Managing Nitrogen in Marine Embayments
A Deeper Dive into the Nitrogen Cycle and
Oyster Aquaculture

Excess nitrogen loading has become one of the most difficult coastal environmental issues for coastal communities throughout the northeast. Federal and State regulations require Towns to comply with Clean Water Act provisions regarding nitrogen and other non-point pollutants, to meet water quality standards. Many semi-enclosed waterbodies along the coast are classified as nitrogen impaired, and Total Maximum Daily Loads (TMDLs) are being derived. Meeting TMDLs, and attaining water quality goals, require that Towns derive appropriate management approaches to reduce nitrogen loading at the source (which is expensive and operationally difficult) or to adopt Alternative Restoration Approaches that enhance the capacity to assimilate nitrogen. These alternative approaches include inlet widening, which increases the flushing and allows greater mixing with marine waters, and shellfish propagation, which enhances the grazing on phytoplankton, sequestering nitrogen in harvestable shellfish tissue. Other measures include constructed wetlands, permeable reactive barriers, and improved stormwater measurement.

This article focuses on shellfish propagation, particularly oyster aquaculture, as a method to increase the capacity of waterbodies to assimilate nitrogen. We emphasize: (1) understanding how shellfish influence nitrogen cycling in coastal embayments, and the processes by which biologically active nitrogen is removed from the embayments, and (2) an accurate accounting of the amount of nitrogen removed from the waterbody when shellfish are harvested.

The aim is to help decision makers considering shellfish propagation as an alternative restoration project by providing an overview of how nitrogen moves through sediments, surface waters and shellfish. This understanding will give decision makers a realistic expectation of the capacity of shellfish to clear phytoplankton from the water column, to sequester nitrogen in tissues, and thus potentially mitigate effects of excess nitrogen.

Shellfish and Nitrogen Cycling in Estuaries
The idea that shellfish strongly affect nitrogen cycling and may help alleviate excess nitrogen in coastal waters was well established by the 1980s (Officer et al. 1982; Dame et al. 1984; Newell, 1988). Early studies showed that oysters act as a major grazer, filtering large amounts of water, and removing particulate nitrogen in the form of phytoplankton. Beyond this removal of particulate nitrogen, oysters can influence the nitrogen cycle in more complex ways.

Figure 1. Overview of Nitrogen Cycling in Coastal Waterbodies with Oysters as a Major Grazer Species.

As shown (Figure 1), nitrogen enters coastal environments from several sources including septic systems, stormwater runoff, fertilizers, and atmospheric deposition.  That nitrogen fuels phytoplankton growth and attached macroalgae.  Phytoplankton are filtered from the water column and ingested by oysters.

The fate of nitrogen ingested by oysters and, very importantly, the amount of nitrogen that the oyster-phytoplankton system can process depends on biological, chemical, and geological (biogeochemical) conditions.  It also depends on the biological properties of the oyster population such as biomass, growth rates, and culture methods.  There is more to the process than the simple sequestration of nitrogen into oysters.  Various amounts of the nitrogen ingested by the oysters may:

  • Be returned to the water column by excretion of ammonium, urea, or other water-soluble waste products.  That excreted portion becomes part of the dissolved inorganic nitrogen in surface water.  As such, it will continue to contribute to the pool of biologically available nitrogen that fuels primary producers.
  • Be assimilated into oyster shell or soft tissue biomass.  That assimilated nitrogen is not biologically available, unless the soft tissue decays and the shell dissolves.
  • Be deposited on the sediment surface as biodeposits (feces and pseudofeces1) from the oysters.

  • The nitrogen contained in biodeposits can be:  

    This latter process of decay to ammonium can result in either or both: (1) a recycling of inorganic nitrogen back to the water column by the loss of ammonium or its conversion products, nitrate and nitrite (which will continue to contribute to the pool of biologically available nitrogen in surface water), and (2) the conversion of all three of these forms of nitrogen due to the conversion to di-nitrogen gas (which will remove the nitrogen from the embayment and decrease the amount of biologically active nitrogen in the sediment-surface water system).   

    Nitrogen Removal Processes
    The goal for oyster propagation is to sequester nitrogen from the surface water so it does not contribute to the deleterious effects associated with eutrophication.  The three main processes by which shellfish can help in removing biologically active nitrogen from the surface waters are: 1) harvest of oyster tissue, 2) denitrification enhancement (enhanced conversion of biologically available nitrogen to nitrogen gas), and 3) long-term (deep) burial in sediment.  These three processes, and the effect of shellfish on each, are not equally understood, and, as of 2014, no studies were found to have quantified all three (Kellog et al. 2014).

    In particular:

    Figure 2 shows the nitrogen removal mechanisms in embayments, with level of certainty associated with each of these estimates.

