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Harmful algal blooms (HABs) cause harm to human health or hinder sustainable use of the marine environment in Blue Economy sectors. HABs are temporally and spatially variable and hence their mitigation is closely linked to effective early warning. The European Union (EU) Interreg Atlantic Area project “PRIMROSE”, Predicting Risk and Impact of Harmful Events on the Aquaculture Sector, was focused on the joint development of HAB early warning systems in different regions along the European Atlantic Area. Advancement of the existing HAB forecasting systems requires development of forecasting tools, improvements in data flow and processing, but also additional data inputs to assess the distribution of HAB species, especially in areas away from national monitoring stations, usually located near aquaculture sites. In this contribution, we review different novel technologies for acquiring HAB data and report on the experience gained in several novel local data collection exercises performed during the project. Demonstrations include the deployment of autonomous imaging flow cytometry (IFC) sensors near two aquaculture areas: a mooring in the Daoulas estuary in the Bay of Brest and pumping from a bay in the Shetland Islands to an inland IFC; and several drone deployments, both of Unmanned Aerial Vehicles (UAV) and of Autonomous Surface vehicles (ASVs). Additionally, we have reviewed sampling approaches potentially relevant for HAB early warning including protocols for opportunistic water sampling by coastguard agencies. Experiences in the determination of marine biotoxins in non-traditional vectors and how they could complement standard routine HAB monitoring are also considered., SI

Across the European Atlantic Arc (Scotland, Ireland, England, France, Spain, and Portugal) the shellfish aquaculture industry is dominated by the production of mussels, followed by oysters and clams. A range of spatially and temporally variable harmful algal bloom species (HABs) impact the industry through their production of biotoxins that accumulate and concentrate in shellfish flesh, which negatively impact the health of consumers through consumption. Regulatory monitoring of harmful cells in the water column and toxin concentrations within shellfish flesh are currently the main means of warning of elevated toxin events in bivalves, with harvesting being suspended when toxicity is elevated above EU regulatory limits. However, while such an approach is generally successful in safeguarding human health, it does not provide the early warning that is needed to support business planning and harvesting by the aquaculture industry. To address this issue, a proliferation of web portals have been developed to make monitoring data widely accessible. These systems are now transitioning from “nowcasts” to operational Early Warning Systems (EWS) to better mitigate against HAB-generated harmful effects. To achieve this, EWS are incorporating a range of environmental data parameters and developing varied forecasting approaches. For example, EWS are increasingly utilizing satellite data and the results of oceanographic modeling to identify and predict the behavior of HABs. Modeling demonstrates that some HABs can be advected significant distances before impacting aquaculture sites. Traffic light indices are being developed to provide users with an easily interpreted assessment of HAB and biotoxin risk, and expert interpretation of these multiple data streams is being used to assess risk into the future. Proof-of-concept EWS are being developed to combine model information with in situ data, in some cases using machine learning-based approaches. This article: (1) reviews HAB and biotoxin issues relevant to shellfish aquaculture in the European Atlantic Arc (Scotland, Ireland, England, France, Spain, and Portugal; (2) evaluates the current status of HAB events and EWS in the region; and (3) evaluates the potential of further improving these EWS though multi-disciplinary approaches combining heterogeneous sources of information.

Apparent increases in harmful algal blooms worldwide have fostered attempts at mitigating their impacts on the aquaculture industry. The dinoflagellate species Azadinium spinosum has been described as the de novo azaspiracid (AZA) toxin producer of AZA-1 and -2 and been implicated in shellfish poisoning incidents (AZP) around Europe, regularly affecting shellfish mariculture operations. Several species of Azadinium have been confirmed in Irish coastal waters, and routine monitoring has shown disparities between Azadinum spp. cell count estimates in the water column and AZA concentrations in shellfish. A survey of bays on the southwest and west coasts of Ireland, carried out in August 2016, investigated the late summer distribution of Azadinium spp. and AZAs. Molecular analysis of water column samples showed very low levels of Az. spinosum. However, AZAs were found in 44% of samples, including in Az. spinosum negative samples. PCR-DGGE analysis was carried out using Amphidomataceae family specific primers on a selection of Az. spinosum negative, but AZA positive, samples. Subsequently sequenced DNA amplicons showed a high level of similarity with other Azadinium species suggesting that the species-specific molecular assays, in current use for monitoring Azadinium spp., are not capturing the likely greater diversity of the genus in Irish waters.

