PhD adventures in Copenhagen, Denmark: revealing past recovery processes of tropical forest systems through ancient environmental DNA 

The lowland tropical rainforests of South-east Asia are complex ecosystems best known for their evergreen forests dominated by the towering dipterocarp trees and unique wildlife. The rainforests are among the most threatened ecosystems on the planet due to climate change, deforestation, logging and agriculture. Many key areas of South-east Asia are also located on the tectonically active Pacific Ring of Fire, which consists of a ‘ring’ of active volcanoes. Volcanic eruptions can be explosive, caused by pressure that has built up over time sending ash, rock and gas into the atmosphere. These eruptions can have an immediate destructive impact on the surrounding environment, negatively affecting forest systems; however, volcanic ash also contains nutrients such as phosphorus, which is essential for plant growth and productivity.  

Ancient environmental DNA

To understand the response and recovery of these tropical forest systems after a volcanic event, I am using lake-sediment cores to explore past records of volcanic activity and forest productivity.  

Lakes act like stores of environmental information, as the sediments found on lake floors are composed of organic and inorganic materials that have accumulated over time. These sediments can provide insights into past nutrient dynamics through geochemical analysis. By extracting ancient environmental DNA (aeDNA), which is genetic material derived from plant material and cells from animals and microorganisms, we can discover how forest biomes have responded to environmental change over time.  

Ancient environmental DNA is typically highly degraded, vulnerable to hydrolysis and oxidation, and easily contaminated by modern DNA. It is therefore crucial to work in a clean environment where the risk of contaminating the samples is minimal.  

Sample handling 

Before splitting the lake sediment core and subsamples for aeDNA extraction, it was first radiographically scanned at the Core Scanning Facility at the BGS campus in Keyworth, Nottinghamshire. Radiographic scanning was also carried out to identify past volcanic events without opening the core, to avoid any potential contamination. I then travelled with the lake sediment core from BGS to the Globe Institute, part of the Faculty of Health and Medical Sciences of the University of Copenhagen, Denmark, which specialises in geogenetics, for aeDNA extraction. 

The institute is located in the heart of Denmark’s capital city. It is surrounded by the Botanical Garden, the National Gallery for Arts, and the King’s Garden, where Rosenborg Castle is located. On arrival, you are met by one of the largest iron meteorites in the world, before entering the Centre for Geogenetics, where the clean aeDNA laboratories are.  

A strict protocol must be followed to avoid any form of modern contamination when working in these laboratories. This includes wearing a full protective outfit consisting of a hazmat suit, face mask, gloves, overshoes, extra protective sleeves and an extra pair of gloves. After suiting up for working the in laboratory, everything must be cleaned in bleach (and washed in ethanol afterwards). The selected samples and all laboratory equipment are then placed in a special clean fume hood, where the aeDNA can be extracted and prepared for sequencing.  

The core was not cut open until it arrived at the Globe Institute, where aeDNA samples were taken at 1 cm intervals using sterile syringes. The samples were taken from intervals pre-eruption, right after the eruption, and several intervals post-eruption, to help understand the forest system’s response to volcanic events. The selected samples were incubated overnight and purified the next day, after which the concentration was measured. Finally, the samples went through another preparation process, the crucial step that converts raw DNA into a library of adapter-ligated, standardised fragments that have been amplified to ensure enough copies are available for genetic sequencing.  

Next steps 

While the prepared DNA samples are awaiting sequencing, the final work for geochemical analysis and stable isotopes measurements is being completed at BGS’s laboratories back in Keyworth. These analyses will help explore the history of past nutrient inputs from volcanic events and improve our understanding of how such inputs influence the tropical rainforest system.  

Copenhagen, Denmark 

From working intensely in the laboratories to exploring the city surrounding the Globe Institute, I enjoyed my time in Copenhagen. It’s a vibrant city known for its blend of historic charm and modern design, exceptional cycling culture and world-class food. The city offers attractions like Tivoli Gardens, Amalienborg Slot (the royal castle), Nyhavn and Free Town Christiania, which are, in my opinion, places you must see while walking around with a Ristet med det hele (a hot dog with the works) and a cocio (Danish chocolate milk). And of course, you can never go wrong by entering one of the many bakeries to make the impossible decision of which pastry to choose… 

Thanks 

A big thank you goes to Dr Ana Prohaska for hosting me at the Globe Institute, training me in new skills in molecular biology, and giving me the tools to help me understand the processes of the work. Another big thanks must go to the rest of the team at the Globe Institute for making me feel a part of the group, even though I was only there for a short amount of time.