National Centers for Coastal Ocean Science

The National Centers for Coastal Ocean Science 

(NCCOS) is the focal point for NOAA’s coastal 

ocean science efforts. NCCOS helps NOAA to meet 

its coastal stewardship and management 

responsibilities, and provides coastal managers with 

the scientific information necessary to decide how 

best to protect environmental resources and public 

health, preserve valued habitats, and improve the 

way that communities interact with coastal 

ecosystems. NCCOS major focus areas include 

coastal change: vulnerability, mitigation, and 

restoration; marine spatial ecology; social science, 

and stressor impacts and mitigation. NCCOS 

additionally funds external research through its 

Competitive Research Program. Included below are 

ten highlighted projects by NCCOS, NCCOSsupported researchers, and their partners.

Kachemak Bay Ecological Assessment: Supporting 

Alaska Coastal Resource Management

NOAA NCCOS has conducted a Kachemak 

Bay, Alaska ecological assessment project to 

knit together a broad range of spatial habitat 

and environmental data into new information 

tools for Alaska coastal resource management 

and planning. Kachemak Bay is a productive, 

subarctic estuary in southcentral Alaska that 

contains all the coastal habitats found in the 

Gulf of Alaska, with fish, shellfish, marine 

mammal, and bird populations that support

recreational and commercial harvests. 

Kachemak Bay has seen an increase in 

ecotourism activities and tourism is a 

significant economic driver for the region. 

NOAA, along with federal, state, tribal, 

industry, and non-governmental organization partners, has produced a pilot “State of Kachemak Bay” report, 

developed online tools to improve public data access and visualization of spatial data, and is producing an 

ecological status report in 2021 to highlight regional coastal changes over the past two decades. The project’s 

goal is to provide information tools that help Alaska communities deal with challenges from changing fish and 

shellfish populations, climate change, harmful algal blooms, and to explore opportunities in shellfish and kelp 

mariculture. 

FY20 Accomplishment(s): As part of the assessment, the FY20 pilot “State of Kachemak Bay” report 

summarizes information on marine conditions and resources for state, Alaska Native and public coastal 

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Kachemak Bay is a "natural laboratory" of Alaska coastal habitats, 

with sandy clam beds, seagrass meadows, and rocky, deep fjords 

lined with kelp forests. Image credit: Kris Holderied, NOAA 
stakeholders. In addition, an updated online data visualization tool (BioMapper) improves access to 

spatial information on coastal habitats, environmental conditions and resources. 

State of Kachemak Bay Report: 

https://cdn.coastalscience.noaa.gov/projects-attachments/396/StateofKachemakBay_2019Highlights.pdf

State of Kachemak Bay Report News Item:

https://coastalscience.noaa.gov/news/state-of-kachemak-bay-report-highlights-long-term-monitoring-data/

Project URL: 

https://coastalscience.noaa.gov/project/ecological-assessment-for-kachemak-bay-alaska-science-tools-to-informmanagement/

Testing Alternative Oyster Restoration Strategies 

using Novel Chemical Marking Tools 

NOAA NCCOS 

is leading 

research that 

uses novel 

chemical tagging

tools to test 

alternative oyster 

setting methods. 

Oyster setting is 

the process in 

which larvae 

attach to a setting material such as shell. In partnership with the U.S. Naval Academy and the Maryland 

Department of Natural Resources, research divers used fluorescently-marked larvae to test releasing oyster 

(Crassostrea virginica) larvae directly onto planted oyster shells in the Chesapeake Bay. Oyster larvae are 

marked by placing them in a calcein (fluorescent dye) bath prior to release, after which the dye acts as a tag 

once absorbed by the oyster shell. NCCOS has been examining the utility of chemical markers in late-stage 

larval oysters to determine specific oyster recruitment and in evaluating oyster reef restoration strategies. The 

research shows that juvenile oysters can be established from larvae set directly at the site without using 

enclosures. The techniques developed in this portfolio may reduce the requirement for scarce shell or other 

setting material, and reduce the logistical and material handling costs associated with traditional spat-on-shell 

oyster practices in both restoration and aquaculture sectors. These reductions have the potential to avoid 

challenges commonly associated with publicly funded restoration projects using alternative substrate, and can 

make restoration and aquaculture seeding practices more economical. Tagging methods utilized for larval origin 

confirmation build on methods developed in the NCCOS funded Oyster Marking Methodology Study.

