ALBERT

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

Description: Center for Coastal Monitoring and Assessment

Description: 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: 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: The instrument described in this report is an updated version of the high precision, automated Winkler titration system described by Friederich et al.(1984). The original instrument was based on the work of Bryan et al. (1976) who developed a colorimetric endpointdetector and on the work of Williams and Jenkinson (1982) who produced an automated system that used this detector.The goals of our updated version of the device described by Friederich et al. (1984) were as follows:1) Move control of the system to the MS-DOS environment because HP-85 computers are no longer in production and because more user-friendly programs could be written using the IBM XT or AT computers that control the new device.2) Use more "off the shelf" components and reduce the parts count in the new system so that it could be easily constructed and maintained.This report describes how to construct and use the new automated Winkler titration device. It also includes information on the chemistry of the Winkler titration, and detailed instructions on how to prepare reagents, collect samples, standardize and perform the titrations (Appendix I: Codispoti, L.A. 1991 On the determination of dissolved oxygen in sea water, 15pp.). A disk containing the program needed to operate the new device is also included. (pdf contains 33 pages)

Description: This report contains inorganic nutrient chemistry, sulfide and oxygen data collected during cruises 2 through 5 of the 1988 Black Sea Oceanographic Expedition aboard the R/V Knorr. Continuous nutrient and sulfide data were obtained in the upper 375 m using a pumped profiling system. Discrete samples were collected from rosette-CTD casts. The corresponding physical oceanographic data have been presented by White et al. (1989). Although all of the data reported has been edited at least twice, errors may remain. We encourage queries and plan to distribute updates on electronic media if there are any non-trivial changes.

Description: This report documents the methods used at the Monterey Bay Aquarium Research Institute (MBARI) for analyzing seawater nutrient samples with an Alpkem Series 300 Rapid Flow Analyzer (RFA) system. The methods have been optimized for the particular requirements of this laboratory.The RFA system has been used to analyze approximately 20,000 samples during the past two years. The methods have been optimized to run nutrient analyses in a routine manner with a detection limit of better than -±1% and a within run precision of -±1% of the full scale concentration range. The normal concentration ranges are 0-200 ~M silicate, 0-5 ~M phosphate, 0-50 ~M nitrate, 0-3 ~M nitrite, and 0-10 ~M ammonium.The memorandum is designed to be used in a loose-leaf binder format. Each page is dated and as revisions are made, they should be inserted into the binder. The revisions should be added into the binder. Retain the old versions in order to maintain a historical record of the procedures. (88 pages)

Description: In October 1970, Moss Landing Marine Laboratories began an observational program to determine/the seasonal changes in the water chemistry of Elkhorn Slough and Moss Landing Harbor. This data report contains the first year of data (October 1970 - November 1971). These data are of immediate interest in determining the flushing and mixing mechanisms ofthe slough and in establishing the effect that local domestic and industrial effluents have on the distribution of these chemical parameters. (Document contains 78 Pages)

Description: Office of Sea Grant Programs

Description: National Oceanic and Atmospheric Administration

Description: Department of Commerce

Description: Document has 78 pages.

