CHAPTER ONE

1.1 INTRODUCTION

Estuary is a semi enclosed coastal body of water which has a free connection with the

open sea and within which sea water is measurably diluted with fresh water derived from

land drainage (Pritchard 1967). Pritchard’s definition does not specifically mention tide, even

though the mixing of seawater and fresh water implies this. There are, however, many

nontidal or minimally tidal seas, such as the Mediterranean Sea and the Black Sea, where

fresh and salt water mix. There are several ways to define what an estuary is. Most likely the

simplest definition is that an estuary is a partially enclosed coastal bay where fresh water and

sea water meet and mix (Mateus et al., 2008). The estuaries are subject to constant changes

in wind, radiation, rainfall, water level and freshwater runoff. In addition, estuaries are often

used and affected by humans, used as (natural) harbors, fish farming, recreation, sewage

reservoirs,

Estuaries generally resemble marine environments more than freshwater

environments, trophodynamic structures and functions are very similar in all aquatic systems,

with the exception of gelatinous plankton, which are not found in freshwater systems. Many

estuaries are degraded by a variety of factors, including soil erosion, deforestation,

overgrazing, overfishing, and wetland deposition. Eutrophication can lead to excess nutrients

from wastewater and animal waste; pollutants, including heavy metals, polychlorinated

biphenyls, radionuclides and hydrocarbons from wastewater inlet; and levees or dams for

flood control or diversion (Wolanski, 2007; Silva et al., 2017). Estuaries form a major

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transition zone with steep gradients in energy and physicochemical properties at the interface

between land and sea (Jennerjahn and Mitchell, 2013). Freshwater entering estuaries can

contain large amounts of alluvium eroded from coastal basins and stream banks. This

material has grain sizes ranging from coarse gravel to fine powder and clay. The finer

sediments are easier to transport and play an important role in influencing the relative

proportions of sand and silt deposits in the estuary. They can also lead to a marked reduction

in water clarity in the upper estuaries, which appear visibly cloudy (Thrush et al., 2014).

They are of ecological importance for various population, including economic importance for

commercial fishing and subsistence. People value the estuary for recreation, scientific

knowledge, education, aesthetics and traditional practices. Boating, fishing, swimming,

surfing and bird watching are just a few of the many recreational activities that people enjoy

in estuaries. Considering the totality of human activities dependent on the existence of

estuaries and their ecosystem services (Barbier et al., 2011), their total economic value to

society is vast (Costanza et al., 2014).

Estuaries maintain water quality that is beneficial to both humans and marine life.

They provide a natural buffer between land and ocean, absorbing floodwaters and storm

surges. Estuaries help maintain biodiversity by providing a range of unique habitats,

including mangroves, salt marshes, mudflats and seagrass beds, critical for the survival of

many species. Many commercially important fish and shellfish species use estuarine habitats

as nurseries for spawning and young growth. The estuaries also create jobs through tourists,

who are drawn to the estuaries for their aesthetics and water activities they provide (Cooper

et al., 2003). However, subsistence fishers still struggle to be identified in developing

2
countries because they almost always fish illegally (Chapsos et al., 2019) or even without a

fishing license. In developing countries, the majority of subsistence fishermen are poor

(Pérez-Ramírez et al., 2012) and sell their illegal catches in local markets to earn extra

income and support their families (Palomares, and Pauly 2019). Despite the fact that humans

benefit from estuary ecosystem services, it is important to note that individuals often

overlook ecosystems because they do not directly pay for them (Summers et al., 2018). As a

result, humans can easily disrupt and overexploit the ecosystems, leaving them impoverished

and unable to offer resources as efficiently as they previously did. Human involvement has a

negative impact on the ecosystems, preventing them from growing or even evolving (Farley,

2012).

Climate change impacts ecosystems by affecting water quality, migration patterns and

plant growth (James et al., 2013), Climate change is reducing the productivity of ecosystems

and making it more difficult for ecosystems to improve water quality and control freshwater

runoff, and it has direct impacts on people, livelihood and culture (Spalding et al., 2014).

