ECOHAB 2008-2009: Project Summaries

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Title: ECOHAB: Remote detection of harmful algal blooms in the eastern Gulf of Mexico

Investigators:  Chuanmin Hu, Kendall L Carder, Jennifer Cannizzaro, Zhongping Lee

Institutions:  University of South Florida; Naval Research Lab at Stennis, Mississippi

Funded:  NASA

Satellite remote sensing can provide more synoptic and frequent information on Karenia brevis occurrence over traditional shipboard techniques, and thus has been both an active research area and used routinely by researchers and agencies like NOAA for monitoring harmful algal blooms (HABs). However, because of the uncertainties associated with remote sensing algorithms and data products, current approaches to detect HABs from space often yield false information, and therefore the full potential of remote sensing is yet to be realized. Here we propose a dedicated effort to refine and further develop several existing, yet preliminary HAB classification algorithms.

Objectives:  Specifically, we have three objectives:

1) Develop an improved method to detect K. brevis HABs and quantify cell concentrations by fine-tuning and combining the existing candidate methods based on: chlorophyll-a concentration (Chl) and Chl-anomaly; fluorescence line height (FLH); particulate backscattering over Chl ratio (bbp/Chl); and computer artificial intelligence;

2) Establish a record of HAB characteristics (timing, duration, size, and intensity) in the eastern GOM (EGOM) by combining modern satellite remote sensing (SeaWiFS, MODIS, MERIS) and field sampling data. This is to help understand HAB trends in the region, the question of which has been constantly debated within the scientific community;

3) Explore the potential of using Lidar (CALIOP) data in detecting HABs. Our study area will focus on the EGOM, but data from the western GOM will also be tested.

Approach:  We will take a rigorous  approach to explicitly differentiate the various oceanic constituents using customized, finely tuned algorithms, developed from both in situ and remote measurements and combined with radiative transfer theory and artificial intelligence. There are several novel aspects in the approach. First, MODIS fluorescence line height (FLH) has shown great promise in detecting blooms in coastal waters rich in colored dissolved organic matter (CDOM), and this product will be refined and tested extensively. Second, MERIS bands at 620-nm and 709-nm have shown superior value to other data in correcting bottom effects and in detecting intense blooms, but their use for the GOM is rare. Indeed, for continuity reasons the use of MERIS is critical for the US. Third, the approach to use artificial intelligence (computer neural networks) by combining the advantages of the various methods is expected to yield better performance than any single method. Finally, the potential of active satellite remote sensing (CALIOP) to detect subsurface blooms will be explored.


Expected Results:  We anticipate two major results: 1) an improved, autonomous method to detect and quantify HABs at various concentration levels from space, which will be delivered to NOAA CoastWatch to improve monitoring efforts; 2) the combination of historical in situ K. brevis data and modern remote sensing data will provide a novel view of HAB occurrence in recent years, and will provide baseline data for future evaluation of the coastal environment. This project will add significant value to the existing ECOHAB projects and EPA’s GOM program.



Title: Deposition and resuspension of Alexandrium fundyense resting cysts in the Gulf of Maine: Phase II

Institutions: Woods Hole Oceanographic Institution, University of Massachusetts, United States Geological Survey

Investigators:  D. Anderson, D McGillicuddy, C. Pilskaln, R. Signell, B.Butman, A. Solow


The Gulf of Maine (GOM) supports productive shellfisheries frequently impacted by paralytic shellfish poisoning (PSP) - a serious threat to human health caused by the toxic dinoflagellate Alexandrium fundyense. PSP is the most widespread of the poisoning syndromes associated with harmful algal blooms (HABs). Blooms of A. fundyense in the GOM are highly seasonal, consistent with the view that life history transformations between cysts and vegetative cells are major regulatory factors. The ecology and oceanography of A. fundyense have been relatively well studied, but encystment and excystment dynamics remain poorly understood. This project is the second phase of a continuing study focusing on several aspects of that dynamic – the processes controlling the delivery, deposition, resuspension, and accumulation of resting cysts. In the parent project, researchers mapped the distribution of A. fundyense cysts in GOM bottom sediments and the benthic nepheloid layer (BNL) and obtained trap data on the sedimentation and resuspension fluxes of cysts through time.

