DNA metabarcoding of deep-sea sediment communities using COI: community assessment, spatio-temporal patterns and comparison with 18S rDNA
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. We assessed 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 (900-1,750 m) at two seasons. A fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI) was used as marker for such assessments. 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 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 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, 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. 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 noted that COI reference databases for deep-sea organisms have important gaps, and their completeness is essential in order to successfully apply metabarcoding techniques.
Steps to reproduce
File Canyons_COI.fasta contains the paired-end aligned, demultiplexed and dereplicated metabarcoding sequences of the COI marker used in this work. Metadata for "sample" attributes of the sequences are in file Metadata_Canyons_COI.csv. The fasta file was obtained using the OBITools pipeline from Miseq raw reads. First, the illuminapairedend command was used and only reads with an alignment quality score > 40 were selected. Then the ngsfilter command was used, to demultiplex the samples and remove primer sequences. The "sample" attribute with the sample information for every read was created by ngsfilter during the demultiplexing step. A length filtering step (with command obigrep) was then applied, keeping only sequences with lengths between 309 and 318 bp. Finally, the unique sequences were dereplicated using the command obiuniq.