ALBERT

Description: We have recently exchanged and integrated into a single database tag detections for conch, teleost and elasmobranch fish from four separately maintained arrays in the U.S. Virgin Islands including the NMFS queen conch array (St. John nearshore), NOAA’s Biogeography Branch array (St. John nearshore & midshelf reef); UVI shelf edge arrays (Marine Conservation District, Grammanik & other shelf edge); NOAA NMFS Apex Predator array COASTSPAN (St. John nearshore). The integrated database has over 7.5 million hits. Data is shared only with consent of partners and full acknowledgements. Thus, the summary of integrated data here uses data from NOAA and UVI arrays under a cooperative agreement.The benefits of combining and sharing data have included increasing the total area of detection resulting in an understanding of broader scale connectivity than would have been possible with a single array. Partnering has also been cost-effectiveness through sharing of field work, staff time and equipment and exchanges of knowledge and experience across the network. Use of multiple arrays has also helped in optimizing the design of arrays when additional receivers are deployed. The combined arrays have made the USVI network one of the most extensive acoustic arrays in the world with a total of 150+ receivers available, although not necessarily all deployed at all times. Currently, two UVI graduate student projects are using acoustic array data.

Description: The overall purpose of this project was to collect available information on the characteristics of essential fish habitats in protected and non-protected marine areas around the islands of Puerto Rico. Specifically, this project compiled historical information on benthic habitats and the status of marine resources into a Geographic Information System (GIS) by digitizing paper copies of existing marine geologic maps that were developed for the Caribbean Fishery Management Council (CFMC) for areas around the Commonwealth of Puerto Rico. In addition, information on benthic habitat types, Essential Fish Habitat (EFH) requirements, and fishing and non-fishing impacts to marine resources were compiled for two priority areas: La Parguera and Vieques. The information obtained will help to characterize and select habitats for future monitoring of impacts of fishing and non-fishing activities and to develop management recommendations for conservation of important marine habitats. The project focused specifically on areas identified as priorities for conservation by the Puerto Rico Department of Natural and Environmental Resources (DNER) and the Local Action Strategy Overfishing Group.

Description: The intent of this field mission was to continue ongoing efforts: (1) to spatially characterize and monitor the distribution, abundance and size of both reef fishes and conch within and around the waters of the Virgin Islands National Park (VIIS) and newly established Virgin Islands Coral Reef National Monument (VICR), (2) to correlate this information to in-situ data collected on associated habitat parameters, (3) to use this information to establish the knowledge base necessary for enacting management decisions in a spatial setting and to establish the efficacy of those management decisions. This work is supported by the National Park Service and NOAA’s Coral Reef Conservation Program’s Caribbean Coral Reef Ecosystem Monitoring Project.

Description: The United States Coral Reef Task Force (USCRTF) was established in 1998 by Presidential Executive Order 13089 to lead U.S. efforts to preserve and protect coral reef ecosystems. Current, accurate, and consistent maps greatly enhance efforts to preserve and manage coral reef ecosystems. With comprehensive maps and habitat assessments, coral reef managers can be more effective in designing and implementing a variety of conservation measures, including:• Long-term monitoring programs with accurate baselines from which to track changes;• Place-based conservation measures such as marine protected areas (MPAs); and• Targeted research to better understand the oceanographic and ecological processes affecting coral reef ecosystem health.The National Oceanic and Atmospheric Administration’s (NOAA) National Ocean Service (NOS) is tasked with leading the coral ecosystem mapping element of the U.S. Coral Reef Task Force (CRTF) under the authority of the Presidential Executive Order 13089 to map and manage the coral reefs of the United States.

Description: NOAA/NCCOS is conducting the following work for the NOAA California Current Integrated Ecosystem Assessment, in support of the NOAA/NMFS Northwest Fisheries Science Center.

Description: This report presents an initial characterization of chemical contamination in coral tissues (Porites astreoides) from southwest Puerto Rico. It is the second technical report from a project to characterize chemical contaminants and assess linkages between contamination and coral condition. The first report quantified chemical contaminants in sediments from southwest Puerto Rico. This document summarizes the analysis of nearly 150 chemical contaminants in coral tissues. Although only eight coral samples were collected, some observations can be made on the correlations between observed tissue and sediment contaminant concentrations. The concentrations of polycyclic aromatic hydrocarbons (PAHs), typically associated with petroleum spills and the combustion of fossil fuels, and polychlorinated biphenyls (PCBs) in the coral tissues were comparable to concentrations found in adjacent sediments. However, the concentration of a chemical contaminant (e.g., PAHs) in the coral tissues at a particular site was not a good predictor of what was in the adjacent sediments. In addition, the types of PAHs found in the coral tissues were somewhat different (higher ratios of alkylated PAHs) than in sediments. The levels of PCBs and DDT in coral tissues appeared higher just outside of Guanica Bay, and there was evidence of a downstream concentration gradient for these two contaminant classes. The trace elements copper, zinc and nickel were frequently detected in coral tissues, and the concentration in the corals was usually comparable to that found in adjacent sediments. Chromium was an exception in that it was not detected in any of the coral tissues analyzed. Additional work is needed to assess how spatial patterns in chemical contamination affect coral condition, abundance and distribution.

Description: National Status and Trends Program for Marine Environmental Quality

Description: In May 2006, the NOAA National Ocean Service (NOS), in conjunction with the EPA National Health and Environmental Effects Laboratory (NHEERL), conducted an assessment of the status of ecological condition of soft-bottom habitat and overlying waters throughout the mid-Atlantic Bight (MAB) portion of the eastern U.S. continental shelf. The study area encompassed the region from Cape Cod, MA and Nantucket Shoals in the northeast to Cape Hatteras in the south, and was defined using a one nautical mile buffer of the shoreline extended seaward to the shelf break (~100-m depth contour). A total of 50 stations were targeted for sampling using standard methods and indicators applied in prior NOAA coastal studies and EPA’s Environmental Monitoring and Assessment Program (EMAP) and National Coastal Assessment (NCA). A key feature adopted from these studies was the incorporation of a random probabilistic sampling design. Such a design provides a basis for making unbiased statistical estimates of the spatial extent of ecological condition relative to various measured indicators and corresponding thresholds of concern. Indicators included multiple measures of water quality, sediment quality, and biological condition (benthic fauna). Through coordination with the NOAA Fisheries Service/Northeast Fisheries Science Center (NFS/NEFSC), samples of summer flounder (Paralichthys dentatus) also were obtained from 30 winter 2007 bottom-trawl survey stations in overlapping portions of the study area and used for analysis of chemical-contaminant body burdens.

Description: EPA 600/R-09/159

Description: NOAA’s Mussel Watch Program was designed to monitor the status and trends of chemical contamination of U.S. coastal waters, including the Great Lakes. The Program began in 1986 and is one of the longest running, continuous coastal monitoring programs that is national in scope. NOAA established Mussel Watch in response to a legislative mandate under Section 202 of Title II of the Marine Protection, Research and Sanctuaries Act (MPRSA) (33 USC 1442). In addition to monitoring contaminants throughout the Nation’s coastal shores, Mussel Watch stores samples in a specimen bank so that trends can be determined retrospectively for new and emerging contaminants of concern.In recent years, flame retardant chemicals, known as polybrominated diphenyl ethers (PBDEs), have generated international concern over their widespread distribution in the environment, their potential to bioaccumulate in humans and wildlife, and concern for suspected adverse human health effects. The Mussel Watch Program, with additional funding provided by NOAA’s Oceans and Human Health Initiative, conducted a study of PBDEs in bivalve tissues and sediments.This report, which represents the first national assessment of PBDEs in the U.S. coastal zone, shows that they are widely distributed. PBDE concentrations in both sediment and bivalve tissue correlate with human population density along the U.S. coastline. The national and watershed perspectives given in this report are intended to support research, local monitoring, resource management, and policy decisions concerning these contaminants.

Description: NOAA National Status & Trends Mussel Watch Program

Description: This cruise report is a summary of a field survey conducted within the Sapelo Island National Estuarine Research Reserve (SINERR), located on the Georgia coastline, June 7 – June 13, 2009. Multiple indicators of ecological condition and human dimensions were sampled synoptically at each of 30 stations throughout SINERR using a random probabilistic sampling design. Samples were collected for the analysis of benthic community structure and composition; concentrations of chemical contaminants (metals, pesticides, PAHs, PCBs, PBDEs) in sediments and target demersal biota; nutrient and chlorophyll levels in the water column; bacterial contaminants in the water column; and other basic habitat characteristics such as depth, salinity, temperature, dissolved oxygen, turbidity, total suspended solids, pH, sediment grain size, and organic carbon content. In addition to the fish samples that were collected for analysis of chemical contaminants relative to human-health consumption limits, other human-dimension indicators were sampled as well including presence or absence of fishing gear, vessels, surface trash, and noxious sediment odors. The overall purpose of the survey was to collect data to assess the status of ecosystem condition and potential stressor impacts throughout SINERR, based on these various indicators and corresponding management thresholds, and to provide this information as a baseline for determining how such conditions may be changing with time. While sample analysis is still ongoing a few preliminary results and observations are reported here. A final report will be completed once all data have been processed. The results will provide a comprehensive weight-of-evidence basis for evaluating current condition (aka a “state-of-the-SINEER environmental report”) and serve as a quantitative benchmark for tracking any future changes due to either natural or human disturbances. Another goal of the study is to demonstrate its utility as a possible model for assessing the status of condition at other NEERS sites using similar and consistent methods to promote system-wide regional and national comparisons.

Description: Coral reef ecosystems of the Virgin Islands Coral Reef National Monument, Virgin Islands National Park and the surrounding waters of St. John, U.S. Virgin Islands are a precious natural resource worthy of special protection and conservation. The mosaic of habitats including coral reefs, seagrasses and mangroves, are home to a diversity of marine organisms. These benthic habitats and their associated inhabitants provide many important ecosystem services to the community of St. John, such as fishing, tourism and shoreline protection. However, coral reef ecosystems throughout the U.S. Caribbean are under increasing pressure from environmental and anthropogenic stressors that threaten to destroy the natural heritage of these marine habitats.Mapping of benthic habitats is an integral component of any effective ecosystem-based management approach. Through the implementation of a multi-year interagency agreement, NOAA’s Center for Coastal Monitoring and Assessment - Biogeography Branch and the U.S. National Park Service (NPS) have completed benthic habitat mapping, field validation and accuracy assessment of maps for the nearshore marine environment of St. John. This work is an expansion of ongoing mapping and monitoring efforts conducted by NOAA and NPS in the U.S. Caribbean and replaces previous NOAA maps generated by Kendall et al. (2001) for the waters around St. John. The use of standardized protocols enables the condition of the coral reef ecosystems around St. John to be evaluated in context to the rest of the Virgin Island Territories and other U.S. coral ecosystems. The products from this effort provide an accurate assessment of the abundance and distribution of marine habitats surrounding St. John to support more effective management and conservation of ocean resources within the National Park system.This report documents the entire process of benthic habitat mapping in St. John. Chapter 1 provides a description of the benthic habitat classification scheme used to categorize the different habitats existing in the nearshore environment. Chapter 2 describes the steps required to create a benthic habitat map from visual interpretation of remotely sensed imagery. Chapter 3 details the process of accuracy assessment and reports on the thematic accuracy of the final maps. Finally, Chapter 4 is a summary of the basic map content and compares the new maps to a previous NOAA effort.Benthic habitat maps of the nearshore marine environment of St. John, U.S. Virgin Islands were created by visual interpretation of remotely sensed imagery. Overhead imagery, including color orthophotography and IKONOS satellite imagery, proved to be an excellent source from which to visually interpret the location, extent and attributes of marine habitats. NOAA scientists were able to accurately and reliably delineate the boundaries of features on digital imagery using a Geographic Information System (GIS) and fi eld investigations.The St. John habitat classification scheme defined benthic communities on the basis of four primary coral reef ecosystem attributes: 1) broad geographic zone, 2) geomorphological structure type, 3) dominant biological cover, and 4) degree of live coral cover. Every feature in the benthic habitat map was assigned a designation at each level of the scheme. The ability to apply any component of this scheme was dependent on being able to identify and delineate a given feature in remotely sensed imagery.

Description: Project report produced by NOAA’s Biogeography Branch in cooperation with U.S. National Park Service.

Description: Shallow coral reefs in the IndoPacific contain the highest diversity of marine organisms in the world, with approximately 1500 described species of fish, over 500 species of scleractinian corals, and an estimated 1-10 million organisms yet to be characterized (Reaka-Kudla et al. 1994). These centers of marine biodiversity are facing significant, multiple threats to reef community and habitat structure and function, resulting in local to wide-scale regional damage. Wilkinson (2004) characterized the major pressures as including (1) global climate change, (2) diseases, plagues and invasive species, (3) direct human pressures, (4) poor governance and lack of political will, and (5) international action or inaction. Signs that the natural plasticity of reef ecosystems has been exceeded in many areas from the effects of environmental (e.g., global climate change) and anthropogenic (e.g., land use, pollution) stressors is evidenced by the loss of 20% of the world’s coral reefs (Wilkinson 2004). Predictions are that another 24% (Wilkinson 2006) are under imminent risk of collapse and an additional 26% are under a longer term threat from reduced fitness, disease outbreaks, and increased mortality. These predictions indicate that the current list of approximately 30-40 fatal diseases impacting corals will expand as will the frequency and extent of “coral bleaching” (Waddell 2005; Wilkinson 2004). Disease and corallivore outbreaks, in combination with multiple, concomitant human disturbances are compromising corals and coral reef communities to the point where their ability to rebound from natural disturbances is being lost.

Description: NOAA Technical Memorandum Coral Reef Conservation Program 7

Description: Models that help predict fecal coliform bacteria (FCB) levels in environmental waters can be important tools for resource managers. In this study, we used animal activity along with antibiotic resistance analysis (ARA), land cover, and other variables to build models that predict bacteria levels in coastal ponds that discharge into an estuary. Photographic wildlife monitoring was used to estimate terrestrial and aquatic wildlife activity prior to sampling. Increased duck activity was an important predictor of increased FCB in coastal ponds. Terrestrial animals like deer and raccoon, although abundant, were not significant in our model. Various land cover types, rainfall, tide, solar irradiation, air temperature, and season parameters, in combination with duck activity, were significant predictors of increased FCB. It appears that tidal ponds allow for settling of bacteria under most conditions. We propose that these models can be used to test different development styles and wildlife management techniques to reduce bacterial loading into downstream shellfish harvesting and contact recreation areas.

Description: Nonindigenous species (NIS) are a major threat to marine ecosystems, with possible dramatic effects on biodiversity, biological productivity, habitat structure and fisheries. The Papahānaumokuākea Marine National Monument (PMNM) has taken active steps to mitigate the threats of NIS in Northwestern Hawaiian Islands (NWHI). Of particular concern are the 13 NIS already detected in NWHI and two invasive species found among the main Hawaiian Islands, snowflake coral (Carijoa riseii) and a red alga (Hypnea musciformis).Much of the information regarding NIS in NWHI has been collected or informed by surveys using conventional SCUBA or fishing gear. These technologies have significant drawbacks. SCUBA is generally constrained to depths shallower than 40 m and several NIS of concern have been detected well below this limit (e.g., L. kasmira – 256 m) and fishing gear is highly selective. Consequently, not all habitats or species can be properly represented.Effective management of NIS requires knowledge of their spatial distribution and abundance over their entire range. Surveys which provide this requisite information can be expensive, especially in the marine environment and even more so in deepwater. Technologies which minimize costs, increase the probability of detection and are capable of satisfying multiple objectives simultaneously are desired.This report examines survey technologies, with a focus on towed camera systems (TCSs), and modeling techniques which can increase NIS detection and sampling efficiency in deepwater habitats of NWHI; thus filling a critical data gap in present datasets. A pilot study conducted in 2008 at French Frigate Shoals and Brooks Banks was used to investigate the application of TCSs for surveying NIS in habitats deeper than 40 m. Cost and data quality were assessed. Over 100 hours of video was collected, in which 124 sightings of NIS were made among benthic habitats from 20 to 250 m. Most sightings were of a single cosmopolitan species, Lutjanus kasmira, but Cephalopholis argus, and Lutjanus fulvus, were also detected.The data expand the spatial distributions of observed NIS into deepwater habitats, identify algal plain as an important habitat and complement existing data collected using SCUBA and fishing gear. The technology’s principal drawback was its inability to identify organisms of particular concern, such as Carijoa riseii and Hypnea musciformis due to inadequate camera resolution and inability to thoroughly inspect sites. To solve this issue we recommend incorporating high-resolution cameras into TCSs, or using alternative technologies, such as technical SCUBA diving or remotely operated vehicles, in place of TCSs. We compared several different survey technologies by cost and their ability to detect NIS and these results are summarized in Table 3.

Description: The National Oceanic and Atmospheric Administration’s (NOAA) Center for Coastal Monitoring and Assessment’s (CCMA) Biogeography Branch and the U.S. National Park Service (NPS) have completed mapping the moderate-depth marine environment south of St. John. This work is an expansion of ongoing mapping and monitoring efforts conducted by NOAA and NPS in the U.S. Caribbean. The standardized protocols used in this effort will enable scientists and managers to quantitatively compare moderate-depth coral reef ecosystems around St. John to those throughout the U.S. Territories. These protocols and products will also help support the effective management and conservation of the marine resources within the National Park system.

