Baseline assessment of Fish and Coral bays, St. John, U.S. Virgin Islands in support of watershed restoration activities, part I: fish, coral and benthic habitats

This report provides baseline biological data on fishes, corals and habitats in Coral and Fish Bays, St. John, USVI. A similar report with data on nutrients and contaminants in the same bays is planned to be completed in 2013. Data from NOAA’s long-term Caribbean Coral Reef Ecosystem Monitoring program was compiled to provide a baseline assessment of corals, fishes and habitats from 2001 to 2010, data needed to assess the impacts of erosion control projects installed from 2010 to 2011. The baseline data supplement other information collected as part of the USVI Watershed Stabilization Project, a project funded by the American Recovery and Reinvestment Act of 2009 and distributed through the NOAA Restoration Center, but uses data which is not within the scope of ARRA funded work. We present data on 16 ecological indicators of fishes, corals and habitats. These indicators were chosen because of their sensitivity to changes in water quality noted in the scientific literature (e.g., Rogers 1990, Larsen and Webb 2009). We report long-term averages and corresponding standard errors, plot annual averages, map indicator values and list inventories of coral and fish species identified among surveys. Similar data will be needed in the future to make rigorous comparisons and determine the magnitude of any impacts from watershed stabilization.

Porphyrin detection in denatured cnidarian tissue extracts

Porphyrin metabolic disruption from exposure to xenobiotic contaminants such as heavy metals, dioxins, and aromatic hydrocarbons can elicit overproduction of porphyrins. Measurement of porphyrin levels, when used in conjunction with other diagnostic assays, can help elucidate an organism’s physiological condition and provide evidence for exposure to certain toxicants. A sensitive microplate fluorometric assay has been optimized for detecting total porphyrin levels in detergent solubilized protein extracts from symbiotic, dinoflagellate containing cnidarian tissues. The denaturing buffer used in this modified assay contains a number of potentially interfering components (e.g., sodium dodecyl sulfate (SDS), dithiothreitol (DTT), protease inhibitors, and chlorophyll from the symbiotic zooxanthellae), which required examination and validation. Examination of buffer components were validated for use in this porphyrin assay; while the use of a specific spectrofluorometric filter (excitation 400 ± 15 nm; emission 600 ± 20 nm) minimized chlorophyll interference. The detection limit for this assay is 10 fmol of total porphyrin per μg of total soluble protein and linearity is maintained up to 5000 fmol. The ability to measure total porphyrins in a SDS protein extract now allows a single extract to be used in multiple assays. This is an advantage over classical methods, particularly when tissue samples are limiting, as is often the case with coral due to availability and collection permit restrictions.

Saline-saturated DMSO-EDTA as a storage medium for microbial DNA analysis from coral mucus swab samples

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.

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.

Quantifying seascape structure: extending terrestrial spatial pattern metrics to the marine realm

Spatial pattern metrics have routinely been applied to characterize and quantify structural features of terrestrial landscapes and have demonstrated great utility in landscape ecology and conservation planning. The important role of spatial structure in ecology and management is now commonly recognized, and recent advances in marine remote sensing technology have facilitated the application of spatial pattern metrics to the marine environment. However, it is not yet clear whether concepts, metrics, and statistical techniques developed for terrestrial ecosystems are relevant for marine species and seascapes. To address this gap in our knowledge, we reviewed, synthesized, and evaluated the utility and application of spatial pattern metrics in the marine science literature over the past 30 yr (1980 to 2010). In total, 23 studies characterized seascape structure, of which 17 quantified spatial patterns using a 2-dimensional patch-mosaic model and 5 used a continuously varying 3-dimensional surface model. Most seascape studies followed terrestrial-based studies in their search for ecological patterns and applied or modified existing metrics. Only 1 truly unique metric was found (hydrodynamic aperture applied to Pacific atolls). While there are still relatively few studies using spatial pattern metrics in the marine environment, they have suffered from similar misuse as reported for terrestrial studies, such as the lack of a priori considerations or the problem of collinearity between metrics. Spatial pattern metrics offer great potential for ecological research and environmental management in marine systems, and future studies should focus on (1) the dynamic boundary between the land and sea; (2) quantifying 3-dimensional spatial patterns; and (3) assessing and monitoring seascape change.