1) Determine the sinking characteristics and depositional behavior of resuspended cysts in bottom sediments;
2) Incorporate the USGS Community Sediment Transport Model into the existing physical-biological model for Alexandrium dynamics in the GOM;
3) Use this model formulation to explore the relationship between existing maps of cyst distribution and sediment type, and the thickness and cyst content of the BNL at different locations in the GOM;
4) Characterize cyst content and residence time in the BNL at different locations in the GOM with varying BNL thicknesses, taking into account both resuspension fluxes and lateral advection;
5) Conduct numerical experiments to explore the processes involved in the sedimentation of newly formed A. fundyense cysts, their deposition, reworking, and eventual redeposition in major cyst seedbeds in the GOM; and
6) Optimize cyst mapping strategies to minimize cost without unacceptable loss of accuracy in model forecasts.

Approach: Researchers will use observations from the parent project as well as new laboratory experiments and numerical model simulations to characterize cyst dynamics in surface waters, the BNL, and bottom sediments of the GOM.

Expected results: The expected results of this project will support NOAA’s planned operational forecasting system for PSP in the GOM, and fit perfectly with NOAA and ECOHAB priorities to provide “Quantitative understanding of HABs…… in relation to the surrounding environment ….. leading to development of operational ecological forecasting capabilities in areas with severe, recurrent blooms along the US coast”. Continued expansion and refinement of the coupled numerical models will greatly enhance the capability for HAB forecasting in the GOM.



Title: Mechanism of harmful algal bloom initiation in the western Gulf of Mexico

Institutions: Texas A&M University, NOAA, Woods Hole Oceanographic Institution

Investigators: L.Campbell, R. Hetland, R. Stumpf; R. Olson; H. Sosik


The toxic dinoflagellate Karenia brevis is the primary harmful algal bloom (HAB) species in the Gulf of Mexico. One curious feature of K. brevis blooms is that although they occur regularly in the eastern Gulf, they occur only sporadically in the western Gulf along the Texas coast. This difference is unexpected since temperature, salinity, and nutrient conditions are similar in the two regions.

Objectives: The central hypothesis of this project is that the primary mechanism of bloom initiation in the western Gulf of Mexico is convergence and consequent downwelling at the coast, which physically concentrates Karenia cells because they swim upwards toward light. This mechanism differs from the blooms in the eastern Gulf off Florida, where blooms result from upwelling favorable winds and concentration at nearshore frontal boundaries. Specific objectives are to (1) correlate wind and bloom events using an existing hydrodynamic model to test the hypothesis that K. brevis bloom events are linked to seasonal downwelling along the Texas coast and that upwelling events may play an important role in dispersing the bloom; (2) test downwelling index predictions with field data on bloom development, including sampling targeted by the model predictions; and (3) develop a “Downwelling Index” for improved predictive capability based on local wind conditions.

Approach: A multi-investigator interdisciplinary program is proposed to develop better tools for prediction and to apply a novel imaging technology for detection and quantification of K. brevis. A numerical simulation of surface currents in the Gulf of Mexico suggested that increases in algal concentrations due to downwelling circulation may be comparable to (or, exceed) population increases due to growth alone. To investigate the relationship between K. brevis blooms and wind events, field samples will be collected by an extensive volunteer network combined with a targeted sampling program guided by model results and satellite data. Cell abundances will be analyzed in near-real time with the Imaging FlowCytobot (IFCB) and automated classification. Finally, results will enable creation of a ‘downwelling index’ based on local wind conditions that will provide a new tool to predict the likelihood of K. brevis bloom formation. This index will take into account the net accumulation of plankton near the coast due to downwelling circulation. Measured environmental conditions and observed bloom events, as well as simulated bloom events using the hydrodynamic model, will be used to develop and refine the downwelling index.

Expected results: Important outcomes of this project include new fundamental knowledge on the mechanism of bloom formation in the western Gulf and demonstration of the IFCB as a powerful technique for identification and quantification of HABs in near real time. Once validated, the downwelling Index will be made available to managers via the NOAA HAB Forecast System for prediction/ early warning of HAB events. A better understanding of how K. brevis blooms form will lead to improved prediction of harmful algal blooms throughout the Gulf.