Within the continuum of land, rivers and coastal shelves, estuaries perform many important

functions, such as pollutant filtration, nutrient transformation, and elemental biogeochemical

cycling. Therefore, they can have a significant impact on the environmental quality of coastal

waters. Estuaries also protect coastal watersheds and infrastructure from damage from

storms, floods, waves and erosion. With more than 4 billion people living within 60 km of

the world's coasts (Kennish et al., 2008), many of whom live in estuaries, these buffering

effects are crucial for sustaining coastal communities. important to

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 .Three main types of estuaries can be recognized, which are positive, negative or

neutral estuaries. In active estuaries, the amount of evaporation from the surface of the

estuary is less than the amount of fresh water entering the estuary from rivers and land-based

drainage systems.

1.2 Classification based on geomorphology

 DROWNED RIVER VALLEYS: Drowned River valley is also known as coastal

delta estuary. In places where sea level rises relative to land, sea water gradually

enters river valleys, and the topography of estuaries remains similar to river valleys.

This is the most common type of estuary in temperate climates (Kunneke, and Palik

1984). In these systems, the stress divergence that balances the pressure gradient

mainly comes from tidal currents interacting with the bed. Such an interaction

represents a vertical mixing agent that is momentum and mass. In

In some cases, it is possible that mixing at the pycnocline, from the internal stress (or

the stress within the water column around the pycnocline region), also helps to

equalize the pressure gradient (Valle-Levinson, 2010).

 FJORD-TYPE: Fjord-like estuaries form in deeply eroded valleys formed by

glaciers. These U-shaped estuaries typically have steep edges, rocky bottoms, and

submarine sills shaped by ice movement. This tidal distortion yields a two-layer or

three-layer (depending on the specific geometry of the basin) residual flow, as

observed in several fjords and channels of southern Chile (Valle-Levinson et al.,

2007).

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 TECTONIC ESTUARIES: These estuaries are formed by subsidence or land is

separated from the ocean by landslides combined with faults, volcanoes and

landslides. Floods caused by sea level rise during the Holocene also contributed to the

formation of these estuaries. only a small number of tectonic estuaries; These

estuaries are dynamic in many ways, similar to coastal plain estuaries. The processes

and dynamics described in coastal plain estuaries, for example, largely apply to the

San Francisco Bay, a tectonic estuary. However, there are tectonic estuaries, such as

some on the northwest coast of Spain (Gilcoto et al., 2007), where the gravity

circulation is not as developed as in the estuaries coastal plain river.

 BAR-BUILT ESTUARIES: These estuaries tend to be shallow (several meters

deep) with low river discharge and tidal energy being dissipated rapidly as tidal

waves enter the estuary. They are mainly found in subtropical and temperate lowlands

with little surface area for a well-developed watershed, i.e. small catchment area.

Gravitational circulation may be restricted near the freshwater source but should not

cut vertically through the rest of the system. Tidal currents and mixing are often

associated with transitions with ocean but weakened within the basin. These systems

are mainly driven by the force of the wind, but the dynamics remain between the

pressure gradient and the friction, with the exception of the frictional force acting

both on the surface, through the wind and at below, by the stress generated by the

currents due to the wind (Valle-Levinson, 2010).

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 CHAPTER TWO

2.1 BIODIVERSITY OF ESTUARIES

Biodiversity includes the variety of life and its interactions environment, from

genotype to ecosystem. Dominated by marine life, our estuaries are diverse and contains

representatives of many different types of phyla, from microorganisms to whales. By marine

standards estuaries are generally considered species-poor ecosystems. Nevertheless, the

resident species, the strong physical and chemical gradients found within estuaries and the

supply of nutrients from the adjacent catchment make estuaries functionally diverse. In

general, freshwater entering an estuary has a nutrient concentration many times greater than

that of adjacent coastal seawater. Thus, retaining nutrient-rich freshwater in a semi-enclosed

estuary provides an opportunity for key producers to thrive, especially in shallow surface

waters where sunlight is brightest and water is warm. Part of this primary output will be used

by primary and secondary consumers in the estuary and a part may be exported to the

adjacent coastal area (Thrush et al., 2014).