Description: The intent of this field mission was to continue ongoing efforts: (1) to spatially characterize and monitor the distribution, abundance and size of reef fishes, and the abundance of macroinvertebrates (conch, Diatema, lobster) within and around the waters of the Virgin Islands National Park (VIIS) and newly established Virgin Islands Coral Reef National Monument (VICR), (2) to correlate this information to in-situ data collected on associated habitat parameters, (3) to use this information to establish the knowledge base necessary for enacting management decisions in a spatial setting and (4) to establish the efficacy of those management decisions.An additional focus this year, was to evaluate a new habitat data collection method for RHA sites (MSR and some Coral Bay sites). There are concerns that the cylinder habitat data are not reflective of the fish transect habitat. To address this, we collected habitat data at 5x4 m increments along the transect in addition to data collected using the cylinder method. We are currently assessing the potential differences between these methods and preliminary results indicate that the average difference of coral cover estimates between the two methods was 4.1% (range 0-11%) based on 16 sample sites.In addition, Erinn Muller, a Nancy Foster Fellowship recipient, collaborated with the Biogeography Branch to examine the spatial distribution of coral diseases, to provide baseline information on disease prevalence over varying spatial scales and to establish spatial distributions of coral diseases around St. John.

Description: A baseline environmental characterization of the inner Kachemak Bay, Alaska was conducted using the sediment quality triad approach based on sediment chemistry, sediment toxicity, and benthic invertebrate community structure. The study area was subdivided into 5 strata based on geophysical and hydrodynamic patterns in the bay (eastern and western intertidal mud flats, eastern and western subtidal, and Homer Harbor). Three to seven locations were synoptically sampled within each stratum using a stratified random statistical design approach. Three sites near the village of Port Graham and two sites in the footprint of a proposed Homer Harbor expansion were also collected for comparison. Concentrations of over 120 organic and metallic contaminants were analyzed. Ambient toxicity was assessed using two amphipod bioassays. A detailed benthic community condition assessment was performed. Habitat parameters (depth, salinity, temperature, dissolved oxygen, sediment grain size, and organic carbon content) that influence species and contaminant distribution were also measured at each sampling site.Sediments were mostly mixed silt and sand; characteristic of high energy habitats, with pockets of muddy zones. Organic compounds (PAHs, DDTs, PCBs, cyclodienes, cyclohexanes) were detected throughout the bay but at relatively low concentrations. Tributyltin was elevated in Homer Harbor relative to the other strata. With a few exceptions, metals concentrations were relatively low and probably reflect the input of glacial runoff. Relative to other sites, Homer Harbor sites were shown to have elevated concentrations of metallic and organic contaminants. The Homer Harbor stratum however, is a deep, low energy depositional environment with fine grained sediment. Concentrations of organic contaminants measured were five to ten times higher in the harbor sites than in the open bay sites. Concentration of PAHs is of a particular interest because of the legacy of oil spills in the region. There was no evidence of residual PAHs attributable to oil spills, outside of local input, beyond the confines of the harbor. Concentrations were one to ten times below NOAA sediment quality guidelines. Selected metal concentrations were found to be relatively elevated compared to other data collected in the region. However, levels are still very low in the scale of NOAA’s sediment quality guidelines, and therefore appear to pose little or no ecotoxicity threat to biota.Infaunal assessment showed a diverse assemblage with more than 240 taxa recorded and abundances greater than 3,000 animals m-22 in all but a few locations. Annelid worms, crustaceans, snails, and clams were the dominant taxa accounting for 63 %, 19%, 5%, and 7 % respectively of total individuals. Specific benthic community assemblages were identified that were distributed based on depth and water clarity. Species richness and diversity was lower in the eastern end of the bay in the vicinity of the Fox River input. Abundance was also generally lower in the eastern portion of the study area, and in the intertidal areas near Homer. The eastern portions of the bay are stressed by the sediment load from glacial meltwater. Significant toxicity was virtually absent.Conditions at the sites immediately outside the existing Homer Harbor facility did not differ significantly from other subtidal locations in the open Kachemak Bay. The benthic fauna at Port Graham contained a significant number of species not found in Kachemak Bay. Contaminant conditions were variable depending on specific location. Selected metal concentrations were elevated at Port Graham and some were lower relative to Kachemak Bay, probably due to local geology. Some organic contaminants were accumulating at a depositional site.

Description: This report presents the results of a two-year investigation and summary of oceanographic satellite data obtained from multiple operational data providers and sources, spanning years of operational data collection. Long-term summaries of Sea Surface Temperature (SST) and SST fronts, Sea Surface Height Anomalies (SSHA), surface currents, ocean color chlorophyll and turbidity, and winds are provided.Merged satellite oceanographic data revealed information on: (1) seasonal cycles and timing of transition periods; (2) linkages between seasonal effects (warming and cooling), upwelling processes and transport; and (3) nutrient/sediment sources, sinks, and physical limiting factors controlling surface response for Olympic Coast marine environments. These data and information can be used for building relevant hind cast models, ecological forecasts, and regional environmental indices (e.g. upwelling, climate, “hot spot”) on biological distribution and/or response in the PNW.

Description: The Flower Garden Banks National Marine Sanctuary (FGBNMS) is located in the northwestern Gulf of Mexico approximately 180 km south of Galveston, Texas. The sanctuary’s distance from shore combined with its depth (the coral caps reach to within approximately 17 m of the surface) result in limited exposure of this coral reef ecosystem to natural and human-induced impacts compared to other coral reefs of the western Atlantic. In spite of this, the sanctuary still confronts serious impacts including hurricanes events, recent outbreaks of coral disease, an increase in the frequency of coral bleaching and the massive Diadema antillarum die-off during the mid-1980s. Anthropogenic impacts include large vessel anchoring, commercial and recreational fishing, recreational scuba diving, and oil and gas related activities. The FGBNMS was designated in 1992 to help protect against some of these impacts.Basic monitoring and research efforts have been conducted on the banks since the 1970s. Early on, these efforts focused primarily on describing the benthic communities (corals, sponges) and providing qualitative characterizations of the fish community. Subsequently, more quantitative work has been conducted; however, it has been limited in spatial scope. To complement these efforts, the current study addresses the following two goals put forth by sanctuary management: 1) to develop a sampling design for monitoring benthic fish communities across the coral caps; and 2) to obtain a spatial and quantitative characterization of those communities and their associated habitats.

Description: The National Marine Fisheries Service (NMFS) Northeast Fisheries Science Center (NEFSC) Fisheries Sampling Branch (FSB) collects, maintains, and distributes data for scientific and management purposes in the northwest Atlantic Ocean. FSB manages three separate but related observer programs: the Northeast Fisheries Observer Program (NEFOP), the Industry Funded Scallop (IFS) Observer Program, and the At Sea Monitoring (ASM) Program. For the purposes of this manual, “observers” refers to any observer/monitor working for the FSB.In 2011, FSB trained and deployed over 200 observers, provided coverage on a variety of fisheries, and completed over 15,000 sea days. Observed trips are required under many of the region's fishery management plans, and for some fisheries by other federal laws and authorities such as Amendment 16 and Framework 44, Magnuson-Stevens Fishery Conservation and Management Act, Marine Mammal Protection Act, the Endangered Species Act, the and the Sustainable Fisheries Act.The purpose of this guide is to provide FSB observers, as well as end users of NEFSC Observer Program data, with a detailed description of each data field collected. In addition to this manual, the NEFSC Observer Program Biological Sampling and Catch Estimation Manual provides summaries and tables intended to enable observers to quickly determine the correct sampling protocols and methods while at sea.This manual represents a revision of the data forms, collection procedures, and protocols described in the 1996 NEFSC Observer Program Manual. For documentation of other changes see Documentation of changes made to the NEFSC Fisheries Observer Program Manual, 2013.

Description: This report is a result of long-term fish monitoring studies supported by the National Park Service (NPS) at the Virgin Islands National Park since 1988 and is now a joint NPS and NOAA collaboration. Reef fish monitoring data collected from 1988 to 2006 within Virgin Islands National Park (VINP) and adjacent reefs around St. John, U.S. Virgin Islands (USVI) were analyzed to provide information on the status of reef fishes during the monitoring period. Monitoring projects were initiated by the National Park Service (NPS) in the 1980s to provide useful data for evaluation of resources and for development of a long-term monitoring program.Monthly monitoring was conducted at two reef sites (Yawzi Point and Cocoloba Cay) starting in November 1988 for 2.5 years to document the monthly/seasonal variability in reef fish assemblages. Hurricane Hugo (a powerful Category 4 storm) struck the USVI in September 1989 resulting in considerable damage to the reefs around St. John. Abundance of fishes was lower at both sites following the storm, however, a greater effect was observed at Yawzi Point, which experienced a more direct impact from the hurricane. The storm affected species differently, with some showing only small, short-term declines in abundance, and others, such as the numerically abundant blue chromis (Chromis cyanea), a planktivorous damselfish, exhibiting a larger and longer recovery period.This report provides: 1) an evaluation of sampling methods, sample size, and methods used during the sampling period, 2) an evaluation of the spatial and temporal variability in reef fish assemblages at selected reef sites inside and outside of VINP, and 3) an evaluation of trends over 17 years of monitoring at the four reference sites. Comparisons of methods were conducted to standardize assessments among years. Several methods were used to evaluate sample size requirements for reef fish monitoring and the results provided a statistically robust justification for sample allocation.

Description: This report is divided into six sections, the first of which provides information on documents that emphasize the need for education/training of minorities in the sciences including marine science. Also provided is material students can use to find out about careers in the sciences, some universities that offer marine science education, and curricula that should be considered. The second section deals with existing programs designed to train pre-college students and prepare them either for further education or potential employment in the sciences. The next four sections deal with existing programs in the marine sciences for college-level students, scholarships and scholarship programs, examples of loan programs, and internships and internship programs.

Description: The National Status and Trends (NS&T) Program has conducted studies to determine the spatial extent and severity of chemical contamination and associated adverse biological effects in coastal bays and estuaries of the United States since 1991. Sediment contamination in U.S. coastal areas is a major environmental issue because of its potential toxic effects on biological resources and often, indirectly, on human health. Thus, characterizing and delineating areas of sediment contamination and toxicity and demonstrating their effect(s) on benthic living resources are therefore important goals of coastal resource management at NOAA.The National Centers for Coastal Ocean Science, and the Office of National Marine Sanctuaries, in cooperation with the U.S. Geological Survey (USGS), University of California Moss Landing Marine Lab (MLML), and the Monterey Bay Aquarium Research Institute (MBARI), conducted ecosystem monitoring and characterization studies within and between marine sanctuaries along the California coast in 2002 and 2004 on the NOAA RV McArthur. One of the objectives was to perform a systematic assessment of the chemical and physical habitats and associated biological communities in soft bottom habitats on the continental shelf and slope in the central California region. This report addresses the magnitude and extent of chemical contamination, and contaminant transport patterns in the region. Ongoing studies of the benthic community are in progress and will be reported in an integrated assessment of habitat quality and the parameters that govern natural resource distributions on the continental margin and in canyons in the region.

Description: This memorandum has four parts. The first is a review and partial synthesis of Phase 1 and Phase 2 Reports by Dr. Ernest Estevez of the Mote Marine Laboratory to the Board of County Commissioners of Sarasota County, Florida. The review and synthesis emphasizes identification of the most important aspects of the structure of the Myakka system in terms of forcing functions, biological components, and major energy flows. In this context, the dominant primary producers, dominant fish species and food habits, and major environmental variables were of articular interest. A major focus of the review and synthesis was on the river zonations provided in the report and based on salinity and various biological indicators. The second part of this memorandum is a review of a draft report by Mote Marine Laboratory on evaluation of potential water quality impacts on the Myakka River from proposed activities in the watershed. This Memorandum's third part is a review of resource-management related ecosystem models in the context of possible future models of the Myakka River Ecosystem. The final part of this memorandum is proposed future work as an extension of the initial reports.

Description: Coastal and Estuarine Data Archaeology and Rescue Program

Description: In the past decade, increased awareness regarding the declining condition of U.S. coral reefs has prompted various actions by governmental and non-governmental organizations. Presidential Executive Order 13089 created the U.S. Coral Reef Task Force (USCRTF) in 1998 to coordinate federal and state/territorial activities (Clinton, 1998), and the Coral Reef Conservation Act of 2000 provided Congressional funding for activities to conserve these important ecosystems, including mapping, monitoring and assessment projects carried out through the support of NOAA’s CRCP. Numerous collaborations forged among federal agencies and state, local, non-governmental, academic and private partners now support a variety of monitoring activities. This report shares the results of many of these monitoring activities, relying heavily on quantitative, spatially-explicit data that has been collected in the recent past and comparisons with historical data where possible. The success of this effort can be attributed to the dedication of over 270 report contributors who comprised the expert writing teams in the jurisdictions and contributed to the National Level Activities and National Summary chapters. The scope and content of this report are the result of their dedication to this considerable collaborative effort.Ultimately, the goal of this report is to answer the difficult but vital question: what is the condition of U.S. coral reef ecosystems? The report attempts to base a response on the best available science emerging from coral reef ecosystem monitoring programs in 15 jurisdictions across the country. However, few monitoring programs have been in place for longer than a decade, and many have been initiated only within the past two to five years. A few jurisdictions are just beginning to implement monitoring programs and face challenges stemming from a lack of basic habitat maps and other ecosystem data in addition to adequate training, capacity building, and technical support. There is also a general paucity of historical data describing the condition of ecosystem resources before major human impacts occurred, which limits any attempt to present the current conditions within an historical context and contributes to the phenomenon of shifting baselines (Jackson, 1997; Jackson et al., 2001; Pandolfi et al., 2005).

Description: The Biogeography Branch’s Sampling Design Tool for ArcGIS provides a means to effectively develop sampling strategies in a geographic information system (GIS) environment. The tool was produced as part of an iterative process of sampling design development, whereby existing data informs new design decisions. The objective of this process, and hence a product of this tool, is an optimal sampling design which can be used to achieve accurate, high-precision estimates of population metrics at a minimum of cost. Although NOAA’s Biogeography Branch focuses on marine habitats and some examples reflects this, the tool can be used to sample any type of population defined in space, be it coral reefs or corn fields.

Description: Land-based pollution is commonly identified as a major contributor to the observed deterioration of shallow-water coral reef ecosystem health. Human activity on the coastal landscape often induces nutrient enrichment, hypoxia, harmful algal blooms, toxic contamination and other stressors that have degraded the quality of coastal waters. Coral reef ecosystems throughout Puerto Rico, including Jobos Bay, are under threat from coastal land uses such as urban development, industry and agriculture. The objectives of this report were two-fold: 1. To identify potentially harmful land use activities to the benthic habitats of Jobos Bay, and 2. To describe a monitoring plan for JobosBay designed to assess the impacts of conservation practices implemented on the watershed.This characterization is a component of the partnership between the U.S. Department of Agriculture (USDA) and the National Oceanic and Atmospheric Administration (NOAA) established by the Conservation Effects Assessment Project (CEAP) in Jobos Bay. CEAP is a multi-agency effort to quantify the environmental benefits of conservation practices used by private landowners participating in USDA programs. The Jobos Bay watershed, located in southeastern Puerto Rico, was selected as the first tropical CEAP Special Emphasis Watershed (SEW). Both USDA and NOAA use their respective expertise in terrestrial and marine environments to model and monitor Jobos Bay resources.This report documents NOAA activities conducted in the first year of the three-year CEAP effort in Jobos Bay. Chapter 1 provides a brief overview of the project and background information on Jobos Bay and its watershed. Chapter 2 implements NOAA’s Summit to Sea approach to summarize the existing resource conditions on the watershed and in the estuary. Summit to Sea uses a GIS-based procedure that links patterns of land use in coastal watersheds to sediment and pollutant loading predictions at the interface between terrestrial and marineenvironments. The outcome of Summit to Sea analysis is an inventory of coastal land use and predicted pollution threats, consisting of spatial data and descriptive statistics, which allows for better management of coral reef ecosystems. Chapters 3 and 4 describe the monitoring plan to assess the ecological response to conservationpractices established by USDA on the watershed.Jobos Bay is the second largest estuary in Puerto Rico, but has more than three times the shoreline of any other estuarine area on the island. It is a natural harbor protected from offshore wind and waves by a series of mangrove islands and the Punta Pozuelo peninsula. The Jobos Bay marine ecosystem includes 48 km² of mangrove, seagrass, coral reef and other habitat types that span both intertidal and subtidal areas. Mapping of Jobos Bay revealed 10 different benthic habitats of varying prevalence, and a large area of unknown bottom type covering 38% of the entire bay. Of the known benthic habitats, submerged aquatic vegetation, primarily seagrass, is the most common bottom type, covering slightly less than 30% of the bay. Mangroves are the dominant shoreline feature, while coral reefs comprise only 4% of the total benthic habitat. However, coral reefs are some of the most productive habitats found in Jobos Bay, and provide important habitat and nursery grounds for fish and invertebrates of commercial and recreational value.

