Coastal Lagoons - Chapter 4 docx

Biogeochemical Cycles Melike Gürel, Aysegul Tanik, Rosemarie C. Russo, and I. Ethem Gönenç CONTENTS 4.1 Nutrient Cycles 4.1.1 Nitrogen Cycle 4.1.1.1 Uptake of Nitrogen Forms 4.1.1.2 Nitrification 4.1.1.3 Denitrification 4.1.1.4 Nitrate Ammonification 4.1.1.5 Mineralization of Organic Nitrogen (Ammonium Regeneration) 4.1.1.6 Ammonia Release from Sediment 4.1.1.7 Nitrogen Fixation 4.1.2 Phosphorus Cycle 4.1.2.1 Uptake of Phosphorus 4.1.2.2 Phytoplankton Death and Mineralization 4.1.2.3 Phosphorus Release from Sediment 4.1.2.4 Sorption of Phosphorus 4.1.2.5 Significance of N/P Ratio 4.1.3 Silicon Cycle 4.1.3.1 Uptake of Silicon 4.1.3.2 Settling of Diatoms 4.1.3.3 Dissolution of Silica 4.1.4 Dissolved Oxygen 4.1.4.1 Processes Affecting the Dissolved Oxygen Balance in Water 4.1.4.1.1 Reaeration 4.1.4.1.2 Photosynthesis—Respiration 4.1.4.1.3 Oxidation of Organic Matter 4.1.4.1.4 Oxidation of Inorganic Matter 4.1.4.1.5 Sediment Oxygen Demand 4.1.4.1.6 Nitrification 4.1.4.2 Redox Potential 4.1.5 Modeling of Nutrient Cycles 4.1.5.1 Modeling Nitrogen Cycle 4.1.5.1.1 Phytoplankton Nitrogen 4 L1686_C04.fm Page 79 Monday, November 15, 2004 1:38 PM © 2005 by CRC Press 4.1.5.1.2 Organic Nitrogen 4.1.5.1.3 Ammonium Nitrogen 4.1.5.1.4 Nitrate Nitrogen 4.1.5.1.5 Organic Nitrogen (Benthic) 4.1.5.1.6 Ammonia Nitrogen (Benthic) 4.1.5.1.7 Nitrate Nitrogen (Benthic) 4.1.5.2 Modeling of Phosphorus Cycle 4.1.5.2.1 Inorganic Phosphorus 4.1.5.2.2 Phytoplankton Phosphorus 4.1.5.2.3 Organic Phosphorus 4.1.5.2.4 Organic Phosphorus (Benthic) 4.1.5.2.5 Inorganic Phosphorus (Benthic) 4.1.5.3 Modeling of Silicon Cycle 4.1.5.4 Modeling of Dissolved Oxygen 4.1.5.4.1 Dissolved Oxygen 4.1.5.4.2 Dissolved Oxygen (Benthic) 4.1.5.4.3 Sediment Oxygen Demand 4.2 Organic Chemicals 4.2.1 Sources of Organic Chemicals 4.2.2 Classification of Organic Chemicals That Might Appear in Aquatic Environments 4.2.3 Fate of Organic Chemicals in Aquatic Environments 4.2.3.1 Volatilization 4.2.3.2 Ionization 4.2.3.3 Sorption 4.2.3.4 Hydrolysis 4.2.3.5 Oxidation 4.2.3.6 Photolysis 4.2.3.7 Biodegradation 4.2.4 Governing Equations of Reactions To Be Used in Modeling 4.2.4.1 Volatilization 4.2.4.2 Sorption 4.2.4.3 Computation of Partition Coefficients 4.2.4.4 Hydrolysis 4.2.4.5 Oxidation 4.2.4.6 Photolysis 4.2.4.7 Biodegradation Acknowledgments References 4.1 NUTRIENT CYCLES Among the most productive ecosystems in the biosphere, coastal lagoons cover 13% of world’s coastal zone 1 and constitute an interface between terrestrial and marine environments. 2,3 Nutrient loadings coming from both boundaries to lagoon ecosystems have increased considerably in recent years, and they have a major impact on L1686_C04.fm Page 80 Monday, November 15, 2004 1:38 PM © 2005 by CRC Press water quality and ecology. 4,5 Control of nutrients is thus one of the major problems faced by those responsible for the management of these sensitive ecosystems. In order to develop appropriate modeling strategies for making scientifically sound approaches to reduce the risk of environmental degradation of these ecosystems, a better understanding of nutrient cycles is required. In this section, nutrient cycles and their associated mechanisms and major reactions in coastal marine environments are described. Additional information on eutrophication caused by nutrient loading will be presented in Chapter 5. 4.1.1 N ITROGEN C YCLE Among nutrients, nitrogen is of particular importance because it is one of the major factors regulating primary production in coastal marine environments. 6–8 Nutrients are imported to coastal lagoons via atmosphere, agricultural lands, forests, rivers, urban and suburban run-off, domestic and industrial wastewater discharges, groundwater, and the sea. Nutrients are exported via tidal exchange, sediment accumulation, and denitrification. An additional source is nitrogen fixation. Internal sources of nitrogen include benthic and pelagic regeneration. In general, little is known about the supply of nutrients from the atmosphere and groundwater to coastal lagoons. 