Time-series metabarcoding analysis of zooplankton diversity of the NW Atlantic continental shelf

Abstract

Biodiversity of zooplankton is central to the functioning of ocean ecosystems, yet morphological taxonomic analysis requires teams of experts and detailed examination of many samples. Metabarcoding (DNA sequencing of short amplified regions of one or a few genes from environmental samples) is a powerful tool for analysis of the composition and diversity of natural communities. The 18S rRNA V9 hypervariable region was sequenced for 26 zooplankton samples collected from the Gulf of Maine, Georges Bank, and Mid-Atlantic Bight during ecosystem monitoring surveys by the U.S. Northeast Fisheries Science Center during 2002–2012. A total of 7 648 033 sequences and 22 072 operational taxonomic units (OTUs) were identified and classified into 28 taxonomic groups of plankton. Comparative analysis of molecular (V9 sequence numbers) and morphological (abundance counts) focused on seven taxonomic groups and revealed similar patterns of variation among years and regions. Sequence numbers and abundance counts showed positive correlation for all groups, with significant correlations (p < 0.05) for Calanoida, Gastropoda, and Chaetognatha. Shannon diversity index values calculated using sequence numbers and abundance counts showed highly significant correlation (r = 0.625; p < 0.001) across all regions during 2002–2012. This study demonstrates the potential of metabarcoding for time-series analysis of zooplankton biodiversity, ocean ecosystem assessment, and fisheries management.

Exploring the Use of Environmental DNA (eDNA) to Detect Animal Taxa in the Mesopelagic Zone

“…Our results suggest that eDNA analysis is an informative and highly efficient approach for invertebrate biodiversity detection in the mesopelagic that complements net sampling. Our sequence results were based on the 18S V9 marker, which detects a comprehensive and phylogenetically diverse range of animals (Wu et al, 2015;Bucklin et al, 2019;Blanco-Bercial, 2020). The 18S V9 marker is well-suited for broadly focused eDNA surveys due to its relatively short length, as eDNA is likely degraded and thus comprised of relatively small fragments (Jo et al, 2017).…”

“…obs.). For some taxa, there is a mismatch between traditional barcode efforts that focus on the COI and 16S genes (Cristescu, 2014;Lindsay et al, 2015;Elbrecht et al, 2016;Leray and Knowlton, 2016), and metabarcoding analyses which often instead utilize 18S markers to capture a broad range of higher level taxa (de Vargas et al, 2015;Kelly et al, 2017;Djurhuus et al, 2018;Bucklin et al, 2019;Sawaya et al, 2019;Blanco-Bercial, 2020). Additionally, nominal species on Genbank may be misidentified, either due to mistakes in identification due to lack of taxonomic expertise or to the existence of cryptic species (Lindsay et al, 2015(Lindsay et al, , 2017Abad et al, 2017).…”

Metabarcoding Analyses and Seasonality of the Zooplankton Community at BATS

“…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.…”

Comparison of invertebrate diversity in lake waters and their resting eggs in sediments, as revealed by high-throughput sequencing (HTS)

“…DNA metabarcoding provides an alternative method for rapidly identifying species and assessing biodiversity (Elías-Gutiérrez et al, 2018;Bucklin et al, 2019;Carroll et al, 2019). Using 18S rRNA gene sequences, Sun et al (2014) investigated the community dynamics of prokaryotic and eukaryotic microbes in an estuary reservoir.…”