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Estuarine and Coastal Sediments – Coupled Biogeochemical Cycling DJ Burdige, Old Dominion University, Norfolk, VA, USA

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Estuarine and Coastal Sediments – Coupled Biogeochemical Cycling DJ Burdige, Old Dominion University, Norfolk, VA, USA 5.09 Estuarine and Coastal Sediments – Coupled Biogeochemical Cycling DJ Burdige, Old Dominion University, Norfolk, VA, USA © 2011 Elsevier Inc. All rights reserved. 5.09.1 Introduction 279 5.09.2 Introduction to Biogeochemical Processes in Sediments 280 5.09.2.1 Organic Matter Remineralization Processes 280 5.09.2.1.1 The anaerobic food chain for organic matter remineralization 281 5.09.2.2 Chemolithotrophic Reactions 281 5.09.2.2.1 Aerobic processes 281 5.09.2.2.2 Anaerobic processes 282 5.09.2.3 Linkages between Chemolithotrophic and Organic Matter Remineralization Processes 283 5.09.2.4 Seasonality and Non-Steady-State Processes in Estuarine and Coastal Sediments 284 5.09.3 Linkages of Biogeochemical Processes and Transport Processes and the Occurrence of Mixed Redox Conditions in Sediments 285 5.09.4 The Classification of Estuarine and Coastal Sediments 285 5.09.4.1 Steadily Accumulating Sediments 287 5.09.4.2 Sediments Subject to Extensive Physical Reworking 289 5.09.4.3 High Permeability, Sandy Sediments 289 5.09.4.4 Bypass Zone Sediments 291 5.09.4.5 Macrophyte-Dominated Sediments 291 5.09.4.6 Intertidal Mudflats and Sandflats 292 5.09.5 Sediment Oxygen Consumption 293 5.09.6 Organotrophic Denitrification, Anammox and Anoxic Nitrification 293 5.09.6.1 Anammox 295 5.09.6.2 Anoxic Nitrification 295 5.09.6.3 Nitrogen Loss from Sediments: Closing Thoughts 296 5.09.7 Iron and Manganese Reduction 296 5.09.8 Sulfate Reduction and Sulfide Mineral Formation 300 5.09.8.1 Pyrite Formation in Sediments 301 5.09.8.2 Pyrite Burial and Sulfur Burial Efficiency 302 5.09.9 Methanogenesis, Methane Oxidation, and Methane Fluxes to the Atmosphere 303 5.09.10 Trace Metal Cycling 304 5.09.11 Concluding Remarks 307 References 308 Abstract A variety of macroscopic physical and biological forcing functions act on estuarine and coastal sediments across a range of time and space scales, and can have a profound effect on the processes associated with the remineralization of sedimentary organic matter. These interactions exert a strong influence on the cycling of biogeochemically reactive elements (C, N, S, P and trace metals such as Mn and Fe), and result in linkages between and within these cycles that are far more complex than once envisioned. Biogeochemical processes in estuarine and coastal sediments also have implications on benthic–pelagic coupling in estuaries and the coastal ocean, and on some global oceanic cycles and biogeochemical budgets. 5.09.1 Introduction processes directly or indirectly associated with the reminerali­ zation of sedimentary organic matter has a significant impact Estuarine and coastal marine sediments are impacted by a wide on the biogeochemical cycling of elements such as carbon, range of macroscopic physical and biological forcings that nitrogen, phosphorus, sulfur, and many trace metals, including occur over a broad range of time and space scales. These manganese and iron. Furthermore, because estuarine and include, for example, bioturbation and bioirrigation by benthic coastal systems are relatively shallow, biogeochemical pro­ macrofauna, pore-water advective exchange driven by near- cesses that occur in the underlying sediments tend to have a seabed pressure gradients, oxygen input through macrophyte greater overall impact on the dynamics of estuaries and the roots, and large-scale physical mixing (reworking) of the sedi- coastal ocean as a whole. ments by tides, surface currents, or storms. The interplay With this in mind, the goal of this chapter is to present between these forcings and biological (largely microbial) an integrated view of estuarine and coastal sediment 279 280 Estuarine and Coastal Sediments – Coupled Biogeochemical Cycling biogeochemistry, focusing on these considerations. First, the 5.09.2.1 Organic Matter Remineralization Processes chapter briefly describes the key biogeochemical processes that The occurrence of specific organic matter remineralization occur in these sediments, using the biogeochemical zonation (respiratory) processes in any natural system appears to be model (Claypool and Kaplan, 1974; Froelich et al., 1979)as controlled by the free energy yield per mole of organic carbon the framework for the discussion. Next, it discusses how an understanding of the physical and biological forcings outlined oxidized by a specific individual electron acceptor (Claypool above can be used to characterize estuarine and coastal sediments and Kaplan, 1974; Froelich et al., 1979). Based on this bio­ based on their functional diagenetic characteristics (e.g., Aller, geochemical zonation model, the oxidant that provides the 2004). The remaining sections then link these two discussions greatest amount of free energy will be utilized first, and when together to provide a unified discussion of the coupled biogeo­ this oxidant is depleted then the next most efficient oxidant chemical processes that occur in estuarine and coastal sediments. will be used (Table 1). In principle, this will continue until either all available oxidants are consumed or all oxidizable (metabolizable) organic carbon is utilized (e.g., Aller and Mackin, 1984). 