Using Environmental DNA to understand how biodiversity of the oceans has changed over time
Posted on: 27/09/2021 By: Luke Holman
Understanding the biodiversity of past oceans is a tricky task. In SEACHANGE we are using a range of powerful and novel techniques to learn about how humans have affected marine life through time. Here in at the University of Copenhagen, we are leading the environmental DNA work within the project. Read on to learn about environmental DNA, how we will use it in SECHANGE and what opportunities and challenges we might face in coming years.
As organisms move through the air, across the land or through streams, lakes and oceans they leave genetic material in the environment. This material can be fragments of cells, lost skin, feathers, hair, faeces or mucus. We call this genetic material environmental DNA (eDNA), and it can be extracted from a range of samples, for example water, sediment and air. We can analyse the composition of eDNA to find out which animals, plants, fungi or bacteria shed DNA into our collected environmental samples. Some marine species can be challenging to detect with non-DNA methods, for example deep-sea fish that avoid humans, or microscopic plankton that require expertise to identify correctly. We can avoid these problems by using eDNA analyses to detect taxa within the samples instead. However, there are a number of unique challenges to working with eDNA too!
Environmental DNA is a mixture of different biological components from tissue to extracellular DNA.
One of the first sets of samples we are working on in SEACHANGE is marine sediment. As eDNA sinks to the bottom of the ocean it gathers over time in sediment resulting in layers of accumulated material where each layer of sediment corresponds with a particular time-period – like a kind of biological time capsule. Our first challenge is to match these slices of sediment with dates provided from radioisotope dating. We can then identify species from the eDNA extracted from each sediment sample. Finally, we will combine our results with additional data collected by the other SEACHANGE partners to learn how marine biodiversity has changed across each of the key cultural transitions explored in the project.
We carefully remove the top section of sediment from each core to collect uncontaminated material from the centre.
One major challenge in our work is to avoid contamination. The techniques for identifying the extracted eDNA are incredibly sensitive and can detect tiny amounts of DNA. This means that we need to be careful to prevent cross-contamination from previous experiments, avoid contaminating the sample with our own DNA and store our eDNA samples separate from more concentrated sources of DNA. When we work on these samples we wear several layers of protective clothing which can get very hot and sweaty during long days in the lab!
As the project progresses we look forward to seeing what our work on eDNA can contribute to our knowledge of how humanity has changed marine biodiversity and ecosystem function. If you want to learn more about ancient and environmental DNA you can look at recent publications from the group here.