Title: Linking biogeochemistry to harmful algal bloom nutritional physiology with gene expression analyses: a case study with Aureococcus anophagefferens

Institutions: Woods Hole Oceanographic Institution, SUNY Stony Brook

Investigators: S. Dyhrman, C. Gobler


Harmful algal blooms (HABs) represent a significant threat to fisheries, public health, and economies around the world. Despite many years of study, fundamental questions remain regarding how nutrients drive HABs, such as the brown tides caused by Aureococcus anophagefferens. What species of dissolved inorganic nitrogen and phosphorus, or dissolved organic nitrogen and phosphorus are preferentially transported and metabolized by cells during blooms? How does nutrient transport and metabolism change as a function of ambient conditions as blooms initiate, are sustained, and decline? This project capitalizes on the recent completion of the first HAB genome sequence (A. anophagefferens) and our preliminary gene expression work with this species to develop and apply assays of gene expression to track the nutritional physiology of A. anophagefferens in its natural environment. By concurrently examining nutrient dynamics (e.g. supply, composition etc.), bloom dynamics, and gene expression we will create a clearer understanding of how nutrients influence HABs.

1) Optimize qRT-PCR methods for the quantification of the expression of genes involved in nutrient transport and metabolism.
2) In laboratory experiments, validate how the expression of the target genes are regulated by nutritional physiology and changes in exogenous nutrients.
3) Track gene expression patterns in parallel with nutrient dynamics through the course of a bloom.
4) In field incubations, examine gene expression patterns during nutrient addition bioassays.

Approach:  In this targeted research study, investigators will validate and apply quantitative gene expression assays to examine how nutrients influence bloom initiation, sustenance, and decline. The project will link nutrient dynamics to the expression of genes involved in nutrient transport and metabolism in culture controls and through the course of a brown tide.

Expected results:  Parameterization of nutrient influences on HABs provided by the development and application of the approach described herein would 1) provide information that will enhance HAB forecasting efforts (e.g. better modeling of how eutrophication and nutrient inputs influence bloom dynamics), 2) provide decision makers with the information needed to control and mitigate blooms (e.g. assays of the effects of nutrient loading), and 3) help facilitate bloom prevention through an advanced understanding of how nutrients promote bloom formation, sustenance, and decline in different systems. Although this study uses brown tide as a model, we underscore that the approach developed and validated herein has never been conducted for any algal species and may be used as a blue-print for application to other HABs.

Title: Causes and consequences of cell death in the toxic dinoflagellate Alexandrium tamarense

Institutions: University of Texas Marine Science Institute

Investigators: D. Erdner


Harmful Algal Blooms (HABs) in estuarine and coastal waters can endanger both public and ecosystem health, and their incidence and extent are increasing worldwide. The toxic dinoflagellate Alexandrium tamarense is responsible for outbreaks of paralytic shellfish poisoning, one of the most widespread HAB syndromes. While numerous laboratory and field studies have greatly increased our understanding of the biological and physical processes that lead to the initiation of blooms and their subsequent growth and transport, very little is known about the causes of bloom decline and termination. Preliminary results suggest that Alexandrium may initiate programmed cell death in response to nutrient stress, leading to the hypothesis that an active cell death pathway in Alexandrium may contribute to the decline of blooms in situ.

Objectives: The overall goal of this project is to evaluate the relationship between nutrient stress, programmed cell death (PCD), and encystment in Alexandrium by: (1) documenting the PCD process in Alexandrium, including the genetic, biochemical, and morphological changes that occur; (2) identifying the triggers of PCD in Alexandrium; (3) investigating the link between PCD and the encystment process; and (4) assessing the presence and magnitude of PCD in a natural Alexandrium bloom.

Approach: A suite of genetic and biochemical assays will be used to determine the existence of the PCD process in Alexandrium under conditions that result in nutrient stress or encystment. These include measures of caspase activity, DNA fragmentation, maintenance of membrane integrity, inversion of phosphatidylserine in the cell membrane, and metacaspase gene expression. These analyses will also be used with natural bloom populations, to assess the role of PCD in bloom decline in situ.

