DNA barcoding plankton

Dr Bruce Deagle in his laboratory.
Dr Bruce Deagle is using advances in DNA technology to identify hundreds of plankton species at once. (Photo: Glenn Jacobson)
Krill captured on a silk mesh.

Genetic technologies pioneered by the Human Genome Project are opening up new realms of discovery for scientists studying microscopic Antarctic marine plants and animals.

Australian Antarctic Division molecular ecologist, Dr Bruce Deagle, said advances in DNA sequencing are enabling scientists to simultaneously identify hundreds of phytoplankton and zooplankton species (collectively called plankton) in a single sample.

Such samples include the stomach contents of fish, water and plankton-net samples collected from the Southern Ocean, and potentially even aquaculture feeds.

‘New methods of sequencing mean that we can sequence hundreds of thousands of genes at once, compared to the old days when we could only sequence one at a time,’ Dr Deagle said.

The approach for identifying plankton relies on ‘barcodes’, which are segments of DNA unique to different species. These genetic markers are amplified from the total DNA extracted from a sample and the resulting sequences are then compared to a reference database to identify the organisms.

Dr Deagle and post-doctoral fellow Dr Laurence Clarke, from the Antarctic Climate and Ecosystems Cooperative Research Centre, will use the technology on the K-Axis voyage (see Spotlight on the K-Axis) to monitor plankton biodiversity in different habitats and regions of the study.

‘The main goal of the K-Axis study is to look at the shift from a krill-based ecosystem to the fish/copepod-based ecosystem as you move north from Antarctica,’ Dr Deagle said.

‘We’ll be measuring different things that tell us about that change, and we’ll provide a genetic perspective on which plankton species are shifting within the study region.’

To do this the pair will analyse the DNA in water and plankton-net samples collected in the study area, and in the stomach contents of small ‘mesopelagic’ fish (these fish live in the top 200-1000 m of ocean and are an important food source for seals and penguins).

Dr Deagle said the new DNA methods have already revealed some exciting findings in other marine systems.

‘Recent research has highlighted that up to a third of the small unicellular organisms in temperate and tropical marine plankton surveys are being overlooked when using only morphological [physical] identification methods,’ he said.

A closely related study underway at the Antarctic Division compares DNA-based identification with traditional morphological identification of organisms collected using an almost century-old technology – the continuous plankton recorder, or CPR.

‘The CPR is towed behind the ship and catches plankton on a silk mesh that slowly winds through the instrument,’ Dr Deagle said.

‘We can then identify organisms captured in the silk, under the microscope, or using genetics.

‘Our DNA methodology won’t replace this morphological identification, but it will complement it, allowing us to identify species that look physically identical, but that are genetically different.

‘The high-throughput nature of the genetic analysis means in the future we should be able to process many more samples to enhance our understanding of Southern Ocean plankton dynamics.’

Dr Deagle will also apply the technology to look at bycatch in the krill fishing industry. Krill fishing vessels filter large volumes of water to collect krill, catching tiny larval fish in the process.

‘The fish are a relatively small bycatch, but it’s easy to identify the species with DNA barcoding and this can tell you about the distribution of fish larvae and the impact the krill fishery could have on the species,’ he said.

Dr Deagle is working with a Norwegian krill fishing company to trial the technology as a quality control for their krill meal.

‘DNA barcoding allows us to confirm whether their product is entirely Antarctic krill – Euphasia superba – or whether it contains other krill species,’ he said.

‘The krill are taken from different areas of the fishery at different times, so in theory we could identify which areas have a high proportion of bycatch or non-target krill species. This could allow the company to adjust where they fish to minimise those effects.’

Wendy Pyper
Australian Antarctic Division