typically considered very limited or non-filter estuarine systems (Meybeck et al., 2004;Laruelle, 2009; Dürr et al., 2011). On the other hand, an overall higher, but variable filtering efficiency is associated to internal filter estuaries (Laruelle, 2009;Dürr et al., 2011). Among them, tidal systems, covering about 25% of the river basin areas on continents and having the second largest coastline (>20% of the global coastline), account for about half of the global water discharge passing through internal filter estuaries (Dürr et al., 2011). Moreover, they are typically heavy polluted systems since their drainage areas correspond to the most populated in the world and, contributing one-third to the CO₂ emissions from internal filter estuaries, they act as the most important estuarine sources for atmospheric CO2 (Laruelle et al., 2013).

Other internal filter estuaries such as small deltas, although widely represented worldwide (≈30% of the global coastline), are generally associated to a smaller filtering efficiency due to their relatively short residence time, while lagoons and fjords, despite their high filtering capacity, have virtually a weak impact on the global elemental cycle because they are confined to a limited number of regions (Wollast, 2003; Laruelle, 2009; Dürr et al.,

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Figure1.5:Globaloverviewofnearshorecoastaltypes.a fromDürretal.(2011).b fromLaruelle(2009).c fromLaruelleetal.(2013).

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1.4. SCIENTIFIC CONTEXT

Figure 1.6: Worldwide distribution of the coastline types, as proposed byDürr et al.(2011).

2011).

The wide geographical extension of tidal estuaries and their higher CO₂ emissions, as well as their relatively important filtering capacity suggest a strong potential effect of such systems on the coastal and global biogeochemical cycling. Moreover, the high population density hosted by their drainage basins (>35% of the global population), which is expected to increase in the future with likely consequences on the estuarine environment (IPCC Report, 2013), highlights a strong reliance of human benefits on the environmental quality of tidal systems. The understanding of the biogeochemical functioning of tidal estuaries becomes thus a central task in estuarine science not only to refine the quantitative assessment of the global elemental cycles, but also to improve our ability to forecast their evolution in the light of future climate and land-use changes and to help establish mitigation policies. As a consequence, tidal estuaries are chosen as the main subject of this dissertation.

1.4 Scientific context

The crucial role of estuaries on the fate of major elements and, thus, on their global cycle, as well as the estuarine great commercial and priceless ecological value, fuelled a

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particular interest in protecting and monitoring these systems since decades. However, due to their intrinsic variability, managing and studying estuaries is particularly challenging.

Stationary monitoring stations, which are typically sparsely distributed along estuarine channels, although able to measure the estuarine variability at the appropriate temporal scale, only provide local information. On the other hand, field surveys, such as for instance those carrying out measures along longitudinal transects, can describe the spatial estuarine variability. However, they should be repeatedly performed in order to fully capture the temporal evolution of the estuarine dynamics, which ranges from hours (e.g. tidal forcing), months (e.g. discharge, seasonal temperature), and longer time scales (e.g. historical continent loads, morphological evolution). Therefore, measurement campaigns are often time and energy consuming, as well as very expensive.

Although some estuaries have been extensively investigated, the global estuarine research effort is largely biased towards highly anthropogenically-impacted countries (e.g.

U.S., Europe and South Asia). As a consequence, any regional and/or global upscaling estimate of the biogeochemical functioning of estuaries is typically characterized by a large uncertainty resulting from their skewed spatial distribution. For instance, Laruelle et al.

(2013) reduced by more than 70% their previous calculation of CO2emissions from fjords (Laruelle et al., 2010) owing to an increase in data availability and highlighted how global upscaling can be affected by a poor representativeness of observations. Nowadays, reactive- transport models (RTMs), by providing a mechanistic description of process interactions in terms of energy and matter fluxes, are generally regarded as the most suitable tool to ideally complement field observations in high variable Earth’s sub-systems, such as estuaries (Steefel et al., 2005). Based on numerical solutions, RTMs provide the integrative and prognostic strength required for resolving and quantifying process rates that are often difficult or impossible to measure (Soetaert and Meysman, 2012) and can be used for predicting the estuarine response to future climate and land-use changes (Regnier et al., 2003).

