Showing papers by "National Ocean Service published in 2007"

RECOGNIZING DINOFLAGELLATE SPECIES USING ITS rDNA SEQUENCES1

Abstract: Dinoflagellate taxonomy is based primarily on morphology and morphometric data that can be difficult to obtain. In contrast, molecular data can be rapidly and cost-effectively acquired, which has led to a rapid accumulation of sequence data in GenBank. Currently there are no systematic criteria for utilizing taxonomically unassigned sequence data to identify putative species that could in turn serve as a basis for testable hypotheses concerning the taxonomy, diversity, distribution, and toxicity of these organisms. The goal of this research was to evaluate whether simple, uncorrected genetic distances (p) calculated using ITS1/5.8S/ITS2 (ITS region) rDNA sequences could be used to develop criteria for recognizing putative species before formal morphological evaluation and classification. The current analysis used sequences from 81 dinoflagellate species belonging to 14 genera. For this diverse assemblage of dinoflagellate species, the within-species genetic distances between ITS region copies (p=0.000–0.021 substitutions per site) were consistently less than those observed between species (p=0.042–0.580). Our results indicate that a between-species uncorrected genetic distance of p≥0.04 could be used to delineate most free-living dinoflagellate species. Recently evolved species, however, may have ITS p values <0.04 and would require more extensive morphological and genetic analyses to resolve. For most species, the sequence of the dominant ITS region allele has the potential to serve as a unique species-specific “DNA barcode” that could be used for the rapid identification of dinoflagellates in field and laboratory studies.

Standard reporting requirements for biological samples in metabolomics experiments: environmental context

Abstract: Metabolomic technologies are increasingly being applied to study biological questions in a range of different settings from clinical through to environmental. As with other high-throughput technologies, such as those used in transcriptomics and proteomics, metabolomics continues to generate large volumes of complex data that necessitates computational management. Making sense of this wealth of information also requires access to sufficiently detailed and well annotated meta-data. Here we provide standard reporting requirements for describing biological samples, taken from an environmental context and involved in metabolomic experiments. It is our intention that these reporting requirements should guide and support the standardised annotation, dissemination and interpretation of environmental metabolomics meta-data.

Toxicity of fipronil and its enantiomers to marine and freshwater non-targets.

Abstract: Fipronil is a phenylpyrazole insecticide used in agricultural and domestic settings for controlling various insect pests in crops, lawns, and residential structures. Fipronil is chiral; however, it is released into the environment as a racemic mixture of two enantiomers. In this study, the acute toxicity of the (S,+) and (R,-) enantiomers and the racemic mixture of fipronil were assessed using Simulium vittatum IS-7 (black fly), Xenopus laevis (African clawed frog), Procambarus clarkii (crayfish), Palaemonetes pugio (grass shrimp), Mercenaria mercenaria (hardshell clam), and Dunaliella tertiolecta (phytoplankton). Results showed that S. vittatum IS-7 was the most sensitive freshwater species to the racemic mixture of fipronil (LC50 = 0.65 microg/L) while P. pugio was the most sensitive marine species (LC50 = 0.32 microg/L). Procambarus clarkii were significantly more sensitive to the (S,+) enantiomer while larval P. pugio were significantly more sensitive to the (R,-) enantiomer. Enantioselective toxicity was not observed in the other organisms tested. Increased mortality and minimal recovery was observed in all species tested for recovery from fipronil exposure. These results indicate that the most toxic isomer of fipronil is organism-specific and that enantioselective toxicity may be more common in crustaceans than in other aquatic organisms.

Assessment of specific binding proteins suitable for the detection of paralytic shellfish poisons using optical biosensor technology.

