NOAA Technical Memorandum NMFS-AFSC-317 doi:10.7289/V5/TM-AFSC-317 The Applicability of Sonars for Habitat Mapping: a Bibliography T. A. Smith and R. A. McConnaughey U.S. DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration National Marine Fisheries Service Alaska Fisheries Science Center April 2016 NOAA Technical Memorandum NMFS The National Marine Fisheries Service's Alaska Fisheries Science Center uses the NOAA Technical Memorandum series to issue informal scientific and technical publications when complete formal review and editorial processing are not appropriate or feasible. Documents within this series reflect sound professional work and may be referenced in the formal scientific and technical literature. The NMFS-AFSC Technical Memorandum series of the Alaska Fisheries Science Center continues the NMFS-F/NWC series established in 1970 by the Northwest Fisheries Center. The NMFS-NWFSC series is currently used by the Northwest Fisheries Science Center. This document should be cited as follows: Smith, T. A., and R. A. McConnaughey. 2016. The applicability of sonars for habitat mapping: a bibliography. U.S. Dep. Commer., NOAA Tech. Memo. NMFS-AFSC-317, 129 p. doi:10.7289/V5/TM-AFSC-317. Document available: http://www.afsc.noaa.gov/Publications/AFSC-TM/NOAA-TM-AFSC-317.pdf Reference in this document to trade names does not imply endorsement by the National Marine Fisheries Service, NOAA. NOAA Technical Memorandum NMFS-AFSC-317 doi:10.7289/V5/TM-AFSC-317 The Applicability of Sonars for Habitat Mapping: a Bibliography by T. A. Smith and R. A. McConnaughey Resource Assessment Conservation Engineering Alaska Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration 7600 Sand Point Way N.E. Seattle, WA 98115 www.afsc.noaa.gov U.S. DEPARTMENT OF COMMERCE Penny. S. Pritzker, Secretary National Oceanic and Atmospheric Administration Kathryn D. Sullivan, Under Secretary and Administrator National Marine Fisheries Service Eileen Sobeck, Assistant Administrator for Fisheries April 2016 This document is available to the public through: National Technical Information Service U.S. Department of Commerce 5285 Port Royal Road Springfield, VA 22161 www.ntis.gov Introduction- The Applicability of Sonars for Habitat Mapping: A Bibliography A great variety of biotic and abiotic factors define the habitats of marine species such that knowledge of their spatial and temporal variability can be used to understand biological patterns of distribution and abundance. The importance of habitats for the sustainable management of fishery stocks was formally acknowledged in the United States with passage of the Sustainable Fisheries Act in 1996. At that time, the Magnuson-Stevens Fishery Conservation and Management Act was amended to include new requirements to identify and protect essential fish habitat (EFH). By legal definition, EFH means those waters and substrate necessary to fish for spawning, breeding, feeding, or growth to maturity. Using the best scientific information, federal fishery management plans must describe and identify EFH in text that clearly states the habitats or habitat types determined to be EFH for each life stage of the managed species. In so doing, the plans should explain the physical, biological, and chemical characteristics of EFH and must also identify the specific geographic location or extent of habitats described as EFH. The broad scope of the EFH mandate requires an efficient process for describing and mapping the habitats of federally managed species. Factors such as temperature, salinity, and depth are generally accepted as habitat-defining characteristics for marine fish and invertebrates, and synoptic data sets are frequently available. Research also indicates that surficial sediments are an important habitat factor for many species, with both direct and indirect effects on survival and growth. Traditional sampling with grabs and cores is, however, impractical over large areas and the availability of geo-referenced data is usually limited as a result. Acoustic methods, on the other hand, are suitable for large-scale surveying and show great promise as a substitute for direct-sampling methods, but they are still at a “nascent” stage of development (Anderson et al. 2008) and have not been proven for EFH purposes. The complex relationship between acoustic returns and seafloor sediments has been actively 1 studied for decades. According to Holliday (2007) , as many as 80 different parameters have been used to describe the physical and material properties of the seafloor, of which 6 to 12 of these may have major influence on acoustic returns from the seabed. This complexity limits the utility of conventional ground-truthing with grabs. Overall, each seabed type has a characteristic acoustic return, although that return is not unique because many of the