The oceans play a key role in global issues such as climate change, food security, and human health. Given their vast dimensions and internal complexity, efficient monitoring and predicting of the planet’s ocean must be a collaborative effort of both regional and global scale. A first and foremost requirement for such collaborative ocean observing is the need to follow well-defined and reproducible methods across activities: from strategies for structuring observing systems, sensor deployment and usage, and the generation of data and information products, to ethical and governance aspects when executing ocean observing. To meet the urgent, planet-wide challenges we face, methods across all aspects of ocean observing should be broadly adopted by the ocean community and, where appropriate, should evolve into “Ocean Best Practices.” While many groups have created best practices, they are scattered across the Web or buried in local repositories and many have yet to be digitized. To reduce this fragmentation, we introduce a new open access, permanent, digital repository of best practices documentation (oceanbestpractices.org) that is part of the Ocean Best Practices System (OBPS). The new OBPS provides an opportunity space for the centralized and coordinated improvement of ocean observing methods. The OBPS repository employs user-friendly software to significantly improve discovery and access to methods. The software includes advanced semantic technologies for search capabilities to enhance repository operations. In addition to the repository, the OBPS also includes a peer reviewed journal research topic, a forum for community discussion and a training activity for use of best practices. Together, these components serve to realize a core objective of the OBPS, which is to enable the ocean community to create superior methods for every activity in ocean observing from research to operations to applications that are agreed upon and broadly adopted across communities. Using selected ocean observing examples, we show how the OBPS supports this objective. This paper lays out a future vision of ocean best practices and how OBPS will contribute to improving ocean observing in the decade to come.

24 pages, 8 figures, 1 table, supplementary material https://doi.org/10.3389/fmars.2019.00250, Harmful algal blooms (HABs) produce local impacts in nearly all freshwater and marine systems. They are a problem that occurs globally requiring an integrated and coordinated scientific understanding, leading to regional responses and solutions. Given that these natural phenomena will never be completely eliminated, an improved scientific understanding of HAB dynamics coupled with monitoring and ocean observations, facilitates new prediction and prevention strategies. Regional efforts are underway worldwide to create state-of-the-art HAB monitoring and forecasting tools, vulnerability assessments, and observing networks. In the United States, these include Alaska, Pacific Northwest, California, Gulf of Mexico, Gulf of Maine, Great Lakes, and the United States Caribbean islands. This paper examines several regional programs in the United States, European Union, and Asia and concludes that there is no one-size-fits-all approach. At the same time, successful programs require strong coordination with stakeholders and institutional sustainability to maintain and reinforce them with new automating technologies, wherever possible, ensuring integration of modeling efforts with multiple regional to national programs. Recommendations for scaling up to a global observing system for HABs can be summarized as follows: (1) advance and improve cost-effective and sustainable HAB forecast systems that address the HAB-risk warning requirements of key end-users at global and regional levels; (2) design programs that leverage and expand regional HAB observing systems to evaluate emerging technologies for Essential Ocean Variables (EOVs) and Essential Biodiversity Variables (EBVs) in order to support interregional technology comparisons and regional networks of observing capabilities; (3) fill the essential need for sustained, preferably automated, near real-time information from nearshore and offshore sites situated in HAB transport pathways to provide improved, advanced HAB warnings; (4) merge ecological knowledge and models with existing Earth System Modeling Frameworks to enhance end-to-end capabilities in forecasting and scenario-building; (5) provide seasonal to decadal forecasts to allow governments to plan, adapt to a changing marine environment, and ensure coastal industries are supported and sustained in the years ahead; and (6) support implementation of the recent calls for action by the United Nations Decade 2010 Sustainable Development Goals (SDGs) to develop indicators that are relevant to an effective and global HAB early warning system

In the summer of 2005 an exceptional bloom of the dinoflagellate Karenia mikimotoi occurred along Ireland's Atlantic seaboard and was associated with the mass mortality of both benthic and pelagic marine life. Oxygen depletion, cellular toxicity and physical smothering, are considered to be the main factors involved in mortality. In this paper we use a theoretical approach based on stoichiometry (the Anderson ratio) and an average K. mikimotoi cellular carbon content of 329 pg C cell−1 (n = 20) to calculate the carbonaceous and nitrogenous oxygen demand following bloom collapse. The method was validated against measurements of biochemical oxygen demand and K. mikimotoi cell concentration. The estimated potential oxygen utilisation (POU) was in good agreement with field observations across a range of cell concentrations. The magnitude of POU following bloom collapse, with the exception of three coastal areas, was considered insufficient to cause harm to most marine organisms. This indicates that the widespread occurrence of mortality was primarily due to other factors such as cellular toxicity and/or mucilage production, and not oxygen depletion or related phenomena. In Donegal Bay, Kilkieran Bay and inner Dingle Bay, where cell densities were in the order of 106 cells L−1, estimated POU was sufficient to cause hypoxia. Of the three areas, Donegal Bay is considered to be the most vulnerable due to its hydrographic characteristics (seasonally stratified, weak residual flow) and hypoxic conditions (2.2 mg L−1 O2) were directly observed in the Bay post bloom collapse. Here, depending on the time of bloom collapse, depressed DO levels could persist for weeks and continue to have a potentially chronic impact on the Bay.

