Showing papers by "National Ocean Service published in 2016"

A synthesis of genetic connectivity in deep-sea fauna and implications for marine reserve design

Abstract: With anthropogenic impacts rapidly advancing into deeper waters, there is growing interest in establishing deep-sea marine protected areas (MPAs) or reserves. Reserve design depends on estimates of connectivity and scales of dispersal for the taxa of interest. Deep-sea taxa are hypothesized to disperse greater distances than shallow-water taxa, which implies that reserves would need to be larger in size and networks could be more widely spaced; however, this paradigm has not been tested. We compiled population genetic studies of deep-sea fauna and estimated dispersal distances for 51 studies using a method based on isolation-by-distance slopes. Estimates of dispersal distance ranged from 0.24 km to 2028 km with a geometric mean of 33.2 km and differed in relation to taxonomic and life-history factors as well as several study parameters. Dispersal distances were generally greater for fishes than invertebrates with the Mollusca being the least dispersive sampled phylum. Species that are pelagic as adults were more dispersive than those with sessile or sedentary lifestyles. Benthic species from soft-substrate habitats were generally less dispersive than species from hard substrate, demersal or pelagic habitats. As expected, species with pelagic and/or feeding (planktotrophic) larvae were more dispersive than other larval types. Many of these comparisons were confounded by taxonomic or other life-history differences (e.g. fishes being more dispersive than invertebrates) making any simple interpretation difficult. Our results provide the first rough estimate of the range of dispersal distances in the deep sea and allow comparisons to shallow-water assemblages. Overall, dispersal distances were greater for deeper taxa, although the differences were not large (0.3-0.6 orders of magnitude between means), and imbalanced sampling of shallow and deep taxa complicates any simple interpretation. Our analyses suggest the scales of dispersal and connectivity for reserve design in the deep sea might be comparable to or slightly larger than those in shallow water. Deep-sea reserve design will need to consider the enormous variety of taxa, life histories, hydrodynamics, spatial configuration of habitats and patterns of species distributions. The many caveats of our analyses provide a strong impetus for substantial future efforts to assess connectivity of deep-sea species from a variety of habitats, taxonomic groups and depth zones.

Vertical distribution of buoyant Microcystis blooms in a Lagrangian particle tracking model for short‐term forecasts in Lake Erie

Abstract: Cyanobacterial harmful algal blooms (CHABs) are a problem in western Lake Erie, and in eutrophic fresh waters worldwide. Western Lake Erie is a large (3000 km2), shallow (8 m mean depth), freshwater system. CHABs occur from July to October, when stratification is intermittent in response to wind and surface heating or cooling (polymictic). Existing forecast models give the present location and extent of CHABs from satellite imagery, then predict two-dimensional (surface) CHAB movement in response to meteorology. In this study, we simulated vertical distribution of buoyant Microcystis colonies, and 3-D advection, using a Lagrangian particle model forced by currents and turbulent diffusivity from the Finite Volume Community Ocean Model (FVCOM). We estimated the frequency distribution of Microcystis colony buoyant velocity from measured size distributions and buoyant velocities. We evaluated several random-walk numerical schemes to efficiently minimize particle accumulation artifacts. We selected the Milstein scheme, with linear interpolation of the diffusivity profile in place of cubic splines, and varied the time step at each particle and step based on the curvature of the local diffusivity profile to ensure that the Visser time step criterion was satisfied. Inclusion of vertical mixing with buoyancy significantly improved model skill statistics compared to an advection-only model, and showed greater skill than a persistence forecast through simulation day 6, in a series of 26 hindcast simulations from 2011. The simulations and in situ observations show the importance of subtle thermal structure, typical of a polymictic lake, along with buoyancy in determining vertical and horizontal distribution of Microcystis.

