ALBERT

Description: An activity book for children highlighting coral reef issues. The book includes coral reef information, fun facts, drawings to color, connect the dots, find a word, images, matching, etc. Target audience is K-6th graders.

Description: Digital maps of the shallow (〈~30m deep) coral reef ecosystems of Majuro Atoll, Republic of the Marshall Islands, were created through visual interpretation of remote sensing imagery acquired between 2004 and 2006. Reef ecosystem features were digitized directly into a Geographic Information System. Benthic features were categorized according to a classification scheme with attributes including zone (location such as lagoon or forereef, etc.), structure (bottom type such as sand or patch reef, etc.) and percent hard bottom. This atlas consists of 27 detailed maps displaying reef zone and structure of coral ecosystems around Majuro. Adjacent maps in the atlas overlap slightly to ensure complete coverage. Maps and associated products can be used to support science and management activities on Majuro reef ecosystems including inventory, monitoring, conservation, and sustainable development applications. Maps are not to be used for navigation.

Description: Coastal and marine ecosystems support diverse and important fisheries throughout the nation’s waters, hold vast storehouses of biological diversity, and provide unparalleled recreational opportunities. Some 53% of the total U.S. population live on the 17% of land in the coastal zone, and these areas become more crowded every year. Demands on coastal and marine resources arerapidly increasing, and as coastal areas become more developed, the vulnerability of human settlements to hurricanes, storm surges, and flooding events also increases.Coastal and marine environments are intrinsically linked to climate in many ways. The ocean is an important distributor of the planet’s heat, and this distribution could be strongly influenced by changes in global climate over the 21st century. Sea-level rise is projected to accelerate during the 21st century, with dramatic impacts in low-lying regions where subsidence and erosion problems already exist. Many other impacts of climate change on the oceans are difficult to project, such as the effects on ocean temperatures and precipitation patterns, although the potential consequences of various changes can be assessed to a degree. In other instances, research is demonstrating that global changes may already be significantly impacting marine ecosystems, such as the impact of increasing nitrogen on coastal waters and the direct effect of increasing carbon dioxide on coral reefs.Coastal erosion is already a widespread problem in much of the country and has significant impacts on undeveloped shorelines as well as on coastal development and infrastructure. Along the Pacific Coast, cycles of beach and cliff erosion have been linked to El Niño events that elevate average sea levels over the short term and alter storm tracks that affect erosion and wave damage along thecoastline. These impacts will be exacerbated by long-term sea-level rise. Atlantic and Gulf coastlines are especially vulnerable to long-term sea-level rise as well as any increase in the frequency of storm surges or hurricanes. Most erosion events here are the result of storms and extreme events, and the slope of these areas is so gentle that a small rise in sea level produces a large inland shiftof the shoreline. When buildings, roads and seawalls block this natural migration, the beaches and shorelines erode, threatening property and infrastructure as well as coastal ecosystems.

Description: In this report we analyze the Topic 5 report’s recommendations for reducing nitrogen losses to the Gulf ofMexico (Mitsch et al. 1999). We indicate the relative costs and cost-effectiveness of different control measures, and potential benefits within the Mississippi River Basin. For major nonpoint sources, such as agriculture, we examine both national and basin costs and benefits.Based on the Topic 2 economic analysis (Diaz and Solow 1999), the direct measurable dollar benefits to Gulf fisheries of reducing nitrogen loads from the Mississippi River Basin are very limited at best. Although restoring the ecological communities in the Gulf may be significant over the long term, we do not currently have information available to estimate the benefits of such measures to restore the Gulf’s long-term health. For these reasons, we assume that measures to reduce nitrogen losses to the Gulf will ultimately prove beneficial, and we concentrate on analyzing the cost-effectiveness of alternative reduction strategies.We recognize that important public decisions are seldom made on the basis of strict benefit–cost analysis, especially when complete benefits cannot be estimated. We look at different approaches and different levels of these approaches to identify those that are cost-effective and those that have limited undesirable secondary effects, such as reduced exports, which may result in lost market share.We concentrate on the measures highlighted in the Topic 5 report, and also are guided by the source identification information in the Topic 3 report (Goolsby et al. 1999). Nonpoint sources that are responsible for the bulk of the nitrogen receive most of our attention. We consider restrictions on nitrogen fertilizer levels, and restoration of wetlands and riparian buffers for denitrification. We also examine giving more emphasis to nitrogen control in regions contributing a greater share of the nitrogen load.

Description: The overall goal of this assessment was to evaluate the effects of nutrient-source reductions that may be implemented in the Mississippi River Basin (MRB) to reduce the problem of low oxygen conditions (hypoxia) in the nearshore Gulf of Mexico. Such source reductions would affect the quality of surface waters—streams, rivers, and reservoirs—in the drainage basin itself, as well as nearshore Gulf waters. The task group’s work was divided into addressing the effects of nutrient-source reductions on: (1) surface waters in the MRB and (2) hypoxia in the Gulf of Mexico.

Description: Ths report addresses the following two questions:1) What are the loads (flux) of nutrients transported from the Mississippi-Atchafalaya River Basin to the Gulf of Mexico, and where do they come from within the basin?2) What is the relative importance of specific human activities, such as agriculture, point-source discharges, and atmospheric deposition in contributing to these loads?These questions were addressed by first estimating the flux of nutrients from the Mississippi-Atchafalaya River Basin and about 50 interior basins in the Mississippi River system using measured historical streamflow and water quality data. Annual nutrient inputs and outputs to each basin were estimated using data from the National Agricultural Statistics Service, National Atmospheric Deposition Program, and point-source data provided by the USEPA. Next, a nitrogen mass balance was developed using agricultural statistics, estimates of nutrient cycling in agricultural systems, and a geographic information system. Finally, multiple regression models were developed to estimate the relative contributions of the major input sources to the flux of nitrogen and phosphorus to the Gulfof Mexico.

Description: Nutrient overenrichment from human activities is one of the major stresses affecting coastal ecosystems. There is increasing concern in many areas around the world that an oversupply of nutrients from multiple sources is having pervasive ecological effects on shallow coastal and estuarine areas. These effects include reduced light penetration, loss of aquatic habitat, harmfid algal blooms, a decrease in dissolved oxygen (or hypoxia), and impacts on living resources. The largest zone of oxygen-depleted coastal waters in the United States, and the entire western Atlantic Ocean, is found in the northern Gulf of Mexico on the Louisiana-Texas continental shelf. This zone is influenced by the freshwater discharge and nutrient flux of the Mississippi River system.This report describes the seasonal, interannual, and long-term variability in hypoxia in the northern Gulf of Mexico and its relationship to nutrient loading. It also documents the relative roles of natural and human-induced factors in determining the size and duration of the hypoxic zone.

Description: The continental shelf adjacent to the Mississippi River is a highly productive system, often referred to as the fertile fisheries crescent. This productivity is attributed to the effects of the river, especially nutrient delivery. In the later decades of the 2oth century, though, changes in the system were becoming evident. Nutrient loads were seen to be increasing and reports of hypoxia were becoming more frequent.During most recent summers, a broad area (up to 20,000 krn2) of near bottom, inner shelf waters immediately west of the Mississippi River delta becomes hypoxic (dissolved oxygen concentrations less than 2 mgll). In 1990, the Coastal Ocean Program of the National Oceanic and Atmospheric Administration initiated the Nutrient Enhanced Coastal Ocean Productivity (NECOP) study of this area to test the hypothesis that anthropogenic nutrient addition to the coastal ocean has contributed to coastal eutrophication with a significant impact on water quality. Three major goals of the study were to determine the degree to which coastal productivity in the region is enhanced by terrestrial nutrient input, to determine the impact of enhanced productivity on water quality, and to determine the fate of fixed carbon and its impact on living marineresources. The study involved 49 federal and academic scientists from 14 institutions and cost $9.7 million. Field work proceeded from 1990 through 1993 and analysis through 1996, although some analyses continue to this day.The Mississippi River system delivers, on average, 19,000 m3/s of water to the northern Gulf of Mexico. The major flood of the river system occurs in spring following snow melt in the upper drainage basin. This water reaches the Gulf of Mexico through the Mississippi River birdfootdelta and through the delta of the Atchafalaya River. Much of this water flows westward along the coast as a highly stratified coastal current, the Louisiana Coastal Current, isolated from the bottom by a strong halocline and from mid-shelf waters by a strong salinity front. This stratification maintains dissolved and particulate matter from the rivers, as well as recycled material, in a well-defined flow over the inner shelf. It also inhibits the downward mixing of oxygenated surface waters from the surface layer to the near bottom waters. This highlystratified flow is readily identifiable by its surface turbidity, as it carries much of the fine material delivered with the river discharge and resuspended by nearshore wave activity. A second significant contribution to the turbidity of the surface waters is due to phytoplankton in these waters. This turbidity reduces the solar radiation penetrating to depth through the watercolumn. These two aspects of the coastal current, isolation of the inner shelf surface waters and maintenance of a turbid surface layer, precondition the waters for the development of near bottom summer hypoxia.

Description: In this report we have attempted to evaluate the ecological and economic consequences of hypoxia in the northern Gulf of Mexico. Although our initial approach was to rely on published accounts, we quickly realized that the body of published literature deahng with hypoxia was limited,and we would have to conduct our own exploratory analysis of existing Gulf data, or rely on published accounts from other systems to infer possible or potential effects of hypoxia.For the economic analysis, we developed a conceptual model of how hypoxia-related impacts could affect fisheries. Our model included both supply and demand components. The supplymodel had two components: (1) a physical production function for fish or shrimp, and (2) the cost of fishing. If hypoxia causes the cost of a unit of fishing effort to change, then this will result in a shift in supply. The demand model considered how hypoxia might affect the quality of landed fish or shrimp. In particular, the market value per pound is lower for small shrimp thanfor large shrimp.Given the limitations of the ecological assessment, the shallow continental shelf area affected by hypoxia does show signs of hypoxia-related stress. While current ecological conditions are a response to a variety of stressors, the effects of hypoxia are most obvious in the benthos that experience mortality, elimination of larger long-lived species, and a shifting of productivity to nonhypoxic periods (energy pulsing). What is not known is whether hypoxia leads to higher productivity during productive periods, or simply to a reduction of productivity during oxygen-stressed periods.The economic assessment based on fisheries data, however, failed to detect effects attributable to hypoxia. Overall, fisheries landings statistics for at least the last few decades have been relatively constant. The failure to identify clear hypoxic effects in the fisheries statistics does not necessarily mean that they are absent. There are several possibilities: (1) hypoxic effects are small relative to the overall variability in the data sets evaluated; (2) the data and the power of the analyses are not adequate; and (3) currently there are no hypoxic effects on fisheries.Lack of identified hypoxic effects in available fisheries data does not imply that effects would not occur should conditions worsen. Experience with other hypoxic zones around the globe shows that both ecological and fisheries effects become progressively more severe as hypoxia increases. Several large systems around the globe have suffered serious ecological and economic consequencesfrom seasonal summertime hypoxia; most notable are the Kattegat and Black Sea. The consequences range from localized loss of catch and recruitment failure to complete system-wide loss of fishery species. If experiences in other systems are applicable to the Gulf of Mexico, thenin the face of worsening hypoxic conditions, at some point fisheries and other species will decline, perhaps precipitously.

Description: There is nothing mysterious about how coastal rivers, their estuaries, and their relationship with the sea all work to satisfy many of our greatest needs, including drinkable water, fish and shellfish, and soils essential for sustaining the production of food and fiber. Nor are the methods that have proved successful in the protection andrestoration of watershed health difficult to understand. It is difficult, however, to imagine how we are to survive without healthy watersheds. Each watershed alongCalifornia’s coast shows signs of increasing abuse from road construction and maintenance, livestock grazing, residential development, timber harvesting, and a dozen other human activities. In some cases whole streams have simply been wiped away.This document has been created to guide and support every person in the community, from homemaker to elected official, who wants her or his watershed to provide cleanwater, harvestable fish resources and other proof that life in the watershed cannot only be maintained but also enjoyed. It is based on years of experience with watershedprotection and restoration in California. If citizen involvement is to be effective, it must draw not only on scientific knowledge but also on an understanding of how totranslate individual views into commitments and capable group action.This guide briefly reviews the condition of California’s coastal watersheds, identifies the kinds of concerns that have led citizens to successful watershed protection efforts, explains why citizen, in addition to government, effort is essential for watershed protection and restoration to succeed, and puts in the reader’s hands both the technical and organizational “tools of the trade” in the hope that those who use this guide will be encouraged to join in efforts to make their watershed serve this and future generations better.

Description: Over the past one hundred and fifty years, the landscape and ecosystems of the Pacific Northwest coastal region, already subject to many variable natural forces, have been profoundly affected by human activities. In virtually every coastal watershed from the Strait of Juan de Fuca to CapeMendocino, settlement, exploitation and development of resou?-ces have altered natural ecosystems. Vast, complex forests that once covered the region have been largely replaced by tree plantations or converted to non-forest conditions. Narrow coastal valleys, once filled withwetlands and braided streams that tempered storm runoff and provided salmon habitat, were drained, filled, or have otherwise been altered to create land for agriculture and other uses. Tideflats and saltmarshes in both large and small estuaries were filled for industrial, commercial,and other urban uses. Many estuaries, including that of the Columbia River, have been channeled, deepened, and jettied to provide for safe, reliable navigation. The prodigious rainfall in the region, once buffered by dense vegetation and complex river and stream habitat, now surges down sirfiplified stream channels laden with increased burdens of sediment and debris. Although these and many other changes have occurred incrementally over time and in widely separated areas, their sum can now be seen to have significantly affected the natural productivity of theregion and, as a consequence, changed the economic structure of its human communities. This activity has taken place in a region already shaped by many interacting and dynamic natural forces. Large-scale ocean circulation patterns, which vary over long time periods, determine the strength and location of currents along the coast, and thus affect conditions in the nearshoreocean and estuaries throughout the region. Periodic seasonal differences in the weather and ocean act on shorter time scales; winters are typically wet with storms from the southwest while summers tend to be dry with winds from the northwest. Some phenomena are episodic, such asEl Nifio events, which alter weather, marine habitats, and the distribution and survival of marine organisms. Other oceanic and atmospheric changes operate more slowly; over time scales of decades, centuries, and longer. Episodic geologic events also punctuate the region, such asvolcanic eruptions that discharge widespread blankets of ash, frequent minor earthquakes, and major subduction zone earthquakes each 300 to 500 years that release accumulated tectonic strain, dropping stretches of ocean shoreline, inundating estuaries and coastal valleys, and triggering landslides that reshape stream profiles. While these many natural processes have altered, sometimes dramatically, the Pacific Northwest coastal region, these same processes haveformed productive marine and coastal ecosystems, and many of the species in these systems have adapted to the variable environmental conditions of the region to ensure their long-term survival.

