Northeast Habitat Ecology Research

At the Habitat Ecology Branch of the Northeast Fisheries Science Center, our research includes multi-disciplinary and multi-agency expertise, and encourages collaborations with managers, academic researchers, and industry partners.

Offshore Wind Energy Areas

In search of renewable energy sources, we are helping the Bureau of Ocean Energy Management characterize the ocean floor as a potential and suitable location for wind energy platforms. In order to assess the ocean floor we collected multitudes of ocean data and took many ground-truthing samples to confirm our discoveries. 

Bathymetry map.

One of our sampling techniques is the collection and annotation of millions of still images captured from llohe HabCam IV and School for Marine Science & Technology’s pyramid camera systems. These images provided both 2D and 3D visual imagery. We also used grab and core sediment samplers to ground-truth to our visual images. The use of side scan and high-resolution multibeam sonar provided vital topographic features enable us to map and define the ocean floor. We also calculated terrain metrics to determine the ground’s slope, roughness, and aspect.

In addition to our visual data, we applied hydrographic CTD (temperature, salinity, and depth) and sediment (mud, silt, clay, sand, gravel, shell hash, and cobble) data into our analysis. We then combine this information with our data on bottom-dwelling animals and our fish and shellfish abundance data.

By building all these important facets into our dataset, we were able to measure and describe the biological and physical features of our ocean environment. In order to conserve habitat, is essential for our researchers to know what species lives in those areas, the physical structure of the areas, and how manmade structures might affect them.

Collaborator: University of Massachusetts/School for Marine Science & Technology

Black Sea Bass Habitat

Black sea bass. Photo: NOAA Fisheries

One species that researchers believe will benefit greatly from offshore wind energy area development is black sea bass. This species is commonly found along the Atlantic coast from Maine to Florida, and on the eastern coast of the Gulf of Mexico. Its preferred habitat is in and around rocky structures, which is why wind energy areas would provide an ideal location. 

Researchers are interested in black sea bass because they are a commercially important species. Those caught in the wild are sustainably managed and considered a “smart” food choice by NOAA’s FishWatch.

Our researchers continue to apply shipboard methods to collect data and analyze bottom habitats using HabCam IV, a specially designed towed camera. HabCam is capable of shooting six images per second while being piloted along the ocean floor. We combine the visual images with associated acoustic and hydrographic data, which enables researchers to better define habitat used by black sea bass and other bottom-dwelling species.

Habitat Climate Vulnerability Assessment

The climate along the Eastern seaboard is changing dramatically. NOAA Fisheries is responsible for preserving and conserving habitats that support fisheries and protected species. 

Several researchers from the Northeast Fisheries Science Center are part of regional working group. They are developing an important tool used to assess the vulnerability of habitats experiencing climate change. Marine fish and invertebrate species, marine mammals, and sea turtles are all subjected to changes in climate. It is important for us to understand how these changes create vulnerabilities to species, habitats, and communities.

Our goal is to provide fishery management councils, researchers, and other stakeholders with the means to assess proficiently the relative vulnerability of species habitats due to climate shifts. This information will help determine long-term effects, identify the most vulnerable habitats, and create the measures necessary to protect existing habitats and communities.

Habitat Suitability Modeling

Using Computers to Help Define the Dynamics of Fish Populations and Their Environment

The Northeast U.S. region is one of the most valued fisheries environments in the world. Nearly 95 percent of our commercially harvested fish are directly linked and originate from local coastal environments. However, the state of our fish stocks is a primary concern. Fish populations fluctuate between years because of:

• Changes in primary production.
• Low reproductive output.
• Predator-prey interaction.
• Habitat disturbance.
• Harvesting
• Disease.
• Mortality.
• Climate change. 

The response to these variables may be cyclic or episodic. In cases where population levels do not remain the same from year to year, it may be because of condition changes in the environment. We hope to illustrate how change in thermal habitat of commercially important species along the Northeast U.S. continental shelf marine ecosystem can potentially influence the fisheries.

Researchers in the Image Modeling and Assessment Group use computers to help provide necessary information to the New England and Mid-Atlantic Fishery Management councils. This information aids strategic development of ecosystem-based management. The use of habitat suitability modeling and the application of various computer training techniques allows us to apply powerful statistical methods for estimating the spatial and temporal abundance of species, and also to display them as maps in response to various temperature scenarios. Climate change is believed to be a strong influence in the distribution patterns of fish populations. Using these tools, we can potentially see how species respond during a specific season, year, and under various environmental conditions.

Components keyed into the models include current and historic fish species data and hydrographic (which could include temperature, salinity, conductivity, and depth) data. The model helps researchers identify which predicator variables are associated with the species’ abundance and ultimate distribution. An additional goal is to use these models to assess the estimated probability and characterize the response patterns of fish species in estuarine, coastal and offshore regions.