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 Sea water doesn't just move in and out of estuaries with the tides. The speed and

direction of tidal currents at estuary entrances are influenced by the narrowing and depth of

the mouth and can be deflected and altered by sandbars, rocky outcrops, shorelines, man-

made structures and biological coral reefs. As a result, plankton often congregate on separate

fronts or eddies. These areas, which can be stable or ephemeral, are often places of increased

feeding activity by carnivorous fish and their predators, including large fish, birds and

marine mammals (Thrush et al., 2014). There is more to estuary bottom habitats than just

rocks, sand, and mud. Like terrestrial habitats, estuarine habitats are more fully defined based

on dominant species and habitat structure. These habitats can include tube mats, oyster beds,

oyster reefs, crab-cutting mudflats, oyster fields, mussel beaches, sponge gardens, kelp reefs

and seaweeds. These descriptive habitat designations often provide clues to the dominant

ecological processes that underlie the delivery of ecosystem services. The rapid rate of

biodiversity loss has raised concerns about the impact on ecosystem processing and, by

natural extension, the delivery of ecosystem services (Balvanera et al., 2006; Airoldi and

Beck 2007). Globally, 60% of ecosystem services are deteriorating or have been over-

exploited.

There is increasing recognition of a positive relationship between aspects of

biodiversity and many ecosystem processes (Solan et al., 2004; Stachowicz et al., 2008).

Essentially, species diversity is required to maintain functional diversity, lead to more

complete resource utilization, and provide resilience and time stability through functional

offsets. Despite the long history of use and the effects stemming from both land and sea, our

estuarine ecosystems still exhibit high biodiversity values and are still essential to our

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tourism and our sense of national identity. Estuary bed habitats often form a mosaic in steep

slopes related to salinity, wave and tidal energy and depth, and the biological processes that

create these landscapes. Habitat inequalities and their connectivity make a very important

contribution to the delivery of estuarine ecosystem services. Many organisms change their

habitat use, daily or as they grow older, balancing their access to food sources against the

risk of predation or using a range of different food sources. as their size increases and their

energy requirements change (Thrush et al., 2014).

2.2 ANTHROPOGENIC IMPACTS ON ESTUARIES

Estuaries, due to their transitional nature between river basins and marine

environments, are susceptible to human impact from diverse geographical sources from

watershed boundaries to distant marine sources. They are also historical sites where human

activity is concentrated, albeit to varying degrees of intensity and involving different

activities over time. As ecosystems, estuaries are threatened by human activities such as

pollution and overfishing. They are also threatened by sewage, coastal colonization, land

clearing and more. Estuaries are affected by events far upstream and concentrate materials

such as pollutants and sediments (Branch, 1999). Runoff water and industrial, agricultural

and domestic wastes pour into rivers and are discharged into estuaries. Pollutants that can be

introduced without rapidly degrading in the marine environment, such as plastics, pesticides,

furans, dioxins, phenols, and heavy metals.

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 These toxins can accumulate in the tissues of many aquatic species in a process

known as bioaccumulation. They also accumulate in benthic environments, such as estuaries

and bay mud: a geological record of human activities over the past century. Pesticides,

automobile fluids such as antifreeze, oil or grease, and metals such as mercury or lead pollute

all estuaries. These substances can enter estuaries through industrial waste, runoff, streets,

farmland and storm drains. Eutrophication can also cause toxic algal blooms such as red

tides, brown tides, and Pfiesteria growth. Pfiesteria is a single-celled organism that can

release very powerful toxins into the water, causing bleeding wounds on fish and even killing

them. Although the consumption of fish affected by this toxin is not harmful to humans,

exposure to waters where Pfisteria blooms can cause serious health problems (NOAA, 2017).