This study investigated the application of a three-dimensional physical hydrodynamic model in a harmful algal bloom forecast system for Bantry Bay, southwest Ireland. Modelled oceanographic conditions were studied and used to help understand observed changes in the chemical and biological patterns from the national biotoxins and phytoplankton monitoring program. The study focused on two toxic events in 2013. An upwelling event was predicted by the model prior to the appearance and population increase of potentially toxic diatoms, Pseudo-nitzschia, and associated domoic acid in shellfish. A downwelling episode was provided as a forecast in the model prior to the arrival of a Dinophysis bloom and detection of its associated biotoxins in Bay shellfish. The modelled forecast products developed included expected surface, mid-depth and bottom current pathways at the mouth of the Bay and on the adjacent shelf. The rate and direction of water volume flow at the mouth and mid-bay sections were produced by the model to examine predicted upwelling and downwelling pulses. The model also calculated the evolution of water properties (temperature, salinity and density) with depth along the Bay axis and on the adjacent continental shelf. Direct measurements of water properties at a fixed point, mid-bay, were comparable to model calculations. The operational model for southwest Ireland produces a reliable 3-day physical hydrodynamic forecast of the dominant regional physical processes that result in water exchange events between Bantry Bay and its adjacent shelf. While simulated physical hydrodynamics were provided as a 3-day forecast, the upwelling and downwelling signals from the model, closely linked to toxic HAB episodes, were evident up to 10 days prior to the contamination of shellfish in the Bay.

The “Applied Simulations and Integrated Modelling for the Understanding of Harmful Algal Blooms” (Asimuth) project sought to develop a harmful algal bloom (HAB) alert system for Atlantic Europe. This was approached by combining, at a national or regional level, regulatory monitoring phytoplankton and biotoxin data with satellite remote sensing and other information on current marine conditions, coupled with regional scale models that included a representation of HAB transport. Synthesis of these products was achieved by expert interpretation within HAB risk alert bulletins that were prepared on a regular basis (typically weekly) for use by the aquaculture industry. In this preface to the Asimuth Special Issue we outline the main HAB species of concern in the region and the strengths and limitations of different methodologies to provide early warning of their blooms.

Toxic and non-toxic Pseudo-nitzschia blooms are common in coastal waters worldwide including Ireland. Off southwest Ireland, the timing of blooms on a weekly scale is highly variable, while the seasonal pattern is more regular with a bimodal distribution. Upwelling conditions are closely linked to Pseudo-nitzschia blooms. The work presented here describes a mathematical model, a Zero-Inflated Negative Binomial Model, employed to forecast the onset, abundance and duration of Pseudo-nitzschia blooms in the bays of southwest Ireland. Variables used in the model included field observations of Pseudo-nitzschia , sea surface temperature and wind. The estimated model reveals that, on average, cell levels on a given day depend on sea surface temperature, the value of a wind index on the previous day and the number of Pseudo-nitzschia in the water the previous week. The model forecast performed well for the onset and duration of blooms. However, the magnitude of blooms was sometimes underestimated by the model.

A 3D primitive equation coastal ocean model for southwest Ireland, called the Bantry Bay model, was developed and implemented operationally. Validated model outputs have multiple uses. One of the incentives to develop the model was to explore the possible transport pathways that carry harmful algae blooms (HAB) into Bantry Bay. The model is nested offline in a regional North East Atlantic operational model. Surface forcing is taken from the half-degree Global Forecasting System, available at three-hourly intervals. Heat fluxes are calculated from the bulk formulae. Surface freshwater fluxes are obtained from the prescribed rainfall rates and the evaporation rates calculated by the model. Freshwater discharges from five rivers are included in the model. Model validation and the model skill in representing the water level, currents, temperature and salinity in the bay are reported. A scoring system based on the average adjusted relative mean absolute error for the predicted currents was used. An upgrade to a higher score was achieved through the incorporation of local winds into the surface forcing and by varying the bottom roughness coefficient. The model, designed to work in forecast mode, can replicate the main oceanographic features in the region. The model forecast is used in a decision support system for HAB alerts. An operational HAB alert system did not exist in Ireland prior to the use of this model.