Description: A significant fraction of the total nitrogen entering coastal and estuarine ecosystems along the eastern U.S. coast arises from atmospheric deposition; however, the exact role of atmospherically derived nitrogen in the decline of the health of coastal, estuarine, and inland waters is still uncertain. From the perspective of coastal ecosystem eutrophication, nitrogen compounds from the air, along with nitrogen from sewage, industrial effluent, and fertilizers, become a source of nutrients to the receiving ecosystem. Eutrophication, however, is only one of the detrimental impacts of the emission of nitrogen containing compounds to the atmosphere. Other adverse effects include the production of tropospheric ozone, acid deposition, and decreased visibility (photochemical smog).Assessments of the coastal eutrophication problem indicate that the atmospheric deposition loading is most important in the region extending from Albemarle/Parnlico Sounds to the Gulf of Maine; however, these assessments are based on model outputs supported by a meager amount of actual data. The data shortage is severe. The National Research Council specifically mentions the atmospheric role in its recent publication for the Committee on Environmental and NaturalResources, Priorities for Coastal Ecosystem Science (1994). It states that, "Problems associated with changes in the quantity and quality of inputs to coastal environments from runoff and atmospheric deposition are particularly important [to coastal ecosystem integrity]. These includenutrient loading from agriculture and fossil fuel combustion, habitat losses from eutrophication, widespread contamination by toxic materials, changes in riverborne sediment, and alteration of coastal hydrodynamics. "

Description: Professionals who are responsible for coastal environmental and natural resource planning and management have a need to become conversant with new concepts designed to provide quantitative measures of the environmental benefits of natural resources. These amenities range from beaches to wetlands to clean water and other assets that normally are not bought and sold in everyday markets.At all levels of government — from federal agencies to townships and counties — decisionmakers are being asked to account for the costs and benefits of proposed actions. To non-specialists, the tools of professional economists are often poorly understood and sometimes inappropriatefor the problem at hand. This handbook is intended to bridge this gap.The most widely used organizing tool for dealing with natural and environmental resource choices is benefit-cost analysis — it offers a convenient way to carefully identify and array, quantitatively if possible, the major costs, benefits, and consequences of a proposed policy or regulation.The major strength of benefit-cost analysis is not necessarily the predicted outcome, which depends upon assumptions and techniques, but the process itself, which forces an approach to decision-making that is based largely on rigorous and quantitative reasoning.However, a major shortfall of benefit-cost analysis has been the difficulty of quantifying both benefits and costs of actions that impact environmental assets not normally, nor even regularly, bought and sold in markets. Failure to account for these assets, to omit them from the benefit-costequation, could seriously bias decisionmaking, often to the detriment of the environment. Economists and other social scientists have put a great deal of effort into addressing this shortcoming by developing techniques to quantify these non-market benefits.The major focus of this handbook is on introducing and illustrating concepts of environmental valuation, among them Travel Cost models and Contingent Valuation. These concepts, combined with advances in natural sciences that allow us to better understand how changes in the naturalenvironment influence human behavior, aim to address some of the more serious shortcomings in the application of economic analysis to natural resource and environmental management and policy analysis.Because the handbook is intended for non-economists, it addresses basic concepts of economic value such as willingness-to-pay and other tools often used in decision making such as costeffectiveness analysis, economic impact analysis, and sustainable development. A number of regionally oriented case studies are included to illustrate the practical application of these concepts and techniques.

Description: Professionals who are responsible for coastal environmental and natural resource planning and management have a need to become conversant with new concepts designed to provide quantitative measures of the environmental benefits of natural resources. These amenities range from beaches to wetlands to clean water and other assets that normally are not bought and sold in everyday markets.At all levels of government — from federal agencies to townships and counties — decisionmakers are being asked to account for the costs and benefits of proposed actions. To non-specialists, the tools of professional economists are often poorly understood and sometimes inappropriatefor the problem at hand. This handbook is intended to bridge this gap.The most widely used organizing tool for dealing with natural and environmental resource choices is benefit-cost analysis — it offers a convenient way to carefully identify and array, quantitatively if possible, the major costs, benefits, and consequences of a proposed policy or regulation.The major strength of benefit-cost analysis is not necessarily the predicted outcome, which depends upon assumptions and techniques, but the process itself, which forces an approach to decision-making that is based largely on rigorous and quantitative reasoning.However, a major shortfall of benefit-cost analysis has been the difficulty of quantifying both benefits and costs of actions that impact environmental assets not normally, nor even regularly, bought and sold in markets. Failure to account for these assets, to omit them from the benefit-costequation, could seriously bias decisionmaking, often to the detriment of the environment. Economists and other social scientists have put a great deal of effort into addressing this shortcoming by developing techniques to quantify these non-market benefits.The major focus of this handbook is on introducing and illustrating concepts of environmental valuation, among them Travel Cost models and Contingent Valuation. These concepts, combined with advances in natural sciences that allow us to better understand how changes in the naturalenvironment influence human behavior, aim to address some of the more serious shortcomings in the application of economic analysis to natural resource and environmental management and policy analysis.Because the handbook is intended for non-economists, it addresses basic concepts of economic value such as willingness-to-pay and other tools often used in decision making such as costeffectiveness analysis, economic impact analysis, and sustainable development. A number of regionally oriented case studies are included to illustrate the practical application of these concepts and techniques.

Description: What Are ~umulat iveE ffects?Coastal managers now recognize that many of the most serious resource degradation problems have built up gradually as the combined outcome of numerous actions and choices which alone may have had relatively minor impacts. For example, alteration of essential habitat throughwetland loss, degradation of water quality from nonpoint source pollution, and changes in salinity of estuarine waters from water diversion projects can be attributed to numerous small actions and choices. These incremental losses have broad spatial and temporal dimensions,resulting in the gradual alteration of structure and functioning of biophysical systems. In the environmental management field, the term "cumulative effects" is generally used to describe this phenomenon of changes in the environment that result from numerous, small-scale alterations.

Description: Extensive losses of coastal wetlands in the United States caused by sea-level rise, land subsidence, erosion, and coastal development have increased hterest in the creation of salt marshes within estuaries. Smooth cordgrass Spartina altemiflora is the species utilized most for salt marsh creation and restoration throughout the Atlantic and Gulf coasts of the U.S., while S. foliosa and Salicomia virginica are often used in California. Salt marshes have many valuable functions such as protecting shorelines from erosion, stabilizing deposits of dredged material, dampening flood effects, trapping water-born sediments, serving as nutrient reservoirs, acting as tertiary watertreatment systems to rid coastal waters of contaminants, serving as nurseries for many juvenile fish and shellfish species, and serving as habitat for various wildlife species(Kusler and Kentula 1989). The establishment of vegetation in itself is generally sufficient to provide the functions of erosion control, substrate stabilization, and sediment trapping. The development of other salt marsh functions, however, is more difficult to assess. For example, natural estuarine salt marshes support a wide variety of fish and shellfish, and the abundance of coastal marshes has been correlated with fisheries landings (Turner 1977, Boesch and Turner 1984). Marshes function for aquatic species by providing breeding areas, refuges from predation, and rich feeding grounds (Zimmerman and Minello 1984, Boesch and Turner 1984, Kneib 1984, 1987, Minello and Zimmerman 1991). However, the relative value of created marshes versus that of natural marshes for estuarine animals has been questioned (Carnmen 1976, Race and Christie 1982, Broome 1989, Pacific Estuarine Research Laboratory 1990, LaSalle et al. 1991, Minello and Zimmerman 1992, Zedler 1993). Restoration of all salt marsh functions is necessary to prevent habitat creation and restoration activities from having a negative impact on coastal ecosystems.

Description: The intersection of social and environmental forces is complex in coastal communities. The well-being of a coastal community is caught up in the health of its environment, the stability of its economy, the provision of services to its residents, and a multitude of other factors. With this in mind, the project investigators sought to develop an approach that would enable researchers to measure these social and environmental interactions. The concept of well-being proved extremely useful for this purpose. Using the Gulf of Mexico as a regional case study, the research team developed a set of composite indicators to be used for monitoring well-being at the county-level. The indicators selected for the study were: Social Connectedness, Economic Security, Basic Needs, Health, Access to Social Services, Education, Safety, Governance, and Environmental Condition. For each of the 37 sample counties included in the study region, investigators collected and consolidated existing, secondary data representing multiple aspects of objective well-being. To conduct a longitudinal assessment of changing wellbeing and environmental conditions, data were collected for the period of 2000 to 2010. The team focused on the Gulf of Mexico because the development of a baseline of well-being would allow NOAA and other agencies to better understand progress made toward recovery in communities affected by the Deepwater Horizon oil spill. However, the broader purpose of the project was to conceptualize and develop an approach that could be adapted to monitor how coastal communities are doing in relation to a variety of ecosystem disruptions and associated interventions across all coastal regions in the U.S. and its Territories. The method and models developed provide substantial insight into the structure and significance of relationships between community well-being and environmental conditions. Further, this project has laid the groundwork for future investigation, providing a clear path forward for integrated monitoring of our nation’s coasts. The research and monitoring capability described in this document will substantially help counties, local organizations, as well state and federal agencies that are striving to improve all facets of community well-being.

Description: This report is the second in a series from a project to assess land-based sources of pollution (LBSP) and effects in the St. Thomas East End Reserves (STEER) in St. Thomas, USVI, and is the result of a collaborative effort between NOAA’s National Centers for Coastal Ocean Science, the USVI Department of Planning and Natural Resources, the University of the Virgin Islands, and The Nature Conservancy.Passive water samplers (POCIS) were deployed in the STEER in February 2012. Developed by the US Geological Survey(USGS) as a tool to detect the presence of water solublecontaminants in the environment, POCIS samplers were deployed in the STEER at five locations. In addition to the February 2012 deployment, the results from an earlier POCIS deployment in May 2010 in Turpentine Gut, a perennial freshwater stream which drains to the STEER, are also reported.A total of 26 stormwater contaminants were detected at least once during the February 2012 deployment in the STEER. Detections were high enough to estimate ambient water concentrations for nine contaminants using USGS sampling rate values. From the May 2010 deployment in Turpentine Gut, 31 stormwater contaminants were detected, and ambient water concentrations could be estimated for 17 compounds.Ambient water concentrations were estimated for a numberof contaminants including the detergent/surfactant metabolite 4-tert-octylphenol, phthalate ester plasticizers DEHP and DEP, bromoform, personal care products including menthol, indole, n,n-diethyltoluamide (DEET), along with the animal/plant sterol cholesterol, and the plant sterol beta-sitosterol. Only DEHP appeared to have exceeded a water quality guideline for the protection of aquatic organisms.

Description: This report contains a chemical and biological characterization of sediments from the St. Thomas East End Reserves (STEER) in St. Thomas, U.S. Virgin Islands (USVI). The STEER Management Plan (published in 2011) identified chemical contaminants and habitat loss as high or very high threats and called for a characterization of chemical contaminants as well as an assessment of their effects on natural resources. The baseline information contained in this report on chemical contaminants, toxicity and benthic infaunal community composition can be used to assess current conditions, as well as the efficacy of future restoration activities. In this phase of the project, 185 chemical contaminants, including a number of organic (e.g., hydrocarbons and pesticides) and inorganic (e.g., metals) compounds, were analyzed from 24 sites in the STEER. Sediments were also analyzed using a series of toxicity bioassays, including amphipod mortality, sea urchin fertilization impairment, and the cytochrome P450 Human Reporter Gene System (HRGS), along with a characterization of the benthic infaunal community. Higher levels of chemical contaminants were found in Mangrove Lagoon and Benner Bay in the western portion of the study area than in the eastern area. The concentrations of polychlorinated biphenyls (PCBs), DDT (dichlorodiphenyltrichloroethane), chlordane, zinc, copper, lead and mercury were above a NOAA sediment quality guideline at one or more sites, indicating impacts may be present in more sensitive species or life stages in the benthic environment. Copper at one site in Benner Bay, however, was above a NOAA guideline indicating that effects on benthic organisms were likely. The antifoulant boat hull ingredient tributyltin, or TBT, was found at the third highest concentration in the history of NOAA’s National Status and Trends (NS&T) Program, which monitors the Nation’s coastal and estuarine waters for chemical contaminants and bioeffects. Unfortunately, there do not appear to be any established sediment quality guidelines for TBT. Results of the bioassays indicated significant sediment toxicity in Mangrove Lagoon and Benner Bay using multiple tests. The benthic infaunal communities in Mangrove Lagoon and Benner Bay appeared severely diminished.