Abstract: Paralytic shellfish poisoning (PSP) toxin monitoring in shellfish is currently performed using the internationally accredited AOAC mouse bioassay. Due to ethical and performance-related issues associated with this bioassay, the European Commission has recently published directives extending procedures that may be used for official PSP control. The feasibility of using a surface plasmon resonance optical biosensor to detect PSP toxins in shellfish tissue below regulatory levels was examined. Three different PSP toxin protein binders were investigated: a sodium channel receptor (SCR) preparation derived from rat brains, a monoclonal antibody (GT13-A) raised to gonyautoxin 2/3, and a rabbit polyclonal antibody (R895) raised to saxitoxin (STX). Inhibition assay formats were used throughout. Immobilization of STX to the biosensor chip surface was achieved via amino-coupling. Specific binding and inhibition of binding to this surface was achieved using all proteins tested. For STX calibration curves, 0-1000 ng/mL, IC50 values for each binder were as follows: SCR 8.11 ng/mL; GT13-A 5.77 ng/mL; and R895 1.56 ng/mL. Each binder demonstrated a different cross-reactivity profile against a range of STX analogues. R895 delivered a profile that was most likely to detect the widest range of PSP toxins at or below the internationally adopted regulatory limits.

Sublethal effects of the toxic dinoflagellate Karenia brevis on marine copepod behavior

Abstract: Apart from grazing interactions, little is known regarding the sublethal effects of Karenia brevis cells on copepod behavior. We conducted grazing and mortality experiments with K. brevis cells and brevetoxins (PbTx-2), establishing routes of toxicity for the copepods Acartia tonsa, Temora turbinata and Centropages typicus. Subsequent behavioral experiments determined whether copepod swimming and photobehavior, both behaviors involved in predator avoidance, were impaired at sublethal K. brevis and PbTx-2 levels. Copepods variably grazed toxic K. brevis and non-toxic Prorocentrum minimum at bloom concentrations. Although copepods accumulated brevetoxins, significant mortality was only observed in T turbinata at the highest test concentration (1 x 10 7 K. brevis cells L -1 ). Acartia tonsa exhibited minimal sublethal behavioral effects. However, there were significant effects on the swimming and photobehavior of T. turbinata and C. typicus at the lowest sublethal concentrations tested (0.15 μg PbTx-2 L -1 , 1 x 10 5 K. brevis cells L -1 ). Although physiological incapacitation may have altered copepod behavior, starvation likely played a major role as well. These data suggest that sublethal effects of K. brevis and brevetoxin on copepod behavior occur and predicting the role of zooplankton grazers in trophic transfer of algal toxins requires knowledge of species-specific sublethal effects.

Brevetoxin exposure in bottlenose dolphins (Tursiops truncatus) associated with Karenia brevis blooms in Sarasota Bay, Florida

Abstract: Bottlenose dolphins (Tursiops truncatus) face a variety of threats, including risk of exposure to brevetoxins produced by blooms of the harmful alga Karenia brevis. This study investigated brevetoxin exposure in a population of dolphins inhabiting Sarasota Bay, Florida, USA (27°N, 82°W), utilizing tissues from dolphins recovered between 1994 and 2003. Brevetoxin levels detected by ELISA in tissues, gastric samples and excreta from dolphin carcasses (n = 19) associated with K. brevis blooms were compared with with levels in carcasses (n = 16) associated with background K. brevis conditions. In the K. brevis-exposed set, 84% of dolphin carcasses recovered during K. brevis blooms had detectable brevetoxin levels, with values ranging between 7 and 2,896 ng PbTx-3 eq g−1. Over 50% of dolphin carcasses recovered during non-bloom conditions also tested positive by ELISA for brevetoxins, with concentrations ranging from 6 to 44 ng PbTx-3 eq g−1. Control samples from the east coast of Florida were negative by the ELISA. Results from this study establish baseline brevetoxin body burdens in a dolphin population frequently exposed to K. brevis blooms, and data indicate that dolphin carcasses not associated with large-scale mortality events can contain levels of brevetoxins comparable to carcasses stranding during such events.

