Zooplankton diversity monitoring strategy for the urban coastal region using metabarcoding analysis

Abstract

Marine ecosystems in urban coastal areas are exposed to many risks due to human activity. Thus, long-term and continuous monitoring of zooplankton diversity is necessary. High-throughput DNA metabarcoding has gained recognition as an efficient and highly sensitive approach to accurately describing the species diversity of marine zooplankton assemblages. In this study, we collected 30 zooplankton samples at about 2-week intervals for 1 year. Zooplankton diversity showing a typical four season pattern. Of the “total” and “common” zooplankton, we assigned 267 and 64 taxa. The cluster structure and seasonal diversity pattern were rough when only the “common” zooplankton was used. Our study examined how to maximize the benefits of metabarcoding for monitoring zooplankton diversity in urban coastal areas. The results suggest that to take full advantage of metabarcoding when monitoring a zooplankton community, it is necessary to carefully investigate potential ecosystem threats (non-indigenous species) through sufficient curation rather than disregarding low-abundance operational taxonomic units.

Evaluating Metabarcoding Markers for Identifying Zooplankton and Ichthyoplankton Communities to Species in the Salish Sea: Morphological Comparisons and Rare, Threatened or Invasive Species

“…Our research aims to contribute genetic identification methodology, ground-truthed with zooplankton morphological identifications, towards understanding and monitoring the dynamic responses of zooplankton and ichthyoplankton species and their communities in future studies. Here we employ a high-throughput sequence (HTS) metabarcoding assay approach, which prior studies have indicated can capture a broad diversity of taxa that are often difficult to identify using microscopy and/or other morphological techniques; these include many larval bivalves, gastropods, polychaetes, copepods, and fishes [28][29][30][31][32]. Metabarcoding can also detect species that are low in abundance and/or cryptic [3,9,[29][30][31][32][33][34][35][36].…”

“…Here we employ a high-throughput sequence (HTS) metabarcoding assay approach, which prior studies have indicated can capture a broad diversity of taxa that are often difficult to identify using microscopy and/or other morphological techniques; these include many larval bivalves, gastropods, polychaetes, copepods, and fishes [28][29][30][31][32]. Metabarcoding can also detect species that are low in abundance and/or cryptic [3,9,[29][30][31][32][33][34][35][36].…”

“…Effective metabarcoding gene regions (markers) require an appropriate level of sequence variability to distinguish among species/taxa of interest, and the primers that flank these diagnostic sequences must anneal to conserved sequences on either end [31][32][33][34][35][36]. When the appropriate gene region/marker and primers are selected, the internal sequence region contains nucleotide variants that can be used to distinguish among the species/taxa in a sample in comparison to reference sequence databases [28][29][30][31][32][33][34][35][36].…”

“…Researchers thus aim to select the metabarcoding markers and corresponding primers that are most likely to identify the target taxa/species at the desired taxonomic level [13,[28][29][30][31][32][33][34][35][36]. However, some markers are limited to higher systematic levels because they lack distinctive sequence variation (i.e., the gene region is either too conserved or the marker length is too short to include enough variant nucleotides), and/or available DNA sequence reference repositories are incomplete [13,[31][32][33][34][35][36][37].…”

“…In other words, these are dynamic communities upon which other organisms depend for food [25][26][27], and they are critical to ecosystem services and seafood resources [12,13,16]. However, the sheer numbers of plankton samples required, and the diverse taxonomic coverage needed to identify their component species and monitor such complex community changes are prohibitive using traditional morphological analyses alone (see [12,[28][29][30]).…”