Abstract
We assessed spatio-temporal patterns of diversity in deep-sea sediment communities using metabarcoding. We chose a recently developed eukaryotic marker based on the v7 region of the 18S rRNA gene. Our study was performed in a submarine canyon and its adjacent slope in the Northwestern Mediterranean Sea, sampled along a depth gradient at two different seasons. We found a total of 5,569 molecular operational taxonomic units (MOTUs), dominated by Metazoa, Alveolata and Rhizaria. Among metazoans, Nematoda, Arthropoda and Annelida were the most diverse. We found a marked heterogeneity at all scales, with important differences between layers of sediment and significant changes in community composition with zone (canyon vs slope), depth, and season. We compared the information obtained from metabarcoding DNA and RNA and found more total MOTUs and more MOTUs per sample with DNA (ca. 20% and 40% increase, respectively). Both datasets showed overall similar spatial trends, but most groups had higher MOTU richness with the DNA template, while others, such as nematodes, were more diverse in the RNA dataset. We provide metabarcoding protocols and guidelines for biomonitoring of these key communities in order to generate information applicable to management efforts.
Highlights
The use of environmental DNA is revolutionizing the way we assess biodiversity and has the potential to change practices and policies in management and conservation (Bohmann et al, 2014; Kelly et al, 2014; Handley, 2015; Creer et al, 2016)
After further filtering based on cumulative frequencies, elimination of molecular operational taxonomic units (MOTUs) that could not be assigned to Super-Group or lower rank, and non-marine organisms, the final dataset consisted of 5,569 MOTUs with a total of 5,728,801 reads (Table S1)
Rarefaction curves (Fig. S2) showed that a plateau in the number of MOTUs was achieved in general at ca. 20,000 reads which, considering that the mean number of reads obtained per sample was 35,362, indicated an overall sequencing depth adequate to capture the number of MOTUs present
Summary
The use of environmental DNA (eDNA) is revolutionizing the way we assess biodiversity and has the potential to change practices and policies in management and conservation (Bohmann et al, 2014; Kelly et al, 2014; Handley, 2015; Creer et al, 2016). Several technical and methodological challenges remain, such as those related to contamination, primer biases, sequencing artefacts, delineation of taxonomic units, or databases’ depth (Thomsen & Willerslev, 2015; Carugati et al, 2015; Pawlowski, Lejzerowicz & Esling, 2014a; Leray & Knowlton, 2016; Wangensteen & Turon, 2016), metabarcoding has important advantages relative to morphology-based studies. The field is ripe for the move from descriptive, academic objectives to applied biomonitoring goals (Bohmann et al, 2014; Pawlowski et al, 2016; Bucklin et al, 2016)
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