Benthic marine diatoms from French coastal and transitional waters

Latest version published by Université de Nantes on 26 January 2022 Université de Nantes
Publication date:
26 January 2022
Published by:
Université de Nantes
CC-BY 4.0

Download the latest version of this resource data as a Darwin Core Archive (DwC-A) or the resource metadata as EML or RTF:

Data as a DwC-A file download 11,511 records in English (917 KB) - Update frequency: unknown
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Metadata as an RTF file download in English (14 KB)


The objective of this dataset is to compile the historic records of marine and brackish diatom current species and genera reported for French coastal areas since the last quarter of the 19th century. The main focus is marine benthic diatoms, as occurrence datasets for phytoplankton (REPHY dataset) and for freshwater benthic diatoms (SEEE-Diatomées dataset) already exist for French coastal and inland waters, respectively. The dataset aims to fill this gap in knowledge by compiling reports that have been more difficult to reach (e.g., books, PhD theses and other grey literature), but also published papers on microphytobenthos research. The current version of the dataset has 11511 taxonomic entries found in 49 different references, dating from 1888 to 2019. A total of 2846 different taxa were compiled, 97% to species level or below, 3% to genus level. The dataset also offers information on geographic locations at 4 different levels, namely: site, county (i.e., département), region and seaboard. It also provides data on ecology (e.g., sampled substrate, habitat, growth forms) for most taxa. Moreover, a linkage to DiatomBase and WoRMS is given via AphiaID, their unique numerical database identifier. This linkage added relevant information for each species, such as higher taxonomic ranks or its accepted valid synonym.

Data Records

The data in this occurrence resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 11,511 records.

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.


The table below shows only published versions of the resource that are publicly accessible.

How to cite

Researchers should cite this work as follows:

Ribeiro L, Figueira R, Oiry S, Buchet R, Sabbe K, Barillé L (2022): Benthic marine diatoms from French coastal and transitional waters. v1.3. No organisation. Dataset/Occurrence. http://ipt.gbif.pt/ipt/resource?r=benthic-marine-diatoms&v=1.3


Researchers should respect the following rights statement:

The publisher and rights holder of this work is Université de Nantes. This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: 64a375e9-aa8a-4727-9ea2-a548d33d903b.  Université de Nantes publishes this resource, and is itself registered in GBIF as a data publisher endorsed by GBIF France.


Bacillariophyceae; Diatoms; Benthic; Marine and Coastal waters; France; Occurrence


Lourenço Ribeiro
  • Metadata Provider
  • Originator
  • Point Of Contact
MARE - ULisboa
Rui Figueira
  • Originator
Instituto Superior de Agronomia
Simon Oiry
  • Originator
ISOMer, Nantes Université
Rémi Buchet
  • Originator
IFREMER, Service Valorisation de l'Information pour la Gestion Intégrée et la Surveillance (PDG-ODE-VIGIES), Centre Atlantique
Rue de l'Ile d'Yeu
Koen Sabbe
  • Originator
Laurent Barillé
  • Originator
  • Point Of Contact
ISOMer, Nantes Université

Geographic Coverage

metropolitan France

Bounding Coordinates South West [-90, -180], North East [90, 180]

Taxonomic Coverage

Diatoms (Bacillariophyceae) are listed to genus or species level. Nomenclature follows DiatomBase and higher classification is according to Cox (2015).

Class Bacillariophyceae (Diatoms)

Temporal Coverage

Start Date / End Date 1888-01-01 / 2019-10-31

Project Data

No Description available

Title Étude de la pertinence des peuplements du microphytobenthos estuarien pour la mise en place d’un bio-indicateur de la qualité des eaux de transition
Funding This research was funded by a grant by the L’Agence Française pour la Biodiversité, AFB grant number 180906 − Convention Microphytobenthos Phase II, and had the financial support of the Fundação para a Ciência e a Tecnologia (FCT) through UID/MAR/04292/2020.

The personnel involved in the project:

Simon Oiry
  • Author

Sampling Methods

Data inventory and compilation: Data sources were identified based on literature research and web-based search engines (e.g., Google or Web of Science). Both English and French languages were used when entering key terms during the search process, which included terms such as “diatoms” or “microphytobenthos” and was limited geographically to metropolitan France. The applicable data sources were digitally available in pdf format or in paper. Relevant information was manually transferred to a standard format in MS Excel.

Study Extent Compilation of the historic records of marine and brackish diatom current species and genera reported for French coastal areas since the last quarter of the 19th century.
Quality Control Each taxonomic entry is unique, as it refers to a single taxonomic unit found in each one of the 49 references used in the dataset and reported for a specific location (at one to four geographical levels). A thorough cross-checking of species names and clean-up of duplicates was made. In order to standardize the taxonomic entries, the nomenclatural format of the taxa found in the original sources was adapted to the one used in DiatomBase and the World Register of Marine Species (WoRMS), thanks to the taxon match option available on the website of the latter (www.marinespecies.org). DiatomBase (Kociolek et al. 2022) is primarily a nomenclatural database that updated and extended the Catalogue of Diatom Names (Fourtanier and Kociolek 2011), but it is also an authoritative open-access reference system for diatom taxa, which is universally recognized, and it is edited by 23 taxonomic editors world-wide. It is managed by VLIZ and shares with WoRMS a unique identifier, known as the AphiaID, for every species name. This identifier enables to link the species name to an internationally accepted standardized name and associated taxonomic information, such as accepted names, synonyms and current classification. The linkage of the current dataset to DiatomBase/WoRMS was made through a “worms” R package (version 0.2.2, J. Holstein 2018) that allows to retrieve the taxonomic information available for each AphiaID. The dataset was adjusted to the Darwin Core specifications (Wieczorek et al. 2012) in order to be published in the GBIF network.

Method step description:

  1. NA

Bibliographic Citations

  1. Cox, E. (2015). "Diatoms, Diatomeae (Bacillariophyceae s.l., Bacillariophyta)," in Syllabus of Plant Families. Adolf Engler’s Syllabus of Plant Families, ed. W. Frey. 13 ed (Stuttgart: Borntraeger), 64–103.
  2. Fourtanier, E. & Kociolek, J.P. (2011). Catalogue of Diatom Names, California Academy of Sciences, On-line Version updated18 September 2011. Available online at http://researcharchive.calacademy.org/research/diatoms/names/index.asp
  3. Holstein J., (2018). worms: Retrieving Aphia Information from World Register of Marine Species. R package version 0.2.2. https://CRAN.R-project.org/package=worms
  4. Kociolek, J.P.; Blanco, S.; Coste, M.; Ector, L.; Liu, Y.; Karthick, B.; Kulikovskiy, M.; Lundholm, N.; Ludwig, T.; Potapova, M.; Rimet, F.; Sabbe, K.; Sala, S.; Sar, E.; Taylor, J.; Van de Vijver, B.; Wetzel, C.E.; Williams, D.M.; Witkowski, A. & Witkowski, J. (2022). DiatomBase. Accessed at http://www.diatombase.org on 2022-01-03. https://doi.org/10.14284/504
  5. Wieczorek, J.; Bloom, D.; Guralnick, R.; Blum, S.; Döring, M.; Giovanni, R.; Robertson, T. & Vieglais D. (2012) Darwin Core: An evolving community-developed biodiversity data standard. PLOS One 7: e29715. https://doi.org/10.1371/journal.pone.0029715 https://doi.org/10.1371/journal.pone.0029715

Additional Metadata

Alternative Identifiers 64a375e9-aa8a-4727-9ea2-a548d33d903b