9 The nitrogen forms that are important in aquatic environments are ammonia/ ammonium (NH 4 + /NH 3 ), nitrate (NO 3 − ), nitrite (NO 2 − ), nitrogen gas (N 2 ), and organic nitrogen. These different forms of nitrogen, present in different oxidation states, undergo oxidation and reduction reactions. Ammonia and oxidized forms of nitrogen (NO 2 − , NO 3 − ) constitute dissolved inorganic nitrogen (DIN), which can be utilized by phytoplankton for growth or by bacteria as an electron acceptor. Typical concentrations of NH 4 + and NO 3 − in coastal waters range from <1–10 µM and <2–25 µM, respectively. 10 The various nitrogen compounds and their oxidation states, together with their molecular formulas, are given in Table 4.1. Ammonia exists in two forms: ammonium ion (NH 4 + ) and unionized ammonia (NH 3 ). The latter form is toxic to aquatic organisms and is in equilibrium with the ammonium and hydrogen cations. The concentrations of these forms vary considerably as a function of pH and temperature in natural water bodies. The method of calculation of the percent of total ammonia that is unionized at different pH and temperature is given in Emerson et al. 11 (4.1) TABLE 4.1 Forms of Nitrogen and Their Oxidation States Forms of Nitrogen Molecular Formula Oxidation State of N Ammonium NH 4 + −3 Unionized ammonia NH 3 −3 Nitrogen gas N 2 0 Nitrite NO 2 − +3 Nitrate NO 3 − +5 NH NH H 43 + + + L1686_C04.fm Page 81 Monday, November 15, 2004 1:38 PM © 2005 by CRC Press Nitrogen compounds can be classified into organic and inorganic nitrogen. Organic nitrogen in water bodies can be found in both dissolved and particulate forms. The particulate organic nitrogen (PON) is composed of organic detritus particles and phytoplankton and has two possible fates. Dead plant cells lyse and bacteria degrade the resulting dissolved organic nitrogen (DON) or protozoa/zooplankton to consume PON. 12 Most of the DON in seawater is still chemically uncharacterized, and its chemical and biological properties are becoming better known. 7 Except for amino acids and urea, which comprise only a small fraction of DON, most of the DON may be resistant to decomposers. 10 Excretion by animals also releases dissolved nitrogen. Zooplanktons excrete free amino acids, ammonia, and urea. Fish excrete ammonia, urea, and other organic compounds. 7 In aquatic ecosystems, a very complex biogeochemical nitrogen cycle is observed (Figure 4.1). The following sections give information about the processes involved in the biogeochemical cycling of nitrogen in the aquatic environment. 4.1.1.1 Uptake of Nitrogen Forms Primary production in coastal waters is largely regulated by the availability of NH 4 + and NO 3 − for growth. Ammonium is preferred by phytoplankton, as its oxidation FIGURE 4.1 Nitrogen cycle. denitrification uptake excretion excretion grazing grazing death death Fish Sediment anoxia settling Zoo- plankton Phyto- plankton Organic Detritus uptake N 2 N 2 fixation d e n i t r i f i c a t i o n n i t r i f i c a t i o n n i t r i f i c a t i o n a m m o n i f i c a t i o n a m m o n i f i c a t i o n NO 2 − NO 3 − NH 4 + m i n e r a l i z a t i o n death L1686_C04.fm Page 82 Monday, November 15, 2004 1:38 PM © 2005 by CRC Press state is equivalent to that of cellular nitrogen (−3) and thus requires the least energy for assimilation. 12,13 Ammonia concentrations above 1–2 µM tend to inhibit assimilation of other nitrogen species. 10 On the other hand, if nitrate is to be assimilated for the synthesis of cellular materials, it should be reduced to ammonia with the aid of several enzymes including nitrate reductase (enzyme catalyzed reduction) within the cell. This reduction process is called “assimilatory nitrate reduction” and requires energy. 