Description: Conservation Effects Assessment Project, in partnership with U.S. Department of Agriculture

Description: Hurricanes can cause extensive damage to the coastline and coastal communities due to wind-generated waves and storm surge. While extensive modeling efforts have been conducted regarding storm surge, there is far less information about the effects of waves on these communities and ecosystems as storms make landfall. This report describes a preliminary use of NCCOS’ WEMo (Wave Exposure Model; Fonseca and Malhotra 2010) to compute the wind wave exposure within an area of approximately 25 miles radius from Beaufort, North Carolina for estuarine waters encompassing Bogue Sound, Back Sound and Core Sound during three hurricane landfall scenarios. The wind wave heights and energy of a site was a computation based on wind speed, direction, fetch and local bathymetry. We used our local area (Beaufort, North Carolina) as a test bed for this product because it is frequently impacted by hurricanes and we had confidence in the bathymetry data. Our test bed conditions were based on two recent Hurricanes that strongly affected this area. First, we used hurricane Isabel which made landfall near Beaufort in September 2003. Two hurricane simulations were run first by passing hurricane Isabel along its actual path (east of Beaufort) and second by passing the same storm to the west of Beaufort to show the potential effect of the reversed wind field. We then simulated impacts by a hurricane (Ophelia) with a different landfall track, which occurred in September of 2005. The simulations produced a geographic description of wave heights revealing the changing wind and wave exposure of the region as a consequence of landfall location and storm intensity. This highly conservative simulation (water levels were that of low tide) revealed that many inhabited and developed shorelines would receive wind waves for prolonged periods of time at heights far above that found during even the top few percent of non-hurricane events. The simulations also provided a sense for how rapidly conditions could transition from moderate to highly threatening; wave heights were shown to far exceed normal conditions often long before the main body of the storm arrived and importantly, at many locations that could impede and endanger late-fleeing vessels seeking safe harbor. When joined with other factors, such as storm surge and event duration, we anticipate that the WEMo forecasting tool will have significant use by local emergency agencies and the public to anticipate the relative exposure of their property arising as a function of storm location and may also be used by resource managers to examine the effects of storms in a quantitative fashion on local living marine resources.

Description: On July 12-15, 2008, researchers and resource managers met in Jupiter, Florida to discuss and review the state of knowledge regarding mesophotic coral ecosystems, develop a working definition for these ecosystems, identify critical resource management information needs, and develop a Mesophotic Coral Ecosystems Research Strategy to assist the U.S. National Oceanic and Atmospheric Administration (NOAA) and other agencies and institutions in their research prioritization and strategic planning for mesophotic coral ecosystems. Workshop participants included representatives from international, Federal, and state governments; academia; and nongovernmental organizations. The Mesophotic Coral Ecosystems Workshop was hosted by the Perry Institute for Marine Science (PIMS) and organized by NOAA and the U.S. Geological Survey (USGS). The workshop goals, objectives, schedule, and products were governed by a Steering Committee consisting of members from NOAA (National Centers for Coastal Ocean Science’s Center for Sponsored Coastal Ocean Research, the Office of Ocean Exploration and Research’s NOAA Undersea Research Program, and the National Marine Fisheries Service), USGS, PIMS, the Caribbean Coral Reef Institute, and the Bishop Museum.

Description: NOAA Technical Memorandum OAR OER 2

Description: The National Oceanic and Atmospheric Administration (NOAA) National Ocean Service (NOS) initiated a coral reef research program in 1999 to map, assess, inventory, and monitor U.S. coral reef ecosystems (Monaco et al. 2001). These activities were implemented in response to requirements outlined in the Mapping Implementation Plan developed by the Mapping and Information Synthesis Working Group (MISWG) of the Coral Reef Task Force (CRTF) (MISWG 1999). As part of the MISWG of the CRTF, NOS' Biogeography Branch has been charged with the development and implementation of a plan to produce comprehensive digital coral-reef ecosystem maps for all U.S. States, Territories, and Commonwealths within five to seven years. Joint activities between Federal agencies are particularly important to map, research, monitor, manage, and restore coral reef ecosystems. In response to the Executive Order 13089 and the Coral Reef Conservation Act of 2000, NOS is conducting research to digitally map biotic resources and coordinate a long-term monitoring program that can detect and predict change in U.S. coral reefs, and their associated habitats and biological communities.Most U.S. coral reef resources have not been digitally mapped at a scale or resolution sufficient for assessment, monitoring, and/or research to support resource management. Thus, a large portion of NOS' coral reef research activities has focused on mapping of U.S. coral reef ecosystems. The map products will provide the fundamental spatial organizing framework to implement and integrate research programs and provide the capability to effectively communicate information and results to coral reef ecosystem managers. Although the NOS coral program is relatively young, it has had tremendous success in advancing towards the goal to protect, conserve, and enhance the health of U.S. coral reef ecosystems. One objective of the program was to create benthic habitat maps to support coral reef research to enable development of products that support management needs and questions. Therefore this product was developed in collaboration with many U.S. Pacific Territory partners. An initial step in producing benthic habitat maps was the development of a habitat classification scheme. The purpose of this document is to outline the benthic habitat classification scheme and protocols used to map American Samoa, Guam and the Commonwealth of the Northern Mariana Islands.Thirty-two distinct benthic habitat types (i.e., four major and 14 detailed geomorphological structure classes; eight major and 18 detailed biological cover types) within eleven zones were mapped directly into a geographic information system (GIS) using visual interpretation of orthorectified IKONOS satellite imagery. Benthic features were mapped that covered an area of 263 square kilometers. In all, 281 square kilometers of unconsolidated sediment, 122 square kilometers of submerged vegetation, and 82.3 square kilometers of coral reef and colonized hardbottom were mapped.

Description: Perhaps the most difficult job of the ecotoxicologist is extrapolating data calculated from laboratory experiments with high precision and accuracy into the real world of highly-dynamics aquatic environments. The establishment of baseline laboratory toxicity testing data for individual compounds and ecologically important and field studies serve as a precursor to ecosystem level studies needed for ecological risk assessment. The first stage in the field portion of risk assessment is the determination of actual environmental concentrations of the contaminant being studied and matching those concentrations with laboratory toxicity tests. Risk estimates can be produced via risk quotients that would determine the probability that adverse effects may occur.In this first stage of risk assessment, environmental realism is often not achieved. This is due, in part, to the fact that single-species laboratory toxicity tests, while highly controlled, do not account for the complex interactions (Chemical, physical, and biological) that take place in the natural environment. By controlling as many variables in the laboratory as possible, an experiment can be produced in such a fashion that real effects from a compound can be determined for a particular test organism. This type of approach obviously makes comparison with real world data most difficult. Conversely, field oriented studies fall short in the interpretation of ecological risk assessment because of low statistical power, lack of adequate replicaiton, and the enormous amount of time and money needed to perform such studies. Unlike a controlled laboratory bioassay, many other stressors other than the chemical compound in question affect organisms in the environment. These stressors range from natural occurrences (such as changes in temperature, salinity, and community interactions) to other confounding anthropogenic inputs. Therefore, an improved aquatic toxicity test that will enhance environmental realism and increase the accuracy of future ecotoxicological risk assessments is needed.

Description: Estuaries provide critical nursery habitat for many commercially and recreationally important fish and shellfish species. These productive, diverse ecosystems are particularly vulnerable to pollution because they serve as repositories for non–point-source contaminants from upland sources, such as pesticide runoff. Atrazine, among the most widely used pesticides in the United States, has also been one of the most extensively studied. There has not, however, been a specific assessment of atrazine in marine and estuarine ecosystems. This document characterizes the presence and transformation of atrazine in coastal waters, and the effects of atrazine on marine organisms. Review of marine and estuarine monitoring data indicate that atrazine is chronically present in U.S. coastal waters at relatively low concentrations. The concentrations detected have typically been below acute biological effects levels, and below the U.S. EPA proposed water quality criteria for atrazine. While direct risk of atrazine impacts are low, uncertainty remains regarding the effects of long-term low levels of atrazine in mixture with other contaminants. It is recommended that best management practices, such as the use of vegetative buffers and public education about pesticide use, be encouraged in the coastal zone to minimize runoff of atrazine into marine and estuarine waters.

Description: Marine mammals, such as dolphins, can serve as key indicator species in coastal areas by reflecting the effects of natural and anthropogenic stressors. As such they are often considered sentinels of environmental and ecosystem health (Bossart 2006; Wells et al. 2004; Fair and Becker 2000). The bottlenose dolphin is an apex predator and a key component of many estuarine environments in the southeastern United States (Woodward-Clyde Consultants 1994; SCDNR 2005). Health assessments of dolphins areespecially critical in areas where populations are depleted, show signs of epidemic disease and/or high mortality and/or where habitat is being altered or impacted by human activities.Recent assessments of environmental conditions in the Indian River Lagoon, Florida (IRL) and the estuarine waters surrounding Charleston, South Carolina (CHS) highlightthe need for studies of the health of local bottlenose dolphins. While the condition of southeastern estuaries was rated as fair in the National Coastal Condition Report (U.S.EPA 2001), it was noted that the IRL was characterized by poorer than expected benthic communities, significant sediment toxicity and increased nutrient concentrations.Similarly, portions of the CHS estuary have sediment concentrations of aliphatic aromatic hydrocarbons, select inorganic metals, and some persistent pesticides far in excess of reported bioeffect levels (Hyland et al. 1998). Long-term trends in water quality monitoring and recent scientific research suggest that waste load assimilation, non-point source runoff impacts, contaminated sediments, and toxic pollutants are key issues in the CHS estuary system. Several ‘hot spots’ with high levels of heavy metals and organic compounds have been identified (Van Dolah et al. 2004). High concentrations of anthropogenic trace metals, polychlorinated biphenyls (PCB’s) and pesticides have been found in the sediments of Charleston Harbor, as well as the Ashley and Cooper Rivers (Long et al. 1998). Two superfund sites are located within the CHS estuary and the key contaminants of concern associated with these sites are: polycyclic aromatic hydrocarbons (PAH), lead, chromium, copper, arsenic, zinc and dioxin.Concerns related to the overall health of IRL dolphins and dermatologic disease observed in many dolphins in the area (Bossart et al. 2003) initiated an investigation of potential factors which may have impacted dolphin health. From May-August 2001, 35 bottlenose dolphins died in the IRL during an unusual mortality event (MMC 2003). Many of these dolphins were diagnosed with a variety of skin lesions including proliferative ulcerative dermatitis due to protozoa and fungi, dolphin pox and a vesicular dermatopathy of unknown etiology (Bossart et al. 2003). Multiple species from fish to dolphins in the IRL system have exhibited skin lesions of various known and unknown etiologies (Kane et al. 2000; Bossart et al. 2003; Reif et al. 2006). On-going photo-identification (photo-ID)studies have documented skin diseases in IRL dolphins (Mazzoil et al. 2005). In addition, up to 70% of green sea turtles in the IRL exhibit fibropapillomas, with the highest rates of occurrence being seen in turtles from the southern IRL (Hirama 2001).

Description: High salinity estuaries in the southeastern U.S. have experienced increased inputs of contaminants from nonpoint source (NPS) urban runoff and decreases in habitat due tofilling of wetlands and dock/bulkhead construction. Urbanization may pose significant risks to estuarine fauna, particularly crustaceans. The grass shrimp of the genusPalaemonetes, is one of the dominant species found in estuarine tidal creeks, accounting for greater than 50% of all macropelagic fauna on an annual basis. Spatial analytical and geographic information system techniques were used to determine which factors influenced the Palaemonetes population structures in a South Carolina bar-built estuary surrounded by urban development. Impacts from land use practices were investigated using concentric circular buffers around study sites. Factors investigated included sediment-associated polycyclic aromatic hydrocarbons concentration, land use classification, percent impervious surfaces, and other selected urban factors. Geographic information system and statistical modeling showed quantitative relationships betweenland use class and impacts on Palaemonetes density. The study suggests that habitat loss is a major factor influencing grass shrimp densities. Multiple regression modeling suggests a significant relationship between habitat alterations and Palaemonetes densities.

Description: In March-April 2004, the National Oceanic and Atmospheric Administration (NOAA), U.S. Environmental Protection Agency (EPA), and State of Florida (FL) conducted a study to assessthe status of ecological condition and stressor impacts throughout the South Atlantic Bight (SAB) portion of the U.S. continental shelf and to provide this information as a baseline for evaluating future changes due to natural or human-induced disturbances. The boundaries of thestudy region extended from Cape Hatteras, North Carolina to West Palm Beach, Florida and from navigable depths along the shoreline seaward to the shelf break (~100m). The studyincorporated standard methods and indicators applied in previous national coastal monitoring programs — Environmental Monitoring and Assessment Program (EMAP) and National Coastal Assessment (NCA) — including multiple measures of water quality, sediment quality, andbiological condition. Synoptic sampling of the various indicators provided an integrative weight-of-evidence approach to assessing condition at each station and a basis for examining potential associations between presence of stressors and biological responses. A probabilisticsampling design, which included 50 stations distributed randomly throughout the region, was used to provide a basis for estimating the spatial extent of condition relative to the various measured indicators and corresponding assessment endpoints (where available).Conditions of these offshore waters are compared to those of southeastern estuaries, based on data from similar EMAP/NCA surveys conducted in 2000-2004 by EPA, NOAA, and partnering southeastern states (Florida, Georgia, South Carolina, North Carolina, Virginia) (NCA database for estuaries, EPA Gulf Ecology Division, Gulf Breeze FL). Data from a total of 747 estuarine stations are included in this database. As for the offshore sites, the estuarine samples were collected using standard methods and indicators applied in previous coastal EMAP/NCA surveys including the probabilistic sampling design and multiple indicators of water quality, sediment quality, and biological condition (benthos and fish).The majority of the SAB had high levels of DO in near-bottom water (〉 5 mg L-1) indicative of "good" water quality. DO levels in bottom waters exceeded this upper threshold at all sites throughout the coastal-ocean survey area and in 76% of estuarine waters. Twenty-one percent ofestuarine bottom waters had moderate levels of DO between 2 and 5 mg L-1 and 3% had DO levels below 2 mg L-1. The majority of sites with DO in the low range considered to be hypoxic (〈 2 mg L-1) occurred in North Carolina estuaries. There also was a notable concentration of stations with moderate DO levels (2 – 5 mg L-1) in Georgia and South Carolina estuaries.Approximately 58% of the estuarine area had moderate levels of chlorophyll a (5-10 μg L-1) and about 8% of the area had higher levels, in excess of 10 μg L-1, indicative of eutrophication. The elevated chlorophyll a levels appeared to be widespread throughout the estuaries of the region.In contrast, offshore waters throughout the region had relatively low levels of chlorophyll a with 100% of the offshore survey area having values 〈 5 μg L-1.

Description: EPA 600/R-10/046

Description: This Handbook has been prepared to inform you of the National Ocean Service’s history, philosophy, policies, and expectations of you and the NOS.No volunteer handbook can answer every question, so we hope through regular conversations between you and your supervisor we can continue to add to the Handbook as conditions warrant. We hope this Handbook will help you feel comfortable with us. We depend on you in an ever shrinking workforce - your success is our success. Please do not hesitate to ask questions. Your direct supervisor or Volunteer Coordinator will gladly answer them.We ask that you read this Handbook carefully, and refer to it whenever questions arise. The NOS policies, benefits and rules, as explained herein, may be changed from time to time as business, volunteer legislation, and economic conditions dictate. If and when changes are made, you will be made aware of the changes.

Description: Ghost shrimp and mud shrimp in the decapod infraorder Thalassinidea are ecologically important members of manybenthic intertidal and shallow subtidal infaunal communities, largely due to the sediment filtration and mixing that result from their burrowing and feeding behavior. These activities considerably modify their immediate environment and have made these cryptic animals extremely interesting to scientists in terms of their behavior, ecology, and classification.Over 20 years ago, seven species of thalassinideans were known from the South Atlantic Bight (Cape Hatteras, NC to Cape Canaveral, FL). During this study, the examinationof extensive collections from the National Museum of Natural History (NMNH), the Southeastern Regional Taxonomic Center (SERTC), and regional institutions, resultedin the identification of 14 species of thalassinideanscurrently known to occur within this region. The family Axiidae is represented by three species: Axius armatus, Calaxius jenneri, and Paraxiopsis gracilimana; the Callianassidae by six: Biffarius biformis, B. cf. fragilis, Callichirus major, Cheramus marginatus, Gilvossius setimanus, and Necallianassa berylae; the Calocarididae by two: Calocaris templemani and Acanthaxius hirsutimanus; andthe families Laomediidae, Thomassiniidae, and Upogebiidae are each represented by one: Naushonia crangonoides, Crosniera wennerae, and Upogebia affinis, respectively. Anillustrated key is presented for species level identification and supplemental notes on the ecology, distribution, and taxonomy of the species are provided.(PDF file contains 38 pages.)

Description: Pelagic juvenile rockfish (Sebastes spp.) collected in surveys designed to assess juvenile salmonids and other species in the Gulf of Alaska in 1998 and 2000–2003provide an opportunity to document the occurrence of the pelagic juveniles of several species of rockfish. Often, species identification of rockfish is difficult or impossible at this stage of development (~20 to 60 mm),and few species indigenous to Alaska waters have been described. Use of mitochondrial DNA markers for rockfish species allowed unequivocal identification of ten species (S. aleutianus, S. alutus, S. borealis, S. entomelas, S.flavidus, S. melanops, S. pinniger, S. proriger, S. reedi, and S. ruberrimus) in subsamples from the collections. Other specimens were genetically assignable to groups of two or three species. Sebastes borealis, S. crameri, and S. reedi were identified using morphological data. Combining genetic and morphological data allowed successful resolution of the other species as S. emphaeus, probably S. ciliatus (although S. polyspinis cannot be totally ruled out), and S. polyspinis. Many specimens were initially morphologically indistinguishable from S. alutus, and several morphological groups included fish geneticallyidentified as S. alutus. This paper details the characteristics of these pelagic juveniles to facilitate morphological identification of these species in future collections. (PDF file contains 32 pages.)