There is a perception that anthropogenically-driven changes in nutrient supply to coastal waters influences the abundance, frequency and toxicity of harmful algal blooms (HABs) through a change in the form or ratio of nutrient that limits phytoplankton growth. If nutrient concentrations are not limiting for growth, then ratios do not influence floristic composition. At non-limiting concentrations, evidence that alteration of nitrogen: phosphorus (N:P) ratios has stimulated HABs is limited, and primarily based on hypothesised relationships in relatively few locations (in particular: Tolo Harbour Hong Kong and Dutch Coastal Waters). In all cases, an unequivocal causal link between an increase in HABs (frequency, magnitude or duration) and change in N or P as the limiting nutrient is difficult to establish. The silicon (Si) limitation hypothesis is generally supported by experimental evidence and field data on the nuisance flagellate Phaeocystis. We found little evidence that high N:Si ratios preferentially promote harmful dinoflagellates over benign species. Laboratory studies demonstrate that nutrient ratios can influence toxin production, but genus and species specific differences and environmental control make extrapolation of these data to the field difficult. Studies of the role of dissolved and particulate organic nutrients in the growth of HAB species, while limited, demonstrate the potential for organic nutrients (especially organic N) to support the growth of a range of HAB species. There is a clear need for better understanding of the role of mixotrophy in the formation of HABs and for studies of HAB and non-HAB species in competition for environmentally realistic concentrations of organic nutrients.

A simple model is described which predicts harmful algal events in the bays of southwestern Ireland. Fundamental to the model is the physical forcing of circulation in these bays in summer. The predominant hydrographic feature at this time is a wind-driven two-layer oscillatory flow acting in a thermally stratified water column. This mechanism exchanges substantial proportions of the bays' volumes, and harmful algal events arise with the associated transport of harmful populations into them. The model is therefore based on the criterion that wind-driven water exchanges result in exchanges of phytoplankton, which, if the time of year is correct, result in toxic events. Utilising Bantry Bay as an example, hindcasting showed that the model has a high degree of success using a wind index based on the sequence of winds that results in water exchange. The model was implemented by estimating indices from the five-day weather forecast, and trialled in 2005. Results were published on the web in real time, during which a predicted water exchange event in mid-June was accompanied by an influx of Dinophysis acuminata into Bantry Bay with an associated contamination of shellfish with Diarrheic Shellfish Poisoning toxins.

Peer-reviewed. Released with a Creative Commons Attribution Non-Commercial No Derivatives License, This paper presents a description of three of the proposed phytoplankton indices under investigation as part of a classification framework for UK and ROI marine waters. The three indices proposed for the classification process are (i) phytoplankton biomass measured as chlorophyll, (ii) the frequency of elevated phytoplankton counts measuring individual species and total cell counts and (iii) seasonal progression of phytoplankton functional groups through the year. Phytoplankton biomass is calculated by a 90th percentile measurement of chlorophyll over the growing season (April to September) compared to a predetermined reference value. Calculation of functional groups and cell counts are taken as proportional counts derived from the presence of the indicator species or group as compared to the total phytoplankton count. Initial boundary conditions for the assessment of high/good status were tested for each index. Chlorophyll reference conditions were taken from thresholds developed for previous EU directives with the setting of offshore concentrations as a reference condition. Thresholds for elevated counts of phytoplankton taxa were taken from previous EU assessments describing counts that could be impact negatively on the environment. Reference seasonal growth curves are established using phytoplankton counts from ‘‘high status’’ waterbodies. To test the preliminary boundaries for each index, a risk assessment integrating nutrient enrichment and susceptibility for coastal and transitional waters was carried out to identify WFD waterbodies in England and Wales at different levels of risk. Waterbodies assessed as having low or medium risk from nutrient enrichment were identified as type 1 and type 2 waterbodies, and waterbodies assessed as high risk were identified as type 3 waterbodies. Phytoplankton data was extracted from the risk assigned waterbodies and applied to each phytoplankton index to test the robustness of the preliminary classification ranges for each phytoplankton index., Environment Agency Water Framework Directive Program and the Scottish and Northern Ireland Forum for Environmental Research (SNIFFER)

A review of the distribution of phytoplankton in coastal, shelf and estuarine waters around Ireland was undertaken to consolidate our understanding of the ecology of these organisms in the region. In broad terms, the review has highlighted the relative importance of vertical water column stability and horizontal transport processes in influencing the abundance and composition of phytoplankton. In coastal waters, the seasonal stabilization and de-stabilization of the water column accounts for most of the natural variation in both phytoplankton species composition and biomass. Much of the remaining natural variability can be explained by the interaction of phytoplankton with a number of oceanographic features and processes such as the presence of tidal and thermohaline fronts, wind and topographically associated coastal upwelling, advection landward of offshore water masses and the flow of coastal and oceanic currents. In estuarine waters, the scenario is somewhat reversed, and although seasonality is important in broad terms, the structure of phytoplankton populations is determined more by local factors operating over much smaller time-scales in the order of days and weeks. The interplay of these factors, such as the periodic rise and fall of the tide and episodic changes in river flow, creates a broad range of conditions that result in greater variation in phytoplankton biomass, while at the same time selecting for a reduced number of species that are adapted to survive in this highly changeable environment.