Description: Washington depends on a healthy coastal and marine ecosystem to maintain a thriving economy and vibrant communities. These ecosystems support critical habitats for wildlife and a growing number of often competing ocean activities, such as fishing, transportation, aquaculture, recreation, and energy production. Planners, policy makers and resource managers are being challenged to sustainably balance ocean uses, and environmental conservation in a finite space and with limited information. This balancing act can be supported by spatial planning.Marine spatial planning (MSP) is a planning process that enables integrated, forward looking, and consistent decision making on the human uses of the oceans and coasts. It can improve marine resource management by planning for human uses in locations that reduce conflict, increase certainty, and support a balance among social, economic, and ecological benefits we receive from ocean resources.In March 2010, the Washington state legislature enacted a marine spatial planning law (RCW §43.372) to address resource use conflicts in Washington waters. In 2011, a report to the legislature and a workshop on human use data provided guidance for the marine spatial planning process. The report outlines a set of recommendations for the State to effectively undertake marine spatial planning and this work plan will support some of these recommendations, such as: federal integration, regional coordination, developing mechanisms to integrate scientific and technical expertise, developing data standards, and accessing and sharing spatial data.In 2012 the Governor amended the existing law to focus funding on mapping and ecosystem assessments for Washington’s Pacific coast and the legislature provided $2.1 million in funds to begin marine spatial planning off Washington’s coast. The funds are appropriated through the Washington Department of Natural Resources Marine Resources Stewardship Account with coordination among the State Ocean Caucus, the four Coastal Treaty Tribes, four coastal Marine Resource Committees and the newly formed stakeholder body, the Washington Coastal Marine Advisory Council.

Description: NOAA’s Center for Coastal Monitoring and Assessment’s Biogeography Branch has mapped and characterized large portions of the coral reef ecosystems inside the U.S. coastal and territorial waters, including the U.S. Caribbean. The complementary protocols used in these efforts have enabled scientists and managers to quantitatively compare different marine ecosystems in tropical U.S. waters. The Biogeography Branch used these same general protocols to generate three seamless habitat maps of the Bank/Shelf (i.e., from 0 ≤50 meters) and the Bank/Shelf Escarpment (i.e., from 50 ≤1,000 meters and from 1,000 ≤ 1,830 meters) inside Buck Island Reef National Monument (BIRNM). While this mapping effort marks the fourth time that the shallow-water habitats of BIRNM have been mapped, it is the first time habitats deeper than 30 meters (m) have been characterized. Consequently, this habitat map provides information on the distribution of mesophotic and deep-water coral reef ecosystems and serves as a spatial baseline for monitoring change in the Monument.A benthic habitat map was developed for approximately 74.3 square kilometers or 98% of the BIRNM using a combination of semi-automated and manual classification methods. The remaining 2% was not mapped due to lack of imagery in the western part of the Monument at depths ranging from 1,000 to 1,400 meters. Habitats were interpreted from orthophotographs, LiDAR (Light Detection and Ranging) imagery and four different types of MBES (Multibeam Echosounder) imagery. Three minimum mapping units (MMUs) (100, 1,000 and 5,000 square meters) were used because of the wide range of depths present in the Monument. The majority of the area that was characterized was deeper than 30 m on the Bank/Shelf Escarpment. This escarpment area was dominated by uncolonized sand which transitioned to mud as depth increased. Bedrock was exposed in some areas of the escarpment, where steep slopes prevented sediment deposition. Mesophotic corals were seen in the underwater video, but were too sparsely distributed to be reliably mapped from the source imagery. Habitats on the Bank/Shelf were much more variable than those seen on the Bank/Shelf Escarpment. The majority of this shelf area was comprised of coral reef and hardbottom habitat dominated by various forms of turf, fleshy, coralline or filamentous algae. Even though algae was the dominant biological cover type, nearly a quarter (24.3%) of the Monument’s Bank/Shelf benthos hosted a cover of 10%-〈50% live coral.In total, 198 unique combinations of habitat classes describing the geography, geology and biology of the sea-floor were identified from the three types of imagery listed above. No thematic accuracy assessment was conducted for areas deeper than about 50 meters, most of which was located in the Bank/Shelf Escarpment. The thematic accuracy of classes in waters shallower than approximately 50 meters ranged from 81.4% to 94.4%. These thematic accuracies are similar to those reported for other NOAA benthic habitat mapping efforts in St. John (〉80%), the Main Eight Hawaiian Islands (〉84.0%) and the Republic of Palau (〉80.0%). These digital maps products can be used with confidence by scientists and resource managers for a multitude of different applications, including structuring monitoring programs, supporting management decisions, and establishing and managing marine conservation areas. The final deliverables for this project, including the benthic habitat maps, source imagery and in situ field data, are available to the public on a NOAA Biogeography Branch website (http://ccma.nos.noaa.gov/ecosystems/coralreef/stcroix.aspx) and through an interactive, web-based map application (http://ccma.nos.noaa.gov/explorer/biomapper/biomapper.html?id=BUIS).This report documents the process and methods used to create the shallow to deep-water benthic habitat maps for BIRNM. Chapter 1 provides a short introduction to BIRNM, including its history, marine life and ongoing research activities. Chapter 2 describes the benthic habitat classification scheme used to partition the different habitats into ecologically relevant groups. Chapter 3 explains the steps required to create a benthic habitat map using a combination of semi-automated and visual classification techniques. Chapter 4 details the steps used in the accuracy assessment and reports on the thematic accuracy of the final shallow-water map. Chapter 5 summarizes the type and abundance of each habitat class found inside BIRNM, how these habitats compare to past habitat maps and outlines how these new habitat maps may be used to inform future management activities.

Description: The St. Croix East End Marine Park (STXEEMP) was established in 2003 as the first multi-use marine park managed by the U.S. Virgin Islands Department of Planning and Natural Resources. It encompasses an area of approximately 155 km2 and is entirely within Territorial waters which extend up to 3 nautical miles from shore. As stated in the 2002 management plan, the original goals were to: protect and maintain the biological diversity and other natural values of the area; promote sound management practices for sustainable production purposes; protect the natural resource base from being alienated for other land use purposes that would be detrimental to the area’s biological diversity; and to contribute to regional and national development (The Nature Conservancy, 2002). At the time of its establishment, there were substantial data gaps in knowledge about living marine resources in the St. Croix, and existing data were inadequate for establishing baselines from which to measure the future performance of the various management zones within the park.In response to these data gaps, National Centers for Coastal Ocean Science (NCCOS), Center for Coastal Monitoring and Assessment, Biogeography Branch (CCMA-BB) worked with territorial partners to characterize and assess the status of the marine environment in and around the STXEEMP and land-based stressors that affect them. This project collected and analyzed data on the distribution, diversity and landscape condition of marine communities across the STXEEMP. Specifically, this project characterized (1) landscape and adjacent seascape condition relevant to threats to coral reef ecosystem health, and (2) the marine communities within STXEEMP zones to increase local knowledge of resources exposed to different regulations and stressors.

Description: The Monitor National Marine Sanctuary (MNMS) was the nation’s first sanctuary, originally established in 1975 to protect the famous civil war ironclad shipwreck, the USS Monitor. Since 2008, sanctuary sponsored archeological research has branched out to include historically significant U-boats and World War II shipwrecks within the larger Graveyard of the Atlantic off the coast of North Carolina. These shipwrecks are not only important for their cultural value, but also as habitat for a wide diversity of fishes, invertebrates and algal species. Additionally, due to their unique location within an important area for biological productivity, the sanctuary and other culturally valuable shipwrecks within the Graveyard of the Atlantic are potential sites for examining community change. For this reason, from June 8-30, 2010, biological and ecological investigations were conducted at four World War II shipwrecks (Keshena, City of Atlanta, Dixie Arrow, EM Clark), as part of the MNMS 2010 Battle of the Atlantic (BOTA) research project. At each shipwreck site, fish community surveys were conducted and benthic photo-quadrats were collected to characterize the mobile conspicuous fish, smaller prey fish, and sessile invertebrate and algal communities. In addition, temperature sensors were placed at all four shipwrecks previously mentioned, as well as an additional shipwreck, the Manuela. The data, which establishes a baseline condition to use in future assessments, suggest strong differences in both the fish and benthic communities among the surveyed shipwrecks based on the oceanographic zone (depth). In order to establish these shipwrecks as sites for detecting community change it is suggested that a subset of locations across the shelf be selected and repeatedly sampled over time. In order to reduce variability within sites for both the benthic and fish communities, a significant number of surveys should be conducted at each location. This sampling strategy will account for the natural differences in community structure that exist across the shelf due to the oceanographic regime, and allow robust statistical analyses of community differences over time.

Description: The Gap Analysis of Marine Ecosystem Data project is a review of available geospatial data which can assist in marine natural resource management for eight park units. The project includes the collection of geospatial information and its incorporation in a single consistent geodatabase format. The project also includes a mapping portal which can be seen at: http://ccma.nos.noaa.gov/explorer/gapanalysis/gap_analysis.htmlIn addition to the collection of geospatial information and mapping portal we have conducted a gap analysis of a standard suite of available information for managing marine resources. Additional gap were identified by interviewing park service staff.

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: Source of the Nile Fish farm (SON) is located at Bugungu area in Napoleon Gulf, northern Lake Victoria. The proprietors of the farm requested for technical assistance of NaFIRRI to undertake regular environment monitoring of the cage site as is mandatory under the NEMA conditions. Thus, NAFIRRI undertakes quarterly environment surveys in the cage area covering selected physical-chemical factors i.e. water column depth, water transparency, water column temperature, dissolved oxygen, pH and conductivity; nutrient status, algal and invertebrate communities (zooplankton and macro-benthos) as well as fish community. The first environmental survey was undertaken in February 2011. Results/observations made during the second quarter (April-June 2011) field survey are presented in this technical report along with a scientific interpretation and discussion of the results with reference to possible impacts of the cage facilities on the water environment and the different aquatic biota in and around the cages including natural fish communities.

Description: Tullow Oil plc is to launch an onshore Early Production System (EPS) of oil drilling rated at 4,000 barrels of oil per day by 2009. The location of the EPS is in the Kaiso-Tonya area of Block 2 Oil Exploration Zone along Lake Albert within the Albertine graben. Tullow Oil plc contracted Environmental Resources Management (ERM) Southern Africa (Pty) Ltd in conjunction with Environmental Assessment Consult Limited (EACL) to undertake an Environmental Impact Assessment (EIA) for pre-construction and operation of the proposed EPS. ERM in association with EACL requested National Fisheries Resources Research Institute (NaFIRRI) to conduct a baseline survey of water quality and invertebrates in River Hohwa. This study was requested as part of an earlier baseline survey conducted at the Kaiso-Ngassa spit oil exploration area in Block 2. It was conducted at five selected sites (Fig. 1 & Table 1) within the Hohwa River basin in the Kaiso-Tonya Exploration Area 2. The study was pertinent because the targeted oil wells for EPS are upstream this river which drains the Kaiso-Ngassa valley into Ngassa lagoon.

Description: Environmental Assessment Consult Limited (EACL)

Description: Following the commencement of construction works of a 250 MW hydropower plant at Dumbbell Island in the Upper Victoria Nile in September 2007, BEL requested NaFIRRI to conduct continuous monitoring of fish catches at two transects i.e. the immediate upstream transect of the project site (Kalange-Makwanzi) and the immediate downstream .transect (Buyala-Kikubamutwe). The routine monitoring surveys were designed to be conducted twice a week at each of the tWo transects. It was anticipated that major immediate impacts were to occur during construction, and these needed to be known by BEL as part of a mitigation strategy. For example, the construction of it cofferdam could be accompanied by rapid changes in water quality and quantity downstream of the construction. These changes in turn could affect the fish catch and would probably be missed by the quarterly monitoring already in place. Therefore, a major cbjective of the more regular and rapid monitoring was to discern immediate impacts of construction activities by focusing on selected water quality parameters (total suspended solids, water conductivity, temperature, dissolved oxygen and pH) and fish catch characteristics (total catch, catch rates and value of the catch)

Description: Prepared for Bujagali Energy Limited (BEL)

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: 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: A two year, comprehensive, quantitative investigation was conducted to analyze and identify the spatial distribution of petrogenic and biogenic hydrocarbons in sediments, surface waters, fish and shellfish of Biscayne Bay, Florida. The goal for the first year of the project was to establish baseline information to support oil spill impact assessment and clean-up. One hundred fifty-five sediment and eleven biota samples were collected. The areas sampled included the Miami River, Intracoastal Waterway, tidal flats, access canals and environmentally sensitive shorelines. The second year of the study centered on areas exhibiting petroleum contamination. These areas included the Miami River, Little River, Goulds Canal, Black Creek and Military Canal. Surface and subsurface sediment, biota and surface water were collected. Sample collection, analyses, and data handling for the two year project were conducted so that all information was court-competent and scientifically accurate. Chain of custody was maintained for all samples. Total hydrocarbon content of surface sediments ranged from below detection limits to a high of 2663.44 pg/g. Several sample stations contained petroleum contamination. The majority of biota samples exhibited hydrocarbon concentrations and characteristics that indicated little, if any, petroleum contamination. Surface water samples ranged from 0.78 to 64.47 μg/L and several samples contained petroleum hydrocarbons. Our results indicate several areas of petroleum contamination. These areas are characterized by industrial complexes, port facilities, marinas, major boating routes and many of the major tributaries emptying into Biscayne Bay.

Description: Source of the Nile Fish farm (SON) is located at Bugungu area in Napoleon Gulf, northern LakeVictoria. The proprietors of the farm have a collaborative arrangement with NaFIRRI to undertake quarterly environment monitoring of the cage site as is mandatory under the NEMA conditions. The monitoring surveys cover selected physical-chemical factors i.e. water column depth, water transparency, water column temperature, dissolved oxygen, pH and conductivity; nutrient status, algal and invertebrate communities (micro-invertebrates/zooplankton and macroinvertebrates/macro-benthos) as well as fish community. The second quarter survey for the calendar year 2015, which is the subject of this report, was undertaken in June 2015.Results/observations made are presented in this technical report along with a scientificinterpretation and discussion of the results with reference to possible impacts of the cage facilities to the water environment and aquatic biota.

