Glossary C – D

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Carbon Cycle

What is the Carbon Cycle?

The carbon cycle is related to all of the other nutrient cycles discussed on the Oz Estuaries indicator pages. Carbon is processed both chemically and biologically, from the atmosphere, soils and in water, to form compounds which are in turn either recycled or stored in some form.

digramtic represntation of the carbon cycle showing  the processes involved and thier magnitude

Figure 1. A representation of the processes involved and their magnitude (Illustration courtesy NASA Earth Science Enterprise).

How is the Carbon Cycle Changing?

As discussed in the climate change indicator page, the major human impacts on the carbon cycle are: 1) Deforestation which decreases the capture and storage carbon from the atmosphere and can also release carbon dioxide if the wood is burnt or biodegraded; 2) the burning of fossil fuels which releases carbon dioxide and 3) the production of cement which releases carbon dioxide when lime is produced from heating calcium carbonate (CaCO3 + heat Þ CaO (lime) + CO2 ).

There are other human impacts such as the change in land use from forest or grassland (net stores of carbon) to residential or agricultural (net releasers of carbon). Increased production of livestock such as cows and pigs which produce methane, a greenhouse gas that absorbs more heat per molecule that CO2 , is another growing area of concern.

Considerations for measurement and interpretation

Accurate measurements for sources and sinks
A source of greenhouse gas is an activity or process that releases that gas into the atmosphere. A sink is a process or physical mass in which a greenhouse gas, usually carbon dioxide, is removed or sequestered from the atmosphere and stored. Both sources and sinks can be natural, such as the growing of a forest (a sink) or a forest fires (a source), or human activities such as burning fossil fuels (source) or geosequestration (sink).

Because of the sources and sinks are not only geographically large and diverse but also highly dependant on other factors such as temperature, rainfall, population growth and technology development, it can be very difficult to measure the masses of carbon stored or being released at any one time. Accurate and complete data sets are required to make an assessment of the current status of sources and sinks but also to be able to monitor the rate of change in both.

Carbon cycle feedbacks
A feedback is when the product of a process has an impact on the continuing rate of the process that produced it. The impact can be either positive, and make the rate of the process faster, or negative, and slow it down. There are many examples of feedbacks in the carbon cycle. If the level of CO2 in the atmosphere is increased, the average temperature of the atmosphere will go up (Climate Change), increasing temperatures will melt permafrost releasing methane (another greenhouse gas) which will further increase temperature, melting permafrost and so on.

It is unclear at the moment how all of the feedbacks in the carbon cycle will interact with another and ultimately impact the earth's climate.

Sinks changing to sources
As discussed above a sink is when carbon is stored away from the atmosphere, preventing it from impacting climate. However, most sinks, particularly fossil fuels but also forests, grasslands and permafrost, can become sources given the right conditions. With fossil fuels, humans play the major role in removing it from it storage and burning it. For forests, grasslands and permafrost, climate change on its own maybe enough to turn these important sinks into sources of carbon dioxide and methane. It unclear at this time what level of climate change will be necessary to produce the conditions needed for the swap to occur and which vegetation types or areas are most vulnerable to conversion.

Existing information and Data

One of the biggest programs examining the carbon cycle in Australia is the National Carbon Accounting System or NCAS. NCAS tracks emissions (sources) and removals (sinks) of greenhouse gases from Australian land based systems. The system underpins National Greenhouse Gas Inventory reporting, and provides a basis for emissions projections to assess progress towards meeting Australia's emissions target (Kyoto). NCAS also produces the National Carbon Accounting Toolbox which provides the tools for tracking greenhouse gas emissions and carbon stock changes from land use and management. It includes the Full Carbon Accounting Model (FullCAM), that is derived from Australia's National Carbon Accounting System, and all supporting technical documentation. ( )

Through the Toolbox, users may identify changes in emissions resulting from: soil cultivation, fire management, fertiliser application, climate variability and reliability etc. Users may access: carbon accounting data for a range of plant species and land management systems; historic climate records; and search all technical reports relating to development of the National Carbon Accounting System. Developed in collaboration with the CSIRO, the Australian National University and supported by NASA, the Toolbox draws on the latest of scientific advancements.

