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Overview of Public Protist Trait Databases

Please reach out if we are missing relevant databases or other data sources

Since version 5.1.0 PR2 introduced the following: mixoplankton species (already available in release 5.0) HAB (Harmful Algal Bloom) species - from https://www.marinespecies.org/hab/index.php ecological function - from Sommeria-Klein et al. 2021 (Global drivers of eukaryotic plankton biogeography in the sunlit ocean) - see Table S1 from the paper.

Dumack et al. (2019) — Cercozoa and Endomyxa

This dataset was ingested using read.delim() and served as a core reference for morpho-trophic traits in Rhizaria-related lineages.

Freundenthal et al. (2025) — Amoebozoa Trait Database

This dataset complements Dumack et al. (2019) by extending trait coverage to Amoebozoa using a structurally comparable framework.

Ramond et al. (2018, 2019) — Marine Protist Functional Traits

  • Reference: Ramond et al. 2019, Environmental Microbiology (DOI: 10.1111/1462-2920.14537)
  • Data repository: SEANOE (dataset 56963)
  • Trait domains: morphology, trophic strategy, habitat, life history
  • Data format: semicolon-separated CSV

Traits in this dataset were manually curated from the literature, resulting in high interpretative value but heterogeneous terminology.

Schneider et al. (2020) — Trophic Modes of Aquatic Protists

  • Reference: Schneider et al. 2020, Biodiversity Data Journal (DOI: 10.3897/BDJ.8.e56648)
  • Focus: trophic mode classification, including mixotrophy
  • Structure: main trait table plus a separate citation table

Both tables were ingested to enable explicit linkage between trait assertions and their bibliographic sources.

Giachello et al. (2023) — Functional Traits of Soil Protists

  • Reference: Giachello et al. 2023, Soil Biology & Biochemistry (DOI: 10.1016/j.soilbio.2023.109207)
  • Trait domains: trophic mode, feeding strategy, morphology, locomotion, size, habitat, life history
  • Data format: Excel workbook with multiple sheets

Two sheets were used:

  • the complete trait dataset,
  • the reference table documenting literature sources for trait assignments.

Mitra et al. (2023) — The Mixoplankton Database (MDB)

  • Reference: Mitra et al. 2023, Journal of Eukaryotic Microbiology (DOI: 10.1111/jeu.12972)
  • Database: Zenodo record 7839780
  • Scope: photo-phago-trophic plankton across the global ocean
  • Data format: Excel workbook

For Step 1, only host-related trait columns were retained. Occurrence data and prey-related columns were explicitly excluded to avoid conflating organismal traits with interaction networks.

Bjørbækmo et al. (2019) — Protist Interaction DAtabase (PIDA)

Authors examined the available scientific literature spanning the last ~150 years, and recorded ~2500 ecological interactions from ~500 publications going back to the late 1800s.

Only host-side trait and taxonomic information was retained. Prey taxonomy columns were removed to maintain consistency with a host-centric trait framework.

Põlme et al. (2020) — FungalTraits Database

  • Reference: Põlme et al. 2020, Fungal diveristy (DOI: 10.1007/s13225-020-00466-2)
  • Database: FungalTraits (Google Sheets)
  • Taxonomic scope: Fungi and fungus-like Stramenopiles

This dataset provides a comprehensive, genus-level compilation of ecological and functional traits for fungi, including lifestyle classifications (e.g. saprotrophic, symbiotic, pathogenic), morpho-anatomical features, substrate associations, and ectomycorrhizal characteristics.

Lentendu et al. (2025) — EukFunc: A Holistic Eukaryotic Functional Reference for Automated Profiling of Soil Eukaryotes

This dataset provides comprehensive functional classes and aims to combine functional information across the entire soil eukaryome as compared to focusing on fungi, protists or nematodes individually.

despite enourmous taxonomic coverage, there are very little references that couple the assertions directly to publication sources, making it a little bit troublesome for our framework. exploration of what could be mined is still ongoing.

Rimet et al. (2018) — Trait Database for Phytoplankton of Temperate Lakes

  • Reference: Rimet et al. 2018, Annales de Limnologie – International Journal of Limnology (DOI: 10.1051/limn/2018009)
  • Data repository: (Zenodo: https://zenodo.org/records/1164834)
  • Taxonomic scope: Freshwater phytoplankton (primarily algae) from temperate lakes
  • Taxonomic backbone: Expert-curated taxonomy, largely consistent with contemporary algal systematics
  • Trait domains: morphology, size, life form, colony formation, motility, ecological strategy
  • Data format: CSV (open access)

This database represents a long-term, expert-maintained compilation of phytoplankton functional traits, originally developed for ecological assessment and bioindication in temperate lake ecosystems. Trait definitions are largely categorical and morpho-functional, reflecting classical phytoplankton functional ecology.

Laplace-Treyture et al. (2021) — Phytoplankton Morpho-Functional Trait Dataset from French Water Bodies

Reference: Laplace-Treyture et al. 2021, Scientific Data (DOI: 10.1038/s41597-021-00814-0)

  • Data file: FRENCH_PHYTOPLANKTON_TRAITS.csv (DOI: 10.15454/GJGIAH)
  • Taxonomic scope: Freshwater phytoplankton from French rivers, lakes, and reservoirs
  • Taxonomic backbone: AlgaeBase
  • Trait domains: morphology, size, motility, colony formation, ecological strategy
  • Data format: CSV

This dataset provides a harmonized morpho-functional trait table for phytoplankton taxa occurring in French water bodies, with taxonomy explicitly aligned to AlgaeBase. Traits are predominantly categorical and focus on structural and ecological characteristics commonly used in biomonitoring and functional classification schemes.