Ecological assessment of aquatic ecosystems is one of the key elements for their effective management and conservation. Morphological identification of benthic invertebrates as indicators of ecological status, is still used in monitoring programmes, requiring significant expertise and time. We were interested in comparing these methods with modern sequencing approaches and assessing their applicability in the context of monitoring. We collected samples of benthic invertebrates from the littoral of Lake Bohinj and compared the method of morphological identification with metabarcoding of bulk samples and preservative liquid (eDNA – environmental DNA). Our findings show that the differences between calculated Lake Biotic Indices (LBI) across the three methods are not statistically significant. We detected more invertebrate families using morphological identification but achieved higher taxonomic resolution using bulk or eDNA methods. Morphological identification was the most time consuming, followed by bulk sample metabarcoding, with eDNA metabarcoding being the fastest. Additionally advantages and disadvantages of molecular methods were reviewed.
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