Interview with the author: Broadening the taxonomic scope of coral reef palaeoecological studies using ancient DNA

Imagine being able to take a small handful of sediment from the bottom of the ocean, and from that seemingly lifeless material, be able to reconstruct the dynamic history of life in that area over the past decades and millenia. No, that’s not quite science fiction– advances in DNA sequencing technology have now made this possible. Hidden inside that sediment is what’s known as palaeoenvironmental DNA (aeDNA), or ancient fragments of DNA that come from the organisms that used to occupy the area, which when sequenced and combined with fossil records, allows us this amazing insight into the past.

In this blog post, we go behind the scenes with Dr. Maria del Carmen (K-le) Gomez Cabrera to talk about their recent publication in Molecular Ecology using aeDNA in a coral reef off the coast of Australia to paint a picture of the historic and complex communities that have inhabited these diverse ecosystems over the past hundreds of years.

Coring marine sediments using an aluminium pipe. Acknowledgement Dr. Brian Beck

What led to your interest in this topic / what was the motivation for this study? 
I have previously study the coral-zooxanthellae symbiosis and for this I have used molecular techniques, since it is impossible to identify the symbiont otherwise, I spent endless hours in the lab extracting tiny amounts of DNA. Then I changed fields and started working with Prof. Pandolfi and the Marine Palaeoecology Lab at The University of Queensland. The tools of the trade are rock hammers and chisels. I ended up surrounded by an inordinate amount of large rocks. But been dependant on only fossils to reconstruct the past leaves a lot of the story out since soft bodied organisms are very unlikely to leave a fossil record, this was very frustrating for me. When I attended a talk by Prof. Alan Cooper (a co-authors of this study) on ancient DNA from plaque in ancient human teeth, and considering my background, I decided we needed to try this on coral reefs. Ancient environmental DNA opened a new world for us to study ancient marine ecosystems of which we only know the story that fossilised organisms tell.

What difficulties did you run into along the way? 
Been the first study of its kind that we have undertaken, we ran into many difficulties. Extracting DNA from our samples was the first hurdle. Although we had a well-resourced molecular lab, we could not use it for this study since any trace of modern DNA was a potential contaminant. We had to repurpose a room in a remote campus where no molecular work was carried out, to use it as a clean space for subsampling the sediment cores, we then sent these samples to the Australian Centre for Ancient DNA to be processed. Making sense of the data was also difficult; there is little genetic information about most marine organisms. Although a steep learning curve, now we are better prepared and it is incredible the amount of DNA sequences been generated around the world on marine organisms at present that will greatly benefit this type of studies in the future.

CT scan of a core with coral fragments marked in colour. Each colour represents a different coral genera. Acknowledgement Dr. George Roff

What is the biggest or most surprising finding from this study? 
That we managed to actually extract workable ancient environmental DNA from reef sediment cores that were not even collected with this purpose in mind. This really blew our minds and opened so many new possibilities to answer important ecological questions that otherwise would have remained unanswered. Moreover considering that these sediment cores were collected from tropical environments, we were really pushing the limits of this technique.

Moving forward, what are the next steps for this research?
This study was a proof of concept, it allowed us understand the capabilities of this technique in the context of coral reefs. We are now establishing a new line of research, incorporating a team of amazing PhD students to explore ecological interactions in the past between key marine organisms such as coral and seaweed, we are also working on a more accurate picture of ecological baselines of natural resources such as fish before European colonization of the Australian continent. These studies will give managers better tools to assist with the management of the Great Barrier Reefs and its resources.

Dr. K-le Gomez Cabrera in the field. Acknowledgement Dr. George Roff

What would your message be for students about to start their first research projects in this topic? 
Read profusely and cover many subjects, do not stick just to your particular area of research because your eureka moment may come from something you read on a different field (think about the connection between ancient DNA in plaque from human teeth and coral reefs’ biodiversity). Take the time to understand the capabilities of the techniques you are planning to use. Researching ancient DNA is very expensive, so you need to really know what you want to achieve and how before you start extracting DNA, preparing DNA libraries or even collecting samples.

What have you learned about science over the course of this project? 
I’ve learn that lateral thinking is very important for the scientific endeavour. That it is crucial not to be boxed in your small bubble in your field of research but to keep thinking big, reading broadly, and scouting for opportunities to apply new approaches from other fields.

Describe the significance of this research for the general scientific community in one sentence.
This study opened new avenues of research that can be used to help us understand meaningful ecological interactions between tropical marine organisms hundreds of years in the past that would not have been possible with traditional methods.

Describe the significance of this research for your scientific community in one sentence.
By incorporating ancient environmental DNA into palaeoecological studies of coral reefs, we can better understand ecological interactions involving soft bodied organisms, a feat not possible with traditional palaeoecological tools.

Maria del Carmen Gomez Cabrera, Jennifer M. Young, George Roff, Timothy Staples, Juan Carlos Ortiz, John M. Pandolfi, & Alan Cooper. (2019). Broadening the taxonomic scope of coral reef palaeoecological studies using ancient DNA. Molecular Ecology, 28(10), 2636-2652.

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