Description: This publication of the NOAA Professional Paper NMFS Seriesis the product of a special symposium on “Emerging Technologies for Reef Fisheries Research and Management” held during the 56th annual Gulf and Caribbean Fisheries Institute meeting in Tortola, British Virgin Islands, November 2003. The purpose of this collection is to highlight the diversity of questions and issues in reeffisheries management that are benefiting from applications of technology. Topics cover a wide variety of questions and issues from the study of individual behavior, distribution and abundance of groups and populations, and associations between habitats and fish and shellfish species.(PDF files contains 124 pages.)

Description: This atlas presents information on fish eggs and temperature data collected from broadscale ichthyoplankton surveys conducted off the U.S. northeast coast from ]977 to1987. Distribution and abundance information is provided for 33 taxa in the form of graphs and contoured egg-density maps by month and survey. Comments are included on interannual and interseasonal trends in spawning intensity. Data on 14 additional but less numerous taxa are provided in tabular form. (PDF file contains 316 pages.)

Description: Identification problems are common for many sharks due to a general lack of meristic characteristics that are typicallyuseful for separating species. Other than number of vertebrae and number and shape of teeth, identifications are frequently based on external features that are often shared among species. Identification problems in the field are most prevalent when live specimens are captured and releasing them with a minimum of stress is a priority (e.g., shark tagging programs). Identifications mustbe accurate and conducted quickly but this can be challenging, especially if specimens are very active or too large to be landed without physical damage. This field guide was designed primarily for use during field studies and presents a simplified method for identifying the 21 species of western North Atlantic Ocean sharks belonging to the family Carcharhinidae (carcharhinids). To assist with identifications a dichotomous key to Carcharhinidae was developed, and for the more problematic Carcharhinus species (12 species), separation sheets based on importantdistinguishing features were constructed. Descriptive text and illustrations provided in the species accounts were developed from field observations, photographs, andpublished references. (PDF file contains 36 pages.)

Description: Information on the biology, fishery resources, explotiation patterns, management, and conservation status of two species of grouper-the Nassau grouper, Epinephelus striatus, and the jewfish, Epinephelus itajara-is compiled, reviewed, and analyzed. (PDF file contains 68 pages.)

Description: An investigation was conducted into the deaths of more than 220 bottlenose dolphins (Tursiops truncatus) that occurred within the coastal bay ecosystem of mid-Texas between January and May 1992. The high mortality rate was unusual in that it was limited to a relatively small geographical area, occurred primarily within an inshore bay system separated from the Gulf of Mexico by barrier islands, and coincided with deaths of other taxa including birds and fish. Factors examined to determine the potential causes of the dolphin mortalities included microbial pathogens, natural biotoxins, industrial pollutants, other environmental contaminants, and direct human interactions. Emphasis was placed on nonpoint source pesticide runoff from agricultural areas, which had resulted from record rainfall that occurred during the period of increased mortality.Analytical results from sediment, water, and biota indicated that biotoxins, trace metals, and industrial chemical contamination were not likely causative factors in this mortality event. Elevated concentrations of pesticides (atrazine and aldicarb) were detected in surface water samples from bays within the region, and bay salinities were reduced to 〈10 ppt from December 1991 through April 1992 due to record rainfall and freshwater runoff exceeding any levels since 1939. Prolonged exposure to low salinity could have played a significant role in the unusual mortalities because low salinity exposure may cause disruption of the permeability barrier in dolphin skin. The lack of established toxicity data for marine mammals, particularly dermal absorption and bioaccumulation, precludes accurate toxicological interpretation of results beyond a simple comparison to terrestrial mammalian models. Results clearly indicated that significant periods of agricultural runoff and accompanying low salinities co-occurred with the unusual mortality event in Texas, but no definitive cause of the mortalities was determined. (PDF file contains 25 pages.)

Description: This cruise report is a summary of a field survey conducted in coastal-ocean waters of the Mid-Atlantic Bight from Nags Head, North Carolina to Cape Cod, Massachusetts and from approximately 1 nautical mile (nm) of shore seaward to the shelf break (100 m). The survey was conducted May 12 - May 21, 2006 on NOAA Ship NANCY FOSTER Cruise NF-06-06-NCCOS. Multiple indicators of ecological condition were sampled synoptically at each of 49 stations throughout the region using a random probabilistic sampling design. Samples were collected for the analysis of benthic community structure and composition; concentrations of chemical contaminants (metals, pesticides, PAHs, PCBs, PBDEs) in sediments and target demersal biota; nutrient and chlorophyll levels in the water column; and other basic habitat characteristics such as depth, salinity, temperature, dissolved oxygen, pH, sediment grain size, and organic carbon content. The overall purpose of the survey was to collect data to assess the status of ecological condition in coastal-ocean waters of the region, based on these various indicators, and to provide this information as a baseline for determining how environmental conditions may be changing with time. The results will be of value in helping to broaden our understanding of the status of ecological resources and their controlling factors, including impacts of potential ecosystem stressors, in such strategic coastal areas. (18pp.) (PDF contains 24 pages)

Description: Center for Coastal Environmental Health and Biomolecular Research

Description: Executive Summary:The western National Coastal Assessment (NCA-West) program of EPA, in conjunction with the NOAA National Ocean Service (NOS), conducted an assessment of the status of ecological condition of soft sediment habitats and overlying waters along the western U.S. continental shelf, between the target depths of 30 and 120 m, during June 2003. NCA-West and NOAA/NOS partnered with the West Coast states(Washington (WA), Oregon (OR), and California (CA)), and the Southern California Coastal Water Research Project (SCCWRP) Bight ’03 program to conduct the survey. A total of 257 stations were sampled from Cape Flattery, WA to the Mexican border using standard methods and indicators applied in previous coastal NCA projects. A key study feature was the incorporation of a stratified-random sampling design with stations stratified by state and National Marine Sanctuary (NMS) status. Each of the threestates was represented by at least 50 random stations. There also were a total of 84 random stations located within NOAA’s five NMSs along the West Coast including theOlympic Coast NMS (OCNMS), Cordell Bank NMS (CBNMS), Gulf of Farallones NMS (GFNMS), Monterey Bay NMS (MBNMS), and Channel Islands NMS (CINMS). Collection of flatfish via hook-and-line for fish-tissue contaminant analysis wassuccessful at 50 EMAP/NCA-West stations. Through a collaboration developed with the FRAM Division of the Northwest Fisheries Science Center, fish from an additional 63 stations in the same region and depth range were also analyzed for fish-tissue contaminants. Bottom depth throughout the region ranged from 28 m to 125 m for most stations. Two slightly deeper stations from the Southern California Bight (SCB) (131, 134 m) were included in the data set. About 44% of the survey area had sediments composed of sands (〈 20% silt-clay), about 47% was composed of intermediate muddy sands (20-80% silt-clay), and about 9% was composed of muds (〉 80% silt-clay). The majority ofthe survey area (97%) had relatively low percent total organic carbon (TOC) levels of 〈 2%, while a small portion (〈 1%) had high TOC levels (〉 5%), in a range potentiallyharmful to benthic fauna.Salinity of surface waters for 92% of the survey area were 〉 31 psu, with most stations 〈 31 psu associated with the Columbia River plume. Bottom salinities ranged only between 31.6 and 34.4 psu. There was virtually no difference in mean bottom salinities among states or between NMS and non-NMS stations. Temperatures of surface water (range 8.5 -19.9 °C) and bottom water (range 5.8 -14.7 °C) averagedseveral degrees higher in CA in comparison to WA and OR. The Δσt index of watercolumn stratification indicated that about 31% of the survey area had strong verticalstratification of the water column. The index was greatest for waters off WA and lowest for CA waters.Only about 2.6 % of the survey area had surface dissolved oxygen (DO) concentrations ≤ 4.8 mg/L, and there were no values below the lower threshold (2.3 mg/L) considered harmful to the survival and growth of marine animals. Surface DO concentrations were higher in WA and OR waters than in CA, and higher in the OC NMS than in the CA sanctuaries. An estimated 94.3% of the area had bottom-water DO concentrations ≤ 4.8 mg/L and 6.6% had concentrations ≤ 2.3 mg/L. The high prevalence of DO from 2.3 to 4.8 mg/L (85% of survey area) is believed to beassociated with the upwelling of naturally low DO water across the West Coast shelf.Mean TSS and transmissivity in surface waters (excluding OR due to sample problems) were slightly higher and lower, respectively, for stations in WA than for those in CA. There was little difference in mean TSS or transmissivity between NMS and non-NMS locations. Mean transmissivity in bottom waters, though higher in comparison to surface waters, showed little difference among geographic regions or between NMS and non-NMS locations.Concentrations of nitrate + nitrite, ammonium, total dissolved inorganic nitrogen (DIN) and orthophosphate (P) in surface waters tended to be highest in CA compared toWA and OR, and higher in the CA NMS stations compared to CA non-sanctuary stations. Measurements of silicate in surface waters were limited to WA and CA (exclusive of the SCB) and showed that concentrations were similar between the twostates and approximately twice as high in CA sanctuaries compared to OCNMS or nonsanctuary locations in either state. The elevated nutrient concentrations observed atCA NMS stations are consistent with the presence of strong upwelling at these sites at the time of sampling. Approximately 93% of the area had DIN/P values ≤ 16, indicative of nitrogen limitation. Mean DIN/P ratios were similar among the three states, although the mean for the OCNMS was less than half that of the CA sanctuaries or nonsanctuary locations. Concentrations of chlorophyll a in surface waters ranged from 0 to 28 μg L-1, with 50% of the area having values 〈 3.9 μg L-1 and 10% having values 〉14.5 μg L-1. The mean concentration of chlorophyll a for CA was less than half that of WA and OR locations, and concentrations were lowest in non-sanctuary sites in CA andhighest at the OCNMS.Shelf sediments throughout the survey area were relatively uncontaminated with the exception of a group of stations within the SCB. Overall, about 99% of the total survey area was rated in good condition (〈5 chemicals measured above corresponding effect range low (ERL) concentrations). Only the pesticides 4,4′-DDE and total DDT exceeded corresponding effect range-median (ERM) values, all at stations in CA near Los Angeles. Ten other contaminants including seven metals (As, Cd, Cr, Cu, Hg, Ag, Zn), 2-methylnaphthalene, low molecular weight PAHs, and total PCBs exceeded corresponding ERLs. The most prevalent in terms of area were chromium (31%), arsenic (8%), 2-methylnaphthalene (6%), cadmium (5%), and mercury (4%). Thechromium contamination may be related to natural background sources common to the region. The 2-methylnaphthalene exceedances were conspicuously grouped around the CINMS. The mercury exceedances were all at non-sanctuary sites in CA, particularly in the Los Angeles area.Concentrations of cadmium in fish tissues exceeded the lower end of EPA’s non-cancer, human-health-risk range at nine of 50 EMAP/NCA-West and nine of 60 FRAM groundfish-survey stations, including a total of seven NMS stations in CA and two in the OCNMS. The human-health guidelines for all other contaminants were only exceeded for total PCBs at one station located in WA near the mouth of the Columbia River.Benthic species richness was relatively high in these offshore assemblages, ranging from 19 to 190 taxa per 0.1-m2 grab and averaging 79 taxa/grab. The high species richness was reflected over large areas of the shelf and was nearly three times greater than levels observed in estuarine samples along the West Coast (e.g NCA-Westestuarine mean of 26 taxa/grab). Mean species richness was highest off CA (94 taxa/grab) and lower in OR and WA (55 and 56 taxa/grab, respectively). Mean species richness was very similar between sanctuary vs. non-sanctuary stations for both the CA and OR/WA regions. Mean diversity index H′ was highest in CA (5.36) and lowest in WA (4.27). There were no major differences in mean H′ between sanctuary vs. nonsanctuary stations for both the CA and OR/WA regions.A total of 1,482 taxa (1,108 to species) and 99,135 individuals were identified region-wide. Polychaetes, crustaceans and molluscs were the dominant taxa, both bypercent abundance (59%, 17%, 12% respectively) and percent species (44%, 25%, 17%, respectively). There were no major differences in the percent composition of benthic communities among states or between NMSs and corresponding non-sanctuary sites. Densities averaged 3,788 m-2, about 30% of the average density for West Coast estuaries. Mean density of benthic fauna in the present offshore survey, averaged by state, was highest in CA (4,351 m-2) and lowest in OR (2,310 m-2). Mean densities were slightly higher at NMS stations vs. non-sanctuary stations for both the CA and OR/WA regions.The 10 most abundant taxa were the polychaetes Mediomastus spp., Magelona longicornis, Spiophanes berkeleyorum, Spiophanes bombyx, Spiophanes duplex, and Prionospio jubata; the bivalve Axinopsida serricata, the ophiuroid Amphiodia urtica, the decapod Pinnixa occidentalis, and the ostracod Euphilomedes carcharodonta. Mediomastus spp. and A. serricata were the two most abundant taxa overall. Although many of these taxa have broad geographic distributions throughout the region, the same species were not ranked among the 10 most abundant taxa consistently across states. The closest similarities among states were between OR and WA. At least half of the 10 most abundant taxa in NMSs were also dominant in corresponding nonsanctuary waters.Many of the abundant benthic species have wide latitudinal distributions along the West Coast shelf, with some species ranging from southern CA into the Gulf of Alaska or even the Aleutians. Of the 39 taxa on the list of 50 most abundant taxa that could be identified to species level, 85% have been reported at least once from estuaries of CA, OR, or WA exclusive of Puget Sound. Such broad latitudinal and estuarine distributions are suggestive of wide habitat tolerances.Thirteen (1.2%) of the 1,108 identified species are nonindigenous, with another 121 species classified as cryptogenic (of uncertain origin), and 208 species unclassified with respect to potential invasiveness. Despite uncertainties of classification, the number and densities of nonindigenous species appear to be much lower on the shelf than in the estuarine ecosystems of the Pacific Coast. Spionid polychaetes and the ampharetid polychaete Anobothrus gracilis were a major component of thenonindigenous species collected on the shelf.NOAA’s five NMSs along the West Coast of the U.S. appeared to be in good ecological condition, based on the measured indicators, with no evidence of major anthropogenic impacts or unusual environmental qualities compared to nearby nonsanctuary waters. Benthic communities in sanctuaries resembled those in corresponding non-sanctuary waters, with similarly high levels of species richness and diversity and low incidence of nonindigenous species. Most oceanographic features were also similar between sanctuary and non-sanctuary locations. Exceptions (e.g., higher concentrations of some nutrients in sanctuaries along the CA coast) appeared to be attributable to natural upwelling events in the area at the time of sampling. In addition, sediments within the sanctuaries were relatively uncontaminated, with none of the samples having any measured chemical in excess of ERM values. The ERL valuefor chromium was exceeded in sediments at the OCNMS, but at a much lower percentage of stations (four of 30) compared to WA and OR non-sanctuary areas (31 of 70 stations). ERL values were exceeded for arsenic, cadmium, chromium, 2-methylnaphthalene, low molecular weight PAHs, total DDT, and 4,4′-DDE at multiple sites within the CINMS. However, cases where total DDT, 4,4′-DDE, and chromium exceeded the ERL values were notably less prevalent at CINMS than in non-sanctuary waters of CA. In contrast, 2-methylnaphthalene above the ERL was much more prevalent in sediments at the CINMS compared to non-sanctuary waters off the coast ofCA. While there are natural background sources of PAHs from oil seeps throughout the SCB, this does not explain the higher incidence of 2-methylnaphthalene contaminationaround CINMS. Two stations in CINMS also had levels of TOC (〉 5%) potentially harmful to benthic fauna, though none of these sites exhibited symptoms of impaired benthic condition.This study showed no major evidence of extensive biological impacts linked to measured stressors. There were only two stations, both in CA, where low numbers of benthic species, diversity, or total faunal abundance co-occurred with high sediment contamination or low DO in bottom water. Such general lack of concordance suggests that these offshore waters are currently in good condition, with the lower-end values of the various biological attributes representing parts of a normal reference range controlled by natural factors. Results of multiple linear regression, performed using full model procedures to test for effects of combined abiotic environmental factors, suggested that latitude and depth had significant influences on benthic variables regionwide. Latitude had a significant inverse influence on all three of the above benthic variables, i.e. with values increasing as latitude decreased (p〈 0.01), while depth had a significant direct influence on diversity (p 〈 0.001) and inverse effect on density (p 〈0.01). None of these variables varied significantly in relation to sediment % fines (at p〈 0.1), although in general there was a tendency for muddier sediments (higher % fines) to have lower species richness and diversity and higher densities than coarser sediments.Alternatively, it is possible that for some of these sites the lower values of benthic variables reflect symptoms of disturbance induced by other unmeasured stressors. Theindicators in this study included measures of stressors (e.g., chemical contaminants, eutrophication) that are often associated with adverse biological impacts in shallower estuarine and inland ecosystems. However, there may be other sources of humaninduced stress in these offshore systems (e.g., bottom trawling) that pose greater risks to ambient living resources and which have not been captured. Future monitoring efforts in these offshore areas should include indicators of such alternative sources ofdisturbance. (137pp.) (PDF contains 167 pages)

Description: U.S. EPA, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Western Ecology Division, Newport OR, 97365; EPA 620/R-08/001,

