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First reference library of DNA barcodes of pelagic copepods from the Algoa Bay Sentinel Site

By Dr Paula Pattrick and Dr Shaun H.P. Deyzel, SAEON Elwandle Coastal Node
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Marine copepods form a major component of the plankton in the world’s oceans. Pelagic copepods provide functionally important links in the marine food chain by consuming phytoplankton and serving as food for planktivores, including the commercially important sardine and anchovy, and even some whales.

As most planktonic copepod species are short lived, there is a tight coupling between environmental change and plankton dynamics. Few species are commercially exploited, therefore long-term changes are readily attributed to climate change.

As such, marine copepods play a critical role in ocean ecosystems and are good indicators of climate change.

The high species diversity (>2500 described species of planktonic marine copepods), together with their small size (adults typically have a body length of 1–2 mm, but some species can be as short as 0.2 mm), makes morphological identification of copepod species a challenging task. This leads to a major stumbling block in the study of the structure and function of these species-rich pelagic ecosystems.

However, using information encoded in the DNA of copepods, researchers can now make precise species identifications. With sequencing technology, species can be identified strictly from DNA, allowing for a rapid and accurate catalogue of copepod biodiversity.

DNA barcoding is the process that assumes that with unique nucleotide sequences, different species can be identified. Therefore, with DNA barcodes, researchers are not only able to determine species identification, but also discover new species, or new distribution records of known species (so-called range extensions).

Studying pelagic copepods in Algoa Bay 

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SAEON and Nelson Mandela University PhD student, Mfundo Bizani, receives a completed zooplankton haul from a reference station in the Algoa Bay Sentinel Site. (Image © Shaun Deyzel)

The Algoa Bay Pelagic Ecosystem Long-term Ecological Research Programme (PELTER), is a comprehensive research and monitoring initiative aimed at providing a holistic understanding of the spatial and temporal dynamics of the pelagic ecosystem of Algoa Bay. The copepod community in Algoa Bay is a component of this ecosystem.

Zooplankton, among a suite of essential ocean and biodiversity variables (EOVs, EBVs), are sampled on a monthly basis in the Algoa Bay Sentinel Site by researchers from the SAEON Elwandle Coastal Node and partners. These efforts serve as the ideal time-series required for understanding the dynamics of coastal plankton including: 1) sub-mesoscale drivers of productivity; 2) the influence of mesoscale oceanographic phenomena; 3) time phases and spatial impacts of episodic physical and biological events (outfalls, cold/warming events, harmful algal blooms); and 4) understanding rates and states of change over time.

“Optimising our understanding of plankton biodiversity dynamics will be a primary objective as the PELTER initiative approaches its second decade of operations in Algoa Bay,” says Sentinel Site Coordinator, Dr Shaun Deyzel.

Building a database of coastal plankton species

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Darkfield image of a typical zooplankton sample from Algoa Bay at 50x magnification. Coastal zooplankton is teeming with a great variety of organisms occupying the pelagic space alongside copepods (white arrows). (Image © Shaun Deyzel)

A vital starting point will be to develop a database on copepods found within the Algoa Bay Sentinel Site. The goal is to provide an inventory of copepod species identified, along with their respective DNA barcodes and detailed images.

By determining DNA barcodes for several copepod species using a portion of the mitochondrial cytochrome oxidase I (COI) gene, the researchers are growing a barcode database that can serve as an invaluable reference library, that can be used as a basis for next-generation environmental sequencing.

DNA barcodes will be accessioned and published with the Barcode of Life Database (BOLD) via the South African node of the International Barcode of Life (iBOL) network.

Our initial sequencing was supported by funding from the Foundational Biodiversity Information Programme (Small Grants: NRF110958), for which the authors are most grateful.

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Image from the electropherogram results of the specimen Temora turbinata, showing the peaks representing the colour and signal intensity of each DNA band. From these data, the sequence can be determined, as shown above the peaks.

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