Description: Source of the Nile (SON) Cage Fish farm is located at Bugungu in Napoleon Gulf, northern Lake Victoria, near the headwaters of the River Nile. NaFIRRI has, through a Public-Private collaborative partnership with SON management, undertaken quarterly monitoring of the cage fish farm since 2011. The objective of the environment monitoring is to track possible environment and biological changes as a result of fish cage operations in the area. The agreed study areas cover selected physical-chemical parameters i.e. water depth, transparency, column temperature, dissolved oxygen, pH and conductivity; nutrient status; and biological parameters i.e. algae, zooplankton, macro-benthos and fish communities. The fourth quarter survey, which is the subject of this report was undertaken during December 2015. Results/observations made are presented in this technical report along with a scientific interpretation and discussion of the results with reference to possible impacts of the cage facilities to the water environment and aquatic biota.The present report presents field observations made for the fourth quarter survey undertaken in December 2015 and provides a scientific interpretation and discussion of the results with reference to possible impacts of the cage facilities to the water environment and the different aquatic biota in and around the fish cage site.

Description: This monitoring survey No. 11 undertaken between 4th and 9th September 2012 is the second one to be conducted after completion of construction of Bujagali HydropowerDam. Two pre-construction baseline surveys in April 2000 and April 2006 were conducted and during construction phase, eight monitoring surveys (September 2007,April 2008, April 2009, October 2009, April 2010, September 2010, April 2011, September 2011) were conducted.

Description: Carried out on behalf of Bujagali Energy Limited (BEL)

Description: The results reported on were from a monitoring survey No. 9 undertaken between 9th and 12th September 2011 during construction period of the Bujagali Hydropower Project (BHPP). Two pre-construction, baseline surveys in April 2000 and April 2006 were conducted and so far, during construction phase of the project, eight monitoring surveys have been undertaken i.e. in September 2007, April 2008, April 2009, October 2009, April 2010, September 2010, April 2011 and the present one, in September 2011. Since 2009 biannual monitoring surveys have been conducted at an upstream and a downstream transect of the BHPP with emphasis on the following aspects:water quality determinants biology and ecology of fishes and food webs fish stock and fish catch including economic aspects of catch and sanitation/vector studies (bilharzias and river blindness)in addition to the above mentioned studies, a soil pH survey was undertaken on 15th October 2011 in the area behind the reservoir whose filling started a week earlier. The findings of pH status in the catchment of the dam are also contained in this report.

Description: Kariba weed (Salvinia molesta) is an invasive alien waterweedthat was first recorded in Uganda in sheltered bays of LakeKyoga in June 2013. This waterweed has become a commonfeature on Lake Kyoga and its associated rivers, streams andswamps, and has spread to other lakes notably Kwania and Albert in addition to Lake Kimira in Bugiri district.

Description: Source of the Nile Fish farm (SON) is located at Bugungu area in Napoleon Gulf, northern Lake Victoria. The proprietors of the farm requested for technical assistance of NaFIRRI to undertake regular environment monitoring of the cage site as is mandatory under the NEMA conditions. As the SON is a key collaborator/client of the institute, NAFIRRI agreed to undertake the assignment subject to facilitation by the client. The institute agreed to conduct quarterly surveys of key environmental parameters at the site including selected physical-chemical and biological factors, nutrient status, column depth, water transparency and sedimentation. Samples and field measurements were to be taken at 3 sites: within and/or close to the fish cages (WIC), upstream (USC) and downstream (DSC) of the cages. The first environmental monitoring survey was undertaken in February 2011; the second in May 2011 and the third in September 2011. The surveys cover physical-chemical parameters, nutrient status, invertebrate and fish communities. The present report presents field observations made for the fourth quarter survey undertaken in November 2011 and provides a scientific interpretation and discussion of the results with reference to possible impacts of the cage facilities to the water environment and the different aquatic biota at and around the cage site including natural fish communities.

Description: The specific objectives were to:WATER QUALITY1. To measure the water physical variables as indicators of environmental conditions in the upstream and downstream transects of Kalange (1) and Buyala (2), respectively,2. To determine the concentrations of total suspended solids as a major constituent likely to be released into the waters at any time during the construction activities, by comparing the concentrations at the two transects.FISH CATCH1. To follow up trends in fish catch as construction activity progresses, and to precision of the estimate;2. To estimate the prevailing fish catch rates, total fish catches and the total value of the fish catch to the local fishers at the two transects.

Description: On title page: Environmental and Social Impact Monitoring of the Bujagali Hydropower Project (BHPP), Uganda Fisheries Component

Description: National Fisheries Resources Research Institute (NaFIRRI) undertakes quarterly monitoring of the water environment at Source of the Nile (SON) fish farm. The activity which is through a collaborative arrangement between SON fish farm and NaFIRRI aims at assessing possible changes in the water environment at SON cage area. The fish rearing activity at SON fish farm involves keeping fish in cages often under high stocking densities and feeding them on artificial feeds that are not the natural food eaten by wild fish. Cages being open systems means that all wastes such as faeces, uneaten feed and fish excretes such as ammonia are shed into the water column (Fernandes et al., 2001). The consequence is increased nutrient input which may result into high algal growth (bloom). Although this may mean more food available to primary consumers such as zooplankton, blooms caused by blue-green algae may be harmful as certain species are associated with production of toxins. In addition, the degradation of excessive phytoplankton biomass can lead to anoxic conditions in sediments underlying the cages thus changing the abundance and composition of the resident fauna. Napoleon Gulf being a shallow bay at the exit of River Nile from Lake Victoria harbours a wide variety of wild fish species that are cherished by riparian human populations. The wild fishes living close to cages are bound to be affected by activities associated with this method of fish farming. Cage farming is likely to affect the presence, abundance, diet and residence time of organisms in given vicinity (Carss, 1990; Dempster et al., 2002). Floating structures including cages may act as Fish Attracting Devices (FADs) and most pelagic fishes are known to be strongly attracted to floating objects (Freon and Dagorn, 2000; Castro et al., 2002). Wild fish could be attracted to these sites by for example plenty of food available to the cultured fishes (Bjordal & Skar, 1992). In the process, other ecological interactions between cultured and wild fish may be possible. Wild fish may also be instrumental in cleaning the environment close to the cages through eating any excess uneaten food left by cultured fishes. Caged fish under crowded conditions is susceptible to waterborne diseases and could infect wild fish or vice versa. While diseases breaking out among cultured fishes may be controlled through treatment, the wild fishes cannot undergo treatment and may thus spread diseases to other fishes, hence affecting yields from capture fishery. Furthermore, escape of cultured fish may cause genetic dilution hence decreasing genetic diversity of fish. These and other possible impacts of cages on the water environment may consequently result into conflicts 2 with other resource users especially due to deteriorating water quality and effect on wild fishes, consequently affecting the cage aquaculture industry. Therefore, the following were established as key parameters to be monitored: water temperature, dissolved oxygen, pH, conductivity, water transparency, total suspended solids, nutrient status, algae, zooplankton, benthic macro invertebrates and fish communities. The present report presents field observations made at the two cage sites of Source of the Nile fish farm including upstream, downstream and reference points, for the second quarter (April to June) undertaken in June 2017. The report provides a scientific interpretation and discussion of the results with reference to possible impacts of the cage facilities on the water environment and the different aquatic biota in and around the fish cage site.

Description: The monitoring of water quality and biotic communities at Source of the Nile (SON) fish farm area, for quarter 4 (October – December) was undertaken in December 2017. The activity aimed at assessing possible changes in the water environment at SON cage area. The following parameters were assessed: water physico-chemicals and nutrients, algae, zooplankton, benthic macro invertebrates, and fish communities. Total depth was above 5.0 m (range: 5.63 – 9.74 m) at all sampled points and decreased towards the downstream of cages. Water transparency ranged from 1.26 – 1.48 in the cage area and 1.08 to 1.34 m away from the cages. Within the cage area, Dissolved Oxygen ranged from 5.7 – 6.4 mg/L at the surface, and 5.1 – 6.4 mg/L at the bottom, while in the non-cage areas, the range was 5.5 – 7.5 mg/L at the surface and 2.6 – 7.0 mg/L at the bottom. Temperature ranged from 27.0 – 28.0 o C at the surface and 25.5 – 27.5 o C at the bottom waters for all sites, and were within the optimal range (25 – 32 o C). pH in both surface and bottom waters was above 7.0 (range: 7.5 – 9.2) at all sites. Conductivity within cage area ranged from 100.5 – 102.6 μScm-1 in surface water and 101.8 – 112.1 μScm-1 in bottom water. In the non-cage areas conductivity ranged from 11.0 – 104.4 μScm-1 in surface water and 100.2 – 110.0 μScm-1 at the bottom. Ammonium nitrogen concentration during December was less than 0.02 mg/L at all sites (0.007 – 0.018 mg/L within the cage sites, and 0.012 – 0.019 mg/L in the non-cage sites). Nitrite nitrogen ranged from 0.002 – 0.169 mg/L in the cage area, and 0.003 – 0.057 mg/L in the non-cage areas. Similar to previous records of June and September 2017, nitrate nitrogen concentration generally increased towards the downstream site, being lowest at RPT (0.041 mg/L) and highest at DSC (0.204 mg/L). Soluble reactive phosphorus was less than 0.005 mg/L at all sites, and varied within narrow margin (range: 0.003 – 0.0048 mg/L in cage sites, and 0.0032 – 0.0047 mg/L in non-cage sites). The TP concentration ranged from 0.085 – 0.107 mg/L in the cages, and 0.090 – 0.118 mg/L in the non-cage sites and was higher than recorded in September (0.038 – 0.044 mg/L in the cages and 0.04 to 0.109 mg/L away from cages). Total nitrogen concentration was in the range of 0.138 – 0.553 mg/L within cage area and 0.421 – 0.513 mg/L in non-cage areas. The concentration of TSS ranged from 0.76 – 4.33 mg/L in the cage area and 0.57 – 2.76 mg/L in the non-cage areas. The phytoplankton community was composed of blue-green algae, green algae and diatoms, dominated by blue-green algae. The abundance of algae was higher in the non-cage areas (mean:7.20 ± 2.14 mm3L-1, Range: 5.15 – 10.20 mm3L-1) than recorded in the cage areas (mean: 6.0 ± 0.71 mm3L-1, Range: 5.30 – 6.98 mm3L-1), similar to observations of September 2017 (〈 5 mm3L1 within the cages and 〉5.6 mm3L-1 in the non-cage sites). At all sampled points, blue-green algae contributed 〉70% of total abundance. Total zooplankton abundance ranged from 982,213 – 1,310,830 ind.m-2 in the non-cage sites, and 740,601 – 1,503,130 ind.m-2 in the cage areas. Similar to observations of September 2017, the upper cage site (WIC3 and WIC4) presented lower zooplankton abundance (mean: 788,954 ± 68,381 ind.m-2) when compared to the lower cage site with mean abundance of 1,128,232 ± 530,186 ind.m-2. Like in the previous sampling periods, copepods were the numerically dominant group (92.69 – 97.22 % of total zooplankton abundance) at all sampled points, with no major differences between cage and non-cage areas. The high abundance of copepods was attributed to the abundance of the juvenile stages (copepodites and Nauplius larvae) which contributed 83.72 – 92.78% of the total zooplankton abundance and this was mainly due to the Nauplius larvae (66.4 – 83.2 %). Cladocera relative abundance ranged from 0.32 – 3.98% while that of rotifers ranged from 1.55 – 3.74%. The macro-benthic community comprised molluscs, annelids and arthropods. Taxa richness ranged from 5 – 11 taxa in the cage area, and 7 – 9 taxa in the non-cage areas. The abundance of benthic invertebrates within the cage area ranged from 1,134 – 2,416 ind.m-2 and this was higher than previously recorded in September (294 – 1,415 ind.m-2). In the non-cage sites abundance was in the range of 420 – 3,992 ind.m-2. Oligochaete annelids which are reported to be very tolerant to pollution contributed 0 - 28 % of the abundance of benthos at cage sites and 3 - 20% at the non-cage sites. Diptera made the greatest contribution at almost all sites, with the percent abundance being higher in non-cage sites (40 – 86%) than what was recorded in the cage sites (37 – 82%). Chironomus spp. and Chaoborus sp. were the main contributors to the observed Diptera abundance at all sites. Six fish species, including haplochromines (Nkejje) as a single species group, were recorded in the vicinity of the cages during December 2017. Five fish species were recorded from upstream the cage site, four species from within cage area, and two species from downstream the cages. Overall mean catch rates were 1.8 fish/net/night and 148.6g/net/night compared to 1.7 fish/net/night and 175.4g/net/night recorded in September 2017. By weight, catch rates in December 2017 were highest upstream the cage site (312.1g/net/night) and also by numbers (3.1 fish/net/night). Four species of haplochromines were recorded in the vicinity of the cages during the survey of December 2017 compared to six species recorded in September 2017. The overall catch rate for the haplochromines, in December 2017 was 1.7fish/net/night and 27.5g/net/night compared to 3.4 fish/net/night and 62.3g/net/night recorded in the previous survey of September 2017. Among the fish species examined during December 2017 survey, most of the haplochromine cichlids (88.9%) were mature but only 50% breeding. Only one specimen of L. niloticus was mature and breeding. All S. afrofischeri and S. victoriae specimens examined were mature and in breeding condition while M. kannume was immature. The diet of fishes encountered comprised mostly of fish and insects, which are known natural foods of the fish species. Infection by fish parasites during the survey of December 2017 was not noticed in any fish recorded from the experimental gillnets. The overall observation on concentrations of nutrients, levels of physico-chemical variables, and biotic communities indicated minimal impact of cages on water quality. The farm should therefore continue adhering to the best environmentally sustainable aquaculture practices, especially continuing with fallowing or rotation of cages to allow resident organisms maintain their natural population densities, distribution and community structure in the area; reducing excess uneaten feed and other suspended materials which would impact on nutrient status and biota; as well as wise use of any chemicals in the area.

