Central Coast Region South District Basin Planning & Habitat Mapping Project

This is a report to the California Department of Fish and Game. Between 2003 and 2008, the Foundation of CSUMB produced fish habitat maps and GIS layers for CDFG based on CDFG field data. This report describes the data entry, mapping, and website construction procedures associated with the project. Included are the maps that have been constructed. This report marks the completion of the Central Coast region South District Basin Planning and Habitat Mapping Project. (Document contains 40 pages)

Wetland Tracker Data Collection Central Coast (Morro Bay Region)

The goal of this project was to gather information on wetland restoration projects in the Moro Bay, California, region. Data provided to the San Francisco Estuary Institute (SFEI) will be used to enhance a web-based, public access database, the Bay Area Wetland Project Tracker. Wetland Tracker provides information on the location, size, sponsors, habitats, contact persons, and status of included projects. Its website provides an interactive map of planned and completed wetland projects (http://www.wetlandtracker.org). (Document contains 4 pages)

Roots of prosperity: the Pacific Coast Watershed Partnership

pdf contains 16 pages

Florida's West Coast inlets: shoreline effects and recommended action

This report responds to the 1986 Beaches Bill which, in recognition of the potential deleterious impact on Florida's beaches of inlets modified for navigation, mandated a study of those inlets with identification of recommended action to reduce the impacts. This report addresses west Coast inlets; East Coast inlets are the subject of a companion report. There are 37 inlets along that portion of Florida's West Coast commencing from Pensacola Bay Entrance to Caxambas Pass at the south end of Marco Island. Compared to those on the East Coast, most West Coast inlets have not had the deleterious effects on the adjacent beaches, yet all modified inlets without proper management have the potential of impacting unfavorably on the adjacent shorelines. Moreover, at present there is interest in opening three West Coast entrances which either have been open in the past (Midnight Pass) or which have opened occasionally (Navarre Pass and Entrance to Phillips Lake). A review of inlets in their natural condition demonstrates the presence of a shallow broad outer bar across which the longshore transport Occurs. These shallow and shifting bar features were unsuitable for navigation which in many cases has led to the deepening of the channels and fixing with one or two jetty structures. Inlets in this modified state along with inappropriate maintenance practices have the potential of placing great ero$ional stress along the adjacent beaches. Moreover. channel dredging can reduce wave sheltering of the shoreline by ebb tidal shoals and alter the equilibrium of the affected shoreline segments. The ultimate in poor sand management practice is the placement of good quality beach sand in water depths too great for the sand to reenter the longshore system under natural forces; depths of 12 ft. or less are considered appropriate for Florida in order to maintain the sand in the system. With the interference of the nearshore sediment transport processes by inlets modified for navigation, if the adjacent beaches are to be stabilized there must be an active monitoring program with commitment to placement of dredged material of beach quality on shoreline segments of documented need. Several East Coast inlets have such transfer facilities; however. the quantities of sand transferred should be increased. Although an evolution and improvement in the technical capability to manage sand resources in the vicinity of inlets is expected, an adequate capability exists today and a concerted program should be made to commence a scheduled implementation of this capability at those entrances causing greatest erosional stress on the adjacent shorelines. A brief summary review for each of the 37 West Coast inlets is presented including: a scaled aerial photograph, brief historical information, several items related to sediment losses at each inlet and special characteristics relevant to State responsibilities. For each inlet, where appropriate, the above infor~tion is utilized to develop a recommenced action. (PDF has 101 pages.)

The frequency of muscle protein polymorphism in Menidia menidia (Atherinidae) along the Atlantic coast

(PDF has 6 pages.)

