Abstract
Environmental conditions, such as nutrient concentrations, salinity, elevation etc., shape diatom assemblages of periphytic biofilms. These assemblages respond rapidly to environmental changes, a fact which makes diatoms valuable bioindicators. Hence, freshwater biomonitoring programmes currently use diatom indices (e.g. EU Water Framework Directive - WFD). To date, microscopy-based assessments require high taxonomic expertise for diatom identification at the species level. High-throughput technologies now provide cost-effective identification approaches that are promising, complementary or alternative tools for bioassessment. The suitability of the metabarcoding method is evaluated for the first time in the Cyprus streams WFD monitoring network, an eastern Mediterranean country with many endemic species and results are compared to the results acquired from the morphotaxonomic analysis. Morphotaxonomic identification was conducted microscopically, using the most updated taxonomic concepts, literature and online resources. At the same time, DNA metabarcoding involved the use of the rbcL 312 bp barcode, high-throughput sequencing and bioinformatic analysis. The ecological status was calculated using the IPS Index. Results show a positive correlation between morpho-taxonomic and molecular IPS scores. Discrepancies between the two methodologies are related to the limitations of both techniques. This study confirmed that Fistulifera saprophila can have a crucial role in key differences observed, as it negatively influences IPS scores and microscopy methods frequently overlook it. Importantly, gaps in the DNA barcoding reference databases lead to a positive overestimation in IPS scores. Overall, we conclude that DNA metabarcoding offsets the morphotaxonomic methodology for the ecological quality assessment of freshwaters.
Highlights
Freshwater ecosystems are transient environments, featuring hotspots of biodiversity and supporting about 10% of the total known species on the earth (Strayer and Dudgeon 2010)
The DNA metabarcoding analysis identified a total of four classes, 13 orders, 28 families, 53 genera, 106 species and 136 strains amongst 1,553,538 reads for the 32 stations studied
A Correction Factor (CF) was applied to take into account the biovolume of diatom frustules to make DNA metabarcoding counts fit better with those estimated by microscopic counts (Charles et al 2021)
Summary
Freshwater ecosystems are transient environments, featuring hotspots of biodiversity and supporting about 10% of the total known species on the earth (Strayer and Dudgeon 2010). Due to the extensive urbanisation and advancement in human activities in recent decades, these ecosystems are subjected to environmental degradation and impacted by anthropogenic pressures (Hupało et al 2021) As a result, these freshwater biodiversity hotspots are declining. The Mediterranean region fosters a unique combination of geography, geological history and climate, making it an excellent example of a freshwater biodiversity hotspot This is estimated to result from a distinctly cool and wet season, followed by a warm and dry season influenced by a sequence of regular and often. Panayiota Pissaridou et al.: Morpho- versus MolecularID of diatom communities extreme flooding and drying periods and relatively rare snowfall It is characterised by intense human activities. Studies focus mainly on vertebrates, macroinvertebrate orders and macrophytes of the northern and north-western domain (Figueroa et al 2012)
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