Task 3.1

Task 3.1 Automated platform for the observation of Phytoplankton diversity in relation to ecosystem services 
Task 3.2 Developments on current observations from HF radars
Task 3.3 Profiling coastal waters 
Task 3.4 Microbial and molecular sensors
Task 3.5 Combined sensors for carbonate systems
Task 3.6 Benthic compartment and process
Task 3.7 OSE/OSSE (Observing System Experiment/Observing System Simulation Experiment) technology

Automated platform for the observation of Phytoplankton diversity in relation to ecosystem services 

Lead: CNRS (Felipe Artigas)

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The objective of this task is to combine and improve the use of innovative (semi)-automated observation techniques for addressing phytoplankton dynamics in several European coastal and shelf seas, at high resolution, in (near) real-time, in key monitoring platforms. The focus will be on innovative sensors, which can provide new insights into phytoplankton detection and characterisation in the field. For achieving this task, there is a need to improve the operability and discrimination of existing innovative techniques focusing on phytoplankton diversity, functional groups distribution and/or photosynthetic parameters assessed in coastal marine waters, based on phytoplankton morphology and/or single cell or bulk optical characteristics.

Three main approaches will be explored and used in combination in order to build automated platforms: 1) image acquisition and analysis (in flow/in situ imaging), 2) single-cell optical analysis (scanning flow cytometry), 3) a combination of optical techniques (fluorescence induction, spectrophotometry and spectrofluorometry) for assessing phytoplankton functional groups and photosynthetic activity and physiological status. We shall critically compare different techniques in conditions where failure is likely in order to better define the applicability in different conditions and constrain the range of usability of each technique in terms of cell size, concentration, speed of measurement, background light, background signal, algae pigmentation, morphology etc.

Two workshops, including presentations, discussion of methods for assessing phytoplankton diversity and productivity (open to invited experts from Europe and abroad) and test/inter comparison of techniques (on both cultured micro-algae and natural samples) will be organised in order to establish the most suitable method and technics, as wells as their limits, and how to implement them in a complementary way on combined platforms. Especially we aim to investigate best methods, or combination of them, most suitable for various European coastal seas (link to WP4 JRAP4.1 and 4.5.) taking into account their differences in optical properties and in phytoplankton community structure and biomass.

  • SubTask 3.1.1 Imagery Instrumentation (led by SMHI): Four techniques based on inflow/in situ imaging analysis will be explored and compared in their sensitivity to discriminate phytoplankton taxa and in their accuracy in counting phytoplankton cells/colonies: Imaging Flow Cytometry-Imaging FlowCytobot (by a collaboration with WHOI in the U.S.A.), Imaging Flow Cytometry-CytoSense, FlowCAM and Underwater Vision Profiler (UVP5). The imaging inflow machines will be presented, discussed and tested on discrete samples and all machines will be tested in continuous flow or in situ field exercises, according to the location of the workshops. Classifiers for phytoplankton in general and for selected HAB-species will be developed in the laboratory, before testing them in field conditions.

  • SubTask 3.1.2 Single-cell optical characterization (led by CEFAS): A major challenge in studies of optical properties of phytoplankton cells in the field (marine coastal systems) is to develop means of discrimination between populations and (when possible) taxa, but also to derive insights into phytoplankton functional group, definition of biological traits (based on pigments composition, size, shapes, free-living or colonial status) and, if possible, physiological state. Partners currently working with Scanning “pulse-shape recording” Cytometers (CytoSense-Cytobuoy) will participate in the inter calibration workshops and will work on updating the implementation of this technique into automated platforms, as well as on the better automation of data classification and analysis, in collaboration with SMEs.

  • SubTask 3.1.3 Optical Instrumentation combination (led by SYKE): New optical techniques will be developed and tested to study phytoplankton biomass, taxonomy and productivity, and other optically active in-water constituents. Algorithms for in vivo spectrophotometric (PsiCAM) and spectrofluorometric (Fluoroprobe, AOA) determination of chlorophyll-a, algae groups, particulate matter and colored dissolved organic matter will be compared and developed further. To approach primary production using variable fluorescence (FRRF, PAM) data we determine constrains of the conversion factors from electron transport rate to C-fixation at various spatio-temporal scales including different phytoplankton communities.


Deliverable 3.1: Synthesis report after developments dedicated to the observation of the phytoplankton diversity from automated plateforms (M24). It will gather results of: 

  • methodology assessment after comparison of imaging and single-cell optical “pulse shape recording” techniques addressing phytoplankton functional/taxonomical diversity, as well as recommendations for technical and analytical improvements.
  • methodology assessment after inter comparison of automated bulk optical (fluorescence induction, spectrophotometry and spectrofluorometry) techniques addressing phytoplankton functional diversity and phytoplankton productivity, as well as recommendations for technical and analytical improvements

Deliverable 3.2: Report on the technical and analytical improvements carried out for the implementation of innovative techniques for assessing phytoplankton diversity and productivity and will summarize recommendations on their use according to the coastal system considered and the type of platform available (M42)