Description: As part of an ongoing program of benthic sampling and related assessments of sediment quality at Gray’s Reef National Marine Sanctuary (GRNMS) off the coast of Georgia, a survey of soft-bottom benthic habitats was conducted in spring 2005 to characterize condition of macroinfaunal assemblages and levels of chemical contaminants in sediments and biota relative to a baseline survey carried out in spring 2000. Distribution and abundance of macrobenthos were related foremost to sediment type (median particle size, % gravel), which in turn varied according to bottom-habitat mesoscale features (e.g., association with live bottom versus flat or rippled sand areas). Overall abundance and diversity of soft-bottom benthic communities were similar between the two years, though dominance patterns and relative abundances of component species were less repeatable. Seasonal summer pulses of a few taxa (e.g., the bivalve Ervilia sp. A) observed in 2000 were not observed in 2005. Concentrations of chemical contaminants insediments and biota, though detectable in both years, were consistently at low, background levels and no exceedances of sediment probable bioeffect levels or FDA action levels for edible fish or shellfish were observed. Near-bottom dissolved oxygen levels and organic-matter content ofsediments also have remained within normal ranges. Highly diverse benthic assemblages were found in both years, supporting the premise that GRNMS serves as an important reservoir of marine biodiversity. A total of 353 taxa (219 identified to species) were collected during the spring 2005 survey. Cumulatively, 588 taxa (371 identified to species) have been recorded in the sanctuary from surveys in 2000, 2001, 2002, and 2005. Species Accumulation Curves indicate that the theoretical maximum should be in excess of 600 species. Results of this study will be of value in advancing strategic science and management goals for GRNMS, including characterization and long-term monitoring of sanctuary resources and processes, as well as supporting evolving interests in ecosystem-based management of the surrounding South Atlantic Bight (SAB) ecosystem. (PDF contains 46 pages)

Description: Center for Coastal Environmental Health and Biomolecular Research

Description: A study was conducted in October 2006 in the Charleston, South Carolina area to test the movements of three different buoy line types to determine which produced a preferred profile that could reduce the risk of dolphin entanglement. Tests on diamond-braided nylon commonly used in the crab pot fishery were compared with stiffened line of Esterpro and calf types in both shallow and deep water environments using DSTmilli data loggers. Loggers were placed at intervals along the lines to record depth, and thus movements, over a 24 hour period. Three observers viewed video animations and charts created for each of the six trial days from the collected logger data and provided their opinions on the most desirable line type that fit set criteria. A quantitative analysis (ANCOVA) of the data was conducted taking into consideration daily tidal fluctuations and logger movements. Loggers tracking the tides had an r2 value approaching 1.00 and produced little movement other than with the tides. Conversely, r2 values approaching 0.00 were less affected by tidal movement and influenced by currents that cause more erratic movement. Results from this study showed that stiffened line, in particular the medium lay Esterpro type, produced the more desirable profiles that could reduce risk of dolphin entanglement. Combining the observer’s results with the ANCOVA results, Esterpro was chosen nearly 60% of the time as opposed to the nylon line which was only chosen 10% of the time. ANCOVA results showed that the stiffened lines performed better in both the shallow and deep water environments, while the nylon line only performed better during one trial in a deep water set, most probably due to the increased current velocities experienced that day. (58pp.)(PDF contains 68 pages)

Description: Center for Coastal Environmental Health and Biomolecular Research

Description: Summary:The offshore shelf and canyon habitats of the OCNMS (Fig. 1) are areas of high primary productivity and biodiversity that support extensive groundfish fisheries. Recent acoustic surveys conducted in these waters have indicated the presence of hard-bottom substrates believed to harbor unique deep-sea coral and sponge assemblages. Such fauna are often associated with shallow tropical waters, however an increasing number of studies around the world have recorded them in deeper, cold-water habitats in both northern and southern latitudes. These habitats are of tremendous value as sites of recruitment for commercially important fishes. Yet, ironically, studies have shown how the gear used in offshore demersal fishing, as well as other commercial operations on the seafloor, can cause severe physical disturbances to resident benthic fauna. Due to their exposed structure, slow growth and recruitment rates, and long life spans, deep-sea corals and sponges may be especially vulnerable to such disturbances, requiring very long periods to recover. Potential effects of fishing and other commercial operations in such critical habitats, and the need to define appropriate strategies for the protection of these resources, have been identified as a high-priority management issue for the sanctuary.To begin addressing this issue, an initial pilot survey was conducted June 1-12, 2004 at six sites in offshore waters of the OCNMS (Fig. 2, average depths of 147-265 m) to explore for the presence of deep-sea coral/sponge assemblages and to look for evidence of potential anthropogenic impacts in these critical habitats. The survey was conducted on the NOAA Ship McARTHUR-II using the Navy’s Phantom DHD2+2 remotely operated vehicle (ROV), which was equipped with a video camera, lasers, and a manipulator arm for the collection of voucher specimens. At each site, a 0.1-m2 grab sampler also was used to collect samples of sediments for the analysis of macroinfauna (〉 1.0 mm), total organic carbon (TOC), grain size, and chemical contaminants. Vertical profiles of salinity, dissolved oxygen (DO), temperature, and pressure were recorded at each site with a small SeaCat conductivity-temperature-depth (CTD) profiler. Niskin bottles attached to the CTD also obtained near-bottom water samples in support of a companion study of microbial indicators of coral health and general ecological condition across these sites. All samples except the sediment-contaminant samples are being analyzed with present project funds.Original cruise plans included a total of 12 candidate stations to investigate (Fig. 3). However, inclement weather and equipment failures restricted the sampling to half of these sites. In spite of the limited sampling, the work completed was sufficient to address key project objectives and included several significant scientific observations. Foremost, the cruise was successful in demonstrating the presence of target deepwater coral species in these waters. Patches of the rare stony coral Lophelia pertusa, more characteristic of deepwater coral/sponge assemblages in the North Atlantic, were observed for the first time in OCNMS at a site in 271 meters of water. A large proportion of these corals consisted of dead and broken skeletal remains, and a broken gorgonian (soft coral) also was observed nearby. The source of these disturbances is not known. However, observations from several sites included evidence of bottom trawl marks in the sediment and derelict fishing gear (long lines). Preliminary results also support the view that these areas are important reservoirs of marine biodiversity and of value as habitat for demersal fishes. For example, onboard examination of 18 bottom-sediment grabs revealed benthic infaunal species representative of 14 different invertebrate phyla. Twenty-eight species of fishes from 11 families, including 11 (possibly 12) species of ommercially important rockfishes, also were identified from ROV video footage. These initial discoveries have sparked considerable interests in follow-up studies to learn more about the spatial extent of these assemblages and magnitude of potential impacts from commercial-fishing and other anthropogenic activities in the area. It is essential to expand our knowledge of these deep-sea communities and their vulnerability to potential environmental risks in order to determine the most appropriate management strategies.The survey was conducted under a partnership between NOAA’s National Centers for Coastal Ocean Science (NCCOS) and National Marine Sanctuary Program (NMSP) and included scientists from NCCOS, OCNMS, and several other west-coast State, academic, private, and tribal research institutions (see Section 4 for a complete listing of participating scientists). (PDF contains 20 pages)

Description: Center for Coastal Environmental Health and Biomolecular Research

Description: Executive Summary:Baseline characterization of resources is an essential part of marine protected area (MPA) management and is critical to inform adaptive management. Gray’s Reef National Marine Sanctuary (GRNMS) currently lacks adequate characterization of several key resources as identified in the 2006 Final Management Plan. The objectives of this characterization were to fulfill this need by characterizing the bottom fish, benthic features, marine debris, and the relationships among them for the different bottom types within the sanctuary: ledges, sparse live bottom, rippled sand, and flat sand. Particular attention was given to characterizing the different ledge types, their fish communities, and the marine debris associated with them given the importance of this bottom type to the sanctuary.The characterization has been divided into four sections. Section 1 provides a brief overview of the project, its relevance to sanctuary needs, methods of site selection, and general field procedures. Section 2 provides the survey methods, results, discussion, and recommendations for monitoring specific to the benthic characterization. Section 3 describes the characterization of marine debris. Section 4 is specific to the characterization of bottom fish. Field surveys were conducted during August 2004, May 2005, and August 2005. A total of 179 surveys were completed over ledge bottom (n=92), sparse live bottom (n=51), flat sand (n=20), and rippled sand (n=16). There were three components to each field survey: fish counting, benthic assessment, and quantification of marine debris. All components occurred within a 25 x 4 m belt transect. Two divers performed the transect at each survey site. One diver was responsible for identification of fish species, size, and abundance using a visual survey. The second diver was responsible for characterization of benthic features using five randomly placed 1 m2 quadrats, measuring ledge height and other benthic structures, and quantifying marine debris within the entire transect.GRNMS is composed of four main bottom types: flat sand, rippled sand, sparsely colonized live bottom, and densely colonized live bottom (ledges). Independent evaluation of the thematic accuracy of the GRNMS benthic map produced by Kendall et al. (2005) revealed high overall accuracy (93%). Most discrepancies between map and diver classification occurred during August 2004 and likely can be attributed to several factors, including actual map or diver errors, and changes in the bottom type due to physical forces.The four bottom types have distinct physical and biological characteristics. Flat and rippled sand bottom types were composed primarily of sand substrate and secondarily shell rubble. Flat sand and rippled sand bottom types were characterized by low percent cover (0-2%) of benthic organisms at all sites. Although the sand bottom types were largely devoid of epifauna, numerous burrows indicate the presence of infaunal organisms. Sparse live bottom and ledges were colonized by macroalgae and numerous invertebrates, including coral, gorgonians, sponges, and “other” benthic species (such as tunicates, anemones, and bryozoans). Ledges and sparse live bottom were similar in terms of diversity (H’) given the level of classification used here. However, percent cover of benthic species, with the exception of gorgonians, was significantly greater on ledge than on sparse live bottom. Percent biotic cover at sparse live bottom ranged from 0.7-26.3%, but was greater than 10% at only 7 out of 51 sites. Colonization on sparse live bottom is likely inhibited by shifting sands, as most sites were covered in a layer of sediment up to several centimeters thick. On ledge bottom type, percent cover ranged from 0.42-100%, with the highest percent cover at ledges in the central and south-central region of GRNMS.Biotic cover on ledges is influenced by local ledge characteristics. Cluster analysis of ledge dimensions (total height, undercut height, undercut width) resulted in three main categories of ledges, which were classified as short, medium, and tall. Median total percent cover was 97.6%, 75.1%, and 17.7% on tall, medium, and short ledges, respectively. Total percent cover and cover of macroalgae, sponges, and other organisms was significantly lower on short ledges compared to medium and tall ledges, but did not vary significantly between medium and tall ledges. Like sparse live bottom, short ledges may be susceptible to burial by sand, however the results indicate that ledge height may only be important to a certain threshold. There are likely other factors not considered here that also influence spatial distribution and community structure (e.g., small scale complexity, ocean currents, differential settlement patterns, and biological interactions).GRNMS is a popular site for recreational fishing and boating, and there has been increased concern about the accumulation of debris in the sanctuary and potential effects on sanctuary resources. Understanding the types, abundance, and distribution of debris is essential to improving debris removal and education efforts. Approximately two-thirds of all observed debris items found during the field surveys were fishing gear, and about half of the fishing related debris was monofilament fishing line. Other fishing related debris included leaders and spear gun parts, and non-gear debris included cans, bottles, and rope. The spatial distribution of debris was concentrated in the center of the sanctuary and was most frequently associated with ledges rather than at other bottom types. Several factors may contribute to this observation. Ledges are often targeted by fishermen due to the association of recreationally important fish species with this bottom type. In addition, ledges are structurally complex and are often densely colonized by biota, providing numerous places for debris to become stuck or entangled. Analysis of observed boat locations indicated that higher boat activity, which is an indication of fishing, occurs in the center of the sanctuary. On ledges, the presence and abundance of debris was significantly related to observed boat density and physiographic features including ledge height, ledge area, and percent cover. While it is likely that most fishing related debris originates from boats inside the sanctuary, preliminary investigation of ocean current data indicate that currents may influence the distribution and local retention of more mobile items.Fish communities at GRNMS are closely linked to benthic habitats. A list of species encountered, probability of occurrence, abundance, and biomass by habitat is provided. Species richness, diversity, composition, abundance, and biomass of fish all showed striking differences depending on bottom type with ledges showing the highest values of nearly all metrics. Species membership was distinctly separated by bottom type as well, although very short, sparsely colonized ledges often had a similar community composition to that of sparse live bottom. Analysis of fish communities at ledges alone indicated that species richness and total abundance of fish were positively related to total percent cover of sessile invertebrates and ledge height. Either ledge attribute was sufficient to result in high abundance or species richness of fish. Fish diversity (H`) was negatively correlated with undercut height due to schools of fish species that utilize ledge undercuts such as Pareques species. Concurrent analysis of ledge types and fish communities indicated that there are five distinct combinations of ledge type and species assemblage. These include, 1) short ledges with little or no undercut that lacked many of the undercut associated species except Urophycis earlii ; 2) tall, heavily colonized, deeply undercut ledges typically with Archosargus probatocephalus, Mycteroperca sp., and Pareques sp.; 3) tall, heavily colonized but less undercut with high occurrence of Lagodon rhomboides and Balistes capriscus; 4) short, heavily colonized ledges typically with Centropristis ocyurus, Halichoeres caudalis, and Stenotomus sp.; and 5) tall, heavily colonized, less undercut typically with Archosargus probatocephalus, Caranx crysos and Seriola sp.. Higher levels of boating activity and presumably fishing pressure did not appear to influence species composition or abundance at the community level although individual species appeared affected. These results indicate that merely knowing the basic characteristics of a ledge such as total height, undercut width, and percent cover of sessile invertebrates would allow good prediction of not only species richness and abundance of fish but also which particular fish species assemblages are likely to occur there. Comparisons with prior studies indicate some major changes in the fish community at GRNMS over the last two decades although the causes of the changes are unknown.Species of interest to recreational fishermen including Centropristis striata, Mycteroperca microlepis, and Mycteroperca phenax were examined in relation to bottom features, areas of assumed high versus low fishing pressure, and spatial dispersion. Both Mycteroperca species were found more frequently when undercut height of ledges was taller. They often were found together in small mixed species groups at ledges in the north central and southwest central regions of the sanctuary. Both had lower mode size and proportion of fish above the fishery size limit in heavily fished areas of the sanctuary (i.e. high boat density) despite the presence of better habitat in that region. Black sea bass, C. striata, occurred at 98% of the ledges surveyed and appeared to be evenly distributed throughout the sanctuary. Abundance was best explained by a positive relationship with percent cover of sessile biota but was also negatively related to presence of either Mycteroperca species. This may be due to predation by the Mycteroperca species or avoidance of sites where they are present by C. striata.Suggestions for monitoring bottom features, marine debris, and bottom fish at GRNMS are provided at the end of each chapter. The present assessment has established quantitative baseline characteristics of many of the key resources and use issues at GRNMS. The methods can be used as a model for future assessments to track the trajectory of GRNMS resources. Belt transects are ideally suited to providing efficient and quantitative assessment of bottom features, debris, and fish at GRNMS. The limited visibility, sensitivity of sessile biota, and linear nature of ledge habitats greatly diminish the utility of other sampling techniques. Ledges should receive the bulk of future characterization effort due to their importance to the sanctuary and high variability in physical structure, benthic composition, and fish assemblages. (PDF contains 107 pages.)