Description: In September 2002, side scan sonar was used to image a portion of the sea floor in the northern OCNMS and was mosaiced at 1-meter pixel resolution using 100 kHz datacollected at 300-meter range scale. Video from a remotely-operated vehicle (ROV), bathymetry data, sedimentary samples, and sonar mapping have been integrated todescribe geological and biological aspects of habitat and polygon features have been created and attributed with a hierarchical deep-water marine benthic classificationscheme (Greene et al. 1999). The data can be used with geographic information system (GIS) software for display, query, and analysis. Textural analysis of the sonar imagesprovided a relatively automated method for delineating substrate into three broad classes representing soft, mixed sediment, and hard bottom. Microhabitat and presence ofcertain biologic attributes were also populated into the polygon features, but strictly limited to areas where video groundtruthing occurred. Further groundtruthing work inspecific areas would improve confidence in the classified habitat map. (PDF contains 22 pages.)

Description: One goal of Gray’s Reef National Marine Sanctuary (NMS) is to protect the unique community found within the Sanctuary’s boundaries. An understanding of the ecologicalinteractions, including trophic structure, among these organisms is necessary to realize this goal. Therefore, diet information for 184 fish species was summarized from 113 published studies. Among the fish included are 84 fish species currently known to reside in Gray’s Reef NMS. Thelocations of these studies ranged from the Atlantic Ocean off the coast of the northeast United States to northern Brazil, the Gulf of Mexico, and the Caribbean. All of the species described in this bibliography occur in the southeast United States and are, therefore, current or potential residents of Gray’s Reef National Marine Sanctuary. Each entry includes the objectives, briefmethods, and conclusions of the article. The bibliography is also indexed by species. (PDF contains 64 pages.)

Description: This report documents abundance and cover for selected elements of the benthic coral reef assemblage at the site of the 1984 grounding of the M/V Wellwood on Molasses Reef,Florida Keys. The purpose of the effort was to establish a pre-construction baseline before the installation of reef modules at the site. The installation process is intended to stabilize fractured substrates that were recently exposed by storm impacts, and to provide three-dimensional relief in order to enhance reef community recovery. It is hoped that the restoration effort will result in a biological assemblage with the character of the transition community that would exist there had the incident not occurred. To date, the assemblage has developed the character of a comparatively featureless hard ground similar in composition to hard ground areas and transitionzones surrounding the grounding site. These data will allow scientists and resource managers to better track the trajectory of recovery following the installation of modules. Direct counts of scleractinian and gorgonian corals, hydrocorals of the genus Millepora, and zoanthids of the genus Palythoa were made in three areas within and around the grounding site. The site is poorly developed with respect to scleractinian colony size and cover compared to surrounding areas. Key scleractinian species necessary for the development of topographic relief in the area denuded by the grounding are not well represented in the current community. Though gorgonian cover and richness is similar in all study areas, gorgonian community recovery in the damaged area is not complete. Unlike surrounding areas, one species, Pseudopterogorgia americana, accounts for over half of all corals at the grounding site, over 80% of all gorgonians, and nearly all the coral cover. Based on these findings and other observations made in the 18 years since the grounding, recommendations are made that should be considered in the course of human intervention targeted at stabilizing and enhancing the site. (PDF contains 24 pages.)

Description: Inputs of toxic chemicals provide one of the major types of anthropogenic stress threatening our Nation's coastal and estuarine waters. To assess this threat, the National Oceanic and Atmospheric Administration's (NOAA’s) National Status and Trends (NS&T) Program Mussel Watch Project monitors the concentrations of more than 70 toxic chemicals in sediments and on the whole soft-parts of mussels and oysters at over 300 sites around the U.S. Twenty of the 25 designated areas that comprise NOAA's National EstuarineResearch Reserve System (NERRS) have one or more Mussel Watch monitoring sites. Trace elements and organic contaminants were quantified including As, Ag, Cd, Cu, Hg, Ni, Pb, Zn, ΣPCBs, ΣPAHs, DDT and its metabolites, and butyltins. The Mussel Watch sites located in or near the 20 Reserves provide for both status and trends. Generally the Reserves have trace element and organic contaminant concentrations that are at or below the median concentration determined for all NS&T Mussel Watch monitoring data. Trends were derived using the Spearman-rank correlation coefficient. It was possible to determine if trends exist for sites at which six or more years of data are available. Generally no trends were found for traceelements but when trends were found they were usually decreasing. The same general conclusion holds for organic contaminants but more decreasing trends were found than for trace elements. The greatest number of decreasing trends were found for tributyltin and its metabolites. (PDF contains 203 pages)

Description: Center for Coastal Monitoring and Assessment

Description: Thirty sites were sampled in southern Biscayne Bay and Manatee Bay in December 1999 to determine the extent of toxicity in sediments. Analyses and assays included: pesticides and phenols in seawater; chemical contaminants in sediment; amphipod mortality, HRGS P450, sea urchin sperm fertilization and embryology, MicrotoxTM, MutatoxTM, grass shrimp AChE and juvenile clam mortality assays; sea urchin sperm, amphipod and oyster DNA damage; and benthic community assessment. Sediment sites near the mouth of canals showed evidence of contamination. Contaminant plumes and associated toxicity do not appear to extend seaward of the mouth of the canals in an appreciable manner. Concentrations of contaminants in the sediments in open areas of Biscayne and Manatee Bays are generally low. (PDF contains 140 pages)

Description: Center for Coastal Monitoring and Assessment

Description: As a component of a three-year cooperative effort of the Washington State Department of Ecology and the National Oceanic and Atmospheric Administration, surficial sediment samples from 100 locations in southern Puget Sound were collected in 1999 to determine their relative quality based on measures of toxicity, chemical contamination, and benthic infaunal assemblage structure. The surveyencompassed an area of approximately 858 km2, ranging from East and Colvos Passages south to Oakland Bay, and including Hood Canal. Toxic responses were most severe in some of the industrialized waterways of Tacoma’s Commencement Bay. Other industrialized harbors in whichsediments induced toxic responses on smaller scales included the Port of Olympia, Oakland Bay at Shelton, Gig Harbor, Port Ludlow, and Port Gamble. Based on the methods selected for this survey, the spatial extent of toxicity for the southern Puget Sound survey area was 0% of the total survey area for amphipod survival, 5.7% for urchin fertilization, 0.2% for microbial bioluminescence, and 5-38% with the cytochrome P450 HRGS assay. Measurements of trace metals, PAHs, PCBs, chlorinated pesticides, other organic chemicals, and other characteristics of the sediments, indicated that 20 of the 100 samples collected had one or more chemical concentrations that exceededapplicable, effects-based sediment guidelines and/or Washington State standards. Chemical contamination was highest in eight samples collected in or near the industrialized waterways of Commencement Bay. Samples from the Thea Foss and Middle Waterways were primarilycontaminated with a mixture of PAHs and trace metals, whereas those from Hylebos Waterway were contaminated with chlorinated organic hydrocarbons. The remaining 12 samples with elevated chemical concentrations primarily had high levels of other chemicals, including bis(2-ethylhexyl)phthalate, benzoic acid, benzyl alcohol, and phenol. The characteristics of benthic infaunal assemblages in south Puget Sound differed considerably among locations and habitat types throughout the study area. In general, many of the small embayments and inlets throughout the studyarea had infaunal assemblages with relatively low total abundance, taxa richness, evenness, and dominance values, although total abundance values were very high in some cases, typically due to high abundance of one organism such as the polychaete Aphelochaeta sp. N1. The majority of thesamples collected from passages, outer embayments, and larger bodies of water tended to have infaunal assemblages with higher total abundance, taxa richness, evenness, and dominance values. Two samples collected in the Port of Olympia near a superfund cleanup site had no living organisms in them. A weight-of-evidence approach used to simultaneously examine all three “sediment qualitytriad” parameters, identified 11 stations (representing 4.4 km2, 0.5% of the total study area) with sediment toxicity, chemical contamination, and altered benthos (i.e., degraded sediment quality), 36 stations (493.5 km2, 57.5% total study area) with no toxicity or chemical contamination (i.e., high sediment quality), 35 stations (274.1 km2, 32.0% total study area) with one impaired sediment triadparameter (i.e., intermediate/high sediment quality), and 18 stations (85.7km2, 10.0% total study area) with two impaired sediment parameters (i.e., intermediate/degraded quality sediments). Generally, upon comparison, the number of stations with degraded sediments based upon the sediment quality triad of data was slightly greater in the central Puget Sound than in the northern and southern Puget Sound study areas, with the percent of the total study area degraded in each region decreasing from central to north to south (2.8, 1.3 and 0.5%, respectively). Overall, the sediments collected in Puget Sound during the combined 1997-1999 surveys were among the least contaminated relative to other marine bays and estuaries studied by NOAA using equivalent methods. (PDF contains 351 pages)

Description: Center for Coastal Monitoring and Assessment; Washington State Department of Ecology Environmental Assessment Program Environmental Monitoring and Trends Section Olympia, Washington Publication No. 02-03-033

Description: Charles M. Breder Jr. “hypothesis” diary is a deviation from the field diaries that form part of the Breder collection housed at the Arthur Vining Davis Library, MoteMarine Laboratory. There are no notes or observations from specific scientific expeditions in the document. Instead, the contents provide an insight into the early meticulous scientific thoughts of this biologist, and how he examines and develops these ideas. It is apparent that among Dr. Breder’s passions was his continual search for knowledge about questions that still besieged many scientists. Topics discussed include symmetry, origin of the atmosphere, origin of life, mechanical analogies of organisms, aquaria as an organism, astrobiology, entropy, evolution of species, and other topics. The diary was transcribed as part of the Coastal Estuarine Data/Document Rescue andArcheology effort for South Florida. (PDF contains 33 pages)

Description: Center for Coastal Monitoring and Assessment; Mote Technical Report No. 860

Description: During the summer of 1929, Dr. Charles M. Breder, Jr., employed at that time by the New York Aquarium and American Museum of Natural History, visited the Carnegie Laboratory in the Dry Tortugas to study the development and habits of flying fishes and their allies. The diary of the trip was donated to the Mote Marine Laboratory Library by his family. Dr. Breder's meticulous handwritten account gives us the opportunity to see the simple yet great details of his observations and field experiments. His notes reveal the findings and thoughts of one of the world's greatest ichthyologists. The diary was transcribed as part of the Coastal Estuarine Data/Document Rescue and Archeologyeffort for South Florida. (PDF contains 75 pages)

Description: Center for Coastal Monitoring and Assessment; Mote Technical Report No. 802

Description: Dr. Charles M. Breder, a well known ichthyologist, kept meticulous field diaries throughout his career. This publication is a transcription of field notes recorded during the Bacon Andros Expeditions, and trips to Florida, Ohio and Illinois during the 1930s. Breder's work in Andros included exploration of a "blue hole", inland ecosystems, and collection of marine and terrestrial specimens. Anecdotes include descriptions of camping on the beach, the "filly-mingoes" (flamingos) of Andros Island, the MarineStudios of Jacksonville, FL, a trip to Havana, and the birth of seahorses. This publication is part of a series of transcriptions of Dr. Breder's diaries. (PDF contains 55 pages)

Description: Mote Technical Report No. 884; Center for Coastal Monitoring and Assessment

Description: Dr. Charles M. Breder participated on the 1934 expedition of the Atlantis from Woods Hole, Massachusetts to Panama and back and kept a field diary of daily activities. The Atlantis expedition of 1934, led by Prof. A. E. Parr, was a milestone in the history of scientific discovery in the Sargasso Sea and the West Indies. Although naturalists had visited the Sargasso Sea for many years, the Atlantis voyage was the first attempt to investigate in detailed quantitative manner biological problems about this varying, intermittent ‘false’ bottom of living, floating plants and associated fauna. In addition to Dr. Breder, the party also consisted of Dr. Alexander Forbes, Harvard University and Trustee of the Woods Hole Oceanographic Institution (WHOI); T. S. Greenwood, WHOI hydrographer; M. D. Burkenroad, Yale University’s Bingham Laboratory, carcinology and Sargasso epizoa; M. Bishop, Peabody Museum of Natural History, Zoology Dept., collections and preparations and H. Sears, WHOI ichthyologist. The itinerary included the following waypoints: Woods Hole, the Bermudas, Turks Islands, Kingston, Colon, along the Mosquito Bank off of Nicaragua, off the north coast of Jamaica, along the south coast of Cuba, Bartlett Deep, to off the Isle of Pines, through the Yucatan Channel, off Havana, off Key West, to Miami, to New York City, and then the return to Woods Hole. During the expedition, Breder collected rare and little-known flying fish species and developed a method for hatching and growing flying fish larvae. (PDF contains 48 pages)

Description: Mote Technical Report No. 949; Center for Coastal Monitoring and Assessment

Description: The Biscayne Bay Benthic Sampling Program was divided into two phases. In Phase I, sixty sampling stations were established in Biscayne Bay (including Dumfoundling Bay and Card Sound) representing diverse habitats. The stations were visited in the wet season (late fall of 1981) and in the dry season (midwinter of 1982). At each station certain abiotic conditions were measured or estimated. These included depth, sources of freshwater inflow and pollution, bottom characteristics, current direction and speed, surface and bottom temperature, salinity and dissolved oxygen, and water clarity was estimated with a secchidisk. Seagrass blades and macroalgae were counted in a 0.1-m2 grid placed so as to best represent the bottom community within a 50-foot radius. Underwater 35-mm photographswere made of the bottom using flash apparatus.Benthic samples were collected using a petite Ponar dredge. These samples were washed through a 5-mm mesh screen, fixed in formalin in the field, and later sorted and identifiedby experts to a pre-agreed taxonomic level.During the wet season sampling period, a nonquantitative one-meter wide trawl was made of the epibenthic community. These samples were also washed, fixed, sorted and identified.During the dry season sampling period, sediment cores were collected at each station not located on bare rock. These cores were analyzed for sediment size and organic composition by personnel of the University of Miami.Data resulting from the sampling were entered into a computer. These data were subjected to cluster analyses, Shannon-Weaver diversity analysis, multiple regression analysis of variance and covariance, and factor analysis.In Phase II of the program, fifteen stations were selected from among the sixty of Phase I. These stations were sampled quarterly. At each quarter, five Petite Ponar dredge samples were collected from each station. As in Phase I, observations and measurements, includingseagrass blade counts, were made at each station. In Phase II, polychaete specimens collected were given to a separate contractor for analysis to the species level. Theseanalyses included mean, standard deviation, coefficient of dispersion, percent of total, and numeric rank for each organism in each station as well as number of species, Shannon-Weaver taxa diversity, and dominance (the compliment of Simpson's Index) for each station. Multiple regression analysis of variance and covariance, and factor analysis were applied to the data to determine effect of abiotic factors measured at each station. (PDF contains 96 pages)