For more information, please contact Tori Kentner or Donna Johnson

Deep Sea Coral Habitat

Exploring Deep-sea Coral and Sponge Habitats off the Northeast Coast

A variety of deep-sea corals found on a ledge in the newly named Kinlan Canyon (< ~ 838 m), including a large white gorgonian Paragorgia (bubblegum coral), the colonial white stony coral Lophelia pertusa around it, and a small red Paragorgia (upper left).

In many deep-water bottom communities, corals and sponges provide habitat for certain commercially important fish and shellfish species. These habitats can be hot-spots of biodiversity in the deeper ocean, and their vulnerability to human impacts has stimulated research, monitoring, mapping, and conservation efforts. 

Our scientists and partners are exploring these habitats on the Northeast U.S. continental shelf, slope, and seamounts at depths from 50 to about 2000 meters. This is a major initiative that involves the use of large NOAA ships like the Henry B. Bigelow and ships of our academic partners. We also use drop cameras and remotely operated camera systems to locate, survey, and characterize these deep-sea communities. Along with our partners, we: 

• Map the seafloor and its habitats.
• Collect seafloor video and still imagery.
• Collect deep-sea coral, sponge, and animals for study.
• Document human impacts to these habitats. 

Example of a high resolution multibeam map of Toms Canyon submarine canyon complex on the continental slope in the mid-Atlantic region. Red areas are shallow compared to the blue. Mapped by various NOAA ships. Circles depict drop camera dive sites.

Mapping the seafloor helps us determine where deep-sea coral and sponge habitats are likely to occur.

We’re documenting human impacts to these habitats because the Magnuson Stevens Act provides a way to protect deep-sea corals in U.S. waters. The New England and Mid-Atlantic Fishery Management Councils take measures to protect corals from fishing gear impacts. We also collaborate with the Northeast Fisheries Observer Program to identify coral bycatch from fisheries.

We have participated in surveys for deep-sea corals and sponges in the northern Gulf of Maine. We found extremely high densities for at least two structure-forming species of coral in relatively shallow waters, a unique discovery for the Northeast U.S. coast. The proximity of these habitats to shore increases their potential to be used  as habitat for commercially important fish species.

Based on these surveys and research, the Mid-Atlantic Fisheries Management Council created the Frank R. Lautenberg Deep-Sea Coral Protection Area. This area covers more than 38,000 square miles and protects deep-sea corals from the impacts of fishing gear.  It is the largest such protected area in the entire U.S. Atlantic.

Common sea pen, Pennatula aculeata, Western Jordan Basin, Gulf of Maine.

The new Northeast Canyons and Seamounts Marine National Monument protects critical deep-sea coral habitat off Georges Bank. The New England Fishery Management Council, again based on our surveys, is developing a range of coral protection alternatives around our Gulf of Maine sites and deep-sea coral habitats found far off the New England shore. 

For more information, please contact Dave Packer

Partners include:

• Northeast Fisheries Ecology Branch (Jeff Pessutti).
• NOAA Fisheries National Systematics Lab (Martha Nizinski, lead, Northeast Deep-sea Coral and Sponge Fieldwork Initiative).
• NOAA Fisheries Office of Habitat Conservation, Deep-sea Coral Research and Technology Program (provided major funding for Fieldwork Initiative).
• NOAA Fisheries Greater Atlantic Regional Fisheries Office.
• NOAA Office of Ocean Exploration and Research.
• NOAA National Ocean Service, National Centers for Coastal Ocean Science (seafloor mapping and deep-sea coral habitat suitability modeling).
• Academic partners (e.g., University of Connecticut, University of Maine, Dalhousie University [Canada]).
• Department of Fisheries and Oceans, Canada.
• Woods Hole Oceanographic Institution.

Chemical Analysis in Marine Habitats

Characterization of Microplastics in the Marine Environment

Microplastics are plastic fragments less than 5 mm in size. Larger plastics in the environment degrade into fragments through weathering by sun, wind, and waves. We find microplastics in the environment as fragments, fibers, foams, or pellets referred to as “nurdles.” 

We are worried about microplastics because they are similar in size to prey ingested by aquatic animals. When accidentally ingested, these microplastics can be transferred to higher predators. The different types of plastics can have different toxicities, and they collect different levels of contaminants. It is critical to understand the nature of the microplastics so we can monitor the quality of fisheries habitats and aquaculture facilities. 

Once we find plastics in the environment, our next step is to identify what kind of plastic it is.  To do this, we use a Pyrolysis GC-MS analyzer system.

Pyrolysis analyzer.

Each plastic has unique chemical markers. To discover which markers a plastic contains, we heat a small piece at high temperatures then analyze it with a mass spectrometer. 

