Sunday 29 March 2020

Deep-Sea Metabarcoding


New Paper On Deep-Sea Metabarcoding

By Xavier Turon

DNA Metabarcoding of Deep-Sea Sediment Communities Using COI: Community Assessment, Spatio-Temporal Patterns and Comparison with 18S rDNA
By Atienza S, Guardiola M, Præbel K, Antich A, Turon X, Wangensteen OS
Diversity 2020, 12:123 DOI 10.3390/d12040123


Our paper on COI metabarcoding of sediment communities in deep-sea canyons in NW Mediterranean has been published in the special issue Molecular Biodiversity Assessment in the Deep Sea of the Diversity Journal.
Metabarcoding highlights our current deep ignorance on deep-sea communities. We know just 2,805 morphological species from deep Mediterranean. But we detected > 15,000 MOTUs in our very local study! COI Leray-XT recovers the same ecological patterns than 18S, but with enhanced potential for development of novel taxonomy-free ecological bioindicators.

Here is the abstract:


Among the complex ecosystems and habitats that form the deep sea, submarine canyons and open slope systems are regarded as potential hotspots of biodiversity. We assessed the spatial and temporal patterns of biodiversity in sediment communities of a NW Mediterranean Canyon and its adjacent open slope (Blanes Canyon) with DNA metabarcoding. We sampled three layers of sediment and four different depths (900–1750 m) at two seasons, and used a fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI) as a metabarcoding marker. The final dataset contained a total of 15,318 molecular operational taxonomic units (MOTUs). Metazoa, Stramenopiles and Archaeplastida were the dominant taxa and, within metazoans, Arthropoda, Nematoda and Cnidaria were the most diverse. There was a trend towards decreasing MOTU richness and diversity in the first few cm (1 to 5) of the sediment, with only 26.3% of the MOTUs shared across sediment layers. Our results show the presence of heterogeneous communities in the studied area, which was significantly different between zones, depths and seasons. We compared our results with the ones presented in a previous study, obtained using the v7 region of the 18S rRNA gene in the same samples. There were remarkable differences in the total number of MOTUs and in the most diverse taxa. COI recovered a higher number of MOTUs, but more remained unassigned taxonomically. However, the broad spatio-temporal patterns elucidated from both datasets coincided, with both markers retrieving the same ecological information. Our results showed that COI can be used to accurately characterize the studied communities and constitute a high-resolution method to detect ecological shifts. We also highlight that COI reference databases for deep-sea organisms have important gaps, and their completeness is essential in order to successfully apply metabarcoding techniques.
Keywords: DNA metabarcoding; COI; 18S rRNA gene; deep-sea; submarine canyons; meiofauna
With this paper PopCOmics contributes to further the development of genetic tools applied to α- and β-diversity studies in marine communities… more to come soon!