Invasion of novel habitats uncouples haplo‐diplontic life cycles

Abstract: Baker's Law predicts uniparental reproduction will facilitate colonization success in novel habitats. While evidence supports this prediction among colonizing plants and animals, few studies have investigated shifts in reproductive mode in haplo-diplontic species in which both prolonged haploid and diploid stages separate meiosis and fertilization in time and space. Due to this separation, asexual reproduction can yield the dominance of one of the ploidy stages in colonizing populations. We tested for shifts in ploidy and reproductive mode across native and introduced populations of the red seaweed Gracilaria vermiculophylla. Native populations in the northwest Pacific Ocean were nearly always attached by holdfasts to hard substrata and, as is characteristic of the genus, haploid–diploid ratios were slightly diploid-biased. In contrast, along North American and European coastlines, introduced populations nearly always floated atop soft-sediment mudflats and were overwhelmingly dominated by diploid thalli without holdfasts. Introduced populations exhibited population genetic signals consistent with extensive vegetative fragmentation, while native populations did not. Thus, the ecological shift from attached to unattached thalli, ostensibly necessitated by the invasion of soft-sediment habitats, correlated with shifts from sexual to asexual reproduction and slight to strong diploid bias. We extend Baker's Law by predicting other colonizing haplo-diplontic species will show similar increases in asexuality that correlate with the dominance of one ploidy stage. Labile mating systems likely facilitate colonization success and subsequent range expansion, but for haplo-diplontic species, the long-term eco-evolutionary impacts will depend on which ploidy stage is lost and the degree to which asexual reproduction is canalized.

Goods and services of extensive aquaculture: shellfish culture and nutrient trading

Abstract: Bivalve shellfish play an important role in top-down control of primary symptoms of eutrophication. This short-circuits the process of organic decomposition and promotes an enhancement of underwater light climate, improved oxygenation of bottom water, and restoration of submerged aquatic vegetation. This review analyses this ecosystem service as a potential actor in watershed-level nutrient credit trading programmes and explores the possibilities of implementation of such programmes in Europe. We examine the different components of the issue, including the eutrophication status of European coastal waters, legal and management instruments, and the use of mathematical models at both the ecosystem and farm scales to evaluate the potential removal of nitrogen by cultivated shellfish such as oysters, mussels, and clams. The annual European bivalve shellfish production of over 700,000 metric tons is estimated to generate a nitrogen removal of 46,800 t year−1, equivalent to 14 × 106 population equivalent, and a minimum value of 507 × 106 €. We discuss future directions for this topic in Europe, drawing from ongoing research in the USA and elsewhere, in the light of the twin challenges of European aquaculture expansion and implementation of EU directives.

Global solutions to regional problems: Collecting global expertise to address the problem of harmful cyanobacterial blooms. A Lake Erie case study

Abstract: In early August 2014, the municipality of Toledo, OH (USA) issued a ‘do not drink’ advisory on their water supply directly affecting over 400,000 residential customers and hundreds of businesses (Wilson, 2014) This order was attributable to levels of microcystin, a potent liver toxin, which rose to 25 mg L1 in finished drinking water The Toledo crisis afforded an opportunity to bring together scientists from around the world to share ideas regarding factors that contribute to bloom formation and toxigenicity, bloom and toxin detection as well as prevention and remediation of bloom events These discussions took place at an NSF- and NOAA-sponsored workshop at Bowling Green State University on April 13 and 14, 2015 In all, more than 100 attendees from six countries and 15 US states gathered together to share their perspectives The purpose of this review is to present the consensus summary of these issues that emerged from discussions at the Workshop As additional reports in this special issue provide detailed reviews on many major CHAB species, this paper focuses on the general themes common to all blooms, such as bloom detection, modeling, nutrient loading, and strategies to reduce nutrients