Description: Center for Coastal Monitoring and Assessment; A.Y. Cantillo, Editor

Description: Polycyclic aromatic hydrocarbons, butyltins, polychlorinated biphenyls, DDT and metabolites, other chlorinated pesticides, trace and major elements, and a number of measures of contaminant effects are quantified in bivalves and sediments collected as part of the NOAA National Status and Trends (NS&T) Program. This document contains descriptions of some of the sampling and analytical protocols used by NS&T contract laboratories from 1993 through 1996. (PDF contains 257 pages)

Description: Coastal Monitoring and Bioeffects Assessment Division

Description: Between 1994 and 1997, 258 tissue and 178 sediment samples were analyzed for chlorpyrifos throughout the coastal United States and the Great Lakes. Subsequently, 95 ofthe 1997 tissue samples were reanalyzed for endosulfan. Tissue chlorpyrifos concentrations, which exceeded the 90th percentile, were found in coastal regions known to have highagricultural use rates but also strongly correlated with sites near high population. The highest concentrations of endosulfans in contrast, were generally limited to agricultural regions of the country. Detections of chlorpyrifos at several Alaskan sites suggest an atmospherictransport mechanism. Many Great Lakes sites had chlorpyrifos tissue concentrations above the 90th percentile which decreased with increasing distance from the Corn Belt region (Iowa, Indiana, Illinois, and Wisconsin) where most agriculturally applied chlorpyrifos is used. Correlation analysis suggests that fluvial discharge is the primary transport pathway on the Atlantic and Gulf of Mexico coasts for chlorpyrifos but not necessarily for endosulfans. (PDF contains 28 pages)

Description: Center for Coastal Monitoring and Assessment

Description: Toxic chemicals can enter the marine environment through numerous routes: stormwater runoff, industrial point source discharges, municipal wastewater discharges, atmosphericdeposition, accidental spills, illegal dumping, pesticide applications and agricultural practices. Once they enter a receiving system, toxicants often become bound to suspended particles and increase in density sufficiently to sink to the bottom. Sediments are one of the major repositoriesof contaminants in aquatic envronments. Furthermore, if they become sufficiently contaminated sediments can act as sources of toxicants to important biota. Sediment quality data are direct indicators of the health of coastal aquatic habitats.Sediment quality investigations conducted by the National Oceanic and Atmospheric Administration (NOAA) and others have indicated that toxic chemicals are found in the sediments and biota of some estuaries in South Carolina and Georgia (NOAA, 1992). This report documents the toxicity of sediments collected within five selected estuaries: Savannah River, Winyah Bay, Charleston Harbor, St. Simons Sound, and Leadenwah Creek (Figure 1). (PDF contains 292 pages)

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: 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: Executive Summary:The Estuary Restoration Act of 2000 (ERA), Title I of the Estuaries and Clean Waters Act of 2000, was created to promote the restoration of habitats along the coast of the United States (including the US protectorates and the Great Lakes). The NOAA National Centers for Coastal Ocean Science was charged with the development of a guidance manual for monitoring plans under this Act.This guidance manual, titled Science-Based Restoration Monitoring of Coastal Habitats, is written in two volumes. It provides technical assistance, outlines necessary steps, and provides useful tools for the development and implementation of sound scientific monitoring of coastal restoration efforts. In addition, this manual offers a means to detect early warnings that the restoration is on track or not, to gauge how well a restoration site is functioning, to coordinate projects and efforts for consistent and successful restoration, and to evaluate the ecological health of specific coastal habitats both before and after project completion (Galatowitsch et al. 1998).The following habitats have been selected for discussion in this manual: water column, rock bottom, coral reefs, oyster reefs, soft bottom, kelp and other macroalgae, rocky shoreline, soft shoreline, submerged aquatic vegetation, marshes, mangrove swamps, deepwater swamps, and riverine forests. The classification of habitats used in this document is generally based on that of Cowardin et al. (1979) in their Classification of Wetlands and Deepwater Habitats of the United States, as called for in the ERA Estuary Habitat Restoration Strategy.This manual is not intended to be a restoration monitoring “cookbook” that provides templates of monitoring plans for specific habitats. The interdependence of a large number of site-specific factors causes habitat types to vary in physical and biological structure within and between regions and geographic locations (Kusler and Kentula 1990). Monitoring approaches used should be tailored to these differences. However, even with the diversity of habitats that may need to be restored and the extreme geographic range across which these habitats occur, there are consistent principles and approaches that form a common basis for effective monitoring.Volume One, titled A Framework for Monitoring Plans under the Estuaries and Clean Waters Act of 2000, begins with definitions and background information. Topics such as restoration, restoration monitoring, estuaries, and the role of socioeconomics in restoration are discussed. In addition, the habitats selected for discussion in this manual are briefly described. (PDF contains 116 pages)

Description: Healthy coastal habitats are not only important ecologically; they also support healthy coastal communities and improve the quality of people’s lives. Despite their many benefits and values, coastal habitats have been systematically modified, degraded, and destroyed throughout the United States and its protectorates beginning with European colonization in the 1600’s (Dahl 1990). As a result, many coastal habitats around the United States are in desperate need of restoration. The monitoring of restoration projects, the focus of this document, is necessary to ensure that restoration efforts are successful, to further the science, and to increase the efficiency of future restoration efforts.

Description: Davidson Seamount is one of the largest seamounts in U.S. waters and the first to be characterized as a “seamount.” In 2002 and 2006, the Monterey Bay National Marine Sanctuary(MBNMS) led two multi-institutional expeditions to characterize the geology and natural history of Davidson Seamount. Results from these expeditions to Davidson Seamount are adding to the scientific knowledge of seamounts, including the discovery of new species. In November 2008, the MBNMS boundary was expanded to include the Davidson Seamount. In addition, a management plan for Davidson Seamount was created to develop resource protection, education, and research strategies for the area. The purpose of this taxonomic guide is to create aninventory of benthic and mid-water organisms observed at the Davidson Seamount to provide a baseline taxonomic characterization. At least 237 taxa were observed and are presented in this guide; including 15 new or undescribed species (8 sponges, 3 corals, 1 ctenophore, 1 nudibranch,1 polychaete, 1 tunicate) recently or currently being described by taxonomic experts. This is the first taxonomic guide to Davidson Seamount, and is intended to be revised in the future as we learn more about the seamount and the organisms that live there. (PDF has 145 pages.)

Description: Executive Summary:Tropical marine ecosystems in the Caribbean region are inextricably linked through the movement of pollutants, nutrients, diseases, and other stressors, which threaten to further degrade coral reef communities. The magnitude of change that is occurring within the region is considerable, and solutions will require investigating pros and cons of networks of marine protected areas (MPAs), cooperation of neighboring countries, improved understanding of howexternal stressors degrade local marine resources, and ameliorating those stressors.Connectivity can be broadly defined as the exchange of materials (e.g., nutrients and pollutants), organisms, and genes and can be divided into: 1) genetic or evolutionary connectivity that concerns the exchange of organisms and genes, 2) demographic connectivity, which is the exchange of individuals among local groups, and 3) oceanographic connectivity, which includes flow of materials and circulation patterns and variability that underpin much of all these exchanges. Presently, we understand little about connectivity at specific locations beyond model outputs, and yet we must manage MPAs with connectivity in mind. A key to successful MPA management is how to most effectively work with scientists to acquire the information managersneed.Oceanography connectivity is poorly understood, and even less is known about the shape of the dispersal curve for most species. Dispersal kernels differ for various systems, species, and life histories and are likely highly variable in space and time. Furthermore, the implications ofdifferent dispersal kernels on population dynamics and management of species is unknown. However, small dispersal kernels are the norm - not the exception. Linking patterns of dispersal to management options is difficult given the present state of knowledge.The behavioral component of larval dispersal has a major impact on where larvae settle. Individual larval behavior and life history details are required to produce meaningful simulations of population connectivity. Biological inputs are critical determinants of dispersal outcomes beyond what can be gleaned from models of passive dispersal.There is considerable temporal and spatial variation to connectivity patterns. New models are increasingly being developed, but these must be validated to understand upstream-downstream neighborhoods, dispersal corridors, stepping stones, and source/sink dynamics. At present,models are mainly useful for providing generalities and generating hypotheses. Low-technology approaches such as drifter vials and oceanographic drogues are useful, affordable options for understanding local connectivity.The “silver bullet” approach to MPA design may not be possible for several reasons. Genetic connectivity studies reveal divergent population genetic structures despite similar larval life histories. Historical stochasticity in reproduction and/or recruitment likely has important, longlasting consequences on present day genetic structure. (PDF has 200 pages.)

Description: This document presents the results of the first three monitoring events to track the recovery of a repaired coral reef injured by the M/V Elpis vessel grounding incident ofNovember 11, 1989. This grounding occurred within the boundaries of what at the time was designated the Key Largo National Marine Sanctuary (NMS), now designated theKey Largo NMS Existing Management Area within the Florida Keys National Marine Sanctuary (FKNMS). Pursuant to the National Marine Sanctuaries Act (NMSA) 16 U.S.C. 1431 et seq., and the Florida Keys National Marine Sanctuary and Protection Act (FKNMSPA) of 1990, NOAA is the federal trustee for the natural and cultural resources of the FKNMS. Under Section 312 of the NMSA, NOAA has the authority to recover monetary damages for injury, destruction, or loss of Sanctuary resources, and to use therecovered monies to restore injured or lost sanctuary resources within the FKNMS. The restoration monitoring program tracks patterns of biological recovery, determines the success of restoration measures, and assesses the resiliency to environmental and anthropogenic disturbances of the site over time. To evaluate restoration success,reference habitats adjacent to the restoration site are concurrently monitored to compare the condition of restored reef areas with natural coral reef areas unimpacted by the vessel grounding. Restoration of the site was completed September 1995, and thus far three monitoring events have occurred; one in the summer of 2004, one in the summer of 2005, and the latest in the summer of 2007. The monitoring in 2004 was in the nature of a “pilot project,” or proof of concept. Only the quantitative results of the 2005 and 2007monitoring are presented and discussed. Monitoring has consisted of assessment of the structural stability of limestone boulders used in the restoration and comparison of the coral communities on the boulders and reference areas. Corals are divided into Gorgonians, Milleporans, and Scleractinians. Coral densities at the Restored andReference areas for the 2005 and 2007 events are compared, and it is shown that the densities of all taxa in the Restored area are greater by 2007, though not significantly so. For the Scleractinians, number and percentage of colonies by species, as well as several common biodiversity indices are provided. The greater biodiversity of the Restored area is evidenced. Also, size-class frequency distributions for Agaricia spp. (Scleractinia) arepresented. These demonstrate the approaching convergence of the Restored and Reference areas in this regard. An inter-annual comparison of densities, within both areas, for all three Orders, is presented. The most noteworthy finding was the relative consistency across time for all taxa in each area. Finally, certain anomalies regarding species settlement patterns are presented. (PDF contains 48 pages.)

Description: Executive Summary:The marine environment plays a critical role in the amount of carbon dioxide (CO2) that remains within Earth’s atmosphere, but has not received as much attention as theterrestrial environment when it comes to climate change discussions, programs, and plans for action. It is now apparent that the oceans have begun to reach a state of CO2saturation, no longer maintaining the “steady-state” carbon cycle that existed prior to the Industrial Revolution. The increasing amount of CO2 present within the oceans and theatmosphere has an effect on climate and a cascading effect on the marine environment. Potential physical effects of climate change within the marine environment, includingocean acidification, changes in wind and upwelling regimes, increasing global sea surface temperatures, and sea level rise, can lead to dramatic, fundamental changes within marine and coastal ecosystems. Altered ecosystems can result in changing coastal economies through a reduction in marine ecosystem services such as commercial fish stocks andcoastal tourism.Local impacts from climate change should be a front line issue for natural resource managers, but they often feel too overwhelmed by the magnitude of this issue to begin totake action. They may not feel they have the time, funding, or staff to take on a challenge as large as climate change and continue to not act as a result. Already, natural resource managers work to balance the needs of humans and the economy with ecosystem biodiversity and resilience. Responsible decisions are made each day that consider a widevariety of stakeholders, including community members, agencies, non-profit organizations, and business/industry. The issue of climate change must be approached as a collaborative effort, one that natural resource managers can facilitate by balancing human demands with healthy ecosystem function through research and monitoring,education and outreach, and policy reform.The Scientific Expert Group on Climate Change in their 2007 report titled, “Confronting Climate Change: Avoiding the Unmanageable and Managing the Unavoidable” chargedgovernments around the world with developing strategies to “adapt to ongoing and future changes in climate change by integrating the implications of climate change into resource management and infrastructure development”. Resource managers must make future management decisions within an uncertain and changing climate based on both physical and biological ecosystem response to climate change and human perception of and response to the issue. Climate change is the biggest threat facing any protected area today and resource managers must lead the charge in addressing this threat. (PDF has 59 pages.)

