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This paper explores the diversity and taxonomy of species within Fragilaria sensu stricto, an abundant and ecologically important diatom genus, taking advantage of cultured and DNA-barcoded material. The goal is to facilitate the identification of European taxa within this complex, providing a unified view on morphological and molecular diversity. There is a general agreement that the separation of species within the group of Fragilaria is difficult because morphological descriptions of species are not consistent between authorities, ongoing taxonomic revisions have resulted in species described with standards of the late 20th and 21st centuries alongside descriptions based on 19th century (light microscopical) criteria, and because not all diagnostic characters can be seen in all specimens encountered in routine analyses. Consequent confusion could blur potentially important ecological distinctions between species. Our study demonstrated that some species defined on morphological criteria could be confirmed using the rbcL chloroplast gene as a genetic marker, for example, Fragilaria gracilis, Fragilaria tenera, Fragilaria perminuta, and Fragilaria subconstricta. However, even for those species, preliminary identifications based on morphology often differed from identifications based on phylogenetic clustering combined with detailed morphological study. Clades were well-defined by rbcL, but based on morphology, the terminal taxa of these clades did not match the currently described Fragilaria species. To clarify recognition of these taxa, we describe three new species: Fragilaria agnesiae, Fragilaria heatherae, and Fragilaria joachimii.

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At weekly intervals from July to October 2006, we measured silica deposition in the summer diatom assemblage at various depths in the eutrophic Rímov Reservoir (Czech Republic) using PDMPO, the 2-(4-pyridyl)-5{[4-(2-dimethylaminoethyl-aminocarbamoyl)-methoxy]phenyl}oxazole labeling technique. Fluorescence microscopy coupled with image analysis allows quantifying silicon (Si) deposition over time and a simple distinction between cells that are actively depositing Si and those that are not. Diatom assemblage was exclusively dominated by Fragilaria crotonensis Kitton, which formed pronounced subsurface maxima (2-6.5 m). Concentrations of the main nutrients (Si and phosphorus, P) were low over the whole season; however, at depth, the nutrient availability was higher than at the surface. Fragilaria silica deposition rates were eight times higher at the surface than at depth. Half the population was involved in silica deposition at the surface, while only 20% active cells were doing so at depth. At the surface, silica deposition was limited by P deficiency; the effect of dissolved Si (DSi) was not statistically significant. Silica deposition at depth was significantly constrained by low light availability despite the 1% average light attenuation at depth, which is supposed sufficient for photosynthesis. This study represents the first attempt to employ the PDMPO technique coupled with quantitative image analysis of PDMPO fluorescence in freshwater ecology. On the basis of our results, PDMPO probe appears to be an appropriate proxy for the study of resource limitation in natural diatom populations.