Optimized plankton imaging, clustering and visualization workflows through integrative data management and application of artificial intelligence

Phytoplankton is a diverse group of photosynthesizing organisms which account for approximately fifty percent of the primary production on Earth. Increasing our knowledge on phytoplankton dynamics (and plankton in general) is therefore of major importance. In the present research, we aimed to reveal the spatiotemporal dynamics of the phyto- and zooplankton community in the Eastern English Channel, Southern Bight of the North Sea and the Thames estuary. To do so, we organized a JERICO-NEXT Lifewatch cruise in May 2017 on board of the RV Simon Stevin and sampled 44 stations, involving five research institutions from France (CNRS-LOG,), The Netherlands (RWS, NIOZ) and Belgium (UGENT, VLIZ). To quantify the biomass of the phytoplankton community we used a unique combination of three flow cytometers and two Fast Repetition Rate Fluorometerss that were coupled to the underway ferrybox system. These observations were complemented with Water Insight Spectrometer and water profile data (by means of a CTD) and samples for zooplankton, pigment and nutrient analysis. A dedicated data workshop was organized with all partners to conduct a joint analysis on both the biotic and abiotic data. A first exploration of the data, by means of regression-based models and multivariate statistics, suggested that mainly nutrient discharges from the rivers influence the plankton structure. Furthermore, water turbidity is controlling photosynthetic activity and horizontal and vertical variations of photosynthetic properties can be discriminated

Comprehensive climate system modeling on massively parallel computers

A better understanding of both natural and human induced changes to the Earth`s climate is necessary for policy makers to make informed decisions regarding energy usage and other greenhouse gas producing activities. To achieve this, substantial increases in the sophistication of climate models are required. Coupling between the climate subsystems of the atmosphere, oceans, cryosphere and biosphere is only now beginning to be explored in global models. the enormous computational expenses of such models is one significant factor limiting progress. A comprehensive climate system model targeted to distributed memory massively parallel processing (MPP) computers is under development at Lawrence Livermore National Laboratory. This class of computers promises the computational power to permit the timely execution of climate models of substantially more sophistication than current generation models. Our strategy for achieving high performance on large numbers of processors is to exploit the multiple layers of parallelism naturally contained within highly coupled global climate models. The centerpiece of this strategy is the concurrent execution of multiple independently parallelized components of the climate system model. This methodology allows the assignment of an arbitrary number of processors to each of the major climate subsystems. Hence, a higher total number of processors may be efficiently used. Furthermore, load imbalances arising from the coupling of submodels may be minimized by adjusting the distribution of processors among the submodels

The silent majority: Pico- and nanoplankton as ecosystem health indicators for marine policy

A healthy marine ecosystem is a fully functioning system, able to supply ecosystem services whilst still maintaining resilience to human-induced environmental change. Monitoring and managing the health of resilient marine ecosystems requires indicators that can assess their biodiversity state and food web functioning. Plankton are crucial components of pelagic habitats, occupying the base of the pelagic food web. Larger plankton have long been used to monitor ecosystem productivity and biodiversity due to their identification via traditional light microscopy. In contrast, the regular monitoring of pico- and nanoplankton (<20 µm; hereafter called “tiny plankton”) only started with the development of flow cytometry techniques, which has limited their inclusion as ecosystem health indicators. Four UK plankton surveys have sampled and identified these tiny plankton for up to 14 years, providing an opportunity to test their suitability as indicators of ecosystem state. We investigated six groups of tiny plankton, including heterotrophic nanoeukaryotes, photosynthetic nanoeukaryotes, photosynthetic picoeukaryotes, and Synechococcus cyanobacteria, and two groups of heterotrophic bacteria. Flow cytometry and light microscopy data from an inshore Western English Channel station revealed that 99.98 % of plankton abundance and 71 % of plankton biomass was derived from tiny plankton cells too small to be quantified accurately under a light microscope and thus not adequately considered in assessments of pelagic habitats. Different UK marine and coastal regions showed consistency in peak abundances of these tiny plankton. We used a novel wavelet coherence method to identify time-based relationships between tiny plankton and environmental variables linked to human pressures. Relationships were found between nitrogenous nutrients and all tiny plankton groups, most commonly at sub-annual to annual time scales. Photosynthetic picoeukaryotes, heterotrophic nanoeukaryotes, and HNA-bacteria were associated with high sea surface temperatures. Given the here established relationship between tiny plankton and environmental variables, and their importance in the full plankton assemblage, we recommend that, alongside existing microplankton lifeforms, tiny plankton groups can be used as plankton lifeforms, either individually or in combination, to inform biodiversity indicators that meet policy obligations under the EU Marine Strategy Framework Directive (MSFD), (Oslo-Paris Convention) OSPAR strategies, and the UK Marine Strategy

