DNA metabarcoding of deep-sea sediment communities using COI: community assessment, spatio-temporal patterns and comparison with the 18S rDNA marker

Abstract

The deep sea is the largest biome on Earth, albeit it is the least studied. Among the complex ecosystems and habitats that form the deep sea, submarine canyons and open slope systems are regarded to be potential hot-spots of biodiversity. The Mediterranean Sea hosts the 8.86% of the inventoried submarine canyons in the global ocean, like the Blanes Canyon, located in its Northwestern section. We assessed spatial (through sediment layers and along a depth gradient) and temporal (in two different seasons) patterns of biodiversity in sediment communities of the Blanes Canyon and its adjacent open slope with eDNA metabarcoding, using a fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI) as a marker. We found a total of 15,318 molecular operational taxonomic units (MOTUs), of which 10,860 could be assigned only to Eukarya. Among those assigned at lower levels, Metazoa, Stramenopiles and Archaeplastida were the dominant taxa. Within metazoans, Arthropoda, Nematoda and Cnidaria were the most diverse among the 28.2% that could be assigned to at least the phylum level. There was a trend towards decreasing 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, significantly different between zones, depths and seasons. We compared our results with the ones presented in Guardiola et al (2016), obtained using the v7 region of the 18S rRNA gene as genetic marker in the exact same samples. There were remarkable differences in the total number of MOTUs, in the most diverse taxa and in MOTU richness. COI recovered a higher number of MOTUs, but more remained unassigned taxonomically. However, broad spatio-temporal patterns elucidated from both datasets coincided, both markers retrieving the same ecological information. The choice of marker depends on a trade-off between marker variability, primer bias, and completeness of reference databases. Our results showed that COI can be used to accurately characterize the studied communities and to develop high-resolution bioindicators to detect ecological shifts. We also noted that COI reference databases for deep-sea organisms have important gaps, and its completeness is essential in order to successfully apply metabarcoding solutions.