However, despite three decades of successful RTM applications in estuarine systems (e.g.

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1.4. SCIENTIFIC CONTEXT

O’Kane, 1980;Lung and Paerl, 1988;Thouvenin et al., 1994;Soetaert and Herman, 1995a;

Billen et al., 2001;Garnier et al., 2007;Lin et al., 2007;Arndt et al., 2009;Cerco et al., 2010), our ability to quantify the role of estuaries in the global biogeochemical cycle and to predict their future behaviors is still scarce (Hobbie, 2000). On the one hand, the limited availability of reiterated data, necessary to constrain and validate model results, led to the development of locally-tuned models and to modelling applications typically biased towards well-surveyed estuaries of populated and industrialized countries, such as the Eastern coast of U.S. and the Western Europe (Regnier et al., 2013b). On the other hand, the typical high computational demand of RTMs generally hampers simulations over timescales larger than one year and limits the scientific questions to site-specific management issues, such as eu- trophication or local elemental budget quantification (Hobbie, 2000;Regnier et al., 2013b).

Hence, no model is currently suitable to represent the wide diversity of estuarine systems and to quantify the anthropogenic effects on their biogeochemistry at regional and/or global scales (Bauer et al., 2013). As a consequence, the biogeochemical role of estuaries in the global elemental cycle assessment is essentially omitted. For instance, Earth-System Models (EMSs; e.g. Fig. 1.7a), designed to simulate and understand the centennial scale evolution of climate including biogeochemical feedbacks, focus on physical, chemical and biological processes within and between atmosphere, ocean, cryosphere and land, but ne- glects biogeochemical transformations occurring in estuaries (Collins et al., 2011;Le Quéré et al., 2013). Similarly, the global C budget reported by the Intergovernmental Panel on Climate Change report (IPCC Report, 2013; Fig. 1.7b) considers estuaries as passive pipes transporting carbon from the land to the sea and essentially unaffected by anthropogenic disturbances, although local and global studies indicate that this assumption is not verified (e.g. Kempe, 1988; Estacio et al., 1999;Cole et al., 2007; Regnier et al., 2013a; Sin and Jeong, 2015).

In this context, there has been a recent call for a “synthesis approach” that, bringing together existing information and integrating modelling research with comparative studies,

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Figure 1.7: a) Example of the schematic structure of an Earth-System Model (ESM).

Modified from Dunne et al. (2012). b) Global carbon cycle as represented in the IPCC Report (2013). In the right figure, black numbers and arrows indicate reservoir masses and exchange fluxes estimated prior to the Industrial Era (year 1750) while red numbers and arrows represent annual anthropogenic fluxes referring to years 2000-2009. Fluxes and carbon stocks are expressed in Pg C yr⁻¹and Pg C, respectively. In both ESM and IPCC’s global carbon cycle schemes, estuaries are neglected.

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1.5. THESIS OUTLINE

could allow identifying common patterns, mechanisms and interactions and developing new concepts that can be applied to all estuaries (Hobbie, 2000; Hofmann, 2000). The latter challenging task could theoretically allow for an extension of results from one estuary to others that have not been the subject of detailed studies (Geyer et al., 2000;Hobbie, 2000) and could thus ultimately improve our ability to assessing the estuarine role at the regional and/or global scale (Regnier et al., 2013b).

1.5 Thesis Outline

The main objectives of the research presented in thesis are to provide an innovative modeling concept that, on the one hand, resolves the overall estuarine dynamics at the relevant spatio-temporal scale, and, on the other hand, provides a flexible tool allowing applications and projections at local, regional and, potentially, global scales and to fill the knowledge gaps in estuarine science by quantifying the estuarine CO2dynamics and its response to future climate and land-use changes, analyzing the contributions of biogeochemical reactions to the estuarine CO₂dynamics and providing uncertainties in estimates.