The elemental composition of biofilms reflects estuarine areas affected by human

activities and, over time, can alter the basic composition of ecosystems and reversible

changes or irreversible in the abiotic and biotic parts of the top basal system (García-Alonso

2017). Estuaries have a natural tendency to eutrophication because runoff water washes

nutrients into estuaries. With human activities, soil runoff now also includes many chemicals

used as fertilizers in agriculture as well as livestock and human waste. Chemicals that reduce

oxygen in excess water can lead to hypoxia and create dead zones. This can lead to reduced

water quality, fish and other animal populations. Overfishing also occurs.

Kennish (2015b) and Kennish et al., (2008) study the impact of human activities on

estuaries. They identified a wide range of anthropogenic stressors to these ecosystems, which

can be grouped into different categories. These include; (1) habitat loss and alteration; (2)

sewage and pathogenic inputs; (3) chemical contaminants; (4) human-induced

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sediment/particulate inputs; (5) human-altered hydrological regimes; (6) overfishing; (7)

climate change effects;

 Habitat Loss and Alteration; Estuaries are particularly vulnerable to habitat loss and

change due to human activities. Examples include physical changes in the Gulf region

associated with construction of lagoons, bulkheads, retaining walls, docks, piers, boat

ramps, marinas, housing, roads and other infrastructure ( Michael, 2017). Protected

areas have been established in some of the most sensitive and valuable estuarine

habitats impacted by human activity. The dredging of lagoons, canals and other

estuary areas disrupts benthic habitat for months or even years.

2.3 IMPLICATIONS OF EUTROPHICATION ON ESTUARIES

2.3.1 Effects of eutrophication on biogeochemical cycles

Nitrogen is often the main cause of eutrophication in estuaries in temperate zones.

(Howarth and Roxanne 2006). During the eutrophication event, biochemical feedback

reduces the amount of silica available. (Howarth et al., 2011) These feedbacks also increase

nitrogen and phosphorus inputs, creating favorable conditions for the existence of harmful

algae. With the current unbalanced nitrogen cycle, estuaries may be phosphorus-limited

instead of nitrogen-limited.

Estuaries can be severely affected by the unbalanced phosphorus cycle, as phosphorus

interacts with the availability of nitrogen and silica. With abundant nutrients in the

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ecosystem, plants and algae proliferate and eventually decompose, producing significant

amounts of carbon dioxide. (Morales-Williams et al., 2021) While releasing CO2 into the

water and atmosphere, these organisms also take away all or most of the available oxygen,

creating a hypoxic environment and an imbalanced oxygen cycle. (Selman et al., 2008)

Excess carbon in the form of CO2 can lead to low pH levels and ocean acidification, further

harming vulnerable coastal areas such as estuaries.

2.3.2 Effects of eutrophication on estuarine plants

Eutrophication has been found to adversely affect many plant communities in

estuarine ecosystems (Deegan et al., 2012). Saltmarshes are a type of ecosystem in some

estuaries adversely affected by eutrophication (Deegan et al., 2012). Corduroy plants

dominate the salt marsh landscape (Donnelly et al., 2001). Excess nutrients cause plants to

grow faster in aboveground biomass, but because they are rich in nutrients, less energy is

allocated to the roots. This leads to a lower biomass in the vegetation below ground which

destabilizes the banks of the marsh causing increased rates of erosion. Similar phenomena

also occur in mangrove swamps, another potential estuarine ecosystem. Increased nitrogen

causes increased shoot growth and decreased root growth (Lovelock et al., 2009).

2.3.3 Effects of eutrophication on estuarine animals

In all biomes, eutrophication often leads to plant death, but the impact doesn't stop

there. Plant death changes the entire food web structure, which can lead to the death of

animals in the affected biome. Estuary estuaries are biodiversity hotspots, containing the

majority of commercial fish catches, making eutrophication impacts in estuaries even greater

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(Waltham et al., 2020). Some specific estuarine animals feel the effects of eutrophication

more strongly than others. Eutrophication reduces oxygen levels in their habitat to the point

where whitefish cannot survive, causing local extinction. However, some animals, such as

carnivorous fish, tend to do well in nutrient-poor environments and can benefit from

eutrophication. This can be seen in sea bass or sea bass populations (Vonlanthen et al.,

2012).

