Cryptic Zooplankton Diversity Revealed by a Metagenetic Approach to Monitoring Metazoan Communities in the Coastal Waters of the Okhotsk Sea, Northeastern Hokkaido

Abstract

Monitoring zooplankton communities is important to understand dynamics in marine ecosystems. However, it is difficult to identify cryptic species and immature stages of zooplankton using morphological classification, which is time-consuming and requires high skill levels. Here, we conducted a metagenetic analysis of the 18S region in 101 zooplankton samples collected weekly throughout 2014 and 2015 at the Okhotsk Tower in Mombetsu, Hokkaido, Japan, and compared the results of this analysis with those provided by morphological analysis. The metagenetic analysis detected 561 molecular taxonomic units (MOTUs), whereas the morphological analysis detected 201 taxonomic groups. Zooplankton communities were dominated by copepods throughout the sampling period; however, non-copepod taxa, which comprised high proportions of both MOTUs (mean 51.1%) and sequence reads (mean 19.1%), were also important. Cryptic diversity detected by the metagenetic analysis was primarily driven by Copepoda and by the larvae of benthic taxa such as Bivalvia, Gastropoda, and Polychaeta. Community structure and diversity varied between periods of warm and cold water, indicating strong correlations with water temperature and thus seasonality. Furthermore, metagenetic analysis revealed detailed seasonal changes in dominant taxa, including larval stages of metazoans with high taxonomic resolutions; these included commercially important organisms such as Japanese scallops. The metagenetic analysis revealed that changes in both water mass and bentho-pelagic interactions sustain ecosystems rich in zooplankton diversity in this area. Metagenetic analysis provides novel insight into zooplankton diversity, and generates massive sequence data that may be used in future research; thus, it is considered an effective tool for monitoring zooplankton communities.

The crossover from microscopy to genes in marine diversity: from species to assemblages in marine pelagic copepods

“…This process is defined as metabarcoding. Compared to DNA barcoding on single specimens, metabarcoding is based on shorter gene fragments, and in general of a single marker, often variable regions of conserved nuclear small-subunit ribosomal RNA genes 18S rRNA (V1-2 [6,96,97]; V4 [98,99]; V9 [9,[100][101][102][103][104][105][106][107] and 28S rRNA [7,8]).…”

Larval assemblages over the abyssal plain in the Pacific are highly diverse and spatially patchy

“…For the first time, we use metabarcoding to investigate the diversity of a larval assemblage in the deep sea. Metabarcoding has routinely been used to characterize the diversity and structure of microbial communities (e.g., Sogin et al, 2006; Huber et al, 2007), with more recent applications to communities of benthic meiofauna and macrofauna (e.g., Fonseca et al, 2010; Leray & Knowlton, 2015), upper ocean zooplankton assemblages (e.g., Lindeque et al, 2013; Sommer et al, 2017; Hirai et al, 2017; Djurhuus et al, 2018), as well as gut contents and sediment communities (e.g., Leray et al, 2013; Deagle et al, 2013; Sinniger et al, 2016). Molecular methods circumvent some of the particular challenges of microscopy-based investigations of deep-sea meroplankton, including the common occurrence of damaged specimens and near ubiquitous lack of identification guides.…”

Environmental DNA identifies marine macrophyte contributions to Blue Carbon sediments

“…Since approximately 3% of cellular organic carbon (C org ) is DNA (Landenmark et al 2015), eDNA‐based methods also provide an approach to estimate contributions to blue carbon stocks (Ortega et al 2019). eDNA analyses provide information on presence‐absence, and can be related to traditional measures of species (Pilliod et al 2013; Thomsen et al 2016; Hirai et al 2017). However, the relationship between eDNA reads and actual species abundance depends on the barcoding primers used and the target taxa because of biases associated with Polymerase Chain Reaction (PCR).…”