Seafloor Ecology

Seafloor ecology research at the Marine School includes seafloor mapping using underwater videography, the effects of marine-protected areas on benthic (bottom) invertebrate communities and fisheries, the impacts of aquaculture activities on benthic communities in the Gulf of Maine, restoration and monitoring of shellfish reefs, quantifying the effects of shellfish reefs on water quality, and the impacts of fishing gear on seafloor habitats.


Environmental monitoring at UNH's open ocean aquaculture demonstration site (Funded by NOAA/Sea Grant; 1999-ongoing.) The University of New Hampshire initiated an open ocean aquaculture site in 1997 to adapt techniques used in other areas to open ocean conditions of New England. The site is located about seven miles offshore of Portsmouth harbor and at present involves four fish cages and two longlines for growing shellfish. The ongoing environmental monitoring program involves sampling the water column and seafloor, and it is part of UNH's CINEMAR program ( Larry Ward, Ray Grizzle, and Jim Irish are the principal investigators.

Collecting water samples using Niskin bottles aboard the R/V GULF CHALLENGERr, UNH's major research vessel (Holly Abeels)

Bryan Soares (Captain), Deb Brewitt (mate) and Paul Pelletier
(substitute Captain/mate) of the

Collecting box core sample of the seabed in the vicinity of UNH's open ocean aquaculture site (Jenn Greene, Ray Grizzle)


Restoration of eelgrass and shellfish habitats in the Great Bay Estuary. (Funded by USDA/Natural Resource Conservation Service; 2005-2008) This project is part of the NRCS Wildlife Habitat Improvement Program (WHIP) and is aimed at implementing multispecies restoration of estuarine habitat consisting mainly of shellfish and eelgrass. David Burdick, Ray Grizzle, Fred Short and Gregg Moore are the principal investigators.

Reef Densities

Ship tracks showing bottom areas imaged with towed, underwater video and classified based on relative shell densities.

Shell Bottom

Classified bottom map showing distributionof oyster shell densities (no live oysters were observed); note three major areas where "shell bottom" occurs

Restoration of shellfish habitats will occur in selected mediumand high density shell areas in 2006 and 2007.

Nannie Island


Nannie Islands


Adams High 


Example stills extracted from video imagery illustrating each of the three relative shell density levels shown on the above maps.

A community-based shellfish habitat Restoration program for New Hampshire. (Funded by NOAA/The Nature Conservancy; 2005-2007) This project will combine experimental and full-scale restoration efforts on an oyster reef in the Bellamy River. It will include implementing an oyster conservationists program that will engage local citizens in helping to raise oysters for future use at restoration sites. Ray Grizzle and Jay Odell (The Nature Conservancy) are the principal investigators.


Training volunteer Oyster Conservationists on how to care
for their oyster spat

Little Bay

Oyster Conservationists, Lois and Dick Roberts, with their oyster cage

Oyster Cage

Oyster Consevationist's cage with 1800 spat floating in Little Bay

The effects of natural and restored oyster reefs on water quality. (Funded by NOAA's National Estuarine Research Reserve, Graduate Research Fellowship Program; awarded to Mark Capone, 2005-2007) This project is focused on various ecological processes associated with restored and natural oyster reefs. It will provide information that will complement other ongoing programs aimed at better understanding the ecology and restoration of the eastern oyster in Great Bay.

Nannie Islands

Nannie Island restoration/study site


In situ fluorometer measuring seston uptake over a restored reef (Nannie Island)

Oysters Mark

Mark displaying 2 year old oysters from a restored reef

Oyster Shell

Oyster shell from 2 areas in Great Bay showing the difference in algal fouling between sites

Developing a protocol for sampling juvenile groundfish in rocky habitat. (Funded by NOAA/Northeast Consortium; 2005-2006) Previous research on the effects of the Western Gulf of Maine fishing closure has indicated substantial recovery of seafloor habitats. This project was designed to determine how gillnets might be used to assess fish populations in rocky habitats. Ray Grizzle, David Berlinsky, and Mike Leary are the principal investigators.

