Northeast Fisheries & Habitat Ecology Research

At the Fisheries and 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.

Deep Sea Coral Habitat

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

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 and characterizing these habitats on the Northeast U.S. continental shelf, slope, and seamounts at depths from about 165-6560 feet (50 to about 2000 meters). This is a major initiative that uses large NOAA research ships like the Henry B. Bigelow and ships of our academic partners. We 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

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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 conducted surveys for deep-sea corals and sponges in the northern Gulf of Maine. We found high densities of at least two structure-forming species of coral in relatively shallow water, 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.

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Based on these surveys and research, our two regional Fishery Management Councils established deep-sea coral protection areas along the continental slope and in the submarine canyons from Maine to North Carolina, as well as in discrete areas in the northern Gulf of Maine. The Mid-Atlantic Fishery Management Council created the Frank R. Lautenberg Deep-Sea Coral Protection Area while the New England Fishery Management Council created the Georges Bank Deep-Sea Coral Protection Area, along with the Gulf of Maine Mount Desert Rock and Outer Schoodic Ridge areas. These areas in total cover about 66,593 square miles of ocean bottom and protect deep-sea corals from the impacts of certain bottom-tending fishing gear. In addition, the New England Council created the 41 square mile Gulf of Maine Jordan Basin Dedicated Habitat Research Area, an area dedicated to deep-sea coral habitat research.

The Northeast Canyons and Seamounts Marine National Monument off Georges Bank also protects distinct geological features (3 canyons and 4 seamounts) that support vulnerable deepwater communities, including deep-sea corals..

Partners include:

• NOAA Fisheries Office of Science & Technology, National Systematics Lab .
• NOAA Fisheries Office of Habitat Conservation, Deep-sea Coral Research and Technology Program (provided major funding for the Northeast Deep Sea Coral Initiative).
• NOAA Fisheries Greater Atlantic Regional Fisheries Office.
• NOAA National Ocean Service, Office of National Marine Sanctuaries.
• NOAA Oceanic and Atmospheric Research, 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, University of Southern Mississippi, Dalhousie University [Canada]).
• Department of Fisheries and Oceans, Canada.

Read our blog.

For more information, please contact Dave Packer

Chemical Analysis in Marine Habitats

Determining Fish Age through Eyeball Chemistry 

Estimating fish age is crucial for stock assessment, and we use several methods to do this. Determining fish age using structures such as scales, otoliths, vertebrae and spines can be tedious, requiring several hours of collecting and processing samples. Amino acid racemization,a tool to determine the age of rocks, sediments, and fossils, is being as a potential tool for estimating the age of fishes., Further studies are needed before the method can be widely applied. Dating using this method could be a powerful tool for fish aging. For comparison, carbon dating can age samples that are about 50,000 years old, while this new method can date specimens that are 2.5 million years old.

When we use this method to determine age, we analyze two different forms of amino acids within the eye lens cores. These cores are ideal structures for aging because they don’t change after development. A NOAA colleague tested the utility of using this method to age temperate fish species in the southeastern U.S.

Assessing Fish Diet, Habitat Use, Migration, and Contamination using Tracer Chemicals 

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 assessing fish diets.

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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 a predator’s diet. Knowing prey types helps scientists understand the nutritional quality of the fish’s diet. Lipids (also referred to as fats) are some of the most important components of a fish’s diet. Lipids are used by fish as the metabolic energy source for swimming, including prey capture, as well as for development, reproduction, and long distance migrations.

The same instruments can be used to examine fish tissues for trace amounts of inorganic contaminants to help us better understand contamination pathways through the environment. For example, we assessed PCB signatures in the tissues of young bluefish collected from U.S. East Coast locations after Super Storm Sandy.

Overwintering Survival of Black Sea Bass

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Black sea bass are a commercially and recreationally important species found along the U.S. East Coast from Cape Cod, Massachusetts, to Florida. Black sea bass’ range has been shifting northward in recent years. In the mid-Atlantic, this federally managed species migrates seasonally as water temperatures change. They move offshore and south in the fall as water temperatures cool and return north to coastal areas and bays in spring as the water warms.