Ammonium uptake and growth limitation in marine phytoplankton

Abstract: We used continuous culture techniques and a sensitive fluorescence method to quantify relationships among ammonium (NH z ) concentration, cellular NH z uptake rates, and growth rate limitation for five marine algal species ranging in diameter from 3 to 11 mm. The growth rate of two high–nutrient-requiring coastal diatoms, Thalassiosira weissflogii and Thalassiosira pseudonana, were limited at NH z concentrations ,90–100 nmol L21, while those of low-nutrient–adapted species, the oceanic coccolithophore Emiliania huxleyi, the coastal pelagophyte Aureoumbra lagunensis, and the coastal trebouxiophyte Nannochloris atomus, were limited at concentrations ,30–40 nmol L21. In the nitrogen-limited cyclostats, the residence times of dissolved ammonium were extremely short (4–12 min at chlorophyll a levels of 20–30 m gL 21), and these short times had to be taken into account to obtain accurate NH z measurements. Ammonium and nitrate concentrations in stratified surface ocean waters (3–15 nmol L21) fall within the range that substantially limited algal growth rates in our experiments, providing evidence for nitrogen limitation in these waters. Ammonium uptake rates and associated specific growth rates were much lower for T. weissflogii (10–11 mm in diameter) than for the other smaller (3.1– 4.5 mm in diameter) species under ammonium limitation owing to the limits imposed by NH z diffusion to the cell surface. Diffusion per unit of cell volume varies with the inverse square of the cell diameter and, thus, greatly restricts growth of large-celled species under NH z limitation. The resultant selection of small-celled algal species in ammonium-limited ocean waters should promote rapid grazing and nutrient cycling and minimum nutrient loss via settling of intact cells and zooplankton fecal material. Competition for limiting nutrients is a fundamental force shaping the composition and structure of phytoplankton communities and planktonic food webs (Sommer 1989; Thingstad and Sakshaug 1990). This competition is based in large measure on differences in relationships among dissolved nutrient concentrations, cellular nutrient uptake rates, and specific growth rates among species. It has been argued that nitrogen (N) is the most important limiting nutrient in coastal waters and the open ocean based on N : phosphorus (P) ratios of inorganic nutrient pools and results of nutrient addition experiments (Dugdale 1967; Ryther and Dunstan 1971; Falkowski and Raven 1997). In low-nitrogen waters, ammonium (NH z )i s often the dominant nitrogen source utilized by phytoplankton, while nitrate, which is energetically more difficult to assimilate, is only a minor source (Harrison et al. 1996; Mulholland and Lomas in press). However, despite the likely importance of

Description of a new genus of pfiesteria-like dinoflagellate, luciella gen. nov. (dinophyceae), including two new species: luciella masanensis sp. nov. and luciella atlantis sp. nov.

Abstract: A new genus of Pfiesteria-like heterotrophic dinoflagellate, Luciella gen. nov., and two new species, Luciella masanensis sp. nov. and Luciella atlantis sp. nov., are described. These species commonly occur with other small (<20 μm) heterotrophic and mixotrophic dinoflagellates in estuaries from Florida to Maryland and the southern coast of Korea, suggesting a possible global distribution. An SEM analysis indicates that members of the genus Luciella have the enhanced Kofoidian plate formula of Po, cp, X, 4′, 2a, 6″, 6c, PC, 5+s, 5‴, 0p, and 2″″. The two four-sided anterior intercalary plates are diamond shaped. The genus Luciella differs from the other genera in the Pfiesteriaceae by a least one plate in the plate tabulation and in the configuration of the two anterior intercalary plates. An SSU rDNA phylogenetic analysis confirmed the genus as monophyletic and distinct from the other genera in the Pfiesteriaceae. The morphology of Luciella masanensis closely resembles Pfiesteria piscicida Steid. et J. M. Burkh. and other Pfiesteria-like dinoflagellates in size and shape, making it easily misidentified using LM. Luciella atlantis, in contrast, has a more distinctive morphology. It can be distinguished from L. masanensis and other Pfiesteria-like organisms by a larger cell size, a more conical-shaped epitheca and hypotheca, larger rhombic-shaped intercalary plates, and an asymmetrical hypotheca. The genus Luciella is assigned to the order Peridiniales and the family Pfiesteriaceae based on plate tabulation, plate pattern, general morphology, and phylogenetic analysis.

