Advances in metabarcoding techniques bring us closer to reliable monitoring of the marine benthos

1. Reliable and accurate biodiversity census methods are essential for
monitoring ecosystem health and assessing potential ecological impacts of
future development projects. Although metabarcoding is increasingly used
to study biodiversity across ecological research, morphology-based
identification remains the preferred approach for marine ecological impact
assessments. Comparing metabarcoding to morphology-based protocols
currently used by ecological surveyors is essential to determine whether
this DNA-based approach is suitable for the long-term monitoring of marine
ecosystems. 2. We compared metabarcoding and morphology-based approaches
for the analysis of invertebrates in low diversity intertidal marine
sediment samples. We used a recently developed bioinformatics pipeline and
two taxonomic assignment methods to resolve and assign amplicon sequence
variants (ASVs) from Illumina amplicon data. We analysed the community
composition recovered by both methods and tested the effects, on the
levels of diversity detected by the metabarcoding method, of sieving
samples prior to DNA extraction. 3. Metabarcoding of the mitochondrial
marker cytochrome c oxidase I (COI) gene recovers the presence of more
taxonomic groups than the morphological approach. We found that sieving
samples results in lower alpha diversity detected and suggests a community
composition that differs significantly from that suggested by un-sieved
samples in our metabarcoding analysis. We found that whilst metabarcoding
and morphological approaches detected similar numbers of species, they are
unable to identify the same set of species across samples. 4. Synthesis
and Applications We show that metabarcoding using the COI marker provides
a more holistic, community-based, analysis of benthic invertebrate
diversity than a traditional morphological approach. We also highlight
current gaps in reference databases and bioinformatic pipelines for the
identification of intertidal benthic invertebrates that need to be
addressed before metabarcoding can replace traditional methods.
Ultimately, with these limitations taken into consideration, resolving
community-wide diversity patterns with metabarcoding could improve the
management of non-protected marine habitats in the U.K.14-Jul-2020