Estuarine Ecosystems, Habitats, and Ecosystem Services

 Project Importance

As more people move to the coast, as the weather continues to impact the inhabitants of the coast and shape the landscape, as sea levels continue to rise, it is important to consider these ecosystems and monitor how they are affected by human and natural elements.  One of the suggestions for the deposition of dredge spoil is the creation of an island.  Creating an island would result in an intertidal area, where the tide sometimes covers the shore and sometimes leaves it exposed.  In those areas creating a marsh may be the best option to develop a new habitat and area for nutrient cycling.  Like seagrass, marshes are known to have high rates of denitrification and in some cases higher than seagrass beds.  Oyster beds are also being considered for the fringes of the island as a way to mitigate erosion and contribute another ecosystem service of value to humans.  Ultimately, when a major engineering project is undertaken on the coast, it is important to keep in mind how we impact the area.  NC DOT is working with Coastal Studies Institute to discover the best options so that if a habitat will be affected by dredging, that habitat can be replaced, or the spoil can be used to augment an already existing productive ecosystem.  To learn more about Estuarine Ecology at Coastal Studies Institute check out the video below.


Pamlico Sound Estuarine System (PSES)

An estuary is a place where freshwater mixes with the sea in a semi-enclosed coastal body of water. The Pamlico Sound is home to a host of unique habitats and is the largest of the North Carolina estuaries. Water from the marshes, forests, and grasslands of eastern North Carolina and southeastern Virginia flow into and mix with ocean water fed from Oregon and Hatteras inlets. The combination of fresh and salt water creates brackish water, which varies in its salinity or salt content hour to hour and day to day.

There are three types of estuaries found in North Carolina:

  • Tributary estuaries – begin at the initial interface of fresh and sea water in a river
  • Trunk estuaries – begin downstream of tributary estuaries and meet at the widening of a river into a sound
  • Back Barrier Sounds – lie parallel to the coast, sandwiched between the mainland and the barrier islands


Each type of estuary is unique and offers conditions that are incredibly changeable, yet remarkably suitable for wildlife. Some creatures move through the different types of estuaries based on the stage of their life cycle.  This project zeroes in on the back barrier Pamlico Sound area and its habitats, ecosystems, and ecosystem services.

Sub-Aquatic Vegetation: Seagrass

Seagrass grows in shallow salty and brackish water like that of the Pamlico sound.  Unlike seaweed, seagrass shares the same composition as terrestrial plants, similar to what you might find on a golf course or in your backyard.  This means that they have roots, stems, and leaves and can also produce flowers and seeds.  Every spring throughout the sound, seagrass appears in a patchwork of underwater meadows, some of which can grow so large they can be seen from space.


Dark swaths of sea grass sprout in spring beneath the brackish waters of the back barrier islands of Pamlico Sound.


These meadows of underwater grasses provide an important habitat for a wide variety of animals.  Many of the fish that are caught locally, both in the sound and out in the ocean, start their life in the sanctuary of the seagrass beds.  This makes seagrass an important ecosystem service provider for the commercial and recreational fisheries in North Carolina.  The habitat created by seagrass acts as a nursery for juvenile creatures of all shapes and sizes including invertebrates, fish, crabs, and turtles.



Sea grass clams

Seagrass clams



Sediment Trapping

Seagrass offers other ecosystem services such as sediment trapping.  Waves and currents are capable of whipping up sand and silt from the sound floor suspending the sediment up in the water column.  The suspended sediment impairs water clarity and prevents sunlight from reaching the sound bottom where life depends on it to grow.  As water rushes over these sub-aqueous meadows, sand and silt become trapped by the flowing grasses and settle to the bottom.  Not only does the seagrass act as a net containing clouds of suspended sediment sweeping across the sound floor, it also acts as an anchor keeping what sediment lies beneath it in place.  In the absence of seagrass, waves and currents can rush through undeterred and stir up more sediment to be carried and deposited elsewhere, like one of the inlets.  The presence of seagrass mitigates the ever constant process of erosion and improves water clarity.



