DNA metabarcoding of Chironomidae pupal exuviae

This study explores the potential of combining DNA metabarcoding with CPET--a traditional sampling method--to create a cost-effective and scalable approach for freshwater biomonitoring, which we call Meta-CPET. We tested how well this new method captures key biodiversity patterns, such as local species richness (alpha diversity) and differences in community composition between sites (beta diversity), as well as how effectively it detects changes in biological communities along environmental gradients.We also paid close attention to the choice of primers, since the PCR amplification step in DNA metabarcoding can introduce significant bias depending on which primers are used. To evaluate our approach, we created 15 artificial mock communities with distinct species mixes and collected 12 real-world samples across both wet and dry seasons, covering a wide geographic range to represent actual chironomid communities.We generated two sets of amplicon data: one using a primer pair specifically designed for chironomids, and another using a highly degenerate universal primer pair. By integrating molecular tools with traditional methods, this work aims to establish a reliable and scalable framework for modern freshwater biomonitoring that can support better ecosystem management.