Integrating Chironomidae SedDNA Metabarcoding and Fossil Remain Identification

Reconstructing past environmental conditions based on identifying organism assemblages insediment core samples can be seen as a central discipline of Paleolimnology. Chironomidae, or so-called non-biting midges, are considered key bioindicators of aquatic ecosystem variability. Data derived from identifying their chitinous remains in sediments is used to document past chironomid larvae assemblages, which are studied to reconstruct ecosystem changes through time. Recent developments in sedimentary DNA (sedDNA) research have demonstrated that molecular techniques are suitable to determine past occurrences of organisms, either independently or in combination with established approaches based on identifying morphological remains. However, sedDNA-based records of changes in chironomid assemblages are still unexplored and have yet to be made available. To close this gap, we aimed to explore the applicability of sedDNA metabarcoding to identify Chironomidae assemblages in lake sediments by sampling and processing three sediment cores from Lake Sempach in Switzerland. With a focus on developing analytical approaches, we compared an invertebrate-universal (FWH) and a newly designed Chironomidae-specific metabarcoding primer set (CH) to assess their performance in detecting Chironomidae DNA. Furthermore, we isolated and identified sub-fossil larval remains and compared the morphotype assemblages with data derived from sedDNA metabarcoding to evaluate the comparability of the different methods. Results showed a good overall agreement of the morphotype assemblage-specific clustering among the sub-fossil remains and metabarcoding datasets. Both methods indicated chironomid assemblage similarity between the two littoral cores in contrast to the considerably different assemblages of the deep lake core. The dataset based on fossil remains resulted in a higher morphotype diversity compared to sedDNA metabarcoding, and we experienced a pronounced primer bias effect with considerably more Chironomidae detections applying the CH primer combination compared to the FWH combination. Overall, we conclude that sedDNA metabarcoding can supplement traditional fossil-remains identifications and potentially provide independent reconstructions of past chironomid assemblage changes. Furthermore, it has the potential of more efficient workflows, better sample standardisation and species-level resolution datasets. Nonetheless, challenges such as reference sequence database quality and species coverage, sampling strategy, and morphotype definitions should be assessed in future research to improve the integrability of the different methodological approaches, resulting in improved environment reconstructions.