2.3.4 Effects of eutrophication on human activities

Eutrophication can affect many marine habitats, which can have economic

consequences. The commercial fishing industry depends on estuaries for about 68% of the

catch value due to the high biodiversity of this ecosystem. During the algal bloom period, the

fishermen noticed a significant increase in the number of fish. A sudden increase in primary

productivity causes fish populations to spike, leading to an increase in oxygen utilization

(Gao, Yang et al., 2012). The continued deoxygenation of the water then causes a decline in

fish populations. These impacts can begin in estuaries and have widespread effects on

surrounding waters. This, in turn, can reduce the revenue of the fishing industry in a region

and across the country (Fay, Gavin et al., 2019).

2.4 IMPLICATIONS FOR MARINE LIFE

Estuaries are amazingly dynamic systems where temperature, salinity, turbidity, depth

and currents change daily in response to the tides. This dynamic makes estuaries a highly

productive habitat, but also makes it difficult for many species to survive year-round. As a

result, large and small estuaries experience dramatic seasonal variation in their fish

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communities (Osborn, 2017). During the winter, the fish community is dominated by hard-

working marine inhabitants, and in the summer a wide variety of marine fish and fish species

move in and out of the estuaries, taking advantage of their high yields. Estuaries provide the

necessary habitat for many species of organisms that depend on estuaries to complete their

life cycles. Pacific herring (Clupea pallasii) are known to spawn in estuaries and bays,

estuarine-born perch, juvenile flatfish and lampreys migrate to estuaries to spawn, and

salamanders and lampreys use estuaries as migratory corridors (Gillanders et al., 2003).

In addition, populations of migratory birds, such as the black-tailed magpie (Gill et

al., 2001), depend on estuaries. Two of the main challenges of estuary life are changes in

salinity and silt. Many fish and invertebrates have different methods of controlling or

obeying changes in salt concentrations and are known as osmoconformers and

osmoregulators. Many animals also burrow to avoid predation and live in more stable

sedimentary environments. However, a large number of bacteria are found in sediments with

very high oxygen requirements. This reduces oxygen levels in the sediment, often resulting

in partial anoxia, which can be exacerbated by limited water flow.

2.5 MICROORGANISMS IN AN ESTUARY

Bacteria were the most abundant organisms in estuaries, with an average of 10^6 to

10^7/ml organisms in water and 10^8 to 10^10 per dry weight of sediment. Soil and salt

marsh sediments often contain more bacteria per unit volume than the water column. In the

water column, high densities can be found in the surface layer rather than the subsurface.

Aerobic and anaerobic anaerobes are the most common, and pseudomonads and Vibrio are

the most common isolates. Sediments and waterlogged soils show very high concentrations
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of bacteria, which decrease with soil depth. Higher concentrations of bacteria were found in

most estuaries than in coastal seawater and nearby river water (John et al., 1989). The

number of fungi living in the estuaries is extremely large. Some species of fungi live only in

estuaries, while others have a wider range of habitats. Aquatic fungi and yeasts predominate

in aquatic species, with a few fungi associated with particles or solids in the water. In

sediments, active fungal species are mainly found in surface aerobic zones. Fungal densities

decrease rapidly with soil depth, but fungal spores are found in all sediments.

Most of the phytoplankton in a typical estuary are closely related to the surrounding

marine or freshwater microbial groups and belong to the phyla Proteobacteria, Bacteroidetes

and Actinobacteria, with phylotypes in this estuary occurs in a range of salinities considered

as mixed freshwater or marine biota, these estuaries. phylotypes are found in a wide range of

mixed marine or freshwater populations (Hollibaugh, 2000). Some estuaries near urban areas

and industrial zones have received high inputs of a variety of trace elements, including

polycyclic aromatic hydrocarbons (PAHs). PAHs are toxic, mutagenic and carcinogenic to

human health and the environment. Therefore, ecological examination of PAH-degrading

microorganisms is essential to prevent ecological damage caused by organic pollutants in

estuarine ecosystems. Research has shown that a large number of bacterial species are

capable of biodegrading PAH, but the diversity of the microbial community is also

significantly reduced due to the availability of a particular carbon source in the biomolecules.