Expected Results: The end results of the work will be: a description of the PCD process in a toxic dinoflagellate; an understanding of the environmental triggers of PCD; elucidation of the link between PCD and encystment pathways in Alexandrium; and assessment of the role of PCD in bloom decline in situ. The results of this project will provide valuable information on the links between nutrient conditions and bloom termination, contributing directly to all three of EPA’s desired outcomes: 1) assessment of the role of PCD in bloom decline will contribute to better modeling of harmful blooms, thereby providing information that will enhance HAB forecasting efforts; 2) data on the links between nutrient conditions and bloom decline (or persistence) will help to provide decision makers with the information needed to control and mitigate blooms; and 3) knowledge of cell death processes in toxic dinoflagellate will help facilitate bloom prevention through an advanced understanding of the conditions and processes that promote their formation, maintenance, and decline.

Title:  PNWTOX–The Columbia River plume and HABs in the Pacific Northwest: bioreactor, barrier, or conduit?

Institutions: University of Washington; Department of Fisheries and Oceans, Pacific Region, Institute of Ocean Sciences, Sidney, B.C., Canada; University of California, Santa Cruz.

B. Hickey, E. Lessard, P. MacCready, N. Banas, M. Foreman, R. Thomson,  D.Masson; R. Kudela

Funded:  NOAA NOS NCCOS CSCOR and National Science Foundation

Project Summary:
Objective: The overall program objective is to improve predictability of Harmful Algal Bloom (HAB) events on Pacific Northwest (PNW) coastal beaches by advancing our understanding of HAB development/dissipation and transport and mixing processes using existing data in parallel with state of the art physical and bio-physical models that include, for the first time, both the Columbia River (CR) plume and potential HAB source regions off both Oregon and Washington.

Approach: This project makes use of results and data from two recently completed, temporally overlapping 5-year, multi-institutional, interdisciplinary studies–ECOHAB PNW (The Ecology and Oceanography of Harmful Algal Blooms in the PNW) and RISE (River Influences on Shelf Ecosystems), to improve predictability of arrival of HABs, in particular, toxigenic Pseudo-nitzschia (PN), on PNW beaches. The overriding conclusion from both studies is that lack of understanding of the effect of the CR plume on cross-shelf and alongshelf transport and mixing is the greatest impediment to understanding how phytoplankton, in particular, HABs, arrive on coastal beaches. In this project, we will build on the wealth of complementary information and enhanced knowledge generated in these two programs to study the transport and mitigation of HABs to the Washington coast from both northern and southern sources and extend our analyses to species other than PN. Hypotheses include: 1) The CR plume is a bioreactor for growth but not for toxin production, 2) During downwelling winds, the CR plume inhibits shoreward transport of toxic blooms, 3) During upwelling winds the CR plume enhances cross-shelf transport of toxic blooms below the surface layer, and 4) The CR plume enhances northward transport of toxic blooms along the coast.

Studies will include idealized process studies addressing these hypotheses, hindcasts of selected HAB events, and development of a forecasting ability. The new Northwest Association of Networked Ocean Observing Systems (NANOOS) will be used for model verification and also model improvement via data assimilation.

Expected Results: A large group of Government and Tribal bodies with interests in coastal shellfish resources will benefit from both the improved HABs understanding as well as a forecasting ability. New information on Alexandrium may allow managers to shorten annual PSP beach closures. Models in ECOHAB PNW did not include the CR plume; those in RISE did not include two known source regions for toxic PN, the Juan de Fuca eddy region (north) and Heceta bank (south). The proposed forecast/hindcast models will include both source regions and the plume as well as the other freshwater sources that impact nutrient and freshwater supply in the region. The imbedded biological model will use a new approach based on measured biological rates, providing a ten fold improvement in skill over most existing models.