Chapter 2presents a detailed overview of the dominant physical and biogeochemical processes controlling biogeochemical transformations and fluxes of carbon and nutrients along the estuarine gradient, together with a broad review of recent developments in the modelling of estuarine biogeochemical dynamics. Moreover, it provides an example of how combining a RTM approach with highly-resolution databases can be used to disentangle the complex process interplay that underlays carbon dynamics in estuaries and a series of simulations is performed to explore biogeochemical trends across different estuarine geometries and environmental scenarios. Results are then discussed in the context of improving the modelling of estuarine carbon and CO2 dynamics at regional and global scales and current limitations to upscaling strategies are highlighted. The chapter was published as a review article by Regnier et al. (2013b). My contribution to this work consisted in collaborating to the development of the reactive-transport model code used to perform simulations and in reviewing the estuarine modelling literature over the past 30

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years, which highlighted how biogeochemical modelling applications are geographically biased towards the East coast of U.S. and Western Europe, often limited to short timescale simulations (<1 year) and designed to resolve scientific questions at local level.

InChapter 3, the one-dimensional, reactive transport model C-GEM (Carbon-Generic Estuary Model), developed during my thesis project, is described together with a protocol for its set-up. C-GEM’s performance in reproducing the estuarine hydrodynamics, the solute and solid transport and the biogeochemical functioning is evaluated by means of steady- state and annual transient applications to the macrotidal Scheldt estuary (BE/NL). Results from a sensitivity analysis are also presented in order to assess the model’s sensitivity to variations in internal parameter values. The strength of C-GEM depends on its simplified structure that, relying on a new theoretical concept based on the interdependence between geometry and hydrodynamics and on the first-order control of the hydrodynamics on the estuarine biogeochemistry, allows for using an idealized representation of the estuarine geometry as support for numerical calculations. Implementation of the geometrical support only requires specification of a few parameters (estuarine width and depth at upstream and downstream limits), typically derivable from maps and bathymetrical charts. Therefore, C-GEM not only reduces data requirements for applications and offers a valid compromise between performance and computational efficiency, but is also proposed as investigation tool to study geometry effects on estuarine biogeochemistry.

InChapter 4, a unified modelling approach, aiming at improving upscaling strategies and enabling projections, is developed and tested on three idealized estuaries covering the main features of tidal systems. Simulations, representing average environmental conditions for temperate tidal estuaries worldwide, are carried out for the present decade, as well as for the mid-21st century using C-GEM. Here, the model uses a unique parameter set extracted from a large literature review of more than 40 local modelling studies, which allows extending the scope of applicability of C-GEM to a wide climatological zone.

Hydrodynamics, solute and solid transport and biogeochemistry in each idealized estuary

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1.6. CONNECTION BETWEEN THESIS CHAPTERS

are fully analyzed and their whole-system biogeochemical indicators (i.e. Net Ecosystem Metabolism, CO2 gas exchange across the air-water interface, carbon and nitrogen filtering capacities) are compared in order to identify possible relationships between estuarine biogeochemical functioning and different hydro-geometrical characteristics. Furthermore, a sensitivity analysis, performed to assess the response of the estuarine biogeochemistry to parameter uncertainties as deduced from the literature review, is performed. Results are then discussed in terms of improving our ability to transfer information from a well-constrained to a poorly-know estuary and to predict the response of the estuarine biogeochemistry to future climate and land-use changes.