The role of 2,4-dihydroxyquinoline (DHQ) in Pseudomonas aeruginosa pathogenicity

Abstract: Bacteria synchronize group behaviors using quorum sensing, which is advantageous during an infection to thwart immune cell attack and resist deleterious changes in the environment. In Pseudomonas aeruginosa, the Pseudomonas quinolone signal (Pqs) quorum-sensing system is an important component of an interconnected intercellular communication network. Two alkylquinolones, 2-heptyl-4-quinolone (HHQ) and 2-heptyl-3-hydroxy-4-quinolone (PQS), activate transcriptional regulator PqsR to promote the production of quinolone signals and virulence factors. Our work focused on the most abundant quinolone produced from the Pqs system, 2,4-dihydroxyquinoline (DHQ), which was shown previously to sustain pyocyanin production and antifungal activity of P. aeruginosa. However, little is known about how DHQ affects P. aeruginosa pathogenicity. Using C. elegans as a model for P. aeruginosa infection, we found pqs mutants only able to produce DHQ maintained virulence towards the nematodes similar to wild-type. In addition, DHQ-only producing mutants displayed increased colonization of C. elegans and virulence factor production compared to a quinolone-null strain. DHQ also bound to PqsR and activated the transcription of pqs operon. More importantly, high extracellular concentration of DHQ was maintained in both aerobic and anaerobic growth. High levels of DHQ were also detected in the sputum samples of cystic fibrosis patients. Taken together, our findings suggest DHQ may play an important role in sustaining P. aeruginosa pathogenicity under oxygen-limiting conditions.

Structure–Activity Relationship Studies Using Natural and Synthetic Okadaic Acid/Dinophysistoxin Toxins

Abstract: Okadaic acid (OA) and the closely related dinophysistoxins (DTXs) are algal toxins that accumulate in shellfish and are known serine/threonine protein phosphatase (ser/thr PP) inhibitors. Phosphatases are important modulators of enzyme activity and cell signaling pathways. However, the interactions between the OA/DTX toxins and phosphatases are not fully understood. This study sought to identify phosphatase targets and characterize their structure–activity relationships (SAR) with these algal toxins using a combination of phosphatase activity and cytotoxicity assays. Preliminary screening of 21 human and yeast phosphatases indicated that only three ser/thr PPs (PP2a, PP1, PP5) were inhibited by physiologically saturating concentrations of DTX2 (200 nM). SAR studies employed naturally-isolated OA, DTX1, and DTX2, which vary in degree and/or position of methylation, in addition to synthetic 2-epi-DTX2. OA/DTX analogs induced cytotoxicity and inhibited PP activity with a relatively conserved order of potency: OA = DTX1 ≥ DTX2 >> 2-epi-DTX. The PPs were also differentially inhibited with sensitivities of PP2a > PP5 > PP1. These findings demonstrate that small variations in OA/DTX toxin structures, particularly at the head region (i.e., C1/C2), result in significant changes in toxicological potency, whereas changes in methylation at C31 and C35 (tail region) only mildly affect potency. In addition to this being the first study to extensively test OA/DTX analogs’ activities towards PP5, these data will be helpful for accurately determining toxic equivalence factors (TEFs), facilitating molecular modeling efforts, and developing highly selective phosphatase inhibitors.

RNA-Seq analysis of seasonal and individual variation in blood transcriptomes of healthy managed bottlenose dolphins.

