Abstract
DNA-based monitoring methods are potentially faster and cheaper compared to traditional morphological benthic identification. DNA metabarcoding involves various methodological choices which can introduce bias leading to a different outcome in biodiversity patterns. Therefore, it is important to harmonize DNA metabarcoding protocols to allow comparison across studies and this requires a good understanding of the effect of methodological choices on diversity estimates. This study investigated the impact of DNA and PCR replicates on the detection of macrobenthos species in locations with high, medium and low diversity. Our results show that two to three DNA replicates were needed in locations with a high and medium diversity to detect at least 80% of the species found in the six DNA replicates, while three to four replicates were needed in the location with low diversity. In contrast to general belief, larger body size or higher abundance of the species in a sample did not increase its detection prevalence among DNA replicates. However, rare species were less consistently detected across all DNA replicates of the location with high diversity compared to locations with less diversity. Our results further show that pooling of DNA replicates did not significantly alter diversity patterns, although a small number of rare species was lost. Finally, our results confirm high variation in species detection between PCR replicates, especially for the detection of rare species. These results contribute to create reliable, time and cost efficient metabarcoding protocols for the characterization of macrobenthos.
Highlights
Marine and coastal ecosystems are highly valuable envi ronments as they deliver many ecosystem services (Daily et al 2009; Duncan et al 2015) and functions (Duncan et al 2015) to society
We evaluated the effect of DNA and PCR replicates, as well as the effect of pooling DNA replicates before PCR amplification on alpha and beta diversity of macrobenthos
We considered that the impact of technical replication may be linked to the diversity of the sampled communities and sampled three macrobenthic communities in the Belgian part of the North Sea, char acterized by low, medium and high diversity (Breine et al 2018)
Summary
Marine and coastal ecosystems are highly valuable envi ronments as they deliver many ecosystem services (Daily et al 2009; Duncan et al 2015) and functions (Duncan et al 2015) to society. Sustainable marine exploitation is important to ensure a healthy marine environment, and evaluation of the potential effects of human activities is needed through environmental impact assess ments (EIAs). Such assessments typically use macroben thic communities as indicators (Van Hoey et al 2010), because they rapidly respond to environmental changes.
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