Chapter 5 presents a novel upscaling strategy developed to derive robust estimates of organic and inorganic carbon fluxes in estuaries at regional scale. Here, the generic modelling approach as presented in Chapter 4, which combines high-resolution databases with an idealized representation of the estuarine geometry and a generic set of model parameters, is adapted to the real world in order to quantify the carbon dynamics of tidal estuaries discharging into the North Sea. A series of simulations is performed to quantify the average efficiency in retaining carbon in the six main tidal estuaries flowing into the region (Scheldt, Elbe, Ems, Weser, Humber, Thames). The same filtering capacity is then applied to the carbon input incoming from upstream rivers discharging into all tidal systems bordering the North Sea and their overall carbon export to the coastal zone, as well as their total CO₂emission is calculated.

Finally, a conclusive chapter (Chapter 6) provides a synthesis of the key findings and arguments projected by the present research work. Moreover, recommendations are given in the light of further applications of the modelling approach developed during this thesis.

1.6 Connection between thesis chapters

While this chapter (Chapter 1) provides an overview of estuaries and their biogeochemical role and describes the scientific context that have motivated this research, chapters 2-5 present results from a series of modeling applications performed to resolve and quantify the

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CO2dynamics from the local to the regional scale and the last chapter (Chapter 6) synthetizes the key findings of the thesis and provides recommendations for future application of our modeling approach. More specifically, Chapter 2, provides a general description of the most important physical and biogeochemical processes that govern carbon and nutrient transformations along the estuarine gradient (pages 25-43) and a review of past modeling studies (i.e. excluding the ones performed in this thesis) that are used to quantify estuarine budgets, fluxes and filtering capacities at local scale (pages 44-54). Next, it presents exploratory results dedicated to the first application of a one-dimensional, generic reactive-transport model for the CO2 dynamics at a scale larger than an individual estuary (pages 54-60).

In this chapter, the applied model is a prototype of the Carbon-Generic Estuary Model (C-GEM) developed in the framework of this thesis, which uses an innovative simplified representation of the estuarine geometry as support for numerical calculations. C-GEM’s prototype is applied to conditions representative of the summer period during 2000’s in the Western European region in three idealized tidal estuaries, which differ in terms of hydro-geometries. Results highlight the potential of combining a generic modeling plat- form with a unique set of model parameters and high-resolution environmental databases to quantify the estuarine CO2dynamics at regional scale. C-GEM modelling strategy and model structure is then fully described in the following chapter (Chapter 3). Results from a local application (i.e. The Scheldt estuary, BE/NL) of the newly developed model are also presented and used to evaluate its performance in reproducing both spatial and temporal trends of the estuarine hydrodynamics and biogeochemistry. Next, the modeling approach applied to the regional scale in Chapter 2 is expanded in Chapter 4. Here, the validated version of C-GEM described in Chapter 3 is used to perform simulations. They cover three idealized estuaries, characterized by hydro-geometrical features that span those observed in tidal estuaries flowing in temperate regions. Similar to chapter 2, the model is forced by spatially resolved databases to deduce biogeochemical boundary conditions and climate forcings. The environmental settings differ as they represent here present-day (year 2000)

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1.6. CONNECTION BETWEEN THESIS CHAPTERS

and future (year 2050) annually averaged conditions rather than a specific season of the year (i.e. summer during 2000’s in Chapter 2). Moreover, a new, generic set of model parameters, derived from an extensive search for estuarine model applications published over the last 30 years, is applied. This is in marked contrast from the set-up in Chapter 2 where a set of parameters calibrated on a specific estuarine system was used. This unique parameter set is likely more representative of temperate tidal estuarine conditions worldwide, thereby extending the scope of C-GEM to a scale larger than those presented in Chapters 2 and 3 and allowing a robust quantification of the biogeochemical role of these estuaries at global and annual scales. Finally, in Chapter 5, the generic approach developed in Chapter 4 is con- served, but C-GEM is used here to explicitly simulate the main tidal estuaries discharging into the North Sea using an idealized, yet realistic representation of the geometry of each system constrained from field observations instead of theoretical, “end-member” systems assumed to be representative of an estuarine class (e.g. funnel-shaped versus prismatic).