Optimization of blood collection card method/enzyme-linked immunoassay for monitoring exposure of bottlenose dolphin to brevetoxin-producing red tides.

Abstract: Blood collection cards have been successfully used as a tool to monitor brevetoxin (PbTx) exposure in several species, including fish, mice, and rats. Previous methanolic methods used for extracting brevetoxin from blood collection cards have shown dolphin blood to have matrix difficulties in several biological assays. To better biomonitor protected marine mammal species in the Florida area, which is historically prone to unusual mortality events caused by brevetoxin exposure, we have modified the previous extraction method to consistently recover brevetoxin with a known efficiency from dolphin blood collection card samples with minimal matrix interference. A combination of phosphate-buffered saline (PBS) with 6% MeOH and 100% acetonitrile was used to elute blood from the cellulose card and precipitate proteins, respectively. Analysis was performed using a newly developed direct enzyme-linked immunoassay (ELISA), which yields a sample limit of quantification of 1 ng PbTx-3 equiv/mL. This extraction method allowed for linear recovery of PbTx-3 spiked into dolphin blood (1-30 ng/mL) with a consistent recovery rate of 58% and has subsequently been used to monitor brevetoxins in dolphins, as well as sea turtles and manatees, in regions endemic to red tides. In addition, two known metabolites of PbTx-2 were isolated and also found to be detectable using the ELISA. The cysteine conjugate (m/z 1018) and cysteine sulfoxide conjugate (m/z 1034) were found to have linear recoveries of 87% and 66%, respectively. In summary, this method of extracting brevetoxins and their metabolites from blood collection cards, in conjunction with the ELISA detection method, is a simple and reliable way to biomonitor physiologically relevant toxin levels in protected marine animals.

Using mummichog (Fundulus heteroclitus) arrays to monitor the effectiveness of remediation at a Superfund site in Charleston, South Carolina, USA

Abstract: We previously developed a cDNA array for mummichogs (Fundulus heteroclitus), an estuarine minnow, that is targeted for identifying differentially expressed genes from exposure to polycyclic aromatic hydrocarbons and several metals, including chromium. A chromium-contaminated Superfund site at Shipyard Creek in Charleston, South Carolina, USA, is undergoing remediation, providing us a unique opportunity to study the utility of arrays for monitoring the effectiveness of site remediation. Mummichogs were captured in Shipyard Creek in Charleston prior to remediation (2000) and after remediation began (2003 and 2005). Simultaneously, mummichogs were collected from a reference site at the Winyah Bay National Estuarine Research Reserve (NERR) in Georgetown, South Carolina, USA. The hepatic gene expression pattern of fish captured at Shipyard Creek in 2000 showed wide differences from the fish captured at NERR in 2000. Interestingly, as remediation progressed the gene expression pattern of mummichogs captured at Shipyard Creek became increasingly similar to those captured at NERR. The arrays acted as multidimensional biomarkers as the number of differentially expressed genes dropped from 22 in 2000 to four in 2003, and the magnitude of differential expression dropped from 3.2-fold in 2000 to no gene demonstrating a difference over 1.5-fold in 2003. Furthermore, the arrays indicated changes in the bioavailability of chromium caused by hydraulic dredging in the summer of 2005. This research is, to our knowledge, the first report using arrays as biomarkers for a weight-of-evidence hazard assessment and demonstrates that arrays can be used as multidimensional biomarkers to monitor site mitigation because the gene expression profile is associated with chromium bioavailability and body burden.

