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Evaluating the ecological status of water courses by sequencing the DNA of diatoms

Since 2009, INRA has been developing the innovative technology of metabarcoding on diatom communities (micro-algae), the aim being to design a rapid method to characterise the ecological status of water courses. This method is currently being standardised at a European level.

Photos de différentes espèces de diatomées en microscopie optique (objectif 100 fois à immersion).. © INRA
Updated on 06/21/2017
Published on 04/10/2017

Diatoms: excellent bio-indicators of the ecological status of freshwater courses

These microscopic algae have an external cell wall made of silica whose shape is characteristic of each species. They develop in water courses by forming thin films (biofilms) on the surface of immersed substrates. Because of their considerable biodiversity (more than 100,000 of extant species) and their sensitivity to numerous environmental factors, which varies from one species to another, diatoms can be excellent indicators to monitor the ecological status of freshwater ecosystems. For this reason, the European Water Framework Directive recommends their use as "bio-indicators". The standardised methods currently employed on a routine basis involve the microscopic observation of samples in order to identify and count the different species present. Depending on the abundance of species and their tolerance to pollution, this then enables the calculation of a quality index, the Biological Diatom Index (BDI). However, these methods remain expensive and time-consuming.  

An innovative method

First of all, the scientists built a "reference database" using diatoms cultivated in the laboratory. This database groups the molecular, morphological, ecological and taxonomic data on many diatom species. It is regularly updated and can be accessed via the R-SYST network (see insert) set up by INRA. As a second stage, the scientists carried out several measurement campaigns in natural environments that were or were not polluted, in the French departments of Mayotte, La Réunion and more recently in mainland France. Conducted in collaboration with ONEMA (French Agency for Biodiversity), the DREAL (Regional Environmental, Planning and Housing Agencies), water agencies and different consultancies, these campaigns confirmed the strong concordance between the method using metabarcoding and the microscopic method used for more than 20 years to assess river quality.

Complementing the reference method

According to Frédéric Rimet, the two methods remain complementary. The taxonomic know-how of technicians has been available for many years when using the reference method. In no case should it be abandoned or a major asset could be lost in many laboratories, but the two approaches might be combined, thus providing supplementary information. The former ensures the classification of diatoms from their morphological characteristics, while the latter uses reduced and specific chloroplast DNA sequences called "DNA barcodes" that are characteristic of each diatom species.  
Although in cost terms the two methods are currently equivalent, the principal value of the new technique resides in its rapidity of implementation.

Currently being standardised at a European level

Since 2012, several teams of scientists have been working to establish European protocols for this metabarcoding method. Currently under validation by the European Committee for Standardization (CEN), these protocols should soon result in the definition of European standards for the collection of samples in fresh water and the construction of a reference database. Indeed, very recently, the constitution of European working groups such as the COST DNAqua-Net network (see insert) should enable development of the application of these molecular methods to ecological evaluation and estimating the biodiversity of freshwater bodies.

Scientific contact(s):

  • Frédéric RIMET INRA-Université Savoie Mont Blanc Alpine Research Centre for Food Webs in Lentic Ecosystems (UMR 0042 CARRTEL).
  • Agnès BOUCHEZ INRA-Université Savoie Mont Blanc Alpine Research Centre for Food Webs in Lentic Ecosystems (UMR 0042 CARRTEL). sur les Réseaux Trophiques et les Ecosystèmes Limniques), Inra et Université Savoie Mont Blanc, 75 avenue de Corzent, BP 511, 74203 Thonon-Les-Bains cedex
Associated Division(s):
Forest, Grassland and Freshwater Ecology
Associated Centre(s):

For more information on INRA's R-SYST network

logo. © INRA

R-SYST  is a national network grouping around a dozen INRA research teams (from the Plant Health and Environment (SPE) and Forest, Grassland and Freshwater Ecology (EFPA Divisions) involved in the molecular and morphological characterisation of organisms (viruses, bacteria, micro-algae, plants, fungi and insects). These teams comprise technicians, research scientists and engineers working in the fields of molecular biology, genetics and bio-informatics. They generate databases and design and make available tools to analyse these taxonomic data.  

For more information on the COST DNAqua-Net network

logo. © INRA

The European Union's COST actions (CO-Operation in Science & Technology programme) enable the federation of communities of research teams (more than 30,000 at present throughout Europe) around a scientific theme by funding their networking activities (conferences, symposia, scientific visits, etc.).  

Agnès Bouchez is Vice-Chair of the COST DNAqua-Net network, which was launched in March 2017.
The purpose of this network is to set up a group of research scientists from different disciplines in order to identify reference genomic tools and develop new genomic indicators and measurement techniques for the evaluation and routine monitoring of the biodiversity of water bodies in Europe. DNAqua-Net should also provide a platform to train future generations of scientists in new technologies. Working with water managers, political decision-makers and other stakeholders, this group of research scientists should develop a conceptual framework for the application of eco-genomic tools in the context of legally required environmental evaluations.