Research has shown that Australia's net primary production (photosynthesis) is much lower than the global average for a land mass of Australia's size, 740 Tg C/yr versus a global average of 2850 Tg C/yr for a comparative size. Other differences including the dominant role of fire in Australian ecosystems and markedly difference plant species from those found in Europe and North America . Models used to project the carbon cycle need to account for these variations in Australia

To better understand the carbon cycle in Australia , flux tower experiments are being carried out in a number of locations. These experiments study the controls on carbon flux (the movement of carbon from the atmosphere to plants and soil and tin the opposite direction), whether there are any sudden or non linear changes to the carbon cycle (eg from droughts or insect attack) and provide valuable high resolution data for carbon models.

The change in tree area as an estimate of carbon uptake for a temperate native forest near Tumbarumba NSW Australia

Figure 2. The change in tree area as an estimate of carbon uptake for a temperate native forest near Tumbarumba NSW Australia. Green bars are live trees; red bars are dead trees; and the blue line is rainfall. From AGO and CSIRO.

Key questions and further research needs

  • More complete modelling of oceanic carbon cycles
  • More complete modelling of terrestrial carbon cycles
  • A better understanding the inputs, transport and fate of carbon estuarine systems
  • What will be the impact of changes to carbon cycle of health of estuaries
  • Will increased CO2 levels increase primary productivity in estuaries?


Chris Hepplewhites, Geoscience Australia

Carbon dioxide partial pressure

The partial pressure of carbon dioxide (PCO2) is the gas phase pressure (i.e. in the air above a waterway) of carbon dioxide which would be in equilibrium with the dissolved carbon dioxide. More information


Minerals containing CO32-, e.g. CaCO3 or limestone.

Caring for our Country

Caring for our Country is an NRM initiative that commenced on 1 July 2008. The aims of the initiative are to integrate delivery of the Commonwealth's previous natural resource management programs including the Natural Heritage Trust and the National Action Plan for Salinity and Water Quality. More


The area of land which collects and transfers rainwater into a waterway.

Catchment action plans

Catchment action plans provide a roadmap to ensure that resources are protected and enhanced for the enjoyment and viability of future generations.

Catchment Management Authority (CMA)

Regional body responsible for strategic planning and coordination of land and water resources.

Central basins

Central basins are uniform, lower energy environments in the deeper and quieter parts of estuaries, and are often formed landward of barrier bar deposits in wave-dominated estuaries. More information


Channels are environments of frequently high energy, in terms of tidal movement (e.g. tidal channels) or fluvial flow (e.g. river channels). More information

Charge balance

The sum of positive charges equals the sum of negative charges in natural waters. If this were not the case, you would get an electrical shock each time you touched water. The 'electroneutrality' or 'charge-balance' equation:

Eq. 1. åzmc = åzma

in which mc and ma are the molalities of cationic and anionic species and z is the ionic valence, can be used to indicate the accuracy of a water sample1. Major ions comprise most of the ionic content of a water sample, and are usually used on their own when assessing charge balance errors. For example, if major cation and anion concentration values (milligrams per litre) are substituted into Eq. 1 as:

Eq. 2. (Na+) + 2(Mg2+) + 2(Ca2+) + (K+) = (Cl-) + (HCO3-) + 2(CO32-) + 2(SO42-)

the right-hand side of the equation should be roughly equal to the left-hand side. Charge balance errors are most often reported as percentages e.g. by substituting Eq. 2 into Eq. 3:

Eq. 3. E = åzmc - åzma / åzmc + åzma * 100

In most cases, charge balance errors of <5% are considered acceptable. Charge balance errors of greater than 5% usually indicate that either an analytical error has occurred, or that an ionic species found in significant concentrations has been excluded from the analysis.

  1. Freeze, R.A. and Cherry, J.A. 1979. Groundwater, Prentice-Hall Inc., Englewood Cliffs, N.J., pp. 604.

Chlorophyll a

Chlorophyll a is a green pigment found in plants. Chlorophyll a concentrations are an indicator of phytoplankton abundance and biomass in coastal and estuarine waters. More information

Chemical weathering

Chemical weathering is the break-down of rocks or minerals by chemical processes operating at the atomic and molecular levels. New substances frequently form during chemical weathering. Solution, silicate hydrolysis and oxidation are some examples of chemical weathering.