FY20 Accomplishment(s): Continued release and monitoring of deployed larvae onto shell-bag reefs 

in the study site and of observed oyster spat recruitment. 

Project URL: 

https://coastalscience.noaa.gov/news/new-technique-shows-oyster-shell-seeding-is-possible-in-open-water/

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Spat on shell produced by direct setting, as seen with the naked eye (left image).The calcein 
NCCOS-funded Research Evaluates Options for Managing 

Dune Systems in North Carolina

An NCCOS-funded observational and dynamic modeling study assessed possible beach and dune management 

actions to help coastal communities make informed decisions in the context of extreme storms and sea level 

rise. The project, led by researchers at Oregon State University and University of North Carolina, evaluated 

dune shape as a function of beach nourishment, dune grass planting, sand fencing, and treatment of the wrack 

line on the Outer Banks, NC. The team discovered that nourishing beaches prior to the storm season, planting 

dunes with certain species of dune grasses, and allowing a wrack line to remain on the beach all led to taller and 

wider dunes systems. In contrast, sand fencing created shorter but wider dunes. The models demonstrate how 

management actions influence dune shape, which has implications for coastal protection during storm events, 

flood protection capacity, and the resilience of beaches and dunes. This study was supported through the 

NCCOS Effects of Sea Level Rise (ESLR) Program.

FY20 Accomplishment(s): The NOAA funded research team delivered their findings on possible dune 

management actions to the management advisory group, composed by beach and dune managers and 

city managers in May of 2020. 

Project URLs:

https://coastalscience.noaa.gov/news/the-effect-of-sand-fencing-on-the-structure-of-natural-dune-systems/

https://coastalscience.noaa.gov/news/grasses-shape-and-protect-coastal-dunes-in-different-ways/

https://coastalscience.noaa.gov/news/new-tool-informs-dune-recovery-after-storms/

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Sand fencing on Bogue Banks, NC. Photo: NOAA NCCOS 
Application of Quantitative Molecular Methods to Characterize 

Abundance and Distribution of Alexandrium cysts for NOAA’s 

HAB Forecasting

NCCOS is developing new methods to better forecast blooms of Alexandrium catenella, a marine alga that 

causes paralytic shellfish poisoning (PSP) along the Pacific and Atlantic coastlines of the U.S. and Canada. This 

project supports development for two lab-based quantitative molecular methods for more rapid, accurate 

detection of Alexandrium catenella resting cysts in sediment. Scientists are working with the University of 

Washington Tacoma, the University of Alaska, and the Woods Hole Oceanographic Institution to map the 

distribution of Alexandrium resting cysts in the Gulf of Maine, Puget Sound, and the waters around Kodiak 

Island and Kachemak Bay, Alaska. Cyst distribution and abundance are used to forecast blooms of Alexandrium 

cells in the water column. Molecular detection methods and training is needed to advance research and HAB 

forecasting applications that reduce effort and turnaround time for cyst enumeration. New methods employing 

molecular-level analytical procedures known as quantitative polymerase chain reaction (qPCR) and fluorescent 

in situ hybridization (FISH) were developed to reduce the time and effort required for cyst identification and 

counting. These molecular tools are being tested to better characterize cyst distribution and speed up the 

forecasting process for Alexandrium blooms. The project will help expand NOAA HAB Operational 

Forecasting to new regions.

FY20 Accomplishment(s): First season of field sampling, initial design of quantitative PCR assay and 

in situ labeling method completed pending method refinement and validation.

Project URL: 

https://coastalscience.noaa.gov/project/application-of-quantitative-molecular-methods-to-characterizeabundance-and-distribution-of-alexandrium-cysts-for-noaas-hab-forecasting/

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 Light micrograph (left) of an Alexandrium resting cyst in the sediment. The same cyst (right) stained with a 
Spatial Predictive Modeling for ESA-listed Corals

NCCOS uses spatial modeling to predict the distributions of threatened coral species in the U.S. Atlantic 

(Florida) and Caribbean (Puerto Rico, U.S. Virgin Islands). NOAA is partnering with scientists in academia and 

the federal government to develop new modeling approaches and interactive mapping applications that provide 

data-driven spatial predictions for the presence, absence, abundance, and population structure of multiple 

threatened coral species. These outputs also include associated estimates of predictive uncertainty, and a spatial 

database of Atlantic coral ecosystem monitoring, in accessible map formats. These products are used to inform 

management decisions that may affect coral species listed under the Endangered Species Act (ESA), such as 

spatial planning for coral restoration and place-based management.

