Development of a General Protocol for Characterizing Subtidal Oyster Reefs Using Remote Sensing Techniques

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Fisheries Resources


Semme Dijkstra UNH - Center for Coastal and Ocean Mapping Associate Investigator
Brian Smith N.H. Fish and Game Department Associate Investigator
Holly Abeels UNH - Department of Biological Sciences Technician
Jennifer Greene UNH - Department of Biological Sciences Technician
Melissa Brodeur University of New Hampshire Technician
Raymond Grizzle UNH - Jackson Estuarine Lab Principal Investigator

Students Involved:

Mike Leo UNH - Center for Coastal and Ocean Mapping
Sarah Mikulak UNH - Department of Biological Sciences
Kaitlin Graiff UNH - Department of Biological Sciences
Krystin Ward UNH - Jackson Estuarine Lab
Mark Capone UNH - Department of Biological Sciences

Populations of the eastern oyster (Crassostrea virginica) have been in long-term decline in many areas along the eastern U.S. coast. A major hindrance to effective oyster management has been the lack of a methodology for effectively and economically obtaining data on distribution and abundance. The overall goal of the proposed project is the development of new and innovative remote sensing technologies culminating in a recommended general protocol for further testing in other areas. We propose to assess the effectiveness of newly developing acoustic, visualization, videographic and GIS-based mapping technologies for characterizing subtidal oyster reef habitat.

The following six major objectives with methods will be addressed:

1) Conduct acoustic surveys of three oyster reefs in New Hampshire using single beam, multibeam and sidescan sonar

2) Determine the spatial extent of each study reef and characteristics (e.g., shell densities) potentially derivable from the acoustics data using sediment characterization and visualization software presently under development

3) Videographically image each study reef at a spatial scale sufficient to determine the boundaries and other characteristics of each reef

4) Carry out groundtruthing of the information obtained from objectives two and three using quadrat sampling by divers

5) Produce ArcGIS-based maps in both electronic and printed forms of all study reefs

6) Develop a recommended general protocol that can be tested in other areas for mapping and characterizing subtidal oyster reefs, emphasizing acoustics and videography while minimizing destructive sampling techniques. This final objective represents the major end product of the proposed research. It will essentially consist of a synthesis of information from the other objectives.


1) Conduct acoustic surveys of oyster reefs

2) Determine reef characteristics (e.g., shell densities) potentially derivable from the acoustics data

3) Videographically image each study reef

4) Carry out groundtruthing using quadrat sampling by divers

5) Produce ArcGIS-based maps

6) Develop a recommended general protocol for mapping and characterizing subtidal oyster reefs


Single beam, multibeam and sidescan sonar; underwater videography; quadrat excavation by divers.


Populations of the eastern oyster have been in long-term decline in many areas along the eastern U.S. coast. A major hindrance to effective oyster management has been the lack of a methodology to effectively and economically obtain data on distribution and abundance.


This project resulted in peer-reviewed publications and additional work and contracts. The partnerships that were formed among the PIs have also led to more interactions, and probably will eventually result in additional collaborative projects.