Simulations are performed to quantify the annually averaged carbon filtering capacity for these main systems and results are up-scaled to the entire North Sea by applying the filtering efficiency to the total carbon input incoming from the upper rivers in all catchments.

A similar application to the East coast of US in currently under way (N. Goossens and co-workers, Université Libre de Bruxelles).

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CHAPTER II

Modelling Estuarine Biogeochemical Dynamics: From the Local to the Global Scale

Regnier, P., S. Arndt, N. Goossens, C. Volta, G. G. Laruelle, R. Lauerwald, and J.

Hartmann. Published in Aquatic Geochemistry, 19, 591-626, 2013, doi: 10.1007/s10498- 013-9218-3.

2.1 Introduction

Situated at the transition between freshwater and marine environments, estuaries are key components of the land-ocean aquatic continuum. They act as strong nutrient and carbon filters and are relevant contributors to the atmospheric CO2budget (e.g.Smith and Hollibaugh, 1993;Cai and Wang, 1998;Wollast, 1998;Rabouille et al., 2001;Borges and Frankignoulle, 2002; Borges et al., 2005; Zhai et al., 2005;Laruelle et al., 2010;Borges and Abril, 2012;Mackenzie et al., 2012;Laruelle et al., 2013;Regnier et al., 2013a). Along the estuarine gradient, oceanic and terrestrial carbon and nutrient inputs are modified by biogeochemical processes, buried in sediments, incorporated into biomineralized structures or, in the case of gaseous species such as CO2, exchanged with the atmosphere. All these transformations are driven by a complex interplay between geological, physical, chemical and biological processes, which are modulated by a wide array of forcing mechanisms, such as wind stress, light, water temperature, waves, tides or freshwater discharge.

The estuarine biogeochemical dynamics, the lateral carbon and nutrient fluxes and the vertical air-water gaseous exchange are characterized by strong spatial gradients from

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the tidally dominated mouth to the river-dominated upstream reaches. A pronounced temporal variability ranging from hours (e.g. tidal forcing) to months (e.g. discharge, seasonal temperature), and longer (e.g. historical nutrient loading) is another distinct feature of estuarine systems. Human activities, in particular, have changed both the quantity and quality of terrestrial carbon and nutrient fluxes to estuaries and the coastal ocean with likely consequences for global biogeochemical cycles and climate (Ver et al., 1999;

Rabouille et al., 2001;Mackenzie et al., 2004, 2012;Regnier et al., 2013a). However, the quantitative significance of the estuarine bioreactor as a regulator of land-ocean carbon and nutrient fluxes or global atmospheric CO2 concentrations remains poorly constrained (e.g. Borges et al., 2005; Mackenzie et al., 2005; Regnier et al., 2013a). This limited quantitative understanding mainly results from the inherent spatial and temporal variability of the estuarine environment that is difficult to resolve on the basis of observations alone.

Observations only provide instantaneous and localized information that cannot easily be extrapolated to the scale of the entire estuarine system. Yet, important whole system properties, such as the net ecosystem metabolism ((NEM, Borges and Abril, 2012) and the estuarine-filtering capacity (Nixon et al., 1996), require spatially integrated assessments at a high temporal resolution over a seasonal or annual cycle (e.g.Arndt et al., 2009).

Reaction-transport models (RTMs) provide ideal tools to resolve the variability inherent in the estuarine environment. RTMs are used as analogues of the real world. Such models are based on a process-functional approach that focuses on energy and matter fluxes, and treats the biogeochemical system as a bioreactor (Haag and Kaupenjohann, 2000). RTMs are generally developed to investigate the transport and transformation of a selected set of constituents in a compartment of the Earth system. Albeit commonly used in the fields of, for example, early diagenesis or groundwater research (Lichtner et al., 1996), the concept has rarely been applied in estuarine and ocean science. Nevertheless, many biogeochemical models developed in these fields are fully consistent with the above definition.