parameters are confounded. As a result, accurate characterization of seabed types from acoustic returns is problematic because different combinations of grain size, surface roughness, and slope, for example, can have the same acoustic properties (the so-called “inverse problem”). The situation is even more complex, given the seabed frequently is not static due to time-varying forces such as waves, currents, certain fishing activities, and natural biological processes. Notwithstanding the challenges of interpretation, many useful applications of sonars for habitat mapping have been reported in the scientific literature. The primary focus of this bibliography is benthic habitat characterization using backscatter and bathymetric data from multibeam echo sounders, single-beam echo sounders, and side scan 1 sonars. The coverage ranges from methods for acquiring and processing data, data extraction and synthesis from imagery, production and use of habitat maps for fishery management and other purposes, modeling species distributions using processed data, and some relevant theoretical treatments. The bibliography was compiled from extensive searches of online literature databases, as well as secondary reviews of literature cited in the selected references. The collection includes peer-reviewed articles, as well as state and Federal reports, conference papers, cruise reports, bulletins, and books. The abstracts and keywords for each reference were obtained from the original source whenever possible. If one or the other was not available for use, a brief summary and/or keywords were added. Links were only provided at the request of the publisher. Some papers were excluded due to lack of availability of copyright permissions. This bibliography can be found online as a searchable, dynamic database at http://access.afsc.noaa.gov/sonarHabMap/search.php . Acknowledgments We would like to thank all of the authors and publishers who granted permission to include copyrighted works, especially ProQuest (www.proquest.com) for their considerable contributions. We would like to thank Jim Lee (AFSC) in his assistance in obtaining style guidelines because of publisher requests. We would like to thank Sarah Schwartz (USDDC Office of General Council) in her assistance in copyright law. 1 Holliday, D. V. 2007. Theory of sound-scattering from the seabed. Pages 13-23 in Anderson, J., Holliday, V., Kloser, R., Reid, D., and Simard, Y. (ed). Acoustic seabed classification of marine physical and biological landscapes. ICES Cooperative Research Report no. 286. Copenhagen. 2 Able, K. W., D. C. Twichell, C. B. Grimes, and R. S. Jones. 1987. Sidescan sonar as a tool for detection of demersal fish habitats. Fish. Bull., U.S. 85:725-737. Keywords: habitat preferences, side scan sonar, sonar, marine, Caulolatilus, habitat selection, Lopholatilus, methodology Abstract: Sidescan sonar can be an effective tool for the determination of the habitat distribution of commercially important species. This technique has the advantage of rapidly mapping large areas of the seafloor. Sidescan images (sonographs) may also help to identify appropriate fishing gears for different types of seafloor or areas to be avoided with certain types of gears. During the early stages of exploration, verification of sidescan sonar sonographs is critical to successful identification of important habitat types. Tilefishes (Lopholatilus and Caulolatilus) are especially good target species because they construct large burrows in the seafloor or live around boulders, both of which are easily detectable on sonographs. In some special circumstances the estimates of tilefish burrow densities from sonographs can be used to estimate standing stock. In many localities the burrow and boulder habitats of tilefish are shared with other commercially important species such as American lobsters. Homarus americanus: cusk. Brosme brosme; and ocean pout. Macrozoarces americanus. Allen, Y. and C. Wilson, H. Roberts, and J. Supan. 2004. Using sidescan sonar to assess the impact and persistence of natural and anthropogenic disturbance to low-relief oyster habitats in coastal Louisiana. In: Proceedings of the Gulf and Caribbean Fisheries Institute. 