ID-Gene Diatoms Molecular Index

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.