The effects of urbanization on populations of grass shrimp Palaemonetes spp. in small, high salinity estuaries

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

A Biogeographic assessment off North/Central California: In support of the National Marine Sanctuaries of Cordell Bank, Gulf of the Farallones and Monterey Bay. Phase II - Environmental setting and update to marine birds and animals

NOAA’s National Centers for Coastal Ocean Science (NCCOS) conducts and supports research, monitoring, assessments, and technical assistance to meet NOAA’s coastal stewardship and management responsibilities. In 2001 the Biogeography Branch of NCCOS partnered with NOAA’s National Marine Sanctuary Program (NMSP) to conduct biogeographic assessments to support the management plan updates for the sanctuaries. The first biogeographic assessment conducted in this partnership focused on three sanctuaries off north/ central California: Cordell Bank, Gulf of the Farallones and Monterey Bay. Phase I of this assessment was conducted from 2001 to 2004, with the primary goal to identify and gather the best available data and information to characterize and identify important biological areas and time periods within the study area. The study area encompasses the three sanctuaries and extends along the coastal ocean off California from Pt. Arena to Pt. Sal (35°-39°N). This partnership project was lead by the NCCOS Biogeography Branch, but included over 90 contributors and 25 collaborating institutions. Phase I results include: 1) a report on the overall assessment that includes hundreds of maps, tables and analyses; 2) an ecological linkage report on the marine and estuarine ecosystems along the coast of north/central California, and 3) related geographic information system (GIS) data and other summary data files, which are available for viewing and download in several formats at the following website: http://ccma.nos.noaa.gov/products/biogeography/canms_cd/welcome.html Phase II (this report) was initiated in the Fall of 2004 to complete the analyses of marine mammals and update the marine bird colony information. Phase II resulted in significant updates to the bird and mammal chapters, as well as adding an environmental settings chapter, which contains new and existing data and maps on the study area. Specifically, the following Phase II topics and items were either revised or developed new for Phase II: •environmental, ecological settings – new maps on marine physiographic features, sea surface temperature and fronts, chlorophyll and productivity •all bird colony or roost maps, including a summary of marine bird colonies •updated at-sea data CDAS data set (1980-2003) •all mammal maps and descriptions •new overall density maps for eight mammal species •new summary pinniped rookery/haulout map •new maps on at-sea richness for cetaceans and pinnipeds •most text in the mammal chapter •new summary tables for mammals on population status and spatial and temporal patterns

Deep-sea benthic footprint of the Deepwater Horizon blowout

The Deepwater Horizon (DWH) accident in the northern Gulf of Mexico occurred on April 20, 2010 at a water depth of 1525 meters, and a deep-sea plume was detected within one month. Oil contacted and persisted in parts of the bottom of the deep-sea in the Gulf of Mexico. As part of the response to the accident, monitoring cruises were deployed in fall 2010 to measure potential impacts on the two main soft-bottom benthic invertebrate groups: macrofauna and meiofauna. Sediment was collected using a multicorer so that samples for chemical, physical and biological analyses could be taken simultaneously and analyzed using multivariate methods. The footprint of the oil spill was identified by creating a new variable with principal components analysis where the first factor was indicative of the oil spill impacts and this new variable mapped in a geographic information system to identify the area of the oil spill footprint. The most severe relative reduction of faunal abundance and diversity extended to 3 km from the wellhead in all directions covering an area about 24 km2. Moderate impacts were observed up to 17 km towards the southwest and 8.5 km towards the northeast of the wellhead, covering an area 148 km2. Benthic effects were correlated to total petroleum hydrocarbon, polycyclic aromatic hydrocarbons and barium concentrations, and distance to the wellhead; but not distance to hydrocarbon seeps. Thus, benthic effects are more likely due to the oil spill, and not natural hydrocarbon seepage. Recovery rates in the deep sea are likely to be slow, on the order of decades or longer.

Sampling design tool for ArcGIS: Instruction manual.[for ESRI ArcGIS 10.0 Service Pack 3 or higher]

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, highprecision 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.

Integrating remote sensing products and GIS tools to support marine spatial management in West Hawai'i

Marine protected areas (MPAs) represent a form of spatial management, and geospatial information on living marine resources and associated habitat is extremely important to support best management practices in a spatially discrete MPA. Benthic habitat maps provide georeferenced information on the geomorphic structure and biological cover types in the marine environment. This information supports an enhanced understanding of ecosystem function and species habitat utilization patterns. Benthic habitat maps are most useful for marine management and spatial planning purposes when they are created at a scale that is relevant to management actions. We sought to improve the resolution of existing benthic habitat maps created during a regional mapping effort in Hawai`i. Our results complemented these existing regional maps and provided more detailed, finer-scale habitat maps for a network of MPAs in West Hawai`i. The map products created during this study allow local planners and managers to extract information at a spatial scale relevant to the discrete management units, and appropriate for local marine management efforts on the Kona Coast. The resultant benthic habitat maps were integrated in a geographic information system (GIS) that also included aerial imagery, underwater video, MPA regulations, summarized ecological data and other relevant and spatially explicit information. The integration of the benthic habitat maps with additional “value added” geospatial information into a dynamic GIS provide a decision support tool with pertinent marine resource information available in one central location and support the application of a spatial approach to the management of marine resources. Further, this work can serve as a case study to demonstrate the integration of remote sensing products and GIS tools at a fine spatial scale relevant to local-level marine spatial planning and management efforts.