FY20 Accomplishment(s): A coral model is in development for Puerto Rico and the U.S. Virgin 

Islands.

Project URL:

https://coastalscience.noaa.gov/project/spatial-predictive-modeling-threatened-esa-corals-u-s-atlantic-caribbean/

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NCCOS is mapping predicted distributions of ESA-listed corals, such as this lobed star coral (Orbicella annularis), 

throughout the U.S. Atlantic. Image credit: NOAA Fisheries. 
Promising HAB Control Method Builds on NCCOS-Funded 

Discovery of Natural Algicide. 

An NCCOS funded project, led by University of Delaware marine scientist Dr. Kathryn Coyne, characterized an 

algicidal compound produced by the bacterium Shewanella, and confirmed the compound can selectively kill 

marine dinoflagellate phytoplankton known to produce harmful algal blooms. Using small-scale microcosm 

experiments, the team found the naturally occurring compound induces programmed cell death in 

dinoflagellates, while having no negative impacts on other phytoplankton, fish, or shellfish. Results pointed to 

the compound as an effective and environmentally safe natural algicidal agent, but additional research was 

needed to determine a cost effective and efficient method to deploy it in the environment. This project is 

supported by the NCCOS Prevention, Control and Mitigation of Harmful Algal Blooms (PCMHAB) Program.

FY20 Accomplishment(s): With additional funding by Delaware Sea Grant, the Coyne team is now 

testing a promising and novel delivery method using mesh bags filled with gel-like alginate beads 

temporarily deployed in coastal waters, where needed, to prevent algal blooms from occurring, or to 

shut down or mitigate blooms already underway.

Project URL: 

https://coastalscience.noaa.gov/news/promising-hab-control-method-builds-on-nccos-funded-discovery-ofnatural-algicide/

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Fluorescent images of a harmful dino
NCCOS Research Provides Scientific Foundation for U.S

Supreme Court Ruling

A recent U.S. Supreme 

Court ruling found that 

pollution discharge 

into groundwater from 

a Maui County (HI) 

sewage treatment plant 

(County of Maui v. 

Hawaii Wildlife Fund) 

fueled macroalgal 

(seaweed) blooms 

along the west side of 

the Island of Maui. At

this location, 

wastewater is injected 

into disposal wells, 

travels underground, 

and ends up in the 

Pacific Ocean, thereby violating the permitting program of the US Clean Water Act. The Act will now apply to 

pollution that funnels through groundwater before reaching a federally regulated waterway. Following a series 

of studies funded by NOAA in the 1990’s, projects supported through the NCCOS Ecology and Oceanography 

of Harmful Algal Blooms (ECOHAB) program and Hawaii Coral Reef Initiative (HCRI) focused research 

efforts on the link between increased nutrients from land-based sources of pollution and the decline in coral 

health. Results showed that all coastal waters near injection wells had high nitrogen values and were impacted 

by sewage effluent high in nutrients (but no pathogens) leaking from deep injection wells. These findings 

demonstrated that substantial nuisance macroalgal blooms in Maui coastal waters were linked to wastewater 

nutrient sources.

FY20 Accomplishment(s): Understanding of the causes and solutions to algal blooms in Maui was the 

result of research led by NOAA and the combined efforts of numerous federal and state agencies, 

institutions, and other contributors over the last 25 years. Thus, the far reaching SCOTUS ruling not 

only highlights the value of the NCCOS Competitive Research Program (CRP), it also points out the 

common occurrence of CRP research providing management outcomes years, and even decades, after 

project funding has ended.

Project URL: 

https://coastalscience.noaa.gov/news/nccos-research-provides-scientific-foundation-for-u-s-supremecourt-ruling/

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Maui County, Hawaii, wastewater treatment facilities at issue in Supreme Court litigation. 

Credit: Warren Gretz/NREL via E&E News. 
Ozone Impregnated Nano-bubble Technology Safely 

Eradicates Harmful Algal Blooms and Mitigates their Impact.