VDatum and Strategies for National Coverage

Abstract: VDatum is a software tool being developed by the National Ocean Service that allows users to vertically transform geospatial data among a variety of ellipsoidal, orthometric and tidal datums. This is important to coastal applications that rely on vertical accuracy in bathymetric, topographic, and coastline data sets. The VDatum software can be applied to a single point location or to a batch data file. Applying VDatum to an entire data set can be particularly useful when merging multiple data sources together, where they must first all be referenced to a common vertical datum. Contemporary technologies, such as lidar and kinematic GPS data collection, can also benefit from VDatum in providing new approaches for efficiently processing shoreline and bathymetric data with accurate vertical referencing. VDatum is currently available for Tampa Bay, New York Bight, Delaware Bay, Louisiana's Calcasieu River and Lake Charles, central California, Puget Sound, Strait of Juan de Fuca, and north/central North Carolina. In addition, VDatum development is near completion for Chesapeake Bay, Mobile Bay to Cape San Bias, Southern California, Long Island Sound and New York Harbor, and projects are also commencing for an area from New Orleans to Mobile Bay, the Gulf of Maine and the Pacific Northwest. Given the numerous applications that can benefit from having a vertical datum transformation tool, the goal is to develop a seamless nationwide VDatum utility that would facilitate more effective sharing of vertical data and also complement a vision of linking such data through national elevation and shoreline databases.

The Use of Geographic Information Systems as a Forensic Tool to Investigate Sources of Marine Mammal Entanglement in Fisheries

Abstract: Commercial fisheries represent a significant anthropogenic threat to marine mammal survival. Causes of marine mammal mortality are commonly determined by detailed necropsies of stranded carcasses. Gross evidence of entanglement in a fishery might include gear attached to the body, internal indications of asphyxiation and trauma, or gear markings on the epidermis. As gear is often fishery-specific, wound patterns on the epidermis that are created by entanglements in fishing gear may serve to identify possible sources of mortality. For this study, tools within the Environmental Systems Research Institute, Inc. (ESRI) ArcMap GIS software were used to create maps that outline impressions that fishing gear can leave on the epidermis of entangled marine mammals. These maps can subsequently be used to identify possible sources of fishery entanglement for the many marine mammals that wash ashore without gear attached to their carcass. Entanglement wound patterns can be visually compared with fishing gear characteristics; however, differences in scale and image quality can introduce subjectivity that might hinder source identification. The technique described herein provides an objective way to outline the unique characteristics of fishing gear and their associated wounds on entangled marine mammals. Additionally, spatial relationships are preserved as the maps are adjusted to varying scales. Whereas the initial protocol required time-consuming digitization of the outline and visual determination of the pattern interface, this new, semiautomated technique saves analyst effort and minimizes error.

A Fast Response Capability within NOAA/NOS/CO-OPS

Abstract: Duuring a maritime emergency, such as an oil spill, it is important to develop an effective response based on sound scientific observations and expertise in order to protect the lives, commerce and environment in the affected area. The National Oceanographic and Atmospheric Administration (NOAA) National Ocean Service's (NOS) Center for Operational Oceanographic Products and Services (CO-OPS), with support from the Emergency Response Division within the Office of Response and Restoration (a.k.a. NOAA Hazmat), has been developing a fast response capability to satisfy this objective. The Quick Response Estuarine Buoy (QREB) has specifically been developed as a rapid-deployment system for the collection of oceanographic and meteorological information at a targeted location in an effort to ensure safe, efficient and environmentally- sound navigation while supporting the environmental needs of Hazmat's response. The QREB is intended to be a self-contained, small moored system that can be easily deployed in coastal waters by a small size vessel. The buoy has a meteorological package and an acoustic Doppler current profiler (ADCP) mounted below its hull. The real time data are communicated through both an IP modem and a GOES satellite antenna for durations up to 30 days. The buoy was deployed during the NOAA Safe Seas 2006 (SS2006) exercise in the Gulf of the Farallones and Monterey Bay National Marine Sanctuaries. Real-time environmental data from the QREB near the site of a simulated oil spill were made available to the Scientific Support Team (SST), Hazmat, the National Weather Service (NWS) and other emergency responders at the Incident Command Post to provide guidance in managing the simulated situation and were also incorporated into the local weather forecasts and used to truth Hazmat's General NOAA Operational Modeling Environment (GNOME) forecasts. Although the Safe Seas drill proved successful, it is evident that improvements are still required for the QREB to become fully operational in response to a real event. Upon successful testing, the QREB will not only be available for event response, but will also be primarily used to collect current velocity data in key navigational areas of the United States in support of the mission of the National Current Observational Program (NCOP) within CO-OPS.

