18S V9 metabarcoding correctly depicts plankton estuarine community drivers

Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding

“…As such, micro‐eukaryotic plankton plays essential roles in the structure and function of marine ecosystems globally (Liu et al, ). Additionally, planktonic communities are often used as indicators of ecosystem change due to their ability to rapidly respond to environmental shifts (Abad, Albaina, Aguirre, & Estonba, ; Taylor, Allen, & Clark, ). This makes the understanding of the composition, dynamics and position in food webs of planktonic communities across space and time, essential.…”

Metabarcoding Analyses and Seasonality of the Zooplankton Community at BATS

“…Another limitation in this particular study is the taxonomic resolution of the V9 region. Despite the fact that it has been widely used for community characterization in the zooplankton (Amaral-Zettler et al, 2009;de Vargas et al, 2015;Abad et al, 2017), its ability to resolve species is somewhat limited in zooplankton (Wu et al, 2015). For the V9 alone, even identification at the genus level would have only an 80% success for Copepoda (Wu et al, 2015).…”

“…If considering at the most modern superfamilies, whose planktonic radiation happened more recently (Bradford-Grieve, 2002), the same V9 is shared by whole families (Calanidae) or even across several families within the most modern superfamily, the Clausocalanoidea. This is a widespread issue (Albaina et al, 2016;Abad et al, 2017), and this asymmetry of the resolution would influence estimates of diversity, with a closer accuracy in areas where the Arietelloidea or Diaptomoidea are dominant groups (e.g., the mesopelagic or coastal environments, respectively) compared to niches where the other superfamilies are more common (e.g., the epipelagic open ocean). In the BATS region, Pleuromamma spp.…”

“…Nowadays, with the aid of high-throughput sequencing, community-level barcoding can be done in a single analysis, an approach known as metabarcoding (Amaral-Zettler et al, 2009;Fonseca et al, 2010;Taberlet et al, 2012). Applied to the zooplankton, this technique has demonstrated its ability to uncover the existing diversity in very complex samples (Lindeque et al, 2013), determine spatial biographical regions based in community structure Bucklin et al, 2019), capture the vertical structure in the open ocean (Sommer et al, 2017), or show the potential for monitoring of estuarine conditions and seasonality (Abad et al, 2016(Abad et al, , 2017. This method is still subject to technical limitations, and there is much to be learn about it, especially the meaning of read counts compared to "classical" studies such as individual counts or biomass (Bucklin et al, 2016;Lamb et al, 2019).…”

“…From the existing data, the best suited would be those from Deevey studies but, unfortunately, the counts were not available in the original publications, and all efforts done to find the original data from her institution, or at the Bermuda Institute of Ocean Sciences, have been unsuccessful. This study analyses the zooplankton community at the BATS location (32.166667 • N, 64.5 • W), in the Sargasso Sea, during the year 2015, by means of metabarcoding, using the hypervariable V9 region of the 18S gene (Amaral-Zettler et al, 2009;de Vargas et al, 2015), a region commonly used for zooplankton metabarcoding (Albaina et al, 2016;Abad et al, 2017;Bucklin et al, 2019). The analyses aim to understand the seasonal response of the zooplankton community to hydrographic conditions, the ability of the metabarcoding approach to detect processes such as seasonal and daily (day/night) changes in the community composition of the zooplankton, and to determine if there is correlation between routine biological oceanographic measurements taken within the BATS program and the changes in the zooplankton community.…”