Taxonomy-free molecular diatom index for high-throughput eDNA biomonitoring.

Current biodiversity assessment and biomonitoring are largely based on the morphological identification of selected bioindicator taxa. Recently, several attempts have been made to use eDNA metabarcoding as an alternative tool. However, until now, most applied metabarcoding studies have been based on the taxonomic assignment of sequences that provides reference to morphospecies ecology. Usually, only a small portion of metabarcoding data can be used due to a limited reference database and a lack of phylogenetic resolution. Here, we investigate the possibility to overcome these limitations by using a taxonomy-free approach that allows the computing of a molecular index directly from eDNA data without any reference to morphotaxonomy. As a case study, we use the benthic diatoms index, commonly used for monitoring the biological quality of rivers and streams. We analysed 87 epilithic samples from Swiss rivers, the ecological status of which was established based on the microscopic identification of diatom species. We compared the diatom index derived from eDNA data obtained with or without taxonomic assignment. Our taxonomy-free approach yields promising results by providing a correct assessment for 77% of examined sites. The main advantage of this method is that almost 95% of OTUs could be used for index calculation, compared to 35% in the case of the taxonomic assignment approach. Its main limitations are under-sampling and the need to calibrate the index based on the microscopic assessment of diatoms communities. However, once calibrated, the taxonomy-free molecular index can be easily standardized and applied in routine biomonitoring, as a complementary tool allowing fast and cost-effective assessment of the biological quality of watercourses. This article is protected by copyright. All rights reserved.


The human genome: reality and fantasy

Wednesday 1st February 2017 to 20 hours, Duboule give a lecture entitled "Road to transhumanism."


Making a difference: Asymmetry, fate and renewal in the stomatal lineage

28.03.2017 16:15, A100 (Sciences II)

Dominique Bergmann (Stanford University, USA).
hosted by: Michael Hothorn.


Our department hosts 12 research laboratories gathering close to 200 scientists, engineers and technical staff. Research topics cover a large variety of topics, such as developmental genetics and neurogenetics, regeneration, evo-devo, physics of biology, phylogenetics or anthropology.



Teaching life sciences at the University of Geneva is an important duty for all staff scientists. In addition to the bachelor programme, we also propose specific masters and PhD specialisations through various programmes.



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