7,14 Nitrogen uptake can be an important process. For example, in Basin d’Arcachon in southern France, due to the high nitrogen uptake rates of the seagrass Zostera noltii, nitrogen uptake is quantitatively more important than denitrification as a nitrogen sink. 15 In shallow water systems, biological organisms larger than phytoplankton turn over slowly, and their metabolism is lower. Nevertheless, these organisms store large amounts of nitrogen, because a substantial amount of nitrogen is tied up in their biology. Thus, nitrogen concentrations in the shallow systems tend to be lower. 16 Nutrient assimilation by macrophytes can be significantly different from that by phytoplankton because macrophytes have the ability to grow for long periods on stored nutrients. Rooted seagrasses can assimilate nutrients from sediment and possibly serve as nutrient pumps 10 (see Chapter 5 for details). 4.1.1.2 Nitrification Nitrification is the microbiological oxidation of ammonium to nitrite and then to nitrate under aerobic conditions, to satisfy the energy requirements of autotrophic microorganisms. Much of the energy released by this oxidation is used to reduce the carbon present in CO 2 to the oxidation state of cellular carbon, during the formation of organic matter. As indicated previously, the first step in nitrification is oxidation of ammonium to nitrite, which is accomplished by Nitrosomonas bacteria. (4.2) The second step is oxidation of nitrite to nitrate by Nitrobacter. This is a faster process. (4.3) The overall nitrification reaction is therefore (4.4) The nitrification process can influence marine primary production by competing with heterotrophs for the limited supply of dissolved oxygen and by decreasing the amount NH O H NO H O 4 1 2 22 + + − +++12 2  NO O NO 32 1 2 2 −− +  NH O NO H O H 2432 22 +− + +++ L1686_C04.fm Page 83 Monday, November 15, 2004 1:38 PM © 2005 by CRC Press of NH 4 + that is needed by phytoplankton for growth. 17 The coupling of the nitrification process with denitrification leads to loss of nitrogen from the atmosphere. Nitrification can take place either in the water column or in the sediment. However, nitrification in the water column of shallow marine and estuarine systems appears to be relatively limited. 17 Nitrification rates in the water column are at least in order of magnitude smaller than the nitrification rates per unit volume in sediment. For example, in coastal waters, nitrification rates range from only ~0.001–0.1 µmol l −1 h −1 , whereas in coastal sediment nitrification rates are often 20 µmol l −1 h −1 . 18 Nitrification rates measured in coastal sediment are usually on the order of 30–100 µmol m −2 h −1 . 17,10 Physico-chemical and biological factors regulating nitrification in coastal marine sediment include temperature, light, NH 4 + concentration, dissolved oxygen concentration, pH, dissolved CO 2 concentration, salinity, the presence of any inhibitory compounds, macrofaunal activity, and the presence of macrophyte roots. 8,17 Temperature influences the metabolic activities of nitrification bacteria. The optimum temperature is in the range of 25–35°C in pure cultures. 17 Due to both seasonal and diurnal changes in temperature in shallow coastal sediment, it is expected that nitrifying bacteria would exhibit optimal growth and/or activity during daytime and in the summer months when temperatures are maximum. 8 The effect of temperature on nitrification rates in pure cultures is usually expressed through Arrhenius type equations. 17 In addition, temperature also affects dissolved oxygen solubility and therefore the process rates. Light may influence the nitrification activity in shallow water sediment. Light availability and the penetration depth of light into sediment may affect benthic nitrification. 