1. Solution

is the process through which minerals and rocks dissolve in water. Carbonic acid formation:

H2CO3 + CO2 = H2CO3

and subsequent solution (or dissolution) of calcium carbonate:

CaCO3 + H2CO3 = Ca2+ + 2HCO3

is an example of solution that affects the carbonate alkalinity, buffering capacity and pH of water.

2. Silicate hydrolysis

is the breakdown of silicate rocks to yield cations, alkalinity, silica and clay minerals:

primary silicate + H2O + CO2 = clay + cations + HCO3 + SiO2

3. Oxidation

is the loss of an electron from an element. Oxidation usually results in the formation of an oxide. The oxidation of pyrite in acid sulphate soils gives rise to acid drainage in the coastal zone.

Chenier, chenier plain

Discrete, elongated, vegetated marine beach ridge, sandy hummock and/or shell bodies stranded on a coastal mudflat or marsh and roughly parallel to a prograding shoreline. When cheniers are distributed across a wide plain, that feature is called a 'chenier plain'.


A weathered form of aluminosilicate mineral particles, less than 0.002 mm in diameter.

Climate Change

Climate change is the term used to describe changes in average weather over time periods ranging from decades to millions of years. More information


An abbreviation commonly used for catchment management authority.

Coarse Sediment

A sediment comprising coarse-grained material such as sand or gravel particles.

Coast, coastal zone

The term 'coast' or 'coastline' have different meanings for different purposes.

The Macquarie dictionary defines 'coast' as the land next to the sea. The "coast" has also been defined as a strip of land of indefinite width that extends inland from the shore to the first change in terrain that is unaffected by marine processes [1], and the land adjacent to the sea upon which waves have an effect [2].

Coast could therefore include bays, inlets and estuaries. The extent that the term coast applies inland can be debated. Options include the various tide heights, the maximum extent of inundation (extent of storm surges etc), the limit of tidal influence on rivers and estuaries, the limit of salt water, and the extent of coastal vegetation.

The extent that the term 'coast' applies offshore is also unclear. Options include the line of lowest astronomical tide, the territorial sea baseline, limit of islands and reefs, continental shelf, etc.

Legally there are also variations on what constitutes the coast. For example, most property boundaries adjoining the coast are limited to the 'high water mark' or 30 metres landward of the high water mark. The limits of each State (and the Northern Territory) are generally the line of 'low water mark'. The term 'low water' also has different meanings in different States. A working group of the Intergovernmental Committee on Surveying and Mapping (ICSM) has identified over 50 different terms relating to the coastline used in Commonwealth and State legislation.

For the purposes of OzCoast and OzEstuaries, we have defined the 'coast' broadly to include areas of related to the coastal environment. OzCoast and OzEstuaries is primarily concerned with estuaries and the broadest limits of the inter-tidal zone. In some cases OzCoast and OzEstuaries covers areas further offshore where environmental studies provide information relevant to coastal management i.e. to the 3 nautical miles offshore (coastal waters) and coastal IMCRA regions.

  1. Duxbury, A. C. and A. B. Duxbury (1991). An Introduction to the Worlds Oceans. Dubuque, Indiana, W C Brown.
  2. Watt, A. (1982). Longman Illustrated Dictionary of Geology. Harlow, Essex, England, Longman Group: 192 pp.

More information on marine & costal maritime boundaries


Bill Hirst
Peter Harris

Coastal CRC

Commonly used abbreviation for The Cooperative Research Centre (CRC) for Coastal Zone, Estuary and Waterway Management.

Coastal Lakes Assessment and Management (CLAM) Tool

Coastal lakes are an important resource for their local and widespread communities because they provide important ecological, social and economic benefits. Uses for the land and water resources within a coastal lake catchment include urban development for local and tourist populations, agricultural and aquaculture production, and conservation of flora and fauna. Increasing demand on resources can create conflict over the use and sustainable management of the lakes. These issues are intricately linked, so the management of coastal lake systems requires knowledge of the processes and interactions between all key components of the system. This is a complex problem requiring the integration of often minimal information from various disciplines.

The Coastal Lake Assessment and Management (CLAM) tool is a decision support tool to inform of the potential impacts of management decisions on all key components of a coastal lake system. It is more than a software product as consultation with local stakeholders is an imperative component throughout the whole CLAM development process. The method used to develop a CLAM decision support tool, in short, involves collecting information about potential management decisions, and the key values of the lake, and integrating this into a single, simple tool. Training in the use and development of CLAM tools is available through the Australian National University.

