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

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

Harmful algal blooms and climate change: exploring future distribution changes

Harmful algae can cause death in fish, shellfish, marine mammals, and humans, via their toxins or from effects associated with their sheer quantity. There are many species, which cause a variety of problems around north-west Europe, and the frequency and distribution of algal blooms have altered in the recent past. Species distribution modelling was used to understand how harmful algal species may respond in the future to climate change, by considering environmental preferences and how these may shift. Most distribution studies to date use low resolution global model outputs. In this study, high resolution, downscaled shelf seas climate projections for the north-west European shelf were nested within lower resolution global projections, to understand how the distribution of harmful algae may change by the mid to end of century. Projections suggest that the habitat of most species (defined by temperature, salinity, depth, and stratification) will shift north this century, with suitability increasing in the central and northern North Sea. An increase in occurrence here might lead to more frequent detrimental blooms if wind, irradiance and nutrient levels are also suitable. Prioritizing monitoring of species in these susceptible areas could help in establishing early-warning systems for aquaculture and health protection schemes

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

Notes sur la biologie et la morphologie de la sardine dans le fond du Golfe de Gascogne

Paul V. Creach nos brinda un estudio muy particularizado sobre la biología y la morfología de la sardina capturada en el golfo de Vizcaya, cuya longitud puede oscilar entre los 9 y los 19 cm. El fondo marino del mencionado golfo es escenario de continuas renovaciones de la población sardinera.Bizkaiko golkoan arrantzatu ohi den sardinaren biologia eta morfologiari buruzko azterlan bereziki zehatza eskaintzen digu Paul V. Creach-ek. 9-19 zentimetro arteko luzera izaten du. Sardina sardak etengabe eraberritzen ari dira golko horretako hondoko uretan.Paul V. Creach se livre à une étude très spécialisée portant sur la biologie et la morphologie des sardines capturées dans le golfe de Gascogne, dont les tailles peuvent varier de 9 à 19 cm de longueur. Le fonds du golfe de Gascogne est le théâtre de renouvellements continuels de la population sardinière.Paul V. Creach offers us a very itemised study on the biology and the morphology of the sardine species captured in the Bay of Biscay, the length of which can oscillate between 9 and 19 cm. The sea bottom in the mentioned bay is the scene of a continuous renovation of the sardine population

Spring activity assessment of parasitoids in western France by experimental exposure of cereal aphids on trap plants in a wheat field

International audienc

Direct estimate of active bacteria: CTC use and limitations

During the last 10 years, the dye 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) has been used to determine the in situ number of "active" bacteria in different ecosystems. A part of this success is due to a simple protocol, which does not require sophisticated equipment. However, it has not been established whether the method determines viable cells, e.g. those capable of growth and cell division, as opposed to cells that are active in the sense of having some detectable metabolic activity. In this study, the number of CTC-positive cells through the growth stages of Escherichia coli was estimated and compared to counts of the total number of bacteria, the culturability (CFU counts) and respiratory activity (CO2 evolution). There was a good correlation between the number of CTC-positive cells and the CFU count, regardless of the growth phase. However, CTC could still be reduced by a large part of the population during the first hours of stationary phase even if the bacteria were no longer releasing CO2. Thus, the reduction of CTC is a good estimator for cell viability, rather than cell activity. Additionally, a review of the literature showed that there is presently no standardized protocol for using CTC, which makes difficult at present the comparison of active bacterial numbers in different samples from different sites. [KEYWORDS: Active bacteria; 5-Cyano-2,3-ditolyl tetrazolium chloride (CTC); Method]

Biodiversity-ecosystem function relationship in microphytobenthic diatoms of the Westerschelde estuary

Studies investigating the role of species diversity in sustaining key ecosystem processes, such as primary production, have until now mainly focused on terrestrial plant and soil communities. Although the relationship remains controversial, most evidence suggests that decreases in species diversity adversely affect ecosystem functions. It is unclear, however, whether conclusions derived from terrestrial systems can be readily transferred to aquatic systems. In the present study, the relationship between the diversity of intertidal benthic diatom biofilms and their estimated net primary production (Pn) in the macrotidal Westerschelde estuary was investigated. Diversity measures were calculated on the basis of relative cell counts down to species level. Biomass was estimated as chlorophyll a, and Pn was modelled using a vertically resolved primary production model on the basis of measurements of photosynthetic activity, biomass and abiotic parameters. Species composition of benthic diatoms differed significantly between sites along the salinity gradient of the estuary. As epipelic species were strongly correlated with photosynthetically active surface biofilm biomass and, hence, also with primary productivity, we focused on the diversity of this functional group. The results indicate that (1) biomass appears to be inversely related to the diversity of the biofilms (Periods of low biomass did not show low diversity [as reported in phytoplankton], possibly because these events were driven by grazing pressure and not by nutrient stress) and (2) relationships between diversity (species richness and Shannon index) and Pn appeared to be site specific, with either a significant positive or a unimodal relationship between both parameters. [KEYWORDS: Benthic diatoms ; Biodiversity ; Biomass ; Net primary production]