Stock assessments for black sea bass have a high degree of uncertainty because some aspects of the species’ biology are not well understood. To improve models and better manage the species, scientists need to know how resilient adult black sea bass are to cold winter temperatures. Using the Howard Lab’s recirculating aquaculture systems, our scientists studied the physiological effects of cold temperatures on the fish. They gradually exposed black sea bass to their lowest known thermal tolerance for 1 day and up to 3 days. They found adult black sea bass to be more resilient to very cold temperatures than previously reported for younger fish. A second experiment exposed adult black sea bass to their thermal limit for a longer period of time. It showed that they were resilient to exposure for up to 5 days. This suggests that more adult black sea bass may survive cold conditions during mid-Atlantic winters than previously understood.

Future research will explore how resilience is affected when black sea bass are acclimated to cold temperatures more quickly versus over a longer period of time. Scientists will also study whether black sea bass from different parts of their north-south range differ in their resilience to cold temperatures. Additional planned experiments hope to identify:

• Threshold cold temperatures that cause adult black sea bass to leave the area
• Whether the rate of temperature decline affects that behavior

Understanding the thermal tolerance and winter survival of adult black sea bass will support more effective fisheries management, ensuring fishermen continue to enjoy catching black sea bass for years to come.

For more information, please contact Andrij Horodysky.

Ocean Acidification

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Many processes can change seawater pH. Offshore, carbon dioxide absorption from the atmosphere is the primary driver of ocean acidification. Human activities are generating more carbon dioxide. As carbon dioxide increases, it mixes into the ocean water and raises its acidity, which can harm marine life.

Closer to shore, coastal acidification can include human inputs on land as well as natural processes. In addition to humans generating more carbon dioxide, excess nutrient run-off in coastal zones and changes in land usage can result in changes in aquatic pH. Local runoff from land ends up in rivers which empty into estuaries and coastal waters. Runoff can be influenced by agriculture, sediment, deforestation, and urbanization. Natural coastal acidification can include coastal upwelling and changes in water column circulation.

We study how these changes affect the survival, growth, and metabolism of economically-important finfish and crustaceans. This can help us anticipate future changes to fishery resources, assess their resiliency, and better manage our ecosystems for the future.

Marine Development and Fish Behavior

We work to understand the interactions among offshore development projects, marine life, and habitats. We have studied the impact noise has on black sea bass behavior with funding from the Bureau of Ocean Energy Management. This research informs management to protect fisheries as offshore development continues.

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Many commercial and recreational fish produce sounds for reproductive and/or alarm communication, including most cod, hake, croakers, and drum. We use a medical testing technique for auditory brainstem response to record how a fish’s brain responds to underwater sounds that vary in intensity (volume) and frequency (pitch) so we can describe what a species can hear. We compare these data to field recordings of marine noise to identify and protect critical spawning habitats, guide quieter marine construction of energy platforms and bridges, create more sustainable low-noise coastal and shoreline development plans, and refine shipping routes—all in support of the sustainable blue economy.

We study fish hearing to

• Better understand reproductive ecology in sound-producing species
• Reveal potential effects of environmental changes such as ocean acidification on auditory ecology
• Predict the possible effects of human activities and coastal development on the ocean’s soundscape and marine life

For more information, contact Andrij Horodysky.

Pollution and Fish Health

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Industrial waste is an ongoing problem in our urban waterways and is harmful to wildlife. We study the effects of industrial pollution on fish health to help managers prevent pollution and clean up and restore polluted rivers. These studies help protect New Jersey's waterways and fish populations along with the U.S. Fish and Wildlife Service and National Ocean Service. We study the environmental impacts of Superfund sites on fish populations in the Lower Passaic River, New Jersey. From studies in Newark Bay and the Elizabeth River to the Superfund sites, our research supports the future of fish and other wildlife in our waters.

For more information, please contact James Vasslides.

Health and Reproduction in Recovering River Herring Populations

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River herring populations are at historic lows despite mitigation efforts such as dam removal and habitat restoration. Are legacy contaminants affecting herring reproduction, recruitment, and population growth in some rivers? We are collecting adult and juvenile river herring from New Jersey, New York, and Maine rivers as part of a pilot study to examine the health and reproductive potential of several river systems. Herring returns are much higher in Maine, especially the Penobscot River, than in New Jersey and New York. We are assessing relationships between contaminants and river herring health, and comparing results across river systems. The data may provide insight into challenges that pollution poses to herring recovery, and information important to improving the habitat of these iconic fish.

Diamond Alkali Natural Resource Damage Assessment

Decades of industrial pollution in the Lower Passaic River have impacted human and wildlife health. NOAA and the U.S. Fish and Wildlife Service are working together to study how pollution affects fish health in the river by measuring white perch reproduction and lifespan. The data will be used as part of a long-term Natural Resource Damage Assessment.