The integration is completed using a Bayesian decision network (BDN). This approach is advantageous over other methods because it is suited to the rapid accumulation and integration of existing information sourced from observed data, model simulation and expert opinion, at various scales, from many disciplines. The BDN framework structure also inherently represents uncertainty in the input data but can be readily up-dated when new information becomes available.

The follow estuaries, creeks and inlets in NSW have had a CLAM developed, or one is under construction:

Back Creek, Back Lake, Belongil Creek, Berowra Estuary, Burrill Lake, Lake Cakora, Lake Cathie-Innes, Cobaki Broadwater, Coffs Creek, Coila Lake, Cudgen Lake, Dalhousie Creek, Deep Creek, Fiddamans Creek, Merimbula Lake, Myall Lake, Narrawallee Inlet, Queens Lake, Smiths Lake, Tallow Creek, Terranora Broadwater, Urunga Lagoon, Wallis Lake, Willis CreekLake Wollumboola, Woolgoolga Lake, Lake Wooloweyah.

For more information on the CLAM tools see

Coastal Lagoon

Coastal waterways in which waves are the principal factor that shapes the overall geomorphology. Characterised by a sandy barrier that can partially or totally constrict the entrance, backed by a mud basin, and typically have negligible river input. More information.

Coastal Protuberance

A prominence or bulging out of the coastline, typically formed from deltaic sediments.

Coastal Waterway

A body of water situated on or near the ocean coast, with some association with the ocean. Includes embayments, wave-and tide-dominated estuaries, wave- and tide-dominated deltas, coastal lagoons, and tidal creeks.


The formation of a complex chemical species by the coordination of ligands to a central ion, usually a metal. Ligands are anions or molecules that contain free pairs of electrons (or bases). The pairs of electrons form covalent or ionic bonds to the central ion. The resulting complex often stays in solution, thus preventing the precipitation of metals.

Conceptual Model

A depiction or representation of the most current understanding of the major ecosystem features and processes (including biological, physical, chemical and geomorphic components) of a particular environment (e.g. estuaries). More information.

Condition (State)

"The state or health of individual animals or plants, communities or ecosystems". [1]

  1. Scheltinga DM, Counihan R, Moss A, Cox M, Bennett J (2004) 'Users' guide for Estuarine, Coastal and Marine indicators for regional NRM monitoring. Cooperative Research Centre for Coastal Zone. Report was commissioned by the Australian Government Department of Environment and Heritage.'


The presence of charged ionic species in solution enables water to conduct an electrical current. This is referred to as conductivity, electrical conductivity (EC) or conductance, and it is directly related to the total dissolved salt concentration. Conductivity is best measured in the field using an electronic probe that applies a voltage between two electrodes. EC is sensitive to water temperature. The international standard temperature for laboratory conductivity measurements is 25 oC. Most modern field instrumentation will correct and standardise conductivity readings to this temperature and then refer to the measurement as specific conductance. It is worth mentioning that different standard temperatures were used in the past, so the water temperature at which the measurement was taken should always be reported. Up until around the late 1970s the units of EC were micromhos per centimetre (mhos cm-2) after which they were changed to microSiemens cm-2 (1S cm-1 = 1 mho cm-1).


Contaminants are chemical (toxicants) and biological (i.e. bacterial and viral pathogens) constituents of the environment capable of producing adverse effects on biological systems.

Contiguous Zone

The Contiguous Zone is a belt of water contiguous to the territorial sea, the outer limit of which does not exceed 24 nautical miles from the territorial sea baseline. More information

Continental Shelf

The Continental Shelf is the area of the seabed and subsoil which extends beyond the territorial sea to a distance of 200 nautical miles from the territorial sea baseline and beyond that distance to the outer edge of the continental margin. More information

Continental shelf, inner

The inner continental shelf environment represents the shallow marine environment directly seaward of the entrance of the estuary/coastal waterway. More information

Cooperative Research Centre for Coastal Zone, Estuary and Waterway Management

The Cooperative Research Centre (CRC) for Coastal Zone, Estuary and Waterway Management (the Coastal CRC) was established in July 1999. It received funding for a period of seven years.

The Coastal CRC provided decision-making tools and knowledge necessary for the effective management and ecosystem health of Australia's coastal zone, estuaries and waterways.