Abstract: The blood transcriptome can reflect both systemic exposures and pathological changes in other organs of the body because immune cells recirculate through the blood, lymphoid tissues, and affected sites. In human and veterinary medicine, blood transcriptome analysis has been used successfully to identify markers of disease or pathological conditions, but can be confounded by large seasonal changes in expression. In comparison, the use of transcriptomic based analyses in wildlife has been limited. Here we report a longitudinal study of four managed bottlenose dolphins located in Waikoloa, Hawaii, serially sampled (approximately monthly) over the course of 1 year to establish baseline information on the content and variation of the dolphin blood transcriptome. Illumina based RNA-seq analyses were carried out using both the Ensembl dolphin genome and a de novo blood transcriptome as guides. Overall, the blood transcriptome encompassed a wide array of cellular functions and processes and was relatively stable within and between animals over the course of 1 year. Principal components analysis revealed moderate clustering by sex associated with the variation among global gene expression profiles (PC1, 22 % of variance). Limited seasonal change was observed, with < 2.5 % of genes differentially expressed between winter and summer months (FDR < 0.05). Among the differentially expressed genes, cosinor analysis identified seasonal rhythmicity for the observed changes in blood gene expression, consistent with studies in humans. While the proportion of seasonally variant genes in these dolphins is much smaller than that reported in humans, the majority of those identified in dolphins were also shown to vary with season in humans. Gene co-expression network analysis identified several gene modules with significant correlation to age, sex, or hematological parameters. This longitudinal analysis of healthy managed dolphins establishes a preliminary baseline for blood transcriptome analysis in this species. Correlations with hematological parameters, distinct from muted seasonal effects, suggest that the otherwise relatively stable blood transcriptome may be a useful indicator of health and exposure. A robust database of gene expression in free-ranging and managed dolphins across seasons with known adverse health conditions or contaminant exposures will be needed to establish predictive gene expression profiles suitable for biomonitoring.

In Tide’s Way: Southeast Florida’s September 2015 Sunny-day Flood

Abstract: The Flood Event. High tides on 27 September 2015 f looded several Miami-region communities with 0.57 m of ocean water. The flooding was concerning because of the sunny-day conditions and awareness that trends of such events are accelerating within U.S. Atlantic Coast cities from rising seas (Sweet et al. 2014; Ezer and Atkinson 2014; Sweet and Marra 2016). It was the sixth largest flood measured by the National Oceanic and Atmospheric Administration (NOAA) tide gauge in Virginia Key, Florida (Miami region), since its 1994 installation (Fig. 6.1a). The five higher floods were in response to hurricanes. The f lood had substantial astronomical underpinnings (Fig. 6.1b); it occurred during spring tides and near the peak of the seasonal mean sea level (MSL), the lunar 8.8-year perigee, and the 18.6-year nodal cycles. These factors explain the 0.24-m NOAA tide prediction relative to mean higher high water (MHHW) tidal datum that delineates typical tidal inundation (Schureman 2001; Parker 2007). Yet, tide forcing alone was insufficient to produce the observed impacts as minor “nuisance” flooding begins in excess of 0.4 meters in this region (Sweet et al. 2014). Other dynamics were at play. A nontidal sea level anomaly (Fig. 6.1b, green line), which exceeded 0.15 m for a month starting September 22, reached 0.33 m during the flood and even higher for weeks afterwards. Strong high pressure over Eastern Canada (Fig. 6.1c) with >15 m s−1 northeasterlies offshore of the mid-Atlantic Bight (not shown) drove an Ekmanrelated setup along much of the U.S. East Coast. During the flood, setup was >20 cm along the southeast Florida coast as modeled by NOAA’s extratropical surge and tide operational forecast system (Funakoshi et al. 2013). Local winds, however, were calm (<3 m s−1; http://tidesandcurrents.noaa.gov/met), inverse barometer effects nonexistent (Fig. 6.1c), and dynamical wave effects minimal as inferred by the ~1 cm standard deviations during tide measurements (Sweet et al. 2015). Interestingly, Gulf Stream transport measured upstream in the Florida Current (FC) slowed to a monthly minimum of 23.4 Sverdrup (Sv; 1 Sv ≡ 106 m3 s−1) on 25 September (Fig. 6.1d), which persisted through the flood. Transport slowdowns raise MSL along the US southeast (Zhao and Johns 2014; Ezer 2016) and Florida coasts (Park and Sweet 2015) from adjustments to meridional Ekman transport (Lee and Williams 1988) and shelf-wave dynamics (Czeschel et al. 2012; Ezer 2016). Previous studies report a 0.5–1.5 cm rise in coastal MSL per 1-Sv decline in Gulf Stream system transport (Ezer et al. 2013; Woodworth et al. 2014; Goddard et al. 2015; Ezer 2016); when it slows, local tidal-flood risks increase (Sweet et al. 2009; Ezer and Atkinson 2014; Wdowinski et al. 2016). Here, we derive a contemporary return period of the flood using a time-dependent extreme value statistical model. Then, we assess the degree that (i) seasonal variability, (ii) tide cycles, (iii) FC monthly transport minimums, and (iv) a multidecadal trend have independently affected Virginia Key’s extreme water level distribution and estimate their attribution during the f lood. We conclude by analyzing how the flood’s return period changes under future SLR projections for the Miami region forced by three representative concentration pathways (RCP).