55:1006-1007. Keywords: sidescan sonar, oyster habitat, Louisiana Abstract: Traditional methods used to assess oyster reef distribution and condition are only able to provide subjective point information which is often poorly georeferenced. Maps of oyster habitat in shallow waters are therefore typically extremely generalized, giving few details about the true distribution, character and dynamics of reefs. Sidescan sonar offers a significant advantage for oyster reef assessment in the turbid waters of coastal Louisiana. We used sidescan sonar in ultra-shallow (<2m) waters to completely image over 19 000 ha in Louisiana estuaries in advance of an impending freshwater diversion project. We also conducted four years of intense annual surveys in a more restricted area (320 ha) with a diversity of reef types and culture intensity to examine natural and anthropogenic impacts on oyster reef extent and character. Our intensive surveys identified older stable reefs which had not been actively worked. Shell abundance and structure on these reefs were high, but oyster meat productivity was low. Areas of intense oyster culture were characterized by low relief reefs that frequently showed distinct evidence of scarring from dredging and other anthropogenic sources. Smaller scars caused by oyster dredging typically healed through the within 3 time period of our study while larger anthropogenic scarring did not diminish over the four years. We also deployed the sonar towfish over an area immediately before and after both seeding and harvesting to establish a quantitative relationship with sonar reflectance. These relationships can be further used to predict the impact of harvesting and seeding on the extent oyster habitat. Demographic comparison of red snapper (Lutjanus campechanus) from the Atlantic and Gulf of Mexico. The citations and abstracts are from Aquatic Sciences and Fisheries Abstracts (ASFA) and are provided with permission of ProQuest LLC. Further reproduction is prohibited. Allen, Y. C., C. A. Wilson, H. H. Roberts, and J. Supan. 2005. High resolution mapping and classification of oyster habitats in nearshore Louisiana using Sidescan Sonar. Estuaries 28:435-446. Keywords and abstract are not provided as requested by Springer Publishing. Please visit the link below for the keywords and abstract. Link: http://link.springer.com/article/10.1007/BF02693925 Anderson, J. T., D. Van Holliday, R. Kloser, D. G. Reid, and Y. Simard. 2008. Acoustic seabed classification: current practice and future directions. ICES J. Mar. Sci. 65:1004-1011. Keywords: acoustic, classification, echosounders, habitat, landscape, mapping, marine, multibeam, seabed, sidescan, single beam, sonar. Abstract: Acoustic remote sensing of the seabed using single-beam echosounders, multibeam echosounders, and sidescan sonars combined and individually are providing technological solutions to marine-habitat mapping initiatives. We believe the science of acoustic seabed classification (ASC) is at its nascence. A comprehensive review of ASC science was undertaken by an international group of scientists under the auspices of ICES. The review was prompted by the growing need to classify and map marine ecosystems across a range of spatial scales in support of ecosystem-based science for ocean management. A review of the theory of sound-scattering from seabeds emphasizes the variety of theoretical models currently in use and the ongoing evolution of our understanding. Acoustic-signal conditioning and data quality assurance before classification using objective, repeatable procedures are important technical considerations where standardization of methods is only just beginning. The issue of temporal and spatial scales is reviewed, with emphasis on matching observational scales to those of the natural world. It is emphasized throughout that the seabed is not static but changes over multiple time-scales as a consequence of natural physical and biological processes. A summary of existing commercial ASC systems provides an introduction to existing capabilities. Verification (ground-truthing) methods are reviewed, emphasizing the difficulties of matching observational scales with acoustic- backscatter data. Survey designs for ASC explore methods that extend beyond traditional oceanographic and fisheries survey techniques. Finally, future directions for 4 acoustic seabed classification science were identified in the key areas requiring immediate attention by the international scientific community. The citations and abstracts are from Aquatic Sciences and Fisheries Abstracts (ASFA) and are provided with permission of ProQuest LLC. Further reproduction is prohibited. Appeldoorn, R. S., J. A. Rivera, and M. C. Prada. 2001. Mapping benthic habitats using side scan sonar. p. 402-414. In Proceedings of the Gulf and Caribbean Fisheries Institute. Gulf and Caribbean Fisheries Institute, Harbor Branch Oceanographic Institution, Inc. Keywords: habitat mapping, active sensors, side scan sonar Abstract: Detailed, but large scale habitat mapping is necessary if fisheries researchers are to investigate habitat-species distributions on spatial scales relevant to fisheries management and marine conservation, and identify essential fish habitats and the qualities that underlie their importance. The latter will include both the immediate structural qualities of a given area and the linkages among surrounding habitats. Knowledge of the underlying structure of