Interactions between adult migratory striped bass (Morone saxatilis) and their prey during winter off the Virginia and North Carolina Atlantic coast from 1994 through 2007

The migratory population of striped bass (Morone saxatilis) (>400 mm total length[TL]) spends winter in the Atlantic Ocean off the Virginia and North Carolina coasts of the United States. Information on trophic dynamics for these large adults during winter is limited. Feeding habits and prey were described from stomach contents of 1154 striped bass ranging from 373 to 1250 mm TL, collected from trawls during winters of 1994-96, 2000, and 2002-03, and from the recreational fishery during 2005-07. Nineteen prey species were present in the diet. Overall, Atlantic menhaden (Brevoortia tyrannus) and bay anchovy (Anchoa mitchilli) dominated the diet by boimass (67.9%) and numerically (68.6%). The percent biomass of Atlantic menhaden during 1994-2003 to 87.0% during 2005-07. Demersal fish species such as Atlantic croaker (Micropogonias undulatus) and spot (Leiostomus xanthurus) represented <15% of the diet biomass, whereas alosines (Alosa spp.) were rarely observed. Invertebrates were least important, contributing <1.0% by biomass and numerically. Striped bass are capable of feeding on a wide range of prey sizes (2% to 43% of their total length). This study outlines the importance of clupeoid fishes to striped bass winter production and also shows that predation may be exerting pressure on one of their dominant prey, the Atlantic menhaden.

Population assessment of two stocks of white grunt, Haemulon plumieri, from the southeastern coast of the United States

Changes in the age structure and population size of white grunt, Haemulon plumieri, from North Carolina through the Florida Keys were examined using records of landings and size frequencies of fish from commercial, re~reational, and headboat fisheries from 1986-1998. Data were stratified into two geographical areas: North Carolina and South Carolina; and southeast Florida. Population size in numbers at age was estimated for each year and geographical area by applying an uncalibrated separable virtual population analysis (SVPA) to the landings in numbers at age. A calibrated virtual population analysis, FADAPT, was also run for data from North Carolina and South Carolina. SVPA and FADAPT were used to estimate annual, age-specific fishing mortality (F) for four levels of natural mortality (M = 0.20, 0.25, 0.30, and 0.35). The best estimate of M for white grunt is 0.30. Landings of white grunt in the Carolinas for the three fisheries have generally decreased in recent years, but have held fairly steady for the species in southeast Florida. Age at entry and age at full recruitment were age-1 and age-4 for the Carolinas, and age-l and age-3 for southeast Florida. With M = 0.30, levels of fishing mortality (F) on the fully-recruited ages were 0.23 for the Carolinas and 0.33 for southeast Florida. Spawning potential ratio (SPR) at M = 0.30 was 57% for the Carolinas and 61% for southeast Florida, which indicates that the species, by definition, has not been over-exploited by fishing. The results of this assessment of the white grunt population off the Carolinas agree with the recent F/FMSY analysis of white grunt (Anonymous, 1999). (PDF contaons 72 pages)

Cruise Report NOAA Ship McARTHUR II Cruise AR-04-04: Leg 2 (June 1-12, 2004): A pilot survey of deepwater coral/sponge assemblages and their susceptibility to fishing/harvest impacts at the Olympic Coast National Marine Sanctuary (OCNMS)

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

Soft-bottom benthic assemblages and levels of contaminants in sediments and biota at Gray's Reef National Marine Sanctuary and nearby shelf waters off the coast of Georgia (2000 and 2001)

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

A comparison of animal abundance and distribution in similar habitats in Rookery Bay, Marco Island and Fakahatchee on the southwest coast of Florida, 1971 - 1972

The three areas in Rookery Bay, near Marco Island and Fakahatchee Bay were sampled from July 1971 through July 1972, and 1,006,640 individual animals were collected, of which the majority (55%) came from the Marco area. The large disparity between the catches at Marco and the remaining study areas was due mainly to the appearance of high numbers of species of polychaetes and echinoderms that were of very minor importance or absent from the catches in Rookery Bay and Fakahatchee Bay. When only the major classes of animals in the catch are considered (i.e., crustaceans, fish and mollusks) the total counts for Fakahatchee (298,830) and Marco (275,075) are quite comparable but both exceed Rookery Bay (119,388) by a considerable margin. The effects of the red tide outbreak in the summer of 1971 were apparently restricted to the Rookery Bay Sanctuary and may account for some of the observed differences. For the purposes of making controlled comparisons between the study areas, three common habitats were selected in each area so that a mud bottom habitat, a sand-shell bottom habitat and a vegetated bottom habitat were located in each of the study areas. Total catches by habitat types for crustaceans, fish and mollusks and certain of the more abundant species show clearly the overwhelming importance of the vegetated bottom as a habitat for animals. By habitat the vegetated areas had the most "indicator species" with five, the mud habitat was next with three and the sand-shell habitat third with two. Thus the vegetated habitat would be the best choice if a single habitat were to be used to detect environmental changes between study areas. (PDF contains 137 pages)