Description: Center for Coastal Monitoring and Assessment

Description: A series of studies was initiated to assess the condition of benthic macroinfauna and chemical contaminant levels in sediments and biota of the Gray’s Reef National Marine Sanctuary (GRNMS) and nearby shelf waters off the coast of Georgia. Four key objectives of the research are (1) todocument existing environmental conditions within the sanctuary in order to provide a quantitative benchmark for tracking any future changes due to either natural or human disturbances; (2) to examine broader cross-shelf spatial patterns in benthic fauna and sediment contaminantconcentrations and to identify potential controlling factors associated with the observed patterns; (3) to assess any between-year temporal variability in benthic fauna; and (4) to evaluate the importance of benthic fauna as prey for higher trophic levels. Such questions are being addressed to help fulfill long-term science and management goals of the GRNMS. However, it is anticipated that theinformation will be of additional value in broadening our understanding of the surrounding South Atlantic Bight (SAB) ecosystem and in bringing the knowledge to bear on related resourcemanagement issues of the region.We have begun to address the first three of these objectives with data from samples collected in spring 2000 at stations within GRNMS, and in spring 2001 at stations within the sanctuary and along three cross-shelf transects extending from the mouths of Sapelo, Doboy, and Altamaha Sounds out to sanctuary depths (about 17-20 m). This report provides a description of baseline conditions withinthe sanctuary, based on results of the spring 2000 survey (Section II), and uses data from both 2000 and 2001 to examine overall spatial and temporal patterns in biological and chemical variables within the sanctuary and surrounding inner-shelf environment (Section III). (PDF contains 65 pages)

Description: Center for Coastal Environmental Health and Biomolecular Research

Description: The mapping and geospatial analysis of benthic environments are multidisciplinary tasks that have become more accessible in recent years because of advances in technology and cost reductions in survey systems. The complex relationships that exist among physical, biological, and chemical seafloor components require advanced, integrated analysis techniques to enable scientists and others to visualize patterns and, in so doing, allow inferences to be made about benthic processes. Effective mapping, analysis, and visualization of marine habitats are particularly important because the subtidal seafloor environment is not readily viewed directly by eye. Research in benthic environments relies heavily, therefore, on remote sensing techniques to collect effective data. Because many benthic scientists are not mapping professionals, they may not adequately consider the links between data collection, data analysis, and data visualization. Projects often start with clear goals, but may be hampered by the technical details and skills required for maintaining data quality through the entire process from collection through analysis and presentation. The lack of technical understanding of the entire data handling process can represent a significant impediment to success.While many benthic mapping efforts have detailed their methodology as it relates to the overall scientific goals of a project, only a few published papers and reports focus on the analysis and visualization components (Paton et al. 1997, Weihe et al. 1999, Basu and Saxena 1999, Bruce et al. 1997). In particular, the benthic mapping literature often briefly describes data collection and analysis methods, but fails to provide sufficiently detailed explanation of particular analysis techniques or display methodologies so that others can employ them. In general, such techniques are in large part guided by the data acquisition methods, which can include both aerial and water-based remote sensing methods to map the seafloor without physical disturbance, as well as physical sampling methodologies (e.g., grab or core sampling).The terms benthic mapping and benthic habitat mapping are often used synonymously to describe seafloor mapping conducted for the purpose of benthic habitat identification. There is a subtle yet important difference, however, between general benthic mapping and benthic habitat mapping. The distinction is important because it dictates the sequential analysis and visualization techniques that are employed following data collection. In this paper general seafloor mapping for identification of regional geologic features and morphology is defined as benthic mapping. Benthic habitat mapping incorporates the regional scale geologic information but also includes higher resolution surveys and analysis of biological communities to identify the biological habitats. In addition, this paper adopts the definition of habitats established by Kostylev et al. (2001) as a “spatially defined area where the physical, chemical, and biological environment is distinctly different from the surrounding environment.” (PDF contains 31 pages)

Description: Science Applications International Corporation Report 623

Description: South Carolina’s oyster reefs are a major component of the coastal landscape. Eastern oysters Crassostrea virginica are an important economic resource to the state and serve many essential functions in the environment, including water filtration, creek bank stabilization and habitat forother plants and animals. Effective conservation and management of oyster reefs is dependent on an understanding of their abundance, distribution, condition, and change over time. In South Carolina, over 95% of the state’s oyster habitat is intertidal. The current intertidal oyster reef database for South Carolina was developed by field assessment over several years. This database was completed in the early 1980s and is in need of an update to assess resource/habitat status and trends across the state. Anthropogenic factors such as coastal development andassociated waterway usage (e.g., boat wakes) are suspected of significantly altering the extent and health of the state’s oyster resources.In 2002 the NOAA Coastal Services Center’s (Center) Coastal Remote Sensing Program (CRS) worked with the Marine Resources Division of the South Carolina Department of Natural Resources (SCDNR) to develop methods for mapping intertidal oyster reefs along the South Carolina coast using remote sensing technology. The objective of this project was to provide SCDNR with potential methodologies and approaches for assessing oyster resources in a moreefficiently than could be accomplished through field digitizing. The project focused on the utility of high-resolution aerial imagery and on documenting the effectiveness of various analysis techniques for accomplishing the update. (PDF contains 32 pages)

Description: Coral reefs exist in warm, clear, and relatively shallow marine waters worldwide. These complex assemblages of marine organisms are unique, in that they support highly diverse, luxuriant, and essentially self-sustaining ecosystems in otherwise nutrient-poor and unproductive waters. Coral reefs are highly valued for their great beauty and for their contribution to marine productivity.Coral reefs are favorite destinations for recreational diving and snorkeling, as well as commercial and recreational fishing activities. The Florida Keys reef tract draws an estimated 2 million tourists each year, contributing nearly $800 million to the economy. However, these reef systems represent a very delicate ecological balance, and can be easily damaged and degraded by direct orindirect human contact. Indirect impacts from human activity occurs in a number of different forms, including runoff of sediments, nutrients, and other pollutants associated with forest harvesting, agricultural practices, urbanization, coastal construction, and industrial activities. Direct impacts occur through overfishing and other destructive fishing practices, mining of corals,and overuse of many reef areas, including damage from souvenir collection, boat anchoring, and diver contact.In order to protect and manage coral reefs within U.S. territorial waters, the National Oceanic andAtmospheric Administration (NOAA) of the U.S. Department of Commerce has been directed to establish and maintain a system of national marine sanctuaries and reserves, and to monitor the condition of corals and other marine organisms within these areas. To help carry out this mandate the NOAA Coastal Services Center convened a workshop in September, 1996, to identify current and emerging sensor technologies, including satellite, airborne, and underwater systems withpotential application for detecting and monitoring corals.For reef systems occurring within depths of 10 meters or less (Figure 1), mapping location and monitoring the condition of corals can be accomplished through use of aerial photography combined with diver surveys. However, corals can exist in depths greater than 90 meters (Figure 2), well below the limits of traditional optical imagingsystems such as aerial or surface photography or videography. Although specialized scuba systems can allow diving to these depths, the thousands of square kilometers included within these management areas make diver surveys for deeper coral monitoring impractical. For these reasons, NOAA is investigating satellite and airborne sensor systems, as well as technologies which can facilitate thelocation, mapping, and monitoring of corals in deeper waters.The following systems were discussed as having potential application for detecting, mapping, and assessing the condition of corals. However, no single system is capable ofaccomplishing all three of these objectives under alldepths and conditions within which corals exist. Systems were evaluated for their capabilities, including advantages and disadvantages, relative to their ability to detect and discriminate corals under a variety of conditions. (PDF contains 55 pages)

Description: This document represents a pilot effort to map socialchange in the coastal United States—a social atlascharacterizing changing population, demographic,housing, and economic attributes. This pilot effortfocuses on coastal North Carolina. The impetus for thisproject came from numerous discussions about theusefulness and need for a graphic representation ofsocial change information for U.S. coastal regions.Although the information presented here will be ofinterest to a broad segment of the coastal community andgeneral public, the intended target audience is coastalnatural resource management professionals, Sea GrantExtension staff, urban and regional land-use planners,environmental educators, and other allied constituentsinterested in the social aspects of how the nation’s coastsare changing.This document has three sections. The first sectionprovides background information about the project. Thesecond section features descriptions of social indicatorsand depictions of social indicator data for 1970, 1980,1990, and 2000, and changes from 1970 to 2000 for allNorth Carolina coastal counties. The third sectioncontains three case studies describing changes in selectsocial attributes for subsets of counties. (PDF contains 67 pages)

Description: While the homes threatened by erosion and the developer illegally filling in marshlands are the projects that make the headlines, for many state regulatory programs, it’s the residential docks and piers that take up the most time. When is a dock too long? What about crossing extended property lines? And at what point does a creek have too many docks?There are no easy answers to these questions. At the request of the Georgia Coastal Management Program, the National Oceanic and Atmospheric Administration (NOAA) Coastal Services Center published in April 2003 an inventory of residential dock and pier management information for the southeastern U.S. This inventory builds upon that effort and includes five New England states and one municipality: Connecticut, Maine, Massachusetts, New Hampshire, Rhode Island, and the Town of Falmouth, Massachusetts. Federal laws, state laws and regulations, permitting policies, and contact information are presented in a tabular format that is easy to use. (PDF contains 16 pages)

Description: While the homes threatened by erosion and the developer illegally filling in marshlands are the projects that make the headlines, for many state regulatory programs, it’s the residential docks and piers that take up the most time. Whenis a dock too long? What about crossing extended property lines? And at what point does a creek have too many docks?There are no easy answers to any of the dock and pier related questions. Each state has to craft the laws and policies that are best for its natural resources and its political and legal environment. At the same time, mistakes in judgment can be costly for the organization, the homeowner, and the natural resources.At the request of the Georgia Coastal Management Program, the National Oceanic and Atmospheric Administration (NOAA) Coastal Services Center compiled an inventory of dock information for four states—Georgia, Florida, North Carolina, and South Carolina. Federal laws, state laws and regulations, permitting policies, and contact information are included in a tabular format that is easy to use.(PDF contaions 18 pages)

Description: This document, Guidance for Benthic Habitat Mapping: An Aerial Photographic Approach, describes proven technology that can be applied in an operational manner by state-level scientists and resource managers. This information is based on the experience gained by NOAA Coastal Services Center staff and state-level cooperators in the production of a series of benthic habitat data sets in Delaware, Florida, Maine, Massachusetts, New York, Rhode Island, the Virgin Islands, and Washington, as well as during Center-sponsored workshops on coral remote sensing and seagrass and aquatic habitat assessment. (PDF contains 39 pages)The original benthic habitat document, NOAA Coastal Change Analysis Program (C-CAP): Guidance for Regional Implementation (Dobson et al.), was published by theDepartment of Commerce in 1995. That document summarized procedures that were to be used by scientists throughout the United States to develop consistent and reliablecoastal land cover and benthic habitat information. Advances in technology and new methodologies for generating these data created the need for this updated report,which builds upon the foundation of its predecessor.

Description: As more people discover coastal and marine protected areas as destinations for leisure-time pursuits, the task of managing coastal resources while providing opportunities for high quality visitor experiences becomes more challenging. Many human impacts occur at these sites; some are caused by recreation and leisure activities on-site, and others by activities such as agriculture, aquaculture, or residential and economic development in surroundingareas. Coastal management professionals are continually looking for effective ways to prevent or mitigate negative impacts of visitor use. (PDF contains 8 pages)Most coastal and marine protected area managers arechallenged with balancing two competing goals—protection of natural and cultural resources and provision of opportunities for public use. In most cases, some level of compromise between the goals is necessary, where one goal constrains or “outweighs” the other. Often there is a lack of clear agreement about the priority of these competing goals. Consequently, while natural resource decisionsshould ultimately be science-based and objective, such decisions are frequently made under uncertainty, relying heavily upon professional judgment. These decisions are subject to a complex array of formal and informal drivers and constraints—data availability, timing, legal mandate, political will, diverse public opinion, and physical, human, and social capital. This paper highlights assessment,monitoring, and planning approaches useful to gauge existing resource and social conditions, determinefeasibility of management actions, and record decision process steps to enhance defensibility. Examples are presented from pilot efforts conducted at the Rookery Bay National Estuarine Research Reserve (NERR) and Ten Thousand Islands National Wildlife Refuge (NWR) in South Florida.

Description: Executive Summary:Information found in this report covers the years 1986 through 2005. Mussel Watch began monitoring a suite of trace metals and organic contaminants such as DDT, PCBs and PAHs. Through time additional chemicals were added, and today approximately 140 analytes are monitored. The Mussel Watch Program is the longest running estuarine and coastal pollutant monitoring effort conducted in the United States that is national in scope each year. Hundreds of scientific journal articles and technical reports based on Mussel Watch data have been written; however, this report is the first that presents local, regional and national findingsacross all years in a Quick Reference format, suitable for use by policy makers, scientists, resource managers and the general public.Pollution often starts at the local scale where high concentrations point to a specific source of contamination, yet some contaminants such as PCBs are atmospherically transported across regional and national scales, resulting in contamination far from their origin. Findings presented here showed few national trends for trace metals and decreasing trends for most organic contaminants; however, a wide variety of trends, both increasing and decreasing, emerge at regional and local levels. For most organic contaminants, trends have resulted from state andfederal regulation. The highest concentrations for both metal and organic contaminants are found near urban and industrial areas.In addition to monitoring throughout the nation’s coastal shores and Great Lakes, Mussel Watch samples are stored in a specimen bank so that trends can be determined retrospectively for new and emerging contaminants ofconcern. For example, there is heightened awareness of a group of flame retardants that are finding their way into the marine environment. These compounds, known as polybrominated diphenyl ethers (PBDEs), are now being studied using historic samples from the specimen bank and current samples to determine their spatial distribution. We will continue to use this kind of investigation to assess new contaminant threats.We hope you find this document to be valuable, and thatyou continue to look towards the Mussel Watch Programfor information on the condition of your coastal waters. (PDF contains 118 pages)

Description: Center for Coastal Monitoring and Assessment

Description: Tidal creek ecosystems are the primary aquatic link between stormwater runoff form the land and estuaries. Small tidal creeks begin in upland areas and drain into larger creeks forming a network. The creeks increase in size until they join a tidal river, sound, bay, or harbor that ultimately conect to the coastal ocean. The upper regions or headwaters of tidal creeks are "first responders" to stormwater runoff and are an important habitat for evaluating the impacts of coastal development on aquatic ecosystems. (PDF contains 22 pages)

Description: Hollings Marine Laboratory

Description: This manual presents geographic information by state of occurrence, and descriptions of the socio-economic impact created by the invasion of non-indigenous and native transplanted animal species in the Laurentian Great Lakes and the coastal waters of the United States. It is not a comprehensive literature review, but rather is intended as a primer for those unfamiliar with the socio-economic impacts of invasive aquatic and marine animals. Readers should also note that the information contained in this manual is current as of its publication date. New information and new species are routinely being added to the wider literature base. Most of the information was gathered from a number of web sites maintained by government agencies, commissions, academic institutions and museums. Additional information was taken from the primary and secondary literature. This manual focuses on socio-economic consequences of invasive species. Thus, ecological impacts, when noted in the literature, are not discussed unless a connection to socio-economic factors can be made. For a majority of the species listed, either the impact of their invasion is not understood, or it is not published in sources surveyed. In the species summaries, sources of information are cited except for information from the U.S. Geological Survey’s (USGS) Nonindigenous Aquatic Species Database http://nas.er.usgs.gov. This website formed the base information used in creating tables on geographic distribution, and in many of the species summaries provided. Thus, whenever information is given without specific author/source and date citation, it has come from this comprehensive source. (PDF contains 90 pages)

Description: As a Federal trust species, the well-being of the striped bass (Morone saxatilis) population along the Eastern Seaboard is of major concern to resource users. Striped bass are an extremely valuable commercial and recreational resource. As a principal piscivore in Chesapeake Bay, striped bass directly or indirectly interact with multiple trophic levels within the ecosystem and are therefore very sensitive to biotic and abiotic ecosystem changes. For reasons that have yet to be defined, the species has a high intrinsic susceptibility to mycobacteriosis. This disease has been impacting Chesapeake Bay striped bass since at least the 1980s as indicated by archived tissue samples. However, it was not until heightened incidences of fish with skin lesions in the Pocomoke River and other tributaries of the Chesapeake Bay were reported in the summer and fall of 1996 and 1997 that a great deal of public and scientific interest was stimulated about concerns for fish disease in the Bay. (PDF contains 50 pages)

Description: Didemnum sp. A is a colonial ascidian or “sea squirt” of unknown geographic origin. Colonies of Didemnum sp. A were first documented in U.S. waters in 1993 at Damariscotta River, Maine and San Francisco Bay, California. An alarming number of colonies have since been found at several locations in New England and along the West Coast of the contiguous continental United States. Originally believed to be restricted to artificial structures in nearshore habitats, such as ports and marinas, colonies of Didemnum sp. A have also been discovered on a gravel-pavement habitat on Georges Bank at depths of 40-65m. The wide distribution of Didemnum sp. A, the presence of colonies on an important offshore fishing ground, and the negative economic impacts that other species of noninidigenous ascidians have had on aquaculture operations have raised concerns about the potential impacts of Didemnum sp. A. We reviewed the available information on the biology and ecology of Didemnum sp. A and potentially closely related species to examine the environmental and socioeconomic factors that may have influenced the introduction, establishment and spread of Didemnum sp. A in U.S. waters, the potential impacts of this colonial ascidian on other organisms, aquaculture, and marine fisheries, and the possibility that it will spread to other U.S. waters. In addition, we present and discuss potential management objectives for minimizing the impacts and spread of Didemnum sp. A.Concern over the potential for Didemnum sp. A to become invasive stems from ecological traits that it shares with other invasive species, including the ability to overgrow benthic organisms, high reproductive and population growth rates, ability to spread by colony fragmentation, tolerance to a wide range of environmental conditions, apparent scarcity of predators, and the ability to survive in human dominated habitats. At relatively small spatial scales, species of Didemnum and other nonindigenous ascidians have been shown to alter the abundance and composition of benthic assemblages. In addition, the Canadian aquaculture industry has reported that heavy infestations of nonindigenous ascidians result in increased handling and processing costs. Offshore fisheries may also suffer where high densities of Didemnum sp. A may alter the access of commercially important fish species to critical spawning grounds, prey items, and refugia. Because colonial ascidian larvae remain viable for only 12–24hrs, the introduction and spread of Didemnum sp. A across large distances is thought to be predominantly human mediated; hull fouling, aquaculture, and ballast water. Recent studies suggest that colony growth rates decline when temperatures exceed 21 ºC for 7 consecutive days. Similarly, water temperatures above 8 to 10 ºC are necessary for colony growth; however, colonies can survive extended periods of time below this temperature threshold as an unidentified overwintering form.A qualitative analysis of monthly mean nearshore water temperatures suggest that new colonies of Didemnum will continue to be found in the Northeast U.S., California Current, and Gulf of Alaska LMEs. In contrast, water temperatures become less favorable for colony establishment in subarctic, subtropical, and tropical areas to the north and south of Didemnum’s current distribution in cool temperate habitats. We recommend that the Aquatic Nuisance Species Task Force serve as the central management authority to coordinate State and Federal management activities. Five objectives for a Didemnum sp. A management and control program focusing on preventing the spread of Didemnum sp. A to new areas and limiting the impacts of existing populations are discussed. Given the difficulty of eradicating large populations of Didemnum sp. A, developing strategies for limiting the access of Didemnum sp. A to transport vectors and locating newly established colonies are emphasized. (PDF contains 70 pages)