The goal of the Coastal CRC was to bridge the gaps between science, the community and policy making organisations. They conducted quality science within five interlinked themes in management study areas using participatory approaches with stakeholders.

Coral bleaching

Coral bleaching is the paling or whitening of corals due to a loss or decline of the symbiotic microalgae (zooxanthellae) that live within the coral polyp, and that give it colour. Coral bleaching is caused by both natural and human-induced variations in the reef environment. Some causes of coral bleaching include changes in water temperature, sub-aerial exposure caused by low tides or ENSO-related changes in sea level and rapid dilution of salinity levels.

Coral reef

Coral reefs are biogenic (aragonite) structures produced by living organisms. They are found in shallow, nutrient-deficient marine waters in the tropics.

Critical success factor

Critical success factor is a business term for a component or element which is necessary for a project (or organization) to achieve its mission. More information

Cusp, cuspate

Short ridges that are separated by crescent-shaped troughs. They are found on the foreshore at relatively evenly spaced intervals. Cuspate pertains to a shoreline which follows smooth arcs in between cups.

Cut-Off Embayment

Typically small basins within wave-dominated estuaries or wave-dominated deltas that have been bypassed by the principal fluvial current flow, and therefore have restricted exchange with the main body of the coastal waterway.

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Decision support tools (or systems)

Decision support tools are interactive computer-based systems that assist decision makers to utilize models and data to identify and solve problems and make decisions by increasing awareness and understanding over a wider range of issues and identify trade-offs.

Decomposition of organic matter

The decomposition of organic matter is variously referred to as oxidation, metabolism, degradation and mineralisation. Organic matter is first oxidised by molecular oxygen, and the products (or metabolites) of the reaction are carbon dioxide and recycled nutrients (i.e. the reaction is the reverse of photosynthesis) [1,2].

For example, the aerobic respiration of Redfield organic matter yields 106 moles of carbon dioxide (CO2), 16 moles of ammonia (NH3) and one mole of orthophosphate (PO4) (reaction 1). If sufficient dissolved oxygen is present, bacteria oxidise the NH4 produced in reaction 1 to nitrite (NO2) (reaction 1a) and then to nitrate (NO3) (reaction 1b) in a process called nitrification.

(1) Oxygen reduction

106(CH2O)16(NH3)(H3PO4) + 106O2 = 106 CO2 + 16 NH3 + PO4

(1a) 16 NH4+ + 24 O2 = 16 NO2- + 16 H2O + 32 H+

(1b) 16 NO2- + 8 O2 = 16 NO3

106(CH2O)16(NH3)(H3PO4) + 138 O2 ------- 106 CO2 + 16 HNO3 + H3PO4 + 122 H2O

When dissolved oxygen is depleted, oxidation proceeds in a series of reactions which represent successively lower pE levels (or redox states; Figure 1). Reactions 2 - 4 occur under sub-oxic conditions.

(2) Manganese reduction

106(CH2O)16(NH3)(H3PO4) + 236 MnO2 + 472 H+ ------- 106 CO2 + 236 Mn2+ + 8 N2 + H3PO4 + 366 H2O

(3a) Nitrate reduction by denitrification

106(CH2O)16(NH3)(H3PO4) + 94.4 HNO3 -------106 CO2 + 55.5 N2 + H3PO4 + 177 H2O

(3b) Dissimilatory nitrate reduction to ammonia

106(CH2O)16(NH3)(H3PO4) + 84.8 HNO3 -------106 CO2 + 42.4 N2 + 16 NH3 + H3PO4 + 148.4 H2O

Iron and sulfate are the last oxidants in the series. Sulfate reduction (5) only occurs under anoxic conditions.

(4) Iron oxyhydroxide reduction

106(CH2O)16(NH3)(H3PO4) + 212 Fe2O3 (or 424 FeOOH) + 848 H+ ------- 106 CO2 + 16NH3 + H3PO4 + 742 H2O + 424 Fe2+

(5) Sulfate reduction

106(CH2O)16(NH3)(H3PO4) + 53SO42- ------- 106 CO2 + 16 NH3 + H3PO4 + 106 H2O + 53 S2-

Figure of Schematic representation of chemical processes with depth in sediment and changes in Eh range.

