ID-Gene™ Diatoms Molecular Index

A new genetic tool for rapid and cost-effective assessment of the biological quality of water courses

the importance of diatoms for biomonitoring

Benthic diatoms are widely used as bioindicators in rivers and streams because of their high sensitivity to environmental changes and well-established taxon-specific ecological tolerances and preferences. The diatoms grow rapidly and respond quickly to changes in chemical, physical, or biological factors. Hence, analyzing the composition of their communities provides an easy method to detect environmental changes due to natural or anthropogenic causes.

ID-GENE™ Diatoms Molecular Index applications

The index has been developed for rivers and streams in Switzerland. However, it is possible to develop its customized versions that can be adapted to other habitats and geographic regions. Such development of customized tests might require an additional step of calibration for local conditions.

what is the Diatom Molecular Index?

The Diatom Molecular Index determines the ecological status of watercourses based on the composition of diatom community inferred from environmental DNA (eDNA) sequences. The diatom DNA is specifically amplified from total eDNA extracted from epilithic biofilm samples and sequenced using the high-throughput sequencing technologies. Thousands of diatom DNA sequences are obtained per sample. The analysis of these samples using specifically tailored computer algorithms allows to predict with high accuracy the Diatom Molecular Index, as well as to provide a list of diatom species present in the sample.

what are the advantages of using the ID-GENE™ Diatom Molecular Index?

Current biodiversity assessment and monitoring are largely based on morphological identification of bioindicator taxa. However, in the case of diatoms, the microscopic identification of tiny and highly variable diatom frustules is time consuming and requires very good taxonomic expertise, which is not always available. These limiting factors contrast with the need of a fast routine assessment for the management of water quality. To overcome these issues, we propose the ID-GENE™ Diatom Molecular Index to assess water quality directly from diatom high-throughput DNA sequence data. This method allows processing a large number of samples over a short period of time.

how does our index perfom in comparison to conventional microscopic approach?

The ID-Gene™ Diatom Molecular Index has been calibrated using the Swiss Diatom Index (DI-CH) that is currently available in Switzerland and recognized by the Swiss Federal Office for the Environment as one of the tools to assess the biological quality of Swiss watercourses. Our index involves an autoecological value and a weighting factor, which are calculated from the relative abundance and the repartition of each DNA sequence across the entire dataset.

The cross-validation study conducted on 87 samples from Swiss rivers and streams show good congruence between the values of diatom index inferred from morphology-based and eDNA-based approaches. For the majority of samples (80/87) the ecological status differs by less than 1.5 from the original microscopic assessment.

what do we offer ?

  • Rapid service – Processing time maximum 2 weeks for 20-50 biofilm samples
  • High quality control
  • Comptetitive prices
  • Final report comprising diatom index value and a list of species for each sample

interested in applying our diatoms molecular index to evaluate the biological quality of watercourses in your area ?

Please contact us and we will provide you with protocols and the material necessary for samples collection and preservation

Contact us

ID-GENE ecodiagnostics

c/o Fondation Eclosion
Ch. des Aulx 14
1228 Plan-les-Ouates
Switzerland

Explore the genetic memory of water