Description: The mission of the National Oceanic and Atmospheric Administration (NOAA) is to understand and predict changes in the Earth’s environment and conserve and manage coastal and marine resources to meet our nation’s economic, social and environmental needs (NOAA, 2004). In meeting its marine stewardship responsibilities, NOAA seeks to ensure the sustainable use of resources and balance competing uses of coastal and marine ecosystems, recognizing both their human and natural components (NOAA, 2004). Authorities for executing these responsibilities come from over 90 separate pieces of Federal legislation, each with unique requirements and responsibilities. Few of these laws explicitly mandate an ecosystem approach to management (EAM) or supporting science. However, resource managers, the science community, and increasingly, the public, are recognizing that significantly greater connectedness among the scientific disciplines is needed to support management and stewardship responsibilities (Browman and Stergiou, 2004; 2005). Neither NOAA nor any other science agency can meet the increasing demand for ecosystem science products addressing each of its mandates individually. Even if it was possible, doing so would not provide the integration necessary to solve the increasingly complex array of management issues. This focus on the integration of science and management responsibilities into an ecosystem view is one of the centerpieces of the U.S. Commission on Ocean Policy’s report (USCOP, 2004), and the Administration’s response to that report in the U.S. Ocean Action Plan (CEQ, 2004). (PDF contains 100 pages)

Description: From a manager’s perspective, oftentimes the publicly held concerns related to small docks and piers are not really related to the environment. They may be more related to visual impacts and aesthetic concerns, a sense of over-development of the shore, or simply change. While individuals may hold personal aesthetic values related to small docks in general or an individual structure in particular, techniques have evolved that appear to provide reproducible, predictive assessments of the visual impacts and aesthetic values of an area and how those might change with development, including an increase in numbers of small docks. These assessments may be used to develop regulatory or non-regulatory methods for the management of small docks based on state or community standards.Visual impact assessments are increasingly used in the regulatory review of proposed development—although this process is still in its infancy as regards small docks and piers. Some political jurisdictions have established visual impact or aesthetic standards as relate to docks and others are in the process of investigating how to go about such an effort. (PDF contains 42 pages)

Description: Few issues confronting coastal resource managers are as divisive or difficult to manage as regulating the construction of private recreational docks and piers associated with residential development. State resource managers face a growing population intent on living on or near the coast, coupled with an increasing desire to have immediate access to the water by private docks or piers. (PDF contains 69 pages)

Description: Executive Summary:For over three decades, scientists have been documenting the decline of coral reef ecosystems, amid increasing recognition of their value in supporting high biological diversity and their many benefits to human society. Coral reef ecosystems are recognized for their benefits on many levels, such as supporting economies by nurturing fisheries and providing for recreational and tourism opportunities, providing substances useful for medical purposes, performing essential ecosystem services that protect against coastal erosion, and provid-ing a diversity of other, more intangible contributions to many cultures. In the past decade, the increased awareness regarding coral reefs has prompted action by governmental and non-governmental organizations, including increased funding from the U.S. Congress for conservation of these important ecosystems and creation of the U.S. Coral Reef Task Force (USCRTF) to coordinate activities and implement conservation measures [Presidential Executive Order 13089].Numerous partnerships forged among Federal agencies and state, local, non-governmental, academic and private partners support activities that range from basic science to systematic monitoring of ecosystem com-ponents and are conducted by government agencies, non-governmental organizations, universities, and the private sector. This report shares the results of many of these efforts in the framework of a broad assessment of the condition of coral reef ecosystems across 14 U.S. jurisdictions and Pacific Freely Associated States. This report relies heavily on quantitative, spatially-explicit data that has been collected in the recent past and comparisons with historical data, where possible. The success of this effort can be attributed to the dedication of over 160 report contributors who comprised the expert writing teams for each jurisdiction. The content of the report chapters are the result of their considerable collaborative efforts.The writing teams, which were organized by jurisdiction and comprised of experts from numerous research and management institutions, were provided a basic chapter outline and a length limit, but the content of each chapter was left entirely to their discretion. Each jurisdictional chapter in the report is structured to: 1) describe how each of the primary threats identified in the National Coral Reef Action Strategy (NCRAS) has manifested in the jurisdiction; 2) introduce ongoing monitoring and assessment activities relative to three major categories of inquiry – water quality, benthic habitats, and associated biological communities – and provide summary results in a data-rich format; and 3) highlight recent management activities that promote conservation of coral reef ecosystems.

Description: The status of the Gulf menhaden, Brevoortia patronus, fishery was assessed with purse-seine landings data from 1946 to 1997 and port sampling data from 1964 to 1997. These data were analyzed to determine growth rates, biological reference points for fi shing mortality from yield per recruit and maximum spawning potential analyses, spawner-recruit relationships, and maximum sustainable yield (MSY). The separable virtual population approach was used for the period 1976–97 (augmented by earlier analyses for 1964–75) to obtain point estimates of stock size, recruits to age 1, spawning stock size, and fishing mortality rates. Exploitation rates for age-1 fi sh ranged between 11% and 45%, for age-2 fi sh between 32% and 72%, and for age-3 fi sh between 32% and 76%. Biological reference points from yield per recruit (F0.1: 1.5–2.5/yr)and spawning potential ratio (F20: 1.3–1.9/yr and F30: 0.8–1.2/yr) were obtained for comparison with recent estimates of F (0.6–0.8/yr). Recent spawning stock estimates (as biomass or eggs) are above the long-term average, while recent recruits to age 1 are comparable to the long-termaverage. Parameters from Ricker-type spawner-recruit relations were estimated, although considerableunexplained variability remained. Recent survival to age-1 recruitment has generally been below that expected based on the Ricker spawner-recruit relation. Estimates of long-termMSY from PRODFIT and ASPIC estimation of production model ranged between 717,000 t and 753,000 t, respectively. Declines in landings between 1988 and 1992 raised concerns about the status of the Gulf menhaden stock. Landings have fl uctuated without trend since 1992, averaging about 571,000 t. However, Gulf menhaden are short lived and highly fecund. Thus, variation in recruitment to age 1, largely mediated by environmental conditions, infl uences fi shing success over the next two years (as age-1 and age-2 fi sh). Comparisons of recent estimates of fi shingmortality to biological reference points do not suggest overfishing. (PDF file contains 22 pages.)

Description: A two day workshop was convened on February 2-3, 1998 in Charleston, SC with 20 invited experts in various areas of sea turtle research. The goal of this workshop was to review current information on sea turtles with repect to health and identify data gaps. The use of a suite of health assessment indicators will provide insight on the health status of sea turtle populations. Since the relationship of health factors of sea turtles is limited, a seconde workshop was planned. Using a tiered approach, the first workshop we identified and reviewed the available, pertinent baseline information and data gaps. The second workshop will focus on developing the framework for the research plan. The workshops will address the use of integrated set of health parameters; specific objectives are: 1) Identify reliable indicators of health in sea turtles: assess advantages and disadvantages; determine new indicators/biomarkers which may be useful; 2) Review existing sea turtle field sampling projects; 3) Identify field projects suitable for inclusion for health assessment sampling; 4) Identify data gaps, particularly environmental characterization; 5) Identify new health assessment sampling sites, including reference site(s); and 6) Develop integrated five-year research plan, with focus on health assessment of environmental characterization. (PDF contains 174 pages)

Description: Developmental stages of 22 species representing 16 genera of agonid fishes occurring in the northeastern Pacific Ocean from San Francisco Bay to the Arctic Ocean are presented. Three of these species also occur in the North Atlantic Ocean. Larval stages of nine species are described for the first time. Additional information or illustrations intended to augment original descriptions are provided for eight species. Information on five other species is provided from the literature for comparative purposes.The primary objective of this guide is to present taxonomic characters to help identify the early life history stages of agonid fishes in field collections. Meristic, morphometric, osteological, and pigmentation characters are used to identify agonid larvae. Meristic features include numbers of median-fin elements, pectoral-fin rays, dermal plates, and vertebrae. Eye diameter, body depth at the pectoral-fin origin, snout to first dorsal-fin length, and pectoral-fin length are the most useful morphological characters. Presence, absence, numbers, and/or patterns of dermal plates in lateral rows or on the ventral surfaceof the gut are also useful. Other important characters are the presence, absence, numbers, and ornamentation of larval head spines. Lastly, distinct pigmentation patterns are often diagnostic. The potential utility of larval characters in phylogenetic analysis of the family Agonidae is discussed. (PDF file contains 92 pages.)

Description: The incidence of four discrete characters of individual sockeye salmon -two genetically inherited proteins (PGM-1*and PGM-2*), freshwater age at migration, and the presenceof the brain-tissue parasite Myxobolus arcticus-in weekly samples from two Alaskan fisheries (Noyes Island in 1986 and Sumner Strait in 1987) were used to infer stockcomposition of the catches based on corresponding character samples from 73 Alaskan and Canadian stocks. Estimated contributions of 13 stock groups, formed on the basis ofcharacter similarity of their members, were roughly consistent with expectations from tagging experiments, knowledge of stock magnitudes, and similar assessments from scales. Imprecision of the estimated contributions by the 13 stock groups limited their practical value; but variability was much reduced for combined estimated contributions by two inclusive categories, namely stock groups whose members had either high or low brainparasiteprevalence. Noyes Island catches consisted predominantly of unparasitized fish, most of which were probably of Canadian origin. The majority of Sumner Strait catches consisted of parasitized fish, whose freshwater origins may have been in Alaska or Canada. (PDF file contains 27 pages.)

Description: The phylum Acanthocephala (intestinal worm parasites of vertebrates) of the Atlantic coast of the United States comprises 43 species and 20 genera belonging to three orders: Echinorhynchida, Neoechinorhynchida, and Polymorphida. Adults are exclusively intestinal parasites of vertebrates. This study includes those species found in vertebrates of marine and estuarine environments along the North American Atlantic coast between Maine and Texas. Species that can be found within that geographical range and those that typically infect freshwater fishes but that are occasionally present in marine or estuarine hosts arealso included. The taxonamy, anatomy, natural history, and ecology of the phylum Acanthocephala are discussed, and an illustrated key to the genera is presented. Techniques, anannotated systematic treatment of all 43 species, and a systematic index are included. No systematic decisions will be made at this time, but areas where such decisions are pending will be indicated and discussed for future reports. (PDF file contains 32 pages.)

Description: In 1992 and 1993, researchers from the National Marine Mammal Laboratory initiated photo-identification studies on Alaskan killer whales, Orcinus orca. Waters from KodiakIsland west to the central and eastern Aleutian Islands and southeastern Bering Sea were surveyed. A total of 289 individual whales were identified. A photographic record of the whales encountered during these surveys is presented. When photographs of the 289 individual whales were compared among various regions in Alaska (Prince William Soundand Southeast Alaska) and areas outside Alaska (British Columbia, Washington, and California), 11 matches were found. The count is conservative because the 1992 and 1993surveys were limited in geographical range, restricted to summer periods, and whales may have been missed along the survey trackline. Future research incorporating both photoidentification studies and line transect surveys will provide reliable abundance estimates of Alaskan killer whales. (PDF file contains 58 pages.)

Description: The abundance and distribution of ichthyoplankton adjacent to live-bottom habitats (rock outcroppings containing rich, sessile invertebrate communities and many species oftropical and subtropical fishes) in open-shelf waters « 55-m isobath) in Onslow Bay, North Carolina, were investigated. Larvae of reef-associated genera, especially the economically important subtropical and tropical members of the families Haemulidae (Haemulon), Lutjanidae (Lutjanus and Rltomboplites), Serranidae (Mycteroperca and Epinephelus), and Sparidae (Calamus and Pagrus) were targeted. Larvae representing 40 families were collected in neuston tows. Commonly collected reef-associated families were Balistidae, Blenniidae (dominated by the reef-associated Parablennius marmoreus) , Mullidae, and Gobiidae. Larvae representing 70 families werecollected in subsurface tows. Reef-associated families commonly collected included Apogonidae, Balistidae, Gobiidae, Haemulidae, LutJanidae, Scaridae, and Serranidae. Larval Haemulon sp (p)., Lutjanus sp(p)., and Rltomboplites aurorubens were commonly collected and thus it is likely that these taxa spawn in Onslow Bay and recruit to live-bottom sites within the area. Other families of fishes commonly collected but generally not considered reef-associated included Bothidae, Callionymidae, Carangidae, Clupeidae, Engraulidae, and Ophidiidae. Estuarine-dependent species (e.g. the clupeid Brevoortia tyrannus and the sciaenids Leiostomus xanthurus and Micropogonias undulatus) were an important component of the ichthyoplankton during late fall and winter. The frequent occurrence of larvae fromoceanic species (e.g. gonostomatids and myctophids) indicated that Gulf Stream waters had intruded onto the shelf, transporting these larvae to open-shelf waters off North Carolina.(PDF file containes 36 pages.)

Description: From 1974 through 1983, we conducted monitoring to provide the first long-term, year-round record of sea water temperatures south of New England from surface to bottom, and from nearshore to the continental slope. Expendable bathythermograph transects were made approximatelymonthly during the ten years by scientists and technicians from numerous institutions, working on research vessels that traversed the continental shelf off southern New England. Ten-year (1974-83) means and variability are presented for coastal and bottom water temperatures, formid-shelf water column temperatures, and for some atmospheric and oceanographic conditions that mayinfluence shelf and upper-slope water temperatures. Possible applications of ocean temperature monitoringto fishery ecology are noted. Some large departures from mean conditions are discussed; particularly notableduring the decade were the response of water temperatures to the passage of Gulf Stream warm-core rings, and the magnitude and persistence of shelf-water cooling associated with air temperatures in three successive very cold winters (1976-77, 1977-78, and 1978-79). (PDF file contains 51 pages.)

Description: (PDF file contains 248 pages.)

Description: At its june 1990 annual meeting, the Technical Subcommittee(TSC) of the Canada-U.S. Groundfish Committee recommended that scientists and managers working on sablefish, Anoplopoma fimbria, issues convene to present and discuss the results of their recent research. Thorough knowledge of the biology and population dynamics of this species is essential for its effective management, especially considering its commercial importance. TSC representatives from both countries recognized that a great deal ofactive research has been conducted on this species since the International Sablefish Symposium was held in Anchorage, Alaska, in March 1983 (Melteff, 1983). As a result of this recommendation, the International Symposium on the Biology and Management of Sablefish (ISBMS) was convened April 13-15, 1993, at the Alaska Fisheries Science Center in Seattle, Washington. (PDF file contains 286 pages.)

Description: Over 100 molluscan species are landed in Mexico. About 30% are harvested on the Pacific coast and 70% on the Atlantic coast. Clams, scallops, and squid predominate on thePacific coast (abalone, limpets, and mussels are landed there exclusively). Conchs and oysters predominate on the Atlantic coast. In 1988, some 95,000 metric tons (t) of mollusks were landed, with a value of $33 million. Mollusks were used extensively in prehispanic Mexico as food, tools, and jewelry. Their use as food and jewelry continues. Except in the States of Baja California and Baja California Sur, where abalone, clams, and scallops provide fishermen with year-round employment, mollusk fishing is done part time. On both the Pacific and Atlantic coasts, many fishermen are nomads, harvesting mollusks wherever theyfind abundant stocks. Upon finding such beds, they build camps, begin harvesting, and continue until the mollusks become so scarce that it no longer pays to continue. They then look for productive beds in other areas and rebuild their camps. Fishermen harvest abalones, mussels, scallops, and clams by free-diving and using scuba and hooka. Landings of clams and cockles have been growing, and 22,000 t were landed in 1988. Fishermen harvest intertidal clams by hand at wading depths, finding them with their feet. In waters up to 5 m, they harvest them by free-diving. In deeper water, they use scuba and hooka. Many species ofgastropods have commercial importance on both coasts. All species with a large detachable muscle are sold as scallops. On the Pacific coast, hatchery culture of oysters prevails. Oyster culture in Atlantic coast lagoons began in the 1950's, when beds were enhanced by spreading shells as cultch for spat. (PDF file contains 228 pages.)

Description: This three-volume monograph represents the first majorattempt in over a century to provide, on regional bases, broad surveys of the history, present condition, and future of the important shellfisheries of North and Central America and Europe. It was about 100 years ago that Ernest Ingersoll wrote extensively about several molluscan fisheries of North America (1881, 1887) and about 100 years ago that Bashford Dean wrote comprehensively about methods of oyster culture in Europe (1893). Since those were published, several reports, books, and pamphlets have been written about the biology and management of individual species or groups ofclosely related mollusk species (Galtsoff, 1964; Korringa, 1976 a, b, c; Lutz, 1980; Manzi and Castagna, 1989; Shumway, 1991). However, nothing has been written during the past century that is comparable tothe approach used by Ingersoll in describing the molluscanfisheries as they existed in his day in North America or, for that matter, in Europe. (PDF file contains 224 pages.)

Description: The Alaska Fisheries Science Center (AFSC), NationalMarine Fisheries Service (NMFS), hosted an internationalworkshop, 'The Importance of Prerecruit Walleye Pollock to the Bering Sea and North Pacific Ecosystems," from 28 to 30 October 1993. This workshop was held in conjunction with the annual International North Pacific Marine Science Organization (PICES) meeting held in Seattle. Nearly 100 representatives from government agencies, universities, and the fishing industry in Canada, Japan, the People's Republic of China, Russia, and the United States took part in the workshop to review and discuss current knowledge on juvenile pollock from the postlarval period to the time they recruit to the fisheries. In addition to its importance to humans as a major commercial species, pollock also serves as a major forage species for many marine fishes, birds, and mammals in the North Pacific region.(PDF file contains 236 pages.)