PAH pollution. Sequence analysis of the 16S rRNA gene confirmed that Cycloclasticus spp.

plays an important role in the degradation of low molecular weight PAHs in the marine

environment. In addition, Pseudomonas spp., considered a good group of PAH-degrading

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bacteria in soil or sediments, also increased its competitive and adaptive ability to degrade

PAH in seawater environment (Maïté Niepceron et al., 2010).

2.5.1 PROCESSES ASSOCIATED WITH MICROORGANISMS

Cycle of energy and matter in estuaries is closely related with microbial activity. It

has been estimated that half of the aerobic and anaerobic transformations of organic matter in

salt marsh are the result of microbial metabolism.

 CARBON CYCLING: Bacteria show a variety of metabolic pathways involved in

carbon efflux and carbon cycling. Photosynthesis is mainly carried out by algae and

phytoplankton in estuaries. The carbon fixation rates of phytoplankton show marked

seasonal fluctuations in hydrological and nutritional parameters. Since many

sediments and wetlands of estuaries are anoxic, anaerobic digestion is important.

Complex organic matter used by fermenters and dissolved oxide denitrifiers. Sulfate

reducers and methane producers were once thought to have a more limited

distribution. Studies have shown the seasonal and annual dynamics of free plankton

and unstable organic carbon available to microorganisms along the salinity of

estuaries. Plankton abundance can be an important indicator of ecosystem health in

eutrophic estuaries, given the positive relationship between plankton abundance,

unstable organic carbon of microorganisms (MLOC) and dissolved oxygen ( Leila and

Robert 2007).

 NITROGEN CYCLING: Nitrogen is a major limiting nutrient for primary production

in estuaries. The N-cycle processes governed by microbial activity include

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nitrification, soluble oxide denitrification, and nitrogen fixation. The nitrogen cycle in

estuaries involves water mixing and microbial community dynamics. The nitrogen

cycle through the gradient of salinity, oxygen and dissolved inorganic nitrogen in

sandy soils and sea margins, coastal permeable sediments, controls both the amount

and form of nitrogen released in the coastal ocean. In one study, the abundance of

ammonia-oxidizing beta-proteobacteria (beta-AOB) was significantly lower in

freshwater than in saltwater stations, while the abundance of ammonia-oxidizing

archaea bacteria ( AOA) is almost constant in the estuary areas. This different

response to salinity changed the beta-AOB to AOA ratio. Analysis of ammonia

oxidation enrichment cultures at a wide range of salinities revealed that AOA exists

only during freshwater enrichment (Santoro et al., 2008).

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 CHAPTER THREE

3.1 ECONOMIC IMPORTANCE OF ESTUARIES

The estuary is a tourist attraction and plays a central role in development (Harbor

View). Estuaries provide natural harbors used for transportation and industry as ideal

locations for large port facilities. They are ecologically important to diverse biota, including

their economic importance to commercial and subsistence fisheries. People value estuaries

for their recreation, scientific knowledge, education, aesthetics, and traditional practices.

Boating, fishing, swimming, surfing and bird watching are just a few of the many

recreational activities people enjoy in the estuaries. Their unique habitat makes them

valuable laboratories for scientists and students. Considering the presence of 4,444 estuaries

and the total human activities that depend on their ecosystem services (Barbier et al., 2011),

their total economic value to society is enormous (Costanza et al., 2014). Some evidence of

the economic value of functioning estuarine ecosystems can be found in examples where

human activities have affected such functioning. An example is the economic loss caused by

human-induced changes in river runoff. The downstream impact of dam construction is often

not fully considered when making decisions to build dams in river systems. Economic losses

due to reduced fisheries landings due to reduced nutrient flow into the Indian Ocean from the

Sofala Bank fisheries (Turpie, 2004). Estuaries provide materials that are useful for many

purposes other than direct human consumption. Vegetation is used as fertiliser, fish-food and

grazing for livestock.

