Diatoms are microalgae, known to present several characteristics that make them excellent bioindicators. In this study, we analyzed the epiphytic diatom communities of shallow lakes, with the aim of exploring the genetic variability explained by physical, chemical or geographical variables. We selected 77 lakes within the Spanish part of the Duero River Basin characterized by wide chemical variability. In each lake, physical parameters were measured in situ and water samples were taken to determine nutrient levels in the laboratory. Diatom communities were collected and identified by both microscopy and DNA-metabarcoding, amplifying a genetic barcode of rbcL gene. We analyzed the phylogenetic signal for several environmental parameters at the genus level for the three most representative genera of these lakes. Our results indicate significant phylogenetic signals that differ from a genus to another. Processes related to spatial scales appear to be the main predictors controlling the genetic diversity of diatom communities in these ponds, with genetic variants deffering among geographical areas for a given species. These molecular studies confirm the enormous diversity present in the diatom communities that inhabit these ecosystems, but further research is needed to apply diatom-based techniques in shallow lakes monitoring or conservation programs. Our results reinforce the view that considering not only morphological but also molecular and ecological characters is necessary to describe new diatom species, especially given the high number of species described each year.

Diatoms are important organisms in aquatic ecosystems due to their position as primary producers and, therefore, analyzing their communities provides relevant information on ecosystem functioning. Diatoms have been historically identified based on morphological traits, which is time-consuming and require well-trained specialists. Nevertheless, DNA barcoding approach offers an alternative to overcome some limitations of the morphological approach. Unfortunately, however, only a few studies have compared beta diversity patterns for both DNA barcoding and morphological approaches. Here, we derive a new take on this issue and assess the ecological mechanisms underlying spatial variation in epiphytic diatom metacommunities using a comprehensive dataset from 22 Mediterranean ponds at different taxonomic resolutions. Our results suggest a relatively poor correspondence in the compositional variation between morphology--based and molecular--based approaches. We speculate that the incompleteness of the reference database and the bioinformatics processing are the biases most likely related to the molecular approach whereas the limited counting effort and the presence of cryptic species are presumably the major biases related to morphological approach. On the other hand, we found that both approaches were strongly related to the environmental template, suggesting that epiphytic diatom communities were mainly controlled by species sorting at regional extents. Overall, this work suggests that both molecular and morphological approaches provide complementary information on diatom metacommunity organization and emphasizes the importance of DNA barcoding to addressing empirical research questions of community ecology in freshwaters.