Significant Findings

What are the strengths and limitations of acoustics methods?
Our project focused on single (narrow) beam sounders for several reasons. The most widespread use of narrow beam sounders (NBS) is in the form of inexpensive fathometers on small boats that typically only sense and process a portion of the overall acoustic signal. However, with the advent of low cost digitizers and mass storage it became possible to collect the envelope of the returned intensities, or even the full waveform. In our project, the major aim was to assess the usefulness of low-cost NBS systems to map and characterize oyster reefs using relatively simple to use software. And the focus was on using the envelope of the returned frequencies rather than the full waveforms because NBS units providing the capability of collecting full waveforms are relatively rare and more expensive. Also this type of data would require an in depth understanding of acoustics and signal processing from the end user. This was also because commercial systems for mapping the seafloor using NBS systems are commercially available and include QTCView and RoxAnn.
The major strengths of NBS units are the significantly lower cost and relative ease of operation, and minimal logistic demands. Although some amount of specific knowledge for successful data acquisition for oyster mapping is required, highly trained operators are not. The major limitations of these units are that they do not allow for analysis of the sonar signal returns as a function of angle of incidence, and the spatial coverage is not as comprehensive as that of multibeam and/or sidescan sonars.
What are the strengths and limitations of underwater videography?
The major strengths of underwater video for oyster reef mapping and monitoring include: (1) ability to provide high resolution imagery showing a variety of oyster reef characteristics; (2) straightforward deployment, image acquisition, and image interpretation; and (3) low cost. The information can be obtained in a straightforward manner using small boats, and with minimal effort involved in image processing, interpretation, and final map production.
The major limitations of video include: (1) image quality strongly affected by water clarity; (2) relatively narrow swath of bottom area imaged; and (3) data acquisition rate limited to relatively slow ship speeds (less than ~2 knots). Of the three, the first is probably the most important from the context of the widespread use of video for oyster reef monitoring because oysters typically occur in estuarine waters characterized by high turbidity levels (Burrell 1986; Stanley and Sellers 1988). Our research has provided a preliminary assessment of this limitation, but more work needs to be done in other areas. The remaining limitations, swath width and ship speed, may be of less concern in most cases but they do place limitations on video and should be considered in determining its adequacy for a particular application.
What are the strengths and limitations of extractive methods?
Extractive methods include quadrat excavation by divers (as in our study), tongs, and dredges. All have the major advantage over remote sensing methods of providing a physical sample of the oyster population for direct inspection and processing. Therefore, remote sensing methods generally should be viewed from the perspective of their potential to complement extractive sampling. From this perspective, there are three important limitations of extractive sampling for monitoring oyster reefs: (1) impractical for use in determining overall reef shape and size; (2) incapable of determining some reef characteristics relevant to assessment of ecosystem services; and (3) destructive.
Can a general protocol be recommended for mapping and characterizing subtidal oyster reefs?
We recognize that no single study could yield a definitive monitoring protocol for the eastern
oyster. Our project, however, has resulted in new comparative knowledge that should be useful for managers seeking to rely more on remote sensing techniques while minimizing extractive sampling methods. Considering the above strengths-and-limitations assessment of acoustic and video techniques, we offer the following general suggestions discussed by major monitoring objectives.
Oyster density and size. Quantitative extractive methods such as diver-excavated quadrats and patent tongs are the only methods for accurate measurement of oyster density and size, as well as other information (e.g., reproductive state, condition) obtainable only by removing oysters for further processing. Therefore, remote sensing methods in general should be viewed as complementary to extractive sampling if data on density and size are needed. Remote sensing methods, however, can be used to improve the design of extractive sampling programs. For example, acoustics and/or towed videography could be used to determine spatial dimensions and variations in features such as total shell density of a reef. Maps could then be produced to show areas of different shell density, and a stratified (based on shell density) random sampling program designed to allocate extractive samples across the different strata.
Reef shape and size. Multibeam and sidescan sonars are capable of differentiating between oyster bottom and other substrate types, particularly soft sediments (Mayer et al. 1999; Wilson et al. 2000; Allen et al. 2005; Grizzle et al. 2005). If practical (considering costs, depth limitations, etc; see above), multibeam and/or sidescan sonars would be the method of choice for obtaining data on the overall size and shape as well as some aspects of spatial heterogeneity of the reef. Because overall size and shape of a reef typically change on time scales of years or even decades in some cases (Grizzle et al. 2002), these surveys could perhaps be conducted less frequently than other monitoring efforts.
Single-beam sonars provide potentially low cost alternatives to multibeam, and reasonably priced commercial units are available that include hardware as well as software for processing and analyzing the data. Single-beam sonars used in seafloor mapping include relatively inexpensive echo-sounders (Kvernevik, et al., 2002), sub-bottom profiling devices (Smith et al. 2001, 2003), and units designed specifically for discriminating different bottom characteristics (Smith et al. 2003; Riegl, et al. 2005). A major difference between multibeam and single-beam sonars is the latter only insonify a narrow swath of the seafloor along each shiptrack. In a typical application, a relatively small portion of the overall survey area is actually sampled and interpolation techniques are used to infer bottom characteristics between shiptracks. The resulting dataset also requires substantial processing and interpretation as well as groundtruthing, as discussed above.
Underwater videography only recently has been explored as a mapping tool for oysters (Grizzle et al. 2005, 2008). It can be deployed in similar fashion to single-beam sonars, simultaneously logging video and position data along multiple shiptracks (transects) across the study area. And when water clarity is sufficient, video can be used with minimal effort involved in image processing and little or no groundtruthing to produce accurate maps of reef shape and size.
Miscellaneous reef characteristics. The recent emphasis on ecosystem services provided by oyster reefs has resulted in the need to characterize reef features not typically measured. The methods assessed in the present project are most relevant for measurement of the following features (all related to habitat value): shell density, vertical structure, and associated organisms. Shell density can be measured by extractive methods and most remote sensing methods. Vertical structure can be estimated to some extent by extractive methods, but information over large areas requires remote sensing. Most sonars and towed video are capable of detecting vertical variations of only a few centimeters. Identification and determination of abundances of organisms associated with oyster reefs can only be accomplished using underwater video.
Outreach and industrial impacts
Our project involved end users in two major ways. First, the software being developed by Dijkstra, particularly TracEd, has considerable marketing potential. Interest in commercialization of this software has been expressed by a number of parties in the private sector, including a sonar manufacturer, a GIS developer, and a company selling seafloor characterization software. The commercial development of TracEd would guarantee the transferability as well as proper documentation of it. Furthermore, Sea Technology magazine (read by over 22,000 ocean professionals in over 105 countries) has approached Dijkstra concerning writing an article for publication, further expanding the exposure of this software tool to the community.
Secondly, the major end users for the general protocol primarily will be state-level managers. The New Hampshire Fish and Game Department was an active participant in the proposed study. The major potential change likely for their regular oyster reef monitoring is the addition of one or more remote sensing techniques to supplement the data obtained by divers. As a result of this project, Grizzle contracted with the New Hampshire Department of Environmental Services in 2003 to provide video mapping of two oyster reefs in the Great Bay Estuary for which areal coverage information was lacking.
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Available from the National Sea Grant Library (use NHU number to search) or NH Sea Grant

Journal Article

  • Grizzle, R., M. Brodeur, H. Abeels and J. Greene (2008). Bottom habitat mapping using towed underwater videography: subtidal oyster reefs as an example application. Journal of Coastal Research 24(1):103-109, January 2008.
  • Grizzle, R., L. Ward, J. Adams, S. Dijkstra and B. Smith (2005). Mapping and characterizing subtidal oyster reefs using acoustic techniques, underwater videography, and quadrat counts. American Fisheries Society Symposium 41:153-159.


  • Grizzle, R. and M. Brodeur (2004). Oyster ("Crassostrea virginica") reef mapping in the Great Bay Estuary, New Hampshire - 2003. A final report to the New Hampshire Estuaries Project.
  • Grizzle, R. and M. Pietrak (2008). Using underwater videography to monitor oyster farms. The Dredge 2(2), Spring 2008, Connecticut Sea Grant.