Seagrass plays another important role vital to the health of an estuarine ecosystem and that is denitrification.  Rainwater washes nutrients on land into rivers and streams which flow into the sound.  These nutrients include nitrogen in the form of nitrites and nitrates which cycle through the estuarine ecosystems.  When large quantities of these nutrients inundate an ecosystem the health of the system is threatened.  Algae, another photosynthetic organism (meaning it relies on the sun for food), propagates in greater numbers when higher concentrations of nutrients are present.  This results in algal blooms.  Algae, which absorbs many of the nutrients cycling through the system, are short-lived and die off quickly.  When this happens the organic material that remains begins to decay, a process which strips the water of dissolved oxygen.  As oxygen levels drop species which depend on O2 to live are threatened and may even result in large fish die-offs.  Studies have shown that seagrass beds produce favorable conditions for a balanced nitrogen cycle maintaining the health of the ecosystem and guarding it against the negative impacts of the influx of nutrients from stormwater.


Research Methods

Core Sampling

Scientists at the Coastal Studies Institute are examining this process at work.  Nutrient cycling is bio-mediated, meaning that the act of denitrification is occurring at the microbial level.  Both biotic (living organisms) and abiotic (physical, non-living) factors play a role in affecting the way nutrients are processed and where they are stored.  This research is concerned with how much is coming in and how much is going out in the areas of the sediment-water interface.  To study this process scientists take core samples at each of the different habitats at the Rodanthe site starting first with the shoreline that has marshes and then shoreline without marshes, and eventually areas without any vegetation at all.  Next, they focus on the seagrass by taking cores from densely vegetated areas of seagrass to less densely vegetated, to areas where seagrass is totally absent.  By taking an array of samples, researchers hope to better understand the role marshes and seagrass play in nutrient cycling.  To see the process of taking a push core sample first-hand check out the video below.


Continuous Flow Core Incubations

After each collection, water and sediment cores with overlying water were transported to the University of North Carolina Institute of Marine Sciences (IMS) in Morehead City, NC.  At IMS cores were submerged in an aerated water bath overnight in an environment chamber set to the average water temperature.  Dark conditions were maintained throughout the course of the incubation to minimize the effects of photosynthetic algae and to prevent the formation of bubbles that would affect gas concentrations in water.  The following morning (12-18 hours) each core was capped with an air-tight plexiglass top equipped with an inflow and outflow port and incubated to a continuous flow system.  During the incubation unfiltered, aerated water was passed over the cores at a flow rate of 1 ml min-1.  The concentration of dissolved constituents entering the cores was determined using a bypass line.  Samples (5ml) were collected from the outflow of each core and the bypass line for dissolved gas analysis at 18, 24, 36 and 48 hours after the start of the incubation to ensure the steady state conditions.  Successive measurements from each core were averaged to give core specific values and reduce pseudo-replication.

Analytical Techniques

Membrane inlet mass spectrometry (MIMS, Balzers Prisma QME 200 quadrupole mass spectrometer) was used to measure N2, O2 and Ar dissolved in water.  The concentration of N2 and O2 was determined using the ratio with Ar.  Once during the 48 hour period 50 ml water smaples were collected for nutrient analysis.  Water was filtered through Whatman GF/F filters (25 mm diameter, 0.7 µm nominal pore size) and the filtrate was analyed with a Lachat Quick-Chem 8000 (Lachate Instruments, Milwaukee, WI, USA) automated ion analyzer for nitrate (NO3- and NO2-) and ammonium (NH4+)(detection limits: 0.04 μM, 0.18 μM, respectively).


Flux calculations were based on the assumption of steady-state conditions and a well-mixed water column.  A poitive flux indicates a production and a negative fluxindicates demand, relative to the water entering the cores.  A positive N2 flux is assumed to be denitrificaiton.  This method does not discern N2, production from denitrificaiton, anammox or any other N2 producing process.  Fluxes of oxygen directed into the sediment were represent rates of sediment oxygen demand (SOD).



Excessive sediment delivery has long been regarded as a pollutant in aquatic ecosystems, however maintaining and enhancing sediment supply to some coastal habitats such as marshes is a recent management priority.  Additionally, as the quantity of undeveloped shoreline decreases, using dredge material to create new, restore degraded shoreline areas is a desirable alternative in many settings.  Researchers assessed critical features of ecosystem function in reference to deposition sites and in sites being considered for additional deposition sites.  Measurements focused on components of ecosystem function that have been found to contribute most to the overall values of ecosystem services and allowed assessment of expected changes in ecosystem function, and the concomitant changes in the values of ecosystem services.


