Water Ecology Service

Canton, Switzerland

Water Ecology Service

Canton, Switzerland
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News Article | April 19, 2017
Site: phys.org

Diatoms between 0.01 and 0.02 mm, consisting of a single cell surrounded by an artificially colored silica skeleton. The alga in green is present in clean environments, while the orange one lives in more polluted water. Credit: Laure Apothéloz-Perret-Gentil, UNIGE Diatoms are unicellular algae particularly sensitive to changes that affect their aquatic environment. This is why they are used as bioindicators for the biological monitoring of water quality. However, their microscopic identification in river samples requires a lot of time and skill. Biologists from the University of Geneva (UNIGE), Switzerland, have succeeded in establishing a water quality index based solely on the DNA sequences of the diatoms present in the samples, without needing to identify each species visually. This study, published in the journal Molecular Ecology Resources, presents a revolutionary tool to process a very large number of samples in parallel, allowing wide coverage of the monitored sites in a reduced time and at a lower cost. The degree of pollution of rivers resulting from human activities is assessed using different biotic indices. The latter reflect the ecological status of a river based on the quantity and diversity of organisms selected as bioindicators, due to their ecological preferences and tolerance to pollution. This is the case of diatoms, algae consisting of a single cell surrounded by a silica skeleton, recommended by the European Union and Switzerland as one of the ideal bioindicators for rivers and lakes. The quality of rivers is determined using the Swiss diatom index (DI-CH), whose value defines the ecological status. "The morphological identification of the different species present in each sample, however, no longer meets the needs of rapid and reliable bioassessment measures introduced to protect aquatic environments. This is why we have tried to develop a new method," says Jan Pawlowski, professor at the Department of Genetics and Evolution of the UNIGE Faculty of Science. In collaboration with the Geneva Water Ecology Service (SECOE) and the PhycoEco environmental office in La Chaux-de-Fonds, Switzerland, the researchers analyzed the 90 or so samples taken in different rivers in Switzerland and determined their ecological status using the DI-CH. They have thus established a reference system in order to validate the molecular index under development. The latter is based on the DNA sequences characteristic of all the diatom species which may be present in these samples. "The whole range of DNA sequences revealed in each sample corresponds to a specific DI-CH quality index. Furthermore, each sequence identified has a different distribution and is detected in variable amounts from one sample to another. By integrating all these data, we were able to calculate an ecological value for each sequence, without having to identify the species to which it belongs," explains Laure Apothéloz-Perret-Gentil, a member of the Geneva group and the first author of the study. This approach makes it possible to determine the quality of water using all of these ecological values. "Our assessment was correct for almost 80 percent of the samples, which is very encouraging. Increasing the number and diversity of samples will allow us to calibrate our method for future routine, large-scale analyses," indicates Jan Pawlowski. The synchronous processing of a large number of samples in record time and at a reduced cost is not the only advantage of this new tool. The molecular index developed by the biologists from UNIGE could easily be adapted to other groups of unicellular bioindicators: a major asset for monitoring various types of aquatic ecosystems. Explore further: Using genetics to measure the environmental impact of salmon farming More information: Laure Apothéloz-Perret-Gentil et al. Taxonomy-free molecular diatom index for high-throughput eDNA biomonitoring, Molecular Ecology Resources (2017). DOI: 10.1111/1755-0998.12668


Cordonier A.,Water Ecology Service | Gallina N.,University of Geneva | Nirel P.M.,Water Ecology Service
Vie et Milieu | Year: 2010

The goal of this study is to evaluate the influence of four Geneva geotypes (characterized by the composition of trace elements in water), of the season and of water quality on the distribution of epilithic diatoms in the main rivers in the canton of Geneva (Switzerland). To achieve this, we used 72 samples of diatoms as well as some physical-chemical and bacteriological analyses. The sampling was conducted in the framework of monitoring the surface water quality between 1998 and 2004. For each of these 72 samples, the season (winter-spring or summer) as well as one of the four geotypes ("Jura", "Plaine", "Alpes", "Marais") was accounted for. Nine sample groups based upon the distribution of 120 diatom taxa were defined by statistical analyses. The flora of these nine groups is mainly composed of common and frequentlyoccurring species in the surface waters of the Swiss Plateau that represents good to average water quality. Nonetheless, some of the rarest species confined to poorly-nourished calcareous regions, were sampled only in certain groups. Our results show that in addition to the water quality, the geochemical signature influences the floral composition of Geneva's diatoms. It would be interesting to expand this type of study to the Swiss hydrographical network, to define its ecoregions, to measure its influence on the assemblage of diatoms and to ultimately adapt it to our objectives of biological quality.


Visco J.A.,University of Geneva | Apotheloz-Perret-Gentil L.,University of Geneva | Cordonier A.,Water Ecology Service | Esling P.,University of Geneva | And 4 more authors.
Environmental Science and Technology | Year: 2015

Diatoms are widely used as bioindicators for the assessment of water quality in rivers and streams. Classically, the diatom biotic indices are based on the relative abundance of morphologically identified species weighted by their autoecological value. Obtaining such indices is time-consuming, costly, and requires excellent taxonomic expertise, which is not always available. Here we tested the possibility to overcome these limitations using a next-generation sequencing (NGS) approach to identify and quantify diatoms found in environmental DNA and RNA samples. We analyzed 27 river sites in the Geneva area (Switzerland), in order to compare the values of the Swiss Diatom Index (DI-CH) computed either by microscopic quantification of diatom species or directly from NGS data. Despite gaps in the reference database and variations in relative abundance of analyzed species, the diatom index shows a significant correlation between morphological and molecular data indicating similar biological quality status for the majority of sites. This proof-of-concept study demonstrates the potential of the NGS approach for identification and quantification of diatoms in environmental samples, opening new avenues toward the routine application of genetic tools for bioassessment and biomonitoring of aquatic ecosystems. (Graph Presented). © 2015 American Chemical Society.


PubMed | University of Geneva and Water Ecology Service
Type: Journal Article | Journal: Environmental science & technology | Year: 2015

Diatoms are widely used as bioindicators for the assessment of water quality in rivers and streams. Classically, the diatom biotic indices are based on the relative abundance of morphologically identified species weighted by their autoecological value. Obtaining such indices is time-consuming, costly, and requires excellent taxonomic expertise, which is not always available. Here we tested the possibility to overcome these limitations using a next-generation sequencing (NGS) approach to identify and quantify diatoms found in environmental DNA and RNA samples. We analyzed 27 river sites in the Geneva area (Switzerland), in order to compare the values of the Swiss Diatom Index (DI-CH) computed either by microscopic quantification of diatom species or directly from NGS data. Despite gaps in the reference database and variations in relative abundance of analyzed species, the diatom index shows a significant correlation between morphological and molecular data indicating similar biological quality status for the majority of sites. This proof-of-concept study demonstrates the potential of the NGS approach for identification and quantification of diatoms in environmental samples, opening new avenues toward the routine application of genetic tools for bioassessment and biomonitoring of aquatic ecosystems.

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