Analyzing and mapping fish assemblages off central California, USA

This study describes fish assemblages and their spatial patterns off the coast of California from Point Arena to Point Sal, by combining the results of the multivariate analyses of several fisheries datasets with a geographic information system. In order to provide comprehensive spatial coverage for the areas of inshore, continental shelf, and continental slope, three fisheries datasets were analyzed: 1) Inshore: the California Department of Fish and Game dataset of fishery-dependent commercial passenger fishing vessel trips that targeted rockfish; 2) Continental Shelf: the National Marine Fisheries Service (NMFS) fishery-independent bottom trawls; and 3) Continental Slope: the NMFS fishery-independent bottom trawls on the continental slope. One-hundred seven species were analyzed. These species represented those captured in at least 5% of the fishing trips or trawls in at least one of the three data sets. We analyzed each of the three datasets separately, and the three sets of results were combined to define 28 species assemblages and 23 site groups. A species assemblage consisted of species caught together, whereas a site group consisted of fishing trips or trawl locations that tended to have the same species assemblages. At the scale of these datasets, 97% of all site groups were significantly segregated by depth.

Shallow-water benthic habitats of St. John, U.S. Virgin Islands

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

Manual for the Sampling Design Tool for ArcGIS

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.

Boundary options for a research area within Gray's Reef National Marine Sanctuary

Gray’s Reef National Marine Sanctuary (GRNMS) is exploring the concept of a research area (RA) within its boundaries. The idea of a research area was first suggested in public scoping meetings held prior to the review of the Gray’s Reef Management Plan. An RA is a region specifically designed for conducting controlled scientific studies in the absence of confounding factors. As a result, a multidisciplinary group gathered by GRNMS was convened to consider the issue. This Research Area Working Group (RAWG) requested that a suite of analyses be conducted to evaluate the issue quantitatively. To meet this need, a novel selection procedure and geographic information system (GIS) was created to find the optimal location for an RA while balancing the needs of research and existing users. This report and its associated GIS files describe the results of the requested analyses and enable further quantitative investigation of this topic by the RAWG and GRNMS.

Spawning cycles and habitats for ballyhoo (Hemiramphus brasiliensis) and balao (H. balao) in south Florida

Two halfbeak species, ballyhoo (Hemiramphus brasiliensis) and balao (H. balao), are harvested as bait in south Florida waters, and recent changes in fishing effort and regulations prompted this investigation of the overlap of halfbeak fishing grounds and spawning grounds. Halfbeaks were sampled aboard commercial fishing vessels, and during fishery-independent trips, to determine spatial and temporal spawning patterns of both species. Cyclic patterns of gonadosomatic indices (GSIs) indicated that both species spawned during spring and summer months. Histological analysis demonstrated that specific stages of oocyte development can be predicted from GSI values; for example, female ballyhoo with GSIs >6.0 had hydrated oocytes that were 2.0−3.5 mm diameter. Diel changes in oocyte diameters and histological criteria demonstrated that final oocyte maturation occurred over a 30- to 36-hour period and that ballyhoo spawned at dusk. Hydration of oocytes began in the morning, and ovulation occurred at sunset of that same day; therefore females with hydrated oocytes were ready to spawn within hours. We compared maps of all locations where fish were collected to maps of locations where spawning females (i.e. females with GSIs >6.0) were collected to determine the degree of overlap of halfbeak fishing and spawning grounds. We also used geographic information system (GIS) data to describe the depth and bottom type of halfbeak spawning grounds. Ballyhoo spawned all along the coral reef tract of the Atlantic Ocean, inshore of the reef tract, and in association with bank habitats within Florida Bay. In the Atlantic Ocean, balao spawned along the reef tract and in deeper, more offshore waters than did ballyhoo; balao were not found inshore of the coral reef tract or in Florida Bay. Both halfbeak species, considered together, spawned throughout the fishing grounds of south Florida.