17 Nitrification may be strongly impeded by hypoxia since it occurs only under aerobic conditions. 19 Nitrifying bacteria, therefore, have to compete with other heterotrophs for the limited supply of dissolved oxygen. The depth distribution of nitrifying bacteria in sediment is ultimately constrained by the downward dissolved oxygen diffusion, which is typically 1–6.5 mm. In Chesapeake Bay, U.S.A., 18,20 Étang du Prévost in southern France, 21 and Danish coastal zones, 8 O 2 penetration into sediment declines due to increased temperature, organic inputs, and decreased macrofaunal activity in summer. Consequently, thinning of the surficial oxidized zone of sediment is responsible for the significant summer reduction in nitrification rates in these systems. The reported dissolved oxygen concentrations, which inhibit nitrification in sediment are in the range 1.1–6.2 µM O 2 . 8 Salinity is another factor influencing nitrification. Although nitrifying bacteria are able to acclimate to a wide range of salinities, such as those found in lagoon systems, short-term fluctuations may have strong regulating effects on nitrification. For example, a marine Nitrosomonas sp. isolated from the Ems-Dollard estuary at 15% salinity was able to adapt to the entire salinity range (0–35%) and grew at the same rate over the range after a lag phase of up to 12 days. 17 Rysgaard et al. 21 reported in their study conducted with the sediment from the Randers Fjord Estuary, Denmark that both nitrifying and denitrifying bacteria were phys- iologically influenced by the presence of sea salt, showing lower activities at higher salinities. L1686_C04.fm Page 84 Monday, November 15, 2004 1:38 PM © 2005 by CRC Press Salinity has another, nonphysiological effect on nitrification processes. As a consequence of higher salinity, the concentration of cations also increases. These compete with NH 4 + for adsorption on the sediment. As a result, the residence time of NH 4 + within the sediment decreases, and the NH 4 + flux from the sediment increases. At higher salinities, NH 4 + might diffuse out of the sediment before nitrification can take place. 21 Rooted benthic macrophytes might also influence nitrification–denitrification processes in deeper sediment because they release O 2 via their roots. This release could stimulate nitrification and thus provide an additional NO 3 − source for denitrification. 15 Sulfide, the product of anaerobic sulfate reduction, is quantitatively the most important toxic sulfur compound in marine sediment. 17 Sulfide concentrations can significantly reduce the activity of nitrifying bacteria by lowering the redox potential, 20 and concentrations between 0.9 and 40 µM can inhibit nitrification completely. 18 HS − concentrations in estuarine sediment commonly range from 7–200 µM, which is much lower than those for organic-rich sediment (>1 mM). The range of HS − concentration in freshwater sediment pore water is much lower (0–30 µM). 22 The presence of nitrifying bacteria in anaerobic sediment at depths well below the zone into which oxygen can penetrate is attributable to macrofaunal irrigation of sediment by physical resuspension and bioturbation. 15,20 4.1.1.3 Denitrification Denitrification is the microbiological reduction of nitrate to nitrogen gas, where facultative heterotrophic organisms use nitrate as the terminal electron acceptor under anoxic conditions: (4.5) Nitrogen gas is largely unavailable to support primary production; therefore, denitrification removes a substantial portion of the biologically available nitrogen and represents a mechanism for partial buffering against coastal eutrophication. 18,22 The nitrification and denitrification processes taking place in the sediment and in the sediment–water interface are schematically shown in Figure 4.2. Several factors affect denitrification rate, including temperature, pH, redox potential, as well as concentrations of oxygen, nitrate, and organic matter. 