Figure 1. Schematic representation of chemical processes with depth in sediment and changes in Eh range (Modified after Millero, 1996) [3]

  1. Froelich, P. N., Klinkhammer, G. P., Bender, M. L., Luedtke, N., Heath, G. R., Cullen, D., Dauphin, P., Hammond, D., Hartman, B., and Maynard, V. (1979). Early oxidation of organic matter in pelagic sediments of the eastern equatorial Atlantic; suboxic diagenesis. Geochimica et Cosmochimica Acta Pergamon, Oxford. 43, 1075-1090.
  2. Drever, J.I. 1982. The Geochemistry of Natural Waters, Prentice-Hall, Inc., Englewoods Cliffs, N.J., pp. 388.
  3. Millero, F.J. 1996. Chemical Oceanography. CRC Press LLC. pp. 469.

Delta, flood- & ebb-tide

Flood and ebb tidal deltas are subtidal to supratidal dunes and channels, typically found in the entrances of wave-dominated estuaries and deltas (adjacent to the barrier), and are formed by redistribution of sediment by tidal movement in and out of the entrance. More information

Delta, fluvial

Fluvial deltas are complex associations of geomorphic settings, sediment types and ecological habitats, at the point where a freshwater source enters an estuarine water body. More information

Demersal fish

Demersal fish are bottom foraging fish that normally live near or on the seabed.


Denitrification is the microbial reduction of nitrate to dinitrogen gas. Denitrification is sometimes referred to as 'dissimilatory' nitrate reduction because it occurs in association with the dissimilation (decomposition) of organic matter [1]. The denitrification reaction for the oxidation of organic matter with Redfield molar proportions is as follows [2]:

106(CH2O)16(NH3) + H3PO4 + 94HNO3= 106CO2 + H3PO4 + 177H2O + 55.2N2

The nitrate (NO3-) is used in the respiratory process of the microbes, and can be derived from the water column or from nitrification occurring during the mineralisation of organic matter in sediments. When nitrate for denitrification is derived from nitrification, the process is called coupled nitrification-denitrification.

Schematic diagram of N cycling in coastal sediments under relatively low levels of carbon loading

Figure 1. Schematic diagram of N cycling in coastal sediments under relatively low levels of carbon loading. Note that some nitrogen is vented to the atmosphere as dinitrogen gas (modified from Heap et al., 2001 [4]).

Significance of denitrification in coastal waterways

Denitrification is an important reaction in coastal waterways because it can permanently remove nitrogen from the system as dinitrogen gas (Figure 1). As such, it can counteract the eutrophication process [3,4,13]. If benthic denitrification ceases, flushing by tides or freshwater becomes the only way to eliminate excess nitrogen [5]. The cessation of nitrification and denitrification is also an important cause of hysteresis in the loading response of estuaries to nutrients [6].

Some controls on denitrification rates

Denitrification in sediments appears highly sensitive to carbon loading (a.k.a. trophic status) [3,9,13,18]. Carbon loading to sediments can be estimated by measuring the carbon dioxide flux from sediments. Denitrification efficiencies become successively lower as carbon loadings move into the mesotrophic, eutrophic and hypertrophic range [3], and more and more nitrogen is recycled in bioavailable forms (such as ammonium). The efficiency of the denitrification process is an 'indicator' of sustainable carbon loading rates in coastal waterways (e.g. the denitrification efficiency) [3].

Denitrifying bacteria are anaerobic but they require an oxidised form of nitrogen (e.g. nitrate). Denitrification can be enhanced by the presence of benthic infauna which increase sediment surface area (burrows) and enhance irrigation (oxidation) of deeper sediments. Benthic invertebrates thus cause localised increases in concentrations of organic matter and solutes (i.e. ammonium) and ultimately enhance microbial activity and oxic/anoxic microenvironments (and therefore coupled nitrification/denitrification) in their burrow linings, excreta and organic particles [7,17].

Seagrasses and other benthic plants and algae may also enhance coupled nitrification-denitrification because they oxygenate the upper sediment layers [8]. However saturating the upper sediment layers with oxygen can also have the reverse effect, and lower denitrification rates during daylight hours. Moreover, if water column nitrogen concentrations are really low, benthic microalgae may inhibit nitrification and denitrification because they compete for nitrate [15].

Denitrifying activity tends to be highest in the summer months coinciding with warmer water temperatures [11]. It also varies inversely with ionic concentration, and is especially high when salinities are <10 ppt [10]. High concentrations of the heavy metals cadmium, copper and zinc in sediment can inhibit denitrification [12].

