A comparative analysis of metabarcoding and morphology‐based identification of benthic communities across different regional seas

Abstract

In a world of declining biodiversity, monitoring is becoming crucial. Molecular methods, such as metabarcoding, have the potential to rapidly expand our knowledge of biodiversity, supporting assessment, management, and conservation. In the marine environment, where hard substrata are more difficult to access than soft bottoms for quantitative ecological studies, Artificial Substrate Units (ASUs) allow for standardized sampling. We deployed ASUs within five regional seas (Baltic Sea, Northeast Atlantic Ocean, Mediterranean Sea, Black Sea, and Red Sea) for 12–26 months to measure the diversity and community composition of macroinvertebrates. We identified invertebrates using a traditional approach based on morphological characters, and by metabarcoding of the mitochondrial cytochrome oxidase I (COI) gene. We compared community composition and diversity metrics obtained using the two methods. Diversity was significantly correlated between data types. Metabarcoding of ASUs allowed for robust comparisons of community composition and diversity, but not all groups were successfully sequenced. All locations were significantly different in taxonomic composition as measured with both kinds of data. We recovered previously known regional biogeographical patterns in both datasets (e.g., low species diversity in the Black and Baltic Seas, affinity between the Bay of Biscay and the Mediterranean). We conclude that the two approaches provide complementary information and that metabarcoding shows great promise for marine monitoring. However, until its pitfalls are addressed, the use of metabarcoding in monitoring of rocky benthic assemblages should be used in addition to classical approaches rather than instead of them.

Lessons from photo analyses of Autonomous Reef Monitoring Structures as tools to detect (bio-)geographical, spatial, and environmental effects

“…In their analyses, metabarcoding was able to differentiate sites while morphological approaches did not show a significant difference in the composition between sites (despite the sessile fraction of all plate-faces having been pooled for metabarcoding). A higher diversity by metabarcoding than traditional approaches was also found in Northwest Mediterranean hard bottoms, both in artificial and natural substrata (Cahill et al, 2018;De Jode, 2018). An ongoing project will present the results of metabarcoding analyses carried out on the ARMS studied here (and including additional European regions).…”

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

“…Several studies have directly compared traditional and metabarcoding approaches to surveying local marine benthic diversity (Aylagas, Borja, Muxika, & Rodriguez-Ezpeleta, 2018;Cahill et al, 2018;Lejzerowicz et al, 2015;Lobo et al, 2017). A metabarcoding approach to sampling benthic macroinvertebrates has been shown to outperform traditional methods in the level of diversity recovered within an ecological sample (Lobo et al, 2017).…”

A practical guide to DNA metabarcoding for entomological ecologists

“…Many eDNA studies have adopted quantitative procedures for field sampling, such as soil sampling with corers (Ritter et al ., ; Zinger et al ., ), filtering fixed volumes of water (Lacoursiere‐Roussel et al ., ; Macher et al ., ), and using artificial substrate units for macroinvertebrate sampling (Cahill et al ., ). Standardised and robust protocols that provide quantitative and reproducible results will increase the uptake of eDNA metabarcoding (Dickie et al ., ).…”