Title: Bloom dynamics of Alexandrium: the roles of resource competition and allelopathy

Institutions: University of Maine

Investigators: L. Karp-Boss, D. Townsend


Toxic species of the dinoflagellate genus Alexandrium are responsible for outbreaks of Paralytic Shellfish Poisoning (PSP), a recurrent and serious problem in the Gulf of Maine (GOM). Hence, understanding bloom dynamics of Alexandrium spp. is a major research focus in the GOM and other coastal areas. Previous ECOHAB-funded studies have documented that the highest Alexandrium cell concentrations are located in offshore waters, well away from most coastal shellfish beds, and are delivered to inshore waters by physical mechanisms. An intriguing question is: What restricts Alexandrium from blooming in inshore waters? One hypothesis suggested by Townsend et al. (2005), is that Alexandrium bloom dynamics may be controlled not only by physical and chemical factors but also by biological interactions with other phytoplankton taxa – in particular, diatoms.

Objectives: This research will test the hypothesis that bloom dynamics of Alexandrium are influenced by competitive interactions with diatoms, and that the interactions are reciprocal. That is, while field observations and preliminary lab studies indicate that high densities or growth rates of diatoms impede the growth of Alexandrium in early spring and in near-shore waters, either by virtue of their rapid growth rate and exploitation of essential resources or via alleopathic interactions, Alexandrium blooms that have been established after the decline of the diatom bloom can prevent a second diatom bloom via allelopathy.

Approach: This project will conduct detailed laboratory studies that will 1) examine allelopathic interactions between the toxic dinoflagellate A. fundyense and diatoms; 2) obtain ecophysiological parameters on nutrient-dependent growth kinetics of A.fundyense and diatoms common to the GOM, and apply them to a resource-based competition model to predict outcome of competition between A. fundyense and diatoms; and, 3) conduct competition experiments between A. fundyense and diatoms over a range of nitrate and silicate concentrations and compare the experimental results to model predictions. Laboratory efforts will be supplemented with field data for the evaluation of distributions of Alexandrium with respect to distributions of other phytoplankton taxonomic groups, in particular diatoms, nutrients and hydrographic condition.

Expected results: Results from this study will provide new information on the interactions of HAB species with other members of the phytoplankton community, which could lead to new insights into potentially novel mechanisms by which HAB blooms may be controlled. On a more basic level, this study will provide physiological data on uptake kinetics of A. fundyense (which are currently lacking) that is necessary for the development and improvement of forecast models for Alexandrium blooms. The study will also provide information on inter- and intra- variations in physiological parameters between Alexandrium strains, new reference material, and will support the training of graduate and undergraduate students.

Title: Effects of Chronic Domoic Acid Exposure on Gene Expression in the Vertebrate CNS

Institutions: NOAA Northwest Fisheries Science Center, University of Washington

Investigators: K. Lefebvre, M. Myers, F. Farin, T. Bammler, R. Beyer

The potential impacts of chronic algal toxin exposure have long been a concern. One HAB toxin, domoic acid (DA), is a potent neurotoxin that interacts with the vertebrate central nervous system (CNS). Although the clinical signs of acute DA toxicity have been well defined, virtually nothing is known about the impacts of chronic, low-level toxin exposure, primarily due to the difficulties associated with long-term exposure studies. It is known that vertebrates such as fish, seabirds, marine mammals, and humans are repeatedly exposed to DA at levels below those that cause outward signs of toxicity, yet it remains unknown how these chronic sub-acute exposures may impact these organisms. This project plans to quantify gene expression patterns in whole brain and characterize histopathological aberrations in major organs as endpoints to examine the effects of chronic exposure in zebrafish. The overall goal of this project is to develop a general model for the characterization of gene expression effects in the vertebrate CNS and morphological damage in major organs associated with long-term, low-level toxin exposure.

Objectives: The objectives of this project are to 1) quantify gene expression changes in the vertebrate CNS and characterize differentially expressed genes based on function to identify potential pathways of chronic disease associated with long-term, low-level algal toxin exposure, 2) quantify circulating blood toxin levels associated with changes in gene expression, and 3) perform histologic examinations of all major organ systems to characterize pathological impacts of chronic toxicity.

Approach: The toxicogenetic approach will be to use microchip gene array technology to quantify differential gene expression in whole brain during a one-year DA exposure study using a vertebrate model system (zebrafish, Danio rerio). Through pilot studies, the investigators have quantified appropriate sub-acute doses, developed effective repetitive dosing procedures, and developed a statistically rigorous experimental design. RNA isolation methods, microchip array procedures, qRT-PCR confirmation procedures, and bioinformatics processes for grouping and identifying gene clusters of interest have also been perfected. In addition to gene expression analyses, this research will employ standard histology procedures to visualize potential pathological aberrations caused by chronic DA exposure.