A multi-component flood risk assessment in the Maresme coast (NW Mediterranean)

Coastal regions are the areas most threatened by natural hazards, with floods being the most frequent and significant threat in terms of their induced impacts, and therefore, any management scheme requires their evaluation. In coastal areas, flooding is a hazard associated with various processes acting at different scales: coastal storms, flash floods, and sea level rise (SLR). In order to address the problem as a whole, this study presents a methodology to undertake a preliminary integrated risk assessment that determines the magnitude of the different flood processes (flash flood, marine storm, SLR) and their associated consequences, taking into account their temporal and spatial scales. The risk is quantified using specific indicators to assess the magnitude of the hazard (for each component) and the consequences in a common scale. This allows for a robust comparison of the spatial risk distribution along the coast in order to identify both the areas at greatest risk and the risk components that have the greatest impact. This methodology is applied on the Maresme coast (NW Mediterranean, Spain), which can be considered representative of developed areas of the Spanish Mediterranean coast. The results obtained characterise this coastline as an area of relatively low overall risk, although some hot spots have been identified with high-risk values, with flash flooding being the principal risk process

Community structure and seasonal dynamics of diatom biofilms and associated grazers in intertidal mudflats

The composition and seasonal dynamics of biofilm-associated eukaryotic communities were analysed at the metre and kilometre scale along a salinity gradient in the Westerschelde estuary (The Netherlands), using microscopy and a genetic fingerprinting technique (PCR-DGGE). Microphytobenthic biomass, measured as chlorophyll a (chl a), varied seasonally over 2 orders of magnitude, being highest in spring. Communities were dominated by epipelic diatoms, in particular by members of the genus Navicula. In spring, a few smaller epipelic diatom species dominated during biomass peaks, while during the rest of the year, communities were more diverse and were characterised by larger species. The microphytobenthic community collapsed when grazers appeared, which happened concomitantly with a rise in temperature. Spring biomass development was associated with marked changes in porewater nutrient concentrations, especially towards the estuary mouth. In the DGGE data, diatoms, ciliates, amoebae, copepods, nematodes, annelids and platyhelminthes were detected. Ordination analysis of the species counts and DGGE data were largely congruent and indicated that on the scale of the whole estuary (i.e. km scale), taxonomic turnover in microphytobenthos composition was mainly associated with the salinity gradient. At smaller spatial scales, the position of sampling localities along the tidal exposure gradient appeared to be the main determinant of species turnover, in particular in the brackish reaches of the estuary.

The silent majority: pico- and nanoplankton as ecosystem health indicators for marine policy

A healthy marine ecosystem is a fully functioning system, able to supply ecosystem services whilst still maintaining resilience to human-induced environmental change. Monitoring and managing the health of resilient marine ecosystems requires indicators that can assess their biodiversity state and food web functioning. Plankton are crucial components of pelagic habitats, occupying the base of the pelagic food web. Larger plankton have long been used to monitor ecosystem productivity and biodiversity due to their identification via traditional light microscopy. In contrast, the regular monitoring of pico- and nanoplankton (<20 µm; hereafter called “tiny plankton”) only started with the development of flow cytometry techniques, which has limited their inclusion as ecosystem health indicators. Four UK plankton surveys have sampled and identified these tiny plankton for up to 14 years, providing an opportunity to test their suitability as indicators of ecosystem state. We investigated six groups of tiny plankton, including heterotrophic nanoeukaryotes, photosynthetic nanoeukaryotes, photosynthetic picoeukaryotes, and Synechococcus cyanobacteria, and two groups of heterotrophic bacteria. Flow cytometry and light microscopy data from an inshore Western English Channel station revealed that 99.98 % of plankton abundance and 71 % of plankton biomass was derived from tiny plankton cells too small to be quantified accurately under a light microscope and thus not adequately considered in assessments of pelagic habitats. Different UK marine and coastal regions showed consistency in peak abundances of these tiny plankton. We used a novel wavelet coherence method to identify time-based relationships between tiny plankton and environmental variables linked to human pressures. Relationships were found between nitrogenous nutrients and all tiny plankton groups, most commonly at sub-annual to annual time scales. Photosynthetic picoeukaryotes, heterotrophic nanoeukaryotes, and HNA-bacteria were associated with high sea surface temperatures. Given the here established relationship between tiny plankton and environmental variables, and their importance in the full plankton assemblage, we recommend that, alongside existing microplankton lifeforms, tiny plankton groups can be used as plankton lifeforms, either individually or in combination, to inform biodiversity indicators that meet policy obligations under the EU Marine Strategy Framework Directive (MSFD), (Oslo-Paris Convention) OSPAR strategies, and the UK Marine Strateg