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Report

Teaser, summary, work performed and final results

Periodic Reporting for period 1 - ICEDNA (Investigating Changes in Antarctic Marine Ecosystems using Environmental DNA)

Teaser

Summary

Polar marine ecosystems are particularly vulnerable to climate change impacts, from the combined effects of both global warming and ocean acidification. Yet practically speaking, these ecosystems are extremely difficult to work in and gather field data from, so there is a strong need to appraise the efficacy of powerful new techniques for studying them.

This study examined the use of environmental DNA for the purpose of understanding Antarctic marine biodiversity and what affects it in nearshore seafloor ecosystems. Environmental DNA (eDNA) is defined as DNA that is isolated from an environmental sample (such as water, sediment, air) rather than directly from specific individual organisms. Because organisms are continually shedding cells and DNA into the environment, eDNA has proven a sensitive and powerful indicator of organism presence. This study examined this in the context of Antarctic nearshore ecosystems exposed to a gradient of human impacts (around an expeditioner station in Antarctica) and by collecting eDNA samples from an experiment that manipulated the acidity of seawater surrounding experimental seafloor communities to acidity levels predicted 100 years from now. This work is important for society on multiple levels; broadly it will help us understand the uses and limits of this new technique in the context of studying Antarctic seafloor ecosystems and specifically it will give insight into how small scale human impacts (such as the ongoing operations of an expeditioner base) and large scale human impacts (climate change and ocean acidification) affect biodiversity in these ecosystems.

The overall objectives of the study were to: 1) Define the scale at which eDNA signals vary from centimetres to kilometres using different sample mediums (seawater collected at 5m depth V seawater/sediment collected from the seafloor and, 2) relate variation in eDNA signals in the context of impacts of the ongoing operation of an expeditioner station and to the likely effects of future ocean acidification on benthic communities.

Work performed

This project leveraged extensively upon a diving season run by a project partner, the Australian Antarctic Division, which took place in the Austral summer of 2014/2015. During this period the Marie Curie Individual Fellow (MCIF) who was the recipient of this award (in 2017) was employed as a scientific diver. During the diving season the MCIF was involved in collecting data and samples from various dive sites around Casey Station, Antarctica, as well as collecting samples and data during an experiment conducted under the sea-ice, that manipulated the acidity of seawater in chambers on the seafloor, called antFOCE. It was during this period the MCIF collected the environmental DNA samples used as the basis for this project. They consisted of seawater and seawater/sediment filtered through syringe filters with very small holes only microns wide. These filters can capture very small particles as well as large molecules, such as DNA.

During the project, the MCIF extracted DNA from the syringe filters and amplified small stretches of DNA that could be used to identify the organisms that the DNA came from. Once the DNA was extracted and amplified, it was sequenced, resulting in over 60 gigabytes of DNA sequence data, representing over 90 million short DNA sequences. This DNA sequence data was then processed to assign specific DNA sequences to specific samples, to remove errors etc, and then to identify the likely organism (or broader group or organisms) that specific DNA sequences came from. These data were then statistically analysed so that relationships between samples, sampling sites and sampling mediums could be understood. The MCIF also performed sequencing of DNA from representative individual organisms from the benthic ecosystems being studied, so that DNA from the eDNA syringe filters could be matched to specific organisms that were underrepresented in current DNA sequence databases.

The results so far indicate eDNA can indeed be a powerful indicator for the biodiversity present in these ecosystems. They show that eDNA signals vary according to the medium sampled (seawater Vs. seawater/sediment from the seafloor) and the location of the sampled medium. The results also show that samples collected closer to one another are more similar to samples collected further away from one another and the nature of this relationship. This is an important step towards understanding the use of eDNA to study these ecosystems. The data also showed some differences in eDNA signals from different experimental treatments of the antFOCE experiment, which may lead to insights into how these ecosystems will respond to ocean acidification in the future.

Final results

This was the first study to examine the use of eDNA for biodiversity studies in these particular ecosystems and the first using eDNA as a biological indicator in an ocean acidification experiment. Once the results are fully analysed and published, we expect them to contribute to our understanding of the uses and limits of eDNA to study these ecosystems, as well as to increase our understanding of the effect of human impacts on the structure and function of these ecosystems.