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 Estuaries are complex ecosystems, providing many essential goods and services that

support a wide range of human uses and values. Services range from the provision of food

and recreation to the more obscure such as the provision of genetic resources. Some we rely

on every day, others are only called upon in difficult times, such as storm protection (Thrush

et al., 2014). There are many examples of specific ecosystem processes directly related to

service delivery. But what seems so simple is often produced by multiple ecological

processes and interactions that contribute to different services. This overlap and

interrelationship complicate the separation of processes or services and highlights the

potential unintended consequences of administrators taking a monolithic or departmental

approach without awareness of connectivity. Balancing usage requires careful management,

and while defining and isolating individual services is useful, their interconnection and high

degree of interdependency make them a system approach to managing. is preferred.

Perhaps one of the most extensive services provided by estuaries is the production of

shellfish and fish harvested by cultural, recreational and commercial fishermen and

aquaculture. Many species of crustaceans live in estuaries (scallops, pee, cockles, etc.) and

often use different habitats for different life stages. Many species of fish also make use of our

estuaries. Some are permanent residents, while others use the estuary as a breeding or

children's day care center. This includes many species of commercial and recreational

importance, such as red snapper and cod (Thrush et al., 2014). High productivity in the

estuary attracts a large number of fish, shorebirds, seabirds and marine mammals. These

species are often top predators, and changes in their numbers can affect the density of

intermediate food-web predators or other species that play important roles in community or

18
ecosystem processes (Thrush et al., 2014). Chemicals extracted from orifice-dependent

species are used in medicines, dietary supplements, and pest control. Examples from New

Zealand are chemicals currently being tested in cancer research, agar, seaweed powder,

chitin, fish oil, calcium powder, fucoidin sulfate, green lipped mussel extract, and collagen

(Thrush et al., 2014).

Organic and inorganic nutrients are stored, cycled and transformed through the

activity of estuarine species. Nutrient recycling occurs in both the water column and

sediment, but sediment processes are of particular importance in most estuaries. Moving

animals in the sediment (bioturbation) affect pore water flow, stimulating microbial

processes and increasing the rate at which organic matter is broken down and nutrients are

remineralized. Bioturbation destabilizes pore water chemical gradients that affect sediment

permeability and erosion, sediments organic matter, affects decomposition rates, and

transfers mineral nutrients from sediments to overlying waters. may also be emitted.

Together these processes maintain a supply of essential nutrients such as carbon, nitrogen,

phosphorus, sulfur and metals. Estuaries contribute to climate regulation through gaseous

exchange between water, sediment and the atmosphere. This includes the balance of oxygen

and carbon dioxide and the correction of some greenhouse gases. The open ocean is

generally recognized for its contribution to climate regulation because of its large surface

area.

Although they generally cover only a small area, estuaries contribute

disproportionately due to high rates of gas exchange. All major estuary producers absorb

carbon dioxide for photosynthesis; however, large vegetation, such as mangroves and

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seagrasses, provides a notable long-term reserve and shows a greater capacity for long-term

storage. Carbon sequestration is an important service that helps to mitigate the acceleration

of climate change caused by anthropogenic emissions (Nellemann et al., 2009). Seaweeds

(e.g kelp forests) also offer a role in carbon sequestration, though the storage potential for

material that is not advected to the deep ocean is not well understood. Vegetated coastal

habitats are estimated to contribute half of the total carbon sequestration in ocean sediments,

though they cover less than 2% of the ocean surface (Lafoley and Grimsditch 2009).

Another important service provided by estuaries is the removal of nutrients from land

and net loss of nitrogen to the atmosphere. Denitrification is the primary mechanism for

nitrogen removal from estuary systems. It is a biochemical process where inorganic forms of

nitrogen dissolve. Denitrification occurs only under anoxic conditions and is mediated by

specialized bacteria present in the sediment (Thrush et al., 2014). Many estuarine flora and

fauna provide habitat structure that is exploited by other species. This provides a nursery for

young organisms, a hiding place to avoid predators, and a long-term habitat structure for

many species.

3.2 PROBLEMS OF ESTUARIES

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