Real Time Currents in the Harbors of the Great Lakes - A Pilot Project

Abstract: NOAA's National Ocean Service's Center for Operational Oceanographic Products and Services (CO-OPS) is responsible for ensuring safe maritime navigation and supporting efficient water-borne commerce CO-OPS oceanographic and environmental data sets also benefit the National Weather Service, coastal zone managers, and the engineering and surveying communities In 2006, a new pilot project was introduced and implemented in the Great Lakes to measure currents in real time, horizontally across the Cuyahoga River in Cleveland, and the Maumee River in Toledo, Ohio This project provides CO-OPS with a variety of new opportunities to expand the National Current Observation Program (NCOP) to the freshwater environment; to enhance partnerships with the Great Lakes shipping community, City of Cleveland, private industry, and federal agencies; and to test a new platform design for a horizontal acoustic Doppler current profiler developed by the US Army Corps of Engineers, Detroit District The pilots of the Lake Carriers and Lakes Pilots Associations requested assistance with navigating the Cuyahoga and Maumee Rivers where winds affect their transit through narrow bridge spans and around sharp bends The real-time current data provides the pilots with advanced knowledge of the conditions to be expected while in transit, and thus affording them the opportunity to load the vessel accordingly before committing to the river The pilots identified the narrowest channel of the Cuyahoga River at the Center Street swing bridge in Cleveland, Ohio as a place where real time current measurements would provide them with a worst-case scenario of current speed prior to entering the river Another area identified by the pilots occurs as vessels inbound from Lake Erie must transit through a narrow span of a railroad swing bridge on the Maumee River as they approach the Archer Daniels Midland (ADM) pier to offload their grain Access to the latest six minute record of current speed and direction at ADM represents conditions just beyond the bridge spans and this allows the pilot to plan an approach through this area The real time data (every 6 minutes) can be accessed by the public through the web on the Great Lakes Online web page (http://glakesonlinenosnoaagov/moncurrenthtml) The data are also available via NOAA's Interactive Voice Response System at 301-713-9596 Data collection of current speed and direction started in July 2006 and continues to the present at both sites A persistent pattern has been noted at the Cuyahoga River site where a seiche oscillates approximately every 15 hours unless sustained winds compromise the current flow Flow is either inbound or outbound (towards the lake) at approximately 08 knots There isn't a real-time water level station upstream of the Center Street swing bridge on the Cuyahoga River so an examination of the variation in volume flow from the downstream NOS water level station located in Lake Erie cannot be simultaneously compared to the current data A significant feature of the acoustic signal attenuation was noted at the ADM pier last winter when water temperatures approached 32 degrees Fahrenheit Normal maximum profiling ranges diminished as the temperature dropped and approached freezing In addition, side lobe interference also increased with the drop in temperature Other seasonal changes in speed, temperature, and spikes in the data due to wind events are observed as well This pilot project may include a third horizontal current meter site at the head of the St Clair River in the vicinity of the Blue Water Bridge in Port Huron, Michigan in late 2007 Since this project is termed a pilot project, the addition of other current meter sites is dependent on follow-on funding from the US Congress or other sources

Meeting Future Marine Challenges: Charting the Course of NOAA's National Ocean Service Science and Technology Enterprise towards Ecosystem Service and Stewardship

Abstract: The National Oceanic and Atmospheric Administration (NOAA) is the premier civilian ocean agency in the United States. To meet its mission, the agency addresses coastal and ocean challenges on a daily basis focusing on issues ranging from fish stock assessments to coastal inundation. NOAA relies upon a broad science and technology enterprise that produces the products and services necessary to make sound management decisions. Comprised of nine programmatic lines, NOAA's national ocean service (NOS) has a wide-range set of inter-related challenges extending from management of estuaries and marine protected areas to operational oceanography and forecasting. In 2006, NOS established a Science and Technology Board to evaluate its diverse scientific enterprise and apply its wide range of skills and centuries of experience to the modern challenge of developing ecosystem based ocean and coastal services.