5.09.2 Introduction to Biogeochemical Processes On much of the Earth’s surface and in the oceans, the in Sediments amount of oxygen is sufficient relative to the amount of reduced (oxidizable) organic carbon, and aerobic respiration This discussion largely focuses on bacterial metabolism, in part, predominates. (Note, however, that this is not necessarily the because there is a much greater diversity of metabolic processes case in all estuaries and coastal waters (see Chapter 5.05 for among prokaryotes than there is among eukaryotes. (As used here, the term ‘bacteria’ is synonymous with ‘prokaryotes’. details).) However, in many estuarine and coastal settings, the Except where specifically noted, it therefore includes organisms flux of reactive organic carbon to the sediments is sufficiently in the group Archaea, cyanobacteria, and true bacteria or eubac­ high relative to O2 transport into the sediments, and anaerobic teria, i.e., organisms in the group Bacteria.) Most bacterial remineralization occurs. Anaerobic remineralization processes processes that impact sediment biogeochemistry result from dis­ are often referred to as suboxic remineralization (organo­ similatory metabolism (energy-acquiring processes), although trophic denitrification, Mn and Fe reduction) and anoxic assimilatory processes (i.e., production of new bacterial biomass) remineralization (sulfate reduction and methanogenesis), may be important in some aspects of sediment organic carbon although strictly speaking suboxic remineralization occurs remineralization and preservation (Burdige, 2006). under anoxic conditions (e.g., in sediments that are devoid of Bacterial biomass dominates the total benthic biomass in oxygen; see Canfield and Thamdrup, 2009 for an alternate view many, but not all, marine sediments (Aller, 1998; Alongi, 1998; of this classification scheme for remineralization processes). If Fenchel et al., 1998). Furthermore, because of their relatively we define denitrification in a general sense as the reduction of large surface-to-volume ratio as compared to higher, eukaryotic combined nitrogen (nitrate or nitrite) to gaseous end-products organisms, bacterial metabolic processes (on a per organism (predominantly N2), then organotrophic denitrification is a volume basis) can have a much greater impact on overall sedi­ process that couples this reduction to the oxidation of organic ment metabolism, even if they represent only a few percent of matter (e.g., Devol, 2008). Recent studies have also shown that the total benthic biomass (Nealson, 1997). Additional aspects denitrification can be coupled with a number of other oxidative of this problem are discussed in Section 5.09.5 processes (Hulth et al., 2005), hence the need for a more All of these considerations are most pronounced in anoxic complete description of denitrifying processes. (oxygen-deficient) sediments, since only a few protozoans and Under most, but not necessarily all, circumstances, anoxic fungi are capable of anaerobic metabolism. Thus, in most sediments are defined as those in which sulfate reduction and estuarine and coastal sediments, which are anoxic within a methanogenesis occur. The biogeochemical zonation illu­ centimeter or two (or less) below the sediment–water interface, strated in Table 1 can also be looked from the standpoint of bacterial metabolism dominates organic matter remineraliza­ the redox or half cell potential (EH) of the reduction of each of tion and, therefore, drives most of the biogeochemical cycles these terminal electron acceptors. This then leads to their being that will be discussed here. a gradient from positive EH values (oxidizing conditions) in a Table 1 Standard state free energy changes for the major organic matter remineralization processes ΔG° −1 b Process Chemical reaction (kJ mol C ) Aerobic respiration C6H12O6 +6O2 → 6CO2 +6H2O −471 − − Organotropic denitrification 5C6H12O6 + 24NO3 → 12N2 + 24HCO3 + 6CO2 + 18H2O −444 2+ − Organotrophic manganese reduction C6H12O6 + 18CO2 +6H2O+12δ-MnO2 → 12Mn + 24HCO3 −397 2+ − Organotrophic iron reduction C6H12O6 + 42CO2 + 24Fe(OH)3 → 24Fe + 48HCO3 + 18H2O −131 2− − Sulfate reduction 2C6H12O6 + 6SO4 → 6H2S + 12HCO3 −76 → − Methanogenesis 2C6H12O6 6CH4 + 6CO2 49 a Data for C6H12O6, δ-MnO2, and Fe(OH)3 are for glucose, fine-grained vernadite, and amorphous ferric oxide, respectively. Values of standard free energies of formation are from
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