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Diatoms are extremely diverse ubiquitous microalgae. This makes them good indicators of the quality of aquatic ecosystems, and they have been used for this purpose for the past 50 years.  Since 2000, the European Water Framework Directive has required them to be used for assessing the ecological quality of watercourses.
A typological framework has to be devised in order to compare rivers that are comparable, i.e. rivers with the same bioclimatic regions, that flow over the same geological substrate at similar altitudes. Various ecoregional classifications have been defined using these parameters. At a scale covering 4 European countries (Spain, France, Italy, and Switzerland) and at a regional scale (north-east France) we show that ecoregions and geology are determinant in explaining communities, and that pollution-related parameters are less important. Unlike some other authors, we did not observe any homogenization of communities as the level of pollution level increased. Moreover, we did not observe geographically restricted communities, which make it possible to pool data from geographically distinct ecoregions with the same physical characteristics.
Diatoms display a very high degree of species diversity, which can be a problem for their routine use as assessment tools. We showed that when the precision of identification was increased from sub-division to species level, pollution assessment performances also increased, but to a much less marked extent than the number of taxa. Assessment performances at the genus and species levels are similar, whereas there are ten time more species than genera. We also showed that simplifying metrics (life-forms, ecological guilds) can be used to assess nutrient levels as effectively as diatom indices based on species. Furthermore, these metrics provide additional information about biofilm structure that is not available from species-based data.
Finally, micropollutant pollution of rivers is of increasing concern to citizens. We hypothesize that diatoms could be good candidates for assessing herbicide pressure. Four experiments lasting 2 months were conducted in lotic mesocosms. We showed that diatoms surrounded by thick exopolysaccharide matrices were more resistant to dissolved pesticides. On the other hand, diatoms with a high cell surface in contact with the water were disadvantaged. This kind of metric could be used in situ at a larger scale.
We conclude that these metrics could be useful for the purposes of diatom bioassessment. However, we also stress the importance of combining phylogeny and ecology to clarify which environmental pressures are forcing diatoms to adapt. Such studies will enhance diatom bioassessment.