7,8,13,14,18 Denitrification rate is highly temperature dependent and generally increases with increasing temperature. 7 However, because of other factors such as nitrification rate and oxygen concentration, which also are temperature dependent it is difficult, especially in sediment, to separate the effect of temperature alone. 18 The rate of denitrification decreases with acidity. 13,23 The pH range, where denitrifiers are most active, is given as 5.8–9.2. 7 In marine systems, one of the most important environmental factors favoring denitrification is the availability of organic matter. 14 Simple organic compounds, such as formate, lactate, or glucose, usually serve as the electron donor in addition to their assimilation. Coastal marine environments act as centers of deposition for NO NO NO N O N 32 22 −− →→→→ L1686_C04.fm Page 85 Monday, November 15, 2004 1:38 PM © 2005 by CRC Press continentally derived organic materials. Thus, most denitrification in marine sediment occurs in coastal regions rather than deep-sea environments. 22 Oxygen concentrations can also affect denitrification rates. Denitrification is generally considered to occur only under low oxygen or anaerobic conditions. 7 To explain coupled nitrification–denitrification processes in sediment, it is often assumed that these processes are separated vertically within the sediment. However, denitrification can also occur within reduced microzones in the aerobic surface layer of sediment. In both freshwater and marine systems, an oxygen concentration of 0.2 mg l −1 or less is required for denitrification to occur in the water or sediment. 18 Bonin and Raymond 24 studied the kinetics of denitrification under different oxygen concentrations using Pseudomonas nautica isolated from marine sediment. They reported that denitrification can take place in the presence of oxygen. However, enzymes associated with denitrification are affected by the presence of oxygen. Nitrate reductase enzyme was completely inhibited at oxygen concentrations greater than 4.05 mg l −1 , compared with 2.15 mg l −1 and 0.25 mg l −1 for nitrite and nitrous oxide reductase enzymes, respectively. Yet, these results must not be generalized to all denitrifying strains because some bacteria are inhibited by oxygen while other species are not. In many coastal environments, seasonal trends in denitrification are determined largely by availability of NO 3 − which is controlled by rates of nitrification. 20 The response of denitrification rates in sediment slurries to increasing nitrate concentrations can often be described by Michaelis-Menten type kinetics. The half-saturation constant for marine sediment generally ranges from 27–53 µM NO 3 − . 18 Supplies of NO 3 − for denitrification in coastal marine sediment appear to be derived almost exclusively from sediment nitrification. 17 Diffusion of nitrate from the overlying water into the sediment is also a potential nitrate source for denitrification, and its rate in the sediment is 3–4 orders of magnitude greater than that of the overlying water. There is also evidence that the release rates of nitrate and ammonium from sediment are greater than their diffusion rates into the sediment. Nitrification is usually observed in the upper 5 cm of sediment, and the nitrate produced diffuses either up to the water or down to the anoxic zone, where denitrification takes place. 18,23 FIGURE 4.2 Nitrification and denitrification in sediments. N 2 flux settling Organic N NH 4 + NH 4 + flux NO 3 − NO 3 − flux N 2 nitrate ammonification burial nitrification denitrificationammonification WATER SEDIMENT L1686_C04.fm Page 86 Monday, November 15, 2004 1:38 PM © 2005 by CRC Press Macrophytes, benthic algae, and certain macrofauna have been shown to influence denitrification rates in both freshwater and marine sediment by affecting the oxygen and/or the nitrate distribution in the sediment. 