Description: Document has 204 pages.Harville is editor

Description: Kaiser Refractories

Description: Office of Sea Grant Programs - NOAA

Description: Moss Landing Marine Labs

Description: Grant No. GH-94

Description: The mucus surface layer of corals plays a number of integral roles in their overall health and fitness. This mucopolysaccharide coating serves as vehicle to capture food, a protective barrier against physical invasions and trauma, and serves as a medium to host a community of microorganisms distinct from the surrounding seawater. In healthy corals the associated microbial communities are known to provide antibiotics that contribute to the coral’s innate immunity and function metabolic activities such as biogeochemical cycling.Culture-dependent (Ducklow and Mitchell, 1979; Ritchie, 2006) and culture-independent methods (Rohwer, et al., 2001; Rohwer et al., 2002; Sekar et al., 2006; Hansson et al., 2009; Kellogg et al., 2009) have shown that coral mucus-associated microbial communities can change with changes in the environment and health condition of the coral. These changes may suggest that changes in the microbial associates not only reflect health status but also may assist corals in acclimating to changing environmental conditions. With the increasing availability of molecular biology tools, culture-independent methods are being used more frequently for evaluating the health of the animal host. Although culture-independent methods are able to provide more in-depth insights into the constituents of the coral surface mucus layer’s microbial community, their reliability and reproducibility rely on the initial sample collection maintaining sample integrity. In general, a sample of mucus is collected from a coral colony, either by sterile syringe or swab method (Woodley, et al., 2008), and immediately placed in a cryovial. In the case of a syringe sample, the mucus is decanted into the cryovial and the sealed tube is immediately flash-frozen in a liquid nitrogen vapor shipper (a.k.a., dry shipper). Swabs with mucus are placed in a cryovial, and the end of the swab is broken off before sealing and placing the vial in the dry shipper. The samples are then sent to a laboratory for analysis. After the initial collection and preservation of the sample, the duration of the sample voyage to a recipient laboratory is often another critical part of the sampling process, as unanticipated delays may exceed the length of time a dry shipper can remain cold, or mishandling of the shipper can cause it to exhaust prematurely. In remote areas, service by international shipping companies may be non-existent, which requires the use of an alternative preservation medium. Other methods for preserving environmental samples for microbial DNA analysis include drying on various matrices (DNA cards, swabs), or placing samples in liquid preservatives (e.g., chloroform/phenol/isoamyl alcohol, TRIzol reagent, ethanol). These methodologies eliminate the need for cold storage, however, they add expense and permitting requirements for hazardous liquid components, and the retrieval of intact microbial DNA often can be inconsistent (Dawson, et al., 1998; Rissanen et al., 2010).A method to preserve coral mucus samples without cold storage or use of hazardous solvents, while maintaining microbial DNA integrity, would be an invaluable tool for coral biologists, especially those in remote areas. Saline-saturated dimethylsulfoxide-ethylenediaminetetraacetic acid (20% DMSO-0.25M EDTA, pH 8.0), or SSDE, is a solution that has been reported to be a means of storing tissue of marine invertebrates at ambient temperatures without significant loss of nucleic acid integrity (Dawson et al., 1998, Concepcion et al., 2007). While this methodology would be a facile and inexpensive way to transport coral tissue samples, it is unclear whether the coral microbiota DNA would be adversely affected by this storage medium either by degradation of the DNA, or a bias in the DNA recovered during the extraction process created by variations in extraction efficiencies among the various community members. Tests to determine the efficacy of SSDE as an ambient temperature storage medium for coral mucus samples are presented here.

Description: In June 2008, the NOAA National Ocean Service (NOS), in conjunction with the EPA National Health and Environmental Effects Laboratory (NHEERL), conducted an assessment of the status of ecological condition of soft-bottom habitat and overlying waters within the boundaries of Stellwagen Bank National Marine Sanctuary (SBNMS). The sanctuary lies approximately 20 nautical miles east of Boston, MA in the southwest Gulf of Maine between Cape Ann and Cape Cod and encompassing 638 square nautical miles (2,181 km2). A total of 30 stations were targeted for sampling using standard methods and indicators applied in prior NOAA coastalstudies and EPA’s Environmental Monitoring and Assessment Program (EMAP) and National Coastal Assessment (NCA). A key feature adopted from these studies was the incorporation of a random probabilistic sampling design. Such a design provides a basis for making unbiased statistical estimates of the spatial extent of ecological condition relative to various measured indicators and corresponding thresholds of concern. Indicators included multiple measures of water quality, sediment quality, and biological condition (benthic fauna, fish tissue contaminant levels).Depths ranged from 31 – 137 m throughout the study area. About 76 % of the area had sediments composed of sands (〈 20 % silt-clay), 17 % of the area was composed of intermediate muddy sands (20 – 80 % silt-clay), and 7 % of the sampled area consisted of mud (〉 80 % siltclay). About 70 % of the area (represented by 21 sites) had sediment total organic carbon (TOC) concentrations 〈 5 mg/g and all but one site (located in Stellwagen Basin) had levels of TOC 〈 20 mg/g, which is well below the range potentially harmful to benthic fauna (〉 50 mg/g).Surface salinities ranged from 30.6 – 31.5 psu, with the majority of the study region (approximately 80 % of the area) having surface salinities between 30.8 and 31.4 psu. Bottom salinities varied between 32.1 and 32.5 psu, with bottom salinities at all sites having values above the range of surface salinities. Surface-water temperatures varied between 12.1 and 16.8 ºC, while near-bottom waters ranged in temperature from 4.4 – 6.2 ºC. An index of densitystratification (Δσt) indicated that the waters of SBNMS were stratified at the time of sampling. Values of Δσt at 29 of the 30 sites sampled in this study (96.7 % of the study area) varied from 2.1 – 3.2, which is within the range considered to be indicative of strong vertical stratification (Δσt 〉 2) and typical of the western Gulf of Maine in summer.Levels of dissolved oxygen (DO) were confined to a fairly narrow range in surface (8.8 – 10.4 mg/L) and bottom (8.5 – 9.6 mg/L) waters throughout the survey area. These levels are within the range considered indicative of good water quality (〉 5 mg/L) with respect to DO. None of these waters had DO at low levels (〈 2 mg/L) potentially harmful to benthic fauna and fish.