Expected results: This research is expected to yield several results that will directly aid assessments of HAB impacts on marine biota. First, this research will provide the only available data on the impacts of chronic, low-level algal toxin exposure using a realistic long-term exposure time scale. It is also likely that new pathways of DA toxicity will be identified since a single dose exposure pilot study has already revealed gene expression patterns unique to sub-acute exposure. The gene lists generated will be widely disseminated and publicly available for researchers to use as a starting point for species-specific studies on chronic HAB toxin exposure effects. Finally, the study will quantify circulating blood toxin levels that are associated with the observed gene expression effects. These blood toxin levels can be used for characterizing the potential risk to other vertebrates exposed to DA in the field.

Title:  Remote Assessment of Algal Functional Groups in the Absence of Extreme Blooms: Application to Alexandrium fundyense in the Gulf of Maine

Investigators:  Collin Roesler, Neal Pettigrew, Edward Laine, Gregory Teegarden

Institutions:  University of Maine, Bowdoin College, Saint Joseph's College

Funded:  NASA

Satellite remote sensing of ocean color has provided an unprecedented temporal/spatial data set of global phytoplankton biomass sufficient for investigations of climate change, climatology, and episodic events. Phytoplankton ecology, in general, and Harmful Algal Bloom (HAB) investigations in particular, would benefit tremendously if taxonomic information could be derived from ocean color. Obtaining time/space distributions of the causative species on scales comparable to environmental observations would provide unprecedented capabilities for quantify forcing functions related to HAB initiation, development and demise. The Gulf of Maine provides an exciting and challenging test site for such work. Closures due to Paralytic Shellfish Poisoning (PSP) occur annually due to the toxic dinoflagellate Alexandrium fundyense, despite the fact that this species does not achieve bloom concentrations and remains a minor member of the phytoplankton community. Coastal waters in the Gulf of Maine are optically complex complicating ocean color remote sensing. However, such challenges can be met with an inverse modeling approach which targets taxonomically-distinct pigment features and is robust in optically complex waters. Ecologically, A. fundyese is found to co-occur with other more numerous dinoflagellate species and thus a dinoflagellate marker will identify when A. fundyense is likely to be present.

Objectives:  Given these observations and capabilities, the specific objectives of this study are to:
1. Optimize, validate and test an existing ocean color functional group model to yield estimates of A. fundyense populations;
2. Apply the model to historical GoM ocean color data obtained from in situ radiometers deployed on the Gulf of Maine Ocean Observing System moored array (a time series starting in 2001) and SeaWiFS and Aqua-MODIS imagery to statistically quantify the temporal and spatial modes of variability in A. fundyense distributions;
3. Use these statistical modes to investigate
•    causative relationships between A. fundyense distributions and environmental forcing associated with hydrographic characteristics (e.g. water masses, stratification indices) and nutrient distributions;
•    impacts of A. fundyense distributions on the temporal/spatial patterns in coastal PSP scores obtained by the Maine Department of Marine Resources.

Approach:  Our approach is (1) modify an existing algal functional group ocean color inversion model to predict the relative contributions of diatoms and dinoflagellates to the total algal community, the latter of which provides the predictor of likely A. fundyese presence; (2) quantify model sensitivity to pigment-based functional group optical properties, constituent optical properties, and spectral resolution; (3) validate the model against quantified ground truth observations of phytoplankton community composition at a test location; (4) apply the model to mooring- and satellite-based ocean color data to derive time/space series data sets of A. fundyese distributions for statistical analyses.

Expected Results:  The anticipated results are that (1) the functional group model will predict A. fundyese distributions from both in situ and remotely sensed ocean color observations; (2) the occurrence of A. fundyense distributions will precede positive PSP scores at adjacent coastal sampling sites; (3) the statistical analyses will form the basis of a forecast model for A. fundyense distributions in coastal and offshore algal populations and PSP events along the coast.


Last updated: July 11, 2016