Nitrogen cycling is an important component of shallow estuarine ecosystem function because nitrogen generally limits primary production in coastal ecosystems.  Nitrogen supplied in excess can also be considered an important coastal pollutant.  Negative impacts linked to excessive nitrogen deliver to coastal regions include, but are not limited to, harmful algal blooms, shifts in primary producer communities and increased hypoxia (oxygen deficiency). In areas where nitrogen loading to estuaries is excessive, any processes that remove nitrogen from the system become increasingly important.  Denitrification is the microbially-mediated process by which nitrate (NO3-, biologically active) is converted to nitrogen gas (N2, biologically inactive).  Results of recent studies show that denitrification can account for significant nitrate removal from estuaries.

Researchers from the Institute took core samples on a seasonal basis in habitats likely to be either affected by dredge deposition or dredged material or created as a part of a material deposition plan. Using a membrane inlet mass spectrometer (MIMS), researchers analyzed samples collected from these varied locations and found that rates were generally low and there was variability in habitat-specific patterns.  The different habitats from which core samples were taken include marsh (M), unvegetated intertidal (UV-I), unvegetated subtidal (UV-S), sea grass sparse (SG-S), and seagrass dense (SG-D).  Rates of nitrogen removal found at these specific sites by season are found in Figure 1.

Figure 1. The graph represents seasonal rates of denitrificaiton in the five habitats.

In summer, denitrification rates were highest in the fringing marsh and zero in the seagrass beds. Fall denitrification rates were all positive but were also all below 20um m-2 h-2.  The highest rates of denitrification were measured in spring, and seagrass had the highest among the habitats.  These data provide site-specific information on the rates of nitrogen removal that can be expected from habitats in the study area as well as being estimates of what could be expected from the habitats that may be restored as a part of dredged material deposition plans.

To inform estimations of impacts of habitat creation using dredge materials future ecosystem function and thus ecosystem services, researchers conducted similar nitrogen flux experiments in habitats restored in the past.  Salt marshes and oyster reefs are often restored on shorelines to prevent coastal erosion and provide ecosystem functions, including denitrification.  Using a chronosequence space-for-time replacement design spanning 0 to 20 years, scientists evaluated nitrogen cycling following restoration.  To do so, scientists again relied on seasonally collected sediment cores and the use of a membrane inlet mass spectrometer (MIMS) to analyze nitrogen fluxes in the overlying water.

The results indicated denitrification always increased at sites found in the 0-7-year-old sites but were inconsistent in 7-20-year-old sites as seen in Figure 2.

Figure 2. Rates of denitrification over a 20 year period.

Sediment oxygen demand (SOD), an important ecosystem service describing the rate of dissolved oxygen removed during the decomposition of organic matter, was significantly correlated with annual denitrification. These data show that restored salt marshes and oyster reefs can augment denitrification and that the increased nitrogen removal should be sustained through time.  Denitrification occurred in all habitats in the study, but rates were on the lower end of those in the literature.  There was evidence that habitat restoration could ameliorate any loss of denitrification potential due to habitat loss.

Primary Producers

Benthic microalgal communities are composed of diverse assemblages that may include benthic diatoms, cyanobacteria, and green algae.  These communities are an important source of primary production and may provide as much as one-third of the total primary productivity in estuarine systems.  They may also be important contributors to the stabilization of bottom sediments, may serve as food source for grazers, and have been demonstrated to reduce fluxes of nitrogen from the sediment to the water in estuaries.  It is in these vital roles that they provide ecosystem services.

Benthic microalgal biomass was quantified in all habitats throughout the study as seen in Figure 3.

Figure 3. Benthic microalgal biomass quantified in all habitats.

Average annual biomass was higher in the marsh than any other habitats.

Seagrass beds also had elevated biomass, with the lowest benthic microalgal biomass in the unstructured habitats (intertidal and subtidal flat).  Though the economic values of ecosystem services provided by benthic microalgae have not been quantified to the level of detail for organisms like oysters or processes like denitrification, there are significant environmental benefits that result from their presence.  Sediment deposition plans will have to consider the potential values of benthic microalgae, particularly marsh restoration as it will result in significant increases in their biomass.