Section outline

  • The LifeWatch Italy Phytoplankton Virtual Research Environment (Phyto VRE) enables researchers to:

    • Access harmonised data on taxonomy and morphological traits by using the Atlas of Phytoplankton, Atlas of Shapes and Phytoplankton Traits Thesaurus;
    • Access, download, and select LifeWatch Italy datasets (published through the LifeWatch Italy Data Portal and distributed by the LifeWatch ERIC Metadata Catalogue) or upload their own datasets structured according to the Phyto template based on the LifeWatch Italy Data Schema in order to execute the services included in the VRE;
    • Facilitate the computation of morphological and demographic traits (such as hidden dimension, biovolume, surface area, surface-volume ratio, cell carbon content, etc.) and investigate their distribution patterns at different levels of data aggregation (i.e. spatial, temporal, taxonomic) by means of services which automate a set of operations written in the R language.

    Besides the Atlas of Phytoplankton and the Atlas of Shapes, the other services provided by the Phyto VRE are:

    1. Phytoplankton Traits Thesaurus
      The first initiative to deal with the semantics of phytoplankton functional traits focusing on morpho-functional traits. PhytoTraits reflects the agreement of a scientific expert community to fix semantic properties (e.g. label, definition) of approximately 120 traits.
    2. Traits Computation
      This workflow calculates Phytoplankton Traits (Biovolume, Surface Area, Surface Volume Ratio, Cells/Liter, Biovolume/Liter/Carbon Content and Carbon Content/Liter) and Selection (for each selected location/groups of locations, the script allows to exclude from the dataset rare taxa based on their rank distribution in density (n of cells per liter), biovolume per liter (μm3 of cells per liter) or carbon content per liter (pgC per liter)).
    3. Data Filtering
      For each selected location/groups of locations, this calculation allows to exclude from the dataset rare taxa based on their rank distribution in density (n of cells per liter), biovolume per liter (μm3 of cells per liter) or carbon content per liter (pgC per liter).
    4. Size Class Distribution
      For any given sampling site and/or sampling time, the script calculates individual abundance of logarithmic size classes the biovolume or biomass distributions.
    5. Size Density Relationships
      This service calculates cross community, global or local size ~ density scaling relationships for any given combination of sites, sampling times and taxonomic level of observations. Both average trend power law and upper quantile boundary regression (quantile 0.95) are computed.
    6. Community Matrix & Analysis
      The workflow converts the LifeWatch dataframe format into a community matrix (site*taxa) for each selected location/groups of locations, finally processes community matrices. Typologies of community composition analysis that can be performed are species rarefaction curve; nonmetric multidimensional scaling (NMDS); cluster analysis; beta diversity; and distance matrix.
    7. Community Indexes
      For any given sampling site and/or sampling time, the workflow also computes several community indices and/or individual size spectra statistics (biovolume in μm3 or biomass in pgC) from an individual or aggregated LifeWatch dataset.

    Access here the LifeWatch Italy Phytoplankton VRE