Metabarcoding is powerful yet still blind: a comparative analysis of morphological and molecular surveys of seagrass communities.

In the context of the sixth wave of extinction, reliable surveys of biodiversity are increasingly needed to infer the cause and consequences of species and community declines, identify early warning indicators of tipping points, and provide reliable impact assessments before engaging in activities with potential environmental hazards. DNA metabarcoding has emerged as having potential to provide speedy assessment of community structure from environmental samples. Here we tested the reliability of metabarcoding by comparing morphological and molecular inventories of invertebrate communities associated with seagrasses through estimates of alpha and beta diversity, as well as the identification of the most abundant taxa. Sediment samples were collected from six Zostera marina seagrass meadows across Brittany, France. Metabarcoding surveys were performed using both mitochondrial (Cytochrome Oxidase I) and nuclear (small subunit 18S ribosomal RNA) markers, and compared to morphological inventories compiled by a long-term benthic monitoring network. A sampling strategy was defined to enhance performance and accuracy of results by preventing the dominance of larger animals, boosting statistical support through replicates, and using two genes to compensate for taxonomic biases. Molecular barcodes proved powerful by revealing a remarkable level of diversity that vastly exceeded the morphological survey, while both surveys identified congruent differentiation of the meadows. However, despite the addition of individual barcodes of common species into taxonomic reference databases, the retrieval of only 36% of these species suggest that the remaining were either not present in the molecular samples or not detected by the molecular screening. This finding exemplifies the necessity of comprehensive and well-curated taxonomic reference libraries and multi-gene surveys. Overall, results offer methodological guidelines and support for metabarcoding as a powerful and repeatable method of characterizing communities, while also presenting suggestions for improvement, including implementation of pilot studies prior to performing full "blind" metabarcoding assessments to optimize sampling and amplification protocols.

Comparison of benthic foraminifera and macrofaunal indicators of the impact of oil-based drill mud disposal.

We compare foraminifera and macrofauna as bio-indicators of oil-based drill mud disposal site off Congo. The most polluted sites are characterized by poor faunas, dominated by some very tolerant taxa. Slightly further from the disposal site, there is an area with strongly increased densities, heavily dominated by opportunistic taxa. Still further, macrofauna appears to be similar to that at the reference area, but the foraminiferal meiofauna still suggests a slight environmental perturbation. The foraminiferal FIEI index, based on the species distribution in the study area, appears to be more discriminative than the macrofaunal ITI index, based on a priori definitions of the trophic guilds of the various taxa. Our comparative approach allows us to point out the benefits of (1) the use of macrofauna and foraminifera together and (2) the definition of the species groups used in biotic indices on the basis of observations made directly in the study area.