Hauling Gillnet

Hauling gill net aboard the fishing vessel LORI B

Measuring Fish

Measuring fish caught in gill net

Big Cod

One of largest cod (50 lbs) caught inside the closed area

Oyster reef restoration project for City of Dover. (Funded by the City of Dover and NH Estuaries Project; 2004-2006) This project was initiated by the City of Dover to restore a portion of a once productive oyster reef in the Bellamy River that suffered drastic declines in recent years, probably due largely to the oyster disease MSX. The Dover funds were partially matched by funds from NHEP. Ray Grizzle is the principal investigator.

Oyster Spat

Oyster spat on mollusc shells in remote setting tank


Nursery raft where spat are held until large enough to survive on constructed reefs


Reef structure alternatives for restoration of oyster (Crassostrea virginica) populations (Funded by USEPA/NH Estuaries Project; 2004-2006.) Restoration of oyster populations is a high priority for environmental managers in New Hampshire, and many other coastal states. This project seeks to determine the most effective approaches with respect to reef size and placement for restoration of natural reefs. It will address the general ecological debate regarding Single Large or Several Small (SLOSS) reefs with respect to reef development success. Ray Grizzle and Dave Burdick are the principal investigators.


Construction of granite bases for Adams Point experimental reefs

Fig 4

Young oysters (1-month old spat) set on concrete/granite rock and used to "seed" Adams Point experimental reefs

Development of a general protocol for characterizing subtidal oyster reefs using remote sensing techniques (Funded by NH Sea Grant; 2004-2006.) Traditional methods for monitoring subtidal oyster reefs rely upon extractive sampling techniques such as dredges, tongs, or quadrat sampling by divers. Remote sensing methods such as acoustic sounders and underwater video have the potential to greatly enhance the amount of detailed spatial information that can be obtained compared to traditional approaches. This project will compare acoustics (single beam, multibeam, and sidescan sonar), video, and quadrat sampling for characterizing the size and structure of three reefs, with the long-term aim being development of a general monitoring protocol. A report (see Grizzle et al. 2005 in RECENT PUBLICATIONS) will be available describing preliminary studies that led to this project. Ray Grizzle, Semme Dijkstra, and Brian Smith are the principal investigators.

Fig 1

Oyster reefs at Adams Point and Nannie Island that were preliminarily mapped using acoustics and underwater video

Fig 2 A comparison of outputs from video and acoustics mapping approaches. A (top): Photomontage produced from stills extracted from stationary video of Adams Point reef. A (bottom): Classification analysis of single beam sounder data showing six classes of bottom types for Adams Point reef, with grid used for video imaging. B (top): Photomontage for Nannie Island reef. B (bottom): Sidescan sonar image clearly showing shape of Nannie Island reef, with overlying grid used for video imaging

Monitoring marine protected areas: intensive study of the Western Gulf of Maine Closure Area (Funded by NOAA/UNH Cooperative Institute for New England Mariculture and Fisheries [CINEMar] and the Northeast Consortium; 2002-2005.) Marine Protected Areas (MPAs) have become a major management tool in attempts to re-build declining fish stocks globally. The Western Gulf of Maine Closure Area was established in 1997 to help re-build groundfish (e.g. cod, flounders) populations in the New England region. This project is one of several funded by the Northeast Consortium and UNH's CINEMAR that seeks to assess the effects of the closure on fisheries, as well as habitat conditions and social impacts. Andy Rosenberg, Ray Grizzle, Larry Mayer, Larry Ward, and Michael Lesser are the principal investigators.

Fig 5

Sampling the seafloor near Jeffreys Ledge with a box corer deployed from fishing vessel (Jamie Adams, Craig Mavrikis)

Fig 6

Developing underwater video system used to image the seafloor

Sample Process

Identifying invertebrates (Kaitlin Graiff)


David Burdick


Interim Director of the Jackson Estuarine Laboratory
Research Associate Professor of Coastal Ecology and Restoration

Department of Natural Resources & the Environment
Jackson Estuarine Laboratory
85 Adams Point Road
Durham, NH 03824