Integration of submersible transect data and high-resolution multibeam sonar imagery for a habitat-based groundfish assessment of Heceta Bank, Oregon

In the face of dramatic declines in groundfish populations and a lack of sufficient stock assessment information, a need has arisen for new methods of assessing groundfish populations. We describe the integration of seafloor transect data gathered by a manned submersible with high-resolution sonar imagery to produce a habitat-based stock assessment system for groundfish. The data sets used in this study were collected from Heceta Bank, Oregon, and were derived from 42 submersible dives (1988–90) and a multibeam sonar survey (1998). The submersible habitat survey investigated seafloor topography and groundfish abundance along 30-minute transects over six predetermined stations and found a statistical relationship between habitat variability and groundfish distribution and abundance. These transects were analyzed in a geographic information system (GIS) by using dynamic segmentation to display changes in habitat along the transects. We used the submersible data to extrapolate fish abundance within uniform habitat patches over broad areas of the bank by means of a habitat classification based on the sonar imagery. After applying a navigation correction to the submersible-based habitat segments, a good correlation with major boundaries on the backscatter and topographic boundaries on the imagery were apparent. Extrapolation of the extent of uniform habitats was made in the vicinity of the dive stations and a preliminary stock assessment of several species of demersal fish was calculated. Such a habitat-based approach will allow researchers to characterize marine communities over large areas of the seafloor.

Report of the training in database and spatial analysis for Marine Protected Areas staff in Indonesia's BOBLME region, Medan, Indonesia, 30 June-4 July, 2015

Training included: Geographic Information System (GIS)concept and software; Global Positioning System (GPS); Ecological Gap Analysis and Marine Protected Area (MPA) design using Marine Reserve Design using Spatially Explicit Annealing (MARXAN); and cartography.

Spatial and temporal analysis of bottlenose dolphin strandings in South Carolina, 1992-2005

This CD contains summary data of bottlenose dolphins stranded in South Carolina using a Geographical Information System (GIS) and contains two published manuscripts in .pdf files. The intent of this CD is to provide data on bottlenose dolphin strandings in South Carolina to marine mammal researchers and managers. This CD is an accumulation of 14 years of stranding data collected through the collaborations of the National Ocean Service, Center for Coastal Environmental Health and Biomolecular Research (CCEHBR), the South Carolina Department of Natural Resources, and numerous volunteers and veterinarians that comprised the South Carolina Marine Mammal Stranding Network. Spatial and temporal information can be visually represented on maps using GIS. For this CD, maps were created to show relationships of stranding densities with land use, human population density, human interaction with dolphins, high geographical regions of live strandings, and seasonal changes. Point maps were also created to show individual strandings within South Carolina. In summary, spatial analysis revealed higher densities of bottlenose dolphin strandings in Charleston and Beaufort Counties, which consist of urban land with agricultural input. This trend was positively correlated with higher human population levels in these coastal counties as compared with other coastal counties. However, spatial analysis revealed that certain areas within a county may have low human population levels but high stranding density, suggesting that the level of effort to respond to strandings is not necessarily positively correlated with the density of strandings in South Carolina. Temporal analysis revealed a significantly higher density of bottlenose dolphin strandings in the northern portion of the State in the fall, mostly due to an increase of neonate strandings. On a finer geographic scale, seasonal stranding densities may fluctuate depending on the region of interest. Charleston Harbor had the highest density of live bottlenose dolphin strandings compared to the rest of the State. This was due in large part to the number of live dolphin entanglements in the crab pot fishery, the largest source of fishery-related mortality for bottlenose dolphins in South Carolina (Burdett and McFee 2004). Spatial density calculations also revealed that Charleston and Beaufort accounted for the majority of dolphins that were involved with human activities. 1

Coastal resource planning system: Integrating evaluation of ecological integrity and ecosystem services valuation

Efficient and effective coastal management decisions rely on knowledge of the impact of human activities on ecosystem integrity, vulnerable species, and valued ecosystem services—collectively, human impact on environmental quality (EQ). Ecosystem-based management (EBM) is an emerging approach to address the dynamics and complexities of coupled social-ecological systems. EBM “is intended to directly address the long-term sustainable delivery of ecosystem services and the resilience of marine ecosystems to perturbations” (Rosenberg and Sandifer, 2009). The lack of a tool that integrates human choices with the ecological connections between contributing watersheds and nearshore areas, and that incorporates valuation of ecosystem services, is a critical missing piece needed for effective and efficient coastal management. To address the need for an integrative tool for evaluation of human impacts on ecosystems and their services, Battelle developed the EcoVal™ Environmental Quality Evaluation System. The EcoVal system is an updated (2009) version of the EQ Evaluation System for Water Resources developed by Battelle for the U.S. Bureau of Reclamation (Dee et al., 1972). The Battelle EQ evaluation system has a thirty-year history of providing a standard approach to evaluate watershed EQ. This paper describes the conceptual approach and methodology of the updated EcoVal system and its potential application to coastal ecosystems. (PDF contains 4 pages)

Human Dimensions of Marine Fisheries: Using GIS to Illustrate Land-Sea Connections in the Northeast U.S. Herring, Clupea harengus, Fishery

Geographic Information Systems can help improve ocean literacy and inform our understanding of the human dimensions of marine resource use. This paper describes a pilot project where GIS is used to illustrate the connections between fish stocks and the social, cultural, and economic components of the fishery on land. This method of presenting and merging qualitative and quantitative data represents a new approach to assist fishery managers, participants, policy-makers, and other stakeholders in visualizing an often confusing and poorly understood web of interactions. The Atlantic herring fishery serves as a case study and maps from this pilot project are presented and methods reviewed.