RTMs complement field observations, because their integrative power provides the

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2.1. INTRODUCTION

required extrapolation means for a system-scale analysis (e.g.Arndt et al., 2007, 2009) over the entire spectrum of changing forcing conditions, including the long-term response to land- use and climate change (Paerl et al., 2006;Thieu et al., 2010). Over the last three decades, RTM approaches have increasingly been used to unravel the biogeochemical dynamics of estuarine systems, including studies on water quality, phytoplankton and bacterial dynamics or elemental mass budgets (e.g. O’Kane, 1980; Soetaert and Herman, 1995b; Lee et al., 2005; Lin et al., 2007; Arndt et al., 2009; Baklouti et al., 2011; Gypens et al., 2013).

Furthermore, the mechanistic understanding gained through these RTM studies allows to identify the important processes and forcings that drive the cycling of bioactive elements.

They thus have the potential to provide important guidelines for the design of global biogeochemical models (e.g. Falkowski et al., 2000; Mackenzie et al., 2012). However, even today, only a few modelling studies incorporate the full suite of interacting physical, biological and chemical processes controlling the coupled transformations of carbon and nutrients along an estuarine gradient (e.g. Cloern, 2001; Tappin et al., 2003; Hofmann et al., 2008a). Estuarine modelling studies are also clearly biased towards anthropogenically impacted systems in industrialized countries such as the East Coast of the USA, Western Europe and Australia (e.g.Cerco and Cole, 1993;Regnier and Steefel, 1999;Cerco, 2000;

Billen et al., 2001;Kim and Cerco, 2003;Margvelashvili et al., 2003; Tappin et al., 2003;

Robson and Hamilton, 2004;Robson et al., 2008;Scavia et al., 2006; Shen, 2006; Wild- Allen et al., 2009;Cerco et al., 2010). Although data availability for other regions is steadily increasing, model applications to estuaries located in Siberia, Alaska, Southeast Asia, the Hudson Bay or along the tropical Western Atlantic are missing (Fig. 2.1).

Our ability to assess the quantitative role of the estuarine environment for global biogeochemical cycles and greenhouse gas budgets, as well as its response to ongoing land-use and climate changes, requires comparative studies that cover a large range of different systems, thus enabling the identification of global patterns (Borges and Abril, 2012). However, model applications are currently limited by data requirements for calibration and validation,

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Figure 2.1: Location of published estuarine biogeochemical model applications (n = 99).

Red: tidal systems (type 2; n = 74); Blue: other types (n = 25) in the classification of Dürr et al.(2011). Watersheds highlighted in grey correspond to tidal systems. Small and big dots correspond to 1 and 1-5 model applications; circles correspond to more than 5 model applications. The bar charts represent the distribution of model dimensions (top) and model span (bottom). Steady-state (orange) and transient (black) simulations are reported separately.

as well as by the high computational needs required to address physical, biogeochemical and geological processes at the relevant temporal and spatial scales. This computational barrier is rapidly exacerbated when seasonal and inter-annual timescales need to be jointly resolved. Therefore, the application of two- or three-dimensional estuarine RTMs generally remains restricted to short simulation timescales (<1 year) and well-known systems for which detailed bathymetric and geometric information is available (Fig. 2.1). Such two- or three-dimensional RTMs have been set up for, among others, the Chesapeake Bay (Cerco and Cole, 1993;Cerco and Noel, 2004;Cerco et al., 2010), the Pearl Estuary (Guan et al., 2001; Zhang and Li, 2010), the St. Lawrence Estuary (Benoit et al., 2006; Lefort et al., 2012) and the Scheldt Estuary (Arndt et al., 2007, 2009;Vanderborght et al., 2007). One-

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2.2. ESTUARIES WITHIN THE CONTEXT OF THE LAND-OCEAN CONTINUUM

dimensional RTMs are computationally less onerous than multi-dimensional approaches.