Use of biosensors for the detection of marine toxins.

Abstract: Increasing occurrences of harmful algal blooms (HABs) in the ocean are a major concern for countries around the globe, and with strong links between HABs and climate change and eutrophication, the occurrences are only set to increase. Of particular concern with regard to HABs is the presence of toxin-producing algae. Six major marine biotoxin groups are associated with HABs. Ingestion of such toxins via contaminated shellfish, fish, or other potential vectors, can lead to intoxication syndromes with moderate to severe symptoms, including death in extreme cases. There are also major economic implications associated with the diverse effects of marine biotoxins and HABs. Thus, effective monitoring programmes are required to manage and mitigate their detrimental global effect. However, currently legislated detection methods are labour-intensive, expensive and relatively slow. The growing field of biosensor diagnostic devices is an exciting area that has the potential to produce robust, easy-to-use, cost-effective, rapid and accurate detection methods for marine biotoxins and HABs. This review discusses recently developed biosensor assays that target marine biotoxins and their microbial producers, both in harvested fish/shellfish samples and in the open ocean. The effective deployment of such biosensor platforms could address the pressing need for improved monitoring of HABs and marine biotoxins, and could help to reduce their global economic impact.

Recovery and identification of Pseudo-nitzschia (Bacillariophyceae) frustules from natural samples acquired using the environmental sample processor

Abstract: Many species within the diatom genus Pseudo-nitzschia are difficult to distinguish without applying molecular analytical or microscopy-based methods. DNA, antibody and lectin probes have previously been used to provide rapid and specific detection of species and strains in complex field assemblages. Recently, however, well-documented cryptic genetic diversity within the group has confounded results of DNA probe tests in particular. Moreover, the number of species descriptions within the genus continues to increase, as do insights into toxin production by both new and previously described species. Therefore, a combination of classical morphological techniques and modern molecular methodologies is needed to resolve ecophysiological traits of Pseudo-nitzschia species. Here, we present an approach to recover and identify frustules from sample collection filters used for toxin analysis onboard the Environmental Sample Processor (ESP), an in situ sample collection and analytical platform. This approach provides a new and powerful tool for correlating species presence with toxin detected remotely and in situ by the ESP, and has the potential to be applied broadly to other sampling configurations. This new technique will contribute to a better understanding of naturally occurring Pseudo-nitzschia community structure with respect to observed domoic acid outbreaks.

Aflatoxin-Exposure of Vibrio gazogenes as a Novel System for the Generation of Aflatoxin Synthesis Inhibitors

Abstract: Aflatoxin is a mycotoxin and a secondary metabolite, and the most potent known liver carcinogen that contaminates several important crops, and represents a significant threat to public health and the economy. Available approaches reported thus far have been insufficient to eliminate this threat, and therefore provide the rational to explore novel methods for preventing aflatoxin accumulation in the environment. Many terrestrial plants and microbes that share ecological niches and encounter the aflatoxin producers have the ability to synthesize compounds that inhibit aflatoxin synthesis. However, reports of natural aflatoxin inhibitors from marine ecosystem components that do not share ecological niches with the aflatoxin producers are rare. Here we show that a non-pathogenic marine bacterium, Vibrio gazogenes, when exposed to low non-toxic doses of aflatoxin B1, demonstrates a shift in its metabolic output and synthesizes a metabolite fraction that inhibits aflatoxin synthesis without affecting hyphal growth in the model aflatoxin producer, Aspergillus parasiticus. The molecular mass of the predominant metabolite in this fraction was also different from the known prodigiosins, which are the known antifungal secondary metabolites synthesized by this Vibrio. Gene expression analyses using RT-PCR demonstrate that this metabolite fraction inhibits aflatoxin synthesis by down-regulating the expression of early-, middle- and late- growth stage aflatoxin genes, the aflatoxin pathway regulator, aflR and one global regulator of secondary metabolism, LaeA. Our study establishes a novel system for generation of aflatoxin synthesis inhibitors, and emphasizes the potential of the under-explored Vibrio’s silent genome for generating new modulators of fungal secondary metabolism.