Monitoring Hawaii’s marine protected areas: examining spatial and temporal trends using a seascape approach

Hawaii’s coastal marine resources have declined dramatically over the past 100 years due to multiple anthropogenic stressors including overfishing, coastal development, pollution, overuse, invasive species and climate change. It is now becoming evident that ecosystem-based management, in the form of marine protected areas (MPAs), is necessary to conserve biodiversity, maintain viable fisheries, and deliver a broad suite of ecosystem services. Over the past four decades, Hawaii has developed a system of MPAs to conserve and replenish marine resources around the state. These Marine Life Conservation Districts (MLCDs) vary in size, habitat quality, and management regimes, providing an excellent opportunity to test hypotheses concerning MPA design and function using multiple discreet sampling units. NOAA/NOS/NCCOS/Center for Coastal Monitoring and Assessment’s Biogeography Branch used digital benthic habitat maps coupled with comprehensive ecological studies between 2002 and 2004 to evaluate the efficacy of all existing MLCDs using a spatially-explicit stratified random sampling design. The results from this work have shown that areas fully protected from fishing had higher fish biomass, larger overall fish size, and higher biodiversity than adjacent areas of similar habitat quality. Other key findings demonstrated that top predators and other important fisheries species were more abundant and larger in the MPAs, illustrating the effectiveness of these closures in conserving these populations. Habitat complexity, protected area size and habitat diversity were the major factors in determining effectiveness among MPAs.

Microbial community analysis of Acropora palamata mucus swabs, water and sediment samples from Hawksnest Bay, St. John, U.S. Virgin Islands

Colonies of the scleractinian coral Acropora palmata, listed as threatened under the US Endangered Species Act in 2006, have been monitored in Hawksnest Bay, within Virgin Islands National Park, St. John, from 2004 through 2010 by scientists with the US Geological Survey, National Park Service, and the University of the Virgin Islands. The focus has been on documenting the prevalence of disease, including white band, white pox (also called patchy necrosis and white patches), and unidentified diseases (Rogers et al., 2008; Muller et al., 2008). In an effort to learn more about the pathologies that might be involved with the diseases that were observed, samples were collected from apparently healthy and diseased colonies in July 2009 for analysis. Two different microbial assays were performed on Epicentre Biotechnologies DNA swabs containing A. palmata coral mucus, and on water and sediment samples collected in Hawksnest Bay. Both assays are based on polymerase chain reaction (PCR) amplification of portions of the small rRNA gene (16S). The objectives were to determine 1) if known coral bacterial pathogens Serratia marcescens (Acroporid Serratiosis), Vibrio coralliilyticus (temperature-dependent bleaching, White Syndrome), Vibrio shiloi (bleaching, necrosis), and Aurantimonas coralicida (White Plague Type II) were present in any samples, and 2) if there were any differences in microbial community profiles of each healthy, unaffected or diseased coral mucus swab. In addition to coral mucus, water and sediment samples were included to show ambient microbial populations. In the first test, PCR was used to separately amplify the unique and diagnostic region of the 16S rRNA gene for each of the coral pathogens being screened. Each pathogen test was designed so that an amplified DNA fragment could be seen only if the specific pathogen was present in a sample. A positive result was indicated by bands of DNA of the appropriate size on an agarose gel, which separates DNA fragments based on the size of the molecule. DNA from pure cultures of each of the pathogens was used as a positive control for each assay.

Use of skeletochronological analysis to estimate the age of leatherback sea turtles Dermochelys coriacea in the western North Atlantic

Although growth rate and age data are essential for leatherback management, estimates of these demographic parameters remain speculative due to the cryptic life history of this endangered species. Skeletochronological analysis of scleral ossicles obtained from 8 captive, known-age and 33 wild leatherbacks originating from the western North Atlantic was conducted to characterize the ossicles and the growth marks within them. Ages were accurately estimated for the known-age turtles, and their growth mark attributes were used to calibrate growth mark counts for the ossicles from wild specimens. Due to growth mark compaction and resorption, the number of marks visible at ossicle section tips was consistently and significantly greater than the number visible along the lateral edges, demonstrating that growth mark counts should be performed at the tips so that age is not underestimated. A correction factor protocol that incorporated the trajectory of early growth increments was used to estimate the number of missing marks in those ossicles exhibiting resorption, which was then added to the number of observed marks to obtain an age estimate for each turtle. A generalized smoothing spline model, von Bertalanffy growth curve, and size-at-age function were used to obtain estimates of age at maturity for leatherbacks in the western North Atlantic. Results of these analyses suggest that median age at maturation for leatherbacks in this part of the world may range from 24.5 to 29 yr. These age estimates are much greater than those proposed in previous studies and have significant implications for population management and recovery.