Description: The status of the gulf menhaden, Brevoortia patronus, fishery was assessed with purseseine landing data from 1946 to 1992 and port sampling data from 1964 to 1992. These datawere analyzed to determine growth rates, biological reference points for fishing mortality from yield per recruit and maximum spawning potential analyses, spawner-recruit relationships, and maximum sustainable yield (MSY). Virtual population approaches were used to obtain point estimates of stock size, recruits to age I, spawning stock size, and fishing mortality rates. Exploitation rates ranged between 14% and 45% for age-1 fish, between30% and 72% for age-2 fish, and between 36% and 71% for age-3 fish. Biological reference points from yield per recruit (FO. I: 0.7-0.9 yr-1) and maximum spawning potential (F20: 1.62.9 yr-l and F30: 1.0-2.1 yr-1) were obtained for comparison with recent estimates of F (0.4-0.8 yr-l). Parameters from Ricker-type spawner-recruit relations were estimated, although considerable unexplained variability remained. Estimates of long-term MSY from fits of thegeneralized production model ranged between 664,000 metric tons (t) and 897,000 t. Declines in landings since 1988 have raised concerns about the status of the gulf menhadenstock. However, gulf menhaden are short lived and highly fecund. Thus, variation in recruitment to age 1 largely mediated by environmental conditions influences fishingsuccess over the next two years (as age-1 and age-2 fish). Comparisons of recent estimates of fishing mortality to biological reference points do not suggest overfishing. (PDF file contains 26 pages.)

Description: This study owes its inception to the wisdom and experienceof the staff of the Northeast Fisheries Science Center who, after several decades of surveys in the New York Bight, recognized a unique opportunity to capitalize on the decision to stop ocean dumping of sewage sludge and designed an innovative field study to evaluate effects on living marine resources and their habitats. For decades ocean dumping was viewed as a cheap and effective means for disposal of wastes generated by urbanized coastal areas. Even after the 12-mile site was closed, sewage sludge continued to be dumped at Deepwater Dumpsite 106. The 6-milesite off the NewJersey coast is still used as a dumpsitefor dredged material from New York Harbor areas. Discussions continue on the propriety of using thedeep ocean spaces for disposal of a variety of materialincluding low level radioactive wastes. Consequently,managers are still faced with critical decisions in this area. It is to be hoped that the results from the 12-mile study will provide the necessary information on which these managers can evaluate future risks associated with ocean waste disposal. (PDF file contains 270 pages.)

Description: Summer flounder, Paralichthys dentatus, scup, Stenotomus chrysops, and black sea bass, Centropristis striata, cooccur within the Middle Atlantic Bight and off southern New England and are important components of commercial and recreational fisheries. The commercial otter trawl fishery for these species is primarily a winter fishery, whereas the recreational fishery takes place between late spring and autumn. The otter trawl fishery generally targetssummer flounder, and less frequently scup, while black sea bass occurs as bycatch. Trips in which all three species were present yielded highest aggregate landings per unit of effort (LPUE) levels and occurred more often than trips landing only one or two species. More than 50% of the trips in the trawl fishery landed at least two of the three species. In contrast, greater than 75% of the recreational landings of each species occurred as a result of tripslanding only one species. Differences in the fisheries resulted from the interactions of seasonal changes in species distributions and gear selectivity. (PDF file contains 18 pages.)

Description: (PDF file contains 112 pages.)

Description: EXECUTIVE SUMMARY: The Coastal Change Analysis Programl (C-CAP) is developinga nationally standardized database on landcover and habitat change in the coastal regions of the United States. C-CAP is part of the Estuarine Habitat Program (EHP) of NOAA's Coastal Ocean Program (COP). C-CAP inventories coastal submersed habitats, wetland habitats, and adjacent uplands and monitors changes in these habitats on a one- to five-year cycle. This type of information and frequency of detection are required to improve scientific understanding of the linkages of coastal and submersed wetland habitats with adjacent uplands and with the distribution, abundance,and health of living marine resources. The monitoringcycle will vary according to the rate and magnitude ofchange in each geographic region. Satellite imagery(primarily Landsat Thematic Mapper), aerial photography,and field data are interpreted, classified, analyzed,and integrated with other digital data in a geographicinformation system (GIS). The resulting landcoverchange databases are disseminated in digital formfor use by anyone wishing to conduct geographic analysisin the completed regions. C-CAP spatial information on coastal change will be input to EHP conceptual and predictive models to support coastal resource policy planning and analysis. CCAP products will include 1) spatially registered digital databases and images, 2) tabular summaries by state, county, and hydrologic unit, and 3) documentation. Aggregations to larger areas (representing habitats, wildlife refuges, or management districts) will be provided on a case-by-case basis. Ongoing C-CAP research will continue to explore techniques for remote determination of biomass, productivity, and functional status of wetlands and will evaluate new technologies (e.g. remote sensor systems, global positioning systems, image processing algorithms) as they become available. Selected hardcopy land-cover change maps will be produced at local (1:24,000) to regional scales (1:500,000) for distribution. Digital land-cover change data will be provided to users for the cost of reproduction.Much of the guidance contained in this document was developed through a series of professional workshopsand interagency meetings that focused on a) coastal wetlands and uplands; b) coastal submersed habitat including aquatic beds; c) user needs; d) regionalissues; e) classification schemes; f) change detectiontechniques; and g) data quality. Invited participantsincluded technical and regional experts and representativesof key State and Federal organizations. Coastal habitat managers and researchers were given an opportunity for review and comment. This document summarizes C-CAP protocols and procedures that are to be used by scientists throughout the United States to develop consistent and reliable coastal change information for input to the C-CAP nationwide database. It also provides useful guidelines for contributors working on related projects. It is considered a working document subject to periodic review and revision.(PDF file contains 104 pages.)

Description: Current information is reviewed that provides clues to the intraspecific structure of dolphin species incidently killed in the yellowfin tuna purse-seine fishery of the eastern tropical Pacific (ETP). Current law requires that management efforts are focused on the intraspecific level, attempting to preserve local and presumably locally adapted populations. Four species are reviewed: pantropical spotted, Stenella attenuata; spinner, S. longirostTis;striped, S. coeruleoalba; and common, Delphinus delphis, dolphins. For each species, distributional, demographic, phenotypic, and genotypic data are summarized, and theputative stocks are categorized based on four hierarchal phylogeographic criteria relative to their probability of being evolutionarily significant units. For spotted dolphins, the morphological similarity of animals from the south and the west argues that stock designations (and boundaries) be changed from the current northernoffshore and southern offshore to northeastern offshore and a combined western and southern offshore. For the striped dolphin, we find little reason to continue the presentdivision into geographical stocks. For common dolphins, we reiterate an earlier recommendation that the long-beaked form (Baja neritic) and the northern short-beaked form bemanaged separately; recent morphological and genetic work provides evidence that they are probably separate species. Finally, we note that the stock structure of ETP spinnerdolphins is complex, with the whitebelly form exhibiting characteristics of a hybrid swarm between the eastern and pantropical subspecies. There is little morphological basis at present for division of the whitebelly spinner dolphin into northern and southern stocks. However, we recommend continued separate management of the pooled whitebelly forms, despite their hybrid/intergrade status. Steps should be taken to ensure that management practices do not reduce the abundance of eastern relative to whitebelly spinner dolphins. To do so may lead to increased invasion of the eastern's stock range and possible replacement of the eastern spinner dolphin genome.(PDF file contains 24 pages.)

Description: The United States and Japanese counterpart panels on aquaculture were formed in 1969 under the United States-Japan Cooperative Program in Natural Resources (UJNR). The panels currently include specialists drawn from the federal departments most concerned with aquaculture. Chargedwith exploring and developing bilateral cooperation, the panels have focused their efforts on exchanginginformation related to aquaculture which could be of benefit to both countries.The UJNR was begun during the Third Cabinet-Level Meeting of the Joint United States-Japan Committee on Trade and Economic Affairs in January 1964, In addition to aquaculture, current subjects in the program include desalination of seawater, toxic microorganisms, air pollution, energy, forage crops, national park management, mycoplasmosis, wind and seismic effects, protein resources,forestry, and several joint panels and committees in marine resources research, development, and utilization.Accomplishments include increased communication and cooperation among technical specialists; exchanges of information, data, and research findings; annual meetings of the panels, a policy-coordinative body; administrative staff meetings; exchanges of equipment, materials, and samples; several major technical conferences; and beneficial effects on international relations. (PDF file contains 150 pages.)

Description: About 72 species of Sebastes (Family Scorpaenidae) are found along the eastern Pacific coast of North America, some of which are heavily exploited by both commercial andsport fisheries. Because of the large number of species, the identification of early life stages has progressed slowly. The objectives of this study were 1) to rear the larvae of four species of rockfish (Sebastes mystinus, S. carnatus, S. atrovirens, and S. rastrelliger); and2) to describe the larvae using morphometric measurements, pigmentation patterns, and head spination.Pigmentation was the most useful feature for identification purposes. Two general patterns were found: 1) a short row of ventral midline melanophores on the tail, and none or very little postero-dorsal pigmentation (S. mystinus); and 2) complete ventral midline pigmentation on the tail, and anterior and postero-dorsal melanophores (S. carnatus, S. atrovirens, and S. rastrelliger). With the exception of very early stages of S. carnatus and S. atrovirens, these species can be readily identified. Morphometric proportionsand head spination did not show major differences among species.Because of the great similarities found among species in this genus, descriptions from field studies are uncertain to some extent. Laboratory rearings, although difficult, canat least provide early larvae from known species which allow precise identification as well as an estimation ofvariability of characters (e.g., pigmentation) within and between broods.(PDF file contains 22 pages.)

Description: This guide was developed to assist with the identification of western North Atlantic grouper species of the genera Alphestes, Cephalopholis, Dermatolepis, Epinephelus,Gonioplectrus, Mycteroperca, and Paranthias. The primary purpose for assembling the guide is for use with projects that deploy underwater video camera systems. The mostvital source of information used to develop the guide was an archive of underwater video footage recorded during fishery projects. These video tapes contain 348 hours ofsurvey activity and are maintained at the National Marine Fisheries Service (NMFS), Pascagoula, Mississippi. This footage spans several years (1980-92) and was recordedunder a wide variety of conditions depicting diverse habitats from areas of the western North Atlantic Ocean, Caribbean Sea, and Gulf of Mexico. Published references wereused as sources of information for those species not recorded on video footage during NMFS projects. These references were also used to augment information collected from video footage to provide broader and more complete descriptions. The pictorial guide presents information for all 25 grouper species reported to occur in the western North Atlantic. Species accounts provide descriptive text and illustrations depicting documented phases for the various groupers. In addition, species separation sheets based on important identification features were constructed to further assist with species identification. A meristic table provides information for specimens captured in conjunction with videoassisted fishery surveys. A computerized version enables guide users to amend, revise,update, or customize the guide as new observations and information become available. (PDF file contains 52 pages.)

Description: Interannual variability caused by the El Nino-Southern Oscillation in the eastern tropical Pacific Ocean (ETP) is analogous to seasonal variability of comparable magnitude.Climatological spatial patterns and seasonal variability of physical variables that may affect the ETP ecosystem are presented and discussed. Surface temperature, surfacesalinity, mixed layer depth, thermocline depth, thermocline strength, and surface dynamic height were derived from bathythermograph, hydrocast, and CTD data. Surface current velocity, divergence, and upwelling velocity were derived from ship drift reports. Surface wind velocity, wind stress, wind divergence, wind stress curl, and Ekman pumpingvelocity were derived from gridded pseudostress data obtained from Florida State University. Seasonal maps of these variables, and their deviations from the annual mean, show different patterns of variation in Equatorial (S°S-SON) and Tropical Surface Water (SOlS0N). Seasonal shifts in the trade winds, which affect the strength of equatorialupwelling and the North Equatorial Countercurrent, cause seasonal variations in most variables. Seasonal and interannual variability of surface temperature, mixed layer depth, thermocline depth and wind stress were quantified. Surface temperature, mixed layer depth and thermocline depth, but not local wind stress, are less variable in Tropical Surface Water than in Equatorial Surface Water. Seasonal and interannual variability are close to equal in most of the ETP, within factors of 2 or less. (PDF file contains 70 pages.)

Description: The 13th Annual Larval Fish Conference and Annual Meeting of the American Fisheries Society Early Life History Section cohosted by Mote Marine Laboratory, United States, and the Instituto Nacional de la Pesca, Mexico, were held 21-26 May 1989, in Merida, Yucatan, Mexico. The purpose of holding the meeting in Mexico was to encourage the participation of our Latin American and Caribbean colleagues and to provide a forum for the exchange of ideas and information among researchers working in the Americas. More than 150 participants represented 24 U.S. states, the District of Columbia, and 13 foreign countries including Mexico, Canada, Puerto Rico, Costa Rico, Panama, Cuba, Columbia, Chile, Peru, Brazil, Argentina, South Africa, and West Germany. The Conference began with registration and a social inthe courtyard patio of the Merida Holiday Inn. Fresh redgrouper, the most important commercial finfish species ofthe State of Yucatan, was prepared and served by the hotelstaff, courtesy of CPI, Itzamex, and the Terramar TradingCompany. (PDF file contains 146 pages.)

Description: This manual includes an introduction to the general biology, a selected bibliography, and an illustrated key to 11 genera and 17 species of copepods of the Crustacea, Subclass Copepoda, Order Cyclopoida, Families Archinotodelphyidae, Notodelphyidae and Ascidicolidae, associated with ascidians from the Atlantic Coast of the United States. Species distributed from the Gulf of Maine to Long Island Sound are emphasized. An annotated systematic list, with statements of the world distribution and new records of association with hosts, and a systematic index are also provided. (PDF file contains 44 pages.)

Description: The United States and Japanese counterpart panels on aquaculture were formed in 1969 under the United States-Japan Cooperative Program in Natural Resources (UJNR). The panels currently include specialists drawn from the federal departments most concerned with aquaculture. Charged with exploring and developing bilateral cooperation, the panels have focused their efforts on exchanging information related to aquaculture which could be of benefitto both countries.The UJNR was begun during the Third Cabinet-Level Meeting of the Joint United States-Japan Committee on Trade and Economic Affairs in January 1964. In addition to aquaculture, current subjects in the program include desalination of seawater, toxic microorganisms, air pollution, energy, forage crops, national park management, mycoplasmosis, wind and seismic effects, protein resources, forestry, and several joint panels and committees in marineresources research, development, and utilization.Accomplishments include: Increased communication and cooperation among technical specialists; exchanges of information, data, and research findings; annual meetings of the panels, a policy-coordinative body; administrative staff meetings; exchanges of equipment, materials, and samples; several major technical conferences; and beneficial effects on international relations. (PDF file contains 88 pages.)

Description: This report is a summary of the results of 883 purse seine sets made for juvenile salmonids during 15 cruises off the coasts of Oregon and Washington during the springs and summers of 1981-1985. Juvenile coho salmon (Oncorhynchus kisutch) occurred most frequently, followed by chinook salmon (0. tshawytscha). The juveniles of these two species co-occurred more frequently than expected. Juvenile chum, pink and sockeye salmon (0. keta, O. gorbuscha, and O. nerka), steelhead (0. mykiss) and cutthroat trout (0. clarki clarki) were caught much less frequently and in lower numbers than coho or chinook salmon. We found no evidence of large schools ofjuvenile salmonids. A northerly movement of juvenile coho salmon wa~ suggested by decreased catches off Oregon and increased catches off Washington between early and late summer. Highest catch per set of juvenile coho salmon was usually found inshore of 37.2 km. Juvenile chinook salmon were usually found within 27.9 km of the coast. Juvenile salmonids were found over a broadrange of surface salinities and temperatures. High catches of juvenile coho salmon occurred in both the low salinity waters of the Columbia River plume and in adjacent higher salinity waters. Preferences for specific salinities or temperatures were not obvious for any species, although catch rates of juvenile coho salmon were highest in years when chlorophyll content was also high. Based on expansions of fish with coded wire tags, we estimated that hatchery coho salmon smolts comprised 74%, on average, of the juvenile coho salmon catches. The remaining 26% were presumably wild fish or hatchery fish released as fingerlings. Hatchery coho salmon were caught roughlyin proportion to the numbers released. However, hatchery fish from the Columbia River and private coastal facilities were caught at slightly higher rates while those from coastal Washington and public coastal Oregon hatcheries were caught at slightly lower rates than expected from thenumbers released. No juvenile coho salmon with coded wire tags were caught that had originated from either California or Puget Sound hatcheries. (PDF file contains 88 pages.)

Description: The crinoid fauna of the continental margin (0-1500 m) of northeastern North America (Georgia to Canada) includes 14 species in 13 genera and 5 families. We introduce the external morphology and natural history of crinoids and include a glossary of terms, an illustrated key to local taxa, annotated systematic list, and an index. The fauna includes 2 species found no further south than New England and 8 that occur no further north than the Carolinas and Blake Plateau. Comactinia meridionalis (Agassiz) is the only species commonly found in shallow water «50 m). Notaxa are endemic to the area. (PDF file contains 34 pages.)