habitat function should allow simple rules to be developed for future identification and protection of critical habitats. Despite over 40 years of concentrated academic investigation in the area of La Parguera, Puerto Rico, including geological mapping, there is no comprehensive habitat map suitable for large- scale biological studies. Developing such a map is now feasible using remote sensing and geographic information system (GIS). We are using side scan sonar (SSS) to develop a habitat map extending from the shoreline to the edge of the insular platform and 2 covering over 20 nautical miles square (nm ). SSS is advantageous over airborne remote sensing in its greater depth range and greater resolution. The SSS associated navigation equipment (computer, software, DGPS) and electric winch are mounted on a 22-ft vessel. A 300 kHz transducer is towed over 100-m wide paths to collect bottom images. To create larger views, georeferenced mosaics are generated from individual images using GIS technology. To date we have identified broad areas of habitat and located unknown patch reefs in otherwise soft-sediment areas. At 300 kHz, metal-frame fish traps were not detected, although evidence of their effect on corals were. Although SSS technology is valuable, its success requires proper logistical set-up, plus expertise in computers and electronics. Armstrong, A. A. and L. Mayer. 2000. The NOAA/UNH Joint Hydrographic Center and the UNH Center for Coastal and Ocean Mapping: An educational and research partnership of the Federal Government, the University of New Hampshire and Ocean Industry. p. 705-709. In Proceedings of the Oceans 2000 MTS/IEEE - Where Marine Science and Technology Meet, Vols 1-3, Heriot-Watt University Ocean Systems Laboratory Keywords: ocean mapping technology, hydrography, C-COM/JHC Abstract: Ocean mapping technology is becoming an increasingly important tool in the full range of ocean-related enterprise. Moving well beyond its initial base in 5 hydrographic surveying and nautical charting, ocean mapping has become a critical component of offshore oil exploration and development, submarine cable routing and installation, and geologic and essential fish habitat mapping. The technology of ocean mapping has blossomed rapidly in the past decade with the introduction of multibeam sonar, high-resolution side scan sonar, airborne lidar bathymeters, and laser line scan recorders. The next decade will likely see increased demand for ocean mapping data and continued demand for even more sophisticated ocean mapping technology. In response to this increased demand for ocean mapping data and the increasing complexity of ocean mapping technology, the National Oceanic and Atmospheric Administration (NOAA) and the University of New Hampshire (UNH) have established the complementary Joint Hydrographic Center (JHC) and Center for Coastal and Ocean Mapping (C-COM). The JHC is a NOAA/UNH partnership, and C-COM is a University organization with growing private sector participation. The citations and abstracts are from Aquatic Sciences and Fisheries Abstracts (ASFA) and are provided with permission of ProQuest LLC. Further reproduction is prohibited. Atallah, L., and P. Probert Smith. 2004. How useful is bathymetric information in the classification of high frequency sonar surveys? J. Acoust. Soc. Am. 116:2487-2487. Keywords: seabed classification, bathymetric data, machine learning Abstract: In a number of sonar studies, bathymetric information is used to correct and visualise amplitude data. This work proposes a method which combines amplitude features (describing backscattering strength and sonar texture) with bathymetric features (indicating seafloor variability) for sonar classification. Features are selected per window (of user defined size) and areas around grab samples in a survey are used for training. The importance of different features is investigated in this study, and highlighted by feature selection algorithms as well as by scatter plots exploring the training areas. Classification rates are significantly improved when both amplitude and bathymetry features are used. The method is applied to a sidescan bathymetric sonar dataset taken in Hopvågen bay-Norway. Copyright 2004, reproduced with permission from Acoustical Society of America. Link: http://scitation.aip.org/content/asa/journal/jasa/116/4/10.1121/1.4784932 Auster, P. J., K. Joy, and P. C. Valentine. 2001. Fish species and community distributions as proxies for seafloor habitat distributions: the Stellwagen Bank National Marine Sanctuary example (Northwest Atlantic, Gulf of Maine). Environ. Biol. Fishes 60:331-346. Keywords and abstract are not provided as requested by Springer Publishing. Please visit the link below for the keywords and abstract. Link: http://link.springer.com/article/10.1023%2FA%3A1011022320818 6