A five-year cooperative research and development agreement (CRADA) with American Marine University 

completes is first year to develop and deploy ozone impregnated nano bubble technology as an algal/microbial/

nutrient remediation strategy. Unlike ordinary bubbles that rise and burst at the surface of the water, 

nanobubbles implode under the pressure of the water, releasing oxygen and ozone that help dissolve harmful 

algae. Referred to as “NBOT”, this patented, precise generation of bubbles of less than one thousandth of a 

millimeter provides efficient transfer of ozone to attack microbes and shreds toxins with oxygen as a byproduct 

in hypoxic systems enhancing overall water quality. This powerful action can be implemented in a manner that 

is safe for humans and wildlife and when coupled with NBOT’s ability to also remove nutrients, provides 

cleaner water for longer periods of time thus minimizing bloom retreatment regimens.

FY20 Accomplishment(s): This first year completed successful demonstration projects in Port Mayaca 

Lock of Lake Okeechobee, Lake Newport in Ohio, Constitution Gardens Pond, Washington DC and 

Loxahatchee River in Jupiter FL.

Project URL: 

https://coastalscience.noaa.gov/news/nccos-validates-nanobubble-technology-for-remediation-of-harmfulfreshwater-algal-blooms/

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Field site before (left) and 24 hours after (right) nanobubble treatment. Credit: NOAA NCCOS. 
Assessment of Fish Habitat in Tidal Waters of the Choptank 

River (Chesapeake Bay, Maryland) to Inform Conservation, 

Restoration, and Fishery Management Decisions

The Choptank watershed is an ecologically and economically valuable resource and one of NOAA’s ten Habitat 

Focus Areas. NCCOS is collecting and synthesizing biological, chemical, and physical data to characterize the 

condition of the watershed and identify land use impacts on the environment. This project builds off previous 

ecological assessments of the Choptank watershed and Chesapeake Bay toward improving water quality, the 

health of estuarine and coastal habitats, conservation and restoration efforts, and fishery management decisions.

FY20 Accomplishment(s): A report of recommendations for extending the tidal analytical/statistical 

framework from candidate tributary (Choptank River) to Chesapeake Bay tidal areas is in development.

Project URL: 

https://coastalscience.noaa.gov/project/ecological-assessment-choptank-complex-habitat-focus-area/

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The Choptank River complex is located on Maryland’s eastern shore, and includes the Choptank River and its major 

tributaries. The watershed was selected as a NOAA Habitat Focus area in 2014. Image credit: NOAA Fisheries. 
A Geospatial Assessment of U.S. Atlantic and Gulf of Mexico 

Essential Fish Habitat in Relation to Offshore Sand Featur

Offshore sand resources, e.g., sand shoals, are 

increasingly being used for beach renourishment, 

barrier island restoration, and other uses to enhance 

resiliency of shorelines. However, the impact of sand 

dredging on fish and other marine resources is poorly 

understood. NCCOS is working with the Bureau of 

Ocean Energy Management (BOEM) and NOAA 

Fisheries to provide information on these effects and 

to develop a geospatial decision support tool that 

helps users determine the relative risk to fisheries 

species that are associated with extraction of these 

sand resources.As the demand for Outer Continental 

Shelf sand increases, BOEM is facing increasingly 

complex issues, such as resource allocation, 

cumulative impacts from repeated use, space/use 

conflicts, protection of archaeological sites, and 

Essential Fish Habitat (EFH) impacts. In particular, 

the Magnuson-Stevens Fishery Conservation and 

Management Act requires that any federal agency 

undertaking or authorizing an action that may 

adversely affect EFH or federally managed fish 

species consult with NOAA. Researchers are using 

and developing geospatial maps to investigate the 

link between geomorphological features (e.g., sand

shoals) and EFH, to better analyze the potential 

impacts of sand relocation. These efforts will help to 

ensure that all necessary and effective precautions are 

taken to reduce impacts during sand dredging and 

conveyance to placement sites.

FY20 Accomplishment(s): Development of 

a model and technical report with BOEM.

Project URL:

https://coastalscience.noaa.gov/project/geospatial-assessment-u-s-atlantic-gulf-mexico-essential-fish-habitatrelation-offshore-sand-features/

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ShoalMATE (Shoal Map Assessment Tool for EFH) is a 

geo-spatial decision-support tool being used to guide 

wise use and dredging of North Carolina o