First Biennial Ocean Climate Summit: Finding Solutions for San Francisco Bay Area’s Coast and Ocean. Proceedings of the Summit: April 29, 2008, Golden Gate Club, The Presidio San Francisco, California

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 the terrestrial 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 CO2 saturation, 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 the atmosphere has an effect on climate and a cascading effect on the marine environment. Potential physical effects of climate change within the marine environment, including ocean 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 and coastal 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 to take 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 wide variety 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” charged governments 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.)

Automated, objective texture segmentation of multibeam echosounder data - Seafloor survey and substrate maps from James Island to Ozette Lake, Washington Outer Coast

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 a description 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 for efficient and reproducible automated segmentation routines to process the data. Using MBES data collected by the Olympic Coast National Marine Sanctuary (OCNMS), and through a contracted seafloor survey, we expanded on the techniques of Cutter et al. (2003) to describe an objective repeatable process that uses parameterized local Fourier histogram (LFH) texture features to automate segmentation of surficial sediments from acoustic imagery using a maximum likelihood decision rule. Sonar signatures and classification performance were evaluated using video imagery obtained from a towed camera sled. Segmented raster images were converted to polygon features and attributed using a hierarchical deep-water marine benthic classification scheme (Greene et al. 1999) for use in a geographical information system (GIS). (PDF contains 41 pages.)

Observations of deep coral and sponge assemblages in Olympic Coast National Marine Sanctuary, Washington. Cruise Report: NOAA Ship McArthur II Cruise AR06-07/07

From May 22 to June 4, 2006, NOAA scientists led a research cruise using the ROPOS Remotely Operated Vehicle (ROV) to conduct a series of dives at targeted sites in the Olympic Coast National Marine Sanctuary (OCNMS) with the goal of documenting deep coral and sponge communities. Dive sites were selected from areas for which OCNMS had side scan sonar data indicating the presence of hard or complex substrate. The team completed 11 dives in sanctuary waters ranging from six to 52 hours in length, at depths ranging from 100 to 650 meters. Transect surveys were completed at 15 pre-selected sites, with additional observations made at five other sites. The survey locations included sites both inside and outside the Essential Fish Habitat (EFH) Conservation Area, known as Olympic 2, established by the Pacific Fishery Management Council, enacted on June 12, 2006. Bottom trawling is prohibited in the Olympic 2 Conservation Area for nontribal fishermen. The Conservation Area covers 159.4 square nautical miles or about 15 percent of the sanctuary. Several species of corals and sponges were documented at 14 of the 15 sites surveyed, at sites both inside and outside the Conservation Area, including numerous gorgonians and the stony corals Lophelia pertusa and Desmophyllum dianthus, as well as small patches of the reef building sponge Farrea occa. The team also documented Lophelia sp. and Desmophyllum sp. coral rubble, dead gorgonians, lost fishing gear, and other anthropogenic debris, supporting concerns over potential risks of environmental disturbances to coral health. (PDF contains 60 pages.)

Survey report of NOAA Ship McArthur II cruises AR-04-04, AR-05-05 and AR-06-03: Habitat classification of side scan sonar imagery in support of deep-sea coral/sponge explorations at the Olympic Coast National Marine Sanctuary

Habitat mapping and characterization has been defined as a high-priority management issue for the Olympic Coast National Marine Sanctuary (OCNMS), especially for poorly known 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, and bathymetry records to describe geological and biological (where possible) aspects of habitat. Using a hierarchical deep-water marine benthic classification scheme (Greene et al. 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 the mapping and groundtruthing efforts as well as results of the image classification procedure for each of the areas surveyed. (PDF contains 60 pages.)

Habitat mapping effort at the Olympic Coast National Marine Sanctuary – Current status and future needs

With elevating interest to establish conservation efforts for groundfish stocks and continued scrutiny over the value of marine protected areas along the west coast, the importance 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) assembled a 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.)