Schematic diagram of N cycling in coastal sediments under relatively high carbon loading rates

Figure 2. Schematic diagram of N cycling in coastal sediments under relatively high carbon loading rates. Note that denitrification is less important, and most nitrogen is recycled as ammonium (NH4) which is available to plants (modified from Heap et al., 2001 [4]).

  1. Postgate, J.R. 1998. Nitrogen Fixation. 3rd Edition. Canbridge University Press, London.
  2. Froelich, P. N., Klinkhammer, G. P., Bender, M. L., Luedtke, N., Heath, G. R., Cullen, D., Dauphin, P., Hammond, D., Hartman, B., and Maynard, V. (1979). Early oxidation of organic matter in pelagic sediments of the eastern equatorial Atlantic; suboxic diagenesis. Geochimica et Cosmochimica Acta Pergamon, Oxford. 43, 1075-1090.
  3. Eyre, B. and A.J.P. Ferguson 2002. Sediment biogeochemical indicators for defining sustainable nutrient loads to coastal ecosystems, Proceedings of Coast to Coast 2002 - "Source to Sea", Tweed Heads, pp. 101-104.
  4. Heap, A., Bryce, S., Ryan, D., Radke, L., Smith, C., Smith, R., Harris, P. and D. Heggie. 2001. Australian Estuaries & Coastal Waterways: A Geoscience Perspective for Improved and Integrated Resource Management. AGSO Record 2001/07, pp. 118.
  5. Harris, G.P. 1999. The response of Australian estuaries and coastal embayments to increased nutrient loadings and changes in hydrology, In Australian Estuarine Systems: Carbon, Nitrogen, and Phosphorus fluxes (Eds., S.V. Smith and C.R. Crossland), LOICZ Reports and Studies No. 12, LOICZ IPO: Texel, The Netherlands, pp. 112-124.
  6. Harris, G.P. 1999. Comparison of the biogeochemistry of lakes and estuaries: ecosystem processes, functional groups, hysteresis effects and interactions between macro- and microbiology. Marine and Freshwater Research 50, 791-811.
  7. Nixon, S.W 1988, cited in Harris 1999. Comparison of the biogeochemistry of lakes and estuaries: ecosystem processes, functional groups, hysteresis effects and interactions between macro- and microbiology. Marine and Freshwater Research 50, 791-811.
  8. Risgaard-Petersen, N. and Jensen, K., 1997. Nitrification and denitrification in the rhizosphere of the aquatic macrophyte Lobelia dortmanna (L.), Limnology and Oceanography 42, 529-537.
  9. Seitzinger, S.P., Nixon, S.W. (1985). Eutrophication and the rate of denitrification and N2O production in coastal marine sediments. Limnol. Oceanogr. 30:1332-1339.
  10. Rysgaard, S., Thastum, P., Dalsgaard, T., Bondo Christensen, P., and Sloth, N.P. 1999. Effects of salinity on NH4+ adsorption capacity, nitrification, and denitrification in Danish Estuarine sediments. Estuaries 22(1), 21-30.
  11. Carpenter, E.J., Dunham, S. (1985). Nitrogenous nutrient uptake, primary production, and species composition of phytoplankton in the Carmans River estuary, Long Island, New York. Limnol. Oceanogr. 30, 513-526.
  12. Sakadevan, K., Huang Zheng, and H.J. Bavor. 1999. Impact of heavy metals on denitrification in surface wetland sediments receiving wastewater. Wat. Sci. Tech 40(3), 349-355.
  13. Heggie, D. T., Skyring, G. W., Orchardo, J., Longmore, A. R., Nicholson, G. J., and Berelson, W M. (1999b). Denitrification and denitrifying efficiencies in sediments of Port Phillip Bay: direct determinations of biogenic N2 and N-metabolite fluxes with implications for water quality. Marine Freshwater Research 50, 589-596.
  14. Seitzinger, S.P., Nixon, S.W., Pilson, M.E.Q. (1984). Denitrification and nitrous oxide production in a coastal marine ecosystem. Limnology and Oceanography 29, 73-83.
  15. Krause-Jensen, D., Bondo-Christensen, P. and Rysgaard, S. 1999. Oxygen and nutrient dynamics within mats of the filamentous macroalga Chaetomorpha linum. Estuaries 22(1), 31-38.
  16. Sundareshwar, P.V., Morris, J.T., Koepfler, E.K., and B. Fornwalt. 2003. Phosphorus limitation of coastal ecosystem processes. Science 299, 563-565.
  17. Haese, R.R. 2002. Macrobenthic activity and its effects on biogeochemical reactions and fluxes. In Wefer, G., NBillet, D., Hebbeln, D., Jorgensen, B.B., Schluter, M, Van Weering, T. (eds) Ocean Margin Systems. Springer-Verlag Berlin Heidelberg, pp. 219-234.
  18. Harris, G.P., Batley, G., Fox, D., Hall, D., Jernakoff, P., Molloy, R., Murray, A., Newell, B., Parslow, J., Skyring, G. and Walker, S. (1996). Port Phillip Bay Environmental Study: final report. CSIRO, Dickson, ACT Australia.


