Sedimentary DNA can reveal the past population dynamics of a pelagic copepod

Abstract

Copepods play a key trophic role as secondary producers in transferring primary production to higher trophic levels such as fish. Copepod production significantly contributes to successful fish recruitment. Despite their importance, knowledge of their dynamics over several decades remains limited due to the difficulty to obtain long-term data series with exhaustive sampling and analysis. However, an understanding long-term copepod dynamic is urgently required to head toward better management for sustainable aquatic ecosystems and fish recruitment. Sedimentary DNA (sedDNA) has been developing a useful tool for reconstructing past plankton dynamics. This study evaluates whether sedDNA targeting the pelagic copepod, Eodiaptomus japonicus, in Lake Biwa (Japan) can be an effective tool for elucidating its past population dynamics. It was applied a quantitative polymerase chain reaction method targeting the mitochondrial cytochrome c oxidase subunit I gene on sediment cores and compared the detected sedDNA concentrations with the unique long-term dataset of demographic traits, biomass, specific growth rate, production, subitaneous eggs, and resting eggs of E. japonicus. The sedDNA concentration of E. japonicus recovered from sediment layers did not correlate significantly with its resting eggs and its specific growth rate but with in situ production, biomass, and subitaneous egg production. The results provided the evidence for the sedDNA as a tracking tool for assessing copepod past production dynamics.

Sediment core DNA-Metabarcoding and chitinous remain identification: Integrating complementary methods to characterise Chironomidae biodiversity in lake sediment archives

“…SedDNA allows for the direct extraction and sequencing of genetic material from sediment samples, overcoming the need to isolate chitinous remains followed by challenging morphological identification, hence enabling the detection of taxa that might otherwise remain undetected. Despite recent developments, i.e., the application of sedDNA approaches to different taxonomic groups such as foraminifera (Pawlowska et al, 2020), plants (Garcés-Pastor et al, 2022, fish and mussels (Thomson-Laing et al, 2023), or crustaceans (copepods; Nakane et al, 2023), the suitability of sedDNA metabarcoding to detect Chironomidae species remains, to our current knowledge, largely unexplored.…”