Yet, their application also remains restricted to individual estuarine systems (e.g.O’Kane, 1980;Garnier et al., 1995, 2007;Hanley et al., 1998;Billen et al., 2001, 2009;Vanderborght et al., 2002; Macedo and Duarte, 2006; Even et al., 2007a,b; Hofmann et al., 2008a,b), partly because regional- and global-scale simulations are currently compromised by the limited availability of comprehensive data sets. Therefore, the development of scaling approaches including new modelling tools that extrapolate knowledge from well-studied to data-poor estuarine systems is required to advance our quantitative understanding of their role in the global climate system.

In this contribution, we review the most important estuarine physical and biogeochemical processes that govern the transformations of carbon and nutrients along the estuarine gradient. We then illustrate, on the basis of examples of local estuarine modelling studies, how RTMs can be used to quantify estuarine budgets, fluxes and filtering capacities. The linkages and interactions between the river network, the estuarine environment and the coastal zone are also briefly analysed. Next, we show how a combination of reaction- transport modelling and high-resolution data can help disentangle the complex process interplay that underlies the estuarine NEM, greenhouse gas fluxes and C-filtering capacities. This approach is then generalized to assess the response of these key biogeochemical indicators to changes in estuarine geometry for different environmental scenarios assuming typical Western European climate conditions. Finally, the results are discussed in the context of the development of mechanistically rooted upscaling strategies, from the local to the regional scale and beyond.

2.2 Estuaries Within the Context of the Land-Ocean Continuum

The land-ocean aquatic continuum is commonly defined as the interface, or transition zone, between terrestrial ecosystems and the open ocean (Billen et al., 1991;Mackenzie et al., 2012;Regnier et al., 2013a). Estuaries are integral part of this continuum, but their patial boundaries are often difficult to delineate without ambiguity (Elliott and McLusky, 2002).

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Although estuaries may comprise coastal environments as diverse as deltas, lagoons and fjords, our analysis exclusively focuses on tidal systems due to their intense biogeochemical processing and long residence times (e.g. Wollast, 1983). In addition, tidal estuaries generally reveal a sharp salinity gradient, thus facilitating model calibration and validation using specific methods that are not easily applicable to other coastal systems.

Tidal estuaries, referred to as type 2 in the typology ofDürr et al.(2011), account for a total surface area of 276 x 10³ km² and 27% of the world’s exorheic freshwater water discharge (Laruelle et al., 2013). Together with large rivers, they are the main conduits through which freshwater is delivered to the sea. They also receive a significant fraction of the global carbon and nutrient load from terrestrial ecosystems. According to the analysis of the GlobalNEWS2 project (Seitzinger et al., 2005;Mayorga et al., 2010), tidal systems receive total organic carbon, nitrogen and phosphorus loads of 81, 12 and 0.7 Tg year⁻¹(an equivalent of 25, 34 and 32% of the global land to ocean fluxes), respectively.

A tidal estuary can be geographically divided into the freshwater tidal river, the brackish to saline estuary and the area of the coastal ocean that is under the direct influence of the estuarine plume (Fig. 2.2). The freshwater part can often be further divided into a pre-oxygen minimum zone and an oxygen minimum zone, where a significant proportion of the terrestrial and riverine matter is processed (e.g.Vanderborght et al., 2002;Amann et al., 2012). As an example, the three major zones are illustrated in Fig. 2.2 for the Delaware and Scheldt watersheds. Their tidal intrusion length and thus the landward extension of the estuarine environment are highly variable as they depend on the amplitude of the tidal wave at the estuarine mouth, the estuarine geometry and the upstream river discharge. In the Delaware and Scheldt watersheds, the estuaries typically extend 170 and 215 km inwards, respectively. The average freshwater residence time is about 60-90 days in the Scheldt (Wollast and Peters, 1978) and 80 days in the Delaware estuary (Fisher et al., 1988), but can vary significantly in response to changes in the freshwater discharge.

Most tidal estuaries are alluvial estuaries, which, from a morphological point of view, are

Carbon cycling at the estuarine interface: