Marine sediment infauna-based environmental assessment using metabarcoding identifies potential impact indicator species

Developing large-scale monitoring strategies for marine habitats with appropriate temporal and spatial resolution is challenging logistically and economically. We compare potential DNA metabarcoding infaunal identification methods with traditional morphological assessment of marine intertidal biodiversity across two protected sites of contrasting anthropogenic impact on the south coast of England. We show that all the methodologies are effective at distinguishing the distinct communities present at each site. While morphological methods provide community abundance and biomass information, data derived from 18S metabarcoding of sediment scrapes showed the strongest discriminations between sites with contrasting anthropogenic pressures. This difference is due to the inclusion of more taxa from a wider spectrum of biodiversity in this dataset. However, 18S OTU abundance was a poor predictor of morphological taxa abundance and biomass. Examination of the presence or absence of taxa at the more or less impacted sites allows us to identify potential indicator taxa for future surveys, such as families in the phyla Ascidiacea, Cnidaria, Nematoda, and Platyhelminthes; taxa which are not traditionally incorporated into morphology-based assessments due to the difficulty and expense of identification. DNA metabarcoding tools provide a more comprehensive snapshot of marine biodiversity compared to morphological surveys, and therefore an opportunity to assess the responses of more organisms to environmental stressors and develop novel metrics for habitat assessment. This could greatly benefit future monitoring programs and the assessment of management impacts in marine habitats.