Decadal comparison of a diminishing coral community: a study using demographics to advance inferences of community status

Abstract: The most common coral monitoring methods estimate coral abundance as percent cover, either via in situ observations or derived from images. In recent years, growing interest and effort has focused on colony-based (demographic) data to assess the status of coral populations and communities. In this study, we relied on two separate data sets (photo-derived percent cover estimates, 2002–12, and opportunistic in situ demographic sampling, 2004 and 2012) to more fully infer decadal changes in coral communities at a small, uninhabited Caribbean island. Photo-derived percent cover documented drastic declines in coral abundance including disproportionate declines in Orbicella spp. While overall in situ estimates of total coral density were not different between years, densities of several rarer taxa were. Meandrina meandrites and Stephanocoenia intersepta increased while Leptoseris cucullata decreased significantly, changes that were not discernable from the photo-derived cover estimates. Demographic data also showed significant shifts to larger colony sizes (both increased mean colony sizes and increased negative skewness of size frequency distributions, but similar maximum colony sizes) for most taxa likely indicating reduced recruitment. Orbicella spp. differed from this general pattern, significantly shifting to smaller colony sizes due to partial mortality. Both approaches detected significant decadal changes in coral community structure at Navassa, though the demographic sampling provided better resolution of more subtle, taxon-specific changes.

ERMA® to the Cloud

Abstract: In 2011, the US White House and Congress challenged the executive departments to be cloud-first with Information Technology (IT). National Oceanic and Atmospheric Administration’s (NOAA) Environmental Response Management Applications (ERMA®) was an early candidate for moving an application from local hardware resources to the cloud. The cloud was an intriguing computing infrastructure option for ERMA because of the "on demand" scaling provided by cloud services. ERMA's cloud migration was early in the Federal Risk and Authorization Management Program (FedRAMP) and therefore included experiences with walking through new technology and contracting services with the organization's IT security specialists. Ultimately, the process of migrating ERMA from physical hardware to infrastructure as a service (IaaS) from a cloud service provider included four focus areas: Security considerations; contracting, procurement, and planning; system design; and project management. The chapter also summarizes lessons learned and recommendations for considering cloud migrations for government systems.

A Bayesian mixture model for missing data in marine mammal growth analysis.

Abstract: Much of what is known about bottle nose dolphin (Tursiops truncatus) anatomy and physiology is based on necropsies from stranding events. Measurements of total body length, total body mass, and age are used to estimate growth. It is more feasible to retrieve and transport smaller animals for total body mass measurement than larger animals, introducing a systematic bias in sampling. Adverse weather events, volunteer availability, and other unforeseen circumstances also contribute to incomplete measurement. We have developed a Bayesian mixture model to describe growth in detected stranded animals using data from both those that are fully measured and those not fully measured. Our approach uses a shared random effect to link the missingness mechanism (i.e. full/partial measurement) to distinct growth curves in the fully and partially measured populations, thereby enabling drawing of strength for estimation. We use simulation to compare our model to complete case analysis and two common multiple imputation methods according to model mean square error. Results indicate that our mixture model provides better fit both when the two populations are present and when they are not. The feasibility and utility of our new method is demonstrated by application to South Carolina strandings data.