    Figure 2. Nitrogen Removal Mechanisms in Coastal Habitats with Oyster Harvest.

    Nitrogen Sequestration in Shellfish Tissue
    Nitrogen content in oyster tissue varies. This variability is related to at least six factors (all of which can be known or estimated before initiating oyster propagation as a means of nitrogen mitigation): (1) origin (cultured or wild stock), (2) genetic makeup (e.g. triploid vs. diploid), (3) body size and condition at time of harvest, (4) relative amount of soft tissue vs. shell in the oysters, (5) culture method (on-bottom vs. off-bottom culture) and (6) season/reproductive status at harvest time (Reitsma et al. 2014). As a rule of thumb, a 100g oyster might be considered to contain on average 0.5g N, but the value can vary by almost a factor of 3 (approximately 0.3 to 0.8g, based on data from Reitsma et al. 2014).

    Implications for Nitrogen Remediation Using Shellfish
    At present, data gaps and uncertainty regarding enhancement of denitrification and deep burial preclude the use of those processes in nitrogen removal estimates. In terms of decision making, a conservative approach is to approximate the removal of nitrogen from an embayment by calculating the nitrogen removed upon harvest.

    Estimating the nitrogen removed via shellfish harvest requires an accounting system that accurately describes nitrogen removal for a given waterbody, species, variety, time of harvest/reproductive status of harvested shellfish, and culture method. This need not be complicated, and it should document the amount of shellfish N harvested accurately. Calculations should be based on the harvested weight (mass) of the shellfish rather than on the number of shellfish harvested because the former is a more reliable indicator of the nitrogen content in the shellfish tissue (Reitsma et al. 2015). In addition, time of year at harvest should be noted since the size, weight, soft tissue content, and %N in soft tissue varies significantly over the growing season.

    Oyster harvest can remove nitrogen from the system, and it is possible to estimate the approximate magnitude of this removal.

    Shellfish propagation does not, however, affect the nitrogen loading to the system. It is not a mechanism for source control, and the amount of nitrogen entering the embayment does not change due to the presence of oyster propagation. The biological activity of the oysters inserts them into the nitrogen cycle because they are major grazers, and they become a temporary “sink” for some fraction of the nitrogen entering the system. When we remove that nitrogen through oyster harvest, we are removing nitrogen that might otherwise become biologically available, and managing problems of eutrophication.

    Ultimately, solutions to the nutrient loading issue for waterbodies should be built on a solid understanding of nitrogen loads, and the various location-specific options for reducing the load and/or increasing the capacity to assimilate that load. Shellfish propagation can be part of a comprehensive wastewater and nitrogen management plan, but should be pursued with a realistic accounting of potential nitrogen removal by appropriate municipal resource managers with experience and knowledge on shellfish propagation.

    Submitted by Co-Authors:

    Heidi Clark, Jerry Cura, and Ted Wickwire
    Woods Hole Group
    81 Technology Park Dr.
    East Falmouth, MA 02536

    1) Carmichael, RH, W Walton, H Clark and C Ramcharan. 2012. Bivalve-enhanced nitrogen removal from coastal estuaries. Canadian Journal of Fisheries and Aquatic Science 69:1131-1149.

    2) DEP. 2016. Massachusetts Department of Environmental Protection, online information regarding nitrogen loading and TMDLs. Dame, R, R Zingmark and E Haskin. 1984. Oyster reefs as processors of estuarine materials. Journal of Experimental Marine Biology and Ecology 83:239-247.

    3) Kellogg, ML, AR Smyth, MW Luckenbach, RH Carmichael, BL Brown, JC Conrwell, MF Piehler, MS Owens, DJ Dalrymple, and CB Higgins. 2014. Use of oysters to mitigate eutrophication in coastal waters. Estuarine, Coastal, and Shelf Science 151:156-168. Luckenbach, M. 2013. Can Oysters Really Provide Nutrient Reductions in Chesapeake Bay? If so, can they help us meet our water quality improvement goals? PowerPoint Presentation available online at

    4) Newell, RIE. 1988. Ecological changes in Chesapeake Bay: are they a result of overharvesting the American Oyster Crassostrea virginica? In: Understanding the Estuary. Advances in Chesapeake Bay Research. Proceedings of a conference. Baltimore MD. 29-31. Officer, C, T Smayda, and R Mann. 1982. Benthic filter feeding: a natural eutrophication control. Marine Ecology Progress Series 9:203-210.

    5) Reistma, J, D Murphy and AF Archer. 2014. Shellfish, Nitrogen, and the Health of Our Coastal Waters. Marine Extension Bulletin: Woods Hole Sea Grant and Cape Cod Cooperative Extension.

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