Graham Skyring, Skyring Environment Enterprises
Arthur Webb, Southern Cross University

Denitrification efficiency

Denitrification efficiency is the percentage of inorganic nitrogen released from the sediment as dinitrogen gas (N2) during the decomposition of organic matter. More information


The dropping of material which has been picked up and transported by wind, water, or other processes.


Depuration is the process whereby harvested shellfish are placed in containers that contain clean estuarine water, where it is intended that they will purge themselves of their gastrointestinal contents. The effectiveness of depuration can vary with salinity, temperature and turbidity.


Drying out, usually due to subaerial exposure of a normally submerged environment.


Diatoms are single-celled predominantly microscopic algae which consist of two halves (valves) which fit one inside the other to make up a cell (or frustule). More information


Dispersibility refers to the susceptibility of soil aggregates to break-down into smaller particles by water. It is usually associated with high levels of exchangeable sodium, and makes the soils more erodible.

Dissolved Inorganic Nitrogen (DIN)

Nitrogen compounds, present post-filtration, that are detectable by accepted analytical chemical methods. These nitriogen compounds include nitrite, nitrate, and ammonium (NO2-+NO3++NH4+). More information.

Dissolved organic matter (DOM)

Dissolved organic matter (DOM) is dissolved and colloidal organic material that passes through a filter with a mesh size of between ~0.1 and 1 microns [1]. Dissolved organic carbon (DOC) is the carbon component of the DOM. It can be found in three pools:

  1. a labile pool that has rapid turn-over rates;
  2. a semi-labile pool that has slower turnover rates (e.g. months); and
  3. a refractory pool that is not readily available biologically.

DOC/DOM is a source of carbon for bacterial growth. They also forms complexes with trace metals [2] and can absorb sunlight, thus reducing the amount of light that is available for phytoplankton and submerged aquatic plants. The solubilities of relatively insoluble toxicants, such as lindane, p,p'-DDT and PCBs can also be enhanced in the presence of DOC/DOM [3].

  1. Najjar. R.G. 1991. Marine biogeochemistry. In K.E. Trenberth (editor), Climate System Modeling, Cambridge University Press, pp. 241-280.
  2. Elder, J.F. 1988. Metal Biogeochemistry in Surface-Water Systems - A Review of Principles and Concepts. U.S. Geological Survey Circular 1013.
  3. Chiou, C.T., Malcolm, R.L., Brinton, T.I., and Kile, D.E. 1986. Water solubility enhancement of some organic pollutants and pesticides by dissolved humic and fulvic acids. Environmental Science and Technology 20, 502-508.

Dissolved organic nitrogen

Dissolved organic nitrogen (DON) is comprises the organic forms of nitrogen including amino acids, proteins, urea and humic acids. More information

Dissolved oxygen

Measures of dissolved oxygen refer to the amount of oxygen contained in water, and define the living conditions for oxygen-requiring (aerobic) aquatic organisms. More information

Drowned River Valley

A bedrock valley which has been submerged by rising sea-level, and has not been significantly infilled by sediment. Also: Embayment.


As with beaches, coastal dunes begin with the accumulation of marine sand that is transported to the coast by waves and currents. However, the sand is subsequently reworked by strong onshore winds (greater than 5 m/sec) and then deposited behind the beach. More information

Dune vegetation

Communities of plants that grow on beaches and dunes are known as dune vegetation. More information

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