Description: Executive Summary:The Connectivity Colloquium evolved from an exhortation by Dan Basta, Director of the National Marine Sanctuary Program, to come together and assess what we know about the condition of our natural resources, identify information gaps and how to fill them, and transform science and management from an emphasis on documentation to a nexus for action. This purpose in some ways reflects the initiation of the Florida Keys National Marine Sanctuary itself, which was designated by an act of the U.S. Congress in 1990 in the aftermath of the 1989 Exxon Valdez oil spill in Alaska and three major ship groundings of the Florida Reef Tract in late 1989. Over the next seven years NOAA worked with federal, state, and local partners to develop a comprehensive management plan for the Sanctuary implemented under a co-trustee partnership between NOAA and the State of Florida. (PDF contains 270 pages; 14Mb)

Description: The Scientific Forum on the Gulf of Mexico: The Islands in the Stream Concept took place in January 2008 in Sarasota, Florida. The purpose of the meeting was to bring together scientists and managers from around the Gulf of Mexico to discuss a range of topics on our knowledge of the Gulf of Mexico, from its geology to larger-scale connectivity to the Caribbean region, and their applications to the concept of a more integrated approach to area-based management.The forum included six panels of invited experts who spoke on the oceanographic and biological features in the Gulf of Mexico, including connections with Mexico and the Mesoamerican barrier reef system, and the legal and regulatory structure currently in place. The charge to the group was to share information, identify gaps in our knowledge, identify additional potential areas forprotection, and discuss available science about connectivity and the potential value of establishing a marine protected area network in the Gulf of Mexico. (PDF has 108 pages.)

Description: Without knowledge of basic seafloor characteristics, the ability to address any number of critical marine and/or coastal management issues is diminished. For example,management and conservation of essential fish habitat (EFH), a requirement mandated by federally guided fishery management plans (FMPs), requires among other things adescription of habitats for federally managed species. Although the list of attributes important to habitat are numerous, the ability to efficiently and effectively describe many, and especially at the scales required, does not exist with the tools currently available. However, several characteristics of seafloor morphology are readily obtainable at multiple scales and can serve as useful descriptors of habitat. Recent advancements in acoustic technology, such as multibeam echosounding (MBES), can provide remote indication of surficial sediment properties such as texture, hardness, or roughness, and further permit highly detailed renderings of seafloor morphology. With acoustic-based surveys providing a relatively efficient method for data acquisition, there exists a need forefficient and reproducible automated segmentation routines to process the data. Using MBES data collected by the Olympic Coast National Marine Sanctuary (OCNMS), andthrough a contracted seafloor survey, we expanded on the techniques of Cutter et al. (2003) to describe an objective repeatable process that uses parameterized local Fourierhistogram (LFH) texture features to automate segmentation of surficial sediments from acoustic imagery using a maximum likelihood decision rule. Sonar signatures andclassification performance were evaluated using video imagery obtained from a towed camera sled. Segmented raster images were converted to polygon features and attributedusing a hierarchical deep-water marine benthic classification scheme (Greene et al. 1999) for use in a geographical information system (GIS). (PDF contains 41 pages.)

Description: Habitat mapping and characterization has been defined as a high-priority management issue for the Olympic Coast National Marine Sanctuary (OCNMS), especially for poorlyknown deep-sea habitats that may be sensitive to anthropogenic disturbance. As a result, a team of scientists from OCNMS, National Centers for Coastal Ocean Science (NCCOS), and other partnering institutions initiated a series of surveys to assess the distribution of deep-sea coral/sponge assemblages within the sanctuary and to look for evidence of potential anthropogenic impacts in these critical habitats. Initial results indicated that remotely delineating areas of hard bottom substrate through acoustic sensing could be a useful tool to increase the efficiency and success of subsequent ROV-based surveys of the associated deep-sea fauna. Accordingly, side scan sonar surveys were conducted in May 2004, June 2005, and April 2006 aboard the NOAA Ship McArthur II to: (1) obtain additional imagery of the seafloor for broader habitat-mapping coverage of sanctuary waters, and (2) help delineate suitable deep-sea coral/sponge habitat, in areas of both high and low commercial-fishing activities, to serve as sites for surveying-in more detail using an ROV on subsequent cruises. Several regions of the sea floor throughout the OCNMS were surveyed and mosaicked at 1-meter pixel resolution. Imagery from the side scan sonar mapping efforts was integrated with other complementary data from a towed camera sled, ROVs, sedimentary samples, andbathymetry records to describe geological and biological (where possible) aspects of habitat. Using a hierarchical deep-water marine benthic classification scheme (Greene etal. 1999), we created a preliminary map of various habitat polygon features for use in a geographical information system (GIS). This report provides a description of themapping and groundtruthing efforts as well as results of the image classification procedure for each of the areas surveyed. (PDF contains 60 pages.)

Description: Executive Summary:Circulation and Exchange of Florida Bay and South Florida Coastal Waters The coastal ecosystem of South Florida is comprised of distinct marine environments. Circulation of surface waters and exchange processes, which respond to both local and regional forcings, interconnect different coastal environments. In addition, re-circulating current systemswithin the South Florida coastal ecosystem such as the Tortugas Gyre contribute to retention of locally spawned larvae.Variability in salinity, chlorophyll, and light transmittance occurs on a wide range of temporal and spatial scales, in response to both natural forcing, such as seasonal precipitation and evaporation and interannual “El Niño” climate signals, and anthropogenic forcing, such as water management practices in south Florida. The full time series of surface property maps are posted at www.aoml.noaa.gov/sfp.Regional surface circulation patterns, shown by satellite-tracked surface drifters, respond to large-scale forcing such as wind variability and sea level slopes. Recent patterns include slow flow from near the mouth of the Shark River to the Lower Keys, rapid flow from the Tortugas tothe shelf of the Carolinas, and flow from the Tortugas around the Tortugas Gyre and out of the Florida Straits.The Southwest Florida Shelf and the Atlantic side of the Florida Keys coastal zone are directly connected by passages between the islands of the Middle and Lower Keys. Movement of water between these regions depends on a combination of local wind-forced currents and gravitydriventransports through the passages, produced by cross-Key sea level differences on time scales of several days to weeks, which arise because of differences in physical characteristics (shape, orientation, and depth) of the shelf on either side of the Keys. A southeastward meanflow transports water from western Florida Bay, which undergoes large variations in water quality, to the reef tract.Adequate sampling of oceanographic events requires both the capability of near real-time recognition of these events, and the flexibility to rapidly stage targeted field sampling. Capacity to respond to events is increasing, as demonstrated by investigations of the 2002 “blackwater”event and a 2003 entrainment of Mississippi River water to the Tortugas. (PDF contains 364 pages.)

Description: With elevating interest to establish conservation efforts for groundfish stocks and continued scrutiny over the value of marine protected areas along the west coast, theimportance of enhancing our knowledge of seabed characteristics through mapping activities is becoming increasingly more important, especially in a timely manner.Shortly after the inception of the Seabed Mapping Initiative instituted with the US Geological Survey (USGS), the National Marine Sanctuary Program (NMSP) assembleda panel of habitat mapping experts. They determined that the status of existing data sets and future data acquisition needs varied widely among the individual sanctuaries and that more detailed site assessments were needed to better prioritize mapping efforts and outline an overall joint strategy. To assist with that specific effort and provide pertinent information for the Olympic Coast National Marine Sanctuary’s (OCNMS) Management Plan Review, this report summarizes the mapping efforts that have taken place at the site to date; calculates a timeframe for completion of baseline mapping efforts when operating under current data acquisition limitations; describes an optimized survey strategy to dramatically reduce the required time to complete baseline surveying; and provides estimates for the needed vessel sea-days (DAS) to accomplish baseline survey completion within a 2, 5 and 10 year timeframe. (PDF contains 38 pages.)

Description: This document presents the results of the monitoring of a repaired coral reef injured by the M/V Jacquelyn L vessel grounding incident of July 7, 1991. This grounding occurredin Florida state waters within the boundaries of the Florida Keys National Marine Sanctuary (FKNMS). The National Oceanic and Atmospheric Administration (NOAA)and the Board of Trustees of the Internal Improvement Trust Fund of the State of Florida, (“State of Florida” or “state”) are the co-trustees for the natural resources within the FKNMS and, thus, are responsible for mediating the restoration of the damaged marine resources and monitoring the outcome of the restoration actions. The restoration monitoring program tracks patterns of biological recovery, determines the success of restoration measures, and assesses the resiliency to environmental and anthropogenic disturbances of the site over time.The monitoring program at the Jacquelyn L site was to have included an assessment of the structural stability of installed restoration modules and biological condition ofreattached corals performed on the following schedule: immediately (i.e., baseline), 1, 3, and 6 years after restoration and following a catastrophic event. Restoration of this site was completed on July 20, 2000. Due to unavoidable delays in the settlement of the case, the “baseline” monitoring event for this site occurred in July 2004. The catastrophic monitoring event occurred on August 31, 2004, some 2 ½ weeks after the passage ofHurricane Charley which passed nearby, almost directly over the Dry Tortugas. In September 2005, the year one monitoring event occurred shortly after the passage ofHurricane Katrina, some 70 km to the NW. This report presents the results of all three monitoring events. (PDF contains 31 pages.)

Description: This document presents the results of the monitoring of a repaired coral reef injured by the M/V Connected vessel grounding incident of March 27, 2001. This groundingoccurred in Florida state waters within the boundaries of the Florida Keys National Marine Sanctuary (FKNMS). The National Oceanic and Atmospheric Administration (NOAA) and the Board of Trustees of the Internal Improvement Trust Fund of the State of Florida, (“State of Florida” or “state”) are the co-trustees for the natural resourceswithin the FKNMS and, thus, are responsible for mediating the restoration of the damaged marine resources and monitoring the outcome of the restoration actions. Therestoration monitoring program tracks patterns of biological recovery, determines the success of restoration measures, and assesses the resiliency to environmental andanthropogenic disturbances of the site over time.The monitoring program at the Connected site was to have included an assessment of the structural stability of installed restoration modules and biological condition of reattached corals performed on the following schedule: immediately (i.e., baseline), 1, 3, and 6 years after restoration and following a catastrophic event. Restoration of this site was completed on July 20, 2001. Due to unavoidable delays in the settlement of the case, the“baseline” monitoring event for this site occurred in July 2004. The catastrophic monitoring event occurred on August 31, 2004, some 2 ½ weeks after the passage of Hurricane Charley which passed nearby, almost directly over the Dry Tortugas. In September 2005, the year one monitoring event occurred shortly after the passage of Hurricane Katrina, some 70 km to the NW. This report presents the results of all three monitoring events. (PDF contains 37 pages.)

Description: This document presents the results of baseline monitoring of a repaired coral reef injured by the M/V Wave Walker vessel grounding incident of January 19, 2001. This grounding occurred in Florida state waters within the boundaries of the Florida Keys National Marine Sanctuary (FKNMS). The National Oceanic and Atmospheric Administration(NOAA) and the Board of Trustees of the Internal Improvement Trust Fund of the State of Florida, (“State of Florida” or “state”) are the co-trustees for the natural resources within the FKNMS. This report documents the efficacy of the restoration effort, the condition of the restored reef area two year and four months post-effort, and provides a picture of surrounding reference areas, so as to provide a basis for future comparisons by which to evaluate the long-term success of the restoration. (PDF contains 25 pages.)

Description: The purpose of this field guide is to provide information on nonindigenous (i.e., non-native) fishes that have been observed in Florida’s marine waters. Introductions of non-native marine fishes into Florida’s waters could be intentional or unintentional, and are likely from a variety of sources, including aquarium releases, escape from aquaculture, loss due to extreme weather events (e.g., flooding from hurricanes), and possibly transfer with ballast water or hull-fouling. Presently the lionfishes (Pterois volitans and P. miles) are the only non-native marine fish species known to be established along the coast of Florida. All other marine fishes in this guide (except the euryhaline species, see below) have infrequent occurrences, occur singly or in small groups, and have not yet become self-sustaining populations. Aquarium releases are one of the major pathways whereby nonindigenous fishes gain access to new environments (Ruiz et al. 1997; Fuller et al. 1999). Most of the nonindigenous marine fishes found in Florida’s waters are thought to be aquarium fishes that either were illegally released into the ocean or escaped captivity (e.g., during severe storm/flooding events). Indeed, south Florida is a hotspot for nonindigenous marine aquarium fishes (Semmens et al. 2004). Increased public awareness of the problems caused by released or escaped aquarium fishes may aid in stemming the frequency of releases. For example, HabitattitudeTM (www.habitattitude.net) is a national public awareness and partnership campaign that encourages aquarists and water gardeners to prevent the release of unwanted aquarium plants, fish and other animals. It prompts hobbyists to adopt alternative actions when dealing with these aquatic plants and animals. (PDF file contains 133 pages.)

Description: The Olympic Coast National Marine Sanctuary (OCNMS) continues to invest significant resources into seafloor mapping activities along Washington’s outer coast (Intelmann and Cochrane 2006; Intelmann et al. 2006; Intelmann 2006). Results from these annual mapping efforts offer a snapshot of current ground conditions, help to guide research and management activities, and provide a baseline for assessing the impacts of various threatsto important habitat. During the months of August 2004 and May and July 2005, we used side scan sonar to image several regions of the sea floor in the northern OCNMS, and thedata were mosaicked at 1-meter pixel resolution. Video from a towed camera sled, bathymetry data, sedimentary samples and side scan sonar mapping were integrated to describe geological and biological aspects of habitat. Polygon features were created and attributed with a hierarchical deep-water marine benthic classification scheme (Greene etal. 1999). For three small areas that were mapped with both side scan sonar and multibeam echosounder, we made a comparison of output from the classified images indicating little difference in results between the two methods. With these considerations, backscatter derived from multibeam bathymetry is currently a costefficient and safe method for seabed imaging in the shallow (〈30 meters) rocky waters ofOCNMS. The image quality is sufficient for classification purposes, the associated depths provide further descriptive value and risks to gear are minimized. In shallow waters (〈30 meters) which do not have a high incidence of dangerous rock pinnacles, a towed multi-beam side scan sonar could provide a better option for obtaining seafloorimagery due to the high rate of acquisition speed and high image quality, however the high probability of losing or damaging such a costly system when deployed as a towedconfiguration in the extremely rugose nearshore zones within OCNMS is a financially risky proposition. The development of newer technologies such as intereferometricmultibeam systems and bathymetric side scan systems could also provide great potential for mapping these nearshore rocky areas as they allow for high speed data acquisition,produce precisely geo-referenced side scan imagery to bathymetry, and do not experience the angular depth dependency associated with multibeam echosounders allowing larger range scales to be used in shallower water. As such, further investigation of these systems is needed to assess their efficiency and utility in these environments compared to traditional side scan sonar and multibeam bathymetry. (PDF contains 43 pages.)

