Abstract
DNA metabarcoding is a promising method to increase cost and time efficiency of marine monitoring. While substantial evidence exists that bulk DNA samples adequately reflect diversity patterns of marine macrobenthos, the potential of eDNA in the ethanol preservative of benthic samples for biodiversity monitoring remains largely unexplored. We investigated species detection in bulk DNA and eDNA from the ethanol preservative in samples from four distinct macrobenthic communities in the North Sea. Bulk DNA and eDNA were extracted with different extraction kits and five COI primer sets were tested. Despite the availability of a nearly complete reference database, at most 22% of the amplicon sequence variants (ASVs) were assigned taxonomy at the phylum level. However, the unassigned ASVs represented only a small fraction of the total reads (13%). The Leray primer set outperformed the four other primer sets in the number of non-chimeric reads and species detected, and in the recovery of beta diversity patterns. Community composition differed significantly between bulk DNA and eDNA samples, but both sample types were able to differentiate the four communities. The probability of detecting a species in the eDNA from the ethanol preservative was significantly lower than for bulk DNA for macrobenthos species having small to medium body size and for species having chitine or CaCO3 in their cuticula. Detection in the bulk DNA samples was not affected by the investigated morphological traits, indicating that monitoring of macrobenthos species will be most robust when using bulk DNA as template for metabarcoding.
Highlights
The characterization of benthic diversity relies mostly on morphological taxonomy, a slow and expensive process due to manual sorting and visual identification of taxa in the samples
We evaluated whether eDNA from the ethanol preservative could be used for monitoring by comparing alpha and beta diversity patterns with those observed in bulk DNA
Since different primer sets can lead to different diversity estimates (Elbrecht and Leese, 2017; Lobo et al, 2017; Braukmann et al, 2019), we evaluated the capacity of five COI primer sets from the literature to capture the morphological species in bulk DNA and eDNA from the ethanol preservative
Summary
The characterization of benthic diversity relies mostly on morphological taxonomy, a slow and expensive process due to manual sorting and visual identification of taxa in the samples. Instead of identifying all specimens morphologically, DNA is extracted from the total community, a short fragment of the genome is amplified through PCR, the resulting library is sequenced using high throughput sequencing and the resulting sequences are processed through bioinformatic pipelines (Pawlowski et al, 2018). Each of these steps may introduce bias and errors (Alberdi et al, 2018), while the final detection of a particular species in the sample largely depends on its biomass and the primers used in the DNA metabarcoding protocol (Elbrecht et al, 2017a; Lobo et al, 2017). Bulk DNA samples may further be sorted in different size fractions to enhance detection of smaller sized animals (Leray and Knowlton, 2015; Elbrecht et al, 2017a), which comes at an extra time cost to process samples
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