Age and growth of the blue shark (Prionace glauca) in the North Atlantic Ocean

Age and growth estimates for the blue shark (Prionace glauca) were derived from 411 vertebral centra and 43 tag-recaptured blue sharks collected in the North Atlantic, ranging in length from 49 to 312 cm fork length (FL). The vertebrae of two oxytetracycline-injected recaptured blue sharks support an annual spring deposition of growth bands in the vertebrae in sharks up to 192 cm FL. Males and females were aged to 16 and 15 years, respectively, and full maturity is attained by 5 years of age in both sexes. Both sexes grew similarly to age seven, when growth rates decreased in males and remained constant in females. Growth rates from tag-recaptured individuals agreed with those derived from vertebral annuli for smaller sharks but appeared overestimated for larger sharks. Von Bertalanffy growth parameters derived from vertebral length-at-age data are L∞ = 282 cm FL, K = 0.18, and t0 = –1.35 for males, and L∞ = 310 cm FL, K = 0.13, and t0 = −1.77 for females. The species grows faster and has a shorter life span than previously reported for these waters.

Validated age and growth of the porbeagle shark (Lamna nasus) in the western North Atlantic Ocean

Growth parameters were estimated for porbeagle shark (Lamna nasus) in the northwest Atlantic Ocean on the basis of vertebral annuli. A total of 578 vertebrae was analyzed. Annuli were validated up to an age of 11 years by using vertebrae from recaptured oxytetracycline-injected and known-age sharks. Males and females grew at similar rates until the size of male sexual maturity, after which the relative growth of the males declined. The growth rate of the females declined in a similar manner at the onset of maturity. Growth curves were consistent with those derived from tag-recapture analyses (GROTAG) of 76 recaptured fish and those based on length-frequency methods with measurements from 13,589 individuals. Von Bertalanffy growth curve parameters (combined sexes) were L∞ = 289.4 cm fork length, K = 0.07 and t0 = –6.06. Maximum age, based on vertebral band pair counts, was 25 and 24 years for males and females, respectively. Longevity calculations, however, indicated a maximum age of 45 to 46 years in an unfished population.

The reproductive biology of the porbeage shark (Lamna nasus) in the western North Atlantic Ocean

Reproductive organs from 393 male and 382 female porbeagles (Lamna nasus), caught in the western North Atlantic Ocean, were examined to determine size at maturity and reproductive cycle. Males ranged in size from 86 to 246 cm fork length (FL) and females ranged from 94 to 288 cm FL. Maturity in males was best described by an inflection in the relationship of clasper length to fork length when combined with clasper calcification. Males matured between 162 and 185 cm FL and 50% were mature at 174 cm FL. In females, all reproductive organ measurements related to body length showed a strong inflection around the size of maturity. Females matured between 210 and 230 cm FL and 50% were mature at 218 cm FL. After a protracted fall mating period (September–November), females give birth to an average of 4.0 young in spring (April−June). As in other lamnids, young are nourished through oophagy. Evidence from this study indicated a one-year reproductive cycle and gestation period lasting 8–9 months.

Interactions between climatic variables controlling subalpine tree growth: implications for climatic history of the Sierra Nevada, California

EXTRACT (SEE PDF FOR FULL ABSTRACT): Tree-ring records from foxtail pine (Pinus balfouriana) and western juniper (Juniperus occidentalis) growing near tree line in the eastern Sierra Nevada, California, show strong correlations with summer temperature and winter precipitation. Response surfaces portraying tree growth as a function of summer temperature and winter precipitation indicate a strong interaction between these variables in controlling growth. ... Above average growth for both foxtail pine and western juniper from AD 1480 to 1570 can be interpreted as indicating an extended period of warm, moist conditions unequalled during the 20th century.

Anomalous atmospheric circulation and large winter floods in six subregions of the southwestern United States

EXTRACT (SEE PDF FOR FULL ABSTRACT): We examined atmospheric circulation conditions conducive to occurrence of winter floods that exceed the 10-year peak discharge on rivers in six hydroclimatic subregions in Arizona, southern Utah, Nevada, and California. ... This relationship between flooding and broad-scale atmospheric patterns in the modern record will aid in paleoclimatic interpretations of paleoflood records over the last few thousand years.

Late Holocene environmental variability in the upper San Francisco Estuary as reconstructed from tidal marsh sediments

EXTRACT (SEE PDF FOR FULL ABSTRACT): Tidal marsh sediments collected from Browns Island in the lower Sacramento/San Joaquin Delta, California, are used to reconstruct environmental variability over the past 6.8 ka. Calibrated radiocarbon dates provide chronostratigraphic control. Trace metal analyses, grain-size variability, organic content, and macrofossils are used to define short- and long-term variations in relative salinity and inundation frequency. Aggradation began in subtidal fresh water conditions about 6.8 ka. Subtidal aggradation of clayey silts continued until about 6.3 ka, when conditions shifted toward a lower intertidal brackish marsh environment. By 5.1 ka, a brackish marsh plain had evolved, with surface water freshening after 4.1 ka. Conditions returned to brackish similar to the present after 2.3 ka.