Abstract
The use of environmental DNA (eDNA) for monitoring aquatic macrofauna allows the non-invasive species determination and measurement of their DNA abundance and typically involves the analysis of eDNA captured from water samples. In this proof-of-concept study, we focused on the novel use of eDNA extracted from archived suspended particulate matter (SPM) for identifying fish species using metabarcoding, which benefits from the prospect of retrospective monitoring and also analysis of fish communities through time. We used archived SPM samples of the German Environmental Specimen Bank (ESB), which were collected using sedimentation traps from different riverine points in Germany. Environmental DNA was extracted from nine SPM samples differing in location, organic content, and porosity (among other factors) using four different methods for the isolation of high-quality DNA. Application of the PowerSoil DNA Isolation Kit with an overnight incubation in lysis buffer, resulted in DNA extraction with the highest purity and eDNA metabarcoding of these eDNA fragments was used to detect a total of 29 fish taxa among the analyzed samples. Here we demonstrated for the first time that SPM is a promising source of eDNA for metabarcoding analysis, which could provide valuable retrospective information (when using archived SPM) for fish monitoring, complementing the currently used approaches.
Highlights
An as yet unexplored component of the aquatic environment for the eDNA monitoring is the Suspended particulate matter (SPM), which, if it behaves to sediment, could benefit from high DNA yields, while offering a contemporary snapshot of the diversity
The German Environmental Specimen Bank (ESB) has archived annual composite samples of SPM from 13 river sites since 200519. These SPM samples could represent a valuable source of material for retrospective seasonal and temporal fish community monitoring. In this proof-of-concept study, we aim to demonstrate, that eDNA extracted from archived SPM samples can be used for identifying fish species using metabarcoding of the 12S rRNA gene
The modified PowerSoil protocol resulted in the best balance between DNA yield and purity of DNA and was chosen as the method to extract DNA from the archival SPM samples, which were subsequently analyzed by eDNA metabarcoding
Summary
An as yet unexplored component of the aquatic environment for the eDNA monitoring is the SPM, which, if it behaves to sediment, could benefit from high DNA yields, while offering a contemporary snapshot of the diversity. The German Environmental Specimen Bank (ESB) has archived annual composite samples of SPM from 13 river sites since 200519 These SPM samples could represent a valuable source of material for retrospective seasonal and temporal fish community monitoring. In this proof-of-concept study, we aim to demonstrate, that eDNA extracted from archived SPM samples can be used for identifying fish species using metabarcoding of the 12S rRNA gene. To our knowledge, this represents the first evaluation of SPM as a source material for eDNA-based evaluation of aquatic macrofauna
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