Description: Although ambient (background) noise in the ocean is a topic that has been widely studied since pre-World War II, the effects of noise on marine organisms has only been afocus of concern for the last 25 years. The main point of concern has been the potential of noise to affect the health and behavior of marine mammals. The Stellwagen BankNational Marine Sanctuary (SBNMS) is a site where the degradation of habitat due to increasing noise levels is a concern because it is a feeding ground and summer haven fornumerous species of marine mammals. Ambient noise in the ocean is defined as “the part of the total noise background observed with an omnidirectional hydrophone.” It isan inherent characteristic of the medium having no specific point source. Ambient noise is comprised of a number of components that contribute to the “noise level” in varyingdegrees depending on where the noise is being measured. This report describes the current understanding of ambient noise and existing levels in the Stellwagen BankNational Marine Sanctuary. (PDF contains 32 pages.)

Description: This report summarizes the results of a characterizationof chemical contaminants in the sediments in southwestPuerto Rico. The report is part of a project to integratevarious analytical specialties to assess linkages betweenchemical contaminants and the condition of coral reefs. In this phase of the project, over 120 chemical contaminants were analyzed in sediments collected, including a number of organic (e.g., hydrocarbons), inorganic (e.g., metals), and biological (bacterial) compounds/analytes. The report also provides a preliminary analysis of the association betweensediment contaminants and coral species richness.Overall, the levels of chemical contaminants in the study area between Guanica Bay and the town of La Parguera were fairly low. At most of the sites sampled, particularlyadjacent to the town of La Parguera, concentrations oforganic and inorganic contaminants were below the median values from NOAA’s National Status and Trends Program, which monitors the Nation’s coastal and estuarine waters for chemical contaminants. Elevated levels of a number of contaminant classes were seen at the two sites sampled within Guanica Bay.An initial analysis of modeled PAH (hydrocarbon) data and coral species richness (reef building species) indicated a strong negative correlation between the presence of PAHs in the sediments and coral species richness. Additional work is needed to assess possible reasons for this observed pattern. (PDF contains 126 pages).

Description: Center for Coastal Monitoring and Assessment

Description: In April 2005, a SHOALS 1000T LIDAR system was used as an efficient alternative for safely acquiring data to describe the existing conditions of nearshore bathymetry and theintertidal zone over an approximately 40.7 km2 (11.8 nm2) portion of hazardous coastline within the Olympic Coast National Marine Sanctuary (OCNMS). Data were logged from1,593 km (860 nm) of track lines in just over 21 hours of flight time. Several islands and offshore rocks were also surveyed, and over 24,000 geo-referenced digital still photos were captured to assist with data cleaning and QA/QC. The 1 kHz bathymetry laser obtained a maximum water depth of 22.2 meters. Floating kelp beds, breaking surf lines and turbid water were all challenges to the survey. Although sea state was favorable for this time of the year, recent heavy rainfall and a persistent low-lying layer of fog reduced acquisition productivity. The existence of a completed VDatum model covering this same geographic region permitted the LIDAR data to be vertically transformed andmerged with existing shallow water multibeam data and referenced to the mean lower low water (MLLW) tidal datum. Analysis of a multibeam bathymetry-LIDAR differencesurface containing over 44,000 samples indicated surface deviations from –24.3 to 8.48 meters, with a mean difference of –0.967 meters, and standard deviation of1.762 meters. Errors in data cleaning and false detections due to interference from surf, kelp, and turbidity likely account for the larger surface separations, while the remaining general surface difference trend could partially be attributed to a more dense data set, and shoal-biased cleaning, binning and gridding associated with the multibeam data for maintaining conservative least depths important for charting dangers to navigation. (PDF contains 27 pages.)

Description: In 2003, twelve marine protected areas were established in state waters (0-3 nmi) surrounding the Channel Islands. NOAA is considering extending this network (3-6 nmi) into deeper waters of the Channel Islands National Marine Sanctuary (CINMS). In order for effective long-termmanagement of the deep water reserves to occur, a well-structured monitoring program is required to assess effectiveness. The CINMS and the National Marine Sanctuary Program (NMSP) hosted a 2-day workshop in April 2005 to develop a monitoring plan for the proposed federal marine reserves in that sanctuary. Conducted at the University of California at Santa Barbara, participants included scientists from academic, state, federal, and private research institutions. Workshop participants developed project ideas that could answer priority questionsposed by the NMSP. This workshop report will be used to develop a monitoring plan for the reserves. (PDF contains 47 pages.)

Description: The largely sedentary behavior of many fishes on coral reefs is well established. Information on the movement behavior of individual fish, over fine temporal and spatialscales, however, continues to be limited. It is precisely this type of information that is critical for evaluating the success of marine reserves designed for the conservation and/or management of vagile fishes. In this pilot study we surgically-tagged eight hogfish(Lachnolaimus maximus Walbaum 1792) with coded-acoustic transmitters inside the Conch Reef Research Only Area (a no-take marine reserve) in the northern Florida KeysNational Marine Sanctuary. Our primary objective was to characterize the movement of L. maximus across Conch Reef in the vicinity of the reserve. All fish were captured,surgically-tagged and released in situ during a saturation mission to the Aquarius Undersea Laboratory, which is located in the center of the reserve. Movement of taggedL. maximus was recorded for up to 95 days by three acoustic receivers deployed on the seafloor. Results showed clear diel patterns in L. maximus activity and regular movementamong the receivers was recorded for seven of the eight tagged fish. Fidelity of tagged fish to the area of release was high when calculated at the scale of days, while within-day fidelity was comparatively low when calculated at the scale of hours. While the number of fish departures from the array also varied, the majority of departures for seven of the eight fish did not exceed 1-hr (with the exception of one 47-day departure), suggesting that when departures occurred, the fish did not travel far. Future efforts will significantly expand the number of receivers at Conch Reef such that fish movement behavior relative to the reserve boundaries can be quantified with increased temporal and spatial resolution. (PDF contains 22 pages.)

Description: This report outlines the potential impacts of coastal protection structures on the resources of the Monterey Bay National Marine Sanctuary. At least 15 miles of the Sanctuary’s 300-mile shoreline are currently armored with seawalls and riprap revetments. Most of these coastalprotection structures are placed above the mean high tide line, the official boundary of the Sanctuary, yet some influences of armoring impinge on the marine realm and on recreational use. In addition, continued sea level rise and accompanying coastal retreat will force many of thesestructures below the high tide line over time. The Monterey Bay National Marine Sanctuary staff has recognized the significance of coastal armoring, identifying it as a critical issue in the Coastal Armoring Action Plan of the draft Joint Management Plan.This summary is intended to provide general background information for Sanctuary policies on coastal armoring. The impacts discussed include: aesthetic depreciation, beach loss due to placement, access restriction, loss of sand supply from eroding cliffs, passive erosion, and activeerosion. In addition, the potential biological impacts are explored. Finally, an appraisal of how differing armor types compare in relation to impacts, expense and engineering is presented. While the literature cited in this report focus predominantly on the California coast, theframework for this discussion could have implications for other actively eroding coastlines. (PDF contains 26 pages.)

Description: This report describes cases relating to the management of national marine sanctuaries in which certain scientific information was required so managers could make decisions that effectively protected trust resources. The cases presented represent only a fraction of difficult issues that marine sanctuary managers deal with daily. They include, among others, problems related to wildlife disturbance, vessel routing, marine reserve placement, watershed management, oil spill response, and habitat restoration. Scientific approaches to address these problems vary significantly, and include literature surveys, data mining, field studies (monitoring, mapping, observations, and measurement), geospatial and biogeographic analysis, and modeling. In most cases there is also an element of expert consultation and collaboration among multiple partners, agencies with resource protection responsibilities, and other users and stakeholders. The resulting management responses may involve direct intervention (e.g., for spill response or habitat restoration issues), proposal of boundary alternatives for marine sanctuaries or reserves, changes in agency policy or regulations, making recommendations to other agencies with resource protection responsibilities, proposing changes to international or domestic shipping rules, or development of new education or outreach programs. (PDF contains 37 pages.)

Description: Since 1999, NOAA’s Biogeography Branch of the Center for Coastal Monitoring and Assessment (CCMA-BB) has beenworking with federal and territorial partners to characterize, monitor, and assess the status of the marine environment around northeastern St. Croix, U.S. Virgin Islands. This effort is part of the broader NOAA Coral Reef Conservation Program’s (CRCP) National Coral Reef Ecosystem Monitoring Program (NCREMP). With support from CRCP’sNCREMP, CCMA conducts the “Caribbean Coral Reef Ecosystem Monitoring project” (CREM) with goals to: (1) spatiallycharacterize and monitor the distribution, abundance, and size of marine fauna associated with shallow water coral reef seascapes (mosaics of coral reefs, seagrasses, sand and mangroves); (2) relate this information to in situ fine-scale habitat data and the spatial distribution and diversity of habitat types using benthic habitat maps; (3) use this information to establish the knowledge base necessary for enacting management decisions in a spatial setting; (4) establish the efficacy of those management decisions; and (5) develop data collection and data management protocols. The monitoring effort in northeastern St. Croix was conducted through partnerships with the National Park Service (NPS) and the Virgin Islands Department of Planning and Natural Resources (VI-DPNR). The geographical focal point of the research is Buck Island Reef National Monument (BIRNM), a protected area originally established in 1961 and greatly expanded in 2001; however, the work also encompassed a large portion of the recently created St. Croix East End Marine Park (EEMP). Project funding is primarily provided by NOAA CRCP, CCMA and NPS.In recent decades, scientific and non-scientific observations have indicated that the structure and function of the coral reef ecosystem around northeastern St. Croix have been adversely impacted by a wide range of environmental stressors. The major stressors have included the mass Diadema die off in the early 1980s, a series of hurricanes beginning with Hurricane Hugo in 1989, overfishing, mass mortality of Acropora corals due to disease and several coral bleaching events, with the most severe mass bleaching episode in 2005. The area is also an important recreational resource supporting boating, snorkeling, diving and other water based activities. With so many potential threats to the marine ecosystem anda dramatic change in management strategy in 2003 when the park’s Interim Regulations (Presidential Proclamation No.7392) established BIRNM as one of the first fully protected marine areas in NPS system, it became critical to identifyexisting marine fauna and their spatial distributions and temporal dynamics. This provides ecologically meaningful data to assess ecosystem condition, support decision making in spatial planning (including the evaluation of efficacy of current management strategies) and determine future information needs. The ultimate goal of the work is to better understand the coral reef ecosystems and to provide information toward protecting and enhancing coral reef ecosystems for the benefit of the system itself and to sustain the many goods and services that it offers society. This Technical Memorandum contains analysis of the first six years of fish survey data (2001-2006) and associated characterization of the benthos (1999-2006). The primary objectives were to quantify changes in fish species and assemblage diversity, abundance, biomass and size structure and to provide spatially explicit information on the distribution of key species or groups of species and tocompare community structure inside (protected) versus outside (fished) areas of BIRNM. (PDF contains 100 pages).

Description: Center for Coastal Monitoring and Assessment

Description: Source of the Nile Fish farm (SON) is located at Bugungu area in Napoleon Gulf, northern Lake Victoria. The proprietors of the farm and the National Fisheries Resources Research Institute (NaFIRRI) have an established collaborative arrangement where NaFIRRI provides technical back-stopping to enable quarterly environment monitoring of the cage site; a mandatory requirement of the National Environment Management Authority (NEMA). The agreed studyareas are physical-chemical factors (water depth, water transparency/secchi depth, water temperature, dissolved oxygen, BOO, pH, conductivity), and selected nutrients), algal community (including primary production), aquatic invertebrates (zooplankton and macrobenthos) and the fish community. This report presents field observations made during the third quarter (July-September) field survey undertaken during August 2014; along with scientificinterpretation and discussion of the results in reference to possible impacts of the cage facility to the water environment quality and aquatic biota.

Description: Source of the Nile Fish farm (SON) is located at Bugungu area in Napoleon Gulf, northern Lake Victoria. The proprietors of the farm requested for technical assistance of NaFIRRI to undertake regular environment monitoring of the cage site as is mandatory under the NEMA conditions. NAFIRRI agreed to undertake quarterly environment surveys in the cage area covering selected physical-chemical factors Like water column depth, water transparency, water column temperature, dissolved oxygen, pH and conductivity; nutrient status, algal and invertebrate communities (microinvertebrates/zooplankton and macro-invertebrates/macro-benthos) as well as fish community. The first quarter survey was undertaken in February 2011; the second in May 2011 and the third quarter survey, which is the subject of this report, in September 2011. Results/observations made are presented in this technical report along with a scientific interpretation and discussion of the results with reference to possible impacts of the cage facilities to the water environment and aq-uatic biota, including the natural fish community at and around the cage site.

Description: The first environmental survey was undertaken in February 2011. The survey covered physical-chemical parameters (Water depth, water transparency, water column temperature, dissolved oxygen, pH and conductivity), nutrient status, algal and invertebrate communities (algae, micro-invertebrates/zooplankton and macro-invertebrates/macro-benthos) and the fish community. This report presents the field observations made and provides a scientific interpretation and discussion of the results with reference to possible impacts of the cage facilities to the water environment and the different aquatic biota at and around the cage site including natural fish communities.