18 A wide range of experimental methodologies has been developed to estimate denitrification rates in shallow marine environments. These techniques are based on different assumptions; therefore, care must be taken when comparing denitrification rates obtained using these different techniques. Seitzinger 18 has given the ranges of denitrification rates as 50–250 µmol N m −2 h −1 in estuarine and coastal marine sediment, 2–171 µmol N m −2 h −1 in lake sediment, and 0–345 µmol N m −2 h −1 in river and stream sediment. In low oxygen hypolimnetic lake waters, denitrification rates were generally 0.2–1.9 µmol N l −1 d −1 . The higher rates were from systems that receive substantial amounts of anthropogenic nutrient input. Groundwater is another nitrate source. 18 4.1.1.4 Nitrate Ammonification Denitrification is widely accepted as the dominant process of nitrate reduction in most shallow marine sediment. An alternate pathway to denitrification is nitrate ammonification, which is the reduction of NO 3 − to NH 4 + by heterotrophic bacteria. In contrast to denitrification, nitrogen is not lost from the system but converted to a readily available nitrogen form. 8 Nitrate ammonification can occur occasionally under anaerobic conditions. 2 Nitrate ammonification is also called dissimilatory nitrate reduction, and it has been described as an important process in marine sediment. 24 In both Bassin d’Arcachon and Étang du Prévost, two coastal lagoons in southern France, rates of nitrate ammonification were quantitatively as important as denitrification. 15 4.1.1.5 Mineralization of Organic Nitrogen (Ammonium Regeneration) The process of transforming organic compounds back to inorganic compounds is generally referred to as mineralization. 25 Through the mineralization of organic nitrogen compounds, nitrogen recycling is accomplished. Recycled nitrogen is primarily in the form of ammonia and urea (a dissolved organic nitrogen compound). Urea is rapidly broken down to ammonia by bacteria or by the extracel- lular enzyme urease. 8,23,25 Ammonium is regenerated from organic compounds by animal excretion and by microbial decomposition of organic matter. It is presumed that excretion contributes to the largest part of NH 4 + regeneration in the water column, while decomposition of organic matter is the most important in the sediment. 10 It is widely accepted that shallow coastal sediments are important sites for the mineralization of organic matter. The difference of shallow coastal waters compared with open seas is that a much larger fraction of the organic matter is mineralized on the bottom rather than in the water column. 2,26 Because of the shallow depth of coastal areas (e.g., 2–20 m) and the relatively rapid settling rates, a significant portion of the primary production is transferred to the sediment. Thus, much of the mineralization of nutrients occurs in the upper layer of the sediment. 2,18,27,28 L1686_C04.fm Page 87 Monday, November 15, 2004 1:38 PM © 2005 by CRC Press Organic compounds are mineralized through both aerobic and anaerobic respiration processes. Aerobic respiration, which takes place in the surface sediment layers (typically 0–5 mm depth), results in a rapid depletion of oxygen. In the sediment, bacteria oxidize a significant fraction of the organic matter using terminal electron acceptors other than oxygen (e.g., nitrate, manganese and iron compounds, sulfate, and carbon dioxide). 8,29 The two dominant anaerobic processes are dissimilatory sulfate reduction and methanogenesis (methane production). Generally, sulfate reduction precedes methanogenesis because sulfate-reducing bacteria out- compete methanogens for substrates. Freshwater has lower sulfate concentrations (10–200 µM) than estuarine water (30 mM). 