Multi-marker metabarcoding approach to study mesozooplankton at basin scale

Abstract

Zooplankton plays a pivotal role in marine ecosystems and the characterisation of its biodiversity still represents a challenge for marine ecologists. In this study, mesozooplankton composition from 46 samples collected in summer along the western Adriatic Sea, was retrieved by DNA metabarcoding analysis. For the first time, the highly variable fragments of the mtDNA COI and the V9 region of 18S rRNA genes were used in a combined matrix to compile an inventory of mesozooplankton at basin scale. The number of sequences retrieved after quality filtering were 824,148 and 223,273 for COI and 18S (V9), respectively. The taxonomical assignment against reference sequences, using 95% (for COI) and 97% (for 18S) similarity thresholds, recovered 234 taxa. NMDS plots and cluster analysis divided coastal from offshore samples and the most representative species of these clusters were distributed according to the dominant surface current pattern of the Adriatic for the summer period. For selected sampling sites, mesozooplankton species were also identified under a stereo microscope providing insights on the strength and weakness of the two approaches. In addition, DNA metabarcoding was shown to be helpful for the monitoring of non-indigenous marine metazoans and spawning areas of commercial fish species. We defined pros and cons of applying this approach at basin scale and the benefits of combining the datasets from two genetic markers.

DNA Metabarcoding of Deep-Sea Sediment Communities Using COI: Community Assessment, Spatio-Temporal Patterns and Comparison with 18S rDNA

“…one fifth of reads. This is coherent with previous findings [33,35,36,74], and is likely due to the much lower variability of the 18S gene, that underestimates the true number of species [35,75]. It can be noted here that the v7 region of the 18S rRNA gene targeted in Guardiola et al [31] is comparatively less used in broad-range studies, compared to regions v1-2 and v9 [75].…”

A flexible pipeline combining clustering and correction tools for prokaryotic and eukaryotic metabarcoding

“…The high complementarity of COI and 18S in terms of targeted taxa (highlighted in Fig. S2), also supports the approach taken by Stefanni et al [91], as subsampling each gene dataset for its "best targeted phyla" and subsequently combining both seems to be a very efficient way to produce comprehensive and non-redundant biodiversity inventories.…”

From metabarcoding to metaphylogeography: separating the wheat from the chaff

“…Their use was hindered by the lack of universal primers (Deagle et al 2014), but new sets of COI primers for general purposes or for specific groups (Leray et al 2013, Gunther et al 2018 are overcoming this problem and COI sequences are now being increasingly used in general biodiversity studies (e.g. Leray and Knowlton 2015, Aylagas et al 2016, Macher et al 2018, Porter and Hajibabaei 2018a, where they typically uncover a much higher degree of a-diversity than 18S rDNA (Stefanni et al 2018, Wangensteen et al 2018a. Furthermore, the use of COI opens the door to taxonomic assignment using the extensive database of the Barcode of Life Datasystems (BOLD), which is continuously increasing in depth and coverage (Ratnasingham andHebert 2007, Porter andHajibabaei 2018b).…”