Sediment Core DNA-Metabarcoding and Chitinous Remain Identification: Integrating Complementary Methods to...

Area of Science:

• Paleolimnology
• Molecular Ecology
• Environmental DNA (eDNA)

Background:

• Chironomidae (non-biting midges) are crucial bioindicators for aquatic ecosystem health.
• Traditional methods rely on morphological identification of larval remains in sediments.
• Sedimentary DNA (sedDNA) offers a molecular approach to study past and present organisms.

Purpose of the Study:

• To evaluate the applicability of sedDNA metabarcoding for identifying Chironomidae assemblages in lake sediments.
• To compare the performance of a universal primer set (FWH) versus a Chironomidae-specific primer set (CH).
• To assess the agreement between sedDNA metabarcoding and traditional morphotype analysis.

Main Methods:

• Analysis of three sediment cores from Lake Sempach, Switzerland.
• Extraction and sequencing of sedDNA using two different primer sets (FWH and CH).
• Morphological identification of chitinous larval remains for comparison.

Main Results:

• Good agreement was observed between sedDNA metabarcoding and morphotype assemblage data.
• Both methods revealed higher assemblage similarity in littoral cores compared to the deep lake core.
• The Chironomidae-specific primer set (CH) detected more Chironomidae DNA than the universal set (FWH), indicating primer bias.

Conclusions:

• SedDNA metabarcoding is a viable tool to supplement traditional Chironomidae identification in paleolimnological studies.
• This molecular approach has the potential for more efficient workflows, standardized sampling, and species-level resolution.
• sedDNA metabarcoding can provide independent reconstructions of past chironomid assemblage dynamics.