22 Decomposition through sulfate reduction occurs deeper in the sediment column (>10 cm) and provides an additional source of NH 4 + . 26 Sulfate reduction, and subsequent inhibition of nitrification and denitrification by HS − , should lead to enhanced ammonium regeneration during summer, when sulfate reduction rates are high compared with those in winter. 22 In all cases, the mineralization of organic nitrogen compounds results in the production of NH 3 /NH 4 + . All living matter contains nitrogenous macromolecules, which become available to decomposer organisms upon the death of cells. Depending upon the structural complexity of the organic matter, mineralization can either be a simple deamination reaction or a complex series of metabolic steps involving a number of hydrolytic enzymes. Thus, mineralization rates depend on the degradability of the organic matter; i.e., whether it is labile or highly refractory. For example, seagrass detritus that has 25–30% lignin containing fibers, has a lower mineralization rate than phytoplankton cells, which contain more labile nitrogenous material. 8 Another parameter affecting the mineralization rate of organic matter is temperature. 7 Sea- sonal patterns of benthic nutrient regeneration generally exhibit strong summer maxima, which correlate well with water temperature. The effects of temperature can be represented by Arrhenius type expressions. 27 Mineralization of organic nitrogen plays a central role in nitrogen recycling in coastal marine environments. Regeneration from the sediment regulates all produc- tivity since inorganic nutrients are the limiting factors for primary production, 30 and much of the primary production of many coastal marine systems is supported by nutrient recycling rather than by nutrient inputs alone. 26 In shallow water ecosystems, benthic recycling may account for 20–80% of the nitrogen requirements of the phytoplankton. 8,27 Nixon 26 reported that nutrient inputs to Narragansett Bay, U.S.A. (without being recycled) could support, at the most, only 24–50% of the annual production, depending on the nutrient considered. Ammonium produced during the deamination of organic nitrogen in sediment is not totally available to the primary producers; some of the ammonium remains dissolved in interstitial water, some is adsorbed and buried into deeper sediment, 7 some is consumed by benthic algae for cell synthesis, 13 and a fraction undergoes nitrification in the surficial oxic zone of the sediment. 8 Denitrification following nitrification produces gaseous forms of nitrogen (N 2 , N 2 O) essentially unavailable to most coastal phytoplankton. 2,31 Thus, the coupled processes of nitrification–denitrification represent a sink that shunts nitrogen away from recycling pathways. 20 L1686_C04.fm Page 88 Monday, November 15, 2004 1:38 PM © 2005 by CRC Press [...]... 1981 Lung, 1992 O’Connor, 1981 O’Connor 94 O’Connor 94 Lung80 O’Connor 94 4.1.5.1.3 Ammonium Nitrogen   ∂ C1 C4 (T = DP1anc (1 − fon )C4 − k71θ 71 −20)  C − GP1a P C4 144 44 244 444  K mPc + C4  7 14nc NH 3 3 4 3 4 44 2 ∂t  Death Nitrification 14 24 3 4 4 Mineralization   C6 (T − k12θ12 −20 )   C1  K NIT + C6  144 44 444 4 2 3 (4. 23) Growth where C1 = ammonium nitrogen concentration [mg N l−1] DP1... [day−1] DP1 = death plus respiration rate constant of phytoplankton [day−1] Vs4 = net settling velocity of phytoplankton [m day−1] D = depth of segment [m] 4. 1.5.1.2 Organic Nitrogen   ∂ C7 vS3 (1 − fD 7 ) C4 (T = DP1anc fon C4 − k71θ 71 −20)  C7  C7 − 142 43 ∂t  KmPc + C4  14D 44 4 2 3 Death 144 4 244 44 4 3 Settling (4. 22) Mineralization where C7 = organic nitrogen concentration [mg N l−1] DP1... Growth 144 44 444 4 2 3 144 4 244 44 4 3 Denitrification Nitrification (4. 