We catalog libraries of polymers. The library database is used to identify plastics found in marine environments, fish, marine mammals, and seabirds.

In the future, we hope to use our technique to identify microplastics found in finfish and shellfish aquaculture.

For more information, please contact Ashok Deshpande

Mercury in Fisheries Habitat, Fish, and Marine Mammals

Direct Mercury Analyzer.

Mercury enters the water column and sediments from a variety of natural and human -made sources. Bacteria converts inorganic mercury into harmful methylmercury which gets stored in a fish’s fat tissue. From there it can be transferred to critical organs and cause toxic effects. If the fish is consumed, methylmercury in its system can be transferred to higher predators and humans.

The most critical issue is mercury in our waterways, oceans, sediments, and fisheries, where it can harm seafood consumers. 

We use a Direct Mercury Analyzer to monitor the sediments of local rivers, bays, and fish for the presence of mercury. We have analyzed a variety of samples collected from different locations. Our results show that mercury can be found at high levels in fish, and sometimes in marine mammals as well. 

Marine Academy of Science and Technology High School student Yaseen Zaky is 2nd from right.

The Governor of New Jersey recognized our work on a proposed natural gas pipeline project, which was a part of a Marine Academy of Science and Technology High School senior student project.

We collected sediment samples along the proposed pipeline to understand the potential release of mercury during construction. Sediments from select locations contained elevated levels of mercury.

The results of our mercury analyses were incorporated in the disapproval of the proposed pipeline. 

For more information, please contact Ashok Deshpande

Tracer Chemicals in the Assessment of Diet, Habitat Use, Migration, and Contamination

We use gas chromatographic instruments and mass spectrometers to analyze trace levels of organic compounds in fish. Patterns of chemicals such as fatty acids can be helpful in the assessment of fish diets. 

While the fish’s body completely digests proteins and carbohydrates, fatty acids are transferred from prey to fish almost intact. The unique signatures of fatty acids in different prey species allow us to assess diet. Knowing prey types helps scientists understand the nutritional quality of the fish’s diet. Although considered not so good for the humans, lipids (also referred to as fats) are some of the most important components of fish diet. Lipids are utilized by fish as the metabolic energy source for swimming activities including prey capture, as well as for the development, reproduction, and long distance migrations.

We used the same instruments to examine PCB signatures in the tissues of young bluefish collected from U.S. East Coast locations after Super Storm Sandy.

Mass spectrometer.

European pesticides differ from those used in the United States. Pesticide and PCB patterns that accumulate in bluefin tuna help us to study their trans-Atlantic migration. Information we get from analyzing harmful PCBs and pesticides in New York Bight sports fish and lobsters provide consumption guidelines for local fishermen and seafood consumers. 

We recently installed a new state-of-the-art mass spectrometer  which we hope to use to analyze chemical samples from aquaculture, seafood safety, and protected species.

For more information, please contact Ashok Deshpande

New Directions in Microplastic Research and Outreach

Microplastics are of particular concern in shellfish, which represent a major part of a commercial fishing industry worth more than $5 billion. Understanding the nature of microplastics is critical to identifying, regulating, and mitigating sources that affect the quality of bivalve habitats and aquaculture facilities. 

Our current studies focus on the presence and abundance of microplastics in hard clams and sea scallops. We collect samples from local waters, offshore, and aquaculture facilities. Preliminary data show that there are microplastics in almost every shellfish species.

Research and education are equally important to address the plastic pollution in our waters. NOAA considers the public a full stakeholder in this mission. At the James J. Howard Lab, our goal is not only to convey the importance of research but also to encourage people to consider alternatives to plastic use. We hope that with this knowledge, everyone will become fully engaged in the quest for viable solutions.

Outreach event.

For more information, please contact Beth Sharack

Mollusk and Fish Population Assessment

We are looking at declines in stocks of bivalve mollusks—oysters, northern quahogs, softshell clams, and bay scallops—and ocean fish, including cod and flounder. These declines appear to be closely linked to a climate cycle termed the North Atlantic Oscillation (NAO) index. This index records that some winters have been substantially warmer than they once were.

The upward swing of the NAO began around 1982 and reached a peak during the mid 1990s. During this time, significant changes occurred in marine environments. This increase in temperature had a negative effect on recruitment of mollusk and fish juveniles. This resulted in a sharp decrease in both commercial stocks. Along with stronger winds and higher cloud coverage, the temperature increase affects marine resource abundance.  

Our studies show that when the food supply for mollusks and fish is very small, it limits their reproduction, survival, and growth. The patterns of continuous cloud covers affect the quantities of phytoplankton in marine waters. Dense clouds result in relatively clear waters. Adequate phytoplankton numbers are essential to provide food for other species up the food chain.

For more information, please contact Clyde L. MacKenzie, Jr.