Abstract
Metabarcoding (large-scale taxonomic identification of complex samples via analysis of one or few orthologous DNA regions, called barcodes) is revolutionizing analysis of biodiversity of marine zooplankton assemblages. Metabarcoding relies on high-throughput DNA sequencing (HTS) technologies, which yield millions of DNA sequences in parallel and allow large-scale analysis of environmental samples. Metabarcoding studies of marine zooplankton have used various regions of nuclear small- (18S) and large-subunit (28S) rRNA, which allow accurate classification of novel sequences and reliable amplification with consensus primers, but- due to their relatively conserved nature- may underestimate species diversity in a community. To discriminate species, more variable genes are needed. A limited number of metabarcoding studies have used mitochondrial cytochrome oxidase I (COI), which ensures detection of species-level diversity, but may require group-specific primers and thus result in inconsistent amplification success rates. Reference databases with sequences for accurately-identified species are critically needed to allow taxonomic designation of molecular operational taxonomic units (MOTU) and comparison with previous studies of zooplankton diversity. Potential and promising applications of metabarcoding include rapid detection of impacts of climate change, monitoring and assessment of ecosystem health, calculation of biotic indices, characterization of food webs and detection of introduced, non-indigenous species.
Highlights
Marine zooplankton are rapid-responders to environmental variation associated with regime shifts and climate change, which may cause significant and potentially accelerating losses in species diversity (Beaugrand et al, 2010; Möllmann and Diekmann, 2012)
The DNA present in the sample is extracted from the whole sample; second, the barcode of choice is amplified using consensus or taxonomic group-specific PCR primers and appropriate amplification conditions; third, the PCR products are sequenced on a high-throughput sequencing platform; and the obtained sequences are processed for quality control, grouped in molecular operational taxonomic units (MOTU), and compared to a reference database for taxonomic assignment
Choice of barcode Metabarcoding studies of zooplankton assemblages have used a number of marker gene regions to characterize biodiversity patterns across different systematic levels and to address specific hypotheses
Summary
Marine zooplankton are rapid-responders to environmental variation associated with regime shifts and climate change, which may cause significant and potentially accelerating losses in species diversity (Beaugrand et al, 2010; Möllmann and Diekmann, 2012). Metabarcoding (i.e., the large-scale taxonomic identification of a complex sample via analysis of one or few orthologous DNA regions, called barcodes) has the significant advantage of detecting the "hidden diversity" of zooplankton assemblages – including mero-, holo- and ichthyoplankton (Lindeque et al, 2013).
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