24) where     KmN C2 PNH3 = C1   + C1  (C + C )( K + C )   1  ( KmN + C1 )( KmN + C2 )  2 2  mN (4. 25) Ammonium preference factor C2 = nitrate–nitrogen concentration [mg N l−1] k12 = nitrification rate constant at 20°C [day−1] θ12 = nitrification temperature coefficient [none] T = water temperature [°C] KNIT = half-saturation... nitrogen (in almost the same or similar format as for other models) are presented below 4. 1.5.1.1 Phytoplankton Nitrogen Phytoplankton nitrogen is the nitrogen contained in phytoplankton cells v ∂ (C4 anc ) = GP1 anc C4 − DP1 anc C4 − S 4 anc C4 1 24 1 24 1 24 4 3 4 3 D ∂t 4 3 Growth Death (4. 21) Settling where C4 = phytoplankton carbon concentration [mg C l−1] anc = nitrogen to carbon ratio [mg N/mg−1... sedimentation. 74 FeS + 4. 1 .4. 1 .4. 2 9 4 O2 + H2O → 1 2 Fe2O3 + H2SO4 (4. 11) Iron Oxidation Fe2+ compounds are more soluble than Fe3+ compounds, and thus exist in the low mg l−1 range in sediment pore waters As a consequence, Fe2+ can diffuse to the oxic layer of the sediment, and via the loss of one electron, can be oxidized to Fe3+ by the oxygen present there. 74 Fe2+ → Fe3+ + e− (4. 12) O2 + 4H+ + 4e− → 2H2O (4. 13)... 4e− → 2H2O (4. 13) Half-reaction for oxygen is followed by the precipitation of iron oxyhydroxide Fe3+ + 2H2O → FeOOH(S) + 3H+ (4. 14) to yield the overall redox reaction Fe2+ + © 2005 by CRC Press 1 4 O2 + 3 2 H2O → FeOOH (S) + 2H+ (4. 15) L1686_C 04. fm Page 103 Monday, November 15, 20 04 1:38 PM Iron oxyhydroxide can react with water. 74 FeOOH (S) + H2O → Fe(OH)3 4. 1 .4. 1 .4. 3 (S) (4. 16) Manganese Oxidation... to NH4+ L1686_C 04. fm Page 110 Monday, November 15, 20 04 1:38 PM TABLE 4. 4 Temperature Correction Factors for Decomposition of Organic Nitrogen to NH4+ (θ ) Average 1.03 Location Reference 1. 045 1.051 Manasquan Estuary Patuxent River Estuary Maryland coastal waters 1.08 1.08 Explanation Brandes, 1976 Texas bays and estuaries As Cited in (1.02–1. 04) , PON to NH4+ O’Connor, 1981 Najarian et al., 19 84 Lung,... semi-enclosed basins with limited water exchange, such as lagoons. 15 4. 1 .4. 1.2 Photosynthesis – Respiration Photosynthesis is the conversion of simple inorganic nutrients into more complex organic molecules by autotrophic organisms Via this reaction oxygen is liberated and CO2 is consumed .45 , 64 106CO2 + 16NH4+ + HPO42− + 108H2O→ C106H263O110N16P1 + 107O2 + 14H+ (4. 9) © 2005 by CRC Press L1686_C 04. fm... KNIT = half-saturation constant for oxygen limitation of nitrification [mg O2 l−1] C6 = dissolved oxygen concentration [mg O2 l−1] Table 4. 6 and Table 4. 7 contain nitrification rate constants and temperature correction factors for nitrification in coastal waters, respectively 4. 1.5.1 .4 Nitrate Nitrogen  K NO3    C6 ∂ C2 (T ( T − 20) = k12θ12 −20)   C2 1 anc (1 44  C1 − GP 44 − PNH3 ) C4 − k2Dθ 2D... Mn4+ compounds, and therefore exist in the mg l−1 range in sediment pore waters As a consequence, Mn2+ can diffuse to the oxic layer of the sediment, and via the loss of two electrons, can be oxidized to Mn4+ by the oxygen present there. 74 Mn2+ → Mn4+ + 2e− (4. 17) O2 + 4H+ + 4e− → 2H2O (4. 18) Half-reaction for oxygen is and the oxidation of manganese can be given as Mn2+ + 1 2 O2 + 2H+→ Mn4+ + H2O (4. 19) . Sorption 4. 2.3 .4 Hydrolysis 4. 2.3.5 Oxidation 4. 2.3.6 Photolysis 4. 2.3.7 Biodegradation 4. 2 .4 Governing Equations of Reactions To Be Used in Modeling 4. 2 .4. 1 Volatilization 4. 2 .4. 2 Sorption 4. 2 .4. 3. Coefficients 4. 2 .4. 4 Hydrolysis 4. 2 .4. 5 Oxidation 4. 2 .4. 6 Photolysis 4. 2 .4. 7 Biodegradation Acknowledgments References 4. 1 NUTRIENT CYCLES Among the most productive ecosystems in the biosphere, coastal lagoons. (Benthic) 4. 1.5.3 Modeling of Silicon Cycle 4. 1.5 .4 Modeling of Dissolved Oxygen 4. 1.5 .4. 1 Dissolved Oxygen 4. 1.5 .4. 2 Dissolved Oxygen (Benthic